diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 2fa3170415fb16e0985d7b2bbd589323e2d19aa7..2fc7fc83078d659837142d213257b0517a55e7b1 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -496,10 +496,44 @@ if(BUILD_LIB) if(LAMMPS_DEPS) add_dependencies(lammps ${LAMMPS_DEPS}) endif() + set(LAMMPS_CXX_HEADERS + angle.h + atom.h + bond.h + citeme.h + comm.h + compute.h + dihedral.h + domain.h + error.h + fix.h + force.h + group.h + improper.h + input.h + kspace.h + lammps.h + lattice.h + lmppython.h + memory.h + modify.h + neighbor.h + neigh_list.h + output.h + pair.h + pointers.h + region.h + timer.h + universe.h + update.h + variable.h) + list(TRANSFORM LAMMPS_CXX_HEADERS PREPEND ${LAMMPS_SOURCE_DIR}/) + set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_LIB_SUFFIX}) set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION}) install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}) install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps) + install(FILES ${LAMMPS_CXX_HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps) configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY) install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY) @@ -550,11 +584,11 @@ include(Documentation) ############################################################################### # Install potential and force field files in data directory ############################################################################### -set(LAMMPS_INSTALL_POTENTIALS_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/potentials) -install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_POTENTIALS_DIR}) - -set(LAMMPS_INSTALL_FRC_FILES_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/frc_files) -install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files/ DESTINATION ${LAMMPS_INSTALL_FRC_FILES_DIR}) +set(LAMMPS_INSTALL_DATADIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps) +install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_DATADIR}) +if(BUILD_TOOLS) + install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files DESTINATION ${LAMMPS_INSTALL_DATADIR}) +endif() configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY) configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY) diff --git a/cmake/Modules/Packages/KIM.cmake b/cmake/Modules/Packages/KIM.cmake index 8815f73881b71e1c98780e62043eaf1e4b4983f2..d9d028f6dce9ef3d337807916319243e76e39632 100644 --- a/cmake/Modules/Packages/KIM.cmake +++ b/cmake/Modules/Packages/KIM.cmake @@ -9,6 +9,9 @@ if(PKG_KIM) if(KIM-API_FOUND) set(DOWNLOAD_KIM_DEFAULT OFF) else() + if (NOT DOWNLOAD_KIM) + message(WARNING "KIM-API package not found. We will download and build our own") + endif() set(DOWNLOAD_KIM_DEFAULT ON) endif() option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT}) @@ -21,8 +24,8 @@ if(PKG_KIM) enable_language(Fortran) include(ExternalProject) ExternalProject_Add(kim_build - URL https://s3.openkim.org/kim-api/kim-api-2.0.2.txz - URL_MD5 537d9c0abd30f85b875ebb584f9143fa + URL https://s3.openkim.org/kim-api/kim-api-2.1.2.txz + URL_MD5 6ac52e14ef52967fc7858220b208cba5 BINARY_DIR build CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} diff --git a/cmake/etc/profile.d/lammps.csh.in b/cmake/etc/profile.d/lammps.csh.in index 42f222d67c859d688d824a2cfaefb639fb0a025d..1c13583914ce9a19f079fb1f0901f3eb504d6abf 100644 --- a/cmake/etc/profile.d/lammps.csh.in +++ b/cmake/etc/profile.d/lammps.csh.in @@ -1,4 +1,4 @@ # set environment for LAMMPS and msi2lmp executables # to find potential and force field files -if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_POTENTIALS_DIR@ -if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY @LAMMPS_FRC_FILES_DIR@ +if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_INSTALL_DATADIR@/potentials +if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY @LAMMPS_INSTALL_DATADIR@/frc_files diff --git a/cmake/etc/profile.d/lammps.sh.in b/cmake/etc/profile.d/lammps.sh.in index c1967cb5b2ec30cb53984275712bd14268e0c655..1542a8982f3db5c037a7622a84a93644af8f5eb1 100644 --- a/cmake/etc/profile.d/lammps.sh.in +++ b/cmake/etc/profile.d/lammps.sh.in @@ -1,5 +1,5 @@ # set environment for LAMMPS and msi2lmp executables # to find potential and force field files -LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@} -MSI2LMP_LIBRARY=${MSI2LMP_LIBRARY-@LAMMPS_FRC_FILES_DIR@} +LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_INSTALL_DATADIR@/potentials} +MSI2LMP_LIBRARY=${MSI2LMP_LIBRARY-@LAMMPS_INSTALL_DATADIR@/frc_files} export LAMMPS_POTENTIALS MSI2LMP_LIBRARY diff --git a/doc/include-file-conventions.md b/doc/include-file-conventions.md new file mode 100644 index 0000000000000000000000000000000000000000..c9f8bd5cb1f89de67e216adb4bbe649770de230f --- /dev/null +++ b/doc/include-file-conventions.md @@ -0,0 +1,133 @@ +# Outline of include file conventions in LAMMPS + +This purpose of this document is to provide a point of reference +for LAMMPS developers and contributors as to what include files +and definitions to put where into LAMMPS source. +Last change 2019-07-05 + +## Table of Contents + + * [Motivation](#motivation) + * [Rules](#rules) + * [Tools](#tools) + * [Legacy Code](#legacy-code) + +## Motivation + +The conventions outlined in this document are supposed to help make +maintenance of the LAMMPS software easier. By trying to achieve +consistency across files contributed by different developers, it will +become easier for the code maintainers to modify and adjust files and, +overall, the chance for errors or portability issues will be reduced. +The rules employed are supposed to minimize naming conflicts and +simplify dependencies between files and thus speed up compilation. They +may, as well, make otherwise hidden dependencies visible. + +## Rules + +Below are the various rules that are applied. Not all are enforced +strictly and automatically. If there are no significant side effects, +exceptions may be possible for cases where a full compliance to the +rules may require a large effort compared to the benefit. + +### Core Files Versus Package Files + +All rules listed below are most strictly observed for core LAMMPS files, +which are the files that are not part of a package, and the files of the +packages MOLECULE, MANYBODY, KSPACE, and RIGID. On the other end of +the spectrum are USER packages and legacy packages that predate these +rules and thus may not be fully compliant. Also, new contributions +will be checked more closely, while existing code will be incrementally +adapted to the rules as time and required effort permits. + +### System Versus Local Header Files + +All system- or library-provided include files are included with angular +brackets (examples: `#include ` or `#include `) while +include files provided with LAMMPS are included with double quotes +(examples: `#include "pointers.h"` or `#include "compute_temp.h"`). + +For headers declaring functions of the C-library, the corresponding +C++ versions should be included (examples: `#include ` or +`#include `). However, these includes are limited to those defined +in the C++98 standard. Some files thus must use the older style until +the minimum C++ standard requirement of LAMMPS is lifted to C++11 or +even beyond (examples: `#include ` versus `#include ` +or `#include ` versus `#include `). + +### C++ Standard Compliance + +LAMMPS core files currently correspond to the C++98 standard. Files +requiring C++11 or later are only permitted in (optional) packages +and particularly packages that are not part of the list of commonly +used packages such as MOLECULE, KSPACE, MANYBODY, or RIGID. + +Also, LAMMPS uses the C-style stdio library for I/O instead of iostreams. +Since using both at the same time can cause problems, iostreams should +be avoided where possible. + +### Lean Header Files + +Header files will typically contain the definition of a (single) class. +These header files should have as few include statements as possible. +This is particularly important for classes that implement a "style" and +thus use a macro of the kind `SomeStyle(some/name,SomeName)`. These will +all be included in the auto-generated `"some_style.h"` files which +results in a high potential for direct or indirect symbol name clashes. + +In the ideal case, the header would only include one file defining the +parent class. That would typically be either `#include "pointers.h"` for +the `Pointers` class, or a header of a class derived from it like +`#include "pair.h"` for the `Pair` class and so on. References to other +classes inside the class should be make through pointers, for which forward +declarations (inside the `LAMMPS_NS` or the new class' namespace) can +be employed. The full definition will then be included into the corresponding +implementation file. In the given example from above, the header file +would be called `some_name.h` and the implementation `some_name.cpp` (all +lower case with underscores, while the class itself would be in camel case +and no underscores `SomeName`, and the style name with lower case names separated by +a forward slash). + +### Implementation Files + +In the implementation files (typically, those would have the same base name +as the corresponding header with a .cpp extension instead of .h) include +statements should follow the "include what you use" principle. + +### Order of Include Statements + +Include files should be included in this order: +* the header matching the implementation (`some_class.h` for file `some_class.cpp`) +* mpi.h +* system and library headers (anything that is using angular brackets; C-library headers first, then C++) +* LAMMPS local headers (preferably in alphabetical order) + +### Special Cases and Exceptions + +#### pointers.h + +The `pointer.h` header file also includes `cstdio` and `lmptype.h` +(and through it `stdint.h`, `intttypes.h`, and `climits`). +This means any header including `pointers.h` can assume that `FILE`, +`NULL`, `INT_MAX` are defined. + +## Tools + +The [Include What You Use tool](https://include-what-you-use.org/) +can be used to provide supporting information about compliance with +the rules listed here. There are some limitations and the IWYU tool +may give incorrect advice. The tools is activated by setting the +CMake variable `CMAKE_CXX_INCLUDE_WHAT_YOU_USE` variable to the +path of the `include-what-you-use` command. When activated, the +tool will be run after each compilation and provide suggestions for +which include files should be added or removed. + +## Legacy Code + +A lot of code predates the application of the rules in this document +and the rules themselves are a moving target. So there are going to be +significant chunks of code that do not fully comply. This applies +for example to the USER-REAXC, or the USER-ATC package. The LAMMPS +developers are dedicated to make an effort to improve the compliance +and welcome volunteers wanting to help with the process. + diff --git a/doc/src/Build_cmake.txt b/doc/src/Build_cmake.txt index a16ba995a85c271dac0f4e402b98d13ae0fb6ca1..6eb23b2bb56aa273ea5e7df326413d1e1c0446b4 100644 --- a/doc/src/Build_cmake.txt +++ b/doc/src/Build_cmake.txt @@ -52,11 +52,17 @@ LAMMPS or need to re-compile LAMMPS repeatedly, installation of the ccache (= Compiler Cache) software may speed up repeated compilation even more. -After compilation, you can optionally copy the LAMMPS executable and -library into your system folders (by default under $HOME/.local) with: +After compilation, you may optionally install the LAMMPS executable into +your system with: make install # optional, copy LAMMPS executable & library elsewhere :pre +This will install the lammps executable and library (if requested), some +tools (if configured) and additional files like library API headers, +manpages, potential and force field files. The location of the installation +tree is set by the CMake variable "CMAKE_INSTALL_PREFIX" which defaults +to $\{HOME\}/.local + :line There are 3 variants of CMake: a command-line version (cmake), a text mode diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt index 3fc23c5618105069aeb19299e2e6a58465c94692..e6791de21b0f7b5266e3e20248b2b12b869954fc 100644 --- a/doc/src/Build_extras.txt +++ b/doc/src/Build_extras.txt @@ -172,22 +172,17 @@ KIM package :h4,link(kim) To build with this package, the KIM library with API v2 must be downloaded and built on your system. It must include the KIM models that you want to -use with LAMMPS. If you want to use the "kim_query"_kim_query.html +use with LAMMPS. If you want to use the "kim_query"_kim_commands.html command, you also need to have libcurl installed with the matching development headers and the curl-config tool. -Note that in LAMMPS lingo, a KIM model driver is a pair style -(e.g. EAM or Tersoff). A KIM model is a pair style for a particular -element or alloy and set of parameters, e.g. EAM for Cu with a -specific EAM potential file. Also note that downloading and installing -the KIM API library with all its models, may take a long time (10s of -minutes to hours) to build. Of course you only need to do that once. +See "Obtaining KIM Models"_http://openkim.org/doc/usage/obtaining-models to +learn how to install a pre-build binary of the OpenKIM Repository of Models. +See the list of all KIM models here: https://openkim.org/browse/models -See the list of KIM model drivers here: -https://openkim.org/browse/model-drivers/alphabetical - -See the list of all KIM models here: -https://openkim.org/browse/models/by-model-drivers +(Also note that when downloading and installing from source +the KIM API library with all its models, may take a long time (tens of +minutes to hours) to build. Of course you only need to do that once.) [CMake build]: diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt index 80f91d529113a550fb34550474572b464b945e96..d0d7657c07250f6400572ea514a2aaf7e7f7c37e 100644 --- a/doc/src/Commands_all.txt +++ b/doc/src/Commands_all.txt @@ -68,7 +68,9 @@ An alphabetic list of all general LAMMPS commands. "improper_style"_improper_style.html, "include"_include.html, "jump"_jump.html, -"kim_query"_kim_query.html, +"kim_init"_kim_commands.html, +"kim_interactions"_kim_commands.html, +"kim_query"_kim_commands.html, "kspace_modify"_kspace_modify.html, "kspace_style"_kspace_style.html, "label"_label.html, diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt index f566702609d0faae099efc2b84fffc3738fb7eb3..e035eb843100377552434aed77999e40aa25464a 100644 --- a/doc/src/Commands_compute.txt +++ b/doc/src/Commands_compute.txt @@ -66,6 +66,7 @@ KOKKOS, o = USER-OMP, t = OPT. "group/group"_compute_group_group.html, "gyration"_compute_gyration.html, "gyration/chunk"_compute_gyration_chunk.html, +"gyration/shape"_compute_gyration_shape.html, "heat/flux"_compute_heat_flux.html, "heat/flux/tally"_compute_tally.html, "hexorder/atom"_compute_hexorder_atom.html, @@ -80,6 +81,7 @@ KOKKOS, o = USER-OMP, t = OPT. "meso/e/atom"_compute_meso_e_atom.html, "meso/rho/atom"_compute_meso_rho_atom.html, "meso/t/atom"_compute_meso_t_atom.html, +"momentum"_compute_momentum.html, "msd"_compute_msd.html, "msd/chunk"_compute_msd_chunk.html, "msd/nongauss"_compute_msd_nongauss.html, diff --git a/doc/src/Eqs/compute_shape_parameters.jpg b/doc/src/Eqs/compute_shape_parameters.jpg new file mode 100644 index 0000000000000000000000000000000000000000..9e2374561b40690173497a2e1c9a28c869b0c819 Binary files /dev/null and b/doc/src/Eqs/compute_shape_parameters.jpg differ diff --git a/doc/src/Eqs/compute_shape_parameters.tex b/doc/src/Eqs/compute_shape_parameters.tex new file mode 100644 index 0000000000000000000000000000000000000000..8298efc6e040d9c73d0bac3eb1ce5f45c92ed6ad --- /dev/null +++ b/doc/src/Eqs/compute_shape_parameters.tex @@ -0,0 +1,13 @@ +\documentclass[12pt]{article} + +\pagestyle{empty} +\begin{document} + +\begin{eqnarray*} + c = l_z - 0.5(l_y+l_x) \\ + b = l_y - l_x \\ + k = \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2} +\end{eqnarray*} + +\end{document} + diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt index c55d3743abe5c56998545f1d4adb1202067bdcce..c131b10ec6b983004623c0cd51caadbbd53aa9f2 100644 --- a/doc/src/Errors_messages.txt +++ b/doc/src/Errors_messages.txt @@ -2438,6 +2438,14 @@ Self-explanatory. :dd Self-explanatory. :dd +{Compute gyration ID does not exist for compute gyration/shape} :dt + +Self-explanatory. Provide a valid compute ID. :dd + +{Compute gyration/shape compute ID does not point to a gyration compute} :dt + +Self-explanatory. Provide and ID of a compute gyration command. :dd + {Compute ID for compute reduce does not exist} :dt Self-explanatory. :dd @@ -5777,6 +5785,16 @@ definitions. :dd The data file header lists improper but no improper types. :dd +{Incompatible KIM Simulator Model} :dt + +The requested KIM Simulator Model was defined for a different MD code +and thus is not compatible with LAMMPS. :dd + +{Incompatible units for KIM Simulator Model} :dt + +The selected unit style is not compatible with the requested KIM +Simulator Model. :dd + {Incomplete use of variables in create_atoms command} :dt The var and set options must be used together. :dd @@ -7047,6 +7065,12 @@ The atom style defined does not have this attribute. :dd The atom style defined does not have these attributes. :dd +{KIM Simulator Model has no Model definition} :dt + +There is no model definition (key: model-defn) in the KIM Simulator +Model. Please contact the OpenKIM database maintainers to verify +and potentially correct this. :dd + {KOKKOS package does not yet support comm_style tiled} :dt Self-explanatory. :dd @@ -7551,6 +7575,18 @@ Self-explanatory. :dd Self-explanatory. :dd +{Must use 'kim_style init' command before simulation box is defined} :dt + +Self-explanatory. :dd + +{Must use 'kim_style define' command after simulation box is defined} :dt + +Self-explanatory. :dd + +{Must use 'kim_style init' command before 'kim_style define'} :dt + +Self-explanatory. :dd + {Must use 'kspace_modify pressure/scalar no' for rRESPA with kspace_style MSM} :dt The kspace scalar pressure option cannot (yet) be used with rRESPA. :dd @@ -9494,6 +9530,11 @@ See the "read_data extra/special/per/atom" command for info on how to leave space in the special bonds list to allow for additional bonds to be formed. :dd +{Species XXX is not supported by this KIM Simulator Model} :dt + +The kim_style define command was referencing a species that is not +present in the requested KIM Simulator Model. :dd + {Specified processors != physical processors} :dt The 3d grid of processors defined by the processors command does not diff --git a/doc/src/Errors_warnings.txt b/doc/src/Errors_warnings.txt index 1507d6b22cf706c8656e699d4f1e5d5d1ee7946b..9f346ba8c136bfedb48bfd95aef6f3fb307a1189 100644 --- a/doc/src/Errors_warnings.txt +++ b/doc/src/Errors_warnings.txt @@ -129,6 +129,16 @@ Self-explanatory. :dd Self-explanatory. :dd +{Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost} :dt + +The communication cutoff defaults to the maximum of what is inferred from +pair and bond styles (will be zero, if none are defined) and what is specified +via "comm_modify cutoff"_comm_modify.html (defaults to 0.0). If this results +to 0.0, no ghost atoms will be generated and LAMMPS may lose atoms or use +incorrect periodic images of atoms in interaction lists. To avoid, either use +"pair style zero"_pair_zero.html with a suitable cutoff or use "comm_modify +cutoff"_comm_modify.html. :dd + {Communication cutoff is too small for SNAP micro load balancing, increased to %lf} :dt Self-explanatory. :dd diff --git a/doc/src/Examples.txt b/doc/src/Examples.txt index fcf01de383736b3f38d545ffccb4277660b29bf8..36d0ac86f9f644fd5c43f312ecd75fe76c4bb944 100644 --- a/doc/src/Examples.txt +++ b/doc/src/Examples.txt @@ -73,7 +73,7 @@ granregion: use of fix wall/region/gran as boundary on granular particles hugoniostat: Hugoniostat shock dynamics hyper: global and local hyperdynamics of diffusion on Pt surface indent: spherical indenter into a 2d solid -kim: use of potentials in Knowledge Base for Interatomic Models (KIM) +kim: use of potentials from the "OpenKIM Repository"_openkim latte: examples for using fix latte for DFTB via the LATTE library meam: MEAM test for SiC and shear (same as shear examples) melt: rapid melt of 3d LJ system @@ -153,3 +153,5 @@ illustrate how to use the command(s) provided in that package. Many of the sub-directories have their own README files which give further instructions. See the "Packages_details"_Packages_details.html doc page for more info on specific USER packages. + +:link(openkim,https://openkim.org) diff --git a/doc/src/Install_mac.txt b/doc/src/Install_mac.txt index 3ab119522cab87f992fb0568b97d469826249e90..773c9ec93a432be68eb64a1cb1836637d1a46172 100644 --- a/doc/src/Install_mac.txt +++ b/doc/src/Install_mac.txt @@ -10,47 +10,34 @@ Documentation"_ld - "LAMMPS Commands"_lc :c Download an executable for Mac :h3 LAMMPS can be downloaded, built, and configured for OS X on a Mac with -"Homebrew"_homebrew. Only four of the LAMMPS packages are unavailable -at this time because of additional needs not yet met: KIM, GPU, -USER-INTEL, USER-ATC. +"Homebrew"_homebrew. The following LAMMPS packages are unavailable at this +time because of additional needs not yet met: GPU, KOKKOS, LATTE, MSCG, +MESSAGE, MPIIO POEMS VORONOI. After installing Homebrew, you can install LAMMPS on your system with the following commands: -% brew tap homebrew/science -% brew install lammps # serial version -% brew install lammps --with-mpi # mpi support :pre +% brew install lammps :pre -This will install the executable "lammps", a python module named -"lammps", and additional resources with all the standard packages. To -get the location of the additional resources type this: - -% brew info lammps :pre - -This command also tells you additional installation options available. -The user-packages are available as options, just install them like -this example for the USER-OMP package: - -% brew install lammps --enable-user-omp :pre - -It is usually best to install LAMMPS with the most up to date source -files, which can be done with the "--HEAD" option: - -% brew install lammps --HEAD :pre - -To re-install the LAMMPS HEAD, run this command occasionally (make sure -to use the desired options). - -% brew install --force lammps --HEAD $\{options\} :pre +This will install the executables "lammps_serial" and "lammps_mpi", as well as +the LAMMPS "doc", "potentials", "tools", "bench", and "examples" directories. Once LAMMPS is installed, you can test the installation with the Lennard-Jones benchmark file: % brew test lammps -v :pre +The LAMMPS binary is built with the "KIM package"_Build_extras#kim which +results in Homebrew also installing the `kim-api` binaries when LAMMPS is +installed. In order to use potentials from "openkim.org"_openkim, you can +install the `openkim-models` package + +% brew install openkim-models :pre + If you have problems with the installation you can post issues to "this link"_homebrew. Thanks to Derek Thomas (derekt at cello.t.u-tokyo.ac.jp) for setting up the Homebrew capability. -:link(homebrew,https://github.com/Homebrew/homebrew-science/issues) +:link(homebrew,https://github.com/Homebrew/homebrew-core/issues) +:link(openkim,https://openkim.org) diff --git a/doc/src/Intro_features.txt b/doc/src/Intro_features.txt index 629e8210b72190d1782a48a6df48cfb1b171c164..d133fd80644b7626d0f56eb9c980c9f39fb2f8df 100644 --- a/doc/src/Intro_features.txt +++ b/doc/src/Intro_features.txt @@ -92,8 +92,8 @@ commands) implicit solvent potentials: hydrodynamic lubrication, Debye force-field compatibility with common CHARMM, AMBER, DREIDING, \ OPLS, GROMACS, COMPASS options - access to "KIM archive"_http://openkim.org of potentials via \ - "pair kim"_pair_kim.html + access to the "OpenKIM Repository"_http://openkim.org of potentials via \ + "kim_init, kim_interactions, and kim_query"_kim_commands.html commands hybrid potentials: multiple pair, bond, angle, dihedral, improper \ potentials can be used in one simulation overlaid potentials: superposition of multiple pair potentials :ul diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index bd5addda6f677bff77f6d51b8b86a42342f172e3..43274a96061861541d8c6d6595f383f68737f57a 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -338,22 +338,37 @@ KIM package :link(PKG-KIM),h4 [Contents:] -A "pair_style kim"_pair_kim.html command which is a wrapper on the -Knowledge Base for Interatomic Models (KIM) repository of interatomic -potentials, enabling any of them to be used in LAMMPS simulations. -Also a "kim_query"_kim_query.html command, which allows to query -the OpenKIM database for stored properties. - -To use this package you must have the KIM library available on your -system. +This package contains a set of commands that serve as a wrapper on the +"Open Knowledgebase of Interatomic Models (OpenKIM)"_https://openkim.org +repository of interatomic models (IMs) +enabling compatible ones to be used in LAMMPS simulations. +This includes "kim_init and kim_interactions"_kim_commands.html +commands to select, initialize and instantiate the IM, and a +"kim_query"_kim_commands.html command to perform web queries +for material property predictions of OpenKIM IMs. +Support for KIM IMs that conform to the +"KIM Application Programming Interface (API)"_https://openkim.org/kim-api/ +is provided by the "pair_style kim"_pair_kim.html command. + +NOTE: The command {pair_style kim} is called by {kim_interactions} and +is not recommended to be directly used in input scripts. + +To use this package you must have the KIM API library available on your +system. The KIM API is available for download on the +"OpenKIM website"_https://openkim.org/kim-api/. +When installing LAMMPS from binary, the kim-api package +is a dependency that is automatically downloaded and installed. Information about the KIM project can be found at its website: -https://openkim.org. The KIM project is led by Ellad Tadmor and Ryan -Elliott (U Minnesota). +"https://openkim.org"_https://openkim.org. +The KIM project is led by Ellad Tadmor and Ryan Elliott (U Minnesota) +and is funded by the "National Science Foundation"_https://www.nsf.gov/. [Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM -API which the "pair_style kim"_pair_kim.html command uses. He -developed the pair style. +API and the {pair_style kim} command. Axel Kohlmeyer (Temple U) and +Ellad Tadmor (U Minnesota) contributed to the "kim_commands"_kim_commands.html +interface in close collaboration with Ryan Elliott. + [Install:] @@ -363,10 +378,11 @@ extras"_Build_extras.html doc page. [Supporting info:] +"kim_commands"_kim_commands.html +"pair_style kim"_pair_kim.html src/KIM: filenames -> commands src/KIM/README lib/kim/README -"pair_style kim"_pair_kim.html examples/kim :ul :line @@ -984,9 +1000,9 @@ USER-ADIOS package :link(PKG-USER-ADIOS),h4 [Contents:] -ADIOS is a high-performance I/O library. This package implements the +ADIOS is a high-performance I/O library. This package implements the dump "atom/adios" and dump "custom/adios" commands to write data using -the ADIOS library. +the ADIOS library. [Authors:] Norbert Podhorszki (ORNL) from the ADIOS developer team. diff --git a/doc/src/comm_modify.txt b/doc/src/comm_modify.txt index 482259142bffa6a3bc67d58fd2019be708f81fc9..5f03636c1db240c439d9cee6256a715926588faf 100644 --- a/doc/src/comm_modify.txt +++ b/doc/src/comm_modify.txt @@ -69,9 +69,15 @@ processors. By default the ghost cutoff = neighbor cutoff = pairwise force cutoff + neighbor skin. See the "neighbor"_neighbor.html command for more information about the skin distance. If the specified Rcut is greater than the neighbor cutoff, then extra ghost atoms will be acquired. -If the provided cutoff is smaller, the provided value will be ignored -and the ghost cutoff is set to the neighbor cutoff. Specifying a -cutoff value of 0.0 will reset any previous value to the default. +If the provided cutoff is smaller, the provided value will be ignored, +the ghost cutoff is set to the neighbor cutoff and a warning will be +printed. Specifying a cutoff value of 0.0 will reset any previous value +to the default. If bonded interactions exist and equilibrium bond length +information is available, then also a heuristic based on that bond length +is computed. It is used as communication cutoff, if there is no pair +style present and no {comm_modify cutoff} command used. Otherwise a +warning is printed, if this bond based estimate is larger than the +communication cutoff used. A The {cutoff/multi} option is equivalent to {cutoff}, but applies to communication mode {multi} instead. Since in this case the communication diff --git a/doc/src/commands_list.txt b/doc/src/commands_list.txt index cf716df9acd0c9d3bd68390ea755ed644d16388f..a5c9b568edb8f871a57b6f073c0735a1c730b5f1 100644 --- a/doc/src/commands_list.txt +++ b/doc/src/commands_list.txt @@ -53,7 +53,7 @@ Commands :h1 include info jump - kim_query + kim_commands kspace_modify kspace_style label diff --git a/doc/src/compute.txt b/doc/src/compute.txt index 53ed373aa58f2abffca806dd784bc7a9adf917a5..2a9b2b82f72f91e8e9bb80d8aa1550283159faa8 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -177,7 +177,7 @@ compute"_Commands_compute.html doc page are followed by one or more of "angle"_compute_angle.html - energy of each angle sub-style "angle/local"_compute_angle_local.html - theta and energy of each angle "angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk -"basal/atom"_compute_basal_atom.html - calculates the hexagonal close-packed “c” lattice vector of each atom +"basal/atom"_compute_basal_atom.html - calculates the hexagonal close-packed "c" lattice vector of each atom "body/local"_compute_body_local.html - attributes of body sub-particles "bond"_compute_bond.html - energy of each bond sub-style "bond/local"_compute_bond_local.html - distance and energy of each bond @@ -213,6 +213,7 @@ compute"_Commands_compute.html doc page are followed by one or more of "group/group"_compute_group_group.html - energy/force between two groups of atoms "gyration"_compute_gyration.html - radius of gyration of group of atoms "gyration/chunk"_compute_gyration_chunk.html - radius of gyration for each chunk +"gyration/shape"_compute_gyration_shape.html - compute shape parameters from radius of gyration tensor "heat/flux"_compute_heat_flux.html - heat flux through a group of atoms "heat/flux/tally"_compute_tally.html - "hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6 @@ -227,6 +228,7 @@ compute"_Commands_compute.html doc page are followed by one or more of "meso/e/atom"_compute_meso_e_atom.html - per-atom internal energy of Smooth-Particle Hydrodynamics atoms "meso/rho/atom"_compute_meso_rho_atom.html - per-atom mesoscopic density of Smooth-Particle Hydrodynamics atoms "meso/t/atom"_compute_meso_t_atom.html - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms +"momentum"_compute_momentum.html - translational momentum "msd"_compute_msd.html - mean-squared displacement of group of atoms "msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk "msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms diff --git a/doc/src/compute_gyration.txt b/doc/src/compute_gyration.txt index 8deeddf5859e7efc8f40f044bcfdd186002768b6..054ac02007391ab323530c3abe63e1a422152ba7 100644 --- a/doc/src/compute_gyration.txt +++ b/doc/src/compute_gyration.txt @@ -67,6 +67,7 @@ distance^2 "units"_units.html respectively. [Related commands:] -"compute gyration/chunk"_compute_gyration_chunk.html +"compute gyration/chunk"_compute_gyration_chunk.html, +"compute gyration/shape"_compute_gyration_shape.html [Default:] none diff --git a/doc/src/compute_gyration_shape.txt b/doc/src/compute_gyration_shape.txt new file mode 100644 index 0000000000000000000000000000000000000000..7c428aea8ad86d6bab938491b188915889c73f2c --- /dev/null +++ b/doc/src/compute_gyration_shape.txt @@ -0,0 +1,86 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +compute gyration/shape command :h3 + +[Syntax:] + +compute ID group-ID gyration compute-ID :pre + +ID, group-ID are documented in "compute"_compute.html command +gyration/shape = style name of this compute command +compute-ID = ID of "compute gyration"_compute_gyration.html command :ul + +[Examples:] + +compute 1 molecule gyration/shape pe :pre + +[Description:] + +Define a computation that calculates the eigenvalues of the gyration tensor of a +group of atoms and three shape parameters. The computation includes all effects +due to atoms passing thru periodic boundaries. + +The three computed shape parameters are the asphericity, b, the acylindricity, c, +and the relative shape anisotropy, k: + +:c,image(Eqs/compute_shape_parameters.jpg) + +where lx <= ly <= lz are the three eigenvalues of the gyration tensor. +The asphericity is always non-negative and zero only when the three principal +moments are equal. This zero condition is met when the distribution of particles +is spherically symmetric (hence the name asphericity) but also whenever the particle +distribution is symmetric with respect to the three coordinate axes, e.g., +when the particles are distributed uniformly on a cube, tetrahedron or other Platonic +solid. The acylindricity is always non-negative and zero only when the two principal +moments are equal. This zero condition is met when the distribution of particles is +cylindrically symmetric (hence the name, acylindricity), but also whenever the particle +distribution is symmetric with respect to the two coordinate axes, e.g., when the +particles are distributed uniformly on a regular prism. the relative shape anisotropy +is bounded between zero (if all points are spherically symmetric) and one +(if all points lie on a line). + +NOTE: The coordinates of an atom contribute to the gyration tensor in +"unwrapped" form, by using the image flags associated with each atom. +See the "dump custom"_dump.html command for a discussion of "unwrapped" +coordinates. See the Atoms section of the "read_data"_read_data.html +command for a discussion of image flags and how they are set for each +atom. You can reset the image flags (e.g. to 0) before invoking this +compute by using the "set image"_set.html command. + +[Output info:] + +This compute calculates a global vector of +length 6, which can be accessed by indices 1-6. The first three values are the +eigenvalues of the gyration tensor followed by the asphericity, the acylindricity +and the relative shape anisotropy. The computed values can be used by any command +that uses global vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output +options. + +The vector values calculated by this compute are +"intensive". The first five vector values will be in +distance^2 "units"_units.html while the sixth one is dimensionless. + +[Restrictions:] + +This compute is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +[Related commands:] + +"compute gyration"_compute_gyration.html + +[Default:] none + +:line + +:link(Theodorou) +[(Theodorou)] Theodorou, Suter, Macromolecules, 18, 1206 (1985). + diff --git a/doc/src/compute_momentum.txt b/doc/src/compute_momentum.txt new file mode 100644 index 0000000000000000000000000000000000000000..2c6ec78cf3056151f8f8cd23b343abe8bdd76c5c --- /dev/null +++ b/doc/src/compute_momentum.txt @@ -0,0 +1,49 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +compute momentum command :h3 + +[Syntax:] + +compute ID group-ID momentum :pre + +ID, group-ID are documented in "compute"_compute.html command +momentum = style name of this compute command :ul + +[Examples:] + +compute 1 all momentum :pre + +[Description:] + +Define a computation that calculates the translational momentum +of a group of particles. + +The momentum of each particles is computed as m v, where m and v are +the mass and velocity of the particle. + +[Output info:] + +This compute calculates a global vector (the summed momentum) of +length 3. This value can be used by any command that uses a global +vector value from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output +options. + +The vector value calculated by this compute is "extensive". The vector +value will be in mass*velocity "units"_units.html. + +[Restrictions:] + +This compute is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +[Related commands:] + +[Default:] none diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt index bd6e38e3922941b150e29c57643a037066112089..9b27413cfcb171edc249d28657c38bbf8e65a34e 100644 --- a/doc/src/compute_pressure.txt +++ b/doc/src/compute_pressure.txt @@ -16,12 +16,13 @@ ID, group-ID are documented in "compute"_compute.html command pressure = style name of this compute command temp-ID = ID of compute that calculates temperature, can be NULL if not needed zero or more keywords may be appended -keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} :ul +keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} or {pair/hybrid} :ul [Examples:] compute 1 all pressure thermo_temp -compute 1 all pressure NULL pair bond :pre +compute 1 all pressure NULL pair bond +compute 1 all pressure NULL pair/hybrid lj/cut :pre [Description:] @@ -67,6 +68,9 @@ extra keywords are listed, then only those components are summed to compute temperature or ke and/or the virial. The {virial} keyword means include all terms except the kinetic energy {ke}. +The {pair/hybrid} keyword means to only include contribution +from a sub-style in a {hybrid} or {hybrid/overlay} pair style. + Details of how LAMMPS computes the virial efficiently for the entire system, including for many-body potentials and accounting for the effects of periodic boundary conditions are discussed in diff --git a/doc/src/computes.txt b/doc/src/computes.txt index 926b8da2229a6115f23a22bdd19977d7107cb107..84fcd13da18c267aaf9b198f768609614c273fcb 100644 --- a/doc/src/computes.txt +++ b/doc/src/computes.txt @@ -44,6 +44,7 @@ Computes :h1 compute_group_group compute_gyration compute_gyration_chunk + compute_gyration_shape compute_heat_flux compute_hexorder_atom compute_improper @@ -57,6 +58,7 @@ Computes :h1 compute_meso_e_atom compute_meso_rho_atom compute_meso_t_atom + compute_momentum compute_msd compute_msd_chunk compute_msd_nongauss diff --git a/doc/src/create_atoms.txt b/doc/src/create_atoms.txt index d80e2d45f1473d2a4a084b35af0140e6a3e0605a..2c97194cbadb5e606d5f9eb293ce085d8aec92cd 100644 --- a/doc/src/create_atoms.txt +++ b/doc/src/create_atoms.txt @@ -242,9 +242,8 @@ write_dump all atom sinusoid.lammpstrj :pre :c,image(JPG/sinusoid_small.jpg,JPG/sinusoid.jpg) -The {rotate} keyword can only be used with the {single} style and -when adding a single molecule. It allows to specify the orientation -at which the molecule is inserted. The axis of rotation is +The {rotate} keyword allows specification of the orientation +at which molecules are inserted. The axis of rotation is determined by the rotation vector (Rx,Ry,Rz) that goes through the insertion point. The specified {theta} determines the angle of rotation around that axis. Note that the direction of rotation for diff --git a/doc/src/fix_adapt.txt b/doc/src/fix_adapt.txt index 0d862a890d0d9f591e1a5152386eaf4df7c193dc..4f047ec42d05503942347789d4fb371f33141fc1 100644 --- a/doc/src/fix_adapt.txt +++ b/doc/src/fix_adapt.txt @@ -149,8 +149,7 @@ meaning of these parameters: "spin/neel"_pair_spin_neel.html: coulombic_cutoff: type global: "table"_pair_table.html: table_cutoff: type pairs: "ufm"_pair_ufm.html: epsilon,sigma: type pairs: -"soft"_pair_soft.html: a: type pairs: -"kim"_pair_kim.html: PARAM_FREE_*:i,j,...: global :tb(c=3,s=:) +"soft"_pair_soft.html: a: type pairs: :tb(c=3,s=:) NOTE: It is easy to add new pairwise potentials and their parameters to this list. All it typically takes is adding an extract() method to diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt index 34f0e6daf7ff06daf52d87d5bcd591f8511162ed..3f428e2103b3f067e31a45e1623ad236c49a0963 100644 --- a/doc/src/fix_bond_react.txt +++ b/doc/src/fix_bond_react.txt @@ -24,7 +24,7 @@ common_keyword = {stabilization} :l {stabilization} values = {no} or {yes} {group-ID} {xmax} {no} = no reaction site stabilization {yes} = perform reaction site stabilization - {group-ID} = user-assigned prefix for the dynamic group of non-reacting atoms + {group-ID} = user-assigned prefix for the dynamic group of atoms not currently involved in a reaction {xmax} = xmax value that is used by an internally-created "nve/limit"_fix_nve_limit.html integrator :pre react = mandatory argument indicating new reaction specification :l react-ID = user-assigned name for the reaction :l @@ -52,6 +52,8 @@ react = mandatory argument indicating new reaction specification :l [Examples:] +For unabridged example scripts and files, see examples/USER/misc/bond_react. + molecule mol1 pre_reacted_topology.txt molecule mol2 post_reacted_topology.txt fix 5 all bond/react react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre @@ -106,6 +108,20 @@ involved in any new reactions. The {xmax} value keyword should typically be set to the maximum distance that non-reacting atoms move during the simulation. +Fix bond/react creates and maintains two important dynamic groups of +atoms when using the {stabilization} keyword. The first group contains +all atoms currently involved in a reaction; this group is +automatically thermostatted by an internally-created +"nve/limit"_fix_nve_limit.html integrator. The second group contains +all atoms currently not involved in a reaction. This group should be +used by a thermostat in order to time integrate the system. The name +of this group of non-reacting atoms is created by appending '_REACT' +to the group-ID argument of the {stabilization} keyword, as shown in +the second example above. + +NOTE: When using reaction stabilization, you should generally not have +a separate thermostat which acts on the 'all' group. + The group-ID set using the {stabilization} keyword can be an existing static group or a previously-unused group-ID. It cannot be specified as 'all'. If the group-ID is previously unused, the fix bond/react @@ -116,20 +132,17 @@ internally-created dynamic group. In both cases, this new dynamic group is named by appending '_REACT' to the group-ID, e.g. nvt_grp_REACT. By specifying an existing group, you may thermostat constant-topology parts of your system separately. The dynamic group -contains only non-reacting atoms at a given timestep, and therefore -should be used by a subsequent system-wide time integrator such as -nvt, npt, or nve, as shown in the second example above. The time -integration command should be placed after the fix bond/react command -due to the internal dynamic grouping performed by fix bond/react. +contains only atoms not involved in a reaction at a given timestep, +and therefore should be used by a subsequent system-wide time +integrator such as nvt, npt, or nve, as shown in the second example +above (full examples can be found at examples/USER/misc/bond_react). +The time integration command should be placed after the fix bond/react +command due to the internal dynamic grouping performed by fix +bond/react. NOTE: If the group-ID is an existing static group, react-group-IDs should also be specified as this static group, or a subset. -NOTE: If the group-ID is previously unused, the internally-created -group applies to all atoms in the system, i.e. you should generally -not have a separate thermostat which acts on the 'all' group, or any -other group. - The following comments pertain to each {react} argument (in other words, can be customized for each reaction, or reaction step): @@ -352,12 +365,13 @@ an atom that is not deleted. In addition to deleting unwanted reaction by-products, this feature can be used to remove specific topologies, such as small rings, that may be otherwise indistinguishable. -Also, it may be beneficial to ensure reacting atoms are at a certain -temperature before being released to the overall thermostat. For this, -you can use the internally-created dynamic group named -"bond_react_MASTER_group." For example, adding the following command -would thermostat the group of all atoms currently involved in a -reaction: +Optionally, you can enforce additional behaviors on reacting atoms. +For example, it may be beneficial to force reacting atoms to remain at +a certain temperature. For this, you can use the internally-created +dynamic group named "bond_react_MASTER_group", which consists of all +atoms currently involved in a reaction. For example, adding the +following command would add an additional thermostat to the group of +all currently-reacting atoms: fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1 :pre diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt new file mode 100644 index 0000000000000000000000000000000000000000..93c4e8c4a89297694f1ea0835947fca9600b4547 --- /dev/null +++ b/doc/src/kim_commands.txt @@ -0,0 +1,522 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +kim_init command :h3 +kim_interactions command :h3 +kim_query command :h3 + +[Syntax:] + +kim_init model user_units unitarg +kim_interactions typeargs +kim_query variable formatarg query_function queryargs :pre + +model = name of the KIM interatomic model (the KIM ID for models archived in OpenKIM) +user_units = the LAMMPS "units"_units.html style assumed in the LAMMPS input script +unitarg = {unit_conversion_mode} (optional) +typeargs = atom type to species mapping (one entry per atom type) or {fixed_types} for models with a preset fixed mapping +variable = name of a (string style) variable where the result of the query is stored +formatarg = {split} (optional) +query_function = name of the OpenKIM web API query function to be used +queryargs = a series of {keyword=value} pairs that represent the web query; supported keywords depend on the query function :ul + + +[Examples:] + +kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal +kim_interactions Si +kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real +kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 metal unit_conversion_mode +kim_interactions C H O +Sim_LAMMPS_IFF_PCFF_HeinzMishraLinEmami_2015Ver1v5_FccmetalsMineralsSolvents Polymers__SM_039297821658_000 real +kim_interactions fixed_types +kim_query a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\] :pre + +[Description:] + +The set of {kim_commands} provide a high-level wrapper around the +"Open Knowledgebase of Interatomic Models (OpenKIM)"_https://openkim.org +repository of interatomic models (IMs) (potentials and force fields), +so that they can be used by LAMMPS scripts. These commands do not implement +any computations directly, but rather generate LAMMPS input commands based +on the information retrieved from the OpenKIM repository to initialize and +activate OpenKIM IMs and query their predictions for use in the LAMMPS script. +All LAMMPS input commands generated and executed by {kim_commands} are +echoed to the LAMMPS log file. + +Benefits of Using OpenKIM IMs :h4 + +Employing OpenKIM IMs provides LAMMPS users with multiple benefits: + +Reliability :h5 + +All content archived in OpenKIM is reviewed by the "KIM Editor"_https://openkim.org/governance/ for quality. +IMs in OpenKIM are archived with full provenance control. Each is associated with a maintainer responsible for the integrity of the content. All changes are tracked and recorded. +IMs in OpenKIM are exhaustively tested using "KIM Tests"_https://openkim.org/doc/evaluation/kim-tests/ that compute a host of material properties, and "KIM Verification Checks"_https://openkim.org/doc/evaluation/kim-verification-checks/ that provide the user with information on various aspects of the IM behavior and coding correctness. This information is displayed on the IM's page accessible through the "OpenKIM browse interface"_https://openkim.org/browse. :ul + +Reproducibility :h5 + +Each IM in OpenKIM is issued a unique identifier ("KIM ID"_https://openkim.org/doc/schema/kim-ids/), which includes a version number (last three digits). Any changes that can result in different numerical values lead to a version increment in the KIM ID. This makes it possible to reproduce simulations since the specific version of a specific IM used can be retrieved using its KIM ID. +OpenKIM is a member organization of "DataCite"_https://datacite.org/ and issues digital object identifiers (DOIs) to all IMs archived in OpenKIM. This makes it possible to cite the IM code used in a simulation in a publications to give credit to the developers and further facilitate reproducibility. :ul + +Convenience :h5 + +IMs in OpenKIM are distributed in binary form along with LAMMPS and can be used in a LAMMPS input script simply by providing their KIM ID in the {kim_init} command documented on this page. +The {kim_query} web query tool provides the ability to use the predictions of IMs for supported material properties (computed via "KIM Tests"_https://openkim.org/doc/evaluation/kim-tests/) as part of a LAMMPS input script setup and analysis. +Support is provided for unit conversion between the "unit style"_units.html used in the LAMMPS input script and the units required by the OpenKIM IM. This makes it possible to use a single input script with IMs using different units without change and minimizes the likelihood of errors due to incompatible units. :ul + +:link(IM_types) +Types of IMs in OpenKIM :h4 + +There are two types of IMs archived in OpenKIM: + +The first type is called a {KIM Portable Model} (PM). A KIM PM is an independent computer implementation of an IM written in one of the languages supported by KIM (C, C++, Fortran) that conforms to the KIM Application Programming Interface ("KIM API"_https://openkim.org/kim-api/) Portable Model Interface (PMI) standard. A KIM PM will work seamlessly with any simulation code that supports the KIM API/PMI standard (including LAMMPS; see "complete list of supported codes"_https://openkim.org/projects-using-kim/). +The second type is called a {KIM Simulator Model} (SM). A KIM SM is an IM that is implemented natively within a simulation code ({simulator}) that supports the KIM API Simulator Model Interface (SMI); in this case LAMMPS. A separate SM package is archived in OpenKIM for each parameterization of the IM, which includes all of the necessary parameter files, LAMMPS commands, and metadata (supported species, units, etc.) needed to run the IM in LAMMPS. :ol + +With these two IM types, OpenKIM can archive and test almost all IMs that +can be used by LAMMPS. (It is easy to contribute new IMs to OpenKIM, see +the "upload instructions"_https://openkim.org/doc/repository/adding-content/.) + +OpenKIM IMs are uniquely identified by a +"KIM ID"_https://openkim.org/doc/schema/kim-ids/. +The extended KIM ID consists of +a human-readable prefix identifying the type of IM, authors, publication year, +and supported species, separated by two underscores from the KIM ID itself, +which begins with an IM code +({MO} for a KIM Portable Model, and {SM} for a KIM Simulator Model) +followed by a unique 12-digit code and a 3-digit version identifier. +By convention SM prefixes begin with {Sim_} to readily identify them. + +SW_StillingerWeber_1985_Si__MO_405512056662_005 +Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 :pre + +Each OpenKIM IM has a dedicated "Model Page" on "OpenKIM"_https://openkim.org +providing all the information on the IM including a title, description, +authorship and citation information, test and verification check results, +visualizations of results, a wiki with documentation and user comments, and +access to raw files, and other information. +The URL for the Model Page is constructed from the +"extended KIM ID"_https://openkim.org/doc/schema/kim-ids/ of the IM: + +https://openkim.org/id/extended_KIM_ID +:pre + +For example for the Stillinger-Weber potential +listed above the Model Page is located at: + +"https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005"_https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005 +:pre + +See the "current list of KIM PMs and SMs archived in OpenKIM"_https://openkim.org/browse/models/by-species. +This list is sorted by species and can be filtered to display only +IMs for certain species combinations. + +See "Obtaining KIM Models"_http://openkim.org/doc/usage/obtaining-models to +learn how to install a pre-build binary of the OpenKIM Repository of Models. + +NOTE: It is also possible to locally install IMs not archived in OpenKIM, +in which case their names do not have to conform to the KIM ID format. + +Using OpenKIM IMs with LAMMPS :h4 + +Two commands are employed when using OpenKIM IMs, one to select the +IM and perform necessary initialization ({kim_init}), and the second +to set up the IM for use by executing any necessary LAMMPS commands +({kim_interactions}). Both are required. + +See the {examples/kim} directory for example input scripts that use KIM PMs +and KIM SMs. + +OpenKIM IM Initialization ({kim_init}) :h5 + +The {kim_init} mode command must be issued [before] +the simulation box is created (normally at the top of the file). +This command sets the OpenKIM IM that will be used and may issue +additional commands changing LAMMPS default settings that are required +for using the selected IM (such as "units"_units.html or +"atom_style"_atom_style.html). If needed, those settings can be overridden, +however, typically a script containing a {kim_init} command +would not include {units} and {atom_style} commands. + +The required arguments of {kim_init} are the {model} name of the +IM to be used in the simulation (for an IM archived in OpenKIM this is +its "extended KIM ID"_https://openkim.org/doc/schema/kim-ids/, and +the {user_units}, which are the LAMMPS "units style"_units.html used +in the input script. (Any dimensioned numerical values in the input +script and values read in from files are expected to be in the +{user_units} system.) + +The selected IM can be either a "KIM PM or a KIM SM"_#IM_types. +For a KIM SM, the {kim_init} command verifies that the SM is designed +to work with LAMMPS (and not another simulation code). +In addition, the LAMMPS version used for defining +the SM and the LAMMPS version being currently run are +printed to help diagnose any incompatible changes to input script or +command syntax between the two LAMMPS versions. + +Based on the selected model {kim_init} may modify the +"atom_style"_atom_style.html. +Some SMs have requirements for this setting. If this is the case, then +{atom_style} will be set to the required style. Otherwise, the value is left +unchanged (which in the absence of an {atom_style} command in the input script +is the "default atom_style value"_atom_style.html). + +Regarding units, the {kim_init} command behaves in different ways depending +on whether or not {unit conversion mode} is activated as indicated by the +optional {unitarg} argument. +If unit conversion mode is [not] active, then {user_units} must +either match the required units of the IM or the IM must be able +to adjust its units to match. (The latter is only possible with some KIM PMs; +SMs can never adjust their units.) If a match is possible, the LAMMPS +"units"_units.html command is called to set the units to +{user_units}. If the match fails, the simulation is terminated with +an error. + +Here is an example of a LAMMPS script to compute the cohesive energy +of a face-centered cubic (fcc) lattice for the Ercolessi and Adams (1994) +potential for Al: + +kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal +boundary p p p +lattice fcc 4.032 +region simbox block 0 1 0 1 0 1 units lattice +create_box 1 simbox +create_atoms 1 box +mass 1 26.981539 +kim_interactions Al +run 0 +variable Ec equal (pe/count(all))/$\{_u_energy\} +print "Cohesive Energy = $\{EcJ\} eV" +:pre + +The above script will end with an error in the {kim_init} line if the +IM is changed to another potential for Al that does not work with {metal} +units. To address this {kim_init} offers the {unit_conversion_mode}. +If unit conversion mode {is} active, then {kim_init} calls the LAMMPS +"units"_units.html command to set the units to the IM's required or +preferred units. Conversion factors between the IM's units and the {user_units} +are defined for all "physical quantities"_units.html (mass, distance, etc.). +(Note that converting to or from the "lj" unit style is not supported.) +These factors are stored as "internal style variables"_variable.html with +the following standard names: + +_u_mass +_u_distance +_u_time +_u_energy +_u_velocity +_u_force +_u_torque +_u_temperature +_u_pressure +_u_viscosity +_u_charge +_u_dipole +_u_efield +_u_density :pre + +If desired, the input script can be designed to work with these conversion +factors so that the script will work without change with any OpenKIM IM. +(This approach is used in the +"OpenKIM Testing Framework"_https://openkim.org/doc/evaluation/kim-tests/.) +For example, the script given above for the cohesive energy of fcc Al +can be rewritten to work with any IM regardless of units. The following +script constructs an fcc lattice with a lattice parameter defined in +meters, computes the total energy, and prints the cohesive energy in +Joules regardless of the units of the IM. + +kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 si unit_conversion_mode +boundary p p p +lattice fcc 4.032e-10*$\{_u_distance\} +region simbox block 0 1 0 1 0 1 units lattice +create_box 1 simbox +create_atoms 1 box +mass 1 4.480134e-26*$\{_u_mass\} +kim_interactions Al +run 0 +variable Ec_in_J equal (pe/count(all))/$\{_u_energy\} +print "Cohesive Energy = $\{Ec_in_J\} J" :pre + +Note the multiplication by $\{_u_distance\} and $\{_u_mass\} to convert +from SI units (specified in the {kim_init} command) to whatever units the +IM uses (metal in this case), and the division by $\{_u_energy\} +to convert from the IM's energy units to SI units (Joule). This script +will work correctly for any IM for Al (KIM PM or SM) selected by the +{kim_init} command. + +Care must be taken to apply unit conversion to dimensional variables read in +from a file. For example if a configuration of atoms is read in from a +dump file using the "read_dump"_read_dump.html command, the following can +be done to convert the box and all atomic positions to the correct units: + +variable xyfinal equal xy*$\{_u_distance\} +variable xzfinal equal xz*$\{_u_distance\} +variable yzfinal equal yz*$\{_u_distance\} +change_box all x scale $\{_u_distance\} & + y scale $\{_u_distance\} & + z scale $\{_u_distance\} & + xy final $\{xyfinal\} & + xz final $\{xzfinal\} & + yz final $\{yzfinal\} & + remap :pre + +NOTE: Unit conversion will only work if the conversion factors are placed in +all appropriate places in the input script. It is up to the user to do this +correctly. + +OpenKIM IM Execution ({kim_interactions}) :h5 + +The second and final step in using an OpenKIM IM is to execute the +{kim_interactions} command. This command must be preceded by a {kim_init} +command and a command that defines the number of atom types {N} (such as +"create_box"_create_box.html). +The {kim_interactions} command has one argument {typeargs}. This argument +contains either a list of {N} chemical species, which defines a mapping between +atom types in LAMMPS to the available species in the OpenKIM IM, or the +keyword {fixed_types} for models that have a preset fixed mapping (i.e. +the mapping between LAMMPS atom types and chemical species is defined by +the model and cannot be changed). In the latter case, the user must consult +the model documentation to see how many atom types there are and how they +map to the chemical species. + +For example, consider an OpenKIM IM that supports Si and C species. +If the LAMMPS simulation has four atom types, where the first three are Si, +and the fourth is C, the following {kim_interactions} command would be used: + +kim_interactions Si Si Si C +:pre + +Alternatively, for a model with a fixed mapping the command would be: + +kim_interactions fixed_types +:pre + +The {kim_interactions} command performs all the necessary steps to set up +the OpenKIM IM selected in the {kim_init} command. The specific actions depend +on whether the IM is a KIM PM or a KIM SM. For a KIM PM, +a "pair_style kim"_pair_kim.html command is executed followed by +the appropriate {pair_coeff} command. For example, for the +Ercolessi and Adams (1994) KIM PM for Al set by the following commands: + +kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal +... +... box specification lines skipped +... +kim_interactions Al :pre + +the {kim_interactions} command executes the following LAMMPS input commands: + +pair_style kim EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 +pair_coeff * * Al :pre + +For a KIM SM, the generated input commands may be more complex +and require that LAMMPS is built with the required packages included +for the type of potential being used. The set of commands to be executed +is defined in the SM specification file, which is part of the SM package. +For example, for the Strachan et al. (2003) ReaxFF SM +set by the following commands: + +kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real +... +... box specification lines skipped +... +kim_interactions C H N O :pre + +the {kim_interactions} command executes the following LAMMPS input commands: + +pair_style reax/c lmp_control safezone 2.0 mincap 100 +pair_coeff * * ffield.reax.rdx C H N O +fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq :pre + +Note that the files {lmp_control}, {ffield.reax.rdx} and {param.qeq} +are specific to the Strachan et al. (2003) ReaxFF parameterization +and are archived as part of the SM package in OpenKIM. +Note also that parameters like cutoff radii and charge tolerances, +which have an effect on IM predictions, are also included in the +SM definition ensuring reproducibility. + +NOTE: When using {kim_init} and {kim_interactions} to select +and set up an OpenKIM IM, other LAMMPS commands +for the same functions (such as pair_style, pair_coeff, bond_style, +bond_coeff, fixes related to charge equilibration, etc.) should normally +not appear in the input script. + +Using OpenKIM Web Queries in LAMMPS ({kim_query}) :h5 + +The {kim_query} command performs a web query to retrieve the predictions +of the IM set by {kim_init} for material properties archived in +"OpenKIM"_https://openkim.org. The {kim_query} command must be preceded +by a {kim_init} command. The result of the query is stored in a +"string style variable"_variable.html, the name of which is given as the first +argument of the {kim_query command}. (For the case of multiple +return values, the optional {split} keyword can be used after the +variable name to separate the results into multiple variables; see +the "example"_#split_example below.) +The second required argument {query_function} is the name of the +query function to be called (e.g. {get_lattice_constant_cubic}). +All following "arguments"_Commands_parse.html are parameters handed over to +the web query in the format {keyword=value}, where {value} is always +an array of one or more comma-separated items in brackets. +The list of supported keywords and the type and format of their values +depend on the query function used. The current list of query functions +is available on the OpenKIM webpage at +"https://openkim.org/doc/repository/kim-query"_https://openkim.org/doc/repository/kim-query. + +NOTE: All query functions require the {model} keyword, which identifies +the IM whose predictions are being queried. This keyword is automatically +generated by {kim_query} based on the IM set in {kim_init} and must not +be specified as an argument to {kim_query}. + +NOTE: Each {query_function} is associated with a default method (implemented +as a "KIM Test"_https://openkim.org/doc/evaluation/kim-tests/) +used to compute this property. In cases where there are multiple +methods in OpenKIM for computing a property, a {method} keyword can +be provided to select the method of choice. See the +"query documentation"_https://openkim.org/doc/repository/kim-query +to see which methods are available for a given {query function}. + +{kim_query} Usage Examples and Further Clarifications: :h6 + +The data obtained by {kim_query} commands can be used as part of the setup +or analysis phases of LAMMPS simulations. Some examples are given below. + +[Define an equilibrium fcc crystal] + +kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal +boundary p p p +kim_query a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\] +lattice fcc $\{a0\} +... :pre + +The {kim_query} command retrieves from "OpenKIM"_https://openkim.org +the equilibrium lattice constant predicted by the Ercolessi and Adams (1994) +potential for the fcc structure and places it in +variable {a0}. This variable is then used on the next line to set up the +crystal. By using {kim_query}, the user is saved the trouble and possible +error of tracking this value down, or of having to perform an energy +minimization to find the equilibrium lattice constant. + +Note that in {unit_conversion_mode} the results obtained from a +{kim_query} would need to be converted to the appropriate units system. +For example, in the above script, the lattice command would need to be +changed to: "lattice fcc $\{a0\}*$\{_u_distance\}". + +:link(split_example) +[Define an equilibrium hcp crystal] + +kim_init EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000 metal +boundary p p p +kim_query latconst split get_lattice_constant_hexagonal crystal=\["hcp"\] species=\["Zr"\] units=\["angstrom"\] +variable a0 equal latconst_1 +variable c0 equal latconst_2 +variable c_to_a equal $\{c0\}/$\{a0\} +lattice custom $\{a0\} a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 $\{c_to_a\} & + basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 +... :pre + +In this case the {kim_query} returns two arguments (since the hexagonal +close packed (hcp) structure has two independent lattice constants). +The default behavior of {kim_query} returns the result as a string +with the values separated by commas. The optional keyword {split} +separates the result values into individual variables of the form +{prefix_I}, where {prefix} is set to the the {kim_query} {variable} argument +and {I} ranges from 1 to the number of returned values. The number and order of +the returned values is determined by the type of query performed. + +[Define a crystal at finite temperature accounting for thermal expansion] + +kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal +boundary p p p +kim_query a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\] +kim_query alpha get_linear_thermal_expansion_coefficient_cubic crystal=\["fcc"\] species=\["Al"\] units=\["1/K"\] temperature=\[293.15\] temperature_units=\["K"\] +variable DeltaT equal 300 +lattice fcc $\{a0\}*$\{alpha\}*$\{DeltaT\} +... :pre + +As in the previous example, the equilibrium lattice constant is obtained +for the Ercolessi and Adams (1994) potential. However, in this case the +crystal is scaled to the appropriate lattice constant at room temperature +(293.15 K) by using the linear thermal expansion constant predicted by the +potential. + +NOTE: When passing numerical values as arguments (as in the case +of the temperature in the above example) it is also possible to pass a +tolerance indicating how close to the value is considered a match. +If no tolerance is passed a default value is used. If multiple results +are returned (indicating that the tolerance is too large), {kim_query} +will return an error. See the +"query documentation"_https://openkim.org/doc/repository/kim-query +to see which numerical arguments and tolerances are available for a +given {query function}. + +[Compute defect formation energy] + +kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal +... +... Build fcc crystal containing some defect and compute the total energy +... which is stored in the variable {Etot} +... +kim_query Ec get_cohesive_energy_cubic crystal=\["fcc"\] species=\["Al"\] units=\["eV"\] +variable Eform equal $\{Etot\} - count(all)*$\{Ec\} +... :pre + +The defect formation energy {Eform} is computed by subtracting from {Etot} the +ideal fcc cohesive energy of the atoms in the system obtained from +"OpenKIM"_https://openkim.org for the Ercolessi and Adams (1994) potential. + +NOTE: {kim_query} commands return results archived in +"OpenKIM"_https://openkim.org. These results are obtained +using programs for computing material properties +(KIM Tests and KIM Test Drivers) that were contributed to OpenKIM. +In order to give credit to Test developers, the number of times results +from these programs are queried is tracked. No other information about +the nature of the query or its source is recorded. + + +Citation of OpenKIM IMs :h4 + +When publishing results obtained using OpenKIM IMs researchers are requested +to cite the OpenKIM project "(Tadmor)"_#kim-mainpaper, KIM API +"(Elliott)"_#kim-api, and the specific IM codes used in the simulations, +in addition to the relevant scientific references for the IM. +The citation format for an IM is displayed on its page on +"OpenKIM"_https://openkim.org along with the corresponding BibTex file, +and is automatically added to the LAMMPS {log.cite} file. + +Citing the IM software (KIM infrastructure and specific PM or SM codes) +used in the simulation gives credit to the researchers who developed them +and enables open source efforts like OpenKIM to function. + + +[Restrictions:] + +The set of {kim_commands} is part of the KIM package. It is only enabled if +LAMMPS is built with that package. A requirement for the KIM package, +is the KIM API library that must be downloaded from the +"OpenKIM website"_https://openkim.org/kim-api/ and installed before +LAMMPS is compiled. When installing LAMMPS from binary, the kim-api package +is a dependency that is automatically downloaded and installed. See the KIM +section of the "Packages details"_Packages_details.html for details. + +Furthermore, when using {kim_commands} to run KIM SMs, any packages required +by the native potential being used or other commands or fixes that it invokes +must be installed. + +[Related commands:] + +"pair_style kim"_pair_kim.html + +:line + +:link(kim-mainpaper) +[(Tadmor)] Tadmor, Elliott, Sethna, Miller and Becker, JOM, 63, 17 (2011). +doi: "https://doi.org/10.1007/s11837-011-0102-6"_https://doi.org/10.1007/s11837-011-0102-6 + +:link(kim-api) +[(Elliott)] Elliott, Tadmor and Bernstein, "https://openkim.org/kim-api"_https://openkim.org/kim-api (2011) +doi: "https://doi.org/10.25950/FF8F563A"_https://doi.org/10.25950/FF8F563A diff --git a/doc/src/kim_query.txt b/doc/src/kim_query.txt deleted file mode 100644 index c581de0ebbee7637b6ce6f160a5f862abc956a03..0000000000000000000000000000000000000000 --- a/doc/src/kim_query.txt +++ /dev/null @@ -1,46 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -kim_query command :h3 - -[Syntax:] - -kim_query variable query_function web_query_flags :pre - -variable = name of a (string style) variable where the result of the query is stored -query_function = name of the OpenKIM web API query function to be used -web_query_flags = a series of keyword=value pairs that represent the web query; supported keywords depend on query function :ul - -[Examples:] - -kim_query latconst get_test_result test=TE_156715955670 model=MO_800509458712 & - prop=structure-cubic-crystal-npt species=\["Al"\] keys=\["a"\] units=\["angstrom"\] :pre - -[Description:] - -The kim_query command allows to retrieve properties from the OpenKIM -through a web query. The result is stored in a string style -"variable"_variable.html, the name of which must be given as the first -argument of the kim_query command. The second required argument is the -name of the actual query function (e.g. {get_test_result}). All following -arguments are parameters handed over to the web query in the format -{keyword=value}. The list of supported keywords and the type of how -the value has to be encoded depends on the query function used. This -mirrors the functionality available on the OpenKIM webpage at -"https://query.openkim.org"_https://query.openkim.org/ - -[Restrictions:] - -This command is part of the KIM package. It is only enabled if -LAMMPS was built with that package. Furthermore, its correct -functioning depends on compiling LAMMPS with libcurl support. -See the "Build package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_style kim"_pair_kim.html, "variable"_variable.html diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 8abe9cffa18cee3d7e6e8850cf85b4e982384b35..ef5a4275dfe479989e619d99e760e97bad4e3fb6 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -42,6 +42,7 @@ Commands_compute.html Commands_pair.html Commands_bond.html Commands_kspace.html +Commands_removed.html Packages.html Packages_standard.html Packages_user.html @@ -167,7 +168,7 @@ if.html include.html info.html jump.html -kim_query.html +kim_commands.html label.html lattice.html log.html @@ -455,6 +456,7 @@ compute_global_atom.html compute_group_group.html compute_gyration.html compute_gyration_chunk.html +compute_gyration_shape.html compute_heat_flux.html compute_hexorder_atom.html compute_improper.html @@ -468,6 +470,7 @@ compute_ke_rigid.html compute_meso_e_atom.html compute_meso_rho_atom.html compute_meso_t_atom.html +compute_momentum.html compute_msd.html compute_msd_chunk.html compute_msd_nongauss.html diff --git a/doc/src/pair_adp.txt b/doc/src/pair_adp.txt index fc888ffbffa7b38779ddaa9730316c787445d3cc..de6717a6c3571923cabf8cb3fbc3386b2f6ae18b 100644 --- a/doc/src/pair_adp.txt +++ b/doc/src/pair_adp.txt @@ -42,16 +42,17 @@ the ADP potential files themselves. Likewise, the ADP potential files list atomic masses; thus you do not need to use the "mass"_mass.html command to specify them. -The NIST WWW site distributes and documents ADP potentials: +[ADP potentials are available from:] -http://www.ctcms.nist.gov/potentials :pre +The NIST WWW site at http://www.ctcms.nist.gov/potentials. +Note that ADP potentials obtained from NIST must be converted +into the extended DYNAMO {setfl} format discussed below. +:l -Note that these must be converted into the extended DYNAMO {setfl} -format discussed below. - -The NIST site is maintained by Chandler Becker (cbecker at nist.gov) -who is good resource for info on interatomic potentials and file -formats. +The OpenKIM Project at https://openkim.org/browse/models/by-type provides +ADP potentials that can be used directly in LAMMPS with the "kim_commands +interface"_kim_commands.html. +:l :line diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt index a415ac606ba7ffef1352b768a222e3a39978f085..41593675babaf137289d23bf06ea597a7bb2fbdf 100644 --- a/doc/src/pair_kim.txt +++ b/doc/src/pair_kim.txt @@ -12,76 +12,72 @@ pair_style kim command :h3 pair_style kim model :pre -model = name of KIM model (potential) +model = name of a KIM model (the KIM ID for models archived in OpenKIM) [Examples:] -pair_style kim ex_model_Ar_P_LJ -pair_coeff * * Ar Ar :pre +pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005 +pair_coeff * * Si :pre [Description:] -This pair style is a wrapper on the "Knowledge Base for Interatomic +This pair style is a wrapper on the "Open Knowledgebase of Interatomic Models (OpenKIM)"_https://openkim.org repository of interatomic -potentials, so that they can be used by LAMMPS scripts. +potentials to enable their use in LAMMPS scripts. -Note that in LAMMPS lingo, a KIM model driver is a pair style -(e.g. EAM or Tersoff). A KIM model is a pair style for a particular -element or alloy and set of parameters, e.g. EAM for Cu with a -specific EAM potential file. +The preferred interface for using interatomic models archived in +OpenKIM is the "kim_commands interface"_kim_commands.html. That +interface supports both "KIM Portable Models" (PMs) that conform to the +KIM API Portable Model Interface (PMI) and can be used by any +simulation code that conforms to the KIM API/PMI, and +"KIM Simulator Models" that are natively implemented within a single +simulation code (like LAMMPS) and can only be used with it. +The {pair_style kim} command is limited to KIM PMs. It is +used by the "kim_commands interface"_kim_commands.html as needed. -See the current list of "KIM model -drivers"_https://openkim.org/browse/model-drivers/alphabetical. +NOTE: Since {pair_style kim} is called by {kim_interactions} as needed, +is not recommended to be directly used in input scripts. -See the current list of all "KIM -models"_https://openkim.org/browse/models/by-model-drivers - -To use this pair style, you must first download and install the KIM -API library from the "OpenKIM website"_https://openkim.org. The KIM -section of the "Packages details"_Packages_details.html doc page has -instructions on how to do this with a simple make command, when -building LAMMPS. - -See the examples/kim dir for an input script that uses a KIM model -(potential) for Lennard-Jones. - :line -The argument {model} is the name of the KIM model for a specific -potential as KIM defines it. In principle, LAMMPS can invoke any KIM -model. You should get an error or warning message from either LAMMPS -or KIM if there is an incompatibility. +The argument {model} is the name of the KIM PM. +For potentials archived in OpenKIM +this is the extended KIM ID (see "kim_commands"_kim_commands.html +for details). LAMMPS can invoke any KIM PM, however there can +be incompatibilities (for example due to unit matching issues). +In the event of an incompatibility, the code will terminate with +an error message. Check both the LAMMPS and KIM log files for details. -Only a single pair_coeff command is used with the {kim} style which -specifies the mapping of LAMMPS atom types to KIM elements. This is -done by specifying N additional arguments after the * * in the -pair_coeff command, where N is the number of LAMMPS atom types: +Only a single {pair_coeff} command is used with the {kim} style, which +specifies the mapping of LAMMPS atom types to the species supported by +the KIM PM. This is done by specifying {N} additional arguments +after the * * in the {pair_coeff} command, where {N} is the number of +LAMMPS atom types: N element names = mapping of KIM elements to atom types :ul -As an example, imagine the KIM model supports Si and C atoms. If your -LAMMPS simulation has 4 atom types and you want the 1st 3 to be Si, -and the 4th to be C, you would use the following pair_coeff command: +For example, consider a KIM PM that supports Si and C species. +If the LAMMPS simulation has four atom types, where the first three are Si, +and the fourth is C, the following {pair_coeff} command would be used: pair_coeff * * Si Si Si C :pre -The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The first three Si arguments map LAMMPS atom types 1,2,3 to Si as -defined within KIM. The final C argument maps LAMMPS atom type 4 to C -as defined within KIM. +The first two arguments must be * * so as to span all LAMMPS atom types. +The first three Si arguments map LAMMPS atom types 1, 2, and 3 to Si as +defined within KIM PM. The final C argument maps LAMMPS atom type 4 to C. :line In addition to the usual LAMMPS error messages, the KIM library itself may generate errors, which should be printed to the screen. In this -case it is also useful to check the kim.log file for additional error -information. The file kim.log should be generated in the same +case it is also useful to check the {kim.log} file for additional error +information. The file {kim.log} should be generated in the same directory where LAMMPS is running. To download, build, and install the KIM library on your system, see -the lib/kim/README file. Once you have done this and built LAMMPS +the {lib/kim/README} file. Once you have done this and built LAMMPS with the KIM package installed you can run the example input scripts -in examples/kim. +in {examples/kim}. :line @@ -103,15 +99,14 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] -This pair style is part of the KIM package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. +This pair style is part of the KIM package. See details on +restrictions in "kim_commands"_kim_commands.html. This current version of pair_style kim is compatible with the kim-api package version 2.0.0 and higher. [Related commands:] -"pair_coeff"_pair_coeff.html +"pair_coeff"_pair_coeff.html, "kim_commands"_kim_commands.html [Default:] none diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index da5c86907557acf3668577a255c0b026a6cdb392..1dea2293938a906af2cd6a054fe30db21154bb19 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -20,6 +20,7 @@ acolor acos Acta actinide +acylindricity addforce Addington addtorque @@ -113,6 +114,7 @@ askoose asphere ASPHERE aspherical +asphericity Asq assignee Asta @@ -481,6 +483,7 @@ cvff cwiggle cygwin Cygwin +cylindrically Cyrot cyrstals Daivis @@ -526,6 +529,7 @@ decrementing deeppink deepskyblue defgrad +defn deformable del deleteIDs @@ -574,6 +578,7 @@ Dihedrals dihydride Dij dimdim +dimensioned dimensionality dimgray dipolar @@ -603,6 +608,7 @@ Dobson Dodds dodgerblue dof +doi Donadio dotc Doty @@ -754,6 +760,7 @@ equilibrating equilibration Equilibria equilization +Ercolessi eradius erate erc @@ -880,6 +887,7 @@ Fogarty Foiles fopenmp forestgreen +formatarg formulae Forschungszentrum Fortran @@ -1514,6 +1522,7 @@ lz Maaravi Mackay Mackrodt +Macromolecules macroparticle Madura Magda @@ -1539,6 +1548,7 @@ Mandelli Manh manifoldforce Manolopoulos +manpages manybody MANYBODY Maras @@ -1619,6 +1629,7 @@ meso mesoparticle mesoscale mesoscopic +metadata metadynamics Metadynamics Methfessel @@ -2257,6 +2268,7 @@ quati quatj quatk quatw +queryargs Queteschiner qw qx @@ -2286,6 +2298,7 @@ rcutfac rdc rdf RDideal +rdx README realtime reamin @@ -2312,6 +2325,8 @@ Rensselaer reparameterizing repo representable +Reproducibility +reproducibility repuls rescale rescaled @@ -2602,6 +2617,7 @@ Stoll stopstep Stouch Straatsma +Strachan Stratford Strathclyde Straub @@ -2629,6 +2645,7 @@ superset supersphere Supinski surfactants +Suter Sutmann svn sw @@ -2690,6 +2707,7 @@ th Thakkar thb thei +Theodorou Theor thermalization thermalize @@ -2812,6 +2830,7 @@ txt typeI typeJ typeN +typeargs Tz Tzou ub @@ -2840,6 +2859,7 @@ undump uniaxial uniaxially unimodal +unitarg unitless Universite unix diff --git a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized similarity index 88% rename from examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon rename to examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized index 73cb2eb27031a7a5798dc53c50bd9160e9794eb3..b152dec00ae6307159939e4f35f521b5ed9b7ef9 100644 --- a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon +++ b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized @@ -38,6 +38,8 @@ fix myrxns all bond/react stabilization yes statted_grp .03 & fix 1 statted_grp_REACT nvt temp 300 300 100 +# optionally, you can customize behavior of reacting atoms, +# by using the internally-created 'bond_react_MASTER_group', like so: fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] diff --git a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized new file mode 100644 index 0000000000000000000000000000000000000000..1e5a4938211a2a6c83c6b8180467b7da153c2d49 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized @@ -0,0 +1,48 @@ +# two monomer nylon example +# reaction produces a condensed water molecule + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data tiny_nylon.data + +velocity all create 300.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.data_template +molecule mol2 rxn1_stp1_reacted.data_template +molecule mol3 rxn1_stp2_unreacted.data_template +molecule mol4 rxn1_stp2_reacted.data_template + +thermo 50 + +# dump 1 all xyz 1 test_vis.xyz + +fix myrxns all bond/react stabilization no & + react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map & + react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map + +fix 1 all nve/limit .03 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] + +# restart 100 restart1 restart2 + +run 1000 + +# write_restart restart_longrun +# write_data restart_longrun.data diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 deleted file mode 100644 index 344439f94c5906e1fc7417921b89434ae0a7b8b5..0000000000000000000000000000000000000000 --- a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 +++ /dev/null @@ -1,370 +0,0 @@ -LAMMPS (20 Apr 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - using 1 OpenMP thread(s) per MPI task -# two monomer nylon example -# reaction produces a condensed water molecule - -units real - -boundary p p p - -atom_style full - -kspace_style pppm 1.0e-4 - -pair_style lj/class2/coul/long 8.5 - -angle_style class2 - -bond_style class2 - -dihedral_style class2 - -improper_style class2 - -read_data tiny_nylon.data - orthogonal box = (-25 -25 -25) to (25 25 25) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 44 atoms - reading velocities ... - 44 velocities - scanning bonds ... - 9 = max bonds/atom - scanning angles ... - 21 = max angles/atom - scanning dihedrals ... - 29 = max dihedrals/atom - scanning impropers ... - 29 = max impropers/atom - reading bonds ... - 42 bonds - reading angles ... - 74 angles - reading dihedrals ... - 100 dihedrals - reading impropers ... - 44 impropers - 4 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 41 = max # of special neighbors - -velocity all create 300.0 4928459 dist gaussian - -molecule mol1 rxn1_stp1_unreacted.data_template -Read molecule mol1: - 18 atoms with max type 8 - 16 bonds with max type 14 - 25 angles with max type 28 - 23 dihedrals with max type 36 - 14 impropers with max type 11 -molecule mol2 rxn1_stp1_reacted.data_template -Read molecule mol2: - 18 atoms with max type 9 - 17 bonds with max type 13 - 31 angles with max type 27 - 39 dihedrals with max type 33 - 20 impropers with max type 1 -molecule mol3 rxn1_stp2_unreacted.data_template -Read molecule mol3: - 15 atoms with max type 9 - 14 bonds with max type 13 - 25 angles with max type 27 - 30 dihedrals with max type 33 - 16 impropers with max type 1 -molecule mol4 rxn1_stp2_reacted.data_template -Read molecule mol4: - 15 atoms with max type 11 - 13 bonds with max type 15 - 19 angles with max type 29 - 16 dihedrals with max type 32 - 10 impropers with max type 13 - -thermo 50 - -# dump 1 all xyz 1 test_vis.xyz - -fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map -WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined - -fix 1 statted_grp nvt temp 300 300 100 - -fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 - -thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] - -# restart 100 restart1 restart2 - -run 10000 -PPPM initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.0534597 - grid = 2 2 2 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0402256 - estimated relative force accuracy = 0.000121138 - using double precision FFTs - 3d grid and FFT values/proc = 343 8 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 10.5 - ghost atom cutoff = 10.5 - binsize = 5.25, bins = 10 10 10 - 2 neighbor lists, perpetual/occasional/extra = 1 1 0 - (1) pair lj/class2/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard - (2) fix bond/react, occasional, copy from (1) - attributes: half, newton on - pair build: copy - stencil: none - bin: none -WARNING: Inconsistent image flags (../domain.cpp:786) -Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.34 | 33.34 Mbytes -Step Temp Press Density f_myrxns[1] f_myrxns[2] - 0 300 346.78165 0.0034851739 0 0 - 50 296.70408 -51.30066 0.0034851739 1 0 - 100 274.25324 46.715512 0.0034851739 1 1 - 150 471.61579 31.321598 0.0034851739 1 1 - 200 362.87766 42.061118 0.0034851739 1 1 - 250 367.58058 65.303109 0.0034851739 1 1 - 300 372.38236 -52.421725 0.0034851739 1 1 - 350 297.69957 17.869945 0.0034851739 1 1 - 400 258.30433 49.19156 0.0034851739 1 1 - 450 253.34384 -5.8162637 0.0034851739 1 1 - 500 269.96465 -43.337517 0.0034851739 1 1 - 550 303.23718 10.180246 0.0034851739 1 1 - 600 329.59579 -48.97461 0.0034851739 1 1 - 650 350.42568 50.983183 0.0034851739 1 1 - 700 342.03272 35.43465 0.0034851739 1 1 - 750 269.23405 -41.873166 0.0034851739 1 1 - 800 245.15025 13.953092 0.0034851739 1 1 - 850 257.85421 -3.1492141 0.0034851739 1 1 - 900 316.15644 7.7798301 0.0034851739 1 1 - 950 299.9124 -15.77014 0.0034851739 1 1 - 1000 302.89968 -17.049693 0.0034851739 1 1 - 1050 308.91651 71.84632 0.0034851739 1 1 - 1100 348.43932 -18.742012 0.0034851739 1 1 - 1150 309.03036 50.536311 0.0034851739 1 1 - 1200 318.9761 -16.905746 0.0034851739 1 1 - 1250 320.42806 -0.057975092 0.0034851739 1 1 - 1300 289.7824 18.200772 0.0034851739 1 1 - 1350 284.79836 -9.1978427 0.0034851739 1 1 - 1400 325.43292 42.082833 0.0034851739 1 1 - 1450 261.5041 -37.823325 0.0034851739 1 1 - 1500 298.88723 -5.1647385 0.0034851739 1 1 - 1550 291.37403 -7.7764201 0.0034851739 1 1 - 1600 293.83475 22.2458 0.0034851739 1 1 - 1650 293.80611 24.202512 0.0034851739 1 1 - 1700 291.70205 -23.397884 0.0034851739 1 1 - 1750 292.32437 -10.671214 0.0034851739 1 1 - 1800 302.01367 -11.671025 0.0034851739 1 1 - 1850 322.1651 24.438331 0.0034851739 1 1 - 1900 310.45076 45.343592 0.0034851739 1 1 - 1950 325.91745 -19.847809 0.0034851739 1 1 - 2000 276.89662 63.387098 0.0034851739 1 1 - 2050 311.33783 -24.683247 0.0034851739 1 1 - 2100 346.2336 -27.526891 0.0034851739 1 1 - 2150 345.30604 -15.722411 0.0034851739 1 1 - 2200 346.7718 -17.857633 0.0034851739 1 1 - 2250 304.28676 -1.9965581 0.0034851739 1 1 - 2300 322.56372 -31.786868 0.0034851739 1 1 - 2350 282.64326 6.1982735 0.0034851739 1 1 - 2400 286.65759 -63.207781 0.0034851739 1 1 - 2450 257.05528 32.931491 0.0034851739 1 1 - 2500 283.64386 26.912373 0.0034851739 1 1 - 2550 299.54005 27.277039 0.0034851739 1 1 - 2600 283.92503 14.660972 0.0034851739 1 1 - 2650 321.93453 -18.977358 0.0034851739 1 1 - 2700 376.7189 31.826935 0.0034851739 1 1 - 2750 372.20075 -32.821697 0.0034851739 1 1 - 2800 361.40604 83.035183 0.0034851739 1 1 - 2850 332.27269 -23.927452 0.0034851739 1 1 - 2900 331.14638 -0.12328446 0.0034851739 1 1 - 2950 303.67489 -24.078857 0.0034851739 1 1 - 3000 311.40462 21.563537 0.0034851739 1 1 - 3050 284.72849 -23.849667 0.0034851739 1 1 - 3100 303.48477 39.347763 0.0034851739 1 1 - 3150 264.2739 -0.22299879 0.0034851739 1 1 - 3200 300.03351 31.545323 0.0034851739 1 1 - 3250 288.56663 5.7225228 0.0034851739 1 1 - 3300 200.13238 -31.239655 0.0034851739 1 1 - 3350 231.32512 16.631728 0.0034851739 1 1 - 3400 260.57402 2.1717992 0.0034851739 1 1 - 3450 301.47128 -42.210623 0.0034851739 1 1 - 3500 321.77414 40.074365 0.0034851739 1 1 - 3550 353.21858 28.387783 0.0034851739 1 1 - 3600 331.45989 -57.800858 0.0034851739 1 1 - 3650 303.88123 44.86596 0.0034851739 1 1 - 3700 329.73833 -0.80615652 0.0034851739 1 1 - 3750 297.55588 -0.49626039 0.0034851739 1 1 - 3800 286.38794 -10.010003 0.0034851739 1 1 - 3850 290.17417 -43.51187 0.0034851739 1 1 - 3900 247.88933 51.23735 0.0034851739 1 1 - 3950 332.31324 -18.194985 0.0034851739 1 1 - 4000 325.56802 18.402825 0.0034851739 1 1 - 4050 338.37593 36.430977 0.0034851739 1 1 - 4100 370.95478 39.290285 0.0034851739 1 1 - 4150 348.47859 -7.0779678 0.0034851739 1 1 - 4200 241.30632 -33.371788 0.0034851739 1 1 - 4250 242.17258 -9.986197 0.0034851739 1 1 - 4300 300.85311 -7.9244294 0.0034851739 1 1 - 4350 273.15684 -21.257283 0.0034851739 1 1 - 4400 305.77463 -5.8720722 0.0034851739 1 1 - 4450 314.97697 45.0373 0.0034851739 1 1 - 4500 310.77723 16.958773 0.0034851739 1 1 - 4550 302.1742 12.156862 0.0034851739 1 1 - 4600 319.74799 6.84889 0.0034851739 1 1 - 4650 270.86805 -13.767905 0.0034851739 1 1 - 4700 249.81731 -31.197487 0.0034851739 1 1 - 4750 285.86481 -9.8916364 0.0034851739 1 1 - 4800 233.98321 7.1338571 0.0034851739 1 1 - 4850 302.60551 49.262889 0.0034851739 1 1 - 4900 316.55056 34.663247 0.0034851739 1 1 - 4950 357.32741 11.583006 0.0034851739 1 1 - 5000 400.21045 -8.1781061 0.0034851739 1 1 - 5050 390.01845 -20.490275 0.0034851739 1 1 - 5100 378.84247 -41.328757 0.0034851739 1 1 - 5150 324.02038 -15.023862 0.0034851739 1 1 - 5200 262.08429 10.937354 0.0034851739 1 1 - 5250 255.75508 16.381455 0.0034851739 1 1 - 5300 277.84989 40.68232 0.0034851739 1 1 - 5350 302.92832 9.1989494 0.0034851739 1 1 - 5400 283.7196 -1.6584671 0.0034851739 1 1 - 5450 300.71266 -4.7030295 0.0034851739 1 1 - 5500 343.5499 -0.30550044 0.0034851739 1 1 - 5550 369.51271 21.691649 0.0034851739 1 1 - 5600 372.69789 -38.67994 0.0034851739 1 1 - 5650 327.41266 11.352137 0.0034851739 1 1 - 5700 278.98614 -23.827304 0.0034851739 1 1 - 5750 308.30054 -20.756187 0.0034851739 1 1 - 5800 341.45594 28.058441 0.0034851739 1 1 - 5850 322.97844 -10.731921 0.0034851739 1 1 - 5900 304.53591 32.825279 0.0034851739 1 1 - 5950 287.1752 -36.780091 0.0034851739 1 1 - 6000 296.52681 18.781896 0.0034851739 1 1 - 6050 314.25442 15.992829 0.0034851739 1 1 - 6100 313.86576 3.4342714 0.0034851739 1 1 - 6150 325.64196 32.392039 0.0034851739 1 1 - 6200 367.42931 -27.160706 0.0034851739 1 1 - 6250 369.30798 39.020934 0.0034851739 1 1 - 6300 328.92285 -23.175157 0.0034851739 1 1 - 6350 305.63077 4.9024453 0.0034851739 1 1 - 6400 241.70341 -13.676629 0.0034851739 1 1 - 6450 265.66717 2.40612 0.0034851739 1 1 - 6500 249.36037 13.420255 0.0034851739 1 1 - 6550 294.53814 10.853462 0.0034851739 1 1 - 6600 308.2025 18.995308 0.0034851739 1 1 - 6650 305.43797 -49.56785 0.0034851739 1 1 - 6700 320.27344 11.336281 0.0034851739 1 1 - 6750 321.78666 -23.463899 0.0034851739 1 1 - 6800 303.40388 7.6224553 0.0034851739 1 1 - 6850 297.18966 51.52256 0.0034851739 1 1 - 6900 284.18909 -8.4947203 0.0034851739 1 1 - 6950 331.03663 13.233655 0.0034851739 1 1 - 7000 311.37928 -43.265479 0.0034851739 1 1 - 7050 286.81661 -14.174683 0.0034851739 1 1 - 7100 302.84119 12.048954 0.0034851739 1 1 - 7150 297.19357 -43.111968 0.0034851739 1 1 - 7200 332.47359 26.048249 0.0034851739 1 1 - 7250 262.70677 41.176242 0.0034851739 1 1 - 7300 250.61405 -23.413982 0.0034851739 1 1 - 7350 296.91117 35.88133 0.0034851739 1 1 - 7400 245.09229 -13.447194 0.0034851739 1 1 - 7450 272.28131 -23.322585 0.0034851739 1 1 - 7500 209.04985 13.871239 0.0034851739 1 1 - 7550 255.00955 4.9325621 0.0034851739 1 1 - 7600 312.30937 -37.368274 0.0034851739 1 1 - 7650 305.65903 55.245496 0.0034851739 1 1 - 7700 325.09504 -18.347711 0.0034851739 1 1 - 7750 363.28282 -22.479686 0.0034851739 1 1 - 7800 350.17429 26.849547 0.0034851739 1 1 - 7850 271.70853 -17.764575 0.0034851739 1 1 - 7900 272.66484 -11.701967 0.0034851739 1 1 - 7950 298.60202 -12.765675 0.0034851739 1 1 - 8000 274.58852 49.641532 0.0034851739 1 1 - 8050 304.72347 -0.55414183 0.0034851739 1 1 - 8100 328.30757 -39.861301 0.0034851739 1 1 - 8150 406.67601 2.8999409 0.0034851739 1 1 - 8200 332.20083 -51.217399 0.0034851739 1 1 - 8250 354.50609 53.128769 0.0034851739 1 1 - 8300 337.2758 20.68562 0.0034851739 1 1 - 8350 361.89708 -54.185869 0.0034851739 1 1 - 8400 305.63496 24.058529 0.0034851739 1 1 - 8450 303.27461 4.304683 0.0034851739 1 1 - 8500 253.53694 -10.909021 0.0034851739 1 1 - 8550 277.03017 23.241479 0.0034851739 1 1 - 8600 291.41844 -22.240665 0.0034851739 1 1 - 8650 307.85368 31.919587 0.0034851739 1 1 - 8700 309.19724 0.53529642 0.0034851739 1 1 - 8750 354.6583 11.565515 0.0034851739 1 1 - 8800 329.78598 19.5996 0.0034851739 1 1 - 8850 240.79198 21.803515 0.0034851739 1 1 - 8900 318.40749 -59.816923 0.0034851739 1 1 - 8950 308.47211 -57.808635 0.0034851739 1 1 - 9000 271.51207 50.943482 0.0034851739 1 1 - 9050 249.4005 6.7529187 0.0034851739 1 1 - 9100 221.8772 47.196092 0.0034851739 1 1 - 9150 297.9351 4.0058184 0.0034851739 1 1 - 9200 274.85051 -24.774393 0.0034851739 1 1 - 9250 336.04757 5.3799028 0.0034851739 1 1 - 9300 380.44956 -22.389381 0.0034851739 1 1 - 9350 336.9824 23.050616 0.0034851739 1 1 - 9400 304.46425 32.530218 0.0034851739 1 1 - 9450 317.55591 -22.265425 0.0034851739 1 1 - 9500 323.70901 -7.0159787 0.0034851739 1 1 - 9550 316.07308 28.062131 0.0034851739 1 1 - 9600 262.74608 -0.78519192 0.0034851739 1 1 - 9650 271.55045 -21.430123 0.0034851739 1 1 - 9700 239.6022 14.483637 0.0034851739 1 1 - 9750 338.1437 -0.72765302 0.0034851739 1 1 - 9800 334.50189 19.495144 0.0034851739 1 1 - 9850 354.87554 19.272719 0.0034851739 1 1 - 9900 334.02141 -22.393457 0.0034851739 1 1 - 9950 293.63651 19.178873 0.0034851739 1 1 - 10000 319.81736 21.904414 0.0034851739 1 1 -Loop time of 1.84987 on 1 procs for 10000 steps with 44 atoms - -Performance: 467.059 ns/day, 0.051 hours/ns, 5405.774 timesteps/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.26152 | 0.26152 | 0.26152 | 0.0 | 14.14 -Bond | 0.74069 | 0.74069 | 0.74069 | 0.0 | 40.04 -Kspace | 0.30505 | 0.30505 | 0.30505 | 0.0 | 16.49 -Neigh | 0.39991 | 0.39991 | 0.39991 | 0.0 | 21.62 -Comm | 0.02261 | 0.02261 | 0.02261 | 0.0 | 1.22 -Output | 0.0034585 | 0.0034585 | 0.0034585 | 0.0 | 0.19 -Modify | 0.099979 | 0.099979 | 0.099979 | 0.0 | 5.40 -Other | | 0.01666 | | | 0.90 - -Nlocal: 44 ave 44 max 44 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 44 ave 44 max 44 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 823 ave 823 max 823 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 823 -Ave neighs/atom = 18.7045 -Ave special neighs/atom = 9.77273 -Neighbor list builds = 10000 -Dangerous builds = 0 - -# write_restart restart_longrun -# write_data restart_longrun.data - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:01 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 deleted file mode 100644 index 377781f48f7091dbc910d9ce1ab0f98723abb7bb..0000000000000000000000000000000000000000 --- a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 +++ /dev/null @@ -1,370 +0,0 @@ -LAMMPS (20 Apr 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - using 1 OpenMP thread(s) per MPI task -# two monomer nylon example -# reaction produces a condensed water molecule - -units real - -boundary p p p - -atom_style full - -kspace_style pppm 1.0e-4 - -pair_style lj/class2/coul/long 8.5 - -angle_style class2 - -bond_style class2 - -dihedral_style class2 - -improper_style class2 - -read_data tiny_nylon.data - orthogonal box = (-25 -25 -25) to (25 25 25) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 44 atoms - reading velocities ... - 44 velocities - scanning bonds ... - 9 = max bonds/atom - scanning angles ... - 21 = max angles/atom - scanning dihedrals ... - 29 = max dihedrals/atom - scanning impropers ... - 29 = max impropers/atom - reading bonds ... - 42 bonds - reading angles ... - 74 angles - reading dihedrals ... - 100 dihedrals - reading impropers ... - 44 impropers - 4 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 41 = max # of special neighbors - -velocity all create 300.0 4928459 dist gaussian - -molecule mol1 rxn1_stp1_unreacted.data_template -Read molecule mol1: - 18 atoms with max type 8 - 16 bonds with max type 14 - 25 angles with max type 28 - 23 dihedrals with max type 36 - 14 impropers with max type 11 -molecule mol2 rxn1_stp1_reacted.data_template -Read molecule mol2: - 18 atoms with max type 9 - 17 bonds with max type 13 - 31 angles with max type 27 - 39 dihedrals with max type 33 - 20 impropers with max type 1 -molecule mol3 rxn1_stp2_unreacted.data_template -Read molecule mol3: - 15 atoms with max type 9 - 14 bonds with max type 13 - 25 angles with max type 27 - 30 dihedrals with max type 33 - 16 impropers with max type 1 -molecule mol4 rxn1_stp2_reacted.data_template -Read molecule mol4: - 15 atoms with max type 11 - 13 bonds with max type 15 - 19 angles with max type 29 - 16 dihedrals with max type 32 - 10 impropers with max type 13 - -thermo 50 - -# dump 1 all xyz 1 test_vis.xyz - -fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map -WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined - -fix 1 statted_grp nvt temp 300 300 100 - -fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 - -thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] - -# restart 100 restart1 restart2 - -run 10000 -PPPM initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.0534597 - grid = 2 2 2 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0402256 - estimated relative force accuracy = 0.000121138 - using double precision FFTs - 3d grid and FFT values/proc = 252 2 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 10.5 - ghost atom cutoff = 10.5 - binsize = 5.25, bins = 10 10 10 - 2 neighbor lists, perpetual/occasional/extra = 1 1 0 - (1) pair lj/class2/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard - (2) fix bond/react, occasional, copy from (1) - attributes: half, newton on - pair build: copy - stencil: none - bin: none -WARNING: Inconsistent image flags (../domain.cpp:786) -Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes -Step Temp Press Density f_myrxns[1] f_myrxns[2] - 0 300 346.78165 0.0034851739 0 0 - 50 296.70408 -51.30066 0.0034851739 1 0 - 100 274.25324 46.715512 0.0034851739 1 1 - 150 471.61579 31.321598 0.0034851739 1 1 - 200 362.87766 42.061118 0.0034851739 1 1 - 250 367.58058 65.303109 0.0034851739 1 1 - 300 372.38236 -52.421725 0.0034851739 1 1 - 350 297.69957 17.869945 0.0034851739 1 1 - 400 258.30433 49.19156 0.0034851739 1 1 - 450 253.34384 -5.8162637 0.0034851739 1 1 - 500 269.96465 -43.337517 0.0034851739 1 1 - 550 303.23718 10.180246 0.0034851739 1 1 - 600 329.59579 -48.97461 0.0034851739 1 1 - 650 350.42568 50.983183 0.0034851739 1 1 - 700 342.03272 35.43465 0.0034851739 1 1 - 750 269.23405 -41.873166 0.0034851739 1 1 - 800 245.15025 13.953092 0.0034851739 1 1 - 850 257.85421 -3.1492141 0.0034851739 1 1 - 900 316.15644 7.7798301 0.0034851739 1 1 - 950 299.9124 -15.77014 0.0034851739 1 1 - 1000 302.89968 -17.049693 0.0034851739 1 1 - 1050 308.91651 71.84632 0.0034851739 1 1 - 1100 348.43932 -18.742012 0.0034851739 1 1 - 1150 309.03036 50.536311 0.0034851739 1 1 - 1200 318.9761 -16.905746 0.0034851739 1 1 - 1250 320.42806 -0.057975092 0.0034851739 1 1 - 1300 289.7824 18.200772 0.0034851739 1 1 - 1350 284.79836 -9.1978427 0.0034851739 1 1 - 1400 325.43292 42.082833 0.0034851739 1 1 - 1450 261.5041 -37.823325 0.0034851739 1 1 - 1500 298.88723 -5.1647385 0.0034851739 1 1 - 1550 291.37403 -7.7764201 0.0034851739 1 1 - 1600 293.83475 22.2458 0.0034851739 1 1 - 1650 293.80611 24.202512 0.0034851739 1 1 - 1700 291.70205 -23.397884 0.0034851739 1 1 - 1750 292.32437 -10.671214 0.0034851739 1 1 - 1800 302.01367 -11.671025 0.0034851739 1 1 - 1850 322.1651 24.438331 0.0034851739 1 1 - 1900 310.45076 45.343592 0.0034851739 1 1 - 1950 325.91745 -19.847809 0.0034851739 1 1 - 2000 276.89662 63.387098 0.0034851739 1 1 - 2050 311.33783 -24.683247 0.0034851739 1 1 - 2100 346.2336 -27.526891 0.0034851739 1 1 - 2150 345.30604 -15.722411 0.0034851739 1 1 - 2200 346.7718 -17.857633 0.0034851739 1 1 - 2250 304.28676 -1.9965581 0.0034851739 1 1 - 2300 322.56372 -31.786868 0.0034851739 1 1 - 2350 282.64326 6.1982735 0.0034851739 1 1 - 2400 286.65759 -63.207781 0.0034851739 1 1 - 2450 257.05528 32.931491 0.0034851739 1 1 - 2500 283.64386 26.912373 0.0034851739 1 1 - 2550 299.54005 27.277039 0.0034851739 1 1 - 2600 283.92503 14.660972 0.0034851739 1 1 - 2650 321.93453 -18.977358 0.0034851739 1 1 - 2700 376.7189 31.826935 0.0034851739 1 1 - 2750 372.20075 -32.821697 0.0034851739 1 1 - 2800 361.40604 83.035183 0.0034851739 1 1 - 2850 332.27269 -23.927452 0.0034851739 1 1 - 2900 331.14638 -0.12328446 0.0034851739 1 1 - 2950 303.67489 -24.078857 0.0034851739 1 1 - 3000 311.40462 21.563537 0.0034851739 1 1 - 3050 284.72849 -23.849667 0.0034851739 1 1 - 3100 303.48477 39.347763 0.0034851739 1 1 - 3150 264.2739 -0.22299878 0.0034851739 1 1 - 3200 300.03351 31.545323 0.0034851739 1 1 - 3250 288.56663 5.7225229 0.0034851739 1 1 - 3300 200.13238 -31.239655 0.0034851739 1 1 - 3350 231.32512 16.631728 0.0034851739 1 1 - 3400 260.57402 2.1717992 0.0034851739 1 1 - 3450 301.47128 -42.210623 0.0034851739 1 1 - 3500 321.77414 40.074365 0.0034851739 1 1 - 3550 353.21858 28.387783 0.0034851739 1 1 - 3600 331.45989 -57.800858 0.0034851739 1 1 - 3650 303.88123 44.86596 0.0034851739 1 1 - 3700 329.73833 -0.8061567 0.0034851739 1 1 - 3750 297.55588 -0.49626022 0.0034851739 1 1 - 3800 286.38794 -10.010003 0.0034851739 1 1 - 3850 290.17417 -43.51187 0.0034851739 1 1 - 3900 247.88933 51.23735 0.0034851739 1 1 - 3950 332.31324 -18.194985 0.0034851739 1 1 - 4000 325.56802 18.402825 0.0034851739 1 1 - 4050 338.37594 36.430977 0.0034851739 1 1 - 4100 370.95478 39.290285 0.0034851739 1 1 - 4150 348.47859 -7.0779683 0.0034851739 1 1 - 4200 241.30632 -33.371789 0.0034851739 1 1 - 4250 242.17258 -9.9861962 0.0034851739 1 1 - 4300 300.85311 -7.924429 0.0034851739 1 1 - 4350 273.15684 -21.257282 0.0034851739 1 1 - 4400 305.77464 -5.8720712 0.0034851739 1 1 - 4450 314.97697 45.037299 0.0034851739 1 1 - 4500 310.77723 16.958771 0.0034851739 1 1 - 4550 302.17421 12.156862 0.0034851739 1 1 - 4600 319.74799 6.8488914 0.0034851739 1 1 - 4650 270.86805 -13.767907 0.0034851739 1 1 - 4700 249.81731 -31.197484 0.0034851739 1 1 - 4750 285.86481 -9.8916332 0.0034851739 1 1 - 4800 233.98321 7.1338518 0.0034851739 1 1 - 4850 302.60551 49.262886 0.0034851739 1 1 - 4900 316.55055 34.663238 0.0034851739 1 1 - 4950 357.32741 11.583013 0.0034851739 1 1 - 5000 400.21044 -8.1780861 0.0034851739 1 1 - 5050 390.01845 -20.490268 0.0034851739 1 1 - 5100 378.84249 -41.328772 0.0034851739 1 1 - 5150 324.02039 -15.023852 0.0034851739 1 1 - 5200 262.08427 10.937367 0.0034851739 1 1 - 5250 255.75506 16.381495 0.0034851739 1 1 - 5300 277.84991 40.682283 0.0034851739 1 1 - 5350 302.92834 9.1989644 0.0034851739 1 1 - 5400 283.71964 -1.6583895 0.0034851739 1 1 - 5450 300.71261 -4.703054 0.0034851739 1 1 - 5500 343.54987 -0.30546396 0.0034851739 1 1 - 5550 369.51272 21.691639 0.0034851739 1 1 - 5600 372.69786 -38.679919 0.0034851739 1 1 - 5650 327.41256 11.352201 0.0034851739 1 1 - 5700 278.9861 -23.82728 0.0034851739 1 1 - 5750 308.30037 -20.756238 0.0034851739 1 1 - 5800 341.4559 28.058314 0.0034851739 1 1 - 5850 322.9786 -10.731862 0.0034851739 1 1 - 5900 304.53598 32.825105 0.0034851739 1 1 - 5950 287.17515 -36.780057 0.0034851739 1 1 - 6000 296.52688 18.782156 0.0034851739 1 1 - 6050 314.25411 15.99272 0.0034851739 1 1 - 6100 313.86572 3.4344108 0.0034851739 1 1 - 6150 325.64197 32.39212 0.0034851739 1 1 - 6200 367.4298 -27.161154 0.0034851739 1 1 - 6250 369.30937 39.020881 0.0034851739 1 1 - 6300 328.92245 -23.175612 0.0034851739 1 1 - 6350 305.6293 4.9011587 0.0034851739 1 1 - 6400 241.70456 -13.675247 0.0034851739 1 1 - 6450 265.66574 2.4049735 0.0034851739 1 1 - 6500 249.3592 13.420453 0.0034851739 1 1 - 6550 294.5367 10.856753 0.0034851739 1 1 - 6600 308.20246 18.992923 0.0034851739 1 1 - 6650 305.43756 -49.57151 0.0034851739 1 1 - 6700 320.27395 11.339101 0.0034851739 1 1 - 6750 321.7875 -23.463361 0.0034851739 1 1 - 6800 303.40316 7.6256997 0.0034851739 1 1 - 6850 297.18652 51.52186 0.0034851739 1 1 - 6900 284.19084 -8.496294 0.0034851739 1 1 - 6950 331.04173 13.227745 0.0034851739 1 1 - 7000 311.38027 -43.26105 0.0034851739 1 1 - 7050 286.82046 -14.171194 0.0034851739 1 1 - 7100 302.81691 12.058085 0.0034851739 1 1 - 7150 297.18018 -43.110658 0.0034851739 1 1 - 7200 332.46131 26.051496 0.0034851739 1 1 - 7250 262.72288 41.161451 0.0034851739 1 1 - 7300 250.62739 -23.440907 0.0034851739 1 1 - 7350 296.92141 35.869216 0.0034851739 1 1 - 7400 245.06807 -13.467896 0.0034851739 1 1 - 7450 272.2659 -23.292836 0.0034851739 1 1 - 7500 209.05776 13.888665 0.0034851739 1 1 - 7550 255.03716 4.9662624 0.0034851739 1 1 - 7600 312.26011 -37.350427 0.0034851739 1 1 - 7650 305.5823 55.208039 0.0034851739 1 1 - 7700 325.13382 -18.370791 0.0034851739 1 1 - 7750 363.24898 -22.473126 0.0034851739 1 1 - 7800 350.19254 26.792307 0.0034851739 1 1 - 7850 271.76418 -17.843445 0.0034851739 1 1 - 7900 272.70301 -11.709349 0.0034851739 1 1 - 7950 298.5993 -12.736235 0.0034851739 1 1 - 8000 274.52611 49.657345 0.0034851739 1 1 - 8050 304.73711 -0.52485689 0.0034851739 1 1 - 8100 328.29239 -39.901891 0.0034851739 1 1 - 8150 406.52096 2.8669076 0.0034851739 1 1 - 8200 332.17309 -51.168754 0.0034851739 1 1 - 8250 354.68419 53.003157 0.0034851739 1 1 - 8300 337.28934 20.766408 0.0034851739 1 1 - 8350 361.81133 -54.159227 0.0034851739 1 1 - 8400 305.59597 24.011667 0.0034851739 1 1 - 8450 303.25823 4.423341 0.0034851739 1 1 - 8500 253.50747 -11.026949 0.0034851739 1 1 - 8550 277.13504 23.204625 0.0034851739 1 1 - 8600 291.40211 -22.253861 0.0034851739 1 1 - 8650 307.93765 32.14162 0.0034851739 1 1 - 8700 309.1529 0.36279434 0.0034851739 1 1 - 8750 355.10326 11.677219 0.0034851739 1 1 - 8800 330.21328 19.235269 0.0034851739 1 1 - 8850 241.29109 21.707386 0.0034851739 1 1 - 8900 319.15363 -60.010115 0.0034851739 1 1 - 8950 308.88552 -57.637014 0.0034851739 1 1 - 9000 272.22373 51.15837 0.0034851739 1 1 - 9050 248.84947 7.3390565 0.0034851739 1 1 - 9100 221.91564 48.387079 0.0034851739 1 1 - 9150 298.03506 2.9058639 0.0034851739 1 1 - 9200 274.25114 -24.597819 0.0034851739 1 1 - 9250 334.08373 5.1079577 0.0034851739 1 1 - 9300 383.07285 -23.274763 0.0034851739 1 1 - 9350 335.00581 20.94212 0.0034851739 1 1 - 9400 309.23862 34.074744 0.0034851739 1 1 - 9450 312.62262 -28.468057 0.0034851739 1 1 - 9500 324.54274 2.851136 0.0034851739 1 1 - 9550 313.32781 22.468182 0.0034851739 1 1 - 9600 269.04372 4.064934 0.0034851739 1 1 - 9650 270.98476 -21.520127 0.0034851739 1 1 - 9700 236.8736 16.250728 0.0034851739 1 1 - 9750 333.94686 1.6864148 0.0034851739 1 1 - 9800 330.91875 12.150018 0.0034851739 1 1 - 9850 343.8603 25.338853 0.0034851739 1 1 - 9900 330.93364 -28.292992 0.0034851739 1 1 - 9950 291.25518 25.795948 0.0034851739 1 1 - 10000 319.25565 25.323846 0.0034851739 1 1 -Loop time of 3.55353 on 4 procs for 10000 steps with 44 atoms - -Performance: 243.139 ns/day, 0.099 hours/ns, 2814.105 timesteps/s -93.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0030422 | 0.10454 | 0.35211 | 44.8 | 2.94 -Bond | 0.0063896 | 0.29222 | 0.94356 | 71.3 | 8.22 -Kspace | 0.88508 | 1.6486 | 1.979 | 35.1 | 46.39 -Neigh | 0.61154 | 0.62212 | 0.63307 | 1.0 | 17.51 -Comm | 0.18944 | 0.24549 | 0.29196 | 7.9 | 6.91 -Output | 0.0050066 | 0.011804 | 0.032134 | 10.8 | 0.33 -Modify | 0.52282 | 0.60522 | 0.69588 | 7.9 | 17.03 -Other | | 0.02359 | | | 0.66 - -Nlocal: 11 ave 44 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 -Nghost: 33 ave 44 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 3 -Neighs: 205.75 ave 823 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 823 -Ave neighs/atom = 18.7045 -Ave special neighs/atom = 9.77273 -Neighbor list builds = 10000 -Dangerous builds = 0 - -# write_restart restart_longrun -# write_data restart_longrun.data - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:03 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..de1167c6523d4ada901d5cf73ff8237da07650df --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 @@ -0,0 +1,148 @@ +LAMMPS (5 Jun 2019) +Reading data file ... + orthogonal box = (-25 -25 -25) to (25 25 25) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.000181113 secs + read_data CPU = 0.0251833 secs +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 14 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 14 impropers with max type 11 +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 20 impropers with max type 1 +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 16 impropers with max type 1 +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 10 impropers with max type 13 +WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785) +WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785) +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp_REACT defined +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:319) + G vector (1/distance) = 0.0534597 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0402256 + estimated relative force accuracy = 0.000121138 + using double precision FFTs + 3d grid and FFT values/proc = 343 8 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 10 10 10 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +WARNING: Inconsistent image flags (../domain.cpp:784) +Per MPI rank memory allocation (min/avg/max) = 34.41 | 34.41 | 34.41 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 293.70542 -52.547388 0.0034851739 1 0 + 100 276.36755 54.81826 0.0034851739 1 1 + 150 448.65869 16.874435 0.0034851739 1 1 + 200 379.84257 11.578545 0.0034851739 1 1 + 250 298.21983 90.656585 0.0034851739 1 1 + 300 333.3111 -30.139607 0.0034851739 1 1 + 350 266.57108 6.4505134 0.0034851739 1 1 + 400 264.05476 10.513204 0.0034851739 1 1 + 450 250.70418 -18.635379 0.0034851739 1 1 + 500 261.21632 10.231013 0.0034851739 1 1 + 550 309.89024 -8.8299506 0.0034851739 1 1 + 600 373.45851 30.368993 0.0034851739 1 1 + 650 338.26242 9.0362267 0.0034851739 1 1 + 700 295.67794 -5.6007538 0.0034851739 1 1 + 750 310.86563 -59.228181 0.0034851739 1 1 + 800 286.22678 -9.9022407 0.0034851739 1 1 + 850 218.42135 27.845352 0.0034851739 1 1 + 900 259.62551 24.216336 0.0034851739 1 1 + 950 250.21307 -14.560985 0.0034851739 1 1 + 1000 274.29245 -0.38768626 0.0034851739 1 1 +Loop time of 0.341061 on 1 procs for 1000 steps with 44 atoms + +Performance: 253.327 ns/day, 0.095 hours/ns, 2932.025 timesteps/s +87.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.031135 | 0.031135 | 0.031135 | 0.0 | 9.13 +Bond | 0.12623 | 0.12623 | 0.12623 | 0.0 | 37.01 +Kspace | 0.036491 | 0.036491 | 0.036491 | 0.0 | 10.70 +Neigh | 0.046395 | 0.046395 | 0.046395 | 0.0 | 13.60 +Comm | 0.0025396 | 0.0025396 | 0.0025396 | 0.0 | 0.74 +Output | 0.07775 | 0.07775 | 0.07775 | 0.0 | 22.80 +Modify | 0.019219 | 0.019219 | 0.019219 | 0.0 | 5.64 +Other | | 0.001306 | | | 0.38 + +Nlocal: 44 ave 44 max 44 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2 ave 2 max 2 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 740 ave 740 max 740 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 740 +Ave neighs/atom = 16.8182 +Ave special neighs/atom = 9.77273 +Neighbor list builds = 1000 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..b9c7a3ba15f29f944251c1cf418d10da2b3c86fb --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 @@ -0,0 +1,148 @@ +LAMMPS (5 Jun 2019) +Reading data file ... + orthogonal box = (-25 -25 -25) to (25 25 25) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.000178751 secs + read_data CPU = 0.0385782 secs +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 14 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 14 impropers with max type 11 +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 20 impropers with max type 1 +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 16 impropers with max type 1 +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 10 impropers with max type 13 +WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785) +WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785) +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp_REACT defined +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:319) + G vector (1/distance) = 0.0534597 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0402256 + estimated relative force accuracy = 0.000121138 + using double precision FFTs + 3d grid and FFT values/proc = 252 2 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 10 10 10 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +WARNING: Inconsistent image flags (../domain.cpp:784) +Per MPI rank memory allocation (min/avg/max) = 34.42 | 34.77 | 35.45 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 293.70542 -52.547388 0.0034851739 1 0 + 100 276.36755 54.81826 0.0034851739 1 1 + 150 448.65869 16.874435 0.0034851739 1 1 + 200 379.84257 11.578545 0.0034851739 1 1 + 250 298.21983 90.656585 0.0034851739 1 1 + 300 333.3111 -30.139607 0.0034851739 1 1 + 350 266.57108 6.4505134 0.0034851739 1 1 + 400 264.05476 10.513204 0.0034851739 1 1 + 450 250.70418 -18.635379 0.0034851739 1 1 + 500 261.21632 10.231013 0.0034851739 1 1 + 550 309.89024 -8.8299506 0.0034851739 1 1 + 600 373.45851 30.368993 0.0034851739 1 1 + 650 338.26242 9.0362267 0.0034851739 1 1 + 700 295.67794 -5.6007538 0.0034851739 1 1 + 750 310.86563 -59.228181 0.0034851739 1 1 + 800 286.22678 -9.9022407 0.0034851739 1 1 + 850 218.42135 27.845352 0.0034851739 1 1 + 900 259.62551 24.216336 0.0034851739 1 1 + 950 250.21307 -14.560985 0.0034851739 1 1 + 1000 274.29245 -0.38768626 0.0034851739 1 1 +Loop time of 0.271242 on 4 procs for 1000 steps with 44 atoms + +Performance: 318.535 ns/day, 0.075 hours/ns, 3686.747 timesteps/s +98.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00023773 | 0.0077322 | 0.016042 | 8.4 | 2.85 +Bond | 0.00073385 | 0.032108 | 0.08446 | 19.4 | 11.84 +Kspace | 0.041659 | 0.098095 | 0.13373 | 12.3 | 36.16 +Neigh | 0.028894 | 0.029247 | 0.029558 | 0.1 | 10.78 +Comm | 0.012367 | 0.013642 | 0.01503 | 0.9 | 5.03 +Output | 0.032475 | 0.040504 | 0.061019 | 5.9 | 14.93 +Modify | 0.032934 | 0.049086 | 0.0577 | 4.3 | 18.10 +Other | | 0.0008281 | | | 0.31 + +Nlocal: 11 ave 21 max 0 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Nghost: 32.5 ave 43 max 23 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 185 ave 376 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 740 +Ave neighs/atom = 16.8182 +Ave special neighs/atom = 9.77273 +Neighbor list builds = 1000 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..14cac1dfad64a617e13e90a05120d22dd3f22cfc --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 @@ -0,0 +1,147 @@ +LAMMPS (5 Jun 2019) +Reading data file ... + orthogonal box = (-25 -25 -25) to (25 25 25) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.000217102 secs + read_data CPU = 0.00630778 secs +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 14 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 14 impropers with max type 11 +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 20 impropers with max type 1 +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 16 impropers with max type 1 +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 10 impropers with max type 13 +WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785) +WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785) +dynamic group bond_react_MASTER_group defined +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:319) + G vector (1/distance) = 0.0534597 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0402256 + estimated relative force accuracy = 0.000121138 + using double precision FFTs + 3d grid and FFT values/proc = 343 8 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 10 10 10 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +WARNING: Inconsistent image flags (../domain.cpp:784) +Per MPI rank memory allocation (min/avg/max) = 34.35 | 34.35 | 34.35 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 416.49412 -20.293038 0.0034851739 1 0 + 100 746.49323 91.912227 0.0034851739 1 1 + 150 515.15907 -1.4024709 0.0034851739 1 1 + 200 441.14572 -19.333087 0.0034851739 1 1 + 250 376.40996 30.717679 0.0034851739 1 1 + 300 326.15127 -3.0433799 0.0034851739 1 1 + 350 326.21116 6.235391 0.0034851739 1 1 + 400 366.48556 3.9807338 0.0034851739 1 1 + 450 313.79097 7.6674629 0.0034851739 1 1 + 500 278.89836 14.102052 0.0034851739 1 1 + 550 267.50214 18.241417 0.0034851739 1 1 + 600 276.28064 7.4649611 0.0034851739 1 1 + 650 255.26713 -8.5258573 0.0034851739 1 1 + 700 258.59752 -5.3341215 0.0034851739 1 1 + 750 263.71264 33.369869 0.0034851739 1 1 + 800 246.22976 -15.349137 0.0034851739 1 1 + 850 255.93887 16.331669 0.0034851739 1 1 + 900 239.72525 -0.20075789 0.0034851739 1 1 + 950 213.73064 12.17619 0.0034851739 1 1 + 1000 218.25094 -9.0955642 0.0034851739 1 1 +Loop time of 0.348252 on 1 procs for 1000 steps with 44 atoms + +Performance: 248.096 ns/day, 0.097 hours/ns, 2871.483 timesteps/s +91.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.031941 | 0.031941 | 0.031941 | 0.0 | 9.17 +Bond | 0.13031 | 0.13031 | 0.13031 | 0.0 | 37.42 +Kspace | 0.037554 | 0.037554 | 0.037554 | 0.0 | 10.78 +Neigh | 0.047397 | 0.047397 | 0.047397 | 0.0 | 13.61 +Comm | 0.0025814 | 0.0025814 | 0.0025814 | 0.0 | 0.74 +Output | 0.083526 | 0.083526 | 0.083526 | 0.0 | 23.98 +Modify | 0.013602 | 0.013602 | 0.013602 | 0.0 | 3.91 +Other | | 0.001336 | | | 0.38 + +Nlocal: 44 ave 44 max 44 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 818 ave 818 max 818 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 818 +Ave neighs/atom = 18.5909 +Ave special neighs/atom = 9.77273 +Neighbor list builds = 1000 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..6b13dd60d381fde758362a2e2e126dc5a32a5c39 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 @@ -0,0 +1,147 @@ +LAMMPS (5 Jun 2019) +Reading data file ... + orthogonal box = (-25 -25 -25) to (25 25 25) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.000163256 secs + read_data CPU = 0.0244579 secs +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 14 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 14 impropers with max type 11 +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 20 impropers with max type 1 +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 16 impropers with max type 1 +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 10 impropers with max type 13 +WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785) +WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785) +dynamic group bond_react_MASTER_group defined +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:319) + G vector (1/distance) = 0.0534597 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0402256 + estimated relative force accuracy = 0.000121138 + using double precision FFTs + 3d grid and FFT values/proc = 252 2 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 10 10 10 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +WARNING: Inconsistent image flags (../domain.cpp:784) +Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 416.49412 -20.293038 0.0034851739 1 0 + 100 746.49323 91.912227 0.0034851739 1 1 + 150 515.15907 -1.4024709 0.0034851739 1 1 + 200 441.14572 -19.333087 0.0034851739 1 1 + 250 376.40996 30.717679 0.0034851739 1 1 + 300 326.15127 -3.0433799 0.0034851739 1 1 + 350 326.21116 6.235391 0.0034851739 1 1 + 400 366.48556 3.9807338 0.0034851739 1 1 + 450 313.79097 7.6674629 0.0034851739 1 1 + 500 278.89836 14.102052 0.0034851739 1 1 + 550 267.50214 18.241417 0.0034851739 1 1 + 600 276.28064 7.4649611 0.0034851739 1 1 + 650 255.26713 -8.5258573 0.0034851739 1 1 + 700 258.59752 -5.3341215 0.0034851739 1 1 + 750 263.71264 33.369869 0.0034851739 1 1 + 800 246.22976 -15.349137 0.0034851739 1 1 + 850 255.93887 16.331669 0.0034851739 1 1 + 900 239.72525 -0.20075789 0.0034851739 1 1 + 950 213.73064 12.17619 0.0034851739 1 1 + 1000 218.25094 -9.0955642 0.0034851739 1 1 +Loop time of 0.254903 on 4 procs for 1000 steps with 44 atoms + +Performance: 338.952 ns/day, 0.071 hours/ns, 3923.053 timesteps/s +99.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00014252 | 0.0090715 | 0.021332 | 9.6 | 3.56 +Bond | 0.00047028 | 0.037261 | 0.10789 | 22.7 | 14.62 +Kspace | 0.051006 | 0.12756 | 0.1693 | 13.6 | 50.04 +Neigh | 0.035644 | 0.036088 | 0.036523 | 0.2 | 14.16 +Comm | 0.013984 | 0.016074 | 0.018676 | 1.6 | 6.31 +Output | 0.0002816 | 0.00033726 | 0.00044251 | 0.0 | 0.13 +Modify | 0.023697 | 0.027803 | 0.033552 | 2.5 | 10.91 +Other | | 0.0007123 | | | 0.28 + +Nlocal: 11 ave 29 max 0 min +Histogram: 1 1 0 0 1 0 0 0 0 1 +Nghost: 25 ave 31 max 12 min +Histogram: 1 0 0 0 0 0 0 0 2 1 +Neighs: 204.5 ave 443 max 0 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 818 +Ave neighs/atom = 18.5909 +Ave special neighs/atom = 9.77273 +Neighbor list builds = 1000 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/USER/misc/momentum/in.momentum b/examples/USER/misc/momentum/in.momentum new file mode 100644 index 0000000000000000000000000000000000000000..5adcbfeff6a2c7379daf212b5d7c9b3c7a82f083 --- /dev/null +++ b/examples/USER/misc/momentum/in.momentum @@ -0,0 +1,65 @@ +# Test compute momentum with by comparing it's output with compute reduce + +# Script will output the two computations of the total momentum as +# thermo vars - they should be identical + +# 3D LJ Poiseuille flow simulation +dimension 3 +boundary p p p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 + +# create geometry +lattice hcp 0.5 +region box block 0 20 0 10 0 10 +create_box 3 box +create_atoms 1 box + +mass 1 1.0 +mass 2 1.0 +mass 3 1.0 + +# LJ potentials +pair_style lj/cut 1.0 +pair_coeff * * 1.0 1.0 1.0 + +# define groups +region 1 block INF INF INF 1.0 INF INF +group lower region 1 +region 2 block INF INF 9.0 INF INF INF +group upper region 2 +group boundary union lower upper +group liquid subtract all boundary + +set group lower type 2 +set group upper type 3 + +# temperature settings +compute mobile liquid temp +velocity liquid create 1.0 100 temp mobile +fix 1 all nve +fix 2 liquid temp/rescale 200 1.0 2.0 0.02 1.0 +fix_modify 2 temp mobile + +velocity boundary set 0.0 0.0 0.0 +fix 4 lower setforce 0.0 0.0 0.0 +fix 5 upper setforce 0.0 0.0 0.0 +fix 6 liquid addforce 0.1 0.0 0.0 + +# Compute total momentum +compute mom liquid momentum + +# Comparison (momentum variables + compute reduce) +variable mx atom mass*vx +variable my atom mass*vy +variable mz atom mass*vz +compute mom_red liquid reduce sum v_mx v_my v_mz + +# Run +timestep 0.003 +thermo 1000 +thermo_style custom step c_mom_red[*] c_mom[*] + +run 100000 diff --git a/examples/kim/.gitignore b/examples/kim/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..63421e4217501ea4fb4464ac6a5b9795f82070e0 --- /dev/null +++ b/examples/kim/.gitignore @@ -0,0 +1 @@ +/kim.log diff --git a/examples/kim/in.kim.lj.newton-on b/examples/kim/in.kim-ex.melt similarity index 79% rename from examples/kim/in.kim.lj.newton-on rename to examples/kim/in.kim-ex.melt index 3a95f1dbb018b40b1fe667976f6109fcad02a7aa..5cc3dbc61bbace34e07c3b51f56323278cfdc9a6 100644 --- a/examples/kim/in.kim.lj.newton-on +++ b/examples/kim/in.kim-ex.melt @@ -14,20 +14,14 @@ variable xx equal 20*$x variable yy equal 20*$y variable zz equal 20*$z -units metal -atom_style atomic -newton on +kim_init LennardJones_Ar real lattice fcc 4.4300 region box block 0 ${xx} 0 ${yy} 0 ${zz} create_box 1 box create_atoms 1 box -#pair_style lj/cut 8.1500 -#pair_coeff 1 1 0.0104 3.4000 - -pair_style kim LennardJones_Ar -pair_coeff * * Ar +kim_interactions Ar mass 1 39.95 velocity all create 200.0 232345 loop geom diff --git a/examples/kim/in.kim-pm-query.melt b/examples/kim/in.kim-pm-query.melt new file mode 100644 index 0000000000000000000000000000000000000000..fa04d9043664d6722f11fde83f0ff085f4332eed --- /dev/null +++ b/examples/kim/in.kim-pm-query.melt @@ -0,0 +1,46 @@ +# 3d Lennard-Jones melt +# +# This example requires that the KIM Portable Model (PM) +# SW_StillingerWeber_1985_Si__MO_405512056662_005 +# is installed. This can be done with the command +# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005 +# If this command does not work, you may need to setup your PATH to find the utility. +# If you installed the kim-api using the LAMMPS CMake build, you can do the following +# (where the current working directory is assumed to be the LAMMPS build directory) +# source ./kim_build-prefix/bin/kim-api-activate +# If you installed the kim-api using the LAMMPS Make build, you can do the following +# (where the current working directory is assumed to be the LAMMPS src directory) +# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate +# (where you should relplace X.Y.Z with the appropriate kim-api version number). +# +# Or, see https://openkim.org/doc/obtaining-models for alternative options. +# + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable yy equal 20*$y +variable zz equal 20*$z + +kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real +kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"] + +lattice fcc ${a0} +region box block 0 ${xx} 0 ${yy} 0 ${zz} +create_box 1 box +create_atoms 1 box + +kim_interactions Si + +mass 1 39.95 +velocity all create 200.0 232345 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 + +run 100 diff --git a/examples/kim/in.kim-pm.melt b/examples/kim/in.kim-pm.melt new file mode 100644 index 0000000000000000000000000000000000000000..9959a66793e1517d74c379ae8b262538614bfb49 --- /dev/null +++ b/examples/kim/in.kim-pm.melt @@ -0,0 +1,45 @@ +# 3d Lennard-Jones melt +# +# This example requires that the KIM Portable Model (PM) +# SW_StillingerWeber_1985_Si__MO_405512056662_005 +# is installed. This can be done with the command +# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005 +# If this command does not work, you may need to setup your PATH to find the utility. +# If you installed the kim-api using the LAMMPS CMake build, you can do the following +# (where the current working directory is assumed to be the LAMMPS build directory) +# source ./kim_build-prefix/bin/kim-api-activate +# If you installed the kim-api using the LAMMPS Make build, you can do the following +# (where the current working directory is assumed to be the LAMMPS src directory) +# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate +# (where you should relplace X.Y.Z with the appropriate kim-api version number). +# +# Or, see https://openkim.org/doc/obtaining-models for alternative options. +# + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable yy equal 20*$y +variable zz equal 20*$z + +kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real + +lattice fcc 4.4300 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +create_box 1 box +create_atoms 1 box + +kim_interactions Si + +mass 1 39.95 +velocity all create 200.0 232345 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 + +run 100 diff --git a/examples/kim/in.kim-sm.melt b/examples/kim/in.kim-sm.melt new file mode 100644 index 0000000000000000000000000000000000000000..0ee8e9a85733e0251db1d222bf66a39a44a87939 --- /dev/null +++ b/examples/kim/in.kim-sm.melt @@ -0,0 +1,45 @@ +# 3d Lennard-Jones melt +# +# This example requires that the KIM Simulator Model (PM) +# Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 +# is installed. This can be done with the command +# kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 +# If this command does not work, you may need to setup your PATH to find the utility. +# If you installed the kim-api using the LAMMPS CMake build, you can do the following +# (where the current working directory is assumed to be the LAMMPS build directory) +# source ./kim_build-prefix/bin/kim-api-activate +# If you installed the kim-api using the LAMMPS Make build, you can do the following +# (where the current working directory is assumed to be the LAMMPS src directory) +# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate +# (where you should relplace X.Y.Z with the appropriate kim-api version number). +# +# See https://openkim.org/doc/obtaining-models for alternative options. +# + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable yy equal 20*$y +variable zz equal 20*$z + +kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real + +lattice fcc 4.4300 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +create_box 1 box +create_atoms 1 box + +kim_interactions O + +mass 1 39.95 +velocity all create 200.0 232345 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 + +run 100 diff --git a/examples/kim/in.kim.lj.lmp.newton-off b/examples/kim/in.kim.lj.lmp.newton-off deleted file mode 100644 index 197755294ac2842cbc0c7f22ee22a6564cd7cac4..0000000000000000000000000000000000000000 --- a/examples/kim/in.kim.lj.lmp.newton-off +++ /dev/null @@ -1,35 +0,0 @@ -# 3d Lennard-Jones melt - -variable x index 1 -variable y index 1 -variable z index 1 - -variable xx equal 20*$x -variable yy equal 20*$y -variable zz equal 20*$z - -units metal -atom_style atomic -newton off - -lattice fcc 4.4300 -region box block 0 ${xx} 0 ${yy} 0 ${zz} -create_box 1 box -create_atoms 1 box - -pair_style lj/cut 8.1500 -pair_coeff 1 1 0.0104 3.4000 - -#pair_style kim LennardJones_Ar -#pair_coeff * * Ar - -mass 1 39.95 -velocity all create 200.0 232345 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve -#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 - -run 100 diff --git a/examples/kim/in.kim.lj.newton-off b/examples/kim/in.kim.lj.newton-off deleted file mode 100644 index 82cf5ba602c2ce15632b9d51e1c5b1b360813182..0000000000000000000000000000000000000000 --- a/examples/kim/in.kim.lj.newton-off +++ /dev/null @@ -1,41 +0,0 @@ -# 3d Lennard-Jones melt -# -# This example requires that the example models provided with -# the kim-api package are installed. see the ./lib/kim/README or -# ./lib/kim/Install.py files for details on how to install these -# example models. -# - -variable x index 1 -variable y index 1 -variable z index 1 - -variable xx equal 20*$x -variable yy equal 20*$y -variable zz equal 20*$z - -units metal -atom_style atomic -newton off - -lattice fcc 4.4300 -region box block 0 ${xx} 0 ${yy} 0 ${zz} -create_box 1 box -create_atoms 1 box - -#pair_style lj/cut 8.1500 -#pair_coeff 1 1 0.0104 3.4000 - -pair_style kim LennardJones_Ar -pair_coeff * * Ar - -mass 1 39.95 -velocity all create 200.0 232345 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve -#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 - -run 100 diff --git a/examples/kim/in.kim.lj.lmp.newton-on b/examples/kim/in.lammps.melt similarity index 91% rename from examples/kim/in.kim.lj.lmp.newton-on rename to examples/kim/in.lammps.melt index f9f79e2bb2ea1dcf39ef2f7d7c81cefad34efa90..5792f3a5db6b1096d6fd51edd3595aec22bd1922 100644 --- a/examples/kim/in.kim.lj.lmp.newton-on +++ b/examples/kim/in.lammps.melt @@ -8,9 +8,7 @@ variable xx equal 20*$x variable yy equal 20*$y variable zz equal 20*$z -units metal -atom_style atomic -newton on +units real lattice fcc 4.4300 region box block 0 ${xx} 0 ${yy} 0 ${zz} diff --git a/examples/kim/in.query b/examples/kim/in.query deleted file mode 100644 index 33272dc29892ffea6315d1785412deec500ab552..0000000000000000000000000000000000000000 --- a/examples/kim/in.query +++ /dev/null @@ -1,11 +0,0 @@ - -# example for performing a query to the OpenKIM test database to retrieve -# a parameter to be used in the input. here it requests the aluminium -# lattice constant for a specific test used for a specific model and then -# assigns it to the variable 'latconst' - -units metal -info variables out log -kim_query latconst get_test_result test=TE_156715955670 species=["Al"] model=MO_800509458712 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"] -info variables out log -lattice fcc ${latconst} diff --git a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.1 b/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.1 deleted file mode 100644 index 5925fd750da44be58c8baa168ede149ec8d5f13d..0000000000000000000000000000000000000000 --- a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.1 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (1 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -Lattice spacing in x,y,z = 4.43 4.43 4.43 -Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) - 1 by 1 by 1 MPI processor grid -Created 32000 atoms - Time spent = 0.004499 secs -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 8.45 - ghost atom cutoff = 8.45 - binsize = 4.225, bins = 21 21 21 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard -Setting up Verlet run ... - Unit style : metal - Current step : 0 - Time step : 0.001 -Per MPI rank memory allocation (min/avg/max) = 20.37 | 20.37 | 20.37 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 200 6290.8194 0 7118.0584 129712.25 - 100 95.179725 6718.814 0 7112.496 133346.59 -Loop time of 2.92885 on 1 procs for 100 steps with 32000 atoms - -Performance: 2.950 ns/day, 8.136 hours/ns, 34.143 timesteps/s -99.1% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.5638 | 2.5638 | 2.5638 | 0.0 | 87.54 -Neigh | 0.31935 | 0.31935 | 0.31935 | 0.0 | 10.90 -Comm | 0.006833 | 0.006833 | 0.006833 | 0.0 | 0.23 -Output | 0.000107 | 0.000107 | 0.000107 | 0.0 | 0.00 -Modify | 0.027806 | 0.027806 | 0.027806 | 0.0 | 0.95 -Other | | 0.01091 | | | 0.37 - -Nlocal: 32000 ave 32000 max 32000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 19911 ave 19911 max 19911 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 2.3705e+06 ave 2.3705e+06 max 2.3705e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2370499 -Ave neighs/atom = 74.0781 -Neighbor list builds = 3 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.4 b/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.4 deleted file mode 100644 index c1ca108c7bcf5f07141409d97f028e8aad79ae8a..0000000000000000000000000000000000000000 --- a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.4 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (1 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -Lattice spacing in x,y,z = 4.43 4.43 4.43 -Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) - 1 by 2 by 2 MPI processor grid -Created 32000 atoms - Time spent = 0.001039 secs -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 8.45 - ghost atom cutoff = 8.45 - binsize = 4.225, bins = 21 21 21 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard -Setting up Verlet run ... - Unit style : metal - Current step : 0 - Time step : 0.001 -Per MPI rank memory allocation (min/avg/max) = 8.013 | 8.013 | 8.013 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 200 6290.8194 0 7118.0584 129712.25 - 100 95.179725 6718.814 0 7112.496 133346.59 -Loop time of 0.778581 on 4 procs for 100 steps with 32000 atoms - -Performance: 11.097 ns/day, 2.163 hours/ns, 128.439 timesteps/s -99.8% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.65171 | 0.65891 | 0.67656 | 1.3 | 84.63 -Neigh | 0.07924 | 0.079548 | 0.07997 | 0.1 | 10.22 -Comm | 0.006755 | 0.0069015 | 0.007072 | 0.2 | 0.89 -Output | 4.6e-05 | 9.725e-05 | 0.000203 | 0.0 | 0.01 -Modify | 0.006841 | 0.006941 | 0.007015 | 0.1 | 0.89 -Other | | 0.02618 | | | 3.36 - -Nlocal: 8000 ave 8018 max 7967 min -Histogram: 1 0 0 0 0 0 1 0 0 2 -Nghost: 9131 ave 9164 max 9113 min -Histogram: 2 0 0 1 0 0 0 0 0 1 -Neighs: 630904 ave 632094 max 628209 min -Histogram: 1 0 0 0 0 0 0 1 0 2 - -Total # of neighbors = 2523614 -Ave neighs/atom = 78.8629 -Neighbor list builds = 3 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.1 b/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.1 deleted file mode 100644 index 53555743d76f0f15947790f8d5ecaf37d70422bc..0000000000000000000000000000000000000000 --- a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.1 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (1 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -Lattice spacing in x,y,z = 4.43 4.43 4.43 -Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) - 1 by 1 by 1 MPI processor grid -Created 32000 atoms - Time spent = 0.003479 secs -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 8.45 - ghost atom cutoff = 8.45 - binsize = 4.225, bins = 21 21 21 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Setting up Verlet run ... - Unit style : metal - Current step : 0 - Time step : 0.001 -Per MPI rank memory allocation (min/avg/max) = 19.23 | 19.23 | 19.23 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 200 6290.8194 0 7118.0584 129712.25 - 100 95.179725 6718.814 0 7112.496 133346.59 -Loop time of 2.17978 on 1 procs for 100 steps with 32000 atoms - -Performance: 3.964 ns/day, 6.055 hours/ns, 45.876 timesteps/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.9892 | 1.9892 | 1.9892 | 0.0 | 91.26 -Neigh | 0.14506 | 0.14506 | 0.14506 | 0.0 | 6.65 -Comm | 0.011049 | 0.011049 | 0.011049 | 0.0 | 0.51 -Output | 9.1e-05 | 9.1e-05 | 9.1e-05 | 0.0 | 0.00 -Modify | 0.02347 | 0.02347 | 0.02347 | 0.0 | 1.08 -Other | | 0.01094 | | | 0.50 - -Nlocal: 32000 ave 32000 max 32000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 19911 ave 19911 max 19911 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 2.12688e+06 ave 2.12688e+06 max 2.12688e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2126875 -Ave neighs/atom = 66.4648 -Neighbor list builds = 3 -Dangerous builds = 0 -Total wall time: 0:00:02 diff --git a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.4 b/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.4 deleted file mode 100644 index f0fdf661939b47169279fe7aba73ad3d2f8bcd75..0000000000000000000000000000000000000000 --- a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.4 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (1 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -Lattice spacing in x,y,z = 4.43 4.43 4.43 -Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) - 1 by 2 by 2 MPI processor grid -Created 32000 atoms - Time spent = 0.000919 secs -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 8.45 - ghost atom cutoff = 8.45 - binsize = 4.225, bins = 21 21 21 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Setting up Verlet run ... - Unit style : metal - Current step : 0 - Time step : 0.001 -Per MPI rank memory allocation (min/avg/max) = 7.632 | 7.632 | 7.632 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 200 6290.8194 0 7118.0584 129712.25 - 100 95.179725 6718.814 0 7112.496 133346.59 -Loop time of 0.63515 on 4 procs for 100 steps with 32000 atoms - -Performance: 13.603 ns/day, 1.764 hours/ns, 157.443 timesteps/s -99.8% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.55365 | 0.5566 | 0.55868 | 0.2 | 87.63 -Neigh | 0.041495 | 0.0418 | 0.04211 | 0.1 | 6.58 -Comm | 0.019086 | 0.021075 | 0.023898 | 1.2 | 3.32 -Output | 4.4e-05 | 5.025e-05 | 6e-05 | 0.0 | 0.01 -Modify | 0.009315 | 0.0093595 | 0.009422 | 0.0 | 1.47 -Other | | 0.006263 | | | 0.99 - -Nlocal: 8000 ave 8018 max 7967 min -Histogram: 1 0 0 0 0 0 1 0 0 2 -Nghost: 9131 ave 9164 max 9113 min -Histogram: 2 0 0 1 0 0 0 0 0 1 -Neighs: 531719 ave 533273 max 529395 min -Histogram: 1 0 0 0 1 0 0 0 0 2 - -Total # of neighbors = 2126875 -Ave neighs/atom = 66.4648 -Neighbor list builds = 3 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/kim/log.06Feb2019.in.kim.lj.newton-off.1 b/examples/kim/log.06Feb2019.in.kim.lj.newton-off.1 deleted file mode 100644 index 0ab258fe0de389fc9dfa8d915e0689634d8c4a2f..0000000000000000000000000000000000000000 --- a/examples/kim/log.06Feb2019.in.kim.lj.newton-off.1 +++ /dev/null @@ -1,59 +0,0 @@ -LAMMPS (1 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -Lattice spacing in x,y,z = 4.43 4.43 4.43 -Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) - 1 by 1 by 1 MPI processor grid -Created 32000 atoms - Time spent = 0.003446 secs -WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) -WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 8.45 - ghost atom cutoff = 8.45 - binsize = 4.225, bins = 21 21 21 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair kim, perpetual - attributes: full, newton off, cut 8.45 - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Setting up Verlet run ... - Unit style : metal - Current step : 0 - Time step : 0.001 -Per MPI rank memory allocation (min/avg/max) = 28.51 | 28.51 | 28.51 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 200 6290.8194 0 7118.0584 129712.25 - 100 95.179725 6718.814 0 7112.496 133346.59 -Loop time of 3.01669 on 1 procs for 100 steps with 32000 atoms - -Performance: 2.864 ns/day, 8.380 hours/ns, 33.149 timesteps/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.6562 | 2.6562 | 2.6562 | 0.0 | 88.05 -Neigh | 0.31903 | 0.31903 | 0.31903 | 0.0 | 10.58 -Comm | 0.00634 | 0.00634 | 0.00634 | 0.0 | 0.21 -Output | 9.1e-05 | 9.1e-05 | 9.1e-05 | 0.0 | 0.00 -Modify | 0.024723 | 0.024723 | 0.024723 | 0.0 | 0.82 -Other | | 0.01032 | | | 0.34 - -Nlocal: 32000 ave 32000 max 32000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 19911 ave 19911 max 19911 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 4253750 -Ave neighs/atom = 132.93 -Neighbor list builds = 3 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/kim/log.06Feb2019.in.kim.lj.newton-off.4 b/examples/kim/log.06Feb2019.in.kim.lj.newton-off.4 deleted file mode 100644 index c17ea6afb709834c385bd56763e396ba45fd2378..0000000000000000000000000000000000000000 --- a/examples/kim/log.06Feb2019.in.kim.lj.newton-off.4 +++ /dev/null @@ -1,65 +0,0 @@ -LAMMPS (1 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -Lattice spacing in x,y,z = 4.43 4.43 4.43 -Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) - 1 by 2 by 2 MPI processor grid -Created 32000 atoms - Time spent = 0.000921 secs -WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) -WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) -WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) -WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) -WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) -WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) -WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) -WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 8.45 - ghost atom cutoff = 8.45 - binsize = 4.225, bins = 21 21 21 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair kim, perpetual - attributes: full, newton off, cut 8.45 - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Setting up Verlet run ... - Unit style : metal - Current step : 0 - Time step : 0.001 -Per MPI rank memory allocation (min/avg/max) = 10.05 | 10.05 | 10.05 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 200 6290.8194 0 7118.0584 129712.25 - 100 95.179725 6718.814 0 7112.496 133346.59 -Loop time of 0.890192 on 4 procs for 100 steps with 32000 atoms - -Performance: 9.706 ns/day, 2.473 hours/ns, 112.335 timesteps/s -99.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.77867 | 0.77906 | 0.7794 | 0.0 | 87.52 -Neigh | 0.087831 | 0.088176 | 0.088805 | 0.1 | 9.91 -Comm | 0.006358 | 0.0065898 | 0.006815 | 0.3 | 0.74 -Output | 4.9e-05 | 5.975e-05 | 6.8e-05 | 0.0 | 0.01 -Modify | 0.010265 | 0.010429 | 0.010678 | 0.2 | 1.17 -Other | | 0.005874 | | | 0.66 - -Nlocal: 8000 ave 8018 max 7967 min -Histogram: 1 0 0 0 0 0 1 0 0 2 -Nghost: 9131 ave 9164 max 9113 min -Histogram: 2 0 0 1 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min -Histogram: 1 0 0 0 0 0 1 0 0 2 - -Total # of neighbors = 4253750 -Ave neighs/atom = 132.93 -Neighbor list builds = 3 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/kim/log.06Feb2019.in.kim.lj.newton-on.1 b/examples/kim/log.06Feb2019.in.kim.lj.newton-on.1 deleted file mode 100644 index 59d018e12a59a8e65219926a6eb17dfb291f91e2..0000000000000000000000000000000000000000 --- a/examples/kim/log.06Feb2019.in.kim.lj.newton-on.1 +++ /dev/null @@ -1,59 +0,0 @@ -LAMMPS (1 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -Lattice spacing in x,y,z = 4.43 4.43 4.43 -Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) - 1 by 1 by 1 MPI processor grid -Created 32000 atoms - Time spent = 0.003089 secs -WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) -WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 8.45 - ghost atom cutoff = 8.45 - binsize = 4.225, bins = 21 21 21 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair kim, perpetual - attributes: full, newton off, cut 8.45 - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Setting up Verlet run ... - Unit style : metal - Current step : 0 - Time step : 0.001 -Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 200 6290.8194 0 7118.0584 129712.25 - 100 95.179725 6718.814 0 7112.496 133346.59 -Loop time of 3.05849 on 1 procs for 100 steps with 32000 atoms - -Performance: 2.825 ns/day, 8.496 hours/ns, 32.696 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.6786 | 2.6786 | 2.6786 | 0.0 | 87.58 -Neigh | 0.33105 | 0.33105 | 0.33105 | 0.0 | 10.82 -Comm | 0.012602 | 0.012602 | 0.012602 | 0.0 | 0.41 -Output | 9.5e-05 | 9.5e-05 | 9.5e-05 | 0.0 | 0.00 -Modify | 0.024858 | 0.024858 | 0.024858 | 0.0 | 0.81 -Other | | 0.01132 | | | 0.37 - -Nlocal: 32000 ave 32000 max 32000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 19911 ave 19911 max 19911 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 4253750 -Ave neighs/atom = 132.93 -Neighbor list builds = 3 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/kim/log.06Feb2019.in.kim.lj.newton-on.4 b/examples/kim/log.06Feb2019.in.kim.lj.newton-on.4 deleted file mode 100644 index da8c9f0faaa4683ff742b7eda06820dc0ca77e84..0000000000000000000000000000000000000000 --- a/examples/kim/log.06Feb2019.in.kim.lj.newton-on.4 +++ /dev/null @@ -1,65 +0,0 @@ -LAMMPS (1 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -Lattice spacing in x,y,z = 4.43 4.43 4.43 -Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) - 1 by 2 by 2 MPI processor grid -Created 32000 atoms - Time spent = 0.000893 secs -WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) -WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) -WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) -WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) -WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) -WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) -WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) -WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 8.45 - ghost atom cutoff = 8.45 - binsize = 4.225, bins = 21 21 21 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair kim, perpetual - attributes: full, newton off, cut 8.45 - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Setting up Verlet run ... - Unit style : metal - Current step : 0 - Time step : 0.001 -Per MPI rank memory allocation (min/avg/max) = 9.789 | 9.789 | 9.789 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 200 6290.8194 0 7118.0584 129712.25 - 100 95.179725 6718.814 0 7112.496 133346.59 -Loop time of 0.903182 on 4 procs for 100 steps with 32000 atoms - -Performance: 9.566 ns/day, 2.509 hours/ns, 110.720 timesteps/s -99.6% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.76173 | 0.76349 | 0.76597 | 0.2 | 84.53 -Neigh | 0.088773 | 0.088938 | 0.089074 | 0.0 | 9.85 -Comm | 0.032018 | 0.03452 | 0.03638 | 0.9 | 3.82 -Output | 4e-05 | 4.425e-05 | 5.2e-05 | 0.0 | 0.00 -Modify | 0.009278 | 0.0093917 | 0.009528 | 0.1 | 1.04 -Other | | 0.006797 | | | 0.75 - -Nlocal: 8000 ave 8018 max 7967 min -Histogram: 1 0 0 0 0 0 1 0 0 2 -Nghost: 9131 ave 9164 max 9113 min -Histogram: 2 0 0 1 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min -Histogram: 1 0 0 0 0 0 1 0 0 2 - -Total # of neighbors = 4253750 -Ave neighs/atom = 132.93 -Neighbor list builds = 3 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/kim/log.22Mar2019.query.g++.1 b/examples/kim/log.22Mar2019.query.g++.1 deleted file mode 100644 index 034bb13bbacc1b67fa4f13bc5e2549494dbece38..0000000000000000000000000000000000000000 --- a/examples/kim/log.22Mar2019.query.g++.1 +++ /dev/null @@ -1,34 +0,0 @@ -LAMMPS (28 Feb 2019) - -# example for performing a query to the OpenKIM test database to retrieve -# a parameter to be used in the input. here it requests the aluminium -# lattice constant for a specific test used for a specific model and then -# assigns it to the variable 'latconst' - -units metal -info variables out log - -Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info -Printed on Fri Mar 22 20:00:56 2019 - - -Variable information: - -Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info - -kim_query latconst get_test_result test=TE_156715955670 species=["Al"] model=MO_800509458712 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"] -info variables out log - -Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info -Printed on Fri Mar 22 20:00:57 2019 - - -Variable information: -Variable[ 0]: latconst , style = string , def = 4.03208274841 - -Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info - -lattice fcc ${latconst} -lattice fcc 4.03208274841 -Lattice spacing in x,y,z = 4.03208 4.03208 4.03208 -Total wall time: 0:00:00 diff --git a/lib/kim/Install.py b/lib/kim/Install.py index c3588241c4df01ace3d795c193c332d2ef7cff34..de22950639cc38a6747d54cb7565f0848930ac2c 100644 --- a/lib/kim/Install.py +++ b/lib/kim/Install.py @@ -18,7 +18,7 @@ parser = ArgumentParser(prog='Install.py', # settings thisdir = fullpath('.') -version = "kim-api-2.0.2" +version = "kim-api-2.1.1" # help message @@ -39,11 +39,8 @@ make lib-kim args="-b -a EAM_ErcolessiAdams_1994_Al__MO_324507536345_002" # Ditt make lib-kim args="-b -a everything" # install KIM API lib with all models make lib-kim args="-n -a EAM_Dynamo_Ackland_2003_W__MO_141627196590_005" # only add one model or model driver -See the list of KIM model drivers here: -https://openkim.org/browse/model-drivers/alphabetical - See the list of all KIM models here: -https://openkim.org/browse/models/by-model-drivers +https://openkim.org/browse/models """ pgroup = parser.add_mutually_exclusive_group() @@ -132,7 +129,7 @@ if buildflag: # build kim-api print("Building kim-api ...") - cmd = 'cd "%s/%s/build" && make' % (thisdir, version) + cmd = 'cd "%s/%s/build" && make -j2' % (thisdir, version) txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) if verboseflag: print(txt.decode("UTF-8")) @@ -140,7 +137,7 @@ if buildflag: # install kim-api print("Installing kim-api ...") - cmd = 'cd "%s/%s/build" && make install' % (thisdir, version) + cmd = 'cd "%s/%s/build" && make -j2 install' % (thisdir, version) txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) if verboseflag: print(txt.decode("UTF-8")) diff --git a/lib/kim/README b/lib/kim/README index d3327537b6cdeb554934d4156b9e9c239a333d0a..3cba4a45977465453e46664d593c9cd2b820e03d 100644 --- a/lib/kim/README +++ b/lib/kim/README @@ -1,11 +1,11 @@ -This directory contains build settings for the KIM API library which -is required to use the KIM package and its pair_style kim command in a -LAMMPS input script. +This directory contains build settings for the KIM API library which is +required to use the KIM package and its kim_init, kim_interactions, kim_query, +and pair_kim commands in a LAMMPS input script. Information about the KIM project can be found at https://openkim.org. The KIM project is lead by Ellad Tadmor and Ryan Elliott (U Minn). Ryan Elliott is the main developer for the KIM API and he also -maintains the code that implements the pair_style kim command. +maintains the code that implements the KIM commands. You can type "make lib-kim" from the src directory to see help on how to download and build this library via make commands, or you can @@ -13,11 +13,9 @@ do the same thing by typing "python Install.py" from within this directory, or you can do it manually by following the instructions below. -As of KIM API version 2, the KIM package also provides a LAMMPS command -to perform queries through the OpenKIM web API. This feature requires -that the CURL library (libcurl) development package and its configuration -query tool, curl-config, are installed. The provided Makefile.lammps -is set up to automatically detect this. +Use of the kim_query command requires that the CURL library (libcurl) +development package and its configuration query tool, curl-config, are +installed. The provided Makefile.lammps is set up to automatically detect this. ----------------- @@ -40,8 +38,8 @@ $ cmake .. -DCMAKE_INSTALL_PREFIX=${PWD}/../../installed-kim-api-X.Y.Z 3. Build and install the kim-api and model -$ make -$ make install +$ make -j2 +$ make -j2 install 4. Remove source and build files @@ -53,7 +51,7 @@ $ rm -rf kim-api-X.Y.Z.txz desired value) $ source ${PWD}/kim-api-X.Y.Z/bin/kim-api-activate -$ kim-api-collections-management install system Pair_Johnson_Fe__MO_857282754307_002 +$ kim-api-collections-management install system EAM_ErcolessiAdams_1994_Al__MO_324507536345_002 ----------------- diff --git a/lib/poems/system.h b/lib/poems/system.h index 1b59395de701a45d87b2ec1a9187c69662b555e8..573044ce337bfdc49edec5f15b03b67693d3426e 100644 --- a/lib/poems/system.h +++ b/lib/poems/system.h @@ -15,7 +15,6 @@ * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ - #ifndef SYSTEM_H #define SYSTEM_H @@ -31,7 +30,6 @@ #include "workspace.h" #include "matrixfun.h" #include "onsolver.h" -#include "system.h" #include "inertialframe.h" #include "rigidbody.h" #include "revolutejoint.h" diff --git a/src/ASPHERE/compute_erotate_asphere.cpp b/src/ASPHERE/compute_erotate_asphere.cpp index afec2a9b28a8af8727a153738ff2f95f5fcc791f..3cf23b87eb70dcaf2c1678af126c5548452d87bb 100644 --- a/src/ASPHERE/compute_erotate_asphere.cpp +++ b/src/ASPHERE/compute_erotate_asphere.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_erotate_asphere.h" +#include #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" @@ -20,7 +20,6 @@ #include "atom_vec_tri.h" #include "update.h" #include "force.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/ASPHERE/compute_temp_asphere.cpp b/src/ASPHERE/compute_temp_asphere.cpp index 651c228e41c882c7e676d807024fd09e4dfea2e7..4350678bbda235c4546254c5603e5b09a005c736 100644 --- a/src/ASPHERE/compute_temp_asphere.cpp +++ b/src/ASPHERE/compute_temp_asphere.cpp @@ -15,9 +15,9 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "compute_temp_asphere.h" #include #include -#include "compute_temp_asphere.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" @@ -26,7 +26,6 @@ #include "domain.h" #include "modify.h" #include "group.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/ASPHERE/fix_nh_asphere.cpp b/src/ASPHERE/fix_nh_asphere.cpp index 828c064a526cb3c8b0c3eb9c8e9341b7db3eed11..2f8f11978ed29436c8441351ac6eb2140db41097 100644 --- a/src/ASPHERE/fix_nh_asphere.cpp +++ b/src/ASPHERE/fix_nh_asphere.cpp @@ -15,15 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include "math_extra.h" #include "fix_nh_asphere.h" +#include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" -#include "group.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/ASPHERE/fix_nph_asphere.cpp b/src/ASPHERE/fix_nph_asphere.cpp index 5f201a8463e325c2ff9bdeae85a1e6687907fd77..70880701ca5b3001d616d5bda3f5fc4c2787db9a 100644 --- a/src/ASPHERE/fix_nph_asphere.cpp +++ b/src/ASPHERE/fix_nph_asphere.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nph_asphere.h" +#include #include "modify.h" #include "error.h" diff --git a/src/ASPHERE/fix_npt_asphere.cpp b/src/ASPHERE/fix_npt_asphere.cpp index 5d528911698f2c045c763163ec2c8912ec1661c5..26d4fff81dfbf6fa17679fbd3f187c96a01c4090 100644 --- a/src/ASPHERE/fix_npt_asphere.cpp +++ b/src/ASPHERE/fix_npt_asphere.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_npt_asphere.h" +#include #include "modify.h" #include "error.h" diff --git a/src/ASPHERE/fix_nve_asphere.cpp b/src/ASPHERE/fix_nve_asphere.cpp index 61e3c35293bb9eb146e4a4b05573f384373ce995..93ccf008f4f20207061cf3ed13a43970784604e4 100644 --- a/src/ASPHERE/fix_nve_asphere.cpp +++ b/src/ASPHERE/fix_nve_asphere.cpp @@ -15,16 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nve_asphere.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" -#include "force.h" -#include "update.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/ASPHERE/fix_nve_asphere_noforce.cpp b/src/ASPHERE/fix_nve_asphere_noforce.cpp index 9cc430592a075bd7e61fbf7fe56f8c9882daf7f9..3a7d7e86e956c4f33ca488dd29b15b1979df1743 100644 --- a/src/ASPHERE/fix_nve_asphere_noforce.cpp +++ b/src/ASPHERE/fix_nve_asphere_noforce.cpp @@ -11,16 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nve_asphere_noforce.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" -#include "group.h" -#include "update.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/ASPHERE/fix_nve_line.cpp b/src/ASPHERE/fix_nve_line.cpp index 51a502df89fffcf4dfacd4407e01934ad41a41ef..5e17cb355fb15b5d79974ef84ebb1f19de7d5706 100644 --- a/src/ASPHERE/fix_nve_line.cpp +++ b/src/ASPHERE/fix_nve_line.cpp @@ -11,9 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nve_line.h" #include "atom.h" #include "atom_vec_line.h" diff --git a/src/ASPHERE/fix_nve_tri.cpp b/src/ASPHERE/fix_nve_tri.cpp index fb9bf64c58bf7cbbede432939718394e7cd73d17..797fea1c5bfcd729af10f1c00a920356de89e33e 100644 --- a/src/ASPHERE/fix_nve_tri.cpp +++ b/src/ASPHERE/fix_nve_tri.cpp @@ -11,9 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nve_tri.h" #include "math_extra.h" #include "atom.h" diff --git a/src/ASPHERE/fix_nvt_asphere.cpp b/src/ASPHERE/fix_nvt_asphere.cpp index 5ef91923ebb396b008b07d274c90c625670713e7..597fb03514ca1fa7c2fa426888bea6aa6ab0212a 100644 --- a/src/ASPHERE/fix_nvt_asphere.cpp +++ b/src/ASPHERE/fix_nvt_asphere.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nvt_asphere.h" +#include #include "group.h" #include "modify.h" #include "error.h" diff --git a/src/ASPHERE/pair_gayberne.cpp b/src/ASPHERE/pair_gayberne.cpp index 3d4ed3f183ae4a6ca88de16294b4e750320a8d26..93b164c5038f7210b92c688f71db3bb0a9b0a2a7 100644 --- a/src/ASPHERE/pair_gayberne.cpp +++ b/src/ASPHERE/pair_gayberne.cpp @@ -15,11 +15,9 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_gayberne.h" +#include +#include #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" @@ -27,7 +25,6 @@ #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "integrate.h" #include "citeme.h" #include "memory.h" #include "error.h" diff --git a/src/ASPHERE/pair_line_lj.cpp b/src/ASPHERE/pair_line_lj.cpp index 4873b44dc420e6a6b71e43a0fd681ae4a3d783ff..fdeb09aac447d07eb5cc504656d07732add191c1 100644 --- a/src/ASPHERE/pair_line_lj.cpp +++ b/src/ASPHERE/pair_line_lj.cpp @@ -11,11 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_line_lj.h" +#include #include "atom.h" #include "atom_vec_line.h" #include "force.h" diff --git a/src/ASPHERE/pair_resquared.cpp b/src/ASPHERE/pair_resquared.cpp index b100a5f184fcd0a3d56161c9e64e2f24eb8b5446..f139564320cc283fef61b969ed54eca0763c4d10 100644 --- a/src/ASPHERE/pair_resquared.cpp +++ b/src/ASPHERE/pair_resquared.cpp @@ -15,11 +15,9 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_resquared.h" +#include +#include #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" @@ -27,7 +25,6 @@ #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "integrate.h" #include "memory.h" #include "error.h" diff --git a/src/ASPHERE/pair_tri_lj.cpp b/src/ASPHERE/pair_tri_lj.cpp index cefd73f9769237a9fe91a524c25dce8f74842062..0984b0a30c6e7347c07120ee67046c41b13977a0 100644 --- a/src/ASPHERE/pair_tri_lj.cpp +++ b/src/ASPHERE/pair_tri_lj.cpp @@ -11,11 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_tri_lj.h" +#include #include "math_extra.h" #include "atom.h" #include "atom_vec_tri.h" diff --git a/src/BODY/body_nparticle.cpp b/src/BODY/body_nparticle.cpp index 10529ad3af8252c713c18bb9914f757aebb5e075..353ce5550ceb919965b70091be5580909425cd22 100644 --- a/src/BODY/body_nparticle.cpp +++ b/src/BODY/body_nparticle.cpp @@ -11,8 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "body_nparticle.h" +#include +#include +#include "my_pool_chunk.h" #include "math_extra.h" #include "atom_vec_body.h" #include "atom.h" diff --git a/src/BODY/body_rounded_polygon.cpp b/src/BODY/body_rounded_polygon.cpp index d352c789d79d8cf803ae3fe60b090593e75ed8fc..caf7e4bb8c2bf1f1c08d4d9c1485374600d9a0ab 100644 --- a/src/BODY/body_rounded_polygon.cpp +++ b/src/BODY/body_rounded_polygon.cpp @@ -15,8 +15,10 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include #include "body_rounded_polygon.h" +#include +#include +#include "my_pool_chunk.h" #include "atom_vec_body.h" #include "atom.h" #include "force.h" diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp index 99a380a932ef50b90010c29c778707a4b3cb81f8..98f79138596fe426717afecfd804cd91bc8ac573 100644 --- a/src/BODY/body_rounded_polyhedron.cpp +++ b/src/BODY/body_rounded_polyhedron.cpp @@ -15,12 +15,14 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include #include "body_rounded_polyhedron.h" +#include +#include +#include +#include "my_pool_chunk.h" #include "atom_vec_body.h" #include "atom.h" #include "force.h" -#include "domain.h" #include "math_extra.h" #include "memory.h" #include "error.h" diff --git a/src/BODY/compute_body_local.cpp b/src/BODY/compute_body_local.cpp index 20f7d7670881779ee25cf204c2d09fff1f375a67..c12502df421d311146b1054120498242709de1c7 100644 --- a/src/BODY/compute_body_local.cpp +++ b/src/BODY/compute_body_local.cpp @@ -11,16 +11,14 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_body_local.h" +#include +#include #include "atom.h" #include "atom_vec_body.h" #include "body.h" #include "update.h" -#include "domain.h" #include "force.h" -#include "bond.h" #include "memory.h" #include "error.h" diff --git a/src/BODY/compute_temp_body.cpp b/src/BODY/compute_temp_body.cpp index b560bdd11dfb920789d4f092af717238efaeb7d6..4cf9ac5009a766ece966207a9e3701b3b4130b4c 100644 --- a/src/BODY/compute_temp_body.cpp +++ b/src/BODY/compute_temp_body.cpp @@ -16,9 +16,9 @@ based on ComputeTempAsphere ------------------------------------------------------------------------- */ +#include "compute_temp_body.h" #include #include -#include "compute_temp_body.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_body.h" @@ -27,7 +27,6 @@ #include "domain.h" #include "modify.h" #include "group.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/BODY/fix_nh_body.cpp b/src/BODY/fix_nh_body.cpp index 97398424193f37d0b4f34e6268ec09b2ad5e60c4..b9a0c81e15aa582abe21c8a9bae459d924d7f604 100644 --- a/src/BODY/fix_nh_body.cpp +++ b/src/BODY/fix_nh_body.cpp @@ -16,15 +16,10 @@ based on FixNHAsphere ------------------------------------------------------------------------- */ -#include -#include -#include -#include "math_extra.h" #include "fix_nh_body.h" +#include "math_extra.h" #include "atom.h" #include "atom_vec_body.h" -#include "group.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/BODY/fix_nph_body.cpp b/src/BODY/fix_nph_body.cpp index e647488bce9ae3de2cc3e232aa7a5bbb8c796679..a65c951c968f4312c2a72e373ce6ef8b83b91fdb 100644 --- a/src/BODY/fix_nph_body.cpp +++ b/src/BODY/fix_nph_body.cpp @@ -15,8 +15,8 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include #include "fix_nph_body.h" +#include #include "modify.h" #include "error.h" diff --git a/src/BODY/fix_npt_body.cpp b/src/BODY/fix_npt_body.cpp index 3c30e9e4e92f3825cd3d89da1a46a6f3798f9130..7e8097486ee19c61b481cf800069f3368d672220 100644 --- a/src/BODY/fix_npt_body.cpp +++ b/src/BODY/fix_npt_body.cpp @@ -15,8 +15,8 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include #include "fix_npt_body.h" +#include #include "modify.h" #include "error.h" diff --git a/src/BODY/fix_nve_body.cpp b/src/BODY/fix_nve_body.cpp index 0c74facf34b83e5c152f8511073c7f56c95b5754..185e397540ee41e668b4045f81546d1ba347397a 100644 --- a/src/BODY/fix_nve_body.cpp +++ b/src/BODY/fix_nve_body.cpp @@ -11,16 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nve_body.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_body.h" -#include "force.h" -#include "update.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/BODY/fix_nvt_body.cpp b/src/BODY/fix_nvt_body.cpp index 273b5e7fffd2ac3bf0750ed6cfd2548b4f4f4465..efb05143a17b1a45423d104a2525bca659eede1c 100644 --- a/src/BODY/fix_nvt_body.cpp +++ b/src/BODY/fix_nvt_body.cpp @@ -15,8 +15,8 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include #include "fix_nvt_body.h" +#include #include "group.h" #include "modify.h" #include "error.h" diff --git a/src/BODY/fix_wall_body_polygon.cpp b/src/BODY/fix_wall_body_polygon.cpp index 221937461bac6632be1ba20c7714f58c3b16ee11..e51476de60f27ca879537f4447453fa6b8865189 100644 --- a/src/BODY/fix_wall_body_polygon.cpp +++ b/src/BODY/fix_wall_body_polygon.cpp @@ -15,19 +15,15 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ +#include "fix_wall_body_polygon.h" #include -#include #include -#include "fix_wall_body_polygon.h" #include "atom.h" #include "atom_vec_body.h" #include "body_rounded_polygon.h" #include "domain.h" #include "update.h" #include "force.h" -#include "pair.h" -#include "modify.h" -#include "respa.h" #include "math_const.h" #include "math_extra.h" #include "memory.h" diff --git a/src/BODY/fix_wall_body_polyhedron.cpp b/src/BODY/fix_wall_body_polyhedron.cpp index 24a9e51dad53dcdaea2954d5f4dae5850a996f27..42c62de436536a3174c3ea04000c1033beea709b 100644 --- a/src/BODY/fix_wall_body_polyhedron.cpp +++ b/src/BODY/fix_wall_body_polyhedron.cpp @@ -15,19 +15,15 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ +#include "fix_wall_body_polyhedron.h" #include -#include #include -#include "fix_wall_body_polyhedron.h" #include "atom.h" #include "atom_vec_body.h" #include "body_rounded_polyhedron.h" #include "domain.h" #include "update.h" #include "force.h" -#include "pair.h" -#include "modify.h" -#include "respa.h" #include "math_const.h" #include "math_extra.h" #include "memory.h" diff --git a/src/BODY/pair_body_nparticle.cpp b/src/BODY/pair_body_nparticle.cpp index f2eb2aa5203586f5c1d1d4ce32151ad87e0fb47d..bd7aba5455d6dc0f32d243ce0cc480810e5f32ca 100644 --- a/src/BODY/pair_body_nparticle.cpp +++ b/src/BODY/pair_body_nparticle.cpp @@ -11,11 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_body_nparticle.h" #include -#include -#include #include -#include "pair_body_nparticle.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_body.h" diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp index 69495ea57fb3ac754c3ce37a696cfc59f2dc6aba..f5e18e9d89696903215c62b38dc5b6cf69241876 100644 --- a/src/BODY/pair_body_rounded_polygon.cpp +++ b/src/BODY/pair_body_rounded_polygon.cpp @@ -18,11 +18,10 @@ the contact history for friction forces. ------------------------------------------------------------------------- */ +#include "pair_body_rounded_polygon.h" +#include #include -#include -#include #include -#include "pair_body_rounded_polygon.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_body.h" diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp index 60f6df358224676a743467f19c7fe82341283cf3..2df58d45cd102b7da87a4212606f2721335dff73 100644 --- a/src/BODY/pair_body_rounded_polyhedron.cpp +++ b/src/BODY/pair_body_rounded_polyhedron.cpp @@ -20,12 +20,10 @@ the contact history for friction forces. ------------------------------------------------------------------------- */ +#include "pair_body_rounded_polyhedron.h" +#include #include -#include -#include #include -#include "pair_body_rounded_polyhedron.h" -#include "math_extra.h" #include "atom.h" #include "atom_vec_body.h" #include "body_rounded_polyhedron.h" @@ -41,7 +39,6 @@ #include "math_const.h" using namespace LAMMPS_NS; -using namespace MathExtra; using namespace MathConst; #define DELTA 10000 diff --git a/src/CLASS2/angle_class2.cpp b/src/CLASS2/angle_class2.cpp index d550767e5e0866116d365cf43e638d30f92b9058..99e1b39c9d186b23eb005f983016ae10dc22e209 100644 --- a/src/CLASS2/angle_class2.cpp +++ b/src/CLASS2/angle_class2.cpp @@ -15,10 +15,10 @@ Contributing author: Eric Simon (Cray) ------------------------------------------------------------------------- */ +#include "angle_class2.h" +#include #include #include -#include -#include "angle_class2.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/CLASS2/angle_class2.h b/src/CLASS2/angle_class2.h index 8444ada057bedffafa495a2382a5b4236685e943..cc155747ac96dcaa010962fdfdb439ca92dd2ccc 100644 --- a/src/CLASS2/angle_class2.h +++ b/src/CLASS2/angle_class2.h @@ -20,7 +20,6 @@ AngleStyle(class2,AngleClass2) #ifndef LMP_ANGLE_CLASS2_H #define LMP_ANGLE_CLASS2_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/CLASS2/bond_class2.cpp b/src/CLASS2/bond_class2.cpp index 26c4e63a4dd5e8f5854b0c6c6a5e4f7ca561e192..cfc1a93bdee8aea5eb4426c6c56a1adf7c3a1931 100644 --- a/src/CLASS2/bond_class2.cpp +++ b/src/CLASS2/bond_class2.cpp @@ -15,12 +15,11 @@ Contributing author: Eric Simon (Cray) ------------------------------------------------------------------------- */ -#include -#include #include "bond_class2.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/CLASS2/bond_class2.h b/src/CLASS2/bond_class2.h index 89d930b54883243fd531d9b429829c4d1e791179..f0fcc6825ef896a5cb6409d6bfb19b576d9b9369 100644 --- a/src/CLASS2/bond_class2.h +++ b/src/CLASS2/bond_class2.h @@ -20,7 +20,6 @@ BondStyle(class2,BondClass2) #ifndef LMP_BOND_CLASS2_H #define LMP_BOND_CLASS2_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/CLASS2/dihedral_class2.cpp b/src/CLASS2/dihedral_class2.cpp index c471b1f353ddcef7e4af00af47fb1f73204e39f0..725228666eea6a5d59868e00c3680ad9a190342b 100644 --- a/src/CLASS2/dihedral_class2.cpp +++ b/src/CLASS2/dihedral_class2.cpp @@ -15,14 +15,13 @@ Contributing author: Eric Simon (Cray) ------------------------------------------------------------------------- */ +#include "dihedral_class2.h" +#include #include #include -#include -#include "dihedral_class2.h" #include "atom.h" #include "neighbor.h" #include "update.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "math_const.h" diff --git a/src/CLASS2/dihedral_class2.h b/src/CLASS2/dihedral_class2.h index a4ea9e4bd9ccb8c464c5435bedeb0771d4a06bb1..32cd28913753001a03c12cc6e57f58b83f4f9698 100644 --- a/src/CLASS2/dihedral_class2.h +++ b/src/CLASS2/dihedral_class2.h @@ -20,7 +20,6 @@ DihedralStyle(class2,DihedralClass2) #ifndef LMP_DIHEDRAL_CLASS2_H #define LMP_DIHEDRAL_CLASS2_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp index ccb81aebd9a672a8a61ba3165b6f760a286db707..ca7ac95239035d3db6100f7c405b0150a55fb66d 100644 --- a/src/CLASS2/improper_class2.cpp +++ b/src/CLASS2/improper_class2.cpp @@ -15,14 +15,13 @@ Contributing author: Eric Simon (Cray) ------------------------------------------------------------------------- */ +#include "improper_class2.h" +#include #include #include -#include -#include "improper_class2.h" #include "atom.h" #include "neighbor.h" #include "update.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "math_const.h" diff --git a/src/CLASS2/improper_class2.h b/src/CLASS2/improper_class2.h index 1cc3417731eeb51d5311d6fac19e7462830d5536..cac805046af001b4a1eec87c3bb584af39715338 100644 --- a/src/CLASS2/improper_class2.h +++ b/src/CLASS2/improper_class2.h @@ -20,7 +20,6 @@ ImproperStyle(class2,ImproperClass2) #ifndef LMP_IMPROPER_CLASS2_H #define LMP_IMPROPER_CLASS2_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp index 60b988926a6f0bc4bcf9aa2da43f9fb1b5b7c177..a0088e52b7eedec7cf8b04d92a088ed0bd5aae71 100644 --- a/src/CLASS2/pair_lj_class2.cpp +++ b/src/CLASS2/pair_lj_class2.cpp @@ -9,11 +9,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_class2.h" +#include #include -#include -#include #include -#include "pair_lj_class2.h" #include "atom.h" #include "comm.h" #include "force.h" @@ -21,7 +20,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory.h" diff --git a/src/CLASS2/pair_lj_class2_coul_cut.cpp b/src/CLASS2/pair_lj_class2_coul_cut.cpp index 8dc038b8fc5e2579772466a25e5a132f05cd0947..e999a3682e44d74ffca1c8f1abe7b5d20dae511d 100644 --- a/src/CLASS2/pair_lj_class2_coul_cut.cpp +++ b/src/CLASS2/pair_lj_class2_coul_cut.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_class2_coul_cut.h" +#include #include -#include -#include #include -#include "pair_lj_class2_coul_cut.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/CLASS2/pair_lj_class2_coul_long.cpp b/src/CLASS2/pair_lj_class2_coul_long.cpp index c92c7b78f193df704f0990a64862d51f24f98c65..b56c0769965db82d3a18a6c6ed805f0447f34713 100644 --- a/src/CLASS2/pair_lj_class2_coul_long.cpp +++ b/src/CLASS2/pair_lj_class2_coul_long.cpp @@ -11,17 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_class2_coul_long.h" +#include #include -#include -#include #include -#include "pair_lj_class2_coul_long.h" #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/COLLOID/fix_wall_colloid.cpp b/src/COLLOID/fix_wall_colloid.cpp index 095d01eef3019b6a5735c93dfa5fb093feeca65d..58593a99b18baef1c414ce3d8822d3c2409df629 100644 --- a/src/COLLOID/fix_wall_colloid.cpp +++ b/src/COLLOID/fix_wall_colloid.cpp @@ -15,13 +15,11 @@ Contributing authors: Jeremy Lechman (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "fix_wall_colloid.h" +#include +#include #include "atom.h" #include "atom_vec.h" -#include "update.h" -#include "respa.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/COLLOID/pair_brownian.cpp b/src/COLLOID/pair_brownian.cpp index aefa96b1fb9ba5c2f90fd892b143620cc93f11b4..71a5f8c0567d4617a0d5c9893d48846ad3bfea6c 100644 --- a/src/COLLOID/pair_brownian.cpp +++ b/src/COLLOID/pair_brownian.cpp @@ -15,23 +15,19 @@ Contributing authors: Amit Kumar and Michael Bybee (UIUC) ------------------------------------------------------------------------- */ +#include "pair_brownian.h" +#include #include -#include -#include #include -#include "pair_brownian.h" #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "domain.h" #include "update.h" #include "modify.h" #include "fix.h" -#include "fix_deform.h" #include "fix_wall.h" #include "input.h" #include "variable.h" diff --git a/src/COLLOID/pair_brownian_poly.cpp b/src/COLLOID/pair_brownian_poly.cpp index 389ae084b71662495bbad073b11e5e3d8d8f0c81..c3eb4f28a5afb21543005085f6e256580e5cecff 100644 --- a/src/COLLOID/pair_brownian_poly.cpp +++ b/src/COLLOID/pair_brownian_poly.cpp @@ -16,14 +16,11 @@ Dave Heine (Corning), polydispersity ------------------------------------------------------------------------- */ +#include "pair_brownian_poly.h" +#include #include -#include -#include #include -#include "pair_brownian_poly.h" #include "atom.h" -#include "atom_vec.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" @@ -32,14 +29,12 @@ #include "update.h" #include "modify.h" #include "fix.h" -#include "fix_deform.h" #include "fix_wall.h" #include "input.h" #include "variable.h" #include "random_mars.h" #include "math_const.h" #include "math_special.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/COLLOID/pair_colloid.cpp b/src/COLLOID/pair_colloid.cpp index 04c35a7c009ccd51ad793add69ccf28ae88e04df..ad25184181731f943aac1078b5eb2c1089bcab26 100644 --- a/src/COLLOID/pair_colloid.cpp +++ b/src/COLLOID/pair_colloid.cpp @@ -15,15 +15,12 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_colloid.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_special.h" #include "memory.h" diff --git a/src/COLLOID/pair_lubricate.cpp b/src/COLLOID/pair_lubricate.cpp index 4e629bd442f1473975e071c94d2df95d8fd4b09b..4492de3cbb58902033ff70e5960312cfa2c83544 100644 --- a/src/COLLOID/pair_lubricate.cpp +++ b/src/COLLOID/pair_lubricate.cpp @@ -16,18 +16,15 @@ Amit Kumar and Michael Bybee (UIUC) ------------------------------------------------------------------------- */ +#include "pair_lubricate.h" +#include #include -#include -#include #include -#include "pair_lubricate.h" #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "domain.h" #include "modify.h" #include "fix.h" @@ -35,7 +32,6 @@ #include "fix_wall.h" #include "input.h" #include "variable.h" -#include "random_mars.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/COLLOID/pair_lubricateU.cpp b/src/COLLOID/pair_lubricateU.cpp index 3ea3d4fe4a16dff0f7d39d7cc48ad1f9ed26ff33..4f7e3917e86d84e92c6716ed58b1665d412da994 100644 --- a/src/COLLOID/pair_lubricateU.cpp +++ b/src/COLLOID/pair_lubricateU.cpp @@ -15,25 +15,20 @@ Contributing authors: Amit Kumar and Michael Bybee (UIUC) ------------------------------------------------------------------------- */ +#include "pair_lubricateU.h" #include #include -#include -#include #include -#include "pair_lubricateU.h" #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "domain.h" #include "update.h" #include "math_const.h" #include "modify.h" #include "fix.h" -#include "fix_deform.h" #include "fix_wall.h" #include "input.h" #include "variable.h" diff --git a/src/COLLOID/pair_lubricateU_poly.cpp b/src/COLLOID/pair_lubricateU_poly.cpp index 4fec95dcd81e5db4f2c25d461d860e96e3a97558..0f16d943005634b323681f24d2eff2a7a66d89ec 100644 --- a/src/COLLOID/pair_lubricateU_poly.cpp +++ b/src/COLLOID/pair_lubricateU_poly.cpp @@ -17,24 +17,19 @@ Dave Heine (Corning), polydispersity ------------------------------------------------------------------------- */ +#include "pair_lubricateU_poly.h" #include #include -#include -#include #include -#include "pair_lubricateU_poly.h" #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "domain.h" -#include "update.h" #include "modify.h" #include "fix.h" -#include "fix_deform.h" #include "fix_wall.h" #include "input.h" #include "variable.h" diff --git a/src/COLLOID/pair_lubricate_poly.cpp b/src/COLLOID/pair_lubricate_poly.cpp index ffbe7fce3c182feb1e1c53020eb25a10750a9a74..e347441cf4a8a226c46f7b44342ac3e6e7e15db6 100644 --- a/src/COLLOID/pair_lubricate_poly.cpp +++ b/src/COLLOID/pair_lubricate_poly.cpp @@ -17,13 +17,11 @@ Dave Heine (Corning), polydispersity ------------------------------------------------------------------------- */ +#include "pair_lubricate_poly.h" +#include #include -#include -#include #include -#include "pair_lubricate_poly.h" #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "force.h" #include "neighbor.h" @@ -33,8 +31,6 @@ #include "modify.h" #include "fix.h" #include "fix_deform.h" -#include "memory.h" -#include "random_mars.h" #include "fix_wall.h" #include "input.h" #include "variable.h" diff --git a/src/COLLOID/pair_yukawa_colloid.cpp b/src/COLLOID/pair_yukawa_colloid.cpp index ab7d08850889e05b34399926134e8ff3a0e17359..1866fa60b57559a376f0577d29022ff2f2053be9 100644 --- a/src/COLLOID/pair_yukawa_colloid.cpp +++ b/src/COLLOID/pair_yukawa_colloid.cpp @@ -15,16 +15,13 @@ Contributing authors: Randy Schunk (Sandia) ------------------------------------------------------------------------- */ -#include -#include #include "pair_yukawa_colloid.h" +#include #include "atom.h" #include "atom_vec.h" #include "force.h" -#include "comm.h" #include "neighbor.h" #include "neigh_list.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_xyz_gz.cpp b/src/COMPRESS/dump_xyz_gz.cpp index 7be1a10fe2b15b19daa5f3b93d0659d75959922f..c76b7afa177189f11eda67b7e218ebdd2fde9265 100644 --- a/src/COMPRESS/dump_xyz_gz.cpp +++ b/src/COMPRESS/dump_xyz_gz.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "dump_xyz_gz.h" -#include "domain.h" #include "error.h" #include "update.h" diff --git a/src/CORESHELL/compute_temp_cs.cpp b/src/CORESHELL/compute_temp_cs.cpp index dac0d60fce62309cf3336fc61940125355bb7cb6..0dc03e47f213b43982239148feeca40e9c3c91ad 100644 --- a/src/CORESHELL/compute_temp_cs.cpp +++ b/src/CORESHELL/compute_temp_cs.cpp @@ -16,11 +16,9 @@ (hendrik.heenen at mytum.com) ------------------------------------------------------------------------- */ +#include "compute_temp_cs.h" #include -#include #include -#include -#include "compute_temp_cs.h" #include "atom.h" #include "atom_vec.h" #include "domain.h" @@ -28,7 +26,6 @@ #include "force.h" #include "group.h" #include "modify.h" -#include "fix.h" #include "fix_store.h" #include "comm.h" #include "memory.h" diff --git a/src/CORESHELL/pair_born_coul_dsf_cs.cpp b/src/CORESHELL/pair_born_coul_dsf_cs.cpp index f4d7447adeb47f2f89f1004a362cd5c22c2f6561..9440bca109b7aa5b1b64b03bbeb17715a752fbe6 100644 --- a/src/CORESHELL/pair_born_coul_dsf_cs.cpp +++ b/src/CORESHELL/pair_born_coul_dsf_cs.cpp @@ -16,19 +16,13 @@ References: Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_born_coul_dsf_cs.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_const.h" -#include "memory.h" -#include "error.h" #include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/CORESHELL/pair_born_coul_long_cs.cpp b/src/CORESHELL/pair_born_coul_long_cs.cpp index a19f8c34a866a1ecb93d7387860176395b6838fc..b56389e18062663fc0073185c6706d1138dcac03 100644 --- a/src/CORESHELL/pair_born_coul_long_cs.cpp +++ b/src/CORESHELL/pair_born_coul_long_cs.cpp @@ -15,23 +15,13 @@ Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_born_coul_long_cs.h" +#include #include "atom.h" -#include "comm.h" #include "force.h" -#include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; #define EWALD_F 1.12837917 #define EWALD_P 9.95473818e-1 diff --git a/src/CORESHELL/pair_born_coul_wolf_cs.cpp b/src/CORESHELL/pair_born_coul_wolf_cs.cpp index 7b52c2866413d08c764b1c2e684b99ec119df66a..398c2ba1ee4e38b41918623aad4cabba135f5ddd 100644 --- a/src/CORESHELL/pair_born_coul_wolf_cs.cpp +++ b/src/CORESHELL/pair_born_coul_wolf_cs.cpp @@ -12,24 +12,16 @@ ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_born_coul_wolf_cs.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_const.h" -#include "math_special.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; using namespace MathConst; -using namespace MathSpecial; #define EPSILON 1.0e-20 diff --git a/src/CORESHELL/pair_buck_coul_long_cs.cpp b/src/CORESHELL/pair_buck_coul_long_cs.cpp index 8df91f39a30ff2bfa797914ed501e249e64e3cd7..1392ec1880c4bca25b574c9cbe7bb36ff58d5587 100644 --- a/src/CORESHELL/pair_buck_coul_long_cs.cpp +++ b/src/CORESHELL/pair_buck_coul_long_cs.cpp @@ -15,23 +15,13 @@ Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_buck_coul_long_cs.h" +#include #include "atom.h" -#include "comm.h" #include "force.h" -#include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; #define EWALD_F 1.12837917 #define EWALD_P 9.95473818e-1 diff --git a/src/CORESHELL/pair_coul_long_cs.cpp b/src/CORESHELL/pair_coul_long_cs.cpp index c8c8387d6d692a28e7ccb3e41b71b7f6269a565d..8280799389ca4e126dfff1942679d12447f1fb75 100644 --- a/src/CORESHELL/pair_coul_long_cs.cpp +++ b/src/CORESHELL/pair_coul_long_cs.cpp @@ -15,22 +15,11 @@ Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_long_cs.h" +#include #include "atom.h" -#include "comm.h" #include "force.h" -#include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/CORESHELL/pair_coul_wolf_cs.cpp b/src/CORESHELL/pair_coul_wolf_cs.cpp index 36e037bfc8fe3c7d6efbff7405e68f608f74e787..20b73394805f57b0a01182410498feff59c1d18a 100644 --- a/src/CORESHELL/pair_coul_wolf_cs.cpp +++ b/src/CORESHELL/pair_coul_wolf_cs.cpp @@ -11,25 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - -#include -#include -#include -#include #include "pair_coul_wolf_cs.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_const.h" -#include "math_special.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; using namespace MathConst; -using namespace MathSpecial; #define EPSILON 1.0e-20 diff --git a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp index 56c75f0f5dd24c4c289875b81d980f0ba5e1944f..7ad544051afd6e22206bf48de8718fe1a73eb3cc 100644 --- a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp +++ b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp @@ -15,27 +15,13 @@ Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cut_coul_long_cs.h" +#include #include "atom.h" -#include "comm.h" #include "force.h" -#include "kspace.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; #define EWALD_F 1.12837917 #define EWALD_P 9.95473818e-1 diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp index a6f454dc98961cccd1a21c90f8aade187e61dd65..0b6a27888f82a26bc808387d5d97db601a275227 100644 --- a/src/DIPOLE/atom_vec_dipole.cpp +++ b/src/DIPOLE/atom_vec_dipole.cpp @@ -11,13 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "atom_vec_dipole.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp index 18b78c55e0e02de605fb56956a1cad021a77f842..14c511c1000354f0c68b0eb29d610a7ba8322b19 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_cut_dipole_cut.h" +#include #include -#include #include -#include "pair_lj_cut_dipole_cut.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/DIPOLE/pair_lj_cut_dipole_long.cpp b/src/DIPOLE/pair_lj_cut_dipole_long.cpp index 42446a3777221eda71a677f71023c729df8b6585..fe020ed2e6bc937458c47357206197f0146c5391 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_long.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_cut_dipole_long.h" +#include #include -#include -#include #include -#include "pair_lj_cut_dipole_long.h" #include "atom.h" #include "comm.h" #include "neighbor.h" diff --git a/src/DIPOLE/pair_lj_long_dipole_long.cpp b/src/DIPOLE/pair_lj_long_dipole_long.cpp index fbdc47a15b44cd7a2d20ddca9f7489360586988c..5e7819c2f43b688bd8d4169dab7e677ded3f3f07 100644 --- a/src/DIPOLE/pair_lj_long_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_long_dipole_long.cpp @@ -15,23 +15,19 @@ Contributing author: Pieter J. in 't Veld and Stan Moore (Sandia) ------------------------------------------------------------------------- */ +#include "pair_lj_long_dipole_long.h" +#include #include -#include -#include #include #include "math_const.h" #include "math_vector.h" -#include "pair_lj_long_dipole_long.h" #include "atom.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" -#include "respa.h" #include "memory.h" #include "error.h" diff --git a/src/GPU/fix_gpu.cpp b/src/GPU/fix_gpu.cpp index f0558e6a025c013bb6b77ed5c4fd7267655bd3ad..d4397503dc8d82afa9c8a5045889363af9947807 100644 --- a/src/GPU/fix_gpu.cpp +++ b/src/GPU/fix_gpu.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_gpu.h" #include #include -#include "fix_gpu.h" #include "atom.h" #include "force.h" #include "pair.h" diff --git a/src/GPU/pair_beck_gpu.cpp b/src/GPU/pair_beck_gpu.cpp index 9f76975ef1fbd7be6919130ce2793f9f017ff9ec..d4d36a5837e6af83bfb3502af34263a71c9c6da7 100644 --- a/src/GPU/pair_beck_gpu.cpp +++ b/src/GPU/pair_beck_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_beck_gpu.h" #include #include #include #include -#include "pair_beck_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_born_coul_long_cs_gpu.cpp b/src/GPU/pair_born_coul_long_cs_gpu.cpp index 291ad8ad1fd20391c9ccffa80f14398cbedb09d2..7314024d71c0f27d4789c0e23eef3f20f33f44c3 100644 --- a/src/GPU/pair_born_coul_long_cs_gpu.cpp +++ b/src/GPU/pair_born_coul_long_cs_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (Northwestern) ------------------------------------------------------------------------- */ +#include "pair_born_coul_long_cs_gpu.h" #include #include #include #include -#include "pair_born_coul_long_cs_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_born_coul_long_gpu.cpp b/src/GPU/pair_born_coul_long_gpu.cpp index eb204691c71fac6b1fffe7df4df50214657c9a9e..79c0d5f147cf75387988d78c3650451f44b1673f 100644 --- a/src/GPU/pair_born_coul_long_gpu.cpp +++ b/src/GPU/pair_born_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_born_coul_long_gpu.h" #include #include #include #include -#include "pair_born_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp index 4877a442b5abe4bbff01ef6aacc1577d03cbbb9b..5f74d3fc7caf21fd03ef7bb4a9e1eef71a827a34 100644 --- a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp +++ b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp @@ -15,11 +15,11 @@ Contributing authors: Trung Dac Nguyen (Northwestern) ------------------------------------------------------------------------- */ +#include "pair_born_coul_wolf_cs_gpu.h" #include #include #include #include -#include "pair_born_coul_wolf_cs_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_born_coul_wolf_gpu.cpp b/src/GPU/pair_born_coul_wolf_gpu.cpp index 851174988b4d0ffe9eec517609d417a87a12c86f..693c2abffb8ab39048bc6628671ef73e52a2bbaa 100644 --- a/src/GPU/pair_born_coul_wolf_gpu.cpp +++ b/src/GPU/pair_born_coul_wolf_gpu.cpp @@ -15,11 +15,11 @@ Contributing authors: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_born_coul_wolf_gpu.h" #include #include #include #include -#include "pair_born_coul_wolf_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_born_gpu.cpp b/src/GPU/pair_born_gpu.cpp index 253d2d728254b68c75f1d2bc1d05aecb959d7e2b..e9edc4f1c223e1775fb37dd164dbd3d7a4b8f608 100644 --- a/src/GPU/pair_born_gpu.cpp +++ b/src/GPU/pair_born_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_born_gpu.h" #include #include #include #include -#include "pair_born_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_buck_coul_cut_gpu.cpp b/src/GPU/pair_buck_coul_cut_gpu.cpp index ed602f9cabb8482a11422fdf889e26115d74b167..182673fb0dc0f9e5d1f2883c5f6a5dc5bdd6ed52 100644 --- a/src/GPU/pair_buck_coul_cut_gpu.cpp +++ b/src/GPU/pair_buck_coul_cut_gpu.cpp @@ -15,11 +15,11 @@ Contributing authors: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_buck_coul_cut_gpu.h" #include #include #include #include -#include "pair_buck_coul_cut_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_buck_coul_long_gpu.cpp b/src/GPU/pair_buck_coul_long_gpu.cpp index d6b9e532822dd53043ed1c1bba375f550be8ace2..75e784fafa8d803987275eeab0b9a5d63e0e3105 100644 --- a/src/GPU/pair_buck_coul_long_gpu.cpp +++ b/src/GPU/pair_buck_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_buck_coul_long_gpu.h" #include #include #include #include -#include "pair_buck_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_buck_gpu.cpp b/src/GPU/pair_buck_gpu.cpp index 8c85407e6e6ae6e854de1c8dab3acac0fe23e208..1559c45b8847a1c06afd9162945f0cd146542615 100644 --- a/src/GPU/pair_buck_gpu.cpp +++ b/src/GPU/pair_buck_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_buck_gpu.h" #include #include #include #include -#include "pair_buck_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_colloid_gpu.cpp b/src/GPU/pair_colloid_gpu.cpp index 0ee8708b5b7f4237c6e80d43577b71aa7aba0e9e..4db18dbc52bea98a4fe96a1ca0160b1b086eb5f1 100644 --- a/src/GPU/pair_colloid_gpu.cpp +++ b/src/GPU/pair_colloid_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_colloid_gpu.h" #include #include #include #include -#include "pair_colloid_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_coul_cut_gpu.cpp b/src/GPU/pair_coul_cut_gpu.cpp index fb50c446b1de699fb622f42756480ec8be11f680..8a3eb12f8da931ce06f2dc2a073c20866ca4b0d7 100644 --- a/src/GPU/pair_coul_cut_gpu.cpp +++ b/src/GPU/pair_coul_cut_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen ------------------------------------------------------------------------- */ +#include "pair_coul_cut_gpu.h" #include #include #include #include -#include "pair_coul_cut_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_coul_debye_gpu.cpp b/src/GPU/pair_coul_debye_gpu.cpp index ec771a9935b5a0e1b9ccda7cd5fdd763a158382d..1fc07f8dacb935c83038d1bae077951f8db9b6cf 100644 --- a/src/GPU/pair_coul_debye_gpu.cpp +++ b/src/GPU/pair_coul_debye_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ndtrung@umich.edu) ------------------------------------------------------------------------- */ +#include "pair_coul_debye_gpu.h" #include #include #include #include -#include "pair_coul_debye_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_coul_dsf_gpu.cpp b/src/GPU/pair_coul_dsf_gpu.cpp index 1753b8a91cb03683d60ef8897870c0cc33bc10d1..408be036dd086060c4ee56d284e0605d652802e8 100644 --- a/src/GPU/pair_coul_dsf_gpu.cpp +++ b/src/GPU/pair_coul_dsf_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_coul_dsf_gpu.h" #include #include #include #include -#include "pair_coul_dsf_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_coul_long_cs_gpu.cpp b/src/GPU/pair_coul_long_cs_gpu.cpp index 6ca00d63615aaa88ea7ec8fabac38abf15c8d3dd..c70424e47282792f400d4c395b4044fd9deaaafa 100644 --- a/src/GPU/pair_coul_long_cs_gpu.cpp +++ b/src/GPU/pair_coul_long_cs_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Nguyen (Northwestern) ------------------------------------------------------------------------- */ +#include "pair_coul_long_cs_gpu.h" #include #include #include #include -#include "pair_coul_long_cs_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_coul_long_gpu.cpp b/src/GPU/pair_coul_long_gpu.cpp index f75d10b6dd2f0fcb40e14f5193402edf432c4458..9623c25f2fc4a9ec70c88b31bb67925935047d0c 100644 --- a/src/GPU/pair_coul_long_gpu.cpp +++ b/src/GPU/pair_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Axel Kohlmeyer (Temple) ------------------------------------------------------------------------- */ +#include "pair_coul_long_gpu.h" #include #include #include #include -#include "pair_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_dpd_gpu.cpp b/src/GPU/pair_dpd_gpu.cpp index b1e45fbecd0c1b57431035836359b2b77b37c2a9..5fcad6a35022b62c83d26b197f4c3082b584e8d1 100644 --- a/src/GPU/pair_dpd_gpu.cpp +++ b/src/GPU/pair_dpd_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_dpd_gpu.h" #include #include #include #include -#include "pair_dpd_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_dpd_tstat_gpu.cpp b/src/GPU/pair_dpd_tstat_gpu.cpp index 0693a27344d9d26084ecaaa4ce1e9c72b16a1613..2d6798a12d5fbfd8c2b728d2c70c652aef1feb2b 100644 --- a/src/GPU/pair_dpd_tstat_gpu.cpp +++ b/src/GPU/pair_dpd_tstat_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_dpd_tstat_gpu.h" #include #include #include #include -#include "pair_dpd_tstat_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp index 9b3412d3d1c26cc42ec7142f0941680aa679af66..bc55c6667682f4c42cce07680c5010d7978f5e67 100644 --- a/src/GPU/pair_eam_alloy_gpu.cpp +++ b/src/GPU/pair_eam_alloy_gpu.cpp @@ -15,10 +15,10 @@ Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL) ------------------------------------------------------------------------- */ +#include "pair_eam_alloy_gpu.h" #include #include #include -#include "pair_eam_alloy_gpu.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp index 11ef28af3e7e56b9dd5d79b8f04f5db36509a585..ac379a9ce6404dc1ac1e3be5f19903a23db8c244 100644 --- a/src/GPU/pair_eam_fs_gpu.cpp +++ b/src/GPU/pair_eam_fs_gpu.cpp @@ -15,10 +15,10 @@ Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL) ------------------------------------------------------------------------- */ +#include "pair_eam_fs_gpu.h" #include #include #include -#include "pair_eam_fs_gpu.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/GPU/pair_eam_gpu.cpp b/src/GPU/pair_eam_gpu.cpp index 4788a7241779e68b9851b7207205aa092c7e90ce..57106f48a4d23bf34fe96b8c53004a14754b0255 100644 --- a/src/GPU/pair_eam_gpu.cpp +++ b/src/GPU/pair_eam_gpu.cpp @@ -15,11 +15,11 @@ Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL) ------------------------------------------------------------------------- */ +#include "pair_eam_gpu.h" #include #include #include #include -#include "pair_eam_gpu.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/GPU/pair_eam_gpu.h b/src/GPU/pair_eam_gpu.h index 099529f3df90c766d0385dcb0319294b6f28c4b4..e4742a3bef578f130fc04fcaaf7dcd487de91c95 100644 --- a/src/GPU/pair_eam_gpu.h +++ b/src/GPU/pair_eam_gpu.h @@ -20,7 +20,6 @@ PairStyle(eam/gpu,PairEAMGPU) #ifndef LMP_PAIR_EAM_GPU_H #define LMP_PAIR_EAM_GPU_H -#include #include "pair_eam.h" namespace LAMMPS_NS { diff --git a/src/GPU/pair_gauss_gpu.cpp b/src/GPU/pair_gauss_gpu.cpp index c596a9d644c69bdbdae2364050ebee7e87f8d4ec..842b84acf256f21e45d007d59d378dea6537a2b7 100644 --- a/src/GPU/pair_gauss_gpu.cpp +++ b/src/GPU/pair_gauss_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_gauss_gpu.h" #include #include #include #include -#include "pair_gauss_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_gayberne_gpu.cpp b/src/GPU/pair_gayberne_gpu.cpp index 4ed2750e57fb40dca142c46c568a6d2ac4cff0f8..f00accda159b0dcff801991cd7a572c081b9d7e5 100644 --- a/src/GPU/pair_gayberne_gpu.cpp +++ b/src/GPU/pair_gayberne_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_gayberne_gpu.h" #include #include #include #include -#include "pair_gayberne_gpu.h" #include "math_extra.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj96_cut_gpu.cpp b/src/GPU/pair_lj96_cut_gpu.cpp index 5bc30c809d81708f3b49fabe822cd96edf4f7fd9..16b6b835c0012d0ab762930d25f3f9f244e6005e 100644 --- a/src/GPU/pair_lj96_cut_gpu.cpp +++ b/src/GPU/pair_lj96_cut_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj96_cut_gpu.h" #include #include #include #include -#include "pair_lj96_cut_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp index 134295c69f7a2371d8f91534fad5f605cb2b5518..bacbb400b1779997dc40f64e334238db76b17b10 100644 --- a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_charmm_coul_long_gpu.h" #include #include #include #include -#include "pair_lj_charmm_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_class2_coul_long_gpu.cpp b/src/GPU/pair_lj_class2_coul_long_gpu.cpp index fdffb06a8d33cb8559ff37ce36abef4bfad769af..e34dbb0f99c90030779a5450dfbaf68359b76936 100644 --- a/src/GPU/pair_lj_class2_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_class2_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_class2_coul_long_gpu.h" #include #include #include #include -#include "pair_lj_class2_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_class2_gpu.cpp b/src/GPU/pair_lj_class2_gpu.cpp index bbb916816999d25991fb4ac8d17314eed8f90759..68f27598f38c974c44f97dc0cba67347d4d37441 100644 --- a/src/GPU/pair_lj_class2_gpu.cpp +++ b/src/GPU/pair_lj_class2_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_class2_gpu.h" #include #include #include #include -#include "pair_lj_class2_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cubic_gpu.cpp b/src/GPU/pair_lj_cubic_gpu.cpp index 95eee6ae8f765396dcd0ce427defe5517135d72a..542de37840c4d4585e17c73b6e9d0ddaf0fecf36 100644 --- a/src/GPU/pair_lj_cubic_gpu.cpp +++ b/src/GPU/pair_lj_cubic_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ +#include "pair_lj_cubic_gpu.h" #include #include #include #include -#include "pair_lj_cubic_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp index 69fefbcdeaf2d20e3a3e65af7aa347d23d34d2d1..cf3dd711dc3c83b545ef16cba119237b59c402b7 100644 --- a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_cut_gpu.h" #include #include #include #include -#include "pair_lj_cut_coul_cut_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp index de86c58647e8751fcd9d0e78e4a9072e5d786b51..20354e732c08d913751509dd64055648f5f8b1a8 100644 --- a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_debye_gpu.h" #include #include #include #include -#include "pair_lj_cut_coul_debye_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp index 87eac527494f3c2bfd95aabd4fc8f225cde6cadd..ccaf86efa683a960ff42017f94232d7c17774521 100644 --- a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_dsf_gpu.h" #include #include #include #include -#include "pair_lj_cut_coul_dsf_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.cpp b/src/GPU/pair_lj_cut_coul_long_gpu.cpp index c854dab83d0422b648c31a539597d2086f5e992d..36c72f11431802f1c86fe188c651b6aaef32e018 100644 --- a/src/GPU/pair_lj_cut_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_long_gpu.h" #include #include #include #include -#include "pair_lj_cut_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp index f87dc0ec916e000a36e425896209c2608ffaaa83..79ca90698ac40f81ee700765d4296a38a32bb631 100644 --- a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_msm_gpu.h" #include #include #include #include -#include "pair_lj_cut_coul_msm_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp index d2c925d95032d37f52cfb22b17f239e662c55d7d..e2c8b8d686358d217e23c34d03a8385ba784577c 100644 --- a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_dipole_cut_gpu.h" #include #include #include #include -#include "pair_lj_cut_dipole_cut_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp index 774ff2fae43c49e6e19e3611234f5ee915511e69..fb76376d343f68938761bf1c7423619a87f20f89 100644 --- a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (Northwestern) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_dipole_long_gpu.h" #include #include #include #include -#include "pair_lj_cut_dipole_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_gpu.cpp b/src/GPU/pair_lj_cut_gpu.cpp index 6dde9689f73b1c9f66fbcd3e5d7bdb66133b9041..809e5cf05ef7feb5c965346edad9d664f82b1647 100644 --- a/src/GPU/pair_lj_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_gpu.h" #include #include #include #include -#include "pair_lj_cut_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_expand_coul_long_gpu.cpp b/src/GPU/pair_lj_expand_coul_long_gpu.cpp index 31f4fd651cfb5774617357a82616bbf92fa8e09c..a530f7ff9a0ec4aba4502c858d1fbb0a6b20f9c1 100644 --- a/src/GPU/pair_lj_expand_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_expand_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Nguyen (Northwestern) ------------------------------------------------------------------------- */ +#include "pair_lj_expand_coul_long_gpu.h" #include #include #include #include -#include "pair_lj_expand_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_expand_gpu.cpp b/src/GPU/pair_lj_expand_gpu.cpp index a2e1cf54e3bf9e6f960a41dcf6301604f5589933..86f8a76b52f4f97c735b5c91cb07411f8b779e04 100644 --- a/src/GPU/pair_lj_expand_gpu.cpp +++ b/src/GPU/pair_lj_expand_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Inderaj Bains (NVIDIA), ibains@nvidia.com ------------------------------------------------------------------------- */ +#include "pair_lj_expand_gpu.h" #include #include #include #include -#include "pair_lj_expand_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_gromacs_gpu.cpp b/src/GPU/pair_lj_gromacs_gpu.cpp index e03f4b2e50db8ce6c8bbfd2bbbd47c1132b444d0..78f8b8b4616460c9a99eaba0c1f2a9ffe6afb28b 100644 --- a/src/GPU/pair_lj_gromacs_gpu.cpp +++ b/src/GPU/pair_lj_gromacs_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_lj_gromacs_gpu.h" #include #include #include #include -#include "pair_lj_gromacs_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp index f5029df5dc5394a96bd035e384d67a90b768c7eb..24ff8a4f28dc52e15c01ffcd883c9b49e1546566 100644 --- a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_sdk_coul_long_gpu.h" #include #include #include #include -#include "pair_lj_sdk_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_sdk_gpu.cpp b/src/GPU/pair_lj_sdk_gpu.cpp index 4797a3440878daa326d076e055ec4c11e99960fa..2621f49aeb6b7c4b5ddbd786dc44f2aaac8a46dc 100644 --- a/src/GPU/pair_lj_sdk_gpu.cpp +++ b/src/GPU/pair_lj_sdk_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_sdk_gpu.h" #include #include #include #include -#include "pair_lj_sdk_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp index dd25a70eeecb86d5eccc9d6ad80d1ae777781968..cf26cdf3b4bc1c2cb8e4fdbd49195f07d3fbc46d 100644 --- a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp +++ b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_lj_sf_dipole_sf_gpu.h" #include #include #include #include -#include "pair_lj_sf_dipole_sf_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_mie_cut_gpu.cpp b/src/GPU/pair_mie_cut_gpu.cpp index 838d28033fb1bbe743873091de96f428c38b7183..f3a384113f77d8d0c5f0e6a940aa543b9559e499 100644 --- a/src/GPU/pair_mie_cut_gpu.cpp +++ b/src/GPU/pair_mie_cut_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_mie_cut_gpu.h" #include #include #include #include -#include "pair_mie_cut_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_morse_gpu.cpp b/src/GPU/pair_morse_gpu.cpp index 1f94643e3a5e81f6816e41962637a5cfa6001676..dcad227045b92b54bd127288dda5492999a72eaf 100644 --- a/src/GPU/pair_morse_gpu.cpp +++ b/src/GPU/pair_morse_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_morse_gpu.h" #include #include #include #include -#include "pair_morse_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_resquared_gpu.cpp b/src/GPU/pair_resquared_gpu.cpp index 5e90f788bf482f807de6946185f33bce4ad9d8af..b12a790c81a252aaf3fb0927ed6fd5833b187fbd 100644 --- a/src/GPU/pair_resquared_gpu.cpp +++ b/src/GPU/pair_resquared_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_resquared_gpu.h" #include #include #include #include -#include "pair_resquared_gpu.h" #include "math_extra.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_soft_gpu.cpp b/src/GPU/pair_soft_gpu.cpp index 42adb02553a1c157c7e3ba51dea1791c44d25aa2..0efcb20c8d40290e653b7a0bee66092f53f38052 100644 --- a/src/GPU/pair_soft_gpu.cpp +++ b/src/GPU/pair_soft_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_soft_gpu.h" #include #include #include #include -#include "pair_soft_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_sw_gpu.cpp b/src/GPU/pair_sw_gpu.cpp index 0cc858e57dafa587e0ee920db00e9caff06ebd8b..8999cb6c47c59447810da14a057f2d7c5ac854c1 100644 --- a/src/GPU/pair_sw_gpu.cpp +++ b/src/GPU/pair_sw_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (ORNL) ------------------------------------------------------------------------- */ +#include "pair_sw_gpu.h" #include #include #include #include -#include "pair_sw_gpu.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/GPU/pair_table_gpu.cpp b/src/GPU/pair_table_gpu.cpp index a0b6562e5e32d12737e80e5045a5c6e7ce2587e7..4432265874b12869bd6c5d723dcbbc56ef2f52cc 100644 --- a/src/GPU/pair_table_gpu.cpp +++ b/src/GPU/pair_table_gpu.cpp @@ -15,11 +15,11 @@ Contributing authors: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_table_gpu.h" #include #include #include #include -#include "pair_table_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_tersoff_gpu.cpp b/src/GPU/pair_tersoff_gpu.cpp index cd0c5e669398532856b6e36fa5f656dfabd589e0..e0dc021b5742ff3f97bd0865ce7f9093955b239f 100644 --- a/src/GPU/pair_tersoff_gpu.cpp +++ b/src/GPU/pair_tersoff_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ +#include "pair_tersoff_gpu.h" #include #include #include #include -#include "pair_tersoff_gpu.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/GPU/pair_tersoff_mod_gpu.cpp b/src/GPU/pair_tersoff_mod_gpu.cpp index fd55ddc6e686e0c4aa2992179bb5509a9b706c41..a17efb55e84a713744821444198e6007218037e1 100644 --- a/src/GPU/pair_tersoff_mod_gpu.cpp +++ b/src/GPU/pair_tersoff_mod_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ +#include "pair_tersoff_mod_gpu.h" #include #include #include #include -#include "pair_tersoff_mod_gpu.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/GPU/pair_tersoff_zbl_gpu.cpp b/src/GPU/pair_tersoff_zbl_gpu.cpp index d3828962e274ac17347d7d600a7ed9f0118998f1..765d25f8e627c4df8a05df3469bbac60295cef81 100644 --- a/src/GPU/pair_tersoff_zbl_gpu.cpp +++ b/src/GPU/pair_tersoff_zbl_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ +#include "pair_tersoff_zbl_gpu.h" #include #include #include #include -#include "pair_tersoff_zbl_gpu.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/GPU/pair_ufm_gpu.cpp b/src/GPU/pair_ufm_gpu.cpp index 31422b0f4da6c0aea4319661a8ed0675d4860e30..97c2eebf2432effbc69b030b80e6fbe77eea2f1f 100644 --- a/src/GPU/pair_ufm_gpu.cpp +++ b/src/GPU/pair_ufm_gpu.cpp @@ -17,11 +17,11 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ +#include "pair_ufm_gpu.h" #include #include #include #include -#include "pair_ufm_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_vashishta_gpu.cpp b/src/GPU/pair_vashishta_gpu.cpp index b496359b8a175cf996eea3b5bf7ec8afd310550c..3b74e5685eee23b8c3446c673ec08c12ac32546e 100644 --- a/src/GPU/pair_vashishta_gpu.cpp +++ b/src/GPU/pair_vashishta_gpu.cpp @@ -14,12 +14,12 @@ /* ---------------------------------------------------------------------- Contributing author: Anders Hafreager (UiO) ------------------------------------------------------------------------- */ -#include + +#include "pair_vashishta_gpu.h" #include #include #include #include -#include "pair_vashishta_gpu.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/GPU/pair_yukawa_colloid_gpu.cpp b/src/GPU/pair_yukawa_colloid_gpu.cpp index 3645f392a285759807aeb7e9c19fd13642b3b135..51c7e683db1203ebd55949944232cfa389daeda2 100644 --- a/src/GPU/pair_yukawa_colloid_gpu.cpp +++ b/src/GPU/pair_yukawa_colloid_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_yukawa_colloid_gpu.h" #include #include #include #include -#include "pair_yukawa_colloid_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_yukawa_gpu.cpp b/src/GPU/pair_yukawa_gpu.cpp index 90317fea34e049291238022801e423aa23278b06..5dc13c7750b8fc33980ec62b1db7009ae558d839 100644 --- a/src/GPU/pair_yukawa_gpu.cpp +++ b/src/GPU/pair_yukawa_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_yukawa_gpu.h" #include #include #include #include -#include "pair_yukawa_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_zbl_gpu.cpp b/src/GPU/pair_zbl_gpu.cpp index 99471cbe902f26f97b65c3eebbdc1535787c1019..5e24281145b76b3daf856ebb65b77feb4ac958f1 100644 --- a/src/GPU/pair_zbl_gpu.cpp +++ b/src/GPU/pair_zbl_gpu.cpp @@ -15,12 +15,12 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_zbl_gpu.h" #include "lmptype.h" #include #include #include #include -#include "pair_zbl_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pppm_gpu.cpp b/src/GPU/pppm_gpu.cpp index 1bb1a39703c90ef664e192089509b5d7b0cec328..bbb270ff8e4380c5970f875ef40a9e27d8c3466a 100644 --- a/src/GPU/pppm_gpu.cpp +++ b/src/GPU/pppm_gpu.cpp @@ -15,12 +15,12 @@ Contributing authors: Mike Brown (ORNL), Axel Kohlmeyer (Temple) ------------------------------------------------------------------------- */ +#include "pppm_gpu.h" #include #include #include #include #include -#include "pppm_gpu.h" #include "atom.h" #include "comm.h" #include "gridcomm.h" diff --git a/src/GRANULAR/fix_freeze.cpp b/src/GRANULAR/fix_freeze.cpp index 73c1c9fc111a3239993ebe88d8154a8698ecdc16..1df5c9d0a8e945ea17ed51bd7deb95a3b6e3c9dd 100644 --- a/src/GRANULAR/fix_freeze.cpp +++ b/src/GRANULAR/fix_freeze.cpp @@ -11,12 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_freeze.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" -#include "comm.h" #include "respa.h" #include "error.h" diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index f7cf408e787112cd2426ec77f515e7b97417ffd4..b62b630be50354b1528db72c2ddda855b48d876a 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_pour.h" +#include #include -#include #include -#include "fix_pour.h" #include "atom.h" #include "atom_vec.h" #include "force.h" diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index 8513fc702b480fd4e2dd4a277cdd8a7e5395a53e..e7464a78a9e0bc15971fad479ab8cd5fe9a8d05e 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -16,15 +16,13 @@ Dan Bolintineanu (SNL) ------------------------------------------------------------------------- */ +#include "fix_wall_gran.h" #include -#include #include -#include "fix_wall_gran.h" #include "atom.h" #include "domain.h" #include "update.h" #include "force.h" -#include "pair.h" #include "modify.h" #include "respa.h" #include "math_const.h" diff --git a/src/GRANULAR/fix_wall_gran_region.cpp b/src/GRANULAR/fix_wall_gran_region.cpp index 72798bf7b782f972b7329b7dad5f1c1a1e2e08bc..95553b83b71c960fd84650c0cd49e536e4296dea 100644 --- a/src/GRANULAR/fix_wall_gran_region.cpp +++ b/src/GRANULAR/fix_wall_gran_region.cpp @@ -15,19 +15,12 @@ Contributing authors: Dan Bolintineanu (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_wall_gran_region.h" +#include #include "region.h" #include "atom.h" #include "domain.h" #include "update.h" -#include "force.h" -#include "pair.h" -#include "modify.h" -#include "respa.h" -#include "math_const.h" #include "memory.h" #include "error.h" #include "comm.h" @@ -35,7 +28,6 @@ using namespace LAMMPS_NS; using namespace FixConst; -using namespace MathConst; // same as FixWallGran diff --git a/src/GRANULAR/pair_gran_hertz_history.cpp b/src/GRANULAR/pair_gran_hertz_history.cpp index 728491c17aac88cfd47dd3f9ac2d70c78098b49c..4a362c092813e8daac23c67498c11c121df15def 100644 --- a/src/GRANULAR/pair_gran_hertz_history.cpp +++ b/src/GRANULAR/pair_gran_hertz_history.cpp @@ -15,11 +15,9 @@ Contributing authors: Leo Silbert (SNL), Gary Grest (SNL) ------------------------------------------------------------------------- */ +#include "pair_gran_hertz_history.h" #include -#include -#include #include -#include "pair_gran_hertz_history.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/GRANULAR/pair_gran_hooke.cpp b/src/GRANULAR/pair_gran_hooke.cpp index cfcc2743ba60a5ef76a5939e6e98ee9a54b13f79..d4be320554cc4e34ae40a51d013d1cb946e93049 100644 --- a/src/GRANULAR/pair_gran_hooke.cpp +++ b/src/GRANULAR/pair_gran_hooke.cpp @@ -15,10 +15,8 @@ Contributing authors: Leo Silbert (SNL), Gary Grest (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_gran_hooke.h" +#include #include "atom.h" #include "force.h" #include "fix.h" diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index 5a78b9d79a0e48d55a48642c6fa1f17d1d7c3037..771a5566df40d3bf362aad8f1cd255e17db101da 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -15,14 +15,11 @@ Contributing authors: Leo Silbert (SNL), Gary Grest (SNL) ------------------------------------------------------------------------- */ +#include "pair_gran_hooke_history.h" +#include #include -#include -#include #include -#include "pair_gran_hooke_history.h" #include "atom.h" -#include "atom_vec.h" -#include "domain.h" #include "force.h" #include "update.h" #include "modify.h" diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index 77b198178622d77ba381ebb7d7ebf07a85251771..b87e64a456c6aa703e94da9c09c37905cb72a6f5 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -16,14 +16,11 @@ See the README file in the top-level LAMMPS directory. Leo Silbert (SNL), Gary Grest (SNL) ----------------------------------------------------------------------- */ +#include "pair_granular.h" +#include #include -#include -#include #include -#include "pair_granular.h" #include "atom.h" -#include "atom_vec.h" -#include "domain.h" #include "force.h" #include "update.h" #include "modify.h" diff --git a/src/KIM/README b/src/KIM/README index a69206596f01e752146d2f26bc25c447572fbf71..e61f47426fe5c81b63b4d05fbce908c7dd6f91f0 100644 --- a/src/KIM/README +++ b/src/KIM/README @@ -1,29 +1,30 @@ -This package provides a pair_style kim command which is a wrapper on -the Knowledge Base for Interatomic Models (KIM) repository of -interatomic potentials, so that they can be used by LAMMPS scripts. +This package provides the kim_init, kim_query, kim_interactions, and +the pair_style kim command which are wrappers on the Knowledgebase of +Interatomic Models (KIM) repository of interatomic potentials, so that +they can be used by LAMMPS scripts. Information about the KIM project can be found at https://openkim.org. -The KIM project is lead by Ellad Tadmor and Ryan Elliott (U Minn) and -James Sethna (Cornell U). Ryan Elliott is the main developer for the -KIM API and he also maintains the code that implements the pair_style -kim command. +The KIM project is lead by Ellad B. Tadmor and Ryan S. Elliott (UMN). +Ryan Elliott is the main developer for the KIM API and he also +maintains the code that implements these commands. -Using this package requires the KIM library and its models +Using this package requires the KIM-API library and its models (interatomic potentials) to be downloaded and installed on your system. The library can be downloaded and built in lib/kim or elsewhere on your system, which must be done before bulding LAMMPS with this package. Details of the download, build, and install -process for KIM are given in the lib/kim/README file, and scripts will -soon be provided to help automate the process. Also see the LAMMPS -manual for general information on building LAMMPS with external +process for the KIM-API are given in the lib/kim/README file, and +scripts are provided to help automate the process. Also see the +LAMMPS manual for general information on building LAMMPS with external libraries. The settings in the Makefile.lammps file in lib/kim must be correct for LAMMPS to build correctly with this package installed. However, the default settings should be correct in most cases and the Makefile.lammps file usually will not need to be changed. Once you have successfully built LAMMPS with this package and the KIM -library you can test it using an input file from the examples dir: +library you can test it using an input files in the examples dir: -./lmp_serial < lammps/examples/kim/in.kim.lj +./lmp_serial -in lammps/examples/kim/in.kim.lj -This pair_style was written by Ryan S. Elliott (U Minn). +These commands were written by Ryan S. Elliott (UMN), Ellad B. Tadmor +(UMN) and Axel Kohlmeyer (Temple U). diff --git a/src/KIM/fix_store_kim.cpp b/src/KIM/fix_store_kim.cpp new file mode 100644 index 0000000000000000000000000000000000000000..16d606d2ed06ddfa8dc1b9c79f068b14519d7b2b --- /dev/null +++ b/src/KIM/fix_store_kim.cpp @@ -0,0 +1,155 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Axel Kohlmeyer (Temple U), + Ryan S. Elliott (UMN) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This program is free software; you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by the Free + Software Foundation; either version 2 of the License, or (at your option) + any later version. + + This program is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for + more details. + + You should have received a copy of the GNU General Public License along with + this program; if not, see . + + Linking LAMMPS statically or dynamically with other modules is making a + combined work based on LAMMPS. Thus, the terms and conditions of the GNU + General Public License cover the whole combination. + + In addition, as a special exception, the copyright holders of LAMMPS give + you permission to combine LAMMPS with free software programs or libraries + that are released under the GNU LGPL and with code included in the standard + release of the "kim-api" under the CDDL (or modified versions of such code, + with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for LAMMPS and the licenses of the other code + concerned, provided that you include the source code of that other code + when and as the GNU GPL requires distribution of source code. + + Note that people who make modified versions of LAMMPS are not obligated to + grant this special exception for their modified versions; it is their choice + whether to do so. The GNU General Public License gives permission to release + a modified version without this exception; this exception also makes it + possible to release a modified version which carries forward this exception. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Designed for use with the kim-api-2.0.2 (and newer) package +------------------------------------------------------------------------- */ + +#include "fix_store_kim.h" +#include +extern "C" { +#include "KIM_SimulatorModel.h" +} +#include "error.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +/* ---------------------------------------------------------------------- */ + +FixStoreKIM::FixStoreKIM(LAMMPS *lmp, int narg, char **arg) + : Fix(lmp, narg, arg), simulator_model(NULL), model_name(NULL), + model_units(NULL), user_units(NULL) +{ + if (narg != 3) error->all(FLERR,"Illegal fix STORE/KIM command"); +} + +/* ---------------------------------------------------------------------- */ + +FixStoreKIM::~FixStoreKIM() +{ + // free associated storage + + if (simulator_model) { + KIM_SimulatorModel *sm = (KIM_SimulatorModel *)simulator_model; + KIM_SimulatorModel_Destroy(&sm); + simulator_model = NULL; + } + + if (model_name) { + char *mn = (char *)model_name; + delete[] mn; + model_name = NULL; + } + + if (model_units) { + char *mu = (char *)model_units; + delete[] mu; + model_units = NULL; + } + if (user_units) { + char *uu = (char *)user_units; + delete[] uu; + user_units = NULL; + } +} + +/* ---------------------------------------------------------------------- */ + +int FixStoreKIM::setmask() +{ + int mask = 0; + return mask; +} + + +/* ---------------------------------------------------------------------- */ + +void FixStoreKIM::setptr(const char *name, void *ptr) +{ + if (strcmp(name,"simulator_model") == 0) { + if (simulator_model) { + KIM_SimulatorModel *sm = (KIM_SimulatorModel *)simulator_model; + KIM_SimulatorModel_Destroy(&sm); + } + simulator_model = ptr; + } else if (strcmp(name,"model_name") == 0) { + if (model_name) { + char *mn = (char *)model_name; + delete[] mn; + } + model_name = ptr; + } else if (strcmp(name,"model_units") == 0) { + if (model_units) { + char *mu = (char *)model_units; + delete[] mu; + } + model_units = ptr; + } else if (strcmp(name,"user_units") == 0) { + if (user_units) { + char *uu = (char *)user_units; + delete[] uu; + } + user_units = ptr; + } else error->all(FLERR,"Unknown property in fix STORE/KIM"); +} + +/* ---------------------------------------------------------------------- */ + +void *FixStoreKIM::getptr(const char *name) +{ + if (strcmp(name,"simulator_model") == 0) return simulator_model; + else if (strcmp(name,"model_name") == 0) return model_name; + else if (strcmp(name,"model_units") == 0) return model_units; + else if (strcmp(name,"user_units") == 0) return user_units; + else return NULL; +} diff --git a/src/KIM/fix_store_kim.h b/src/KIM/fix_store_kim.h new file mode 100644 index 0000000000000000000000000000000000000000..6baf480993cabfaba8afa69431a601627a9d523f --- /dev/null +++ b/src/KIM/fix_store_kim.h @@ -0,0 +1,99 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Axel Kohlmeyer (Temple U), + Ryan S. Elliott (UMN) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This program is free software; you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by the Free + Software Foundation; either version 2 of the License, or (at your option) + any later version. + + This program is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for + more details. + + You should have received a copy of the GNU General Public License along with + this program; if not, see . + + Linking LAMMPS statically or dynamically with other modules is making a + combined work based on LAMMPS. Thus, the terms and conditions of the GNU + General Public License cover the whole combination. + + In addition, as a special exception, the copyright holders of LAMMPS give + you permission to combine LAMMPS with free software programs or libraries + that are released under the GNU LGPL and with code included in the standard + release of the "kim-api" under the CDDL (or modified versions of such code, + with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for LAMMPS and the licenses of the other code + concerned, provided that you include the source code of that other code + when and as the GNU GPL requires distribution of source code. + + Note that people who make modified versions of LAMMPS are not obligated to + grant this special exception for their modified versions; it is their choice + whether to do so. The GNU General Public License gives permission to release + a modified version without this exception; this exception also makes it + possible to release a modified version which carries forward this exception. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Designed for use with the kim-api-2.0.2 (and newer) package +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(STORE/KIM,FixStoreKIM) + +#else + +#ifndef LMP_FIX_STORE_KIM_H +#define LMP_FIX_STORE_KIM_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixStoreKIM : public Fix { + public: + FixStoreKIM(class LAMMPS *, int, char **); + ~FixStoreKIM(); + int setmask(); + + void setptr(const char *, void *); + void *getptr(const char *); + + private: + void *simulator_model; // pointer to KIM simulator model class + void *model_name; // string of KIM model name + void *model_units; // string of unit conversion origin or NULL + void *user_units; // string of unit conversion target or NULL +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +*/ diff --git a/src/KIM/kim_init.cpp b/src/KIM/kim_init.cpp new file mode 100644 index 0000000000000000000000000000000000000000..a4272caa012592526b902b110f76185cb7d867a7 --- /dev/null +++ b/src/KIM/kim_init.cpp @@ -0,0 +1,508 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Axel Kohlmeyer (Temple U), + Ryan S. Elliott (UMN) + Ellad B. Tadmor (UMN) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This program is free software; you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by the Free + Software Foundation; either version 2 of the License, or (at your option) + any later version. + + This program is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for + more details. + + You should have received a copy of the GNU General Public License along with + this program; if not, see . + + Linking LAMMPS statically or dynamically with other modules is making a + combined work based on LAMMPS. Thus, the terms and conditions of the GNU + General Public License cover the whole combination. + + In addition, as a special exception, the copyright holders of LAMMPS give + you permission to combine LAMMPS with free software programs or libraries + that are released under the GNU LGPL and with code included in the standard + release of the "kim-api" under the CDDL (or modified versions of such code, + with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for LAMMPS and the licenses of the other code + concerned, provided that you include the source code of that other code + when and as the GNU GPL requires distribution of source code. + + Note that people who make modified versions of LAMMPS are not obligated to + grant this special exception for their modified versions; it is their choice + whether to do so. The GNU General Public License gives permission to release + a modified version without this exception; this exception also makes it + possible to release a modified version which carries forward this exception. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Designed for use with the kim-api-2.1.0 (and newer) package +------------------------------------------------------------------------- */ + +#include "kim_init.h" +#include +#include +#include +#include +#include "error.h" +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "modify.h" +#include "update.h" +#include "universe.h" +#include "input.h" +#include "variable.h" +#include "citeme.h" +#include "fix_store_kim.h" +#include "kim_units.h" + +extern "C" { +#include "KIM_SimulatorHeaders.h" +} + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +void KimInit::command(int narg, char **arg) +{ + if ((narg < 2) || (narg > 3)) error->all(FLERR,"Illegal kim_init command"); + + if (domain->box_exist) + error->all(FLERR,"Must use 'kim_init' command before " + "simulation box is defined"); + char *model_name = new char[strlen(arg[0])+1]; + strcpy(model_name,arg[0]); + char *user_units = new char[strlen(arg[1])+1]; + strcpy(user_units,arg[1]); + if (narg == 3) { + if (strcmp(arg[2],"unit_conversion_mode")==0) unit_conversion_mode = true; + else { error->all(FLERR,"Illegal kim_init command"); } + } else unit_conversion_mode = false; + + char *model_units; + determine_model_type_and_units(model_name, user_units, &model_units); + + write_log_cite(model_name); + + do_init(model_name, user_units, model_units); +} + + +/* ---------------------------------------------------------------------- */ +namespace { +void get_kim_unit_names( + char const * const system, + KIM_LengthUnit & lengthUnit, + KIM_EnergyUnit & energyUnit, + KIM_ChargeUnit & chargeUnit, + KIM_TemperatureUnit & temperatureUnit, + KIM_TimeUnit & timeUnit, + Error * error) +{ + if ((strcmp(system,"real")==0)) { + lengthUnit = KIM_LENGTH_UNIT_A; + energyUnit = KIM_ENERGY_UNIT_kcal_mol; + chargeUnit = KIM_CHARGE_UNIT_e; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_fs; + } else if ((strcmp(system,"metal")==0)) { + lengthUnit = KIM_LENGTH_UNIT_A; + energyUnit = KIM_ENERGY_UNIT_eV; + chargeUnit = KIM_CHARGE_UNIT_e; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_ps; + } else if ((strcmp(system,"si")==0)) { + lengthUnit = KIM_LENGTH_UNIT_m; + energyUnit = KIM_ENERGY_UNIT_J; + chargeUnit = KIM_CHARGE_UNIT_C; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_s; + } else if ((strcmp(system,"cgs")==0)) { + lengthUnit = KIM_LENGTH_UNIT_cm; + energyUnit = KIM_ENERGY_UNIT_erg; + chargeUnit = KIM_CHARGE_UNIT_statC; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_s; + } else if ((strcmp(system,"electron")==0)) { + lengthUnit = KIM_LENGTH_UNIT_Bohr; + energyUnit = KIM_ENERGY_UNIT_Hartree; + chargeUnit = KIM_CHARGE_UNIT_e; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_fs; + } else if ((strcmp(system,"lj")==0)) { + error->all(FLERR,"LAMMPS unit_style lj not supported by KIM models"); + } else { + error->all(FLERR,"Unknown unit_style"); + } +} +} // namespace +void KimInit::determine_model_type_and_units(char * model_name, + char * user_units, + char ** model_units) +{ + KIM_LengthUnit lengthUnit; + KIM_EnergyUnit energyUnit; + KIM_ChargeUnit chargeUnit; + KIM_TemperatureUnit temperatureUnit; + KIM_TimeUnit timeUnit; + int units_accepted; + KIM_Collections * kim_Coll; + KIM_CollectionItemType itemType; + + int kim_error = KIM_Collections_Create(&kim_Coll); + if (kim_error) { + error->all(FLERR,"Unable to access KIM Collections to find Model."); + } + + kim_error = KIM_Collections_GetItemType(kim_Coll, model_name, &itemType); + if (kim_error) { + error->all(FLERR,"KIM Model name not found."); + } + KIM_Collections_Destroy(&kim_Coll); + + if (KIM_CollectionItemType_Equal(itemType, + KIM_COLLECTION_ITEM_TYPE_portableModel)) + { + get_kim_unit_names(user_units, lengthUnit, energyUnit, + chargeUnit, temperatureUnit, timeUnit, error); + KIM_Model * kim_MO; + int kim_error = KIM_Model_Create(KIM_NUMBERING_zeroBased, + lengthUnit, + energyUnit, + chargeUnit, + temperatureUnit, + timeUnit, + model_name, + &units_accepted, + &kim_MO); + + if (kim_error) + error->all(FLERR,"Unable to load KIM Simulator Model."); + + model_type = MO; + KIM_Model_Destroy(&kim_MO); + + if (units_accepted) { + *model_units = new char[strlen(user_units)+1]; + strcpy(*model_units,user_units); + return; + } else if (unit_conversion_mode) { + int const num_systems = 5; + char const * const systems[num_systems] + = {"metal", "real", "si", "cgs", "electron"}; + for (int i=0; i < num_systems; ++i) { + get_kim_unit_names(systems[i], lengthUnit, energyUnit, + chargeUnit, temperatureUnit, timeUnit, error); + kim_error = KIM_Model_Create(KIM_NUMBERING_zeroBased, + lengthUnit, + energyUnit, + chargeUnit, + temperatureUnit, + timeUnit, + model_name, + &units_accepted, + &kim_MO); + KIM_Model_Destroy(&kim_MO); + if (units_accepted) { + *model_units = new char[strlen(systems[i])+1]; + strcpy(*model_units,systems[i]); + return; + } + } error->all(FLERR,"KIM Model does not support any lammps unit system"); + } else { + error->all(FLERR,"KIM Model does not support the requested unit system"); + } + } + else if (KIM_CollectionItemType_Equal( + itemType, KIM_COLLECTION_ITEM_TYPE_simulatorModel)) { + KIM_SimulatorModel * kim_SM; + kim_error = KIM_SimulatorModel_Create(model_name, &kim_SM); + if (kim_error) + error->all(FLERR,"Unable to load KIM Simulator Model."); + model_type = SM; + + int sim_fields; + int sim_lines; + char const * sim_field; + char const * sim_value; + KIM_SimulatorModel_GetNumberOfSimulatorFields(kim_SM, &sim_fields); + KIM_SimulatorModel_CloseTemplateMap(kim_SM); + for (int i=0; i < sim_fields; ++i) { + KIM_SimulatorModel_GetSimulatorFieldMetadata( + kim_SM,i,&sim_lines,&sim_field); + + if (0 == strcmp(sim_field,"units")) { + KIM_SimulatorModel_GetSimulatorFieldLine(kim_SM,i,0,&sim_value); + int len=strlen(sim_value)+1; + *model_units = new char[len]; strcpy(*model_units,sim_value); + break; + } + } + KIM_SimulatorModel_Destroy(&kim_SM); + + if ((! unit_conversion_mode) && (strcmp(*model_units, user_units)!=0)) { + std::string mesg("Incompatible units for KIM Simulator Model, " + "required units = "); + mesg += *model_units; + error->all(FLERR,mesg.c_str()); + } + } +} + + +/* ---------------------------------------------------------------------- */ + +void KimInit::do_init(char *model_name, char *user_units, char *model_units) +{ + // create storage proxy fix. delete existing fix, if needed. + + int ifix = modify->find_fix("KIM_MODEL_STORE"); + if (ifix >= 0) modify->delete_fix(ifix); + char *fixarg[3]; + fixarg[0] = (char *)"KIM_MODEL_STORE"; + fixarg[1] = (char *)"all"; + fixarg[2] = (char *)"STORE/KIM"; + modify->add_fix(3,fixarg); + ifix = modify->find_fix("KIM_MODEL_STORE"); + + FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix]; + fix_store->setptr("model_name", (void *) model_name); + fix_store->setptr("user_units", (void *) user_units); + fix_store->setptr("model_units", (void *) model_units); + + // Begin output to log file + kim_init_log_delimiter("begin"); + + int kimerror; + KIM_SimulatorModel * simulatorModel; + if (model_type == SM) + { + kimerror = KIM_SimulatorModel_Create(model_name,&simulatorModel); + + char const *sim_name, *sim_version; + KIM_SimulatorModel_GetSimulatorNameAndVersion( + simulatorModel,&sim_name, &sim_version); + + if (0 != strcmp(sim_name,"LAMMPS")) + error->all(FLERR,"Incompatible KIM Simulator Model"); + + if (comm->me == 0) { + std::string mesg("# Using KIM Simulator Model : "); + mesg += model_name; + mesg += "\n"; + mesg += "# For Simulator : "; + mesg += std::string(sim_name) + " " + sim_version + "\n"; + mesg += "# Running on : LAMMPS "; + mesg += universe->version; + mesg += "\n"; + mesg += "#\n"; + + if (screen) fputs(mesg.c_str(),screen); + if (logfile) fputs(mesg.c_str(),logfile); + } + + fix_store->setptr("simulator_model", (void *) simulatorModel); + + // need to call this to have access to (some) simulator model init data. + + KIM_SimulatorModel_CloseTemplateMap(simulatorModel); + } + + // Define unit conversion factor variables and print to log + if (unit_conversion_mode) do_variables(user_units, model_units); + + // set units + + std::string cmd("units "); + cmd += model_units; + input->one(cmd.c_str()); + + if (model_type == SM) { + int sim_fields, sim_lines; + char const *sim_field, *sim_value; + KIM_SimulatorModel_GetNumberOfSimulatorFields(simulatorModel, &sim_fields); + + // init model + + for (int i=0; i < sim_fields; ++i) { + KIM_SimulatorModel_GetSimulatorFieldMetadata( + simulatorModel,i,&sim_lines,&sim_field); + if (0 == strcmp(sim_field,"model-init")) { + for (int j=0; j < sim_lines; ++j) { + KIM_SimulatorModel_GetSimulatorFieldLine( + simulatorModel,i,j,&sim_value); + input->one(sim_value); + } + break; + } + } + + // reset template map. + KIM_SimulatorModel_OpenAndInitializeTemplateMap(simulatorModel); + } + + // End output to log file + kim_init_log_delimiter("end"); + +} + +/* ---------------------------------------------------------------------- */ + +void KimInit::kim_init_log_delimiter(std::string const begin_end) const +{ + if (comm->me == 0) { + std::string mesg; + if (begin_end == "begin") + mesg = + "#=== BEGIN kim-init ==========================================\n"; + else if (begin_end == "end") + mesg = + "#=== END kim-init ============================================\n\n"; + + input->write_echo(mesg.c_str()); + } +} + +/* ---------------------------------------------------------------------- */ + +void KimInit::do_variables(char *user_units, char *model_units) +{ + char *from = user_units, *to = model_units; + Variable *variable = input->variable; + + // refuse conversion from or to reduced units + + if ((strcmp(from,"lj") == 0) || (strcmp(to,"lj") == 0)) + error->all(FLERR,"Cannot set up conversion variables for 'lj' units"); + + // get index to internal style variables. create, if needed. + // set conversion factors for newly created variables. + double conversion_factor; + int ier; + char *args[3]; + std::string var_str; + args[1] = (char *)"internal"; + args[2] = (char *)"1.0"; + int v_unit; + int const nunits = 14; + char *units[nunits] = {(char *)"mass", + (char *)"distance", + (char *)"time", + (char *)"energy", + (char *)"velocity", + (char *)"force", + (char *)"torque", + (char *)"temperature", + (char *)"pressure", + (char *)"viscosity", + (char *)"charge", + (char *)"dipole", + (char *)"efield", + (char *)"density"}; + + if (comm->me == 0) { + std::string mesg("# Conversion factors from "); + mesg += from; + mesg += " to "; + mesg += to; + mesg += ":\n"; + input->write_echo(mesg.c_str()); + } + + for (int i = 0; i < nunits; i++) { + var_str = std::string("_u_") + std::string(units[i]); + args[0] = (char *)var_str.c_str(); + v_unit = variable->find(args[0]); + if (v_unit < 0) { + variable->set(3,args); + v_unit = variable->find(args[0]); + } + ier = lammps_unit_conversion(units[i], + from, + to, + conversion_factor); + if (ier != 0) { + std::string err = std::string("Unable to obtain conversion factor: ") + + "unit = " + units[i] + "; " + "from = " + from + "; " + "to = " + to + "."; + error->all(FLERR,err.c_str()); + } + variable->internal_set(v_unit,conversion_factor); + if (comm->me == 0) { + std::stringstream mesg; + mesg << "variable " << std::setw(15) << std::left << var_str + << " internal " + << std::setprecision(12) << std::scientific << conversion_factor + << std::endl; + input->write_echo(mesg.str().c_str()); + } + } + if (comm->me == 0) input->write_echo("#\n"); +} + +/* ---------------------------------------------------------------------- */ + +void KimInit::write_log_cite(char * model_name) +{ + KIM_Collections * coll; + int err = KIM_Collections_Create(&coll); + if (err) return; + + int extent; + if (model_type == MO) + { + err = KIM_Collections_CacheListOfItemMetadataFiles( + coll,KIM_COLLECTION_ITEM_TYPE_portableModel,model_name,&extent); + } + else if (model_type == SM) + { + err = KIM_Collections_CacheListOfItemMetadataFiles( + coll,KIM_COLLECTION_ITEM_TYPE_simulatorModel,model_name,&extent); + } + else + { + error->all(FLERR,"Unknown model type."); + } + + if (err) + { + KIM_Collections_Destroy(&coll); + return; + } + + for (int i = 0; i < extent;++i) + { + char const * fileName; + int availableAsString; + char const * fileString; + err = KIM_Collections_GetItemMetadataFile( + coll,i,&fileName,NULL,NULL,&availableAsString,&fileString); + if (err) continue; + + if (0 == strncmp("kimcite",fileName,7)) + { + if ((lmp->citeme) && (availableAsString)) lmp->citeme->add(fileString); + } + } + + KIM_Collections_Destroy(&coll); +} diff --git a/src/KIM/kim_init.h b/src/KIM/kim_init.h new file mode 100644 index 0000000000000000000000000000000000000000..2b5dc520c78d679fb5526ea1c125a7c960144de0 --- /dev/null +++ b/src/KIM/kim_init.h @@ -0,0 +1,131 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Axel Kohlmeyer (Temple U), + Ryan S. Elliott (UMN) + Ellad B. Tadmor (UMN) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This program is free software; you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by the Free + Software Foundation; either version 2 of the License, or (at your option) + any later version. + + This program is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for + more details. + + You should have received a copy of the GNU General Public License along with + this program; if not, see . + + Linking LAMMPS statically or dynamically with other modules is making a + combined work based on LAMMPS. Thus, the terms and conditions of the GNU + General Public License cover the whole combination. + + In addition, as a special exception, the copyright holders of LAMMPS give + you permission to combine LAMMPS with free software programs or libraries + that are released under the GNU LGPL and with code included in the standard + release of the "kim-api" under the CDDL (or modified versions of such code, + with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for LAMMPS and the licenses of the other code + concerned, provided that you include the source code of that other code + when and as the GNU GPL requires distribution of source code. + + Note that people who make modified versions of LAMMPS are not obligated to + grant this special exception for their modified versions; it is their choice + whether to do so. The GNU General Public License gives permission to release + a modified version without this exception; this exception also makes it + possible to release a modified version which carries forward this exception. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Designed for use with the kim-api-2.1.0 (and newer) package +------------------------------------------------------------------------- */ + +#ifdef COMMAND_CLASS + +CommandStyle(kim_init,KimInit) + +#else + +#ifndef LMP_KIM_INIT_H +#define LMP_KIM_INIT_H + +#include "pointers.h" +#include + +namespace LAMMPS_NS { + +class KimInit : protected Pointers { + public: + KimInit(class LAMMPS *lmp) : Pointers(lmp) {}; + void command(int, char **); + private: + enum model_type_enum {MO, SM}; + model_type_enum model_type; + bool unit_conversion_mode; + + void determine_model_type_and_units(char *, char *, char **); + void write_log_cite(char *); + void do_init(char *, char *, char *); + void do_variables(char*, char*); + void kim_init_log_delimiter(std::string const begin_end) const; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal kim_init command + +Incorrect number or kind of arguments to kim_init. + +E: Must use 'kim_init' command before simulation box is defined + +Self-explanatory. + +E: KIM Model does not support the requested unit system + +Self-explanatory. + +E: KIM Model does not support any lammps unit system + +Self-explanatory. + +E: KIM model name not found + +Self-explanatory. + +E: Incompatible KIM Simulator Model + +The requested KIM Simulator Model was defined for a different MD code +and thus is not compatible with LAMMPS. + +E: Incompatible units for KIM Simulator Model + +The selected unit style is not compatible with the requested KIM +Simulator Model. + +E: KIM Simulator Model has no Model definition + +There is no model definition (key: model-defn) in the KIM Simulator +Model. Please contact the OpenKIM database maintainers to verify +and potentially correct this. + +*/ diff --git a/src/KIM/kim_interactions.cpp b/src/KIM/kim_interactions.cpp new file mode 100644 index 0000000000000000000000000000000000000000..7dbe5230339d20e732879dc99829c2beda7f45ee --- /dev/null +++ b/src/KIM/kim_interactions.cpp @@ -0,0 +1,387 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Axel Kohlmeyer (Temple U), + Ryan S. Elliott (UMN) + Ellad B. Tadmor (UMN) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This program is free software; you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by the Free + Software Foundation; either version 2 of the License, or (at your option) + any later version. + + This program is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for + more details. + + You should have received a copy of the GNU General Public License along with + this program; if not, see . + + Linking LAMMPS statically or dynamically with other modules is making a + combined work based on LAMMPS. Thus, the terms and conditions of the GNU + General Public License cover the whole combination. + + In addition, as a special exception, the copyright holders of LAMMPS give + you permission to combine LAMMPS with free software programs or libraries + that are released under the GNU LGPL and with code included in the standard + release of the "kim-api" under the CDDL (or modified versions of such code, + with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for LAMMPS and the licenses of the other code + concerned, provided that you include the source code of that other code + when and as the GNU GPL requires distribution of source code. + + Note that people who make modified versions of LAMMPS are not obligated to + grant this special exception for their modified versions; it is their choice + whether to do so. The GNU General Public License gives permission to release + a modified version without this exception; this exception also makes it + possible to release a modified version which carries forward this exception. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Designed for use with the kim-api-2.1.0 (and newer) package +------------------------------------------------------------------------- */ + +#include "kim_interactions.h" +#include +#include +#include +#include "error.h" +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "modify.h" +#include "update.h" +#include "universe.h" +#include "input.h" +#include "variable.h" +#include "fix_store_kim.h" + +extern "C" { +#include "KIM_SimulatorHeaders.h" +} + +#define SNUM(x) \ + static_cast(std::ostringstream() \ + << std::dec << x).str() + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +void KimInteractions::command(int narg, char **arg) +{ + if (narg < 1) error->all(FLERR,"Illegal kim_interactions command"); + + if (!domain->box_exist) + error->all(FLERR,"Must use 'kim_interactions' command after " + "simulation box is defined"); + do_setup(narg,arg); +} + +/* ---------------------------------------------------------------------- */ + +void KimInteractions::kim_interactions_log_delimiter( + std::string const begin_end) const +{ + if (comm->me == 0) { + std::string mesg; + if (begin_end == "begin") + mesg = + "#=== BEGIN kim_interactions ==================================\n"; + else if (begin_end == "end") + mesg = + "#=== END kim_interactions ====================================\n\n"; + + input->write_echo(mesg.c_str()); + } +} + +/* ---------------------------------------------------------------------- */ + +void KimInteractions::do_setup(int narg, char **arg) +{ + bool fixed_types; + if ((narg == 1) && (0 == strcmp("fixed_types",arg[0]))) { + fixed_types = true; + } + else if (narg != atom->ntypes) { + error->all(FLERR,"Illegal kim_interactions command"); + } + else { + fixed_types = false; + } + + char *model_name = NULL; + KIM_SimulatorModel *simulatorModel(NULL); + + // check if we had a kim_init command by finding fix STORE/KIM + // retrieve model name and pointer to simulator model class instance. + // validate model name if not given as NULL. + + int ifix = modify->find_fix("KIM_MODEL_STORE"); + if (ifix >= 0) { + FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix]; + model_name = (char *)fix_store->getptr("model_name"); + simulatorModel = (KIM_SimulatorModel *)fix_store->getptr("simulator_model"); + } else error->all(FLERR,"Must use 'kim_init' before 'kim_interactions'"); + + // Begin output to log file + kim_interactions_log_delimiter("begin"); + + if (simulatorModel) { + + if (!fixed_types) { + std::string delimiter(""); + std::string atom_type_sym_list; + std::string atom_type_num_list; + + for (int i = 0; i < narg; i++) + { + atom_type_sym_list += delimiter + arg[i]; + atom_type_num_list += delimiter + SNUM(species_to_atomic_no(arg[i])); + delimiter = " "; + } + + KIM_SimulatorModel_AddTemplateMap( + simulatorModel,"atom-type-sym-list",atom_type_sym_list.c_str()); + KIM_SimulatorModel_AddTemplateMap( + simulatorModel,"atom-type-num-list",atom_type_num_list.c_str()); + KIM_SimulatorModel_CloseTemplateMap(simulatorModel); + + int len = strlen(atom_type_sym_list.c_str())+1; + char *strbuf = new char[len]; + char *strword; + + // validate species selection + + int sim_num_species; + bool species_is_supported; + char const *sim_species; + KIM_SimulatorModel_GetNumberOfSupportedSpecies( + simulatorModel,&sim_num_species); + strcpy(strbuf,atom_type_sym_list.c_str()); + strword = strtok(strbuf," \t"); + while (strword) { + species_is_supported = false; + if (strcmp(strword,"NULL") == 0) continue; + for (int i=0; i < sim_num_species; ++i) { + KIM_SimulatorModel_GetSupportedSpecies(simulatorModel,i,&sim_species); + if (strcmp(sim_species,strword) == 0) + species_is_supported = true; + } + if (!species_is_supported) { + std::string msg("Species '"); + msg += strword; + msg += "' is not supported by this KIM Simulator Model"; + error->all(FLERR,msg.c_str()); + } + strword = strtok(NULL," \t"); + } + delete[] strbuf; + } + else + { + KIM_SimulatorModel_CloseTemplateMap(simulatorModel); + } + + // check if units are unchanged + + int sim_fields, sim_lines; + const char *sim_field, *sim_value; + KIM_SimulatorModel_GetNumberOfSimulatorFields(simulatorModel, &sim_fields); + for (int i=0; i < sim_fields; ++i) { + KIM_SimulatorModel_GetSimulatorFieldMetadata( + simulatorModel,i,&sim_lines,&sim_field); + + if (0 == strcmp(sim_field,"units")) { + KIM_SimulatorModel_GetSimulatorFieldLine(simulatorModel,i,0,&sim_value); + if (0 != strcmp(sim_value,update->unit_style)) + error->all(FLERR,"Incompatible units for KIM Simulator Model"); + } + } + + int sim_model_idx=-1; + for (int i=0; i < sim_fields; ++i) { + KIM_SimulatorModel_GetSimulatorFieldMetadata( + simulatorModel,i,&sim_lines,&sim_field); + if (0 == strcmp(sim_field,"model-defn")) { + sim_model_idx = i; + for (int j=0; j < sim_lines; ++j) { + KIM_SimulatorModel_GetSimulatorFieldLine( + simulatorModel,sim_model_idx,j,&sim_value); + input->one(sim_value); + } + } + } + + if (sim_model_idx < 0) + error->all(FLERR,"KIM Simulator Model has no Model definition"); + + KIM_SimulatorModel_OpenAndInitializeTemplateMap(simulatorModel); + + } else { + + // not a simulator model. issue pair_style and pair_coeff commands. + + if (fixed_types) + error->all(FLERR,"fixed_types cannot be used with a KIM Portable Model"); + + // NOTE: all references to arg must appear before calls to input->one() + // as that will reset the argument vector. + + std::string cmd1("pair_style kim "); + cmd1 += model_name; + + std::string cmd2("pair_coeff * * "); + for (int i=0; i < narg; ++i) { + cmd2 += arg[i]; + cmd2 += " "; + } + + input->one(cmd1.c_str()); + input->one(cmd2.c_str()); + } + + // End output to log file + kim_interactions_log_delimiter("end"); + +} + +/* ---------------------------------------------------------------------- */ + +int KimInteractions::species_to_atomic_no(std::string const species) const +{ + if (species == "H") return 1; + else if (species == "He") return 2; + else if (species == "Li") return 3; + else if (species == "Be") return 4; + else if (species == "B") return 5; + else if (species == "C") return 6; + else if (species == "N") return 7; + else if (species == "O") return 8; + else if (species == "F") return 9; + else if (species == "Ne") return 10; + else if (species == "Na") return 11; + else if (species == "Mg") return 12; + else if (species == "Al") return 13; + else if (species == "Si") return 14; + else if (species == "P") return 15; + else if (species == "S") return 16; + else if (species == "Cl") return 17; + else if (species == "Ar") return 18; + else if (species == "K") return 19; + else if (species == "Ca") return 20; + else if (species == "Sc") return 21; + else if (species == "Ti") return 22; + else if (species == "V") return 23; + else if (species == "Cr") return 24; + else if (species == "Mn") return 25; + else if (species == "Fe") return 26; + else if (species == "Co") return 27; + else if (species == "Ni") return 28; + else if (species == "Cu") return 29; + else if (species == "Zn") return 30; + else if (species == "Ga") return 31; + else if (species == "Ge") return 32; + else if (species == "As") return 33; + else if (species == "Se") return 34; + else if (species == "Br") return 35; + else if (species == "Kr") return 36; + else if (species == "Rb") return 37; + else if (species == "Sr") return 38; + else if (species == "Y") return 39; + else if (species == "Zr") return 40; + else if (species == "Nb") return 41; + else if (species == "Mo") return 42; + else if (species == "Tc") return 43; + else if (species == "Ru") return 44; + else if (species == "Rh") return 45; + else if (species == "Pd") return 46; + else if (species == "Ag") return 47; + else if (species == "Cd") return 48; + else if (species == "In") return 49; + else if (species == "Sn") return 50; + else if (species == "Sb") return 51; + else if (species == "Te") return 52; + else if (species == "I") return 53; + else if (species == "Xe") return 54; + else if (species == "Cs") return 55; + else if (species == "Ba") return 56; + else if (species == "La") return 57; + else if (species == "Ce") return 58; + else if (species == "Pr") return 59; + else if (species == "Nd") return 60; + else if (species == "Pm") return 61; + else if (species == "Sm") return 62; + else if (species == "Eu") return 63; + else if (species == "Gd") return 64; + else if (species == "Tb") return 65; + else if (species == "Dy") return 66; + else if (species == "Ho") return 67; + else if (species == "Er") return 68; + else if (species == "Tm") return 69; + else if (species == "Yb") return 70; + else if (species == "Lu") return 71; + else if (species == "Hf") return 72; + else if (species == "Ta") return 73; + else if (species == "W") return 74; + else if (species == "Re") return 75; + else if (species == "Os") return 76; + else if (species == "Ir") return 77; + else if (species == "Pt") return 78; + else if (species == "Au") return 79; + else if (species == "Hg") return 80; + else if (species == "Tl") return 81; + else if (species == "Pb") return 82; + else if (species == "Bi") return 83; + else if (species == "Po") return 84; + else if (species == "At") return 85; + else if (species == "Rn") return 86; + else if (species == "Fr") return 87; + else if (species == "Ra") return 88; + else if (species == "Ac") return 89; + else if (species == "Th") return 90; + else if (species == "Pa") return 91; + else if (species == "U") return 92; + else if (species == "Np") return 93; + else if (species == "Pu") return 94; + else if (species == "Am") return 95; + else if (species == "Cm") return 96; + else if (species == "Bk") return 97; + else if (species == "Cf") return 98; + else if (species == "Es") return 99; + else if (species == "Fm") return 100; + else if (species == "Md") return 101; + else if (species == "No") return 102; + else if (species == "Lr") return 103; + else if (species == "Rf") return 104; + else if (species == "Db") return 105; + else if (species == "Sg") return 106; + else if (species == "Bh") return 107; + else if (species == "Hs") return 108; + else if (species == "Mt") return 109; + else if (species == "Ds") return 110; + else if (species == "Rg") return 111; + else if (species == "Cn") return 112; + else if (species == "Nh") return 113; + else if (species == "Fl") return 114; + else if (species == "Mc") return 115; + else if (species == "Lv") return 116; + else if (species == "Ts") return 117; + else if (species == "Og") return 118; + else return -1; +} diff --git a/src/KIM/kim_interactions.h b/src/KIM/kim_interactions.h new file mode 100644 index 0000000000000000000000000000000000000000..8172004d530bbcdab21c5a829d6b11f69b22e071 --- /dev/null +++ b/src/KIM/kim_interactions.h @@ -0,0 +1,117 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Axel Kohlmeyer (Temple U), + Ryan S. Elliott (UMN) + Ellad B. Tadmor (UMN) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This program is free software; you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by the Free + Software Foundation; either version 2 of the License, or (at your option) + any later version. + + This program is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for + more details. + + You should have received a copy of the GNU General Public License along with + this program; if not, see . + + Linking LAMMPS statically or dynamically with other modules is making a + combined work based on LAMMPS. Thus, the terms and conditions of the GNU + General Public License cover the whole combination. + + In addition, as a special exception, the copyright holders of LAMMPS give + you permission to combine LAMMPS with free software programs or libraries + that are released under the GNU LGPL and with code included in the standard + release of the "kim-api" under the CDDL (or modified versions of such code, + with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for LAMMPS and the licenses of the other code + concerned, provided that you include the source code of that other code + when and as the GNU GPL requires distribution of source code. + + Note that people who make modified versions of LAMMPS are not obligated to + grant this special exception for their modified versions; it is their choice + whether to do so. The GNU General Public License gives permission to release + a modified version without this exception; this exception also makes it + possible to release a modified version which carries forward this exception. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Designed for use with the kim-api-2.1.0 (and newer) package +------------------------------------------------------------------------- */ + +#ifdef COMMAND_CLASS + +CommandStyle(kim_interactions,KimInteractions) + +#else + +#ifndef LMP_KIM_INTERACTIONS_H +#define LMP_KIM_INTERACTIONS_H + +#include "pointers.h" +#include + +namespace LAMMPS_NS { + +class KimInteractions : protected Pointers { + public: + KimInteractions(class LAMMPS *lmp) : Pointers(lmp) {}; + void command(int, char **); + private: + void do_setup(int, char **); + int species_to_atomic_no(std::string const species) const; + void kim_interactions_log_delimiter(std::string const begin_end) const; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal kim_interactions command + +Incorrect number or kind of arguments to kim_interactions. + +E: Must use 'kim_interactions' command after simulation box is defined + +Self-explanatory. + +E: Must use 'kim_init' command before 'kim_interactions' + +Self-explanatory. + +E: Species XXX is not supported by this KIM Simulator Model + +The kim_interactions command was referencing a species that is not +present in the requested KIM Simulator Model. + +E: Incompatible units for KIM Simulator Model + +The selected unit style is not compatible with the requested KIM +Simulator Model. + +E: KIM Simulator Model has no Model definition + +There is no model definition (key: model-defn) in the KIM Simulator +Model. Please contact the OpenKIM database maintainers to verify +and potentially correct this. + +*/ diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index fedc9761104caa2587f3a6e13f07c4dece63e79e..cddc81c33374173e6a9ac2e536499154982c7f98 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- Contributing authors: Axel Kohlmeyer (Temple U), Ryan S. Elliott (UMN) @@ -52,17 +51,20 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Designed for use with the kim-api-2.0.2 (and newer) package + Designed for use with the kim-api-2.1.0 (and newer) package ------------------------------------------------------------------------- */ +#include "kim_query.h" #include #include #include -#include "kim_query.h" +#include #include "comm.h" #include "error.h" #include "input.h" +#include "modify.h" #include "variable.h" +#include "fix_store_kim.h" #if defined(LMP_KIM_CURL) #include @@ -78,7 +80,7 @@ struct WriteBuf { size_t sizeleft; }; -static char *do_query(char *, int, char **, int, MPI_Comm); +static char *do_query(char *, char *, int, char **, int, MPI_Comm); static size_t write_callback(void *, size_t, size_t, void *); #endif @@ -91,31 +93,79 @@ void KimQuery::command(int narg, char **arg) if (narg < 2) error->all(FLERR,"Illegal kim_query command"); + // check if we had a kim_init command by finding fix STORE/KIM + // retrieve model name. + char * model_name; + + int ifix = modify->find_fix("KIM_MODEL_STORE"); + if (ifix >= 0) { + FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix]; + model_name = (char *)fix_store->getptr("model_name"); + } else error->all(FLERR,"Must use 'kim_init' before 'kim_query'"); + + varname = arg[0]; + bool split = false; + if (0 == strcmp("split",arg[1])) { + if (narg == 2) error->all(FLERR,"Illegal kim_query command"); + split = true; + arg++; + narg--; + } function = arg[1]; + for (int i = 2; i < narg; ++i) + { + if (0 == strncmp("model=",arg[i], 6)) { + error->all(FLERR,"Illegal 'model' key in kim_query command"); + } + } + #if defined(LMP_KIM_CURL) - value = do_query(function, narg-2, arg+2, comm->me, world); + value = do_query(function, model_name, narg-2, arg+2, comm->me, world); // check for valid result // on error the content of "value" is a '\0' byte // as the first element, and then the error message // that was returned by the web server + char errmsg[1024]; if (0 == strlen(value)) { - char errmsg[512]; - sprintf(errmsg,"OpenKIM query failed: %s",value+1); - error->all(FLERR,errmsg); + error->all(FLERR,errmsg); + } else if (0 == strcmp(value,"EMPTY")) { + sprintf(errmsg,"OpenKIM query returned no results"); + error->all(FLERR,errmsg); } + kim_query_log_delimiter("begin"); char **varcmd = new char*[3]; - varcmd[0] = varname; - varcmd[1] = (char *) "string"; - varcmd[2] = value; + if (split) { + int counter = 1; + std::stringstream ss(value); + std::string token; + varcmd[1] = (char *) "string"; + + while(std::getline(ss, token, ',')) { + token.erase(0,token.find_first_not_of(" \n\r\t")); // ltrim + token.erase(token.find_last_not_of(" \n\r\t") + 1); // rtrim + std::stringstream splitname; + splitname << varname << "_" << counter++; + varcmd[0] = const_cast(splitname.str().c_str()); + varcmd[2] = const_cast(token.c_str()); + input->variable->set(3,varcmd); + echo_var_assign(splitname.str(), varcmd[2]); + } + } else { + varcmd[0] = varname; + varcmd[1] = (char *) "string"; + varcmd[2] = value; + input->variable->set(3,varcmd); - input->variable->set(3,varcmd); + echo_var_assign(varname, value); + } + kim_query_log_delimiter("end"); delete[] varcmd; delete[] value; @@ -148,7 +198,8 @@ size_t write_callback(void *data, size_t size, size_t nmemb, void *userp) return 0; // done } -char *do_query(char *qfunction, int narg, char **arg, int rank, MPI_Comm comm) +char *do_query(char *qfunction, char * model_name, int narg, char **arg, + int rank, MPI_Comm comm) { char value[512], *retval; @@ -174,6 +225,9 @@ char *do_query(char *qfunction, int narg, char **arg, int rank, MPI_Comm comm) url += qfunction; std::string query(arg[0]); + query += "&model=[\""; + query += model_name; + query += "\"]"; for (int i=1; i < narg; ++i) { query += '&'; query += arg[i]; @@ -217,9 +271,19 @@ char *do_query(char *qfunction, int narg, char **arg, int rank, MPI_Comm comm) if (value[0] == '[') { int len = strlen(value)-1; - retval = new char[len]; - value[len] = '\0'; - strcpy(retval,value+1); + if (value[len] == ']') { + retval = new char[len]; + value[len] = '\0'; + if (0 == strcmp(value+1, "")) { + strcpy(retval,"EMPTY"); + } + else + strcpy(retval,value+1); + } else { + retval = new char[len+2]; + retval[0] = '\0'; + strcpy(retval+1,value); + } } else if (value[0] == '\0') { int len = strlen(value+1)+2; retval = new char[len]; @@ -227,11 +291,41 @@ char *do_query(char *qfunction, int narg, char **arg, int rank, MPI_Comm comm) strcpy(retval+1,value+1); } else { // unknown response type. we should not get here. - // copy response without modifications. - int len = strlen(value)+1; + // we return an "empty" string but add error message after it + int len = strlen(value)+2; retval = new char[len]; - strcpy(retval,value); + retval[0] = '\0'; + strcpy(retval+1,value); } return retval; } #endif + +/* ---------------------------------------------------------------------- */ + +void KimQuery::kim_query_log_delimiter(std::string const begin_end) const +{ + if (comm->me == 0) { + std::string mesg; + if (begin_end == "begin") + mesg = + "#=== BEGIN kim-query =========================================\n"; + else if (begin_end == "end") + mesg = + "#=== END kim-query ===========================================\n\n"; + + input->write_echo(mesg.c_str()); + } +} + +/* ---------------------------------------------------------------------- */ + +void KimQuery::echo_var_assign(std::string const & name, + std::string const & value) const +{ + if (comm->me == 0) { + std::string mesg; + mesg += "variable " + name + " string " + value + "\n"; + input->write_echo(mesg.c_str()); + } +} diff --git a/src/KIM/kim_query.h b/src/KIM/kim_query.h index 3644e4519bb630a33389bca4487b1b7888d22482..33a37f5131189c6188e2b99bc01f330746aa311c 100644 --- a/src/KIM/kim_query.h +++ b/src/KIM/kim_query.h @@ -51,7 +51,7 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Designed for use with the kim-api-2.0.2 (and newer) package + Designed for use with the kim-api-2.1.0 (and newer) package ------------------------------------------------------------------------- */ #ifdef COMMAND_CLASS @@ -64,6 +64,7 @@ CommandStyle(kim_query,KimQuery) #define LMP_KIM_QUERY_H #include "pointers.h" +#include namespace LAMMPS_NS { @@ -71,7 +72,10 @@ class KimQuery : protected Pointers { public: KimQuery(class LAMMPS *lmp) : Pointers(lmp) {}; void command(int, char **); - + private: + void kim_query_log_delimiter(std::string const begin_end) const; + void echo_var_assign(std::string const & name, std::string const & value) + const; }; } diff --git a/src/KIM/kim_units.cpp b/src/KIM/kim_units.cpp new file mode 100644 index 0000000000000000000000000000000000000000..45f9b81a3513c0b235836219adc1429e813de20c --- /dev/null +++ b/src/KIM/kim_units.cpp @@ -0,0 +1,1411 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Ellad B. Tadmor (UMN) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This program is free software; you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by the Free + Software Foundation; either version 2 of the License, or (at your option) + any later version. + + This program is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for + more details. + + You should have received a copy of the GNU General Public License along with + this program; if not, see . + + Linking LAMMPS statically or dynamically with other modules is making a + combined work based on LAMMPS. Thus, the terms and conditions of the GNU + General Public License cover the whole combination. + + In addition, as a special exception, the copyright holders of LAMMPS give + you permission to combine LAMMPS with free software programs or libraries + that are released under the GNU LGPL and with code included in the standard + release of the "kim-api" under the CDDL (or modified versions of such code, + with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for LAMMPS and the licenses of the other code + concerned, provided that you include the source code of that other code + when and as the GNU GPL requires distribution of source code. + + Note that people who make modified versions of LAMMPS are not obligated to + grant this special exception for their modified versions; it is their choice + whether to do so. The GNU General Public License gives permission to release + a modified version without this exception; this exception also makes it + possible to release a modified version which carries forward this exception. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Designed for use with the kim-api-2.0.2 (and newer) package +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +using namespace std; + +namespace +{ + +// Constants of nature and basic conversion factors +// Source: https://physics.nist.gov/cuu/Constants/Table/allascii.txt +// Working with NIST values even when there are newer values for +// compatibility with LAMMPS + +/*---------------------- + Fundamental constants +------------------------ */ +double const boltz_si = 1.38064852e-23; // [J K^-1] Boltzmann's factor + // (NIST value) +double const Nav = 6.022140857e23; // [unitless] Avogadro's number + // (NIST value) +// double const Nav = 6.02214076e23; // [unitless] Avogadro's number + // (official value May 2019) +double const me_si = 9.10938356e-31; // [kg] electron rest mass + // (NIST value) +// double me_si = 9.10938291e-31; // [kg] electron rest mass +double const e_si = 1.6021766208e-19; // [C] elementary charge + // (charge of an electron/proton) + // (NIST value) + +/*---------------------- + Distance units +------------------------ */ +double const bohr_si = 5.2917721067e-11; // [m] Bohr unit (distance between + // nucleus and electron in H) + // (NIST value) +double const angstrom_si = 1e-10; // [m] Angstrom +double const centimeter_si = 1e-2; // [m] centimeter +double const micrometer_si = 1e-6; // [m] micrometer (micron) +double const nanometer_si = 1e-9; // [m] nanometer + +/*---------------------- + Mass units +------------------------ */ +double const gram_per_mole_si = 1e-3/Nav; // [kg] gram per mole +double const amu_si = 1e-3/Nav; // [kg] atomic mass unit (molecular + // weight) For example, the mean + // molecular weight of water + // is 18.015 atomic mass units + // (amu), so one mole of water + // weight 18.015 grams. +double const gram_si = 1e-3; // [kg] gram +double const picogram_si = 1e-15; // [kg] picogram +double const attogram_si = 1e-21; // [kg[ attogram + +/*---------------------- + Time units +------------------------ */ +double const atu_si = 2.418884326509e-17; // [s] atomic time unit + // ( = hbar/E_h where E_h is the + // Hartree energy) (NIST value) +double const atu_electron_si = atu_si*sqrt(amu_si/me_si); + // [s] atomic time unit + // used in electron system (see https://sourceforge.net/p/lammps/mailman/lammps-users/thread/BCA2BDB2-BA03-4280-896F-1E6120EF47B2%40caltech.edu/) +double const microsecond_si = 1e-6; // [s] microsecond +double const nanosecond_si = 1e-9; // [s] nanosecond +double const picosecond_si = 1e-12; // [s] picosecond +double const femtosecond_si = 1e-15; // [s] femtosecond + +/*---------------------- + Density units +------------------------ */ +double const gram_per_centimetercu_si = + gram_si/pow(centimeter_si,3); // [kg/m^3] gram/centimeter^3 +double const amu_per_bohrcu_si = amu_si/pow(bohr_si,3); // [kg/m^3] amu/bohr^3 +double const picogram_per_micrometercu_si = + picogram_si/pow(micrometer_si,3); // [kg/m^3] picogram/micrometer^3 +double const attogram_per_nanometercu_si = + attogram_si/pow(nanometer_si,3); // [kg/m^3] attogram/nanometer^3 + +/*---------------------- + Energy/torque units +------------------------ */ +double const kcal_si = 4184.0; // [J] kilocalorie (heat energy + // involved in warming up one + // kilogram of water by one + // degree Kelvin) +double const ev_si = 1.6021766208e-19; // [J] electon volt (amount of + // energy gained or lost by the + // charge of a single electron + // moving across an electric + // potential difference of one + // volt.) (NIST value) +double const hartree_si = 4.359744650e-18; // [J] Hartree (approximately the + // electric potential energy of + // the hydrogen atom in its + // ground state) (NIST value) +double const kcal_per_mole_si = kcal_si/Nav;// [J] kcal/mole +double const erg_si = 1e-7; // [J] erg +double const dyne_centimeter_si = 1e-7; // [J[ dyne*centimeter +double const picogram_micrometersq_per_microsecondsq_si = + picogram_si*pow(micrometer_si,2)/pow(microsecond_si,2); + // [J] picogram*micrometer^2/ + // microsecond^2 +double const attogram_nanometersq_per_nanosecondsq_si = + attogram_si*pow(nanometer_si,2)/pow(nanosecond_si,2); + // [J] attogram*nanometer^2/ + // nanosecond^2 + +/*---------------------- + Velocity units +------------------------ */ +double const angstrom_per_femtosecond_si = + angstrom_si/femtosecond_si; // [m/s] Angstrom/femtosecond +double const angstrom_per_picosecond_si = + angstrom_si/picosecond_si; // [m/s] Angstrom/picosecond +double const micrometer_per_microsecond_si = + micrometer_si/microsecond_si; // [m/s] micrometer/microsecond +double const nanometer_per_nanosecond_si = + nanometer_si/nanosecond_si; // [m/s] nanometer/nanosecond +double const centimeter_per_second_si = + centimeter_si; // [m/s] centimeter/second +double const bohr_per_atu_electron_si = + bohr_si/atu_electron_si; // [m/s] bohr/atu + +/*---------------------- + Force units +------------------------ */ +double const kcal_per_mole_angstrom_si = + kcal_per_mole_si/angstrom_si; // [N] kcal/(mole*Angstrom) +double const ev_per_angstrom_si = + ev_si/angstrom_si; // [N] eV/Angstrom +double const dyne_si = + dyne_centimeter_si/centimeter_si; // [N] dyne +double const hartree_per_bohr_si = + hartree_si/bohr_si; // [N] hartree/bohr +double const picogram_micrometer_per_microsecondsq_si = + picogram_si*micrometer_si/pow(microsecond_si,2); + // [N] picogram*micrometer/ + // microsecond^2 +double const attogram_nanometer_per_nanosecondsq_si = + attogram_si*nanometer_si/pow(nanosecond_si,2); + // [N] attogram*nanometer/ + // nanosecond^2 + +/*---------------------- + Pressure units +------------------------ */ +double const atmosphere_si = 101325.0; // [Pa] standard atmosphere (NIST value) +double const bar_si = 1e5; // [Pa] bar +double const dyne_per_centimetersq_si = + dyne_centimeter_si/pow(centimeter_si,3); + // [Pa] dyne/centimeter^2 +double const picogram_per_micrometer_microsecondsq_si = + picogram_si/(micrometer_si*pow(microsecond_si,2)); + // [Pa] picogram/(micrometer* + // microsecond^2) +double const attogram_per_nanometer_nanosecondsq_si = + attogram_si/(nanometer_si*pow(nanosecond_si,2)); + // [Pa] attogram/(nanometer*nanosecond^2) + +/*---------------------- + Viscosity units +------------------------ */ +double const poise_si = 0.1; // [Pa*s] Poise +double const amu_per_bohr_femtosecond_si = + amu_si/(bohr_si*femtosecond_si); // [Pa*s] amu/(bohr*femtosecond) +double const picogram_per_micrometer_microsecond_si = + picogram_si/(micrometer_si*microsecond_si); + // [Pa*s] picogram/(micrometer* + // microsecond) +double const attogram_per_nanometer_nanosecond_si = + attogram_si/(nanometer_si*nanosecond_si); + // [Pa*s] attogram/(nanometer* + // nanosecond) + +/*---------------------- + Charge units +------------------------ */ +double const echarge_si = e_si; // [C] electron charge unit +double const statcoulomb_si = e_si/4.8032044e-10; // [C] Statcoulomb or esu + // (value from LAMMPS units + // documentation) +double const picocoulomb_si = 1e-12; // [C] picocoulomb + +/*---------------------- + Dipole units +------------------------ */ +double const electron_angstrom_si = echarge_si*angstrom_si; + // [C*m] electron*angstrom +double const statcoulomb_centimeter_si = statcoulomb_si*centimeter_si; + // [C*m] statcoulomb*centimeter +double const debye_si = 1e-18*statcoulomb_centimeter_si; + // [C*m] Debye +double const picocoulomb_micrometer_si = picocoulomb_si*micrometer_si; + // [C*m] picocoulomb*micrometer +double const electron_nanometer_si = echarge_si*nanometer_si; + // [C*m] electron*nanometer + +/*---------------------- + Electric field units +------------------------ */ +double const volt_per_angstrom_si = 1.0/angstrom_si;// [V/m] volt/angstrom +double const statvolt_per_centimeter_si = + erg_si/(statcoulomb_si*centimeter_si); // [V/m] statvolt/centimeter +double const volt_per_centimeter_si = + 1.0/centimeter_si; // [V/m] volt/centimeter +double const volt_per_micrometer_si = + 1.0/micrometer_si; // [V/m] volt/micrometer +double const volt_per_nanometer_si = + 1.0/nanometer_si; // [V/m] volt/nanometer + +// Define enumerations +enum sys_type +{ + real = 1, + metal = 2, + si = 3, + cgs = 4, + electron = 5, + micro = 6, + nano = 7 +}; + +enum unit_type +{ + mass = 1, + distance = 2, + time = 3, + energy = 4, + velocity = 5, + force = 6, + torque = 7, + temperature = 8, + pressure = 9, + viscosity = 10, + charge = 11, + dipole = 12, + efield = 13, + density = 14 +}; + +enum units +{ + // mass + gram_per_mole = 101, + kilogram = 102, + gram = 103, + amu = 104, + picogram = 105, + attogram = 106, + // distance + angstrom = 201, + meter = 202, + centimeter = 203, + bohr = 204, + micrometer = 205, + nanometer = 206, + // time + femtosecond = 301, + picosecond = 302, + second = 303, + microsecond = 304, + nanosecond = 305, + // energy + kcal_per_mole = 401, + ev = 402, + joule = 403, + erg = 404, + hartree = 405, + picogram_micrometersq_per_microsecondsq = 406, + attogram_nanometersq_per_nanosecondsq = 407, + // velocity + angstrom_per_femtosecond = 501, + angstrom_per_picosecond = 502, + meter_per_second = 503, + centimeter_per_second = 504, + bohr_per_atu = 505, + micrometer_per_microsecond = 506, + nanometer_per_nanosecond = 507, + // force + kcal_per_mole_angstrom = 601, + ev_per_angstrom = 602, + newton = 603, + dyne = 604, + hartree_per_bohr = 605, + picogram_micrometer_per_microsecondsq = 606, + attogram_nanometer_per_nanosecondsq = 607, + // torque + newton_meter = 701, + dyne_centimeter = 702, + // temperature + kelvin = 801, + // pressure + atmosphere = 901, + bar = 902, + pascal = 903, + dyne_per_centimetersq = 904, + picogram_per_micrometer_microsecondsq = 905, + attogram_per_nanometer_nanosecondsq = 906, + // viscosity + poise = 1001, + pascal_second = 1002, + amu_per_bohr_femtosecond = 1003, // electron system, not in docs, GUESSED + picogram_per_micrometer_microsecond = 1004, + attogram_per_nanometer_nanosecond = 1005, + // charge + echarge = 1101, + coulomb = 1102, + statcoulomb = 1103, + picocoulomb = 1104, + // dipole + electron_angstrom = 1201, + coulomb_meter = 1202, + statcoulomb_centimeter = 1203, + debye = 1204, + picocoulomb_micrometer = 1205, + electron_nanometer = 1206, + // electric field + volt_per_angstrom = 1301, + volt_per_meter = 1302, + statvolt_per_centimeter = 1303, + volt_per_centimeter = 1304, + volt_per_micrometer = 1305, + volt_per_nanometer = 1306, + // density + gram_per_centimetercu = 1401, + kilogram_per_metercu = 1402, + amu_per_bohrcu = 1403, // electron system, not in docs, GUESSED + picogram_per_micrometercu = 1404, + attogram_per_nanometercu = 1405 +}; + +// Define dictionaries +map system_dic; +map unit_dic; +map units_real_dic; +map units_metal_dic; +map units_si_dic; +map units_cgs_dic; +map units_electron_dic; +map units_micro_dic; +map units_nano_dic; + +/* ---------------------------------------------------------------------- */ + +void initialize_dictionaries() +{ + system_dic["real"] = real; + system_dic["metal"] = metal; + system_dic["si"] = si; + system_dic["cgs"] = cgs; + system_dic["electron"] = electron; + system_dic["micro"] = micro; + system_dic["nano"] = nano; + + unit_dic["mass"] = mass; + unit_dic["distance"] = distance; + unit_dic["time"] = time; + unit_dic["energy"] = energy; + unit_dic["velocity"] = velocity; + unit_dic["force"] = force; + unit_dic["torque"] = torque; + unit_dic["temperature"]= temperature; + unit_dic["pressure"] = pressure; + unit_dic["viscosity"] = viscosity; + unit_dic["charge"] = charge; + unit_dic["dipole"] = dipole; + unit_dic["efield"] = efield; + unit_dic["density"] = density; + + units_real_dic[mass] = gram_per_mole; + units_real_dic[distance] = angstrom; + units_real_dic[time] = femtosecond; + units_real_dic[energy] = kcal_per_mole; + units_real_dic[velocity] = angstrom_per_femtosecond; + units_real_dic[force] = kcal_per_mole_angstrom; + units_real_dic[torque] = kcal_per_mole; + units_real_dic[temperature]= kelvin; + units_real_dic[pressure] = atmosphere; + units_real_dic[viscosity] = poise; + units_real_dic[charge] = echarge; + units_real_dic[dipole] = electron_angstrom; + units_real_dic[efield] = volt_per_angstrom; + units_real_dic[density] = gram_per_centimetercu; + + units_metal_dic[mass] = gram_per_mole; + units_metal_dic[distance] = angstrom; + units_metal_dic[time] = picosecond; + units_metal_dic[energy] = ev; + units_metal_dic[velocity] = angstrom_per_picosecond; + units_metal_dic[force] = ev_per_angstrom; + units_metal_dic[torque] = ev; + units_metal_dic[temperature]= kelvin; + units_metal_dic[pressure] = bar; + units_metal_dic[viscosity] = poise; + units_metal_dic[charge] = echarge; + units_metal_dic[dipole] = electron_angstrom; + units_metal_dic[efield] = volt_per_angstrom; + units_metal_dic[density] = gram_per_centimetercu; + + units_si_dic[mass] = kilogram; + units_si_dic[distance] = meter; + units_si_dic[time] = second; + units_si_dic[energy] = joule; + units_si_dic[velocity] = meter_per_second; + units_si_dic[force] = newton; + units_si_dic[torque] = newton_meter; + units_si_dic[temperature]= kelvin; + units_si_dic[pressure] = pascal; + units_si_dic[viscosity] = pascal_second; + units_si_dic[charge] = coulomb; + units_si_dic[dipole] = coulomb_meter; + units_si_dic[efield] = volt_per_meter; + units_si_dic[density] = kilogram_per_metercu; + + units_cgs_dic[mass] = gram; + units_cgs_dic[distance] = centimeter; + units_cgs_dic[time] = second; + units_cgs_dic[energy] = erg; + units_cgs_dic[velocity] = centimeter_per_second; + units_cgs_dic[force] = dyne; + units_cgs_dic[torque] = dyne_centimeter; + units_cgs_dic[temperature]= kelvin; + units_cgs_dic[pressure] = dyne_per_centimetersq; + units_cgs_dic[viscosity] = poise; + units_cgs_dic[charge] = statcoulomb; + units_cgs_dic[dipole] = statcoulomb_centimeter; + units_cgs_dic[efield] = statvolt_per_centimeter; + units_cgs_dic[density] = gram_per_centimetercu; + + units_electron_dic[mass] = amu; + units_electron_dic[distance] = bohr; + units_electron_dic[time] = femtosecond; + units_electron_dic[energy] = hartree; + units_electron_dic[velocity] = bohr_per_atu; + units_electron_dic[force] = hartree_per_bohr; + units_electron_dic[torque] = hartree; // unknown, GUESSED + units_electron_dic[temperature]= kelvin; + units_electron_dic[pressure] = pascal; + units_electron_dic[viscosity] = pascal_second; // unknown, GUESSED + units_electron_dic[charge] = echarge; + units_electron_dic[dipole] = debye; + units_electron_dic[efield] = volt_per_centimeter; + units_electron_dic[density] = amu_per_bohrcu; // unknown, GUESSED + + units_micro_dic[mass] = picogram; + units_micro_dic[distance] = micrometer; + units_micro_dic[time] = microsecond; + units_micro_dic[energy] = picogram_micrometersq_per_microsecondsq; + units_micro_dic[velocity] = micrometer_per_microsecond; + units_micro_dic[force] = picogram_micrometer_per_microsecondsq; + units_micro_dic[torque] = picogram_micrometersq_per_microsecondsq; + units_micro_dic[temperature]= kelvin; + units_micro_dic[pressure] = picogram_per_micrometer_microsecondsq; + units_micro_dic[viscosity] = picogram_per_micrometer_microsecond; + units_micro_dic[charge] = picocoulomb; + units_micro_dic[dipole] = picocoulomb_micrometer; + units_micro_dic[efield] = volt_per_micrometer; + units_micro_dic[density] = picogram_per_micrometercu; + + units_nano_dic[mass] = attogram; + units_nano_dic[distance] = nanometer; + units_nano_dic[time] = nanosecond; + units_nano_dic[energy] = attogram_nanometersq_per_nanosecondsq; + units_nano_dic[velocity] = nanometer_per_nanosecond; + units_nano_dic[force] = attogram_nanometer_per_nanosecondsq; + units_nano_dic[torque] = attogram_nanometersq_per_nanosecondsq; + units_nano_dic[temperature]= kelvin; + units_nano_dic[pressure] = attogram_per_nanometer_nanosecondsq; + units_nano_dic[viscosity] = attogram_per_nanometer_nanosecond; + units_nano_dic[charge] = echarge; + units_nano_dic[dipole] = electron_nanometer; + units_nano_dic[efield] = volt_per_nanometer; + units_nano_dic[density] = attogram_per_nanometercu; + +} + +/* ---------------------------------------------------------------------- */ + +// Get the enumeration for the unit of type `unit_type_enum` +// for LAMMPS system `system_enum`. +units get_lammps_system_unit(sys_type system_enum, unit_type unit_type_enum) +{ + switch(system_enum) { + case real : + return units_real_dic[unit_type_enum]; + case metal : + return units_metal_dic[unit_type_enum]; + case si : + return units_si_dic[unit_type_enum]; + case cgs : + return units_cgs_dic[unit_type_enum]; + case electron : + return units_electron_dic[unit_type_enum]; + case micro : + return units_micro_dic[unit_type_enum]; + case nano : + default : // This is here to a prevent a compiler warning + return units_nano_dic[unit_type_enum]; + } +} + +/* ---------------------------------------------------------------------- */ + +// Mass conversion +double get_mass_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[kilogram][kilogram] = 1.0; + conv[kilogram][gram_per_mole] = 1.0/gram_per_mole_si; + conv[kilogram][gram] = 1.0/gram_si; + conv[kilogram][amu] = 1.0/amu_si; + conv[kilogram][picogram] = 1.0/picogram_si; + conv[kilogram][attogram] = 1.0/attogram_si; + + to_si = 1.0/conv[kilogram][gram_per_mole]; + conv[gram_per_mole][kilogram] = to_si*conv[kilogram][kilogram]; + conv[gram_per_mole][gram_per_mole] = 1.0; + conv[gram_per_mole][gram] = to_si*conv[kilogram][gram]; + conv[gram_per_mole][amu] = to_si*conv[kilogram][amu]; + conv[gram_per_mole][picogram] = to_si*conv[kilogram][picogram]; + conv[gram_per_mole][attogram] = to_si*conv[kilogram][attogram]; + + to_si = 1.0/conv[kilogram][gram]; + conv[gram][kilogram] = to_si*conv[kilogram][kilogram]; + conv[gram][gram_per_mole] = to_si*conv[kilogram][gram_per_mole]; + conv[gram][gram] = 1.0; + conv[gram][amu] = to_si*conv[kilogram][amu]; + conv[gram][picogram] = to_si*conv[kilogram][picogram]; + conv[gram][attogram] = to_si*conv[kilogram][attogram]; + + to_si = 1.0/conv[kilogram][amu]; + conv[amu][kilogram] = to_si*conv[kilogram][kilogram]; + conv[amu][gram_per_mole] = to_si*conv[kilogram][gram_per_mole]; + conv[amu][gram] = to_si*conv[kilogram][gram]; + conv[amu][amu] = 1.0; + conv[amu][picogram] = to_si*conv[kilogram][picogram]; + conv[amu][attogram] = to_si*conv[kilogram][attogram]; + + to_si = 1.0/conv[kilogram][picogram]; + conv[picogram][kilogram] = to_si*conv[kilogram][kilogram]; + conv[picogram][gram_per_mole] = to_si*conv[kilogram][gram_per_mole]; + conv[picogram][gram] = to_si*conv[kilogram][gram]; + conv[picogram][amu] = to_si*conv[kilogram][amu]; + conv[picogram][picogram] = 1.0; + conv[picogram][attogram] = to_si*conv[kilogram][attogram]; + + to_si = 1.0/conv[kilogram][attogram]; + conv[attogram][kilogram] = to_si*conv[kilogram][kilogram]; + conv[attogram][gram_per_mole] = to_si*conv[kilogram][gram_per_mole]; + conv[attogram][gram] = to_si*conv[kilogram][gram]; + conv[attogram][amu] = to_si*conv[kilogram][amu]; + conv[attogram][picogram] = to_si*conv[kilogram][picogram]; + conv[attogram][attogram] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Distance conversion +double get_distance_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[meter][meter] = 1.0; + conv[meter][angstrom] = 1.0/angstrom_si; + conv[meter][centimeter] = 1.0/centimeter_si; + conv[meter][bohr] = 1.0/bohr_si; + conv[meter][micrometer] = 1.0/micrometer_si; + conv[meter][nanometer] = 1.0/nanometer_si; + + to_si = 1.0/conv[meter][angstrom]; + conv[angstrom][meter] = to_si*conv[meter][meter]; + conv[angstrom][angstrom] = 1.0; + conv[angstrom][centimeter] = to_si*conv[meter][centimeter]; + conv[angstrom][bohr] = to_si*conv[meter][bohr]; + conv[angstrom][micrometer] = to_si*conv[meter][micrometer]; + conv[angstrom][nanometer] = to_si*conv[meter][nanometer]; + + to_si = 1.0/conv[meter][centimeter]; + conv[centimeter][meter] = to_si*conv[meter][meter]; + conv[centimeter][angstrom] = to_si*conv[meter][angstrom]; + conv[centimeter][centimeter] = 1.0; + conv[centimeter][bohr] = to_si*conv[meter][bohr]; + conv[centimeter][micrometer] = to_si*conv[meter][micrometer]; + conv[centimeter][nanometer] = to_si*conv[meter][nanometer]; + + to_si = 1.0/conv[meter][bohr]; + conv[bohr][meter] = to_si*conv[meter][meter]; + conv[bohr][angstrom] = to_si*conv[meter][angstrom]; + conv[bohr][centimeter] = to_si*conv[meter][centimeter]; + conv[bohr][bohr] = 1.0; + conv[bohr][micrometer] = to_si*conv[meter][micrometer]; + conv[bohr][nanometer] = to_si*conv[meter][nanometer]; + + to_si = 1.0/conv[meter][micrometer]; + conv[micrometer][meter] = to_si*conv[meter][meter]; + conv[micrometer][angstrom] = to_si*conv[meter][angstrom]; + conv[micrometer][centimeter] = to_si*conv[meter][centimeter]; + conv[micrometer][bohr] = to_si*conv[meter][bohr]; + conv[micrometer][micrometer] = 1.0; + conv[micrometer][nanometer] = to_si*conv[meter][nanometer]; + + to_si = 1.0/conv[meter][nanometer]; + conv[nanometer][meter] = to_si*conv[meter][meter]; + conv[nanometer][angstrom] = to_si*conv[meter][angstrom]; + conv[nanometer][centimeter] = to_si*conv[meter][centimeter]; + conv[nanometer][bohr] = to_si*conv[meter][bohr]; + conv[nanometer][micrometer] = to_si*conv[meter][micrometer]; + conv[nanometer][nanometer] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Time conversion +double get_time_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[second][second] = 1.0; + conv[second][femtosecond] = 1.0/femtosecond_si; + conv[second][picosecond] = 1.0/picosecond_si; + conv[second][microsecond] = 1.0/microsecond_si; + conv[second][nanosecond] = 1.0/nanosecond_si; + + to_si = 1.0/conv[second][femtosecond]; + conv[femtosecond][second] = to_si*conv[second][second]; + conv[femtosecond][femtosecond] = 1.0; + conv[femtosecond][picosecond] = to_si*conv[second][picosecond]; + conv[femtosecond][microsecond] = to_si*conv[second][microsecond]; + conv[femtosecond][nanosecond] = to_si*conv[second][nanosecond]; + + to_si = 1.0/conv[second][picosecond]; + conv[picosecond][second] = to_si*conv[second][second]; + conv[picosecond][femtosecond] = to_si*conv[second][femtosecond]; + conv[picosecond][picosecond] = 1.0; + conv[picosecond][microsecond] = to_si*conv[second][microsecond]; + conv[picosecond][nanosecond] = to_si*conv[second][nanosecond]; + + to_si = 1.0/conv[second][microsecond]; + conv[microsecond][second] = to_si*conv[second][second]; + conv[microsecond][femtosecond] = to_si*conv[second][femtosecond]; + conv[microsecond][picosecond] = to_si*conv[second][picosecond]; + conv[microsecond][microsecond] = 1.0; + conv[microsecond][nanosecond] = to_si*conv[second][nanosecond]; + + to_si = 1.0/conv[second][nanosecond]; + conv[nanosecond][second] = to_si*conv[second][second]; + conv[nanosecond][femtosecond] = to_si*conv[second][femtosecond]; + conv[nanosecond][picosecond] = to_si*conv[second][picosecond]; + conv[nanosecond][microsecond] = to_si*conv[second][microsecond]; + conv[nanosecond][nanosecond] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Energy conversion +double get_energy_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + + map > conv; + double to_si; + + conv[joule][joule] = 1.0; + conv[joule][kcal_per_mole] = 1.0/kcal_per_mole_si; + conv[joule][ev] = 1.0/ev_si; + conv[joule][erg] = 1.0/erg_si; + conv[joule][hartree] = 1.0/hartree_si; + conv[joule][picogram_micrometersq_per_microsecondsq] = 1.0/picogram_micrometersq_per_microsecondsq_si; + conv[joule][attogram_nanometersq_per_nanosecondsq] = 1.0/attogram_nanometersq_per_nanosecondsq_si; + + to_si = 1.0/conv[joule][kcal_per_mole]; + conv[kcal_per_mole][joule] = to_si*conv[joule][joule]; + conv[kcal_per_mole][kcal_per_mole] = 1.0; + conv[kcal_per_mole][ev] = to_si*conv[joule][ev]; + conv[kcal_per_mole][erg] = to_si*conv[joule][erg]; + conv[kcal_per_mole][hartree] = to_si*conv[joule][hartree]; + conv[kcal_per_mole][picogram_micrometersq_per_microsecondsq] = to_si*conv[joule][picogram_micrometersq_per_microsecondsq]; + conv[kcal_per_mole][attogram_nanometersq_per_nanosecondsq] = to_si*conv[joule][attogram_nanometersq_per_nanosecondsq]; + + to_si = 1.0/conv[joule][ev]; + conv[ev][joule] = to_si*conv[joule][joule]; + conv[ev][kcal_per_mole] = to_si*conv[joule][kcal_per_mole]; + conv[ev][ev] = 1.0; + conv[ev][erg] = to_si*conv[joule][erg]; + conv[ev][hartree] = to_si*conv[joule][hartree]; + conv[ev][picogram_micrometersq_per_microsecondsq] = to_si*conv[joule][picogram_micrometersq_per_microsecondsq]; + conv[ev][attogram_nanometersq_per_nanosecondsq] = to_si*conv[joule][attogram_nanometersq_per_nanosecondsq]; + + to_si = 1.0/conv[joule][erg]; + conv[erg][joule] = to_si*conv[joule][joule]; + conv[erg][kcal_per_mole] = to_si*conv[joule][kcal_per_mole]; + conv[erg][ev] = to_si*conv[joule][ev]; + conv[erg][erg] = 1.0; + conv[erg][hartree] = to_si*conv[joule][hartree]; + conv[erg][picogram_micrometersq_per_microsecondsq] = to_si*conv[joule][picogram_micrometersq_per_microsecondsq]; + conv[erg][attogram_nanometersq_per_nanosecondsq] = to_si*conv[joule][attogram_nanometersq_per_nanosecondsq]; + + to_si = 1.0/conv[joule][hartree]; + conv[hartree][joule] = to_si*conv[joule][joule]; + conv[hartree][kcal_per_mole] = to_si*conv[joule][kcal_per_mole]; + conv[hartree][ev] = to_si*conv[joule][ev]; + conv[hartree][erg] = to_si*conv[joule][erg]; + conv[hartree][hartree] = 1.0; + conv[hartree][picogram_micrometersq_per_microsecondsq] = to_si*conv[joule][picogram_micrometersq_per_microsecondsq]; + conv[hartree][attogram_nanometersq_per_nanosecondsq] = to_si*conv[joule][attogram_nanometersq_per_nanosecondsq]; + + to_si = 1.0/conv[joule][picogram_micrometersq_per_microsecondsq]; + conv[picogram_micrometersq_per_microsecondsq][joule] = to_si*conv[joule][joule]; + conv[picogram_micrometersq_per_microsecondsq][kcal_per_mole] = to_si*conv[joule][kcal_per_mole]; + conv[picogram_micrometersq_per_microsecondsq][ev] = to_si*conv[joule][ev]; + conv[picogram_micrometersq_per_microsecondsq][erg] = to_si*conv[joule][erg]; + conv[picogram_micrometersq_per_microsecondsq][hartree] = to_si*conv[joule][hartree]; + conv[picogram_micrometersq_per_microsecondsq][picogram_micrometersq_per_microsecondsq] = 1.0; + conv[picogram_micrometersq_per_microsecondsq][attogram_nanometersq_per_nanosecondsq] = to_si*conv[joule][attogram_nanometersq_per_nanosecondsq]; + + to_si = 1.0/conv[joule][attogram_nanometersq_per_nanosecondsq]; + conv[attogram_nanometersq_per_nanosecondsq][joule] = to_si*conv[joule][joule]; + conv[attogram_nanometersq_per_nanosecondsq][kcal_per_mole] = to_si*conv[joule][kcal_per_mole]; + conv[attogram_nanometersq_per_nanosecondsq][ev] = to_si*conv[joule][ev]; + conv[attogram_nanometersq_per_nanosecondsq][erg] = to_si*conv[joule][erg]; + conv[attogram_nanometersq_per_nanosecondsq][hartree] = to_si*conv[joule][hartree]; + conv[attogram_nanometersq_per_nanosecondsq][picogram_micrometersq_per_microsecondsq] = to_si*conv[joule][picogram_micrometersq_per_microsecondsq]; + conv[attogram_nanometersq_per_nanosecondsq][attogram_nanometersq_per_nanosecondsq] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Velocity conversion +double get_velocity_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[meter_per_second][meter_per_second] = 1.0; + conv[meter_per_second][angstrom_per_femtosecond] = 1.0/angstrom_per_femtosecond_si; + conv[meter_per_second][angstrom_per_picosecond] = 1.0/angstrom_per_picosecond_si; + conv[meter_per_second][centimeter_per_second] = 1.0/centimeter_per_second_si; + conv[meter_per_second][bohr_per_atu] = 1.0/bohr_per_atu_electron_si; + conv[meter_per_second][micrometer_per_microsecond] = 1.0/micrometer_per_microsecond_si; + conv[meter_per_second][nanometer_per_nanosecond] = 1.0/nanometer_per_nanosecond_si; + + to_si = 1.0/conv[meter_per_second][angstrom_per_femtosecond]; + conv[angstrom_per_femtosecond][meter_per_second] = to_si*conv[meter_per_second][meter_per_second]; + conv[angstrom_per_femtosecond][angstrom_per_femtosecond] = 1.0; + conv[angstrom_per_femtosecond][angstrom_per_picosecond] = to_si*conv[meter_per_second][angstrom_per_picosecond]; + conv[angstrom_per_femtosecond][centimeter_per_second] = to_si*conv[meter_per_second][centimeter_per_second]; + conv[angstrom_per_femtosecond][bohr_per_atu] = to_si*conv[meter_per_second][bohr_per_atu]; + conv[angstrom_per_femtosecond][micrometer_per_microsecond] = to_si*conv[meter_per_second][micrometer_per_microsecond]; + conv[angstrom_per_femtosecond][nanometer_per_nanosecond] = to_si*conv[meter_per_second][nanometer_per_nanosecond]; + + to_si = 1.0/conv[meter_per_second][angstrom_per_picosecond]; + conv[angstrom_per_picosecond][meter_per_second] = to_si*conv[meter_per_second][meter_per_second]; + conv[angstrom_per_picosecond][angstrom_per_femtosecond] = to_si*conv[meter_per_second][angstrom_per_femtosecond]; + conv[angstrom_per_picosecond][angstrom_per_picosecond] = 1.0; + conv[angstrom_per_picosecond][centimeter_per_second] = to_si*conv[meter_per_second][centimeter_per_second]; + conv[angstrom_per_picosecond][bohr_per_atu] = to_si*conv[meter_per_second][bohr_per_atu]; + conv[angstrom_per_picosecond][micrometer_per_microsecond] = to_si*conv[meter_per_second][micrometer_per_microsecond]; + conv[angstrom_per_picosecond][nanometer_per_nanosecond] = to_si*conv[meter_per_second][nanometer_per_nanosecond]; + + to_si = 1.0/conv[meter_per_second][centimeter_per_second]; + conv[centimeter_per_second][meter_per_second] = to_si*conv[meter_per_second][meter_per_second]; + conv[centimeter_per_second][angstrom_per_femtosecond] = to_si*conv[meter_per_second][angstrom_per_femtosecond]; + conv[centimeter_per_second][angstrom_per_picosecond] = to_si*conv[meter_per_second][angstrom_per_picosecond]; + conv[centimeter_per_second][centimeter_per_second] = 1.0; + conv[centimeter_per_second][bohr_per_atu] = to_si*conv[meter_per_second][bohr_per_atu]; + conv[centimeter_per_second][micrometer_per_microsecond] = to_si*conv[meter_per_second][micrometer_per_microsecond]; + conv[centimeter_per_second][nanometer_per_nanosecond] = to_si*conv[meter_per_second][nanometer_per_nanosecond]; + + to_si = 1.0/conv[meter_per_second][bohr_per_atu]; + conv[bohr_per_atu][meter_per_second] = to_si*conv[meter_per_second][meter_per_second]; + conv[bohr_per_atu][angstrom_per_femtosecond] = to_si*conv[meter_per_second][angstrom_per_femtosecond]; + conv[bohr_per_atu][angstrom_per_picosecond] = to_si*conv[meter_per_second][angstrom_per_picosecond]; + conv[bohr_per_atu][centimeter_per_second] = to_si*conv[meter_per_second][centimeter_per_second]; + conv[bohr_per_atu][bohr_per_atu] = 1.0; + conv[bohr_per_atu][micrometer_per_microsecond] = to_si*conv[meter_per_second][micrometer_per_microsecond]; + conv[bohr_per_atu][nanometer_per_nanosecond] = to_si*conv[meter_per_second][nanometer_per_nanosecond]; + + to_si = 1.0/conv[meter_per_second][micrometer_per_microsecond]; + conv[micrometer_per_microsecond][meter_per_second] = to_si*conv[meter_per_second][meter_per_second]; + conv[micrometer_per_microsecond][angstrom_per_femtosecond] = to_si*conv[meter_per_second][angstrom_per_femtosecond]; + conv[micrometer_per_microsecond][angstrom_per_picosecond] = to_si*conv[meter_per_second][angstrom_per_picosecond]; + conv[micrometer_per_microsecond][centimeter_per_second] = to_si*conv[meter_per_second][centimeter_per_second]; + conv[micrometer_per_microsecond][bohr_per_atu] = to_si*conv[meter_per_second][bohr_per_atu]; + conv[micrometer_per_microsecond][micrometer_per_microsecond] = 1.0; + conv[micrometer_per_microsecond][nanometer_per_nanosecond] = to_si*conv[meter_per_second][nanometer_per_nanosecond]; + + to_si = 1.0/conv[meter_per_second][nanometer_per_nanosecond]; + conv[nanometer_per_nanosecond][meter_per_second] = to_si*conv[meter_per_second][meter_per_second]; + conv[nanometer_per_nanosecond][angstrom_per_femtosecond] = to_si*conv[meter_per_second][angstrom_per_femtosecond]; + conv[nanometer_per_nanosecond][angstrom_per_picosecond] = to_si*conv[meter_per_second][angstrom_per_picosecond]; + conv[nanometer_per_nanosecond][centimeter_per_second] = to_si*conv[meter_per_second][centimeter_per_second]; + conv[nanometer_per_nanosecond][bohr_per_atu] = to_si*conv[meter_per_second][bohr_per_atu]; + conv[nanometer_per_nanosecond][micrometer_per_microsecond] = to_si*conv[meter_per_second][micrometer_per_microsecond]; + conv[nanometer_per_nanosecond][nanometer_per_nanosecond] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Force conversion +double get_force_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[newton][newton] = 1.0; + conv[newton][kcal_per_mole_angstrom] = 1.0/kcal_per_mole_angstrom_si; + conv[newton][ev_per_angstrom] = 1.0/ev_per_angstrom_si; + conv[newton][dyne] = 1.0/dyne_si; + conv[newton][hartree_per_bohr] = 1.0/hartree_per_bohr_si; + conv[newton][picogram_micrometer_per_microsecondsq] = 1.0/picogram_micrometer_per_microsecondsq_si; + conv[newton][attogram_nanometer_per_nanosecondsq] = 1.0/attogram_nanometer_per_nanosecondsq_si; + + to_si = 1.0/conv[newton][kcal_per_mole_angstrom]; + conv[kcal_per_mole_angstrom][newton] = to_si*conv[newton][newton]; + conv[kcal_per_mole_angstrom][kcal_per_mole_angstrom] = 1.0; + conv[kcal_per_mole_angstrom][ev_per_angstrom] = to_si*conv[newton][ev_per_angstrom]; + conv[kcal_per_mole_angstrom][dyne] = to_si*conv[newton][dyne]; + conv[kcal_per_mole_angstrom][hartree_per_bohr] = to_si*conv[newton][hartree_per_bohr]; + conv[kcal_per_mole_angstrom][picogram_micrometer_per_microsecondsq] = to_si*conv[newton][picogram_micrometer_per_microsecondsq]; + conv[kcal_per_mole_angstrom][attogram_nanometer_per_nanosecondsq] = to_si*conv[newton][attogram_nanometer_per_nanosecondsq]; + + to_si = 1.0/conv[newton][ev_per_angstrom]; + conv[ev_per_angstrom][newton] = to_si*conv[newton][newton]; + conv[ev_per_angstrom][kcal_per_mole_angstrom] = to_si*conv[newton][kcal_per_mole_angstrom]; + conv[ev_per_angstrom][ev_per_angstrom] = 1.0; + conv[ev_per_angstrom][dyne] = to_si*conv[newton][dyne]; + conv[ev_per_angstrom][hartree_per_bohr] = to_si*conv[newton][hartree_per_bohr]; + conv[ev_per_angstrom][picogram_micrometer_per_microsecondsq] = to_si*conv[newton][picogram_micrometer_per_microsecondsq]; + conv[ev_per_angstrom][attogram_nanometer_per_nanosecondsq] = to_si*conv[newton][attogram_nanometer_per_nanosecondsq]; + + to_si = 1.0/conv[newton][dyne]; + conv[dyne][newton] = to_si*conv[newton][newton]; + conv[dyne][kcal_per_mole_angstrom] = to_si*conv[newton][kcal_per_mole_angstrom]; + conv[dyne][ev_per_angstrom] = to_si*conv[newton][ev_per_angstrom]; + conv[dyne][dyne] = 1.0; + conv[dyne][hartree_per_bohr] = to_si*conv[newton][hartree_per_bohr]; + conv[dyne][picogram_micrometer_per_microsecondsq] = to_si*conv[newton][picogram_micrometer_per_microsecondsq]; + conv[dyne][attogram_nanometer_per_nanosecondsq] = to_si*conv[newton][attogram_nanometer_per_nanosecondsq]; + + to_si = 1.0/conv[newton][hartree_per_bohr]; + conv[hartree_per_bohr][newton] = to_si*conv[newton][newton]; + conv[hartree_per_bohr][kcal_per_mole_angstrom] = to_si*conv[newton][kcal_per_mole_angstrom]; + conv[hartree_per_bohr][ev_per_angstrom] = to_si*conv[newton][ev_per_angstrom]; + conv[hartree_per_bohr][dyne] = to_si*conv[newton][dyne]; + conv[hartree_per_bohr][hartree_per_bohr] = 1.0; + conv[hartree_per_bohr][picogram_micrometer_per_microsecondsq] = to_si*conv[newton][picogram_micrometer_per_microsecondsq]; + conv[hartree_per_bohr][attogram_nanometer_per_nanosecondsq] = to_si*conv[newton][attogram_nanometer_per_nanosecondsq]; + + to_si = 1.0/conv[newton][picogram_micrometer_per_microsecondsq]; + conv[picogram_micrometer_per_microsecondsq][newton] = to_si*conv[newton][newton]; + conv[picogram_micrometer_per_microsecondsq][kcal_per_mole_angstrom] = to_si*conv[newton][kcal_per_mole_angstrom]; + conv[picogram_micrometer_per_microsecondsq][ev_per_angstrom] = to_si*conv[newton][ev_per_angstrom]; + conv[picogram_micrometer_per_microsecondsq][dyne] = to_si*conv[newton][dyne]; + conv[picogram_micrometer_per_microsecondsq][hartree_per_bohr] = to_si*conv[newton][hartree_per_bohr]; + conv[picogram_micrometer_per_microsecondsq][picogram_micrometer_per_microsecondsq] = 1.0; + conv[picogram_micrometer_per_microsecondsq][attogram_nanometer_per_nanosecondsq] = to_si*conv[newton][attogram_nanometer_per_nanosecondsq]; + + to_si = 1.0/conv[newton][attogram_nanometer_per_nanosecondsq]; + conv[attogram_nanometer_per_nanosecondsq][newton] = to_si*conv[newton][newton]; + conv[attogram_nanometer_per_nanosecondsq][kcal_per_mole_angstrom] = to_si*conv[newton][kcal_per_mole_angstrom]; + conv[attogram_nanometer_per_nanosecondsq][ev_per_angstrom] = to_si*conv[newton][ev_per_angstrom]; + conv[attogram_nanometer_per_nanosecondsq][dyne] = to_si*conv[newton][dyne]; + conv[attogram_nanometer_per_nanosecondsq][hartree_per_bohr] = to_si*conv[newton][hartree_per_bohr]; + conv[attogram_nanometer_per_nanosecondsq][picogram_micrometer_per_microsecondsq] = to_si*conv[newton][picogram_micrometer_per_microsecondsq]; + conv[attogram_nanometer_per_nanosecondsq][attogram_nanometer_per_nanosecondsq] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Torque conversion +double get_torque_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[newton_meter][newton_meter] = 1.0; + conv[newton_meter][kcal_per_mole] = 1.0/kcal_per_mole_si; + conv[newton_meter][ev] = 1.0/ev_si; + conv[newton_meter][dyne_centimeter] = 1.0/dyne_centimeter_si; + conv[newton_meter][hartree] = 1.0/hartree_si; + conv[newton_meter][picogram_micrometersq_per_microsecondsq] = 1.0/picogram_micrometersq_per_microsecondsq_si; + conv[newton_meter][attogram_nanometersq_per_nanosecondsq] = 1.0/attogram_nanometersq_per_nanosecondsq_si; + + to_si = 1.0/conv[newton_meter][kcal_per_mole]; + conv[kcal_per_mole][newton_meter] = to_si*conv[newton_meter][newton_meter]; + conv[kcal_per_mole][kcal_per_mole] = 1.0; + conv[kcal_per_mole][ev] = to_si*conv[newton_meter][ev]; + conv[kcal_per_mole][dyne_centimeter] = to_si*conv[newton_meter][dyne_centimeter]; + conv[kcal_per_mole][hartree] = to_si*conv[newton_meter][hartree]; + conv[kcal_per_mole][picogram_micrometersq_per_microsecondsq] = to_si*conv[newton_meter][picogram_micrometersq_per_microsecondsq]; + conv[kcal_per_mole][attogram_nanometersq_per_nanosecondsq] = to_si*conv[newton_meter][attogram_nanometersq_per_nanosecondsq]; + + to_si = 1.0/conv[newton_meter][ev]; + conv[ev][newton_meter] = to_si*conv[newton_meter][newton_meter]; + conv[ev][kcal_per_mole] = to_si*conv[newton_meter][kcal_per_mole]; + conv[ev][ev] = 1.0; + conv[ev][dyne_centimeter] = to_si*conv[newton_meter][dyne_centimeter]; + conv[ev][hartree] = to_si*conv[newton_meter][hartree]; + conv[ev][picogram_micrometersq_per_microsecondsq] = to_si*conv[newton_meter][picogram_micrometersq_per_microsecondsq]; + conv[ev][attogram_nanometersq_per_nanosecondsq] = to_si*conv[newton_meter][attogram_nanometersq_per_nanosecondsq]; + + to_si = 1.0/conv[newton_meter][dyne_centimeter]; + conv[dyne_centimeter][newton_meter] = to_si*conv[newton_meter][newton_meter]; + conv[dyne_centimeter][kcal_per_mole] = to_si*conv[newton_meter][kcal_per_mole]; + conv[dyne_centimeter][ev] = to_si*conv[newton_meter][ev]; + conv[dyne_centimeter][dyne_centimeter] = 1.0; + conv[dyne_centimeter][hartree] = to_si*conv[newton_meter][hartree]; + conv[dyne_centimeter][picogram_micrometersq_per_microsecondsq] = to_si*conv[newton_meter][picogram_micrometersq_per_microsecondsq]; + conv[dyne_centimeter][attogram_nanometersq_per_nanosecondsq] = to_si*conv[newton_meter][attogram_nanometersq_per_nanosecondsq]; + + to_si = 1.0/conv[newton_meter][hartree]; + conv[hartree][newton_meter] = to_si*conv[newton_meter][newton_meter]; + conv[hartree][kcal_per_mole] = to_si*conv[newton_meter][kcal_per_mole]; + conv[hartree][ev] = to_si*conv[newton_meter][ev]; + conv[hartree][dyne_centimeter] = to_si*conv[newton_meter][dyne_centimeter]; + conv[hartree][hartree] = 1.0; + conv[hartree][picogram_micrometersq_per_microsecondsq] = to_si*conv[newton_meter][picogram_micrometersq_per_microsecondsq]; + conv[hartree][attogram_nanometersq_per_nanosecondsq] = to_si*conv[newton_meter][attogram_nanometersq_per_nanosecondsq]; + + to_si = 1.0/conv[newton_meter][picogram_micrometersq_per_microsecondsq]; + conv[picogram_micrometersq_per_microsecondsq][newton_meter] = to_si*conv[newton_meter][newton_meter]; + conv[picogram_micrometersq_per_microsecondsq][kcal_per_mole] = to_si*conv[newton_meter][kcal_per_mole]; + conv[picogram_micrometersq_per_microsecondsq][ev] = to_si*conv[newton_meter][ev]; + conv[picogram_micrometersq_per_microsecondsq][dyne_centimeter] = to_si*conv[newton_meter][dyne_centimeter]; + conv[picogram_micrometersq_per_microsecondsq][hartree] = to_si*conv[newton_meter][hartree]; + conv[picogram_micrometersq_per_microsecondsq][picogram_micrometersq_per_microsecondsq] = 1.0; + conv[picogram_micrometersq_per_microsecondsq][attogram_nanometersq_per_nanosecondsq] = to_si*conv[newton_meter][attogram_nanometersq_per_nanosecondsq]; + + to_si = 1.0/conv[newton_meter][attogram_nanometersq_per_nanosecondsq]; + conv[attogram_nanometersq_per_nanosecondsq][newton_meter] = to_si*conv[newton_meter][newton_meter]; + conv[attogram_nanometersq_per_nanosecondsq][kcal_per_mole] = to_si*conv[newton_meter][kcal_per_mole]; + conv[attogram_nanometersq_per_nanosecondsq][ev] = to_si*conv[newton_meter][ev]; + conv[attogram_nanometersq_per_nanosecondsq][dyne_centimeter] = to_si*conv[newton_meter][dyne_centimeter]; + conv[attogram_nanometersq_per_nanosecondsq][hartree] = to_si*conv[newton_meter][hartree]; + conv[attogram_nanometersq_per_nanosecondsq][picogram_micrometersq_per_microsecondsq] = to_si*conv[newton_meter][picogram_micrometersq_per_microsecondsq]; + conv[attogram_nanometersq_per_nanosecondsq][attogram_nanometersq_per_nanosecondsq] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Temperature conversion +double get_temperature_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[kelvin][kelvin] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Pressure conversion +double get_pressure_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[pascal][pascal] = 1.0; + conv[pascal][atmosphere] = 1.0/atmosphere_si; + conv[pascal][bar] = 1.0/bar_si; + conv[pascal][dyne_per_centimetersq] = 1.0/dyne_per_centimetersq_si; + conv[pascal][picogram_per_micrometer_microsecondsq] = 1.0/picogram_per_micrometer_microsecondsq_si; + conv[pascal][attogram_per_nanometer_nanosecondsq] = 1.0/attogram_per_nanometer_nanosecondsq_si; + + to_si = 1.0/conv[pascal][atmosphere]; + conv[atmosphere][pascal] = to_si*conv[pascal][pascal]; + conv[atmosphere][atmosphere] = 1.0; + conv[atmosphere][bar] = to_si*conv[pascal][bar]; + conv[atmosphere][dyne_per_centimetersq] = to_si*conv[pascal][dyne_per_centimetersq]; + conv[atmosphere][picogram_per_micrometer_microsecondsq] = to_si*conv[pascal][picogram_per_micrometer_microsecondsq]; + conv[atmosphere][attogram_per_nanometer_nanosecondsq] = to_si*conv[pascal][attogram_per_nanometer_nanosecondsq]; + + to_si = 1.0/conv[pascal][bar]; + conv[bar][pascal] = to_si*conv[pascal][pascal]; + conv[bar][atmosphere] = to_si*conv[pascal][atmosphere]; + conv[bar][bar] = 1.0; + conv[bar][dyne_per_centimetersq] = to_si*conv[pascal][dyne_per_centimetersq]; + conv[bar][picogram_per_micrometer_microsecondsq] = to_si*conv[pascal][picogram_per_micrometer_microsecondsq]; + conv[bar][attogram_per_nanometer_nanosecondsq] = to_si*conv[pascal][attogram_per_nanometer_nanosecondsq]; + + to_si = 1.0/conv[pascal][dyne_per_centimetersq]; + conv[dyne_per_centimetersq][pascal] = to_si*conv[pascal][pascal]; + conv[dyne_per_centimetersq][atmosphere] = to_si*conv[pascal][atmosphere]; + conv[dyne_per_centimetersq][bar] = to_si*conv[pascal][bar]; + conv[dyne_per_centimetersq][dyne_per_centimetersq] = 1.0; + conv[dyne_per_centimetersq][picogram_per_micrometer_microsecondsq] = to_si*conv[pascal][picogram_per_micrometer_microsecondsq]; + conv[dyne_per_centimetersq][attogram_per_nanometer_nanosecondsq] = to_si*conv[pascal][attogram_per_nanometer_nanosecondsq]; + + to_si = 1.0/conv[pascal][picogram_per_micrometer_microsecondsq]; + conv[picogram_per_micrometer_microsecondsq][pascal] = to_si*conv[pascal][pascal]; + conv[picogram_per_micrometer_microsecondsq][atmosphere] = to_si*conv[pascal][atmosphere]; + conv[picogram_per_micrometer_microsecondsq][bar] = to_si*conv[pascal][bar]; + conv[picogram_per_micrometer_microsecondsq][dyne_per_centimetersq] = to_si*conv[pascal][dyne_per_centimetersq]; + conv[picogram_per_micrometer_microsecondsq][picogram_per_micrometer_microsecondsq] = 1.0; + conv[picogram_per_micrometer_microsecondsq][attogram_per_nanometer_nanosecondsq] = to_si*conv[pascal][attogram_per_nanometer_nanosecondsq]; + + to_si = 1.0/conv[pascal][attogram_per_nanometer_nanosecondsq]; + conv[attogram_per_nanometer_nanosecondsq][pascal] = to_si*conv[pascal][pascal]; + conv[attogram_per_nanometer_nanosecondsq][atmosphere] = to_si*conv[pascal][atmosphere]; + conv[attogram_per_nanometer_nanosecondsq][bar] = to_si*conv[pascal][bar]; + conv[attogram_per_nanometer_nanosecondsq][dyne_per_centimetersq] = to_si*conv[pascal][dyne_per_centimetersq]; + conv[attogram_per_nanometer_nanosecondsq][picogram_per_micrometer_microsecondsq] = to_si*conv[pascal][picogram_per_micrometer_microsecondsq]; + conv[attogram_per_nanometer_nanosecondsq][attogram_per_nanometer_nanosecondsq] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Viscosity conversion +double get_viscosity_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[pascal_second][pascal_second] = 1.0; + conv[pascal_second][poise] = 1.0/poise_si; + conv[pascal_second][amu_per_bohr_femtosecond] = 1.0/amu_per_bohr_femtosecond_si; + conv[pascal_second][picogram_per_micrometer_microsecond] = 1.0/picogram_per_micrometer_microsecond_si; + conv[pascal_second][attogram_per_nanometer_nanosecond] = 1.0/attogram_per_nanometer_nanosecond_si; + + to_si = 1.0/conv[pascal_second][poise]; + conv[poise][pascal_second] = to_si*conv[pascal_second][pascal_second]; + conv[poise][poise] = 1.0; + conv[poise][amu_per_bohr_femtosecond] = to_si*conv[pascal_second][amu_per_bohr_femtosecond]; + conv[poise][picogram_per_micrometer_microsecond] = to_si*conv[pascal_second][picogram_per_micrometer_microsecond]; + conv[poise][attogram_per_nanometer_nanosecond] = to_si*conv[pascal_second][attogram_per_nanometer_nanosecond]; + + to_si = 1.0/conv[pascal_second][amu_per_bohr_femtosecond]; + conv[amu_per_bohr_femtosecond][pascal_second] = to_si*conv[pascal_second][pascal_second]; + conv[amu_per_bohr_femtosecond][poise] = to_si*conv[pascal_second][poise]; + conv[amu_per_bohr_femtosecond][amu_per_bohr_femtosecond] = 1.0; + conv[amu_per_bohr_femtosecond][picogram_per_micrometer_microsecond] = to_si*conv[pascal_second][picogram_per_micrometer_microsecond]; + conv[amu_per_bohr_femtosecond][attogram_per_nanometer_nanosecond] = to_si*conv[pascal_second][attogram_per_nanometer_nanosecond]; + + to_si = 1.0/conv[pascal_second][picogram_per_micrometer_microsecond]; + conv[picogram_per_micrometer_microsecond][pascal_second] = to_si*conv[pascal_second][pascal_second]; + conv[picogram_per_micrometer_microsecond][poise] = to_si*conv[pascal_second][poise]; + conv[picogram_per_micrometer_microsecond][amu_per_bohr_femtosecond] = to_si*conv[pascal_second][amu_per_bohr_femtosecond]; + conv[picogram_per_micrometer_microsecond][picogram_per_micrometer_microsecond] = 1.0; + conv[picogram_per_micrometer_microsecond][attogram_per_nanometer_nanosecond] = to_si*conv[pascal_second][attogram_per_nanometer_nanosecond]; + + to_si = 1.0/conv[pascal_second][attogram_per_nanometer_nanosecond]; + conv[attogram_per_nanometer_nanosecond][pascal_second] = to_si*conv[pascal_second][pascal_second]; + conv[attogram_per_nanometer_nanosecond][poise] = to_si*conv[pascal_second][poise]; + conv[attogram_per_nanometer_nanosecond][amu_per_bohr_femtosecond] = to_si*conv[pascal_second][amu_per_bohr_femtosecond]; + conv[attogram_per_nanometer_nanosecond][picogram_per_micrometer_microsecond] = to_si*conv[pascal_second][picogram_per_micrometer_microsecond]; + conv[attogram_per_nanometer_nanosecond][attogram_per_nanometer_nanosecond] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Charge conversion +double get_charge_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[coulomb][coulomb] = 1.0; + conv[coulomb][echarge] = 1.0/echarge_si; + conv[coulomb][statcoulomb] = 1.0/statcoulomb_si; + conv[coulomb][picocoulomb] = 1.0/picocoulomb_si; + + to_si = 1.0/conv[coulomb][echarge]; + conv[echarge][coulomb] = to_si*conv[coulomb][coulomb]; + conv[echarge][echarge] = 1.0; + conv[echarge][statcoulomb] = to_si*conv[coulomb][statcoulomb]; + conv[echarge][picocoulomb] = to_si*conv[coulomb][picocoulomb]; + + to_si = 1.0/conv[coulomb][statcoulomb]; + conv[statcoulomb][coulomb] = to_si*conv[coulomb][coulomb]; + conv[statcoulomb][echarge] = to_si*conv[coulomb][echarge]; + conv[statcoulomb][statcoulomb] = 1.0; + conv[statcoulomb][picocoulomb] = to_si*conv[coulomb][picocoulomb]; + + to_si = 1.0/conv[coulomb][picocoulomb]; + conv[picocoulomb][coulomb] = to_si*conv[coulomb][coulomb]; + conv[picocoulomb][echarge] = to_si*conv[coulomb][echarge]; + conv[picocoulomb][statcoulomb] = to_si*conv[coulomb][statcoulomb]; + conv[picocoulomb][picocoulomb] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Dipole conversion +double get_dipole_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[coulomb_meter][coulomb_meter] = 1.0; + conv[coulomb_meter][electron_angstrom] = 1.0/electron_angstrom_si; + conv[coulomb_meter][statcoulomb_centimeter] = 1.0/statcoulomb_centimeter_si; + conv[coulomb_meter][debye] = 1.0/debye_si; + conv[coulomb_meter][picocoulomb_micrometer] = 1.0/picocoulomb_micrometer_si; + conv[coulomb_meter][electron_nanometer] = 1.0/electron_nanometer_si; + + to_si = 1.0/conv[coulomb_meter][electron_angstrom]; + conv[electron_angstrom][coulomb_meter] = to_si*conv[coulomb_meter][coulomb_meter]; + conv[electron_angstrom][electron_angstrom] = 1.0; + conv[electron_angstrom][statcoulomb_centimeter] = to_si*conv[coulomb_meter][statcoulomb_centimeter]; + conv[electron_angstrom][debye] = to_si*conv[coulomb_meter][debye]; + conv[electron_angstrom][picocoulomb_micrometer] = to_si*conv[coulomb_meter][picocoulomb_micrometer]; + conv[electron_angstrom][electron_nanometer] = to_si*conv[coulomb_meter][electron_nanometer]; + + to_si = 1.0/conv[coulomb_meter][statcoulomb_centimeter]; + conv[statcoulomb_centimeter][coulomb_meter] = to_si*conv[coulomb_meter][coulomb_meter]; + conv[statcoulomb_centimeter][electron_angstrom] = to_si*conv[coulomb_meter][electron_angstrom]; + conv[statcoulomb_centimeter][statcoulomb_centimeter] = 1.0; + conv[statcoulomb_centimeter][debye] = to_si*conv[coulomb_meter][debye]; + conv[statcoulomb_centimeter][picocoulomb_micrometer] = to_si*conv[coulomb_meter][picocoulomb_micrometer]; + conv[statcoulomb_centimeter][electron_nanometer] = to_si*conv[coulomb_meter][electron_nanometer]; + + to_si = 1.0/conv[coulomb_meter][debye]; + conv[debye][coulomb_meter] = to_si*conv[coulomb_meter][coulomb_meter]; + conv[debye][electron_angstrom] = to_si*conv[coulomb_meter][electron_angstrom]; + conv[debye][statcoulomb_centimeter] = to_si*conv[coulomb_meter][statcoulomb_centimeter]; + conv[debye][debye] = 1.0; + conv[debye][picocoulomb_micrometer] = to_si*conv[coulomb_meter][picocoulomb_micrometer]; + conv[debye][electron_nanometer] = to_si*conv[coulomb_meter][electron_nanometer]; + + to_si = 1.0/conv[coulomb_meter][picocoulomb_micrometer]; + conv[picocoulomb_micrometer][coulomb_meter] = to_si*conv[coulomb_meter][coulomb_meter]; + conv[picocoulomb_micrometer][electron_angstrom] = to_si*conv[coulomb_meter][electron_angstrom]; + conv[picocoulomb_micrometer][statcoulomb_centimeter] = to_si*conv[coulomb_meter][statcoulomb_centimeter]; + conv[picocoulomb_micrometer][debye] = to_si*conv[coulomb_meter][debye]; + conv[picocoulomb_micrometer][picocoulomb_micrometer] = 1.0; + conv[picocoulomb_micrometer][electron_nanometer] = to_si*conv[coulomb_meter][electron_nanometer]; + + to_si = 1.0/conv[coulomb_meter][electron_nanometer]; + conv[electron_nanometer][coulomb_meter] = to_si*conv[coulomb_meter][coulomb_meter]; + conv[electron_nanometer][electron_angstrom] = to_si*conv[coulomb_meter][electron_angstrom]; + conv[electron_nanometer][statcoulomb_centimeter] = to_si*conv[coulomb_meter][statcoulomb_centimeter]; + conv[electron_nanometer][debye] = to_si*conv[coulomb_meter][debye]; + conv[electron_nanometer][picocoulomb_micrometer] = to_si*conv[coulomb_meter][picocoulomb_micrometer]; + conv[electron_nanometer][electron_nanometer] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Electric field conversion +double get_efield_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[volt_per_meter][volt_per_meter] = 1.0; + conv[volt_per_meter][volt_per_angstrom] = 1.0/volt_per_angstrom_si; + conv[volt_per_meter][statvolt_per_centimeter] = 1.0/statvolt_per_centimeter_si; + conv[volt_per_meter][volt_per_centimeter] = 1.0/volt_per_centimeter_si; + conv[volt_per_meter][volt_per_micrometer] = 1.0/volt_per_micrometer_si; + conv[volt_per_meter][volt_per_nanometer] = 1.0/volt_per_nanometer_si; + + to_si = 1.0/conv[volt_per_meter][volt_per_angstrom]; + conv[volt_per_angstrom][volt_per_meter] = to_si*conv[volt_per_meter][volt_per_meter]; + conv[volt_per_angstrom][volt_per_angstrom] = 1.0; + conv[volt_per_angstrom][statvolt_per_centimeter] = to_si*conv[volt_per_meter][statvolt_per_centimeter]; + conv[volt_per_angstrom][volt_per_centimeter] = to_si*conv[volt_per_meter][volt_per_centimeter]; + conv[volt_per_angstrom][volt_per_micrometer] = to_si*conv[volt_per_meter][volt_per_micrometer]; + conv[volt_per_angstrom][volt_per_nanometer] = to_si*conv[volt_per_meter][volt_per_nanometer]; + + to_si = 1.0/conv[volt_per_meter][statvolt_per_centimeter]; + conv[statvolt_per_centimeter][volt_per_meter] = to_si*conv[volt_per_meter][volt_per_meter]; + conv[statvolt_per_centimeter][volt_per_angstrom] = to_si*conv[volt_per_meter][volt_per_angstrom]; + conv[statvolt_per_centimeter][statvolt_per_centimeter] = 1.0; + conv[statvolt_per_centimeter][volt_per_centimeter] = to_si*conv[volt_per_meter][volt_per_centimeter]; + conv[statvolt_per_centimeter][volt_per_micrometer] = to_si*conv[volt_per_meter][volt_per_micrometer]; + conv[statvolt_per_centimeter][volt_per_nanometer] = to_si*conv[volt_per_meter][volt_per_nanometer]; + + to_si = 1.0/conv[volt_per_meter][volt_per_centimeter]; + conv[volt_per_centimeter][volt_per_meter] = to_si*conv[volt_per_meter][volt_per_meter]; + conv[volt_per_centimeter][volt_per_angstrom] = to_si*conv[volt_per_meter][volt_per_angstrom]; + conv[volt_per_centimeter][statvolt_per_centimeter] = to_si*conv[volt_per_meter][statvolt_per_centimeter]; + conv[volt_per_centimeter][volt_per_centimeter] = 1.0; + conv[volt_per_centimeter][volt_per_micrometer] = to_si*conv[volt_per_meter][volt_per_micrometer]; + conv[volt_per_centimeter][volt_per_nanometer] = to_si*conv[volt_per_meter][volt_per_nanometer]; + + to_si = 1.0/conv[volt_per_meter][volt_per_micrometer]; + conv[volt_per_micrometer][volt_per_meter] = to_si*conv[volt_per_meter][volt_per_meter]; + conv[volt_per_micrometer][volt_per_angstrom] = to_si*conv[volt_per_meter][volt_per_angstrom]; + conv[volt_per_micrometer][statvolt_per_centimeter] = to_si*conv[volt_per_meter][statvolt_per_centimeter]; + conv[volt_per_micrometer][volt_per_centimeter] = to_si*conv[volt_per_meter][volt_per_centimeter]; + conv[volt_per_micrometer][volt_per_micrometer] = 1.0; + conv[volt_per_micrometer][volt_per_nanometer] = to_si*conv[volt_per_meter][volt_per_nanometer]; + + to_si = 1.0/conv[volt_per_meter][volt_per_nanometer]; + conv[volt_per_nanometer][volt_per_meter] = to_si*conv[volt_per_meter][volt_per_meter]; + conv[volt_per_nanometer][volt_per_angstrom] = to_si*conv[volt_per_meter][volt_per_angstrom]; + conv[volt_per_nanometer][statvolt_per_centimeter] = to_si*conv[volt_per_meter][statvolt_per_centimeter]; + conv[volt_per_nanometer][volt_per_centimeter] = to_si*conv[volt_per_meter][volt_per_centimeter]; + conv[volt_per_nanometer][volt_per_micrometer] = to_si*conv[volt_per_meter][volt_per_micrometer]; + conv[volt_per_nanometer][volt_per_nanometer] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Demsity conversion +double get_density_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[kilogram_per_metercu][kilogram_per_metercu] = 1.0; + conv[kilogram_per_metercu][gram_per_centimetercu] = 1.0/gram_per_centimetercu_si; + conv[kilogram_per_metercu][amu_per_bohrcu] = 1.0/amu_per_bohrcu_si; + conv[kilogram_per_metercu][picogram_per_micrometercu] = 1.0/picogram_per_micrometercu_si; + conv[kilogram_per_metercu][attogram_per_nanometercu] = 1.0/attogram_per_nanometercu_si; + + to_si = 1.0/conv[kilogram_per_metercu][gram_per_centimetercu]; + conv[gram_per_centimetercu][kilogram_per_metercu] = to_si*conv[kilogram_per_metercu][kilogram_per_metercu]; + conv[gram_per_centimetercu][gram_per_centimetercu] = 1.0; + conv[gram_per_centimetercu][amu_per_bohrcu] = to_si*conv[kilogram_per_metercu][amu_per_bohrcu]; + conv[gram_per_centimetercu][picogram_per_micrometercu] = to_si*conv[kilogram_per_metercu][picogram_per_micrometercu]; + conv[gram_per_centimetercu][attogram_per_nanometercu] = to_si*conv[kilogram_per_metercu][attogram_per_nanometercu]; + + to_si = 1.0/conv[kilogram_per_metercu][amu_per_bohrcu]; + conv[amu_per_bohrcu][kilogram_per_metercu] = to_si*conv[kilogram_per_metercu][kilogram_per_metercu]; + conv[amu_per_bohrcu][gram_per_centimetercu] = to_si*conv[kilogram_per_metercu][gram_per_centimetercu]; + conv[amu_per_bohrcu][amu_per_bohrcu] = 1.0; + conv[amu_per_bohrcu][picogram_per_micrometercu] = to_si*conv[kilogram_per_metercu][picogram_per_micrometercu]; + conv[amu_per_bohrcu][attogram_per_nanometercu] = to_si*conv[kilogram_per_metercu][attogram_per_nanometercu]; + + to_si = 1.0/conv[kilogram_per_metercu][picogram_per_micrometercu]; + conv[picogram_per_micrometercu][kilogram_per_metercu] = to_si*conv[kilogram_per_metercu][kilogram_per_metercu]; + conv[picogram_per_micrometercu][gram_per_centimetercu] = to_si*conv[kilogram_per_metercu][gram_per_centimetercu]; + conv[picogram_per_micrometercu][amu_per_bohrcu] = to_si*conv[kilogram_per_metercu][amu_per_bohrcu]; + conv[picogram_per_micrometercu][picogram_per_micrometercu] = 1.0; + conv[picogram_per_micrometercu][attogram_per_nanometercu] = to_si*conv[kilogram_per_metercu][attogram_per_nanometercu]; + + to_si = 1.0/conv[kilogram_per_metercu][attogram_per_nanometercu]; + conv[attogram_per_nanometercu][kilogram_per_metercu] = to_si*conv[kilogram_per_metercu][kilogram_per_metercu]; + conv[attogram_per_nanometercu][gram_per_centimetercu] = to_si*conv[kilogram_per_metercu][gram_per_centimetercu]; + conv[attogram_per_nanometercu][amu_per_bohrcu] = to_si*conv[kilogram_per_metercu][amu_per_bohrcu]; + conv[attogram_per_nanometercu][picogram_per_micrometercu] = to_si*conv[kilogram_per_metercu][picogram_per_micrometercu]; + conv[attogram_per_nanometercu][attogram_per_nanometercu] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// This routine returns the unit conversion factor between the +// `from_system_enum` to the `to_system_enum` for the `unit_type_enum`. +double get_unit_conversion_factor(unit_type &unit_type_enum, + sys_type from_system_enum, + sys_type to_system_enum) +{ + units from_unit = get_lammps_system_unit(from_system_enum, unit_type_enum); + units to_unit = get_lammps_system_unit(to_system_enum, unit_type_enum); + switch(unit_type_enum) { + case mass : + return get_mass_conversion_factor(from_unit, to_unit); + case distance : + return get_distance_conversion_factor(from_unit, to_unit); + case time : + return get_time_conversion_factor(from_unit, to_unit); + case energy : + return get_energy_conversion_factor(from_unit, to_unit); + case velocity : + return get_velocity_conversion_factor(from_unit, to_unit); + case force : + return get_force_conversion_factor(from_unit, to_unit); + case torque : + return get_torque_conversion_factor(from_unit, to_unit); + case temperature : + return get_temperature_conversion_factor(from_unit, to_unit); + case pressure : + return get_pressure_conversion_factor(from_unit, to_unit); + case viscosity : + return get_viscosity_conversion_factor(from_unit, to_unit); + case charge : + return get_charge_conversion_factor(from_unit, to_unit); + case dipole : + return get_dipole_conversion_factor(from_unit, to_unit); + case efield : + return get_efield_conversion_factor(from_unit, to_unit); + case density : + default : // This is here to a prevent a compiler warning + return get_density_conversion_factor(from_unit, to_unit); + } +} + +} // end of anonymous name space + +/* ---------------------------------------------------------------------- */ + +// Wrapper to the routine that gets the unit conversion. Translates strings +// to enumerations and then call get_unit_conversion_factor() +int lammps_unit_conversion(string const &unit_type_str, + string const &from_system_str, + string const &to_system_str, + double &conversion_factor) +{ + // initialize + conversion_factor = 0.0; + initialize_dictionaries(); + + // convert input to enumeration + unit_type unit_type_enum; + { + map::const_iterator itr = unit_dic.find(unit_type_str); + if (itr != unit_dic.end()) unit_type_enum = itr->second; + else return 1; // error + } + sys_type from_system_enum; + { + map::const_iterator + itr = system_dic.find(from_system_str); + if (itr != system_dic.end()) from_system_enum = itr->second; + else return 1; // error + } + sys_type to_system_enum; + { + map::const_iterator + itr = system_dic.find(to_system_str); + if (itr != system_dic.end()) to_system_enum = itr->second; + else return 1; + } + + // process unit conversions + conversion_factor = get_unit_conversion_factor(unit_type_enum, + from_system_enum, + to_system_enum); + return 0; +} + + diff --git a/src/KIM/kim_units.h b/src/KIM/kim_units.h new file mode 100644 index 0000000000000000000000000000000000000000..97e81a6222b181606860dc4b883568b8f9366d06 --- /dev/null +++ b/src/KIM/kim_units.h @@ -0,0 +1,59 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Ellad B. Tadmor (UMN) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This program is free software; you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by the Free + Software Foundation; either version 2 of the License, or (at your option) + any later version. + + This program is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for + more details. + + You should have received a copy of the GNU General Public License along with + this program; if not, see . + + Linking LAMMPS statically or dynamically with other modules is making a + combined work based on LAMMPS. Thus, the terms and conditions of the GNU + General Public License cover the whole combination. + + In addition, as a special exception, the copyright holders of LAMMPS give + you permission to combine LAMMPS with free software programs or libraries + that are released under the GNU LGPL and with code included in the standard + release of the "kim-api" under the CDDL (or modified versions of such code, + with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for LAMMPS and the licenses of the other code + concerned, provided that you include the source code of that other code + when and as the GNU GPL requires distribution of source code. + + Note that people who make modified versions of LAMMPS are not obligated to + grant this special exception for their modified versions; it is their choice + whether to do so. The GNU General Public License gives permission to release + a modified version without this exception; this exception also makes it + possible to release a modified version which carries forward this exception. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Designed for use with the kim-api-2.0.2 (and newer) package +------------------------------------------------------------------------- */ + +int lammps_unit_conversion(std::string const &unit_type_str, + std::string const &from_system_str, + std::string const &to_system_str, + double &conversion_factor); diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index a1c13ae81fbd21bd9c611cca28e33a34577aa7f0..d935d994bd71413a78773c119d687c8f99ada2d3 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -13,6 +13,7 @@ /* ---------------------------------------------------------------------- Contributing authors: Ryan S. Elliott (UMinn) + Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- @@ -52,12 +53,10 @@ /* ---------------------------------------------------------------------- Designed for use with the kim-api-2.0.2 (and newer) package ------------------------------------------------------------------------- */ - +#include "pair_kim.h" #include #include - -// includes from LAMMPS -#include "pair_kim.h" +#include #include "atom.h" #include "comm.h" #include "force.h" @@ -74,200 +73,184 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ PairKIM::PairKIM(LAMMPS *lmp) : - Pair(lmp), - settings_call_count(0), - init_style_call_count(0), - kim_modelname(NULL), - lmps_map_species_to_unique(NULL), - lmps_unique_elements(NULL), - lmps_num_unique_elements(0), - lmps_units(METAL), - lengthUnit(KIM_LENGTH_UNIT_unused), - energyUnit(KIM_ENERGY_UNIT_unused), - chargeUnit(KIM_CHARGE_UNIT_unused), - temperatureUnit(KIM_TEMPERATURE_UNIT_unused), - timeUnit(KIM_TIME_UNIT_unused), - pkim(NULL), - pargs(NULL), - kim_model_support_for_energy(KIM_SUPPORT_STATUS_notSupported), - kim_model_support_for_forces(KIM_SUPPORT_STATUS_notSupported), - kim_model_support_for_particleEnergy(KIM_SUPPORT_STATUS_notSupported), - kim_model_support_for_particleVirial(KIM_SUPPORT_STATUS_notSupported), - lmps_local_tot_num_atoms(0), - kim_global_influence_distance(0.0), - kim_number_of_neighbor_lists(0), - kim_cutoff_values(NULL), - modelWillNotRequestNeighborsOfNoncontributingParticles(NULL), - neighborLists(NULL), - kim_particle_codes(NULL), - lmps_maxalloc(0), - kim_particleSpecies(NULL), - kim_particleContributing(NULL), - lmps_stripped_neigh_list(NULL), - lmps_stripped_neigh_ptr(NULL) + Pair(lmp), + settings_call_count(0), + init_style_call_count(0), + kim_modelname(NULL), + lmps_map_species_to_unique(NULL), + lmps_unique_elements(NULL), + lmps_num_unique_elements(0), + lmps_units(METAL), + lengthUnit(KIM_LENGTH_UNIT_unused), + energyUnit(KIM_ENERGY_UNIT_unused), + chargeUnit(KIM_CHARGE_UNIT_unused), + temperatureUnit(KIM_TEMPERATURE_UNIT_unused), + timeUnit(KIM_TIME_UNIT_unused), + pkim(NULL), + pargs(NULL), + kim_model_support_for_energy(KIM_SUPPORT_STATUS_notSupported), + kim_model_support_for_forces(KIM_SUPPORT_STATUS_notSupported), + kim_model_support_for_particleEnergy(KIM_SUPPORT_STATUS_notSupported), + kim_model_support_for_particleVirial(KIM_SUPPORT_STATUS_notSupported), + lmps_local_tot_num_atoms(0), + kim_global_influence_distance(0.0), + kim_number_of_neighbor_lists(0), + kim_cutoff_values(NULL), + modelWillNotRequestNeighborsOfNoncontributingParticles(NULL), + neighborLists(NULL), + kim_particle_codes(NULL), + lmps_maxalloc(0), + kim_particleSpecies(NULL), + kim_particleContributing(NULL), + lmps_stripped_neigh_list(NULL), + lmps_stripped_neigh_ptr(NULL) { - // Initialize Pair data members to appropriate values - single_enable = 0; // We do not provide the Single() function - restartinfo = 0; // We do not write any restart info - one_coeff = 1; // We only allow one coeff * * call - // set to 1, regardless use of fdotr, to avoid ev_set()'s futzing with - // vflag_global - no_virial_fdotr_compute = 1; - - // BEGIN: initial values that determine the KIM state - // (used by kim_free(), etc.) - kim_init_ok = false; - kim_particle_codes_ok = false; - // END - - return; + // Initialize Pair data members to appropriate values + single_enable = 0; // We do not provide the Single() function + restartinfo = 0; // We do not write any restart info + one_coeff = 1; // We only allow one coeff * * call + // set to 1, regardless use of fdotr, to avoid ev_set()'s futzing with + // vflag_global + no_virial_fdotr_compute = 1; + + // BEGIN: initial values that determine the KIM state + // (used by kim_free(), etc.) + kim_init_ok = false; + kim_particle_codes_ok = false; + // END } /* ---------------------------------------------------------------------- */ PairKIM::~PairKIM() { - // clean up kim_modelname - if (kim_modelname != 0) delete [] kim_modelname; - - // clean up lammps atom species number to unique particle names mapping - if (lmps_unique_elements) - for (int i = 0; i < lmps_num_unique_elements; i++) - delete [] lmps_unique_elements[i]; - delete [] lmps_unique_elements; - - if (kim_particle_codes_ok) - { - delete [] kim_particle_codes; - kim_particle_codes = NULL; - kim_particle_codes_ok = false; - } - - // clean up local memory used to support KIM interface - memory->destroy(kim_particleSpecies); - memory->destroy(kim_particleContributing); - memory->destroy(lmps_stripped_neigh_list); - // clean up lmps_stripped_neigh_ptr - if (lmps_stripped_neigh_ptr) - { - delete [] lmps_stripped_neigh_ptr; - lmps_stripped_neigh_ptr = 0; - } - - // clean up allocated memory for standard Pair class usage - // also, we allocate lmps_map_species_to_uniuqe in the allocate() function - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - delete [] lmps_map_species_to_unique; - } - - // clean up neighborlist pointers - if (neighborLists) - { - delete [] neighborLists; - neighborLists = 0; - } - - // clean up KIM interface (if necessary) - kim_free(); - - return; + // clean up kim_modelname + if (kim_modelname != 0) delete [] kim_modelname; + + // clean up lammps atom species number to unique particle names mapping + if (lmps_unique_elements) + for (int i = 0; i < lmps_num_unique_elements; i++) + delete [] lmps_unique_elements[i]; + delete [] lmps_unique_elements; + + if (kim_particle_codes_ok) { + delete [] kim_particle_codes; + kim_particle_codes = NULL; + kim_particle_codes_ok = false; + } + + // clean up local memory used to support KIM interface + memory->destroy(kim_particleSpecies); + memory->destroy(kim_particleContributing); + memory->destroy(lmps_stripped_neigh_list); + // clean up lmps_stripped_neigh_ptr + if (lmps_stripped_neigh_ptr) { + delete [] lmps_stripped_neigh_ptr; + lmps_stripped_neigh_ptr = 0; + } + + // clean up allocated memory for standard Pair class usage + // also, we allocate lmps_map_species_to_uniuqe in the allocate() function + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + delete [] lmps_map_species_to_unique; + } + + // clean up neighborlist pointers + if (neighborLists) { + delete [] neighborLists; + neighborLists = 0; + } + + // clean up KIM interface (if necessary) + kim_free(); } /* ---------------------------------------------------------------------- */ + void PairKIM::set_contributing() { int const nall = atom->nlocal + atom->nghost; for (int i = 0; i < nall; ++i) - { kim_particleContributing[i] = ( (i < atom->nlocal) ? 1 : 0 ); - } } /* ---------------------------------------------------------------------- */ -void PairKIM::compute(int eflag , int vflag) +void PairKIM::compute(int eflag, int vflag) { - ev_init(eflag,vflag); - - // grow kim_particleSpecies and kim_particleContributing array if necessary - // needs to be atom->nmax in length - if (atom->nmax > lmps_maxalloc) { - memory->destroy(kim_particleSpecies); - memory->destroy(kim_particleContributing); - - lmps_maxalloc = atom->nmax; - memory->create(kim_particleSpecies,lmps_maxalloc, - "pair:kim_particleSpecies"); - int kimerror = KIM_ComputeArguments_SetArgumentPointerInteger(pargs, - KIM_COMPUTE_ARGUMENT_NAME_particleSpeciesCodes, - kim_particleSpecies); - memory->create(kim_particleContributing,lmps_maxalloc, - "pair:kim_particleContributing"); - kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerInteger( - pargs, - KIM_COMPUTE_ARGUMENT_NAME_particleContributing, - kim_particleContributing); - if (kimerror) - error->all( - FLERR, - "Unable to set KIM particle species codes and/or contributing"); - } - - // kim_particleSpecies = KIM atom species for each LAMMPS atom - - int *species = atom->type; - int nall = atom->nlocal + atom->nghost; - int ielement; - - for (int i = 0; i < nall; i++) { - ielement = lmps_map_species_to_unique[species[i]]; - kim_particleSpecies[i] = kim_particle_codes[ielement]; - } - - // Set kim contributing flags - set_contributing(); - - // pass current atom pointers to KIM - set_argument_pointers(); - - // set number of particles - lmps_local_tot_num_atoms = (int) nall; - - // compute via KIM model - int kimerror = KIM_Model_Compute(pkim, pargs); - if (kimerror) error->all(FLERR,"KIM Compute returned error"); - - // compute virial before reverse comm! - if (vflag_global) - { - virial_fdotr_compute(); - } - - // if newton is off, perform reverse comm - if (!lmps_using_newton) - { - comm->reverse_comm_pair(this); - } - - if ((vflag_atom) && - KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, - KIM_SUPPORT_STATUS_notSupported) - ) - { // flip sign and order of virial if KIM is computing it - double tmp; - for (int i = 0; i < nall; ++i) - { - for (int j = 0; j < 3; ++j) vatom[i][j] = -1.0*vatom[i][j]; - tmp = vatom[i][3]; - vatom[i][3] = -vatom[i][5]; - vatom[i][4] = -vatom[i][4]; - vatom[i][5] = -tmp; - } - } + ev_init(eflag,vflag); + + // grow kim_particleSpecies and kim_particleContributing array if necessary + // needs to be atom->nmax in length + if (atom->nmax > lmps_maxalloc) { + memory->destroy(kim_particleSpecies); + memory->destroy(kim_particleContributing); + + lmps_maxalloc = atom->nmax; + memory->create(kim_particleSpecies,lmps_maxalloc, + "pair:kim_particleSpecies"); + int kimerror = KIM_ComputeArguments_SetArgumentPointerInteger(pargs, + KIM_COMPUTE_ARGUMENT_NAME_particleSpeciesCodes, + kim_particleSpecies); + memory->create(kim_particleContributing,lmps_maxalloc, + "pair:kim_particleContributing"); + kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerInteger( + pargs, + KIM_COMPUTE_ARGUMENT_NAME_particleContributing, + kim_particleContributing); + if (kimerror) + error->all(FLERR, + "Unable to set KIM particle species codes and/or contributing"); + } + + // kim_particleSpecies = KIM atom species for each LAMMPS atom + + int *species = atom->type; + int nall = atom->nlocal + atom->nghost; + int ielement; + + for (int i = 0; i < nall; i++) { + ielement = lmps_map_species_to_unique[species[i]]; + kim_particleSpecies[i] = kim_particle_codes[ielement]; + } + + // Set kim contributing flags + set_contributing(); + + // pass current atom pointers to KIM + set_argument_pointers(); + + // set number of particles + lmps_local_tot_num_atoms = (int) nall; + + // compute via KIM model + int kimerror = KIM_Model_Compute(pkim, pargs); + if (kimerror) error->all(FLERR,"KIM Compute returned error"); + + // compute virial before reverse comm! + if (vflag_global) + virial_fdotr_compute(); + + // if newton is off, perform reverse comm + if (!lmps_using_newton) { + comm->reverse_comm_pair(this); + } - return; + if ((vflag_atom) && + KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported)) { + // flip sign and order of virial if KIM is computing it + double tmp; + for (int i = 0; i < nall; ++i) { + for (int j = 0; j < 3; ++j) vatom[i][j] = -1.0*vatom[i][j]; + tmp = vatom[i][3]; + vatom[i][3] = -vatom[i][5]; + vatom[i][4] = -vatom[i][4]; + vatom[i][5] = -tmp; + } + } } /* ---------------------------------------------------------------------- @@ -276,22 +259,20 @@ void PairKIM::compute(int eflag , int vflag) void PairKIM::allocate() { - int n = atom->ntypes; + int n = atom->ntypes; - // allocate standard Pair class arrays - memory->create(setflag,n+1,n+1,"pair:setflag"); - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; + // allocate standard Pair class arrays + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; - memory->create(cutsq,n+1,n+1,"pair:cutsq"); + memory->create(cutsq,n+1,n+1,"pair:cutsq"); - // allocate mapping array - lmps_map_species_to_unique = new int[n+1]; + // allocate mapping array + lmps_map_species_to_unique = new int[n+1]; - allocated = 1; - - return; + allocated = 1; } /* ---------------------------------------------------------------------- @@ -300,56 +281,49 @@ void PairKIM::allocate() void PairKIM::settings(int narg, char **arg) { - // This is called when "pair_style kim ..." is read from input - // may be called multiple times - ++settings_call_count; - init_style_call_count = 0; - - if (narg != 1) - { - if ((narg > 0) && ((0 == strcmp("KIMvirial", arg[0])) || - (0 == strcmp("LAMMPSvirial", arg[0])))) - { - error->all(FLERR,"'KIMvirial' or 'LAMMPSvirial' not supported with " - "kim-api."); - } - else - error->all(FLERR,"Illegal pair_style command"); - } - // arg[0] is the KIM Model name - - lmps_using_molecular = (atom->molecular > 0); - - // ensure we are in a clean state for KIM (needed on repeated call) - // first time called will do nothing... - kim_free(); - - // make sure things are allocated - if (allocated != 1) allocate(); - - // clear setflag to ensure coeff() is called after settings() - int n = atom->ntypes; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - // set lmps_* bool flags - set_lmps_flags(); - - // set KIM Model name - int nmlen = strlen(arg[0]); - if (kim_modelname != 0) - { - delete [] kim_modelname; - kim_modelname = 0; - } - kim_modelname = new char[nmlen+1]; - strcpy(kim_modelname, arg[0]); - - // initialize KIM Model - kim_init(); - - return; + // This is called when "pair_style kim ..." is read from input + // may be called multiple times + ++settings_call_count; + init_style_call_count = 0; + + if (narg != 1) { + if ((narg > 0) && ((0 == strcmp("KIMvirial", arg[0])) || + (0 == strcmp("LAMMPSvirial", arg[0])))) { + error->all(FLERR,"'KIMvirial' or 'LAMMPSvirial' not supported with " + "kim-api."); + } else error->all(FLERR,"Illegal pair_style command"); + } + // arg[0] is the KIM Model name + + lmps_using_molecular = (atom->molecular > 0); + + // ensure we are in a clean state for KIM (needed on repeated call) + // first time called will do nothing... + kim_free(); + + // make sure things are allocated + if (allocated != 1) allocate(); + + // clear setflag to ensure coeff() is called after settings() + int n = atom->ntypes; + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + // set lmps_* bool flags + set_lmps_flags(); + + // set KIM Model name + int nmlen = strlen(arg[0]); + if (kim_modelname != 0) { + delete [] kim_modelname; + kim_modelname = 0; + } + kim_modelname = new char[nmlen+1]; + strcpy(kim_modelname, arg[0]); + + // initialize KIM Model + kim_init(); } /* ---------------------------------------------------------------------- @@ -358,99 +332,95 @@ void PairKIM::settings(int narg, char **arg) void PairKIM::coeff(int narg, char **arg) { - // This is called when "pair_coeff ..." is read from input - // may be called multiple times - - int i,j,n; - - if (!allocated) allocate(); - - if (narg != 2 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // insure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - - int ilo,ihi,jlo,jhi; - force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); - force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); - - // read args that map atom species to KIM elements - // lmps_map_species_to_unique[i] = - // which element the Ith atom type is - // lmps_num_unique_elements = # of unique elements - // lmps_unique_elements = list of element names - - // if called multiple times: update lmps_unique_elements - if (lmps_unique_elements) { - for (i = 0; i < lmps_num_unique_elements; i++) - delete [] lmps_unique_elements[i]; - delete [] lmps_unique_elements; - } - lmps_unique_elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) lmps_unique_elements[i] = 0; - - - // Assume all species arguments are valid - // errors will be detected by below - lmps_num_unique_elements = 0; - for (i = 2; i < narg; i++) { - for (j = 0; j < lmps_num_unique_elements; j++) - if (strcmp(arg[i],lmps_unique_elements[j]) == 0) break; - lmps_map_species_to_unique[i-1] = j; - if (j == lmps_num_unique_elements) { - n = strlen(arg[i]) + 1; - lmps_unique_elements[j] = new char[n]; - strcpy(lmps_unique_elements[j],arg[i]); - lmps_num_unique_elements++; - } - } - - int count = 0; - for (int i = ilo; i <= ihi; i++) { - for (int j = MAX(jlo,i); j <= jhi; j++) { - if (lmps_map_species_to_unique[i] >= 0 && - lmps_map_species_to_unique[j] >= 0) { - setflag[i][j] = 1; - count++; - } - } - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); - - // setup mapping between LAMMPS unique elements and KIM species codes - if (kim_particle_codes_ok) - { - delete [] kim_particle_codes; - kim_particle_codes = NULL; - kim_particle_codes_ok = false; - } - kim_particle_codes = new int[lmps_num_unique_elements]; - kim_particle_codes_ok = true; - for(int i = 0; i < lmps_num_unique_elements; i++){ - int supported; - int code; - KIM_Model_GetSpeciesSupportAndCode( - pkim, - KIM_SpeciesName_FromString(lmps_unique_elements[i]), - &supported, - &code); - if (supported) - kim_particle_codes[i] = code; - else - { - std::stringstream msg; - msg << "create_kim_particle_codes: symbol not found: " - << lmps_unique_elements[i]; - error->all(FLERR, msg.str().c_str()); + // This is called when "pair_coeff ..." is read from input + // may be called multiple times + + int i,j,n; + + if (!allocated) allocate(); + + if (narg != 2 + atom->ntypes) + error->all(FLERR,"Incorrect args for pair coefficients"); + + // insure I,J args are * * + + if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) + error->all(FLERR,"Incorrect args for pair coefficients"); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + // read args that map atom species to KIM elements + // lmps_map_species_to_unique[i] = + // which element the Ith atom type is + // lmps_num_unique_elements = # of unique elements + // lmps_unique_elements = list of element names + + // if called multiple times: update lmps_unique_elements + if (lmps_unique_elements) { + for (i = 0; i < lmps_num_unique_elements; i++) + delete [] lmps_unique_elements[i]; + delete [] lmps_unique_elements; + } + lmps_unique_elements = new char*[atom->ntypes]; + for (i = 0; i < atom->ntypes; i++) lmps_unique_elements[i] = 0; + + // Assume all species arguments are valid + // errors will be detected by below + std::string atom_type_sym_list; + lmps_num_unique_elements = 0; + for (i = 2; i < narg; i++) { + atom_type_sym_list += std::string(" ") + arg[i]; + for (j = 0; j < lmps_num_unique_elements; j++) + if (strcmp(arg[i],lmps_unique_elements[j]) == 0) break; + lmps_map_species_to_unique[i-1] = j; + if (j == lmps_num_unique_elements) { + n = strlen(arg[i]) + 1; + lmps_unique_elements[j] = new char[n]; + strcpy(lmps_unique_elements[j],arg[i]); + lmps_num_unique_elements++; + } + } + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + if (lmps_map_species_to_unique[i] >= 0 && + lmps_map_species_to_unique[j] >= 0) { + setflag[i][j] = 1; + count++; } - } + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); - return; + // setup mapping between LAMMPS unique elements and KIM species codes + if (kim_particle_codes_ok) { + delete [] kim_particle_codes; + kim_particle_codes = NULL; + kim_particle_codes_ok = false; + } + kim_particle_codes = new int[lmps_num_unique_elements]; + kim_particle_codes_ok = true; + + for(int i = 0; i < lmps_num_unique_elements; i++) { + int supported; + int code; + KIM_Model_GetSpeciesSupportAndCode( + pkim, + KIM_SpeciesName_FromString(lmps_unique_elements[i]), + &supported, + &code); + if (supported) { + kim_particle_codes[i] = code; + } else { + std::string msg("create_kim_particle_codes: symbol not found: "); + msg += lmps_unique_elements[i]; + error->all(FLERR, msg.c_str()); + } + } } /* ---------------------------------------------------------------------- @@ -459,57 +429,48 @@ void PairKIM::coeff(int narg, char **arg) void PairKIM::init_style() { - // This is called for each "run ...", "minimize ...", etc. read from input - ++init_style_call_count; - - if (domain->dimension != 3) - error->all(FLERR,"PairKIM only works with 3D problems"); - - // setup lmps_stripped_neigh_list for neighbors of one atom, if needed - if (lmps_using_molecular) { - memory->destroy(lmps_stripped_neigh_list); - memory->create(lmps_stripped_neigh_list, - kim_number_of_neighbor_lists*neighbor->oneatom, - "pair:lmps_stripped_neigh_list"); - delete [] lmps_stripped_neigh_ptr; - lmps_stripped_neigh_ptr = new int*[kim_number_of_neighbor_lists]; - for (int i = 0; i < kim_number_of_neighbor_lists; ++i) - { - lmps_stripped_neigh_ptr[i] - = &(lmps_stripped_neigh_list[i*(neighbor->oneatom)]); - } + // This is called for each "run ...", "minimize ...", etc. read from input + ++init_style_call_count; + + if (domain->dimension != 3) + error->all(FLERR,"PairKIM only works with 3D problems"); + + // setup lmps_stripped_neigh_list for neighbors of one atom, if needed + if (lmps_using_molecular) { + memory->destroy(lmps_stripped_neigh_list); + memory->create(lmps_stripped_neigh_list, + kim_number_of_neighbor_lists*neighbor->oneatom, + "pair:lmps_stripped_neigh_list"); + delete [] lmps_stripped_neigh_ptr; + lmps_stripped_neigh_ptr = new int*[kim_number_of_neighbor_lists]; + for (int i = 0; i < kim_number_of_neighbor_lists; ++i) + lmps_stripped_neigh_ptr[i] + = &(lmps_stripped_neigh_list[i*(neighbor->oneatom)]); + } + + // make sure comm_reverse expects (at most) 9 values when newton is off + if (!lmps_using_newton) comm_reverse_off = 9; + + // request full neighbor + for (int i = 0; i < kim_number_of_neighbor_lists; ++i) { + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->id = i; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; - } - - // make sure comm_reverse expects (at most) 9 values when newton is off - if (!lmps_using_newton) comm_reverse_off = 9; - - // request full neighbor - for (int i = 0; i < kim_number_of_neighbor_lists; ++i) - { - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->id = i; - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; - - if (modelWillNotRequestNeighborsOfNoncontributingParticles[i]) - { - neighbor->requests[irequest]->ghost = 0; - } - else - { - neighbor->requests[irequest]->ghost = 1; - - } - // always want all owned/ghost pairs - neighbor->requests[irequest]->newton = 2; - // set cutoff - neighbor->requests[irequest]->cut = 1; - neighbor->requests[irequest]->cutoff - = kim_cutoff_values[i] + neighbor->skin; - } - - return; + if (modelWillNotRequestNeighborsOfNoncontributingParticles[i]) + neighbor->requests[irequest]->ghost = 0; + else + neighbor->requests[irequest]->ghost = 1; + + // always want all owned/ghost pairs + neighbor->requests[irequest]->newton = 2; + + // set cutoff + neighbor->requests[irequest]->cut = 1; + neighbor->requests[irequest]->cutoff + = kim_cutoff_values[i] + neighbor->skin; + } } /* ---------------------------------------------------------------------- @@ -528,154 +489,134 @@ void PairKIM::init_list(int id, NeighList *ptr) double PairKIM::init_one(int i, int j) { - // This is called once of each (unordered) i,j pair for each - // "run ...", "minimize ...", etc. read from input + // This is called once of each (unordered) i,j pair for each + // "run ...", "minimize ...", etc. read from input - if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); - return kim_global_influence_distance; + return kim_global_influence_distance; } /* ---------------------------------------------------------------------- */ int PairKIM::pack_reverse_comm(int n, int first, double *buf) { - int i,m,last; - double *fp; - fp = &(atom->f[0][0]); - - m = 0; - last = first + n; - if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces, - KIM_SUPPORT_STATUS_notSupported) - && - ((vflag_atom == 0) || - KIM_SupportStatus_Equal(kim_model_support_for_particleVirial, - KIM_SUPPORT_STATUS_notSupported))) - { - for (i = first; i < last; i++) - { - buf[m++] = fp[3*i+0]; - buf[m++] = fp[3*i+1]; - buf[m++] = fp[3*i+2]; - } - return m; - } - else if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces, - KIM_SUPPORT_STATUS_notSupported) && - (vflag_atom == 1) && - KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, - KIM_SUPPORT_STATUS_notSupported)) - { - double *va=&(vatom[0][0]); - for (i = first; i < last; i++) - { - buf[m++] = fp[3*i+0]; - buf[m++] = fp[3*i+1]; - buf[m++] = fp[3*i+2]; - - buf[m++] = va[6*i+0]; - buf[m++] = va[6*i+1]; - buf[m++] = va[6*i+2]; - buf[m++] = va[6*i+3]; - buf[m++] = va[6*i+4]; - buf[m++] = va[6*i+5]; - } - return m; - } - else if (KIM_SupportStatus_Equal(kim_model_support_for_forces, - KIM_SUPPORT_STATUS_notSupported) - && - (vflag_atom == 1) && - KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, - KIM_SUPPORT_STATUS_notSupported)) - { - double *va=&(vatom[0][0]); - for (i = first; i < last; i++) - { - buf[m++] = va[6*i+0]; - buf[m++] = va[6*i+1]; - buf[m++] = va[6*i+2]; - buf[m++] = va[6*i+3]; - buf[m++] = va[6*i+4]; - buf[m++] = va[6*i+5]; - } - return m; - } - else - return 0; + int i,m,last; + double *fp; + fp = &(atom->f[0][0]); + + m = 0; + last = first + n; + if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces, + KIM_SUPPORT_STATUS_notSupported) + && + ((vflag_atom == 0) || + KIM_SupportStatus_Equal(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported))) { + for (i = first; i < last; i++) { + buf[m++] = fp[3*i+0]; + buf[m++] = fp[3*i+1]; + buf[m++] = fp[3*i+2]; + } + return m; + } else if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces, + KIM_SUPPORT_STATUS_notSupported) && + (vflag_atom == 1) && + KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported)) { + double *va=&(vatom[0][0]); + for (i = first; i < last; i++) { + buf[m++] = fp[3*i+0]; + buf[m++] = fp[3*i+1]; + buf[m++] = fp[3*i+2]; + + buf[m++] = va[6*i+0]; + buf[m++] = va[6*i+1]; + buf[m++] = va[6*i+2]; + buf[m++] = va[6*i+3]; + buf[m++] = va[6*i+4]; + buf[m++] = va[6*i+5]; + } + return m; + } else if (KIM_SupportStatus_Equal(kim_model_support_for_forces, + KIM_SUPPORT_STATUS_notSupported) + && + (vflag_atom == 1) && + KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported)) { + double *va=&(vatom[0][0]); + for (i = first; i < last; i++) { + buf[m++] = va[6*i+0]; + buf[m++] = va[6*i+1]; + buf[m++] = va[6*i+2]; + buf[m++] = va[6*i+3]; + buf[m++] = va[6*i+4]; + buf[m++] = va[6*i+5]; + } + return m; + } else return 0; } /* ---------------------------------------------------------------------- */ void PairKIM::unpack_reverse_comm(int n, int *list, double *buf) { - int i,j,m; - double *fp; - fp = &(atom->f[0][0]); - - m = 0; - if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces, - KIM_SUPPORT_STATUS_notSupported) - && - ((vflag_atom == 0) || - KIM_SupportStatus_Equal(kim_model_support_for_particleVirial, - KIM_SUPPORT_STATUS_notSupported))) - { - for (i = 0; i < n; i++) - { - j = list[i]; - fp[3*j+0]+= buf[m++]; - fp[3*j+1]+= buf[m++]; - fp[3*j+2]+= buf[m++]; - } - } - else if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces, - KIM_SUPPORT_STATUS_notSupported) - && - (vflag_atom == 1) && - KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, - KIM_SUPPORT_STATUS_notSupported)) - { - double *va=&(vatom[0][0]); - for (i = 0; i < n; i++) - { - j = list[i]; - fp[3*j+0]+= buf[m++]; - fp[3*j+1]+= buf[m++]; - fp[3*j+2]+= buf[m++]; - - va[j*6+0]+=buf[m++]; - va[j*6+1]+=buf[m++]; - va[j*6+2]+=buf[m++]; - va[j*6+3]+=buf[m++]; - va[j*6+4]+=buf[m++]; - va[j*6+5]+=buf[m++]; - } - } - else if (KIM_SupportStatus_Equal(kim_model_support_for_forces, - KIM_SUPPORT_STATUS_notSupported) - && - (vflag_atom == 1) && - KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, - KIM_SUPPORT_STATUS_notSupported)) - { - double *va=&(vatom[0][0]); - for (i = 0; i < n; i++) - { - j = list[i]; - va[j*6+0]+=buf[m++]; - va[j*6+1]+=buf[m++]; - va[j*6+2]+=buf[m++]; - va[j*6+3]+=buf[m++]; - va[j*6+4]+=buf[m++]; - va[j*6+5]+=buf[m++]; - } - } else { - ; // do nothing - } - - return; + int i,j,m; + double *fp; + fp = &(atom->f[0][0]); + + m = 0; + if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces, + KIM_SUPPORT_STATUS_notSupported) + && + ((vflag_atom == 0) || + KIM_SupportStatus_Equal(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported))) { + for (i = 0; i < n; i++) { + j = list[i]; + fp[3*j+0]+= buf[m++]; + fp[3*j+1]+= buf[m++]; + fp[3*j+2]+= buf[m++]; + } + } else if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces, + KIM_SUPPORT_STATUS_notSupported) + && + (vflag_atom == 1) && + KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported)) { + double *va=&(vatom[0][0]); + for (i = 0; i < n; i++) { + j = list[i]; + fp[3*j+0]+= buf[m++]; + fp[3*j+1]+= buf[m++]; + fp[3*j+2]+= buf[m++]; + + va[j*6+0]+=buf[m++]; + va[j*6+1]+=buf[m++]; + va[j*6+2]+=buf[m++]; + va[j*6+3]+=buf[m++]; + va[j*6+4]+=buf[m++]; + va[j*6+5]+=buf[m++]; + } + } else if (KIM_SupportStatus_Equal(kim_model_support_for_forces, + KIM_SUPPORT_STATUS_notSupported) + && + (vflag_atom == 1) && + KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported)) { + double *va=&(vatom[0][0]); + for (i = 0; i < n; i++) { + j = list[i]; + va[j*6+0]+=buf[m++]; + va[j*6+1]+=buf[m++]; + va[j*6+2]+=buf[m++]; + va[j*6+3]+=buf[m++]; + va[j*6+4]+=buf[m++]; + va[j*6+5]+=buf[m++]; + } + } else { + ; // do nothing + } } /* ---------------------------------------------------------------------- @@ -684,8 +625,8 @@ void PairKIM::unpack_reverse_comm(int n, int *list, double *buf) double PairKIM::memory_usage() { - double bytes = 2 * lmps_maxalloc * sizeof(int); - return bytes; + double bytes = 2 * lmps_maxalloc * sizeof(int); + return bytes; } /* ---------------------------------------------------------------------- @@ -695,142 +636,123 @@ double PairKIM::memory_usage() int PairKIM::get_neigh(void const * const dataObject, int const numberOfNeighborLists, double const * const cutoffs, - int const neighborListIndex, int const particleNumber, + int const neighborListIndex, + int const particleNumber, int * const numberOfNeighbors, int const ** const neighborsOfParticle) { - PairKIM const * const Model - = reinterpret_cast(dataObject); - - if (numberOfNeighborLists != Model->kim_number_of_neighbor_lists) - return true; - for (int i = 0; i < numberOfNeighborLists; ++i) - { - if (Model->kim_cutoff_values[i] < cutoffs[i]) return true; - } - - // neighborListIndex and particleNumber are validated by KIM API - - // initialize numNeigh - *numberOfNeighbors = 0; - - NeighList * neiobj = Model->neighborLists[neighborListIndex]; - - int *numneigh, **firstneigh; - numneigh = neiobj->numneigh; // # of J neighbors for each I atom - firstneigh = neiobj->firstneigh; // ptr to 1st J int value of each I atom - - *numberOfNeighbors = numneigh[particleNumber]; - - // strip off neighbor mask for molecular systems - if (!Model->lmps_using_molecular) - *neighborsOfParticle = firstneigh[particleNumber]; - else - { - int n = *numberOfNeighbors; - int *ptr = firstneigh[particleNumber]; - int *lmps_stripped_neigh_list - = Model->lmps_stripped_neigh_ptr[neighborListIndex]; - for (int i = 0; i < n; i++) - lmps_stripped_neigh_list[i] = *(ptr++) & NEIGHMASK; - *neighborsOfParticle = lmps_stripped_neigh_list; - } - return false; + PairKIM const * const Model + = reinterpret_cast(dataObject); + + if (numberOfNeighborLists != Model->kim_number_of_neighbor_lists) + return true; + for (int i = 0; i < numberOfNeighborLists; ++i) { + if (Model->kim_cutoff_values[i] < cutoffs[i]) return true; + } + + // neighborListIndex and particleNumber are validated by KIM API + + // initialize numNeigh + *numberOfNeighbors = 0; + + NeighList * neiobj = Model->neighborLists[neighborListIndex]; + + int *numneigh, **firstneigh; + numneigh = neiobj->numneigh; // # of J neighbors for each I atom + firstneigh = neiobj->firstneigh; // ptr to 1st J int value of each I atom + + *numberOfNeighbors = numneigh[particleNumber]; + + // strip off neighbor mask for molecular systems + if (!Model->lmps_using_molecular) + *neighborsOfParticle = firstneigh[particleNumber]; + else { + int n = *numberOfNeighbors; + int *ptr = firstneigh[particleNumber]; + int *lmps_stripped_neigh_list + = Model->lmps_stripped_neigh_ptr[neighborListIndex]; + for (int i = 0; i < n; i++) + lmps_stripped_neigh_list[i] = *(ptr++) & NEIGHMASK; + *neighborsOfParticle = lmps_stripped_neigh_list; + } + return false; } /* ---------------------------------------------------------------------- */ void PairKIM::kim_free() { - if (kim_init_ok) - { - int kimerror = KIM_Model_ComputeArgumentsDestroy(pkim, &pargs); - if (kimerror) - error->all(FLERR,"Unable to destroy Compute Arguments Object"); + if (kim_init_ok) { + int kimerror = KIM_Model_ComputeArgumentsDestroy(pkim, &pargs); + if (kimerror) + error->all(FLERR,"Unable to destroy Compute Arguments Object"); - KIM_Model_Destroy(&pkim); - } - kim_init_ok = false; - - return; + KIM_Model_Destroy(&pkim); + } + kim_init_ok = false; } /* ---------------------------------------------------------------------- */ void PairKIM::kim_init() { - int kimerror; - - // initialize KIM model - int requestedUnitsAccepted; - kimerror = KIM_Model_Create( - KIM_NUMBERING_zeroBased, - lengthUnit, energyUnit, chargeUnit, temperatureUnit, timeUnit, - kim_modelname, - &requestedUnitsAccepted, - &pkim); - if (kimerror) - error->all(FLERR,"KIM ModelCreate failed"); - else { - if (!requestedUnitsAccepted) { - error->all(FLERR,"KIM Model did not accept the requested unit system"); - } - - // check that the model does not require unknown capabilities - kimerror = check_for_routine_compatibility(); - if (kimerror) - { - error->all(FLERR, - "KIM Model requires unknown Routines. Unable to proceed."); - } - - kimerror = KIM_Model_ComputeArgumentsCreate(pkim, &pargs); - if (kimerror) - { - KIM_Model_Destroy(&pkim); - error->all(FLERR,"KIM ComputeArgumentsCreate failed"); - } - else - { - kim_init_ok = true; - } - } - - // determine KIM Model capabilities (used in this function below) - set_kim_model_has_flags(); - - KIM_Model_GetInfluenceDistance(pkim, &kim_global_influence_distance); - KIM_Model_GetNeighborListPointers( - pkim, - &kim_number_of_neighbor_lists, - &kim_cutoff_values, - &modelWillNotRequestNeighborsOfNoncontributingParticles); - if (neighborLists) - { - delete [] neighborLists; - neighborLists = 0; - } - neighborLists = new NeighList*[kim_number_of_neighbor_lists]; - - kimerror = KIM_ComputeArguments_SetArgumentPointerInteger(pargs, - KIM_COMPUTE_ARGUMENT_NAME_numberOfParticles, - &lmps_local_tot_num_atoms); - if (KIM_SupportStatus_NotEqual(kim_model_support_for_energy, - KIM_SUPPORT_STATUS_notSupported)) - kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble(pargs, - KIM_COMPUTE_ARGUMENT_NAME_partialEnergy, - &(eng_vdwl)); - - kimerror = KIM_ComputeArguments_SetCallbackPointer(pargs, - KIM_COMPUTE_CALLBACK_NAME_GetNeighborList, - KIM_LANGUAGE_NAME_cpp, - reinterpret_cast(get_neigh), - reinterpret_cast(this)); - - if (kimerror) - error->all(FLERR,"Unable to register KIM pointers"); - - return; + int kimerror; + + // initialize KIM model + int requestedUnitsAccepted; + kimerror = KIM_Model_Create( + KIM_NUMBERING_zeroBased, + lengthUnit, energyUnit, chargeUnit, temperatureUnit, timeUnit, + kim_modelname, + &requestedUnitsAccepted, + &pkim); + if (kimerror) error->all(FLERR,"KIM ModelCreate failed"); + else if (!requestedUnitsAccepted) + error->all(FLERR,"KIM Model did not accept the requested unit system"); + + // check that the model does not require unknown capabilities + kimerror = check_for_routine_compatibility(); + if (kimerror) + error->all(FLERR, + "KIM Model requires unknown Routines. Unable to proceed."); + + kimerror = KIM_Model_ComputeArgumentsCreate(pkim, &pargs); + if (kimerror) { + KIM_Model_Destroy(&pkim); + error->all(FLERR,"KIM ComputeArgumentsCreate failed"); + } else kim_init_ok = true; + + // determine KIM Model capabilities (used in this function below) + set_kim_model_has_flags(); + + KIM_Model_GetInfluenceDistance(pkim, &kim_global_influence_distance); + KIM_Model_GetNeighborListPointers( + pkim, + &kim_number_of_neighbor_lists, + &kim_cutoff_values, + &modelWillNotRequestNeighborsOfNoncontributingParticles); + if (neighborLists) { + delete [] neighborLists; + neighborLists = 0; + } + neighborLists = new NeighList*[kim_number_of_neighbor_lists]; + + kimerror = KIM_ComputeArguments_SetArgumentPointerInteger(pargs, + KIM_COMPUTE_ARGUMENT_NAME_numberOfParticles, + &lmps_local_tot_num_atoms); + if (KIM_SupportStatus_NotEqual(kim_model_support_for_energy, + KIM_SUPPORT_STATUS_notSupported)) + kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble(pargs, + KIM_COMPUTE_ARGUMENT_NAME_partialEnergy, + &(eng_vdwl)); + + kimerror = KIM_ComputeArguments_SetCallbackPointer(pargs, + KIM_COMPUTE_CALLBACK_NAME_GetNeighborList, + KIM_LANGUAGE_NAME_cpp, + reinterpret_cast(get_neigh), + reinterpret_cast(this)); + + if (kimerror) error->all(FLERR,"Unable to register KIM pointers"); } /* ---------------------------------------------------------------------- */ @@ -839,16 +761,14 @@ void PairKIM::set_argument_pointers() { int kimerror; kimerror = KIM_ComputeArguments_SetArgumentPointerDouble( - pargs, KIM_COMPUTE_ARGUMENT_NAME_coordinates, &(atom->x[0][0])); + pargs, KIM_COMPUTE_ARGUMENT_NAME_coordinates, &(atom->x[0][0])); // Set KIM pointer appropriately for particalEnergy if (KIM_SupportStatus_Equal(kim_model_support_for_particleEnergy, KIM_SUPPORT_STATUS_required) - && (eflag_atom != 1)) - { + && (eflag_atom != 1)) { // reallocate per-atom energy array if necessary - if (atom->nmax > maxeatom) - { + if (atom->nmax > maxeatom) { maxeatom = atom->nmax; memory->destroy(eatom); memory->create(eatom,comm->nthreads*maxeatom,"pair:eatom"); @@ -856,31 +776,25 @@ void PairKIM::set_argument_pointers() } if (KIM_SupportStatus_Equal(kim_model_support_for_particleEnergy, KIM_SUPPORT_STATUS_optional) - && (eflag_atom != 1)) - { + && (eflag_atom != 1)) { kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble( - pargs, - KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy, - reinterpret_cast(NULL)); - } - else if (KIM_SupportStatus_NotEqual(kim_model_support_for_particleEnergy, - KIM_SUPPORT_STATUS_notSupported)) - { + pargs, + KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy, + reinterpret_cast(NULL)); + } else if (KIM_SupportStatus_NotEqual(kim_model_support_for_particleEnergy, + KIM_SUPPORT_STATUS_notSupported)) { kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble( pargs, KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy, eatom); } // Set KIM pointer appropriately for forces if (KIM_SupportStatus_Equal(kim_model_support_for_forces, - KIM_SUPPORT_STATUS_notSupported)) - { + KIM_SUPPORT_STATUS_notSupported)) { kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble( - pargs, - KIM_COMPUTE_ARGUMENT_NAME_partialForces, - reinterpret_cast(NULL)); - } - else - { + pargs, + KIM_COMPUTE_ARGUMENT_NAME_partialForces, + reinterpret_cast(NULL)); + } else { kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble( pargs, KIM_COMPUTE_ARGUMENT_NAME_partialForces, &(atom->f[0][0])); } @@ -888,11 +802,9 @@ void PairKIM::set_argument_pointers() // Set KIM pointer appropriately for particleVirial if (KIM_SupportStatus_Equal(kim_model_support_for_particleVirial, KIM_SUPPORT_STATUS_required) - && (vflag_atom != 1)) - { + && (vflag_atom != 1)) { // reallocate per-atom virial array if necessary - if (atom->nmax > maxeatom) - { + if (atom->nmax > maxeatom) { maxvatom = atom->nmax; memory->destroy(vatom); memory->create(vatom,comm->nthreads*maxvatom,6,"pair:vatom"); @@ -900,84 +812,72 @@ void PairKIM::set_argument_pointers() } if (KIM_SupportStatus_Equal(kim_model_support_for_particleVirial, KIM_SUPPORT_STATUS_optional) - && (vflag_atom != 1)) - { + && (vflag_atom != 1)) { kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble( - pargs, - KIM_COMPUTE_ARGUMENT_NAME_partialParticleVirial, - reinterpret_cast(NULL)); - } - else if (KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, - KIM_SUPPORT_STATUS_notSupported)) - { + pargs, + KIM_COMPUTE_ARGUMENT_NAME_partialParticleVirial, + reinterpret_cast(NULL)); + } else if (KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported)) { kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble( - pargs, KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy, &(vatom[0][0])); - } - - if (kimerror) - { - error->all(FLERR,"Unable to set KIM argument pointers"); + pargs, KIM_COMPUTE_ARGUMENT_NAME_partialParticleVirial, &(vatom[0][0])); } - return; + if (kimerror) error->all(FLERR,"Unable to set KIM argument pointers"); } /* ---------------------------------------------------------------------- */ void PairKIM::set_lmps_flags() { - // determint if newton is on or off - lmps_using_newton = (force->newton_pair == 1); - - // determine if running with pair hybrid - if (force->pair_match("hybrid",0)) - { - error->all(FLERR,"pair_kim does not support hybrid"); - } - - // determine unit system and set lmps_units flag - if ((strcmp(update->unit_style,"real")==0)) { - lmps_units = REAL; - lengthUnit = KIM_LENGTH_UNIT_A; - energyUnit = KIM_ENERGY_UNIT_kcal_mol; - chargeUnit = KIM_CHARGE_UNIT_e; - temperatureUnit = KIM_TEMPERATURE_UNIT_K; - timeUnit = KIM_TIME_UNIT_fs; - } else if ((strcmp(update->unit_style,"metal")==0)) { - lmps_units = METAL; - lengthUnit = KIM_LENGTH_UNIT_A; - energyUnit = KIM_ENERGY_UNIT_eV; - chargeUnit = KIM_CHARGE_UNIT_e; - temperatureUnit = KIM_TEMPERATURE_UNIT_K; - timeUnit = KIM_TIME_UNIT_ps; - } else if ((strcmp(update->unit_style,"si")==0)) { - lmps_units = SI; - lengthUnit = KIM_LENGTH_UNIT_m; - energyUnit = KIM_ENERGY_UNIT_J; - chargeUnit = KIM_CHARGE_UNIT_C; - temperatureUnit = KIM_TEMPERATURE_UNIT_K; - timeUnit = KIM_TIME_UNIT_s; - } else if ((strcmp(update->unit_style,"cgs")==0)) { - lmps_units = CGS; - lengthUnit = KIM_LENGTH_UNIT_cm; - energyUnit = KIM_ENERGY_UNIT_erg; - chargeUnit = KIM_CHARGE_UNIT_statC; - temperatureUnit = KIM_TEMPERATURE_UNIT_K; - timeUnit = KIM_TIME_UNIT_s; - } else if ((strcmp(update->unit_style,"electron")==0)) { - lmps_units = ELECTRON; - lengthUnit = KIM_LENGTH_UNIT_Bohr; - energyUnit = KIM_ENERGY_UNIT_Hartree; - chargeUnit = KIM_CHARGE_UNIT_e; - temperatureUnit = KIM_TEMPERATURE_UNIT_K; - timeUnit = KIM_TIME_UNIT_fs; - } else if ((strcmp(update->unit_style,"lj")==0)) { - error->all(FLERR,"LAMMPS unit_style lj not supported by KIM models"); - } else { - error->all(FLERR,"Unknown unit_style"); - } - - return; + // determint if newton is on or off + lmps_using_newton = (force->newton_pair == 1); + + // determine if running with pair hybrid + if (force->pair_match("hybrid",0)) + error->all(FLERR,"pair_kim does not support hybrid"); + + // determine unit system and set lmps_units flag + if ((strcmp(update->unit_style,"real")==0)) { + lmps_units = REAL; + lengthUnit = KIM_LENGTH_UNIT_A; + energyUnit = KIM_ENERGY_UNIT_kcal_mol; + chargeUnit = KIM_CHARGE_UNIT_e; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_fs; + } else if ((strcmp(update->unit_style,"metal")==0)) { + lmps_units = METAL; + lengthUnit = KIM_LENGTH_UNIT_A; + energyUnit = KIM_ENERGY_UNIT_eV; + chargeUnit = KIM_CHARGE_UNIT_e; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_ps; + } else if ((strcmp(update->unit_style,"si")==0)) { + lmps_units = SI; + lengthUnit = KIM_LENGTH_UNIT_m; + energyUnit = KIM_ENERGY_UNIT_J; + chargeUnit = KIM_CHARGE_UNIT_C; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_s; + } else if ((strcmp(update->unit_style,"cgs")==0)) { + lmps_units = CGS; + lengthUnit = KIM_LENGTH_UNIT_cm; + energyUnit = KIM_ENERGY_UNIT_erg; + chargeUnit = KIM_CHARGE_UNIT_statC; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_s; + } else if ((strcmp(update->unit_style,"electron")==0)) { + lmps_units = ELECTRON; + lengthUnit = KIM_LENGTH_UNIT_Bohr; + energyUnit = KIM_ENERGY_UNIT_Hartree; + chargeUnit = KIM_CHARGE_UNIT_e; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_fs; + } else if ((strcmp(update->unit_style,"lj")==0)) { + error->all(FLERR,"LAMMPS unit_style lj not supported by KIM models"); + } else { + error->all(FLERR,"Unknown unit_style"); + } } /* ---------------------------------------------------------------------- */ @@ -988,8 +888,7 @@ int PairKIM::check_for_routine_compatibility() int numberOfModelRoutineNames; KIM_MODEL_ROUTINE_NAME_GetNumberOfModelRoutineNames( &numberOfModelRoutineNames); - for (int i = 0; i < numberOfModelRoutineNames; ++i) - { + for (int i = 0; i < numberOfModelRoutineNames; ++i) { KIM_ModelRoutineName modelRoutineName; KIM_MODEL_ROUTINE_NAME_GetModelRoutineName(i, &modelRoutineName); @@ -997,10 +896,9 @@ int PairKIM::check_for_routine_compatibility() int required; int error = KIM_Model_IsRoutinePresent( pkim, modelRoutineName, &present, &required); - if (error) { return true; } + if (error) return true; - if ((present == true) && (required == true)) - { + if ((present == true) && (required == true)) { if (!(KIM_ModelRoutineName_Equal(modelRoutineName, KIM_MODEL_ROUTINE_NAME_Create) || KIM_ModelRoutineName_Equal( @@ -1014,8 +912,9 @@ int PairKIM::check_for_routine_compatibility() modelRoutineName, KIM_MODEL_ROUTINE_NAME_ComputeArgumentsDestroy) || KIM_ModelRoutineName_Equal(modelRoutineName, - KIM_MODEL_ROUTINE_NAME_Destroy))) - { return true; } + KIM_MODEL_ROUTINE_NAME_Destroy))) { + return true; + } } } @@ -1030,8 +929,7 @@ void PairKIM::set_kim_model_has_flags() int numberOfComputeArgumentNames; KIM_COMPUTE_ARGUMENT_NAME_GetNumberOfComputeArgumentNames( &numberOfComputeArgumentNames); - for (int i = 0; i < numberOfComputeArgumentNames; ++i) - { + for (int i = 0; i < numberOfComputeArgumentNames; ++i) { KIM_ComputeArgumentName computeArgumentName; KIM_COMPUTE_ARGUMENT_NAME_GetComputeArgumentName( i, &computeArgumentName); @@ -1040,32 +938,24 @@ void PairKIM::set_kim_model_has_flags() pargs, computeArgumentName, &supportStatus); if (KIM_ComputeArgumentName_Equal(computeArgumentName, - KIM_COMPUTE_ARGUMENT_NAME_partialEnergy) - ) + KIM_COMPUTE_ARGUMENT_NAME_partialEnergy)) kim_model_support_for_energy = supportStatus; else if (KIM_ComputeArgumentName_Equal( - computeArgumentName, KIM_COMPUTE_ARGUMENT_NAME_partialForces) - ) + computeArgumentName, KIM_COMPUTE_ARGUMENT_NAME_partialForces)) kim_model_support_for_forces = supportStatus; - else if - (KIM_ComputeArgumentName_Equal( - computeArgumentName, - KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy)\ - ) + else if (KIM_ComputeArgumentName_Equal( + computeArgumentName, + KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy)) kim_model_support_for_particleEnergy = supportStatus; - else if - (KIM_ComputeArgumentName_Equal( - computeArgumentName, - KIM_COMPUTE_ARGUMENT_NAME_partialParticleVirial) - ) + else if (KIM_ComputeArgumentName_Equal( + computeArgumentName, + KIM_COMPUTE_ARGUMENT_NAME_partialParticleVirial)) kim_model_support_for_particleVirial = supportStatus; - else if (KIM_SupportStatus_Equal(supportStatus, KIM_SUPPORT_STATUS_required) - ) - { - std::stringstream msg; - msg << "KIM Model requires unsupported compute argument: " - << KIM_ComputeArgumentName_ToString(computeArgumentName); - error->all(FLERR, msg.str().c_str()); + else if (KIM_SupportStatus_Equal(supportStatus, + KIM_SUPPORT_STATUS_required)) { + std::string msg("KIM Model requires unsupported compute argument: "); + msg += KIM_ComputeArgumentName_ToString(computeArgumentName); + error->all(FLERR, msg.c_str()); } } @@ -1092,20 +982,15 @@ void PairKIM::set_kim_model_has_flags() int numberOfComputeCallbackNames; KIM_COMPUTE_CALLBACK_NAME_GetNumberOfComputeCallbackNames( &numberOfComputeCallbackNames); - for (int i = 0; i < numberOfComputeCallbackNames; ++i) - { + for (int i = 0; i < numberOfComputeCallbackNames; ++i) { KIM_ComputeCallbackName computeCallbackName; - KIM_COMPUTE_CALLBACK_NAME_GetComputeCallbackName( - i, &computeCallbackName); + KIM_COMPUTE_CALLBACK_NAME_GetComputeCallbackName(i, &computeCallbackName); KIM_SupportStatus supportStatus; - KIM_ComputeArguments_GetCallbackSupportStatus( - pargs, computeCallbackName, &supportStatus); + KIM_ComputeArguments_GetCallbackSupportStatus(pargs, + computeCallbackName, + &supportStatus); if (KIM_SupportStatus_Equal(supportStatus, KIM_SUPPORT_STATUS_required)) - { error->all(FLERR,"KIM Model requires unsupported compute callback"); - } } - - return; } diff --git a/src/KIM/pair_kim.h b/src/KIM/pair_kim.h index 27bab6c687457a88df134898c8cf86933290d29a..aa33b9b27185e27e1025a55f0cdbd02f39c9f6d5 100644 --- a/src/KIM/pair_kim.h +++ b/src/KIM/pair_kim.h @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing authors: Ryan S. Elliott (UMinn) + Contributing authors: Ryan S. Elliott (UMinn), Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- @@ -65,108 +65,107 @@ PairStyle(kim,PairKIM) // includes from KIM & LAMMPS class KIM_API_model; #include "pair.h" + extern "C" { #include "KIM_SimulatorHeaders.h" } -#include - namespace LAMMPS_NS { - class PairKIM : public Pair { - public: - PairKIM(class LAMMPS*); - ~PairKIM(); - - // LAMMPS Pair class virtual function prototypes - virtual void compute(int, int); - virtual void settings(int, char**); - virtual void coeff(int, char**); - virtual void init_style(); - virtual void init_list(int id, NeighList *ptr); - virtual double init_one(int, int); - virtual int pack_reverse_comm(int, int, double*); - virtual void unpack_reverse_comm(int, int*, double*); - virtual double memory_usage(); - - protected: - // (nearly) all bool flags are not initialized in constructor, but set - // explicitly in the indicated function. All other data members are - // initialized in constructor - int settings_call_count; - int init_style_call_count; - - // values set in settings() - char* kim_modelname; - - // values set in coeff() - - // values set in allocate(), called by coeff() - virtual void allocate(); - int* lmps_map_species_to_unique; - - // values set in coeff(), after calling allocate() - char** lmps_unique_elements; // names of unique elements given - // in pair_coeff command - int lmps_num_unique_elements; - - // values set in set_lmps_flags(), called from init_style() - bool lmps_using_newton; - bool lmps_using_molecular; - enum unit_sys {REAL, METAL, SI, CGS, ELECTRON}; - unit_sys lmps_units; - KIM_LengthUnit lengthUnit; - KIM_EnergyUnit energyUnit; - KIM_ChargeUnit chargeUnit; - KIM_TemperatureUnit temperatureUnit; - KIM_TimeUnit timeUnit; - - KIM_Model * pkim; - KIM_ComputeArguments * pargs; - - // values set in set_kim_model_has_flags(), called by kim_init() - KIM_SupportStatus kim_model_support_for_energy; - KIM_SupportStatus kim_model_support_for_forces; - KIM_SupportStatus kim_model_support_for_particleEnergy; - KIM_SupportStatus kim_model_support_for_particleVirial; - - // values set in kim_init() - bool kim_init_ok; - int lmps_local_tot_num_atoms; - double kim_global_influence_distance; // KIM Model cutoff value - int kim_number_of_neighbor_lists; - double const * kim_cutoff_values; - int const * modelWillNotRequestNeighborsOfNoncontributingParticles; - class NeighList ** neighborLists; - - // values set in init_style() - bool kim_particle_codes_ok; - int *kim_particle_codes; - - // values set in compute() - int lmps_maxalloc; // max allocated memory value - int* kim_particleSpecies; // array of KIM particle species - int* kim_particleContributing; // array of KIM particle contributing - int* lmps_stripped_neigh_list; // neighbors of one atom, used when LAMMPS - // is in molecular mode - int** lmps_stripped_neigh_ptr; // pointer into lists - - // KIM specific helper functions - virtual void set_contributing(); - virtual void kim_init(); - virtual void kim_free(); - virtual void set_argument_pointers(); - virtual void set_lmps_flags(); - virtual void set_kim_model_has_flags(); - virtual int check_for_routine_compatibility(); - // static methods used as callbacks from KIM - static int get_neigh( - void const * const dataObject, - int const numberOfCutoffs, double const * const cutoffs, - int const neighborListIndex, int const particleNumber, - int * const numberOfNeighbors, - int const ** const neighborsOfParticle); - }; +class PairKIM : public Pair { + public: + PairKIM(class LAMMPS*); + ~PairKIM(); + + // LAMMPS Pair class virtual function prototypes + virtual void compute(int, int); + virtual void settings(int, char**); + virtual void coeff(int, char**); + virtual void init_style(); + virtual void init_list(int id, NeighList *ptr); + virtual double init_one(int, int); + virtual int pack_reverse_comm(int, int, double*); + virtual void unpack_reverse_comm(int, int*, double*); + virtual double memory_usage(); + + protected: + // (nearly) all bool flags are not initialized in constructor, but set + // explicitly in the indicated function. All other data members are + // initialized in constructor + int settings_call_count; + int init_style_call_count; + + // values set in settings() + char* kim_modelname; + + // values set in coeff() + + // values set in allocate(), called by coeff() + virtual void allocate(); + int* lmps_map_species_to_unique; + + // values set in coeff(), after calling allocate() + char** lmps_unique_elements; // names of unique elements given + // in pair_coeff command + int lmps_num_unique_elements; + + // values set in set_lmps_flags(), called from init_style() + bool lmps_using_newton; + bool lmps_using_molecular; + enum unit_sys {REAL, METAL, SI, CGS, ELECTRON}; + unit_sys lmps_units; + KIM_LengthUnit lengthUnit; + KIM_EnergyUnit energyUnit; + KIM_ChargeUnit chargeUnit; + KIM_TemperatureUnit temperatureUnit; + KIM_TimeUnit timeUnit; + + KIM_Model * pkim; + KIM_ComputeArguments * pargs; + + // values set in set_kim_model_has_flags(), called by kim_init() + KIM_SupportStatus kim_model_support_for_energy; + KIM_SupportStatus kim_model_support_for_forces; + KIM_SupportStatus kim_model_support_for_particleEnergy; + KIM_SupportStatus kim_model_support_for_particleVirial; + + // values set in kim_init() + bool kim_init_ok; + int lmps_local_tot_num_atoms; + double kim_global_influence_distance; // KIM Model cutoff value + int kim_number_of_neighbor_lists; + double const * kim_cutoff_values; + int const * modelWillNotRequestNeighborsOfNoncontributingParticles; + class NeighList ** neighborLists; + + // values set in init_style() + bool kim_particle_codes_ok; + int *kim_particle_codes; + + // values set in compute() + int lmps_maxalloc; // max allocated memory value + int* kim_particleSpecies; // array of KIM particle species + int* kim_particleContributing; // array of KIM particle contributing + int* lmps_stripped_neigh_list; // neighbors of one atom, used when LAMMPS + // is in molecular mode + int** lmps_stripped_neigh_ptr; // pointer into lists + + // KIM specific helper functions + virtual void set_contributing(); + virtual void kim_init(); + virtual void kim_free(); + virtual void set_argument_pointers(); + virtual void set_lmps_flags(); + virtual void set_kim_model_has_flags(); + virtual int check_for_routine_compatibility(); + // static methods used as callbacks from KIM + static int get_neigh( + void const * const dataObject, + int const numberOfCutoffs, double const * const cutoffs, + int const neighborListIndex, int const particleNumber, + int * const numberOfNeighbors, + int const ** const neighborsOfParticle); +}; } #endif @@ -184,7 +183,10 @@ The KIM model was unable, for some reason, to complete the computation. E: 'KIMvirial' or 'LAMMPSvirial' not supported with kim-api. -"KIMvirial or "LAMMPSvirial" found on the pair_style line. These keys are not supported kim-api. (The virial computation is always performed by LAMMPS.) Please remove these keys, make sure the KIM model you are using supports kim-api, and rerun. +"KIMvirial or "LAMMPSvirial" found on the pair_style line. These keys +are not supported kim-api. (The virial computation is always performed +by LAMMPS.) Please remove these keys, make sure the KIM model you are +using supports kim-api, and rerun. E: Illegal pair_style command diff --git a/src/KOKKOS/angle_charmm_kokkos.cpp b/src/KOKKOS/angle_charmm_kokkos.cpp index 0f46c958d6f62654789a7fc6423fe9f5ce4971bd..fd9757aab38c9c923f743ac33314499125f38f66 100644 --- a/src/KOKKOS/angle_charmm_kokkos.cpp +++ b/src/KOKKOS/angle_charmm_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "angle_charmm_kokkos.h" #include #include -#include "angle_charmm_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/angle_class2_kokkos.cpp b/src/KOKKOS/angle_class2_kokkos.cpp index 836714764d2177a123ee4d9b9989405bc2b6c953..809ce7e7dd128bbf63b29b1c755d7026cdf299c8 100644 --- a/src/KOKKOS/angle_class2_kokkos.cpp +++ b/src/KOKKOS/angle_class2_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Ray Shan (Materials Design) ------------------------------------------------------------------------- */ +#include "angle_class2_kokkos.h" #include #include -#include "angle_class2_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/angle_cosine_kokkos.cpp b/src/KOKKOS/angle_cosine_kokkos.cpp index 4a4866948f2979ef287a265ec6226997b59640f5..da0ff398f19b2a94ad901a679bf407bff5bdfb4f 100644 --- a/src/KOKKOS/angle_cosine_kokkos.cpp +++ b/src/KOKKOS/angle_cosine_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "angle_cosine_kokkos.h" #include #include -#include "angle_cosine_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/angle_harmonic_kokkos.cpp b/src/KOKKOS/angle_harmonic_kokkos.cpp index dbe705800c4d9dcafaecdd722aa236a6bd792210..fc274bb89400d97437d82b49ee2a420358feba15 100644 --- a/src/KOKKOS/angle_harmonic_kokkos.cpp +++ b/src/KOKKOS/angle_harmonic_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "angle_harmonic_kokkos.h" #include #include -#include "angle_harmonic_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/atom_kokkos.cpp b/src/KOKKOS/atom_kokkos.cpp index 813c5ddbf26f4f63829a8c51b2115e21256b9737..4637a9a21cc42bd3aec9872bf29d915cdf060d2c 100644 --- a/src/KOKKOS/atom_kokkos.cpp +++ b/src/KOKKOS/atom_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_kokkos.h" +#include #include "atom_vec.h" #include "atom_vec_kokkos.h" #include "comm_kokkos.h" diff --git a/src/KOKKOS/atom_vec_angle_kokkos.cpp b/src/KOKKOS/atom_vec_angle_kokkos.cpp index 06358289b657c6c7fd7eb12bbada975712cf8f43..736e1c1fca434846f337bfc96c5e8a95a2d1eecd 100644 --- a/src/KOKKOS/atom_vec_angle_kokkos.cpp +++ b/src/KOKKOS/atom_vec_angle_kokkos.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_angle_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.cpp b/src/KOKKOS/atom_vec_atomic_kokkos.cpp index 6e530bdbe90d55d4af60d229c4286889bcc60e7f..4fec5740d66d3bc83d54669dd22b64b5ede79178 100644 --- a/src/KOKKOS/atom_vec_atomic_kokkos.cpp +++ b/src/KOKKOS/atom_vec_atomic_kokkos.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_atomic_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp index 3195ea0876227c739aee5f34136b6c3c9109fe1b..74c05a506ca7c37c7605c53126f24def46f8c748 100644 --- a/src/KOKKOS/atom_vec_bond_kokkos.cpp +++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_bond_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_charge_kokkos.cpp b/src/KOKKOS/atom_vec_charge_kokkos.cpp index 77d0c1dae3b8f2b1ff703a7bdec6f8fbfd04b163..3f26b1e9ea4f3504bef56b6743e9e31f4336f025 100644 --- a/src/KOKKOS/atom_vec_charge_kokkos.cpp +++ b/src/KOKKOS/atom_vec_charge_kokkos.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_charge_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp index 317914e4f85ece3ffe642fee6591477ebcc7c67f..144ef26f198b4033a55684917faf8183bcac04f0 100644 --- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp +++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_dpd_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_full_kokkos.cpp b/src/KOKKOS/atom_vec_full_kokkos.cpp index 19443b231f8861c3801fca2fa48480a562c84ab1..1fdbcbec8c9378e2bc3f91145db340d5cba0fa82 100644 --- a/src/KOKKOS/atom_vec_full_kokkos.cpp +++ b/src/KOKKOS/atom_vec_full_kokkos.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_full_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp index c4dd90ce05f581df275be6f988a73ac8b2d595c0..40303051b27f18850dc10ecc734e7e3de48d56a4 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "atom_vec_hybrid_kokkos.h" +#include #include "atom_kokkos.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory_kokkos.h" diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.h b/src/KOKKOS/atom_vec_hybrid_kokkos.h index 1bbbd26319af9da9a7c90de4600d78fefe63f6c6..4cfb186b175d95f856895e3bf5da53fb2b6c302b 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.h +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.h @@ -20,7 +20,6 @@ AtomStyle(hybrid/kk,AtomVecHybridKokkos) #ifndef LMP_ATOM_VEC_HYBRID_KOKKOS_H #define LMP_ATOM_VEC_HYBRID_KOKKOS_H -#include #include "atom_vec_kokkos.h" #include "kokkos_type.h" diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.cpp b/src/KOKKOS/atom_vec_molecular_kokkos.cpp index 9871b1247a95e25616f8b47599e3c6f49fece3e5..f3b4ae98ca3da31484602340f1aa35a51bfc4ffd 100644 --- a/src/KOKKOS/atom_vec_molecular_kokkos.cpp +++ b/src/KOKKOS/atom_vec_molecular_kokkos.cpp @@ -11,14 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_molecular_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" #include "modify.h" #include "fix.h" -#include "force.h" #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp index 3b64ceeb42e4176f0d4f7e96fa79e17b74d896e3..7e217df2a622e2df9e892c86ca2a47388d004550 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -11,16 +11,14 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "atom_vec_sphere_kokkos.h" #include -#include #include -#include "atom_vec_sphere_kokkos.h" #include "atom_kokkos.h" #include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" #include "fix_adapt.h" #include "math_const.h" diff --git a/src/KOKKOS/bond_class2_kokkos.cpp b/src/KOKKOS/bond_class2_kokkos.cpp index 798fb41c920544a3674f5b5def85d4b044acf32b..04281bfdd2f27792d3064d285834ea5658d8df59 100644 --- a/src/KOKKOS/bond_class2_kokkos.cpp +++ b/src/KOKKOS/bond_class2_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Ray Shan (Materials Design) ------------------------------------------------------------------------- */ +#include "bond_class2_kokkos.h" #include #include -#include "bond_class2_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/bond_fene_kokkos.cpp b/src/KOKKOS/bond_fene_kokkos.cpp index b5cdc1a05a5042d9197ba95001cfa4d29ecb2c6a..361bb61f7e05312a5a8e56f139ad4aef0d5449ec 100644 --- a/src/KOKKOS/bond_fene_kokkos.cpp +++ b/src/KOKKOS/bond_fene_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "bond_fene_kokkos.h" #include #include -#include "bond_fene_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/bond_harmonic_kokkos.cpp b/src/KOKKOS/bond_harmonic_kokkos.cpp index 51a9fa4389dcbbc98d470f8d56b9d41d392aa7a5..792d98fe88d2d968084f213320b297eb2b5c7279 100644 --- a/src/KOKKOS/bond_harmonic_kokkos.cpp +++ b/src/KOKKOS/bond_harmonic_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "bond_harmonic_kokkos.h" #include #include -#include "bond_harmonic_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/comm_tiled_kokkos.cpp b/src/KOKKOS/comm_tiled_kokkos.cpp index 81cf1f0563ac799f801a2937afa481227c7d63c4..fc6de0a0d7d08895e80d7d57bc09b5255654fab2 100644 --- a/src/KOKKOS/comm_tiled_kokkos.cpp +++ b/src/KOKKOS/comm_tiled_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "comm_tiled_kokkos.h" +#include #include "comm_brick.h" #include "atom_kokkos.h" #include "atom_vec.h" diff --git a/src/KOKKOS/compute_temp_kokkos.cpp b/src/KOKKOS/compute_temp_kokkos.cpp index 7b76f54f5763a5db388e00226cc1adb8a652ac84..a2fcf631259c94d3c30790b814a46980da7015ef 100644 --- a/src/KOKKOS/compute_temp_kokkos.cpp +++ b/src/KOKKOS/compute_temp_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_temp_kokkos.h" #include #include -#include "compute_temp_kokkos.h" #include "atom_kokkos.h" #include "update.h" #include "force.h" diff --git a/src/KOKKOS/dihedral_charmm_kokkos.cpp b/src/KOKKOS/dihedral_charmm_kokkos.cpp index 61ddcc425adc8a16d1107b03be374ac8d4e45dba..94fd0b9bb721d1e1451f8ca1541acb81fbb3b24b 100644 --- a/src/KOKKOS/dihedral_charmm_kokkos.cpp +++ b/src/KOKKOS/dihedral_charmm_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "dihedral_charmm_kokkos.h" #include #include -#include "dihedral_charmm_kokkos.h" #include "atom_kokkos.h" #include "comm.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/dihedral_class2_kokkos.cpp b/src/KOKKOS/dihedral_class2_kokkos.cpp index 98436bc696cdf595eb49b0e7c4c79fcfcb8051bf..4b8d171f618b85a9a567b515d1fb2c3d396db389 100644 --- a/src/KOKKOS/dihedral_class2_kokkos.cpp +++ b/src/KOKKOS/dihedral_class2_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Ray Shan (Materials Design) ------------------------------------------------------------------------- */ +#include "dihedral_class2_kokkos.h" #include #include -#include "dihedral_class2_kokkos.h" #include "atom_kokkos.h" #include "comm.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/dihedral_opls_kokkos.cpp b/src/KOKKOS/dihedral_opls_kokkos.cpp index f50dea2c369204345ab05dc1a37168fae733c7c1..825d106e04c347cfe192498dc7bc0266f974d0ac 100644 --- a/src/KOKKOS/dihedral_opls_kokkos.cpp +++ b/src/KOKKOS/dihedral_opls_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "dihedral_opls_kokkos.h" #include #include -#include "dihedral_opls_kokkos.h" #include "atom_kokkos.h" #include "comm.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/fix_deform_kokkos.cpp b/src/KOKKOS/fix_deform_kokkos.cpp index 7b9336ed3b03822e78cfa91b4e1e920be550a02d..05eb1c22f66a3af0545dacb94ad114732705a2b6 100644 --- a/src/KOKKOS/fix_deform_kokkos.cpp +++ b/src/KOKKOS/fix_deform_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "fix_deform_kokkos.h" #include #include #include -#include "fix_deform_kokkos.h" #include "atom_kokkos.h" #include "update.h" #include "comm.h" diff --git a/src/KOKKOS/fix_dpd_energy_kokkos.cpp b/src/KOKKOS/fix_dpd_energy_kokkos.cpp index d092cb4802c32ef7bcc3cfc06f955ee2d25dba61..20579a6dc5cd3c435e8f1d7910e99b4523f5a66e 100644 --- a/src/KOKKOS/fix_dpd_energy_kokkos.cpp +++ b/src/KOKKOS/fix_dpd_energy_kokkos.cpp @@ -11,15 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_dpd_energy_kokkos.h" #include "atom_masks.h" #include "atom_kokkos.h" -#include "force.h" #include "update.h" -#include "respa.h" -#include "modify.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/fix_enforce2d_kokkos.cpp b/src/KOKKOS/fix_enforce2d_kokkos.cpp index 346e440f5578f35abae9a2f249a14e4fc27b4ad2..bf2a882539fec55f14ab56e75d871647b1244a38 100644 --- a/src/KOKKOS/fix_enforce2d_kokkos.cpp +++ b/src/KOKKOS/fix_enforce2d_kokkos.cpp @@ -15,11 +15,11 @@ Contributing authors: Stefan Paquay & Matthew Peterson (Brandeis University) ------------------------------------------------------------------------- */ +#include "fix_enforce2d_kokkos.h" #include "atom_masks.h" #include "atom_kokkos.h" #include "comm.h" #include "error.h" -#include "fix_enforce2d_kokkos.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp index 2f730d1193ab20bd9f2c0a6d2874314c2d67b33b..89561c9a9281c048085e9daa836fa35df543656c 100644 --- a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp +++ b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp @@ -15,8 +15,6 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include -#include #include "fix_eos_table_rx_kokkos.h" #include "atom_kokkos.h" #include "error.h" @@ -24,7 +22,6 @@ #include "memory_kokkos.h" #include "comm.h" #include -#include "modify.h" #include "atom_masks.h" #define MAXLINE 1024 diff --git a/src/KOKKOS/fix_langevin_kokkos.cpp b/src/KOKKOS/fix_langevin_kokkos.cpp index 0947fee693f8df3d85dcb154135b7b84edd64435..651f790a25ae1f4e895380434cf881e684abb19f 100644 --- a/src/KOKKOS/fix_langevin_kokkos.cpp +++ b/src/KOKKOS/fix_langevin_kokkos.cpp @@ -11,23 +11,20 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_langevin_kokkos.h" +#include #include "atom_masks.h" #include "atom_kokkos.h" #include "force.h" +#include "group.h" #include "update.h" -#include "respa.h" #include "error.h" #include "memory_kokkos.h" -#include "group.h" -#include "random_mars.h" #include "compute.h" #include "comm.h" #include "modify.h" #include "input.h" +#include "region.h" #include "variable.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/fix_momentum_kokkos.cpp b/src/KOKKOS/fix_momentum_kokkos.cpp index 38500531ca73a06997ed7bcb6997175106d67ca9..2d4911bfda6875cee0a6e32513ab1af7dca65a13 100644 --- a/src/KOKKOS/fix_momentum_kokkos.cpp +++ b/src/KOKKOS/fix_momentum_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_momentum_kokkos.h" #include #include -#include "fix_momentum_kokkos.h" #include "atom_kokkos.h" #include "atom_masks.h" #include "domain.h" diff --git a/src/KOKKOS/fix_nh_kokkos.cpp b/src/KOKKOS/fix_nh_kokkos.cpp index fae9ef8f30e0d49ea7a38e975d024245e09781e3..578f2f5c7079c1f53b4eca8b22bbbca20ca3e15b 100644 --- a/src/KOKKOS/fix_nh_kokkos.cpp +++ b/src/KOKKOS/fix_nh_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "fix_nh_kokkos.h" #include #include #include -#include "fix_nh_kokkos.h" #include "math_extra.h" #include "atom.h" #include "force.h" diff --git a/src/KOKKOS/fix_nph_kokkos.cpp b/src/KOKKOS/fix_nph_kokkos.cpp index c5072e6ae90ece0fdc52c349a89d4578e8db8930..3830860fd70227258e989f5f060037845146cceb 100644 --- a/src/KOKKOS/fix_nph_kokkos.cpp +++ b/src/KOKKOS/fix_nph_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nph_kokkos.h" +#include #include "modify.h" #include "error.h" diff --git a/src/KOKKOS/fix_npt_kokkos.cpp b/src/KOKKOS/fix_npt_kokkos.cpp index c488c8e4f34060621f364632316c906755893e74..5b751c9e4dee7eb61b2fcac923b32e5e63fca95f 100644 --- a/src/KOKKOS/fix_npt_kokkos.cpp +++ b/src/KOKKOS/fix_npt_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_npt_kokkos.h" +#include #include "modify.h" #include "error.h" diff --git a/src/KOKKOS/fix_nve_kokkos.cpp b/src/KOKKOS/fix_nve_kokkos.cpp index ca7f72837075b3386fdab0e2778c9ba6bb58c950..f94b68dbceb78bb6e409dd2ccfdb4bea8b6fb1ff 100644 --- a/src/KOKKOS/fix_nve_kokkos.cpp +++ b/src/KOKKOS/fix_nve_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_nve_kokkos.h" #include #include -#include "fix_nve_kokkos.h" #include "atom_masks.h" #include "atom_kokkos.h" #include "force.h" diff --git a/src/KOKKOS/fix_nvt_kokkos.cpp b/src/KOKKOS/fix_nvt_kokkos.cpp index 4db42a62fbbf73a1088221dd6fdcbe76db759e38..66165dd7bc863e78451dd01440ecc4fc84699ff2 100644 --- a/src/KOKKOS/fix_nvt_kokkos.cpp +++ b/src/KOKKOS/fix_nvt_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nvt_kokkos.h" +#include #include "group.h" #include "modify.h" #include "error.h" diff --git a/src/KOKKOS/fix_property_atom_kokkos.cpp b/src/KOKKOS/fix_property_atom_kokkos.cpp index 6860676911ae37b1a92204a99125b204d1eb3486..ff374b885f909de1bc163343fcfc80671bf3b5e5 100644 --- a/src/KOKKOS/fix_property_atom_kokkos.cpp +++ b/src/KOKKOS/fix_property_atom_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_property_atom_kokkos.h" #include #include -#include "fix_property_atom_kokkos.h" #include "atom_kokkos.h" #include "comm.h" #include "memory_kokkos.h" diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp index 12369261b3ff12aafe80964464e36e6b8fbde4c5..e51fbacaaf90a7b82210400a0062d0bda7cb7b02 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp @@ -16,26 +16,19 @@ Kamesh Arumugam (NVIDIA) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_qeq_reax_kokkos.h" +#include #include "kokkos.h" #include "atom.h" #include "atom_masks.h" #include "atom_kokkos.h" #include "comm.h" #include "force.h" -#include "group.h" -#include "modify.h" #include "neighbor.h" #include "neigh_list_kokkos.h" #include "neigh_request.h" #include "update.h" #include "integrate.h" -#include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "pair_reaxc_kokkos.h" diff --git a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp index 9aed0b9ae4052490b798aad062c3856b0d225b81..51702bc603136a9896a7ac9891b9563b486a9187 100644 --- a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp +++ b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp @@ -15,26 +15,13 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include "fix_ave_atom.h" #include "fix_reaxc_bonds_kokkos.h" #include "atom.h" -#include "update.h" #include "pair_reaxc_kokkos.h" -#include "modify.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "comm.h" #include "force.h" #include "compute.h" -#include "input.h" -#include "variable.h" #include "memory_kokkos.h" #include "error.h" -#include "reaxc_list.h" -#include "reaxc_types.h" #include "reaxc_defs.h" #include "atom_masks.h" diff --git a/src/KOKKOS/fix_reaxc_species_kokkos.cpp b/src/KOKKOS/fix_reaxc_species_kokkos.cpp index bd92251960608a2bdfa6cb47c8a3180ae2356cec..f3bce2f9c0ba723b5f9b1f00cd58037e34e388d7 100644 --- a/src/KOKKOS/fix_reaxc_species_kokkos.cpp +++ b/src/KOKKOS/fix_reaxc_species_kokkos.cpp @@ -15,27 +15,18 @@ Contributing authors: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include -#include +#include "fix_reaxc_species_kokkos.h" #include "atom.h" -#include #include "fix_ave_atom.h" -#include "fix_reaxc_species_kokkos.h" -#include "domain.h" -#include "update.h" +#include "reaxc_defs.h" #include "pair_reaxc_kokkos.h" -#include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "comm.h" #include "force.h" -#include "compute.h" #include "input.h" -#include "variable.h" #include "memory_kokkos.h" #include "error.h" -#include "reaxc_list.h" #include "atom_masks.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/fix_rx_kokkos.cpp b/src/KOKKOS/fix_rx_kokkos.cpp index 80333e1e9b6ee6ad140ed02d87fe9aaac820ff3e..e06fc14585a2d4622d72329ea7b67ff796f8f2d2 100644 --- a/src/KOKKOS/fix_rx_kokkos.cpp +++ b/src/KOKKOS/fix_rx_kokkos.cpp @@ -11,15 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_rx_kokkos.h" +#include #include "atom_masks.h" #include "atom_kokkos.h" #include "force.h" #include "memory_kokkos.h" #include "update.h" -#include "respa.h" #include "modify.h" #include "neighbor.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/fix_setforce_kokkos.cpp b/src/KOKKOS/fix_setforce_kokkos.cpp index 634bc05ac3f825e3f14eceae51942b8ecba9cb6d..6f14a71382344bbe850e125554b1df9b3f5c69a5 100644 --- a/src/KOKKOS/fix_setforce_kokkos.cpp +++ b/src/KOKKOS/fix_setforce_kokkos.cpp @@ -11,22 +11,20 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_setforce_kokkos.h" +#include #include "atom_kokkos.h" #include "update.h" #include "modify.h" #include "domain.h" #include "region.h" -#include "respa.h" #include "input.h" #include "variable.h" #include "memory_kokkos.h" #include "error.h" -#include "force.h" #include "atom_masks.h" #include "kokkos_base.h" +#include "region.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_setforce_kokkos.h b/src/KOKKOS/fix_setforce_kokkos.h index 3cbf3d372085d34b0579f5af52e819a0a7f3cb9a..ecbfd71e3641737fc2f5dd3a807ae0fea1bcee87 100644 --- a/src/KOKKOS/fix_setforce_kokkos.h +++ b/src/KOKKOS/fix_setforce_kokkos.h @@ -23,7 +23,6 @@ FixStyle(setforce/kk/host,FixSetForceKokkos) #define LMP_FIX_SET_FORCE_KOKKOS_H #include "fix_setforce.h" -#include "region.h" #include "kokkos_type.h" namespace LAMMPS_NS { @@ -82,7 +81,7 @@ class FixSetForceKokkos : public FixSetForce { typename AT::t_f_array f; typename AT::t_int_1d_randomread mask; - Region* region; + class Region* region; }; } diff --git a/src/KOKKOS/fix_shardlow_kokkos.cpp b/src/KOKKOS/fix_shardlow_kokkos.cpp index 968f877abd4411aaac30fa587f262f4e4058775a..9bd859434170ed02787ee73e56095a345a6914f8 100644 --- a/src/KOKKOS/fix_shardlow_kokkos.cpp +++ b/src/KOKKOS/fix_shardlow_kokkos.cpp @@ -33,31 +33,23 @@ 135, 204105. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_shardlow_kokkos.h" +#include +#include #include "atom.h" #include "atom_masks.h" #include "atom_kokkos.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" -#include -#include "atom_vec.h" #include "comm.h" #include "neighbor.h" #include "neigh_list_kokkos.h" #include "neigh_request.h" #include "memory_kokkos.h" #include "domain.h" -#include "modify.h" -// #include "pair_dpd_fdt.h" #include "pair_dpd_fdt_energy_kokkos.h" -#include "pair.h" #include "npair_ssa_kokkos.h" -#include "citeme.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_wall_lj93_kokkos.cpp b/src/KOKKOS/fix_wall_lj93_kokkos.cpp index 5dbb05417513aee425ad980bd6da7a7722f2a14b..61346144c87ec0bd8d80052ce9c99125435b5808 100644 --- a/src/KOKKOS/fix_wall_lj93_kokkos.cpp +++ b/src/KOKKOS/fix_wall_lj93_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_wall_lj93_kokkos.h" +#include #include "atom_kokkos.h" #include "error.h" #include "atom_masks.h" diff --git a/src/KOKKOS/fix_wall_reflect_kokkos.cpp b/src/KOKKOS/fix_wall_reflect_kokkos.cpp index 75a5c1a81e51bc9a7fe71aef7ccbf55be44e43bd..ba104d19a955c7e3b7f89fc64592ff1aeb276b85 100644 --- a/src/KOKKOS/fix_wall_reflect_kokkos.cpp +++ b/src/KOKKOS/fix_wall_reflect_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_wall_reflect_kokkos.h" #include #include -#include "fix_wall_reflect_kokkos.h" #include "atom_kokkos.h" #include "comm.h" #include "update.h" diff --git a/src/KOKKOS/gridcomm_kokkos.cpp b/src/KOKKOS/gridcomm_kokkos.cpp index 348217634bc84898dc8aa6bc150520a149d7f671..ac33b15d73905e8aeb0902b34b086279f5cc74df 100644 --- a/src/KOKKOS/gridcomm_kokkos.cpp +++ b/src/KOKKOS/gridcomm_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "gridcomm_kokkos.h" +#include #include "comm.h" #include "kspace.h" #include "memory_kokkos.h" diff --git a/src/KOKKOS/improper_class2_kokkos.cpp b/src/KOKKOS/improper_class2_kokkos.cpp index ad32e6da4e152123826e65d2099fcc87878c12a2..defd5e16f5cbf0a97913d3c813847e4f9c0af0f2 100644 --- a/src/KOKKOS/improper_class2_kokkos.cpp +++ b/src/KOKKOS/improper_class2_kokkos.cpp @@ -15,23 +15,16 @@ Contributing author: Ray Shan (Materials Design) ------------------------------------------------------------------------- */ -#include -#include -#include #include "improper_class2_kokkos.h" +#include #include "atom_kokkos.h" -#include "comm.h" #include "neighbor_kokkos.h" -#include "domain.h" #include "force.h" -#include "update.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define TOLERANCE 0.05 #define SMALL 0.001 diff --git a/src/KOKKOS/improper_harmonic_kokkos.cpp b/src/KOKKOS/improper_harmonic_kokkos.cpp index bb397a2c2f43a1bffacaec450880dc76a84f2b6c..7d6437dbf5b6c862ea05873e760268bece948bb4 100644 --- a/src/KOKKOS/improper_harmonic_kokkos.cpp +++ b/src/KOKKOS/improper_harmonic_kokkos.cpp @@ -15,23 +15,17 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "improper_harmonic_kokkos.h" +#include #include "atom_kokkos.h" #include "comm.h" #include "neighbor_kokkos.h" -#include "domain.h" #include "force.h" -#include "update.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define TOLERANCE 0.05 #define SMALL 0.001 diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index 18a4a3168ff6bf2970ab8ca082ce446d8552fb35..a353c3dd184b4288837b7e8a8693df5305808642 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "kokkos.h" #include #include #include @@ -18,7 +19,6 @@ #include #include #include -#include "kokkos.h" #include "lammps.h" #include "force.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h index 942c2af2412d8de02c2c27c61c73f4b995730dc6..e900bbd6d1afcc0d34cffaa247aaf34ea709c39a 100644 --- a/src/KOKKOS/kokkos_type.h +++ b/src/KOKKOS/kokkos_type.h @@ -14,7 +14,7 @@ #ifndef LMP_LMPTYPE_KOKKOS_H #define LMP_LMPTYPE_KOKKOS_H -#include "lmptype.h" +#include "pointers.h" #include #include diff --git a/src/KOKKOS/math_special_kokkos.cpp b/src/KOKKOS/math_special_kokkos.cpp index 127168ef8bae1bce35a2031fce6077e9d0020e1e..f5fc725347cce3391e343bed13d1e8766e454713 100644 --- a/src/KOKKOS/math_special_kokkos.cpp +++ b/src/KOKKOS/math_special_kokkos.cpp @@ -1,7 +1,7 @@ +#include "math_special_kokkos.h" #include #include -#include "math_special_kokkos.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/nbin_ssa_kokkos.cpp b/src/KOKKOS/nbin_ssa_kokkos.cpp index ecf0e08535ca53de6b1d6547a984b636954b9ef2..0e46f7fc61015497c06e38f3a1598064d6067185 100644 --- a/src/KOKKOS/nbin_ssa_kokkos.cpp +++ b/src/KOKKOS/nbin_ssa_kokkos.cpp @@ -19,11 +19,8 @@ #include "nbin_ssa_kokkos.h" #include "neighbor.h" #include "atom_kokkos.h" -#include "group.h" #include "domain.h" -#include "comm.h" #include "update.h" -#include "error.h" #include "atom_masks.h" // #include "memory_kokkos.h" diff --git a/src/KOKKOS/npair_copy_kokkos.cpp b/src/KOKKOS/npair_copy_kokkos.cpp index 7dde05745ceea4131756524c9c43746ee5617854..0ce0f4d3ff9cd797157bd25aa5c68dbea733e582 100644 --- a/src/KOKKOS/npair_copy_kokkos.cpp +++ b/src/KOKKOS/npair_copy_kokkos.cpp @@ -12,14 +12,7 @@ ------------------------------------------------------------------------- */ #include "npair_copy_kokkos.h" -#include "neighbor.h" #include "neigh_list_kokkos.h" -#include "atom.h" -#include "atom_vec.h" -#include "molecule.h" -#include "domain.h" -#include "my_page.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/npair_skip_kokkos.cpp b/src/KOKKOS/npair_skip_kokkos.cpp index e614e624c91cc738d46b06f29fe147800cbed3b6..bb393c9b95e95fb6b0b255cfd41d41a9634a556c 100644 --- a/src/KOKKOS/npair_skip_kokkos.cpp +++ b/src/KOKKOS/npair_skip_kokkos.cpp @@ -12,13 +12,9 @@ ------------------------------------------------------------------------- */ #include "npair_skip_kokkos.h" -#include "neighbor.h" #include "neigh_list_kokkos.h" #include "atom_kokkos.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" -#include "my_page.h" #include "error.h" #include "atom_masks.h" diff --git a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp index 57ac3a9c57eb9735597cb8546b05071b1f8d7e52..2a72617525f52d94ac1f2a45954cab28ebe6c4f7 100644 --- a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp @@ -15,20 +15,16 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_buck_coul_cut_kokkos.h" #include -#include -#include #include -#include "pair_buck_coul_cut_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory_kokkos.h" diff --git a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp index 349c4c060139fe2d2a5e8b7255920f91454de6c5..fdf395684aae26781a0391b879891a9cad722a85 100644 --- a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp @@ -15,28 +15,22 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_buck_coul_long_kokkos.h" #include -#include -#include #include -#include "pair_buck_coul_long_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_buck_kokkos.cpp b/src/KOKKOS/pair_buck_kokkos.cpp index 02c02c986eeb93f67e27fff80d20d1bf4aa4acaa..375d0dc1eafd7fb7f13326c458a140ffdf332da9 100644 --- a/src/KOKKOS/pair_buck_kokkos.cpp +++ b/src/KOKKOS/pair_buck_kokkos.cpp @@ -15,28 +15,22 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pair_buck_kokkos.h" #include -#include -#include #include -#include "pair_buck_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_coul_cut_kokkos.cpp b/src/KOKKOS/pair_coul_cut_kokkos.cpp index 54ba0b63ce3de907fa71b54399b623fad296ef48..5a1a6eefac9178a628b8aaddcc96df826b47998e 100644 --- a/src/KOKKOS/pair_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_coul_cut_kokkos.cpp @@ -11,28 +11,19 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_cut_kokkos.h" +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_coul_debye_kokkos.cpp b/src/KOKKOS/pair_coul_debye_kokkos.cpp index 8966e30394c94506d5237f69e37b55d81348bb23..8dd7e4f3d2cbacd9ee518fdbe4526de7e71d73f6 100644 --- a/src/KOKKOS/pair_coul_debye_kokkos.cpp +++ b/src/KOKKOS/pair_coul_debye_kokkos.cpp @@ -15,28 +15,22 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_coul_debye_kokkos.h" #include -#include -#include #include -#include "pair_coul_debye_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_coul_dsf_kokkos.cpp index 748fed71a7079aba25eff145c293127db85b7452..836b12ba3943e0163b5e0e651a9a7b5da230b37a 100644 --- a/src/KOKKOS/pair_coul_dsf_kokkos.cpp +++ b/src/KOKKOS/pair_coul_dsf_kokkos.cpp @@ -15,22 +15,15 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_dsf_kokkos.h" +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list_kokkos.h" #include "neigh_request.h" #include "memory_kokkos.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "math_const.h" #include "error.h" #include "atom_masks.h" diff --git a/src/KOKKOS/pair_coul_long_kokkos.cpp b/src/KOKKOS/pair_coul_long_kokkos.cpp index a21cb050ffe90fad62216989f25e0b950b614832..84b89c6373c73d7a0086d6c00133f051d1f079b2 100644 --- a/src/KOKKOS/pair_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_coul_long_kokkos.cpp @@ -15,28 +15,22 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_coul_long_kokkos.h" #include -#include -#include #include -#include "pair_coul_long_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_coul_wolf_kokkos.cpp b/src/KOKKOS/pair_coul_wolf_kokkos.cpp index 20391d95303602974fc58d3a3c403622736ef7b1..3ca8f16a790c509726ecab8a2537a46f9b3cad67 100644 --- a/src/KOKKOS/pair_coul_wolf_kokkos.cpp +++ b/src/KOKKOS/pair_coul_wolf_kokkos.cpp @@ -15,21 +15,14 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_wolf_kokkos.h" +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list_kokkos.h" #include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "math_const.h" #include "memory_kokkos.h" #include "error.h" diff --git a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp index a44ef1790e938c60e4c7717783a3d189114647d3..21fd32a2c8ebb419037aaa8e2cb517fdf958ed35 100644 --- a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp +++ b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp @@ -15,22 +15,16 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ +#include "pair_dpd_fdt_energy_kokkos.h" #include -#include -#include -#include #include "atom_kokkos.h" -#include "atom_vec.h" #include "comm.h" #include "update.h" -#include "fix.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "memory_kokkos.h" -#include "modify.h" -#include "pair_dpd_fdt_energy_kokkos.h" #include "error.h" #include "atom_masks.h" #include "kokkos.h" diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp index b5442c0d29ae604bae9f696d3daa962d426bb6fe..48bf63386a70cb9b76ac57dc19ab3a28ab022448 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp +++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp @@ -15,13 +15,11 @@ Contributing authors: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pair_eam_alloy_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "pair_kokkos.h" -#include "pair_eam_alloy_kokkos.h" #include "atom_kokkos.h" #include "force.h" #include "comm.h" diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.h b/src/KOKKOS/pair_eam_alloy_kokkos.h index 6593ccae734ba038d21b2b85b70522c67512abee..e1dd9ab47d880050a43a494c45176274e6cc3b25 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.h +++ b/src/KOKKOS/pair_eam_alloy_kokkos.h @@ -23,7 +23,6 @@ PairStyle(eam/alloy/kk/host,PairEAMAlloyKokkos) #ifndef LMP_PAIR_EAM_ALLOY_KOKKOS_H #define LMP_PAIR_EAM_ALLOY_KOKKOS_H -#include #include "kokkos_base.h" #include "pair_kokkos.h" #include "pair_eam.h" diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp index 16701febd6d195eb7daa1d4de82a109f8d52fd2c..6536dd745aa27426e5f55e457ed1293547404be0 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.cpp +++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp @@ -15,13 +15,11 @@ Contributing authors: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pair_eam_fs_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "pair_kokkos.h" -#include "pair_eam_fs_kokkos.h" #include "atom_kokkos.h" #include "force.h" #include "comm.h" diff --git a/src/KOKKOS/pair_eam_fs_kokkos.h b/src/KOKKOS/pair_eam_fs_kokkos.h index f75605ff6dbca4a131f14fea488c57164f2d14b1..e93977869e8709bcaecdd68e5513d88441c9177f 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.h +++ b/src/KOKKOS/pair_eam_fs_kokkos.h @@ -23,7 +23,6 @@ PairStyle(eam/fs/kk/host,PairEAMFSKokkos) #ifndef LMP_PAIR_EAM_FS_KOKKOS_H #define LMP_PAIR_EAM_FS_KOKKOS_H -#include #include "kokkos_base.h" #include "pair_kokkos.h" #include "pair_eam.h" diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp index d423f2c9276cb83ef38b583cec88246660020aca..f6eef5b53ce5a90bdd07f72794b748171a6213bf 100644 --- a/src/KOKKOS/pair_eam_kokkos.cpp +++ b/src/KOKKOS/pair_eam_kokkos.cpp @@ -15,13 +15,10 @@ Contributing authors: Stan Moore (SNL), Christian Trott (SNL) ------------------------------------------------------------------------- */ +#include "pair_eam_kokkos.h" #include -#include -#include -#include #include "kokkos.h" #include "pair_kokkos.h" -#include "pair_eam_kokkos.h" #include "atom_kokkos.h" #include "force.h" #include "comm.h" diff --git a/src/KOKKOS/pair_eam_kokkos.h b/src/KOKKOS/pair_eam_kokkos.h index 4040eba8588413c61e5b1984e28026fa9db34372..3bf89c549acf108cea791f69964062ba098c0ad4 100644 --- a/src/KOKKOS/pair_eam_kokkos.h +++ b/src/KOKKOS/pair_eam_kokkos.h @@ -23,7 +23,6 @@ PairStyle(eam/kk/host,PairEAMKokkos) #ifndef LMP_PAIR_EAM_KOKKOS_H #define LMP_PAIR_EAM_KOKKOS_H -#include #include "kokkos_base.h" #include "pair_kokkos.h" #include "pair_eam.h" diff --git a/src/KOKKOS/pair_exp6_rx_kokkos.cpp b/src/KOKKOS/pair_exp6_rx_kokkos.cpp index 3a857a6485ceb75a64267655b3da23bda799ae5a..86986873771f2dd50435f2260633b3965073448a 100644 --- a/src/KOKKOS/pair_exp6_rx_kokkos.cpp +++ b/src/KOKKOS/pair_exp6_rx_kokkos.cpp @@ -15,20 +15,17 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ +#include "pair_exp6_rx_kokkos.h" #include -#include #include #include -#include "pair_exp6_rx_kokkos.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "math_const.h" #include "math_special_kokkos.h" #include "memory_kokkos.h" #include "error.h" -#include "modify.h" #include "fix.h" #include #include "atom_masks.h" @@ -41,7 +38,6 @@ #endif using namespace LAMMPS_NS; -using namespace MathConst; using namespace MathSpecialKokkos; #define MAXLINE 1024 diff --git a/src/KOKKOS/pair_hybrid_kokkos.cpp b/src/KOKKOS/pair_hybrid_kokkos.cpp index 00df4a8f3cf21acd3770d48e7c21847077ecc8b6..b5b0a9d02b7cf271e1554ee1647c675e0eac43c6 100644 --- a/src/KOKKOS/pair_hybrid_kokkos.cpp +++ b/src/KOKKOS/pair_hybrid_kokkos.cpp @@ -11,20 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_hybrid_kokkos.h" +#include #include "atom_kokkos.h" #include "force.h" #include "pair.h" #include "neighbor.h" #include "neigh_request.h" #include "update.h" -#include "comm.h" #include "memory_kokkos.h" -#include "error.h" #include "respa.h" #include "atom_masks.h" #include "kokkos.h" diff --git a/src/KOKKOS/pair_hybrid_kokkos.h b/src/KOKKOS/pair_hybrid_kokkos.h index 94e034f8757618105b8b64cf37af7ec2d0b13dd6..799354cf013eb2f3215a5f6013ec3c4ffcf8dcd9 100644 --- a/src/KOKKOS/pair_hybrid_kokkos.h +++ b/src/KOKKOS/pair_hybrid_kokkos.h @@ -20,7 +20,6 @@ PairStyle(hybrid/kk,PairHybridKokkos) #ifndef LMP_PAIR_HYBRID_KOKKOS_H #define LMP_PAIR_HYBRID_KOKKOS_H -#include #include "pair_hybrid.h" #include "pair_kokkos.h" #include "kokkos_type.h" diff --git a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp index a2c3edab6596061f39cda2e3fb4e1527e36dcd9c..0cebd79c88e6cce0c55f66c66b4c87e097293410 100644 --- a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp +++ b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp @@ -11,14 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "pair_hybrid_overlay_kokkos.h" #include #include -#include "pair_hybrid_overlay_kokkos.h" #include "atom.h" #include "force.h" -#include "neighbor.h" -#include "neigh_request.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp index 510740112a218117f2a4fac0bdf88005b1449c7e..ae6cb61b60cb41d569da9108af28f2f3ec1be17c 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp @@ -15,28 +15,21 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_charmm_coul_charmm_implicit_kokkos.h" +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp index 51c96354f94c8e029eab2729d92f9b9cd98f4d3f..9cdef267e2c37b3c5ce0d0b6621f275b995e1229 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp @@ -15,28 +15,22 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_charmm_coul_charmm_kokkos.h" #include -#include -#include #include -#include "pair_lj_charmm_coul_charmm_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp index 22faa9893519451b4ee7792eb77d6b98e8965326..441070248da13f371ad3a1cdc465a548896a97ce 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp @@ -15,28 +15,22 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_charmm_coul_long_kokkos.h" #include -#include -#include #include -#include "pair_lj_charmm_coul_long_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp index 60d480188b20b2f91e654ac1b8ab7a754f484278..1f7642e96575965016b198c86c0ca2be6feeb4b0 100644 --- a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp @@ -11,11 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_class2_coul_cut_kokkos.h" #include -#include -#include #include -#include "pair_lj_class2_coul_cut_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" @@ -24,15 +22,12 @@ #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp index 4c8aea8e929bd240bd6c912a0e16b952931ef644..c88ff9378e4da87b029c12675d12a632bbccc1f8 100644 --- a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp @@ -11,28 +11,22 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_class2_coul_long_kokkos.h" #include -#include -#include #include -#include "pair_lj_class2_coul_long_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_class2_kokkos.cpp b/src/KOKKOS/pair_lj_class2_kokkos.cpp index dd42baa4e0a4503cacb88faf5dc143aa6c86412c..9900e7361f9b663578fdb27ecd04db5c1972ba9b 100644 --- a/src/KOKKOS/pair_lj_class2_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_kokkos.cpp @@ -15,28 +15,22 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_class2_kokkos.h" #include -#include -#include #include -#include "pair_lj_class2_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp index cb5ab9687138887534c6bcb63beab7344286b720..1601e4a4b2b4811002924ffabafa0b6359f93249 100644 --- a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp @@ -11,28 +11,22 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_cut_kokkos.h" #include -#include -#include #include -#include "pair_lj_cut_coul_cut_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp index 800092a09b5f9fb538238ac8005d10dc08bbdd33..6e7d1eeb8bfeed7647cc38eb817f04c93db7f336 100644 --- a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp @@ -15,28 +15,22 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_debye_kokkos.h" #include -#include -#include #include -#include "pair_lj_cut_coul_debye_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp index f793485b47b83f3bc40a50581d48949bf9e8908c..b7dc7cc26d75e491fdda552650a04fc8416deb2b 100644 --- a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp @@ -15,20 +15,16 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_dsf_kokkos.h" #include -#include -#include #include -#include "pair_lj_cut_coul_dsf_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory_kokkos.h" diff --git a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp index 02150586f43b24025f94c449044076ceba7a5d24..122d59af824294d4564b63768bf2b618be88056e 100644 --- a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp @@ -11,20 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_long_kokkos.h" #include -#include -#include #include -#include "pair_lj_cut_coul_long_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory_kokkos.h" diff --git a/src/KOKKOS/pair_lj_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_kokkos.cpp index 4ba8c00f88517dc3bafc183411ceeb7385dfa852..df750b75240441d665258f9df859413d33f71ff5 100644 --- a/src/KOKKOS/pair_lj_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_kokkos.cpp @@ -11,28 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cut_kokkos.h" +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_expand_kokkos.cpp b/src/KOKKOS/pair_lj_expand_kokkos.cpp index 5ea6c9e438b1ee071febcd8527ce4a9e24e0ebee..38bebc364fe1a2f4bc8fabfb6073ff78dc658cc8 100644 --- a/src/KOKKOS/pair_lj_expand_kokkos.cpp +++ b/src/KOKKOS/pair_lj_expand_kokkos.cpp @@ -15,28 +15,22 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_expand_kokkos.h" #include -#include -#include #include -#include "pair_lj_expand_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp index 2421d059da2c203913f6ac888e4a1db368d274fb..a46a5c04418c18daf3b4b76c425078fed9466f88 100644 --- a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp +++ b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp @@ -15,28 +15,22 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_gromacs_coul_gromacs_kokkos.h" #include -#include -#include #include -#include "pair_lj_gromacs_coul_gromacs_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp index 09a0261ae12e209cfb6bb4f8a3c5438cd5e6ba79..23ed5e5595a7b7333e58ce706102f4af573b9981 100644 --- a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp +++ b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp @@ -15,28 +15,22 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_gromacs_kokkos.h" #include -#include -#include #include -#include "pair_lj_gromacs_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_sdk_kokkos.cpp b/src/KOKKOS/pair_lj_sdk_kokkos.cpp index c2375fa7a83720c931b41ef44442c7f14178e6b7..25f081d2558413631b1385152fe3df99ae8c9be3 100644 --- a/src/KOKKOS/pair_lj_sdk_kokkos.cpp +++ b/src/KOKKOS/pair_lj_sdk_kokkos.cpp @@ -11,22 +11,18 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_sdk_kokkos.h" #include #include -#include #include -#include "pair_lj_sdk_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" @@ -34,7 +30,6 @@ #include "lj_sdk_common.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace LJSDKParms; #define KOKKOS_CUDA_MAX_THREADS 256 diff --git a/src/KOKKOS/pair_morse_kokkos.cpp b/src/KOKKOS/pair_morse_kokkos.cpp index b308330eadc6785ba2d6de535c8eb669b64c841b..d3e3042a340fe62f1a8d4fc74326e32869f72674 100644 --- a/src/KOKKOS/pair_morse_kokkos.cpp +++ b/src/KOKKOS/pair_morse_kokkos.cpp @@ -15,20 +15,16 @@ Contributing authors: Stefan Paquay (Eindhoven University of Technology) ------------------------------------------------------------------------- */ +#include "pair_morse_kokkos.h" #include -#include -#include #include -#include "pair_morse_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory_kokkos.h" diff --git a/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp b/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp index 7d17ac3f4316ea95c4efbd9c208fdef12adacd6f..75247859ed23fbd3a52bbd31ad3a580da9a3da1b 100644 --- a/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp +++ b/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp @@ -21,21 +21,16 @@ The Journal of Chemical Physics, 2016, 144, 104501. ------------------------------------------------------------------------------------------- */ -#include +#include "pair_multi_lucy_rx_kokkos.h" #include -#include "math_const.h" -#include #include -#include "pair_multi_lucy_rx_kokkos.h" +#include "math_const.h" #include "atom_kokkos.h" #include "force.h" #include "comm.h" #include "neigh_list.h" #include "memory_kokkos.h" #include "error.h" -#include "citeme.h" -#include "modify.h" -#include "fix.h" #include "atom_masks.h" #include "neigh_request.h" #include "kokkos.h" diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index 64651be270b1d1441e818aa8ee82e96643ef3b39..d0ad1f1b09a3aaacdd8acd1560b9cc90b691b514 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -15,11 +15,10 @@ Contributing author: Ray Shan (SNL), Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pair_reaxc_kokkos.h" #include -#include #include #include -#include "pair_reaxc_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" @@ -27,9 +26,6 @@ #include "neighbor.h" #include "neigh_request.h" #include "neigh_list_kokkos.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "math_const.h" #include "math_special.h" #include "memory_kokkos.h" @@ -38,7 +34,6 @@ #include "reaxc_defs.h" #include "reaxc_lookup.h" #include "reaxc_tool_box.h" -#include "modify.h" #define TEAMSIZE 128 diff --git a/src/KOKKOS/pair_reaxc_kokkos.h b/src/KOKKOS/pair_reaxc_kokkos.h index 89dfc4d884309eb642a594438ded96e29100c209..783ea33c4ec10bee54376311ebde5ca9fb242c7b 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.h +++ b/src/KOKKOS/pair_reaxc_kokkos.h @@ -23,7 +23,6 @@ PairStyle(reax/c/kk/host,PairReaxCKokkos) #ifndef LMP_PAIR_REAXC_KOKKOS_H #define LMP_PAIR_REAXC_KOKKOS_H -#include #include "pair_kokkos.h" #include "pair_reaxc.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/pair_sw_kokkos.cpp b/src/KOKKOS/pair_sw_kokkos.cpp index da4737a2c146d399ae1b3110b4e4c7442284d17e..e85afa362f9b1f599d95bbf2702256cbd2c5a5ff 100644 --- a/src/KOKKOS/pair_sw_kokkos.cpp +++ b/src/KOKKOS/pair_sw_kokkos.cpp @@ -15,11 +15,8 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_sw_kokkos.h" +#include #include "kokkos.h" #include "pair_kokkos.h" #include "atom_kokkos.h" @@ -30,7 +27,6 @@ #include "memory_kokkos.h" #include "neighbor.h" #include "neigh_list_kokkos.h" -#include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" #include "math_const.h" diff --git a/src/KOKKOS/pair_table_kokkos.cpp b/src/KOKKOS/pair_table_kokkos.cpp index 737d600d1e969a3e0207e4fb93068e8862c7a2a5..5ee24ad4797c381702d65386d6baea5739e1140c 100644 --- a/src/KOKKOS/pair_table_kokkos.cpp +++ b/src/KOKKOS/pair_table_kokkos.cpp @@ -15,15 +15,11 @@ Contributing author: Christian Trott (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_table_kokkos.h" +#include #include "kokkos.h" #include "atom.h" #include "force.h" -#include "comm.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/KOKKOS/pair_table_rx_kokkos.cpp b/src/KOKKOS/pair_table_rx_kokkos.cpp index ec7a2ffb943b5be765cae3ab9a41b44fb1f31834..daebeda8db97bc30fb8fcc1891aa4e7818583931 100644 --- a/src/KOKKOS/pair_table_rx_kokkos.cpp +++ b/src/KOKKOS/pair_table_rx_kokkos.cpp @@ -15,11 +15,10 @@ Contributing author: Dan Ibanez (SNL) ------------------------------------------------------------------------- */ +#include "pair_table_rx_kokkos.h" #include #include -#include #include -#include "pair_table_rx_kokkos.h" #include "kokkos.h" #include "atom.h" #include "force.h" diff --git a/src/KOKKOS/pair_tersoff_kokkos.cpp b/src/KOKKOS/pair_tersoff_kokkos.cpp index 9252e3de5237a6df7e0f95cf729d12ba233947b1..b360b20ef3f5658f3919980e80fe910ea7160fec 100644 --- a/src/KOKKOS/pair_tersoff_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_kokkos.cpp @@ -15,11 +15,8 @@ Contributing author: Ray Shan (SNL) and Christian Trott (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_tersoff_kokkos.h" +#include #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" @@ -27,9 +24,6 @@ #include "neighbor.h" #include "neigh_request.h" #include "neigh_list_kokkos.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "math_const.h" #include "memory_kokkos.h" #include "error.h" diff --git a/src/KOKKOS/pair_tersoff_kokkos.h b/src/KOKKOS/pair_tersoff_kokkos.h index f73d4fe2d89e8990466a0a8edafba1cc3d94a9ab..7d41fe2346902f21b31acb703a69989e791997bf 100644 --- a/src/KOKKOS/pair_tersoff_kokkos.h +++ b/src/KOKKOS/pair_tersoff_kokkos.h @@ -23,7 +23,6 @@ PairStyle(tersoff/kk/host,PairTersoffKokkos) #ifndef LMP_PAIR_TERSOFF_KOKKOS_H #define LMP_PAIR_TERSOFF_KOKKOS_H -#include #include "pair_kokkos.h" #include "pair_tersoff.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp index 585074b12863af62e7f1aa3fb8769dd4acc53cc3..81ef48699995490a2542cb663ac5d05184351a16 100644 --- a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp @@ -15,11 +15,8 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_tersoff_mod_kokkos.h" +#include #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" @@ -27,9 +24,6 @@ #include "neighbor.h" #include "neigh_request.h" #include "neigh_list_kokkos.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "math_const.h" #include "memory_kokkos.h" #include "error.h" diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.h b/src/KOKKOS/pair_tersoff_mod_kokkos.h index d7c94ffc93e62c733b8e4e1f7035721a02f3edef..889e1eadfa103e6c36c6af03f28ea0bb2e1d8955 100644 --- a/src/KOKKOS/pair_tersoff_mod_kokkos.h +++ b/src/KOKKOS/pair_tersoff_mod_kokkos.h @@ -23,7 +23,6 @@ PairStyle(tersoff/mod/kk/host,PairTersoffMODKokkos) #ifndef LMP_PAIR_TERSOFF_MOD_KOKKOS_H #define LMP_PAIR_TERSOFF_MOD_KOKKOS_H -#include #include "pair_kokkos.h" #include "pair_tersoff_mod.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp index e1e2211ab5e5b4cf677dab916abc811674db1060..4593f32e3640951d3154c0e49d5680360c9a0f19 100644 --- a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp @@ -15,11 +15,9 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_tersoff_zbl_kokkos.h" #include -#include -#include #include -#include "pair_tersoff_zbl_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" @@ -28,8 +26,6 @@ #include "neigh_request.h" #include "neigh_list_kokkos.h" #include "update.h" -#include "integrate.h" -#include "respa.h" #include "math_const.h" #include "memory_kokkos.h" #include "error.h" diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.h b/src/KOKKOS/pair_tersoff_zbl_kokkos.h index 3af4e0d8ebd410c9d18ff717340fd32e767c589c..0c7fa2e963843019e7d91fd02642f8e58ff935bd 100644 --- a/src/KOKKOS/pair_tersoff_zbl_kokkos.h +++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.h @@ -23,7 +23,6 @@ PairStyle(tersoff/zbl/kk/host,PairTersoffZBLKokkos) #ifndef LMP_PAIR_TERSOFF_ZBL_KOKKOS_H #define LMP_PAIR_TERSOFF_ZBL_KOKKOS_H -#include #include "pair_kokkos.h" #include "pair_tersoff_zbl.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/pair_vashishta_kokkos.cpp b/src/KOKKOS/pair_vashishta_kokkos.cpp index 4a1f291b17443f8a452ae48f8312e2548f2d99af..614d3334d56c388d3a3d57598b51f04a5e312e64 100644 --- a/src/KOKKOS/pair_vashishta_kokkos.cpp +++ b/src/KOKKOS/pair_vashishta_kokkos.cpp @@ -15,11 +15,9 @@ Contributing author: Anders Hafreager (UiO), andershaf@gmail.com ------------------------------------------------------------------------- */ +#include "pair_vashishta_kokkos.h" #include -#include -#include #include -#include "pair_vashishta_kokkos.h" #include "kokkos.h" #include "pair_kokkos.h" #include "atom_kokkos.h" @@ -28,9 +26,7 @@ #include "force.h" #include "comm.h" #include "memory_kokkos.h" -#include "neighbor.h" #include "neigh_list_kokkos.h" -#include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" #include "math_const.h" diff --git a/src/KOKKOS/pair_yukawa_kokkos.cpp b/src/KOKKOS/pair_yukawa_kokkos.cpp index 27e18533a289c90b0c4deda7db3a5b123be08857..6dfffd4a5499c641693fb7a8b4c4f679b86f6a70 100644 --- a/src/KOKKOS/pair_yukawa_kokkos.cpp +++ b/src/KOKKOS/pair_yukawa_kokkos.cpp @@ -14,26 +14,22 @@ /* ---------------------------------------------------------------------- Contributing authors: Stefan Paquay (Brandeis University) ------------------------------------------------------------------------- */ -#include -#include + #include "pair_yukawa_kokkos.h" +#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_zbl_kokkos.cpp b/src/KOKKOS/pair_zbl_kokkos.cpp index 06c84e5189fa5fd6e480182f5ed2709e41f90f27..5697dd5b00faca83dda7f32d73d1f85a046fabb7 100644 --- a/src/KOKKOS/pair_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_zbl_kokkos.cpp @@ -15,21 +15,16 @@ Contributing authors: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pair_zbl_kokkos.h" #include -#include -#include #include -#include "pair_zbl_kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" @@ -39,7 +34,6 @@ // "The Stopping and Range of Ions in Matter" volume 1, Pergamon, 1985. using namespace LAMMPS_NS; -using namespace MathConst; using namespace PairZBLConstants; /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index c9c0d6d1d496bc4f563941613ef7e84536dfd859..b5539ef6e44d0a47eb35cf553cb9f5e64964edd9 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -15,20 +15,15 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pppm_kokkos.h" #include -#include -#include -#include #include -#include "pppm_kokkos.h" #include "atom_kokkos.h" #include "comm.h" #include "gridcomm_kokkos.h" #include "neighbor.h" #include "force.h" #include "pair.h" -#include "bond.h" -#include "angle.h" #include "domain.h" #include "fft3d_wrap.h" #include "remap_wrap.h" diff --git a/src/KOKKOS/rand_pool_wrap_kokkos.cpp b/src/KOKKOS/rand_pool_wrap_kokkos.cpp index 51ebcb154e6c4aad1d80647111a14ef1fac0151f..2d8865feb0fc34e9eec320cd94f312dde062783a 100644 --- a/src/KOKKOS/rand_pool_wrap_kokkos.cpp +++ b/src/KOKKOS/rand_pool_wrap_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "comm.h" #include "rand_pool_wrap_kokkos.h" +#include "comm.h" #include "lammps.h" #include "kokkos.h" #include "random_mars.h" diff --git a/src/KOKKOS/region_block_kokkos.cpp b/src/KOKKOS/region_block_kokkos.cpp index 730ef81466d698412827962c347265b3a8bdaf21..b28230290e1f89c096b49eeac1152b5047a41cb0 100644 --- a/src/KOKKOS/region_block_kokkos.cpp +++ b/src/KOKKOS/region_block_kokkos.cpp @@ -11,11 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "region_block_kokkos.h" -#include "domain.h" -#include "force.h" #include "atom_kokkos.h" #include "atom_masks.h" diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp index b80d5e0646d02bf3f47581c5d95cf0780b109668..2d2f0a9815e2154a6ac53dc34b41f4f8ae875a5a 100644 --- a/src/KOKKOS/verlet_kokkos.cpp +++ b/src/KOKKOS/verlet_kokkos.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "verlet_kokkos.h" #include "neighbor.h" #include "domain.h" #include "comm.h" -#include "atom.h" #include "atom_kokkos.h" #include "atom_masks.h" #include "force.h" @@ -29,15 +27,10 @@ #include "output.h" #include "update.h" #include "modify.h" -#include "compute.h" -#include "fix.h" #include "timer.h" #include "memory_kokkos.h" -#include "error.h" #include "kokkos.h" -#include - using namespace LAMMPS_NS; template diff --git a/src/KSPACE/ewald.cpp b/src/KSPACE/ewald.cpp index ccbb3ed7087e95195fd49725c7ed2c8dab15266c..d74d90b0d6a728b8a5f091b17857af675ab7d394 100644 --- a/src/KSPACE/ewald.cpp +++ b/src/KSPACE/ewald.cpp @@ -18,12 +18,9 @@ triclinic added by Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "ewald.h" #include -#include -#include -#include #include -#include "ewald.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/KSPACE/ewald_dipole.cpp b/src/KSPACE/ewald_dipole.cpp index 89ef7e39a877df2777608cd7d07955421e423c46..c3442beef51cd5b07e20042673fcf9e2a653ea8e 100644 --- a/src/KSPACE/ewald_dipole.cpp +++ b/src/KSPACE/ewald_dipole.cpp @@ -15,12 +15,10 @@ Contributing authors: Julien Tranchida (SNL), Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "ewald_dipole.h" #include -#include -#include #include #include -#include "ewald_dipole.h" #include "atom.h" #include "comm.h" #include "force.h" @@ -32,9 +30,6 @@ #include "error.h" #include "update.h" -#include "math_const.h" -#include "math_special.h" - using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/KSPACE/ewald_dipole_spin.cpp b/src/KSPACE/ewald_dipole_spin.cpp index 698203c85c047d1322641473d3b04ef08e7133ce..e7d67680a14fc903fc05912d7db1d68d9ecb50a3 100644 --- a/src/KSPACE/ewald_dipole_spin.cpp +++ b/src/KSPACE/ewald_dipole_spin.cpp @@ -15,29 +15,22 @@ Contributing authors: Julien Tranchida (SNL) ------------------------------------------------------------------------- */ +#include "ewald_dipole_spin.h" #include -#include -#include #include #include -#include "ewald_dipole_spin.h" #include "atom.h" #include "comm.h" #include "force.h" #include "pair.h" #include "domain.h" #include "math_const.h" -#include "math_special.h" #include "memory.h" #include "error.h" #include "update.h" -#include "math_const.h" -#include "math_special.h" - using namespace LAMMPS_NS; using namespace MathConst; -using namespace MathSpecial; #define SMALL 0.00001 diff --git a/src/KSPACE/ewald_disp.cpp b/src/KSPACE/ewald_disp.cpp index 0603d68eb2c0698a74bdb38b13008abd45e9b8c3..a7ac66fdd3fe68f8847ef7629130dbe8d3a223b2 100644 --- a/src/KSPACE/ewald_disp.cpp +++ b/src/KSPACE/ewald_disp.cpp @@ -15,12 +15,10 @@ Contributing authors: Pieter in 't Veld (SNL), Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "ewald_disp.h" #include #include -#include -#include #include -#include "ewald_disp.h" #include "math_vector.h" #include "math_const.h" #include "math_special.h" diff --git a/src/KSPACE/fft3d.cpp b/src/KSPACE/fft3d.cpp index 7d3c8c83f2a785e77fe84a10d0658bde2d7a53e6..e4c38a57f51b2c128248da67373e361c7aa18027 100644 --- a/src/KSPACE/fft3d.cpp +++ b/src/KSPACE/fft3d.cpp @@ -19,11 +19,11 @@ Paul Coffman (IBM) added MPI collectives remap ------------------------------------------------------------------------- */ +#include "fft3d.h" #include #include #include #include -#include "fft3d.h" #include "remap.h" #ifdef FFT_KISS diff --git a/src/KSPACE/fft3d.h b/src/KSPACE/fft3d.h index a51818d986f6f4b5a9e5c2e2ead828f04b7acb86..8c3d2f27ad5a2f48a1df6a8379f458b3b84406a8 100644 --- a/src/KSPACE/fft3d.h +++ b/src/KSPACE/fft3d.h @@ -11,6 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include + // User-settable FFT precision // FFT_PRECISION = 1 is single-precision complex (4-byte real, 4-byte imag) diff --git a/src/KSPACE/fft3d_wrap.cpp b/src/KSPACE/fft3d_wrap.cpp index b9a6f0ae4659b1fc93dd9154ae95a2b7fb75da6a..507b23d27d9ca7fd1ec83431dfeda6e82f70bbb8 100644 --- a/src/KSPACE/fft3d_wrap.cpp +++ b/src/KSPACE/fft3d_wrap.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fft3d_wrap.h" +#include #include "error.h" using namespace LAMMPS_NS; diff --git a/src/KSPACE/fix_tune_kspace.cpp b/src/KSPACE/fix_tune_kspace.cpp index 0c726985dc7abc3eca60842b9233ad8d8c86e507..cfd88609b3a14cf3008c7e8e16aff67e9afcadb3 100644 --- a/src/KSPACE/fix_tune_kspace.cpp +++ b/src/KSPACE/fix_tune_kspace.cpp @@ -15,13 +15,11 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "fix_tune_kspace.h" +#include +#include +#include #include "update.h" -#include "domain.h" -#include "atom.h" -#include "comm.h" #include "force.h" #include "kspace.h" #include "pair.h" @@ -31,9 +29,6 @@ #include "neighbor.h" #include "modify.h" #include "compute.h" -#include -#include -#include #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} #define SIGN(a,b) ((b) >= 0.0 ? fabs(a) : -fabs(a)) #define GOLD 1.618034 @@ -101,7 +96,7 @@ void FixTuneKspace::init() double old_acc = force->kspace->accuracy/force->kspace->two_charge_force; char old_acc_str[16]; snprintf(old_acc_str,16,"%g",old_acc); - strcpy(new_acc_str,old_acc_str); + strncpy(new_acc_str,old_acc_str,16); int itmp; double *p_cutoff = (double *) force->pair->extract("cut_coul",itmp); @@ -131,36 +126,37 @@ void FixTuneKspace::pre_exchange() // test Ewald store_old_kspace_settings(); strcpy(new_kspace_style,"ewald"); - sprintf(new_pair_style,"%s/long",base_pair_style); + snprintf(new_pair_style,64,"%s/long",base_pair_style); update_pair_style(new_pair_style,pair_cut_coul); update_kspace_style(new_kspace_style,new_acc_str); } else if (niter == 2) { // test PPPM store_old_kspace_settings(); strcpy(new_kspace_style,"pppm"); - sprintf(new_pair_style,"%s/long",base_pair_style); + snprintf(new_pair_style,64,"%s/long",base_pair_style); update_pair_style(new_pair_style,pair_cut_coul); update_kspace_style(new_kspace_style,new_acc_str); } else if (niter == 3) { // test MSM store_old_kspace_settings(); strcpy(new_kspace_style,"msm"); - sprintf(new_pair_style,"%s/msm",base_pair_style); + snprintf(new_pair_style,64,"%s/msm",base_pair_style); update_pair_style(new_pair_style,pair_cut_coul); update_kspace_style(new_kspace_style,new_acc_str); } else if (niter == 4) { store_old_kspace_settings(); - cout << "ewald_time = " << ewald_time << endl; - cout << "pppm_time = " << pppm_time << endl; - cout << "msm_time = " << msm_time << endl; + if (screen) fprintf(screen,"ewald_time = %g\npppm_time = %g\nmsm_time = %g", + ewald_time, pppm_time, msm_time); + if (logfile) fprintf(logfile,"ewald_time = %g\npppm_time = %g\nmsm_time = %g", + ewald_time, pppm_time, msm_time); // switch to fastest one strcpy(new_kspace_style,"ewald"); - sprintf(new_pair_style,"%s/long",base_pair_style); + snprintf(new_pair_style,64,"%s/long",base_pair_style); if (pppm_time < ewald_time && pppm_time < msm_time) strcpy(new_kspace_style,"pppm"); else if (msm_time < pppm_time && msm_time < ewald_time) { strcpy(new_kspace_style,"msm"); - sprintf(new_pair_style,"%s/msm",base_pair_style); + snprintf(new_pair_style,64,"%s/msm",base_pair_style); } update_pair_style(new_pair_style,pair_cut_coul); update_kspace_style(new_kspace_style,new_acc_str); @@ -243,8 +239,8 @@ void FixTuneKspace::update_pair_style(char *new_pair_style, p_pair_settings_file = tmpfile(); force->pair->write_restart(p_pair_settings_file); rewind(p_pair_settings_file); - - cout << "Creating new pair style: " << new_pair_style << endl; + if (screen) fprintf(screen,"Creating new pair style: %s\n",new_pair_style); + if (logfile) fprintf(logfile,"Creating new pair style: %s\n",new_pair_style); // delete old pair style and create new one force->create_pair(new_pair_style,1); @@ -253,7 +249,8 @@ void FixTuneKspace::update_pair_style(char *new_pair_style, double *pcutoff = (double *) force->pair->extract("cut_coul",itmp); double current_cutoff = *pcutoff; - cout << "Coulomb cutoff for real space: " << current_cutoff << endl; + if (screen) fprintf(screen,"Coulomb cutoff for real space: %g\n", current_cutoff); + if (logfile) fprintf(logfile,"Coulomb cutoff for real space: %g\n", current_cutoff); // close temporary file fclose(p_pair_settings_file); @@ -321,7 +318,8 @@ void FixTuneKspace::adjust_rcut(double time) int itmp; double *p_cutoff = (double *) force->pair->extract("cut_coul",itmp); double current_cutoff = *p_cutoff; - cout << "Old Coulomb cutoff for real space: " << current_cutoff << endl; + if (screen) fprintf(screen,"Old Coulomb cutoff for real space: %g\n",current_cutoff); + if (logfile) fprintf(logfile,"Old Coulomb cutoff for real space: %g\n",current_cutoff); // use Brent's method from Numerical Recipes to find optimal real space cutoff @@ -391,7 +389,8 @@ void FixTuneKspace::adjust_rcut(double time) // report the new cutoff double *new_cutoff = (double *) force->pair->extract("cut_coul",itmp); current_cutoff = *new_cutoff; - cout << "Adjusted Coulomb cutoff for real space: " << current_cutoff << endl; + if (screen) fprintf(screen,"Adjusted Coulomb cutoff for real space: %g\n", current_cutoff); + if (logfile) fprintf(logfile,"Adjusted Coulomb cutoff for real space: %g\n", current_cutoff); store_old_kspace_settings(); update_pair_style(new_pair_style,pair_cut_coul); diff --git a/src/KSPACE/fix_tune_kspace.h b/src/KSPACE/fix_tune_kspace.h index 6f40fc8711e32f501237ef8f629dc3065beaea60..1ccd7353170482fb7385bc770fa0087c6ba345a6 100644 --- a/src/KSPACE/fix_tune_kspace.h +++ b/src/KSPACE/fix_tune_kspace.h @@ -20,7 +20,6 @@ FixStyle(tune/kspace,FixTuneKspace) #ifndef LMP_FIX_TUNE_KSPACE_H #define LMP_FIX_TUNE_KSPACE_H -#include #include "fix.h" namespace LAMMPS_NS { @@ -52,10 +51,10 @@ class FixTuneKspace : public Fix { double ewald_time,pppm_time,msm_time; double pair_cut_coul; - char new_acc_str[12]; - char new_kspace_style[20]; - char new_pair_style[20]; - char base_pair_style[20]; + char new_acc_str[16]; + char new_kspace_style[64]; + char new_pair_style[64]; + char base_pair_style[64]; int old_differentiation_flag; int old_slabflag; diff --git a/src/KSPACE/gridcomm.cpp b/src/KSPACE/gridcomm.cpp index ba08c9be2675cbae8c02365f2b0590a2d0bc7acd..368e7370fee608e6beb3a140a18fb6d78b4d8c4e 100644 --- a/src/KSPACE/gridcomm.cpp +++ b/src/KSPACE/gridcomm.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "gridcomm.h" -#include "comm.h" +#include #include "kspace.h" #include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/KSPACE/msm.cpp b/src/KSPACE/msm.cpp index d7cc3f6876949147fb7822078496fe962b768c46..81dbabdbbd444a35ee0719f3f75061c2e1dd8745 100644 --- a/src/KSPACE/msm.cpp +++ b/src/KSPACE/msm.cpp @@ -15,12 +15,10 @@ Contributing authors: Paul Crozier, Stan Moore, Stephen Bond, (all SNL) ------------------------------------------------------------------------- */ +#include "msm.h" #include #include -#include -#include #include -#include "msm.h" #include "atom.h" #include "comm.h" #include "gridcomm.h" diff --git a/src/KSPACE/msm.h b/src/KSPACE/msm.h index 0f81eb9c3f5e845fbd4b217e8e539efaf4d876ec..bf393473e7a641edaea07f25d2f8bcdb2afc1ed9 100644 --- a/src/KSPACE/msm.h +++ b/src/KSPACE/msm.h @@ -20,9 +20,6 @@ KSpaceStyle(msm,MSM) #ifndef LMP_MSM_H #define LMP_MSM_H -#include "lmptype.h" -#include - #include "kspace.h" namespace LAMMPS_NS { diff --git a/src/KSPACE/msm_cg.cpp b/src/KSPACE/msm_cg.cpp index c7896db50c727f2c309070edefa4cb8f4f42f30a..9119d51878fb5b0b63a1d8cfd0ca23902bff4a3c 100644 --- a/src/KSPACE/msm_cg.cpp +++ b/src/KSPACE/msm_cg.cpp @@ -15,10 +15,9 @@ Contributing authors: Paul Crozier, Stan Moore, Stephen Bond, (all SNL) ------------------------------------------------------------------------- */ +#include "msm_cg.h" #include #include -#include -#include #include #include "atom.h" #include "gridcomm.h" @@ -27,12 +26,8 @@ #include "force.h" #include "neighbor.h" #include "memory.h" -#include "msm_cg.h" - -#include "math_const.h" using namespace LAMMPS_NS; -using namespace MathConst; #define OFFSET 16384 #define SMALLQ 0.00001 diff --git a/src/KSPACE/pair_born_coul_long.cpp b/src/KSPACE/pair_born_coul_long.cpp index f12f5779d942df78a3721c1e71d25d0dd0da193b..e248a24ef73370de57e7638f334118d69789848e 100644 --- a/src/KSPACE/pair_born_coul_long.cpp +++ b/src/KSPACE/pair_born_coul_long.cpp @@ -15,11 +15,9 @@ Contributing author: Ahmed Ismail (SNL) ------------------------------------------------------------------------- */ +#include "pair_born_coul_long.h" #include -#include -#include #include -#include "pair_born_coul_long.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/KSPACE/pair_born_coul_msm.cpp b/src/KSPACE/pair_born_coul_msm.cpp index eaa1c116c1b5cff1e06d49c02af72d1d639aa8b8..7300cd92e067258d028b242f37e152984472626b 100644 --- a/src/KSPACE/pair_born_coul_msm.cpp +++ b/src/KSPACE/pair_born_coul_msm.cpp @@ -15,23 +15,17 @@ Contributing author: Stan Moore (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_born_coul_msm.h" #include -#include -#include #include -#include "pair_born_coul_msm.h" #include "atom.h" -#include "comm.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/KSPACE/pair_buck_coul_long.cpp b/src/KSPACE/pair_buck_coul_long.cpp index 0a1ec88da5daf0630a72a73f39b10d68384a84b1..c97856fa3cfd7fad2bbd9220927d0b39179f0958 100644 --- a/src/KSPACE/pair_buck_coul_long.cpp +++ b/src/KSPACE/pair_buck_coul_long.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_buck_coul_long.h" +#include #include -#include -#include #include -#include "pair_buck_coul_long.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/KSPACE/pair_buck_coul_msm.cpp b/src/KSPACE/pair_buck_coul_msm.cpp index 257d1b661f759dbd67f150b85124b742c293d382..1355a2f13a2c24a9cd1f22ea82df8af008a24580 100644 --- a/src/KSPACE/pair_buck_coul_msm.cpp +++ b/src/KSPACE/pair_buck_coul_msm.cpp @@ -11,23 +11,17 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_buck_coul_msm.h" #include -#include -#include #include -#include "pair_buck_coul_msm.h" #include "atom.h" -#include "comm.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/KSPACE/pair_buck_long_coul_long.cpp b/src/KSPACE/pair_buck_long_coul_long.cpp index c7a4a4b2f6d2397b6f788ae2597b6804f0102449..8127cbc1271645865dcd34671f37c976eba452d3 100644 --- a/src/KSPACE/pair_buck_long_coul_long.cpp +++ b/src/KSPACE/pair_buck_long_coul_long.cpp @@ -15,12 +15,11 @@ Contributing author: Pieter J. in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "pair_buck_long_coul_long.h" +#include #include -#include -#include #include #include "math_vector.h" -#include "pair_buck_long_coul_long.h" #include "atom.h" #include "comm.h" #include "neighbor.h" @@ -29,7 +28,6 @@ #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pair_coul_long.cpp b/src/KSPACE/pair_coul_long.cpp index ae268b985793559464cea9b0829f70877f2cc774..7cedf3d003a34a465e71c743662f7bb085a34d91 100644 --- a/src/KSPACE/pair_coul_long.cpp +++ b/src/KSPACE/pair_coul_long.cpp @@ -15,20 +15,16 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_coul_long.h" +#include #include -#include -#include #include -#include "pair_coul_long.h" #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "neighbor.h" #include "neigh_list.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pair_coul_msm.cpp b/src/KSPACE/pair_coul_msm.cpp index 960505142ce796970fbe17395517ed63e7483150..5d42e1f046e70a529282b3c6806327b13d86ec62 100644 --- a/src/KSPACE/pair_coul_msm.cpp +++ b/src/KSPACE/pair_coul_msm.cpp @@ -15,21 +15,13 @@ Contributing authors: Stan Moore (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_coul_msm.h" #include -#include -#include #include -#include "pair_coul_msm.h" #include "atom.h" -#include "comm.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/KSPACE/pair_lj_charmm_coul_long.cpp b/src/KSPACE/pair_lj_charmm_coul_long.cpp index b40eab244b57286f27c9c8adeaea291127075b85..751ee77388965c1183cd9388634615cffaa0d43c 100644 --- a/src/KSPACE/pair_lj_charmm_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmm_coul_long.cpp @@ -15,17 +15,14 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_charmm_coul_long.h" #include -#include -#include #include -#include "pair_lj_charmm_coul_long.h" #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/KSPACE/pair_lj_charmm_coul_msm.cpp b/src/KSPACE/pair_lj_charmm_coul_msm.cpp index 72a8e340bce19714de6a5aa6a253bece1f70c591..a93a1275f4433e99593fd2bd1c66af7536712591 100644 --- a/src/KSPACE/pair_lj_charmm_coul_msm.cpp +++ b/src/KSPACE/pair_lj_charmm_coul_msm.cpp @@ -15,21 +15,13 @@ Contributing authors: Paul Crozier (SNL), Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_charmm_coul_msm.h" #include -#include -#include #include -#include "pair_lj_charmm_coul_msm.h" #include "atom.h" -#include "comm.h" #include "force.h" #include "kspace.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp index cdde21115742aa9f0ae0bd6b048688397a0fc61c..494a3497686572dbafe2bd50cdb93a6704713963 100644 --- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp @@ -19,18 +19,14 @@ additional assistance from Robert A. Latour, Clemson University ------------------------------------------------------------------------- */ +#include "pair_lj_charmmfsw_coul_long.h" #include -#include -#include #include -#include "pair_lj_charmmfsw_coul_long.h" #include "atom.h" -#include "update.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/KSPACE/pair_lj_cut_coul_long.cpp b/src/KSPACE/pair_lj_cut_coul_long.cpp index fde7fa8e354723f99a11aee5013f2117e7d36303..fb79451b375a3c9ab5ad407321667c1cf24a9a27 100644 --- a/src/KSPACE/pair_lj_cut_coul_long.cpp +++ b/src/KSPACE/pair_lj_cut_coul_long.cpp @@ -15,17 +15,15 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_long.h" +#include #include -#include -#include #include -#include "pair_lj_cut_coul_long.h" #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/KSPACE/pair_lj_cut_coul_msm.cpp b/src/KSPACE/pair_lj_cut_coul_msm.cpp index c2e566a117bddc06f965d662b7d41cfa09a13205..4ebbcb9a3fd808c9f745c7fb88ddc073733ef634 100644 --- a/src/KSPACE/pair_lj_cut_coul_msm.cpp +++ b/src/KSPACE/pair_lj_cut_coul_msm.cpp @@ -15,27 +15,17 @@ Contributing authors: Stan Moore (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_msm.h" #include -#include -#include #include -#include "pair_lj_cut_coul_msm.h" #include "atom.h" -#include "comm.h" #include "force.h" #include "kspace.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/KSPACE/pair_lj_cut_tip4p_long.cpp b/src/KSPACE/pair_lj_cut_tip4p_long.cpp index f5889fd520dd4b330bdd28d59af63850f2390813..c98092f19b455d9cd9907c5ca3d48ac277c4638e 100644 --- a/src/KSPACE/pair_lj_cut_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_cut_tip4p_long.cpp @@ -16,23 +16,18 @@ simpler force assignment added by Rolf Isele-Holder (Aachen University) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_tip4p_long.h" +#include #include -#include -#include #include -#include "pair_lj_cut_tip4p_long.h" #include "angle.h" #include "atom.h" #include "bond.h" #include "comm.h" #include "domain.h" #include "force.h" -#include "kspace.h" -#include "update.h" -#include "respa.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pair_lj_long_coul_long.cpp b/src/KSPACE/pair_lj_long_coul_long.cpp index 493866a895c4764d6275f78c6135c619f4197d20..610fc4e89b5d6c29e6f32dbaeea6e17b58466ca3 100644 --- a/src/KSPACE/pair_lj_long_coul_long.cpp +++ b/src/KSPACE/pair_lj_long_coul_long.cpp @@ -17,12 +17,11 @@ University New Orleans) ------------------------------------------------------------------------- */ +#include "pair_lj_long_coul_long.h" +#include #include -#include -#include #include #include "math_vector.h" -#include "pair_lj_long_coul_long.h" #include "atom.h" #include "comm.h" #include "neighbor.h" @@ -31,7 +30,6 @@ #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pair_lj_long_tip4p_long.cpp b/src/KSPACE/pair_lj_long_tip4p_long.cpp index 3137b9d79ad30863cc8ba90b53044109dc40e99b..08409dce72b038abe92a95ac5c932e4efe3ecb68 100644 --- a/src/KSPACE/pair_lj_long_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_long_tip4p_long.cpp @@ -16,23 +16,18 @@ Rolf Isele-Holder (Aachen University) ------------------------------------------------------------------------- */ +#include "pair_lj_long_tip4p_long.h" +#include #include -#include -#include #include -#include "pair_lj_long_tip4p_long.h" #include "angle.h" #include "atom.h" #include "bond.h" #include "comm.h" #include "domain.h" #include "force.h" -#include "kspace.h" -#include "update.h" -#include "respa.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pair_tip4p_long.cpp b/src/KSPACE/pair_tip4p_long.cpp index 9419fdf19667fd1ca623bd546dba9f14c905cf55..2c47f42beb2e440483cd4523c58f4589a9657e2a 100644 --- a/src/KSPACE/pair_tip4p_long.cpp +++ b/src/KSPACE/pair_tip4p_long.cpp @@ -16,23 +16,18 @@ simpler force assignment added by Rolf Isele-Holder (Aachen University) ------------------------------------------------------------------------- */ +#include "pair_tip4p_long.h" +#include #include -#include -#include #include -#include "pair_tip4p_long.h" #include "angle.h" #include "atom.h" #include "bond.h" #include "comm.h" #include "domain.h" #include "force.h" -#include "kspace.h" -#include "update.h" -#include "respa.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp index 1abb19e947819c229281fa661bb7072e0643bd1d..75470c962f0d20adbf2322d5a87dcf9c6a57e340 100644 --- a/src/KSPACE/pppm.cpp +++ b/src/KSPACE/pppm.cpp @@ -18,12 +18,10 @@ triclinic added by Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pppm.h" #include #include -#include -#include #include -#include "pppm.h" #include "atom.h" #include "comm.h" #include "gridcomm.h" diff --git a/src/KSPACE/pppm.h b/src/KSPACE/pppm.h index 6426b9c22dcaaba780c528a6db6c959fb0b5c530..11b98076d955dc726221d3c4dda20e2f831bec81 100644 --- a/src/KSPACE/pppm.h +++ b/src/KSPACE/pppm.h @@ -20,8 +20,7 @@ KSpaceStyle(pppm,PPPM) #ifndef LMP_PPPM_H #define LMP_PPPM_H -#include "lmptype.h" -#include +#include "kspace.h" #if defined(FFT_FFTW3) #define LMP_FFT_LIB "FFTW3" @@ -42,8 +41,6 @@ typedef double FFT_SCALAR; #define MPI_FFT_SCALAR MPI_DOUBLE #endif -#include "kspace.h" - namespace LAMMPS_NS { class PPPM : public KSpace { diff --git a/src/KSPACE/pppm_cg.cpp b/src/KSPACE/pppm_cg.cpp index 3285dba21c775e427ce38916a8b00275958bcf06..bd23dedef1d0bac1a17198dd289710ad1ee6a0a6 100644 --- a/src/KSPACE/pppm_cg.cpp +++ b/src/KSPACE/pppm_cg.cpp @@ -15,11 +15,10 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "pppm_cg.h" #include #include -#include #include - #include "atom.h" #include "gridcomm.h" #include "domain.h" @@ -27,9 +26,8 @@ #include "force.h" #include "neighbor.h" #include "memory.h" -#include "pppm_cg.h" - #include "math_const.h" +#include "remap.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pppm_dipole.cpp b/src/KSPACE/pppm_dipole.cpp index 21a777dd753d8948cc43c45fa257d0602301b8d2..0eb761d9bef3e3142239c04e5b6feddb86f9be37 100644 --- a/src/KSPACE/pppm_dipole.cpp +++ b/src/KSPACE/pppm_dipole.cpp @@ -15,20 +15,15 @@ Contributing authors: Stan Moore (SNL), Julien Tranchida (SNL) ------------------------------------------------------------------------- */ +#include "pppm_dipole.h" #include #include -#include -#include #include -#include "pppm_dipole.h" #include "atom.h" #include "comm.h" #include "gridcomm.h" -#include "neighbor.h" #include "force.h" #include "pair.h" -#include "bond.h" -#include "angle.h" #include "domain.h" #include "fft3d_wrap.h" #include "remap_wrap.h" diff --git a/src/KSPACE/pppm_dipole_spin.cpp b/src/KSPACE/pppm_dipole_spin.cpp index 878d40c82e5e3d544bf0d44a62bfb93718474331..9e9f07322c2cde472a50dc82bb48ab14826f64d7 100644 --- a/src/KSPACE/pppm_dipole_spin.cpp +++ b/src/KSPACE/pppm_dipole_spin.cpp @@ -15,33 +15,23 @@ Contributing author: Julien Tranchida (SNL) ------------------------------------------------------------------------- */ +#include "pppm_dipole_spin.h" #include #include -#include -#include -#include -#include "pppm_dipole_spin.h" #include "atom.h" #include "comm.h" #include "gridcomm.h" -#include "neighbor.h" #include "force.h" #include "pair.h" -#include "bond.h" -#include "angle.h" #include "domain.h" -#include "fft3d_wrap.h" -#include "remap_wrap.h" #include "memory.h" #include "error.h" #include "update.h" #include "math_const.h" -#include "math_special.h" using namespace LAMMPS_NS; using namespace MathConst; -using namespace MathSpecial; #define MAXORDER 7 #define OFFSET 16384 diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp index ba0e85bbba56c868b0c3bd4cea5d04d2302a1f0f..c30d55dd68aadffac42cd219faad6790690ed99a 100644 --- a/src/KSPACE/pppm_disp.cpp +++ b/src/KSPACE/pppm_disp.cpp @@ -16,12 +16,10 @@ Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pppm_disp.h" #include #include -#include -#include #include -#include "pppm_disp.h" #include "math_const.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pppm_disp.h b/src/KSPACE/pppm_disp.h index 86746692742ddaaceb2d0fa967c6cc3758460870..130671fa28b04716a2a6b65ae78d16161e491cab 100644 --- a/src/KSPACE/pppm_disp.h +++ b/src/KSPACE/pppm_disp.h @@ -20,8 +20,7 @@ KSpaceStyle(pppm/disp,PPPMDisp) #ifndef LMP_PPPM_DISP_H #define LMP_PPPM_DISP_H -#include "lmptype.h" -#include +#include "kspace.h" #if defined(FFT_FFTW3) #define LMP_FFT_LIB "FFTW3" @@ -41,8 +40,6 @@ typedef double FFT_SCALAR; #define MPI_FFT_SCALAR MPI_DOUBLE #endif -#include "kspace.h" - namespace LAMMPS_NS { diff --git a/src/KSPACE/pppm_disp_tip4p.cpp b/src/KSPACE/pppm_disp_tip4p.cpp index 2bc63a84bb7974722dc591f58b56128ba7d95bd0..bc46152e2b61207b51e0f92fef41f0a79a23209b 100644 --- a/src/KSPACE/pppm_disp_tip4p.cpp +++ b/src/KSPACE/pppm_disp_tip4p.cpp @@ -16,13 +16,12 @@ Rolf Isele-Holder (Aachen University) ------------------------------------------------------------------------- */ -#include #include "pppm_disp_tip4p.h" +#include #include "pppm_disp.h" #include "atom.h" #include "domain.h" #include "force.h" -#include "memory.h" #include "error.h" #include "math_const.h" diff --git a/src/KSPACE/pppm_stagger.cpp b/src/KSPACE/pppm_stagger.cpp index a5ed6de6262763448d35c50f368809d777f6572a..7b708d035589c7cb4a2bb6a4901513adc457c1f3 100644 --- a/src/KSPACE/pppm_stagger.cpp +++ b/src/KSPACE/pppm_stagger.cpp @@ -15,15 +15,12 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ +#include "pppm_stagger.h" #include #include -#include -#include #include -#include "pppm_stagger.h" #include "atom.h" #include "gridcomm.h" -#include "force.h" #include "domain.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pppm_tip4p.cpp b/src/KSPACE/pppm_tip4p.cpp index b9fe3e648859dc9511c0d027b52c1d9be5b5a780..f664a0dca3b0d2c45a30c8bac943389784b18612 100644 --- a/src/KSPACE/pppm_tip4p.cpp +++ b/src/KSPACE/pppm_tip4p.cpp @@ -15,12 +15,12 @@ Contributing authors: Amalie Frischknecht and Ahmed Ismail (SNL) ------------------------------------------------------------------------- */ -#include #include "pppm_tip4p.h" +#include +#include #include "atom.h" #include "domain.h" #include "force.h" -#include "memory.h" #include "error.h" #include "math_const.h" diff --git a/src/KSPACE/remap.cpp b/src/KSPACE/remap.cpp index 26541f121e0f735e1b094d2e19edbdd5a68764b9..d4cfdea2b0a21330f67eaee9f6bf77059286cb20 100644 --- a/src/KSPACE/remap.cpp +++ b/src/KSPACE/remap.cpp @@ -11,9 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "remap.h" +#include #include #include -#include "remap.h" #define PACK_DATA FFT_SCALAR diff --git a/src/KSPACE/remap_wrap.cpp b/src/KSPACE/remap_wrap.cpp index 8ea2918d7f58b6bb9d5bcf4a1c4f7dd0439a2f41..7929cd053c7dd81943739b8ffdb1e497a2636c7d 100644 --- a/src/KSPACE/remap_wrap.cpp +++ b/src/KSPACE/remap_wrap.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "remap_wrap.h" +#include #include "error.h" using namespace LAMMPS_NS; diff --git a/src/LATTE/fix_latte.cpp b/src/LATTE/fix_latte.cpp index 645b298e09b2bc5fce06b9b7605c05bfc3d33214..7d4e89272d22eeb87afb856352f2470477d2d2c1 100644 --- a/src/LATTE/fix_latte.cpp +++ b/src/LATTE/fix_latte.cpp @@ -15,9 +15,9 @@ Contributing author: Christian Negre (LANL) ------------------------------------------------------------------------- */ +#include "fix_latte.h" #include #include -#include "fix_latte.h" #include "atom.h" #include "comm.h" #include "update.h" diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp index 5019e7711ad7467822308630638b98b42f2f3a14..2f324bf09743cd1c9995d6737b0f7909550d9bf4 100644 --- a/src/MANYBODY/fix_qeq_comb.cpp +++ b/src/MANYBODY/fix_qeq_comb.cpp @@ -15,16 +15,13 @@ Contributing authors: Ray Shan (Sandia, tnshan@sandia.gov) ------------------------------------------------------------------------- */ +#include "fix_qeq_comb.h" #include #include -#include #include #include "pair_comb.h" #include "pair_comb3.h" -#include "fix_qeq_comb.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MANYBODY/fix_qeq_comb.h b/src/MANYBODY/fix_qeq_comb.h index dd4c9f729085ad8bc107b748036c57b57cc8c515..c3a0ac08f3916fadf5930a39188743a46f1384cf 100644 --- a/src/MANYBODY/fix_qeq_comb.h +++ b/src/MANYBODY/fix_qeq_comb.h @@ -20,7 +20,6 @@ FixStyle(qeq/comb,FixQEQComb) #ifndef LMP_FIX_QEQ_COMB_H #define LMP_FIX_QEQ_COMB_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp index 68511b87096df8eb8ff4fa9fe30d39213a514cb7..64c778659c80693b64840461becb28b468eb9dde 100644 --- a/src/MANYBODY/pair_adp.cpp +++ b/src/MANYBODY/pair_adp.cpp @@ -16,11 +16,11 @@ Chandra Veer Singh (Cornell) ------------------------------------------------------------------------- */ +#include "pair_adp.h" +#include #include -#include #include #include -#include "pair_adp.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index e3c5a1627b8bef05b978767325d88a6d9a1e7235..fcc3a3efd24a0b607a898543f9e8bcbd30839695 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -20,28 +20,23 @@ Thomas C. O'Connor (JHU) 2014 ------------------------------------------------------------------------- */ +#include "pair_airebo.h" #include -#include -#include #include #include -#include "pair_airebo.h" #include "atom.h" #include "neighbor.h" #include "force.h" #include "comm.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "my_page.h" -#include "math_const.h" #include "math_special.h" #include "memory.h" #include "error.h" #include "utils.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace MathSpecial; #define MAXLINE 1024 @@ -3198,6 +3193,7 @@ double PairAIREBO::piRCSpline(double Nij, double Nji, double Nijconj, dN3[0]=0.0; dN3[1]=0.0; dN3[2]=0.0; + piRC=0.0; if (typei==0 && typej==0) { @@ -4348,70 +4344,70 @@ void PairAIREBO::Sptricubic_patch_coeffs( ) { const double C_inv[64][32] = { // output_matrix(2, 8*4, get_matrix(3)) - 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, - -3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -2, -1, 0, 0, 0, 0, 0, 0, - 2, -2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, -2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - -3, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -2, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -3, 0, 3, 0, 0, 0, 0, 0, - 9, -9, -9, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 6, -6, 3, -3, 0, 0, 0, 0, 6, 3, -6, -3, 0, 0, 0, 0, - -6, 6, 6, -6, 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0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 9, -9, -9, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, -6, 6, 6, -6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, -2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, -6, 6, 6, -6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 4, -4, -4, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + {-3, 0, 0, 0, 3, 0, 0, 0, -2, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -3, 0, 0, 0, 3, 0, 0, 0}, + { 9, -9, 0, 0, -9, 9, 0, 0, 6, -6, 0, 0, 3, -3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 6, 3, 0, 0, -6, -3, 0, 0}, + {-6, 6, 0, 0, 6, -6, 0, 0, -4, 4, 0, 0, -2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -3, -3, 0, 0, 3, 3, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -3, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, -9, 0, 0, -9, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -6, 6, 0, 0, 6, -6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 9, 0, -9, 0, -9, 0, 9, 0, 6, 0, -6, 0, 3, 0, -3, 0, 6, 0, 3, 0, -6, 0, -3, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0, -9, 0, -9, 0, 9, 0}, + {-27,27, 27,-27, 27,-27,-27, 27,-18, 18, 18,-18, -9, 9, 9, -9,-18, 18, -9, 9, 18,-18, 9, -9,-18, -9, 18, 9, 18, 9,-18, -9}, + {18,-18,-18, 18,-18, 18, 18,-18, 12,-12,-12, 12, 6, -6, -6, 6, 12,-12, 6, -6,-12, 12, -6, 6, 9, 9, -9, -9, -9, -9, 9, 9}, + {-6, 0, 6, 0, 6, 0, -6, 0, -4, 0, 4, 0, -2, 0, 2, 0, -3, 0, -3, 0, 3, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -6, 0, 6, 0, 6, 0, -6, 0}, + {18,-18,-18, 18,-18, 18, 18,-18, 12,-12,-12, 12, 6, -6, -6, 6, 9, -9, 9, -9, -9, 9, -9, 9, 12, 6,-12, -6,-12, -6, 12, 6}, + {-12,12, 12,-12, 12,-12,-12, 12, -8, 8, 8, -8, -4, 4, 4, -4, -6, 6, -6, 6, 6, -6, 6, -6, -6, -6, 6, 6, 6, 6, -6, -6}, + { 2, 0, 0, 0, -2, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, -2, 0, 0, 0}, + {-6, 6, 0, 0, 6, -6, 0, 0, -3, 3, 0, 0, -3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -4, -2, 0, 0, 4, 2, 0, 0}, + { 4, -4, 0, 0, -4, 4, 0, 0, 2, -2, 0, 0, 2, -2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 0, 0, -2, -2, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, -2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -6, 6, 0, 0, 6, -6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, -4, 0, 0, -4, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + {-6, 0, 6, 0, 6, 0, -6, 0, -3, 0, 3, 0, -3, 0, 3, 0, -4, 0, -2, 0, 4, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -6, 0, 6, 0, 6, 0, -6, 0}, + {18,-18,-18, 18,-18, 18, 18,-18, 9, -9, -9, 9, 9, -9, -9, 9, 12,-12, 6, -6,-12, 12, -6, 6, 12, 6,-12, -6,-12, -6, 12, 6}, + {-12,12, 12,-12, 12,-12,-12, 12, -6, 6, 6, -6, -6, 6, 6, -6, -8, 8, -4, 4, 8, -8, 4, -4, -6, -6, 6, 6, 6, 6, -6, -6}, + { 4, 0, -4, 0, -4, 0, 4, 0, 2, 0, -2, 0, 2, 0, -2, 0, 2, 0, 2, 0, -2, 0, -2, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, -4, 0, -4, 0, 4, 0}, + {-12,12, 12,-12, 12,-12,-12, 12, -6, 6, 6, -6, -6, 6, 6, -6, -6, 6, -6, 6, 6, -6, 6, -6, -8, -4, 8, 4, 8, 4, -8, -4}, + { 8, -8, -8, 8, -8, 8, 8, -8, 4, -4, -4, 4, 4, -4, -4, 4, 4, -4, 4, -4, -4, 4, -4, 4, 4, 4, -4, -4, -4, -4, 4, 4} }; double dx = xmax - xmin; double dy = ymax - ymin; @@ -4461,22 +4457,22 @@ void PairAIREBO::Spbicubic_patch_coeffs( ) { const double C_inv[16][12] = { // output_matrix(1, 4*3, get_matrix(2)) - 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, - -3, 3, 0, 0, 0, 0, 0, 0,-2,-1, 0, 0, - 2,-2, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, - 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0,-3, 3, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 2,-2, 0, 0, 0, 0, 0, 0, - -3, 0, 3, 0,-2, 0,-1, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0,-3, 0, 3, 0, - 9,-9,-9, 9, 6,-6, 3,-3, 6, 3,-6,-3, - -6, 6, 6,-6,-4, 4,-2, 2,-3,-3, 3, 3, - 2, 0,-2, 0, 1, 0, 1, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 2, 0,-2, 0, - -6, 6, 6,-6,-3, 3,-3, 3,-4,-2, 4, 2, - 4,-4,-4, 4, 2,-2, 2,-2, 2, 2,-2,-2, + { 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0}, + {-3, 3, 0, 0, 0, 0, 0, 0,-2,-1, 0, 0}, + { 2,-2, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0}, + { 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0,-3, 3, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 2,-2, 0, 0, 0, 0, 0, 0}, + {-3, 0, 3, 0,-2, 0,-1, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0,-3, 0, 3, 0}, + { 9,-9,-9, 9, 6,-6, 3,-3, 6, 3,-6,-3}, + {-6, 6, 6,-6,-4, 4,-2, 2,-3,-3, 3, 3}, + { 2, 0,-2, 0, 1, 0, 1, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 2, 0,-2, 0}, + {-6, 6, 6,-6,-3, 3,-3, 3,-4,-2, 4, 2}, + { 4,-4,-4, 4, 2,-2, 2,-2, 2, 2,-2,-2} }; double dx = xmax - xmin; double dy = ymax - ymin; diff --git a/src/MANYBODY/pair_airebo.h b/src/MANYBODY/pair_airebo.h index 8e92807afb03100e4325c8bd53a4b0008da70e21..04d3fc399f1f60fdf631d102ccf17643d22907f6 100644 --- a/src/MANYBODY/pair_airebo.h +++ b/src/MANYBODY/pair_airebo.h @@ -21,7 +21,6 @@ PairStyle(airebo,PairAIREBO) #define LMP_PAIR_AIREBO_H #include "pair.h" -#include "my_page.h" #include #include "math_const.h" diff --git a/src/MANYBODY/pair_airebo_morse.cpp b/src/MANYBODY/pair_airebo_morse.cpp index a39f7df82e3b3ad4b246607da09beeae43241497..121f9557fd2e91a0312eb89eb89a55b64e89e2e0 100644 --- a/src/MANYBODY/pair_airebo_morse.cpp +++ b/src/MANYBODY/pair_airebo_morse.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "pair_airebo_morse.h" -#include "force.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp index c157e0763c8115159b134403873e7b50e4c7458d..e604f44003c6d8ff0747d39d4325fe8758eaa9ab 100644 --- a/src/MANYBODY/pair_atm.cpp +++ b/src/MANYBODY/pair_atm.cpp @@ -15,8 +15,9 @@ Contributing author: Sergey Lishchuk ------------------------------------------------------------------------- */ -#include #include "pair_atm.h" +#include +#include #include "atom.h" #include "citeme.h" #include "comm.h" diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index 39f48cd05e2222a83b3a52ef9a1dedf560686ed4..6b7468558e6dd7c73d326570944f05b2733ffa7f 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -32,24 +32,19 @@ Rules"_http://lammps.sandia.gov/open_source.html ------------------------------------------------------------------------- */ +#include "pair_bop.h" #include -#include -#include #include +#include #include -#include "pair_bop.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" #include "force.h" #include "comm.h" -#include "domain.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" -#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_bop.h b/src/MANYBODY/pair_bop.h index 3bd9b8cea970da0ea9ede32c54c3290cf10c4644..eca0ec52b80270aabebece6e12fef727f52553c0 100644 --- a/src/MANYBODY/pair_bop.h +++ b/src/MANYBODY/pair_bop.h @@ -26,8 +26,6 @@ PairStyle(bop,PairBOP) #define LMP_PAIR_BOP_H #include "pair.h" -#include -#include "update.h" namespace LAMMPS_NS { @@ -44,20 +42,20 @@ class PairBOP : public Pair { private: int me; - int maxneigh; // maximum size of neighbor list on this processor - int maxneigh3; // maximum size of neighbor list on this processor - int update_list; // check for changing maximum size of neighbor list - int maxbopn; // maximum size of bop neighbor list for allocation - int maxnall; // maximum size of bop neighbor list for allocation - int *map; // mapping from atom types to elements - int nelements; // # of unique elments - int nr; // increments for the BOP pair potential - int ntheta; // increments for the angle function - int npower; // power of the angular function - int nBOt; // second BO increments - int bop_types; // number of elments in potential - int npairs; // number of element pairs - char **elements; // names of unique elements + int maxneigh; // maximum size of neighbor list on this processor + int maxneigh3; // maximum size of neighbor list on this processor + int update_list; // check for changing maximum size of neighbor list + int maxbopn; // maximum size of bop neighbor list for allocation + int maxnall; // maximum size of bop neighbor list for allocation + int *map; // mapping from atom types to elements + int nelements; // # of unique elments + int nr; // increments for the BOP pair potential + int ntheta; // increments for the angle function + int npower; // power of the angular function + int nBOt; // second BO increments + int bop_types; // number of elments in potential + int npairs; // number of element pairs + char **elements; // names of unique elements int ***elem2param; int nparams; int bop_step; @@ -66,23 +64,22 @@ class PairBOP : public Pair { int allocate_neigh; int nb_pi,nb_sg; int ago1; -// int cnt1; - - int *BOP_index; // index for neighbor list position - int *BOP_total; // index for neighbor list position - int *BOP_index3; // index for neighbor list position - int *BOP_total3; // index for neighbor list position - int *neigh_index; // index for neighbor list position - int *neigh_index3; // index for neighbor list position - int neigh_total; // total number of neighbors stored - int neigh_total3; // total number of neighbors stored - int *cos_index; // index for neighbor cosine if not using on the fly - int *neigh_flag; // index for neighbor cosine if not using on the fly - int *neigh_flag3; // index for neighbor cosine if not using on the fly - int cos_total; // number of cosines stored if not using on the fly - int neigh_ct; // limit for large arrays - -/*Parameters variables*/ + + int *BOP_index; // index for neighbor list position + int *BOP_total; // index for neighbor list position + int *BOP_index3; // index for neighbor list position + int *BOP_total3; // index for neighbor list position + int *neigh_index; // index for neighbor list position + int *neigh_index3; // index for neighbor list position + int neigh_total; // total number of neighbors stored + int neigh_total3; // total number of neighbors stored + int *cos_index; // index for neighbor cosine if not using on the fly + int *neigh_flag; // index for neighbor cosine if not using on the fly + int *neigh_flag3; // index for neighbor cosine if not using on the fly + int cos_total; // number of cosines stored if not using on the fly + int neigh_ct; // limit for large arrays + + // Parameters variables int ncutoff,nfunc; int a_flag; @@ -98,51 +95,50 @@ class PairBOP : public Pair { double beta3,rsmall,rbig,rcore; char **words; - double cutmax; //max cutoff for all elements - int otfly; //Defines whether to do on the fly - //calculations of angles and distances - //on the fly will slow down calculations - //but requires less memory on = 1, off=0 + double cutmax; // max cutoff for all elements + int otfly; // Defines whether to do on the fly + // calculations of angles and distances + // on the fly will slow down calculations + // but requires less memory on = 1, off=0 -/* Neigh variables */ + // Neigh variables double *rcut,*rcut3,*dr,*rdr,*dr3,*rdr3; double *rcutsq,*rcutsq3; double **disij,*rij; double rcutall,rctroot; -/*Triple variables */ + // Triple variables double *cosAng,***dcosAng,***dcAng; -/*Double variables */ + // Double variables double *betaS,*dBetaS,*betaP; double *dBetaP,*repul,*dRepul; -/*Sigma variables */ + // Sigma variables int *itypeSigBk,nSigBk; double sigB,sigB_0; double sigB1; - -/*Pi variables */ + // Pi variables int *itypePiBk,nPiBk; double piB,piB_0; -/*Grids1 variables */ + // Grids1 variables double **pBetaS,**pBetaS1,**pBetaS2,**pBetaS3; double **pBetaS4,**pBetaS5,**pBetaS6; -/*Grids2 variables */ + // Grids2 variables double **pBetaP,**pBetaP1,**pBetaP2,**pBetaP3; double **pBetaP4,**pBetaP5,**pBetaP6; -/*Grids3 variables */ + // Grids3 variables double **pRepul,**pRepul1,**pRepul2,**pRepul3; double **pRepul4,**pRepul5,**pRepul6; @@ -155,13 +151,13 @@ class PairBOP : public Pair { double ****gfunc4,****gfunc5,****gfunc6; double dtheta,rdtheta; -/*Grids4 variables */ + // Grids4 variables double **FsigBO,**FsigBO1,**FsigBO2,**FsigBO3; double **FsigBO4,**FsigBO5,**FsigBO6; double dBO,rdBO; -/* End of BOP variables */ + // End of BOP variables double **rcmin,**rcmax,**rcmaxp; struct B_PI{ @@ -211,14 +207,6 @@ class PairBOP : public Pair { void memory_theta_destroy(); void memory_theta_grow(); double cutoff(double, double, int, double); -/* - double betaSfunc(int, double); - double dBetaSfunc(int, double, double, double); - double betaPfunc(int, double); - double dBetaPfunc(int, double, double, double); - double repulfunc(int, double); - double dRepulfunc(int, double, double, double); -*/ void read_table(char *); void allocate(); @@ -229,9 +217,7 @@ class PairBOP : public Pair { void grow_pi(int,int); void grow_sigma(int,int); }; - } - #endif #endif diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp index 980aa84b2a886cdd5b3b49f1f5986d2cdaef3cb6..2fc4caec7b303bae8de37cfefdd57764f13fe96d 100644 --- a/src/MANYBODY/pair_comb.cpp +++ b/src/MANYBODY/pair_comb.cpp @@ -18,11 +18,11 @@ and Aidan Thompson's Tersoff code in LAMMPS ------------------------------------------------------------------------- */ +#include "pair_comb.h" +#include #include -#include #include #include -#include "pair_comb.h" #include "atom.h" #include "comm.h" #include "force.h" @@ -30,7 +30,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "group.h" -#include "update.h" #include "my_page.h" #include "math_const.h" #include "memory.h" diff --git a/src/MANYBODY/pair_comb.h b/src/MANYBODY/pair_comb.h index c798d5f347698ee1b2809457b5118d08c5bd65f1..19788dfab17190a6a028df2e59d1ea6602e7ecd2 100644 --- a/src/MANYBODY/pair_comb.h +++ b/src/MANYBODY/pair_comb.h @@ -21,7 +21,6 @@ PairStyle(comb,PairComb) #define LMP_PAIR_COMB_H #include "pair.h" -#include "my_page.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp index 097f235ff2007e9cd55833d8fe54d609be192ab3..6f1732dbb74cf8038fada15c09679355c909604f 100644 --- a/src/MANYBODY/pair_comb3.cpp +++ b/src/MANYBODY/pair_comb3.cpp @@ -17,19 +17,19 @@ Dundar Yilmaz (dundar.yilmaz@zirve.edu.tr) ------------------------------------------------------------------------- */ +#include "pair_comb3.h" +#include #include -#include #include #include -#include "pair_comb3.h" #include "atom.h" #include "comm.h" #include "force.h" +#include "my_page.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "group.h" -#include "update.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/MANYBODY/pair_comb3.h b/src/MANYBODY/pair_comb3.h index 5d7e5d6beb1ca2659ae72f8bf6567a3f724c4e52..210f84313961c9fd09f1764f96fb22114306af9e 100644 --- a/src/MANYBODY/pair_comb3.h +++ b/src/MANYBODY/pair_comb3.h @@ -21,7 +21,6 @@ PairStyle(comb3,PairComb3) #define LMP_PAIR_COMB3_H #include "pair.h" -#include "my_page.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index b7957349b6482c68ea7c781ae474a78ba24f20a6..acb0e654d864d85c1f4746dd2a83d3c37c4c6a5d 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -15,11 +15,11 @@ Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL) ------------------------------------------------------------------------- */ +#include "pair_eam.h" +#include #include -#include #include #include -#include "pair_eam.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/MANYBODY/pair_eam.h b/src/MANYBODY/pair_eam.h index 234552157b305e7c439d0b04bf529c5c07a62934..8bcb44c347fad0ebf72c3c3d21b3515a5089d66a 100644 --- a/src/MANYBODY/pair_eam.h +++ b/src/MANYBODY/pair_eam.h @@ -20,7 +20,6 @@ PairStyle(eam,PairEAM) #ifndef LMP_PAIR_EAM_H #define LMP_PAIR_EAM_H -#include #include "pair.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp index c004030240a2925733abba3a1d6b7e8a98e4e82c..5b7f9877d7067e1b0747be7e16f01dfde5a6fcb3 100644 --- a/src/MANYBODY/pair_eam_alloy.cpp +++ b/src/MANYBODY/pair_eam_alloy.cpp @@ -15,10 +15,9 @@ Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_eam_alloy.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MANYBODY/pair_eam_cd.cpp b/src/MANYBODY/pair_eam_cd.cpp index c111c6d950fcfe0a2eeb96a3d3e2d73d85012bc2..28004eae7f653842fa318604019c9489cbc29e48 100644 --- a/src/MANYBODY/pair_eam_cd.cpp +++ b/src/MANYBODY/pair_eam_cd.cpp @@ -17,15 +17,14 @@ Germany Department of Materials Science ------------------------------------------------------------------------- */ +#include "pair_eam_cd.h" +#include #include -#include #include #include -#include "pair_eam_cd.h" #include "atom.h" #include "force.h" #include "comm.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp index bbda84fdf1ac6305159e4272dc29f22c974f1aa6..7e007839227b7a59e77266e445738843fac19800 100644 --- a/src/MANYBODY/pair_eam_fs.cpp +++ b/src/MANYBODY/pair_eam_fs.cpp @@ -15,10 +15,9 @@ Contributing authors: Tim Lau (MIT) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_eam_fs.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index f1c028ef3841916d6bb6f7c0d6b20d53ac938405..dd65d92cddc07bbb96170083ef1f02ba4bbbc7f6 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -15,11 +15,10 @@ Contributing author: Xiaowang Zhou (SNL) ------------------------------------------------------------------------- */ +#include "pair_eim.h" +#include #include -#include -#include #include -#include "pair_eim.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/MANYBODY/pair_eim.h b/src/MANYBODY/pair_eim.h index 50f9934c44b94ad6c74533bba1e9684ddfe15ade..f9fb2d5a773f67572708fbac35afced0ec418dd0 100644 --- a/src/MANYBODY/pair_eim.h +++ b/src/MANYBODY/pair_eim.h @@ -20,7 +20,6 @@ PairStyle(eim,PairEIM) #ifndef LMP_PAIR_EIM_H #define LMP_PAIR_EIM_H -#include #include "pair.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp index e4b74f7a2997b40fc80d7c567af405a5adc7f6ac..667311812ba743a35fcc18fe0ae825a6148f728a 100644 --- a/src/MANYBODY/pair_gw.cpp +++ b/src/MANYBODY/pair_gw.cpp @@ -16,11 +16,11 @@ based on PairTersoff by Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "pair_gw.h" +#include #include -#include #include #include -#include "pair_gw.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/MANYBODY/pair_gw_zbl.cpp b/src/MANYBODY/pair_gw_zbl.cpp index f3dd1bc04b5dddc2c2e505ec2423f5290f0ec81b..d39bf53b993d9cdc7739ed956ab51fda64131d79 100644 --- a/src/MANYBODY/pair_gw_zbl.cpp +++ b/src/MANYBODY/pair_gw_zbl.cpp @@ -16,16 +16,13 @@ Based on PairTersoffZBL by Aidan Thompson (SNL) and David Farrell (NWU) ------------------------------------------------------------------------- */ +#include "pair_gw_zbl.h" +#include #include -#include #include #include -#include "pair_gw_zbl.h" #include "atom.h" #include "update.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "force.h" #include "comm.h" #include "memory.h" diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp index 05cdea8055514db6783733371b18c412a26ddf7b..873a675cd90ec6fd51c1f0b55375c8479a160167 100644 --- a/src/MANYBODY/pair_lcbop.cpp +++ b/src/MANYBODY/pair_lcbop.cpp @@ -16,27 +16,21 @@ based on pair_airebo by Ase Henry (MIT) ------------------------------------------------------------------------- */ +#include "pair_lcbop.h" +#include #include -#include -#include #include -#include -#include "pair_lcbop.h" #include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" #include "force.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "my_page.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; #define MAXLINE 1024 #define TOL 1.0e-9 @@ -1099,19 +1093,6 @@ void PairLCBOP::read_file(char *filename) init coefficients for TF_conj ------------------------------------------------------------------------- */ -#include -#include -#include -template< class function > void print_function( double x_0, double x_1, size_t n, function f, std::ostream &stream ) { - double dx = (x_1-x_0)/n; - for( double x=x_0; x<=x_1+0.0001; x+=dx ) { - double f_val, df; - f_val = f(x, &df); - stream << x << " " << f_val << " " << df << std::endl; - } - stream << std::endl; -} - void PairLCBOP::spline_init() { for( size_t N_conj_ij=0; N_conj_ij<2; N_conj_ij++ ) // N_conj_ij for( size_t N_ij=0; N_ij<4-1; N_ij++ ) diff --git a/src/MANYBODY/pair_lcbop.h b/src/MANYBODY/pair_lcbop.h index 0d7c7a51b17e220abc290d9d348398894c2dc08c..c7a7fab46d849fce6270db3205712495706149f3 100644 --- a/src/MANYBODY/pair_lcbop.h +++ b/src/MANYBODY/pair_lcbop.h @@ -21,7 +21,6 @@ PairStyle(lcbop,PairLCBOP) #define LMP_PAIR_LCBOP_H #include "pair.h" -#include "my_page.h" #include #include "math_const.h" diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp index a61b4034591f8aba6e5882632a4de3bb8bb12908..92456790cc7b71b9ab73b811a51dd82c5249e619 100644 --- a/src/MANYBODY/pair_nb3b_harmonic.cpp +++ b/src/MANYBODY/pair_nb3b_harmonic.cpp @@ -16,18 +16,16 @@ (based on Stillinger-Weber pair style) ------------------------------------------------------------------------- */ +#include "pair_nb3b_harmonic.h" +#include #include -#include #include #include -#include "pair_nb3b_harmonic.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" #include "force.h" #include "comm.h" -#include "memory.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp index d3aca4e8896712504e771ecec6fbadaef933fd9d..d3964b292c79a7003e370ed985dc03f1f0754c86 100644 --- a/src/MANYBODY/pair_polymorphic.cpp +++ b/src/MANYBODY/pair_polymorphic.cpp @@ -16,11 +16,11 @@ This modifies from pair_tersoff.cpp by Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "pair_polymorphic.h" +#include #include -#include #include #include -#include "pair_polymorphic.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" @@ -30,10 +30,7 @@ #include "memory.h" #include "error.h" -#include "math_const.h" - using namespace LAMMPS_NS; -using namespace MathConst; #define MAXLINE 1024 #define DELTA 4 diff --git a/src/MANYBODY/pair_polymorphic.h b/src/MANYBODY/pair_polymorphic.h index 32f1c5414a6714847f2877a643224d50544cf89f..e7c3cd0d26d9596c34e81d11579d4e0fc5dfedfb 100644 --- a/src/MANYBODY/pair_polymorphic.h +++ b/src/MANYBODY/pair_polymorphic.h @@ -22,6 +22,7 @@ PairStyle(polymorphic,PairPolymorphic) #include "pair.h" #include +#include namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_rebo.cpp b/src/MANYBODY/pair_rebo.cpp index e07a1b349555d3e138677673e89e5d8df2214c23..06357d836826d77e906c7717e4cbd61c57426640 100644 --- a/src/MANYBODY/pair_rebo.cpp +++ b/src/MANYBODY/pair_rebo.cpp @@ -26,7 +26,7 @@ PairREBO::PairREBO(LAMMPS *lmp) : PairAIREBO(lmp) { global settings ------------------------------------------------------------------------- */ -void PairREBO::settings(int narg, char **/*arg*/) +void PairREBO::settings(int narg, char ** /* arg */) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index 5a148fb15271de5b8e9b4eb890b0fcf696d9e216..f1d1a6fa9f5713ee9186f37baee49d8aee56c799 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -15,21 +15,19 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "pair_sw.h" +#include #include -#include #include #include -#include "pair_sw.h" #include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "force.h" #include "comm.h" +#include "error.h" +#include "force.h" #include "memory.h" #include "neighbor.h" #include "neigh_list.h" -#include "memory.h" -#include "error.h" +#include "neigh_request.h" using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp index 213b1037bb531293b753a7bd1e5e65488e3d24af..62c74576e0037a1f9b914d9a259cf5803cf61e31 100644 --- a/src/MANYBODY/pair_tersoff.cpp +++ b/src/MANYBODY/pair_tersoff.cpp @@ -15,11 +15,11 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "pair_tersoff.h" +#include #include -#include #include #include -#include "pair_tersoff.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/MANYBODY/pair_tersoff_mod.cpp b/src/MANYBODY/pair_tersoff_mod.cpp index e8fdecfe019ff9b8668990808bae776054d9910d..698dd8fa03dbb642f7c30239c095d3530885ab42 100644 --- a/src/MANYBODY/pair_tersoff_mod.cpp +++ b/src/MANYBODY/pair_tersoff_mod.cpp @@ -16,22 +16,18 @@ Vitaly Dozhdikov (JIHT of RAS) - MOD addition ------------------------------------------------------------------------- */ +#include "pair_tersoff_mod.h" +#include #include -#include #include #include -#include "pair_tersoff_mod.h" #include "atom.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "force.h" #include "comm.h" +#include "math_const.h" #include "memory.h" #include "error.h" -#include "math_const.h" - using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MANYBODY/pair_tersoff_mod_c.cpp b/src/MANYBODY/pair_tersoff_mod_c.cpp index 4a5904c106a91b67e0f27a87e72af52c4a060ccf..6c2c4f4e7a1600bf5bc5dbe1a645b4d4a118130c 100644 --- a/src/MANYBODY/pair_tersoff_mod_c.cpp +++ b/src/MANYBODY/pair_tersoff_mod_c.cpp @@ -15,24 +15,18 @@ Contributing author: Ganga P Purja Pun (George Mason University, Fairfax) ------------------------------------------------------------------------- */ +#include "pair_tersoff_mod_c.h" +#include #include -#include #include #include -#include "pair_tersoff_mod_c.h" #include "atom.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "force.h" #include "comm.h" #include "memory.h" #include "error.h" -#include "math_const.h" - using namespace LAMMPS_NS; -using namespace MathConst; #define MAXLINE 1024 #define DELTA 4 diff --git a/src/MANYBODY/pair_tersoff_zbl.cpp b/src/MANYBODY/pair_tersoff_zbl.cpp index 353e3d22645bd04d4628dc125944b6cef48a6997..ab06e6ec313e8d92af3092494c5637e5ee1ea040 100644 --- a/src/MANYBODY/pair_tersoff_zbl.cpp +++ b/src/MANYBODY/pair_tersoff_zbl.cpp @@ -16,22 +16,19 @@ David Farrell (NWU) - ZBL addition ------------------------------------------------------------------------- */ +#include "pair_tersoff_zbl.h" +#include #include -#include #include #include -#include "pair_tersoff_zbl.h" #include "atom.h" #include "update.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "force.h" #include "comm.h" #include "memory.h" #include "error.h" - #include "math_const.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp index 3d4b1d900efba5d8359fdc046d4002a4a0570113..13b44c58a4cd0a297060bc88b8dba32694143d9e 100644 --- a/src/MANYBODY/pair_vashishta.cpp +++ b/src/MANYBODY/pair_vashishta.cpp @@ -16,21 +16,19 @@ Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "pair_vashishta.h" +#include #include -#include #include #include -#include "pair_vashishta.h" #include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "force.h" #include "comm.h" +#include "error.h" +#include "force.h" #include "memory.h" #include "neighbor.h" #include "neigh_list.h" -#include "memory.h" -#include "error.h" +#include "neigh_request.h" using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_vashishta_table.cpp b/src/MANYBODY/pair_vashishta_table.cpp index d4eaa59f1a1aa2a35ef36a5ee26b7c2dfa30b11d..bf39183b9d5ad9beb1ba3e0246b75385aa79da3f 100644 --- a/src/MANYBODY/pair_vashishta_table.cpp +++ b/src/MANYBODY/pair_vashishta_table.cpp @@ -15,21 +15,14 @@ Contributing author: Anders Hafreager (UiO), andershaf@gmail.com ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_vashishta_table.h" +#include #include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" +#include "error.h" #include "force.h" #include "comm.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp index 7d817ffbb19e87a41299cbbe85e3d12a743db16c..9a4a0b6a7f84500c36ef6abf11773fe47bed8ca1 100644 --- a/src/MC/fix_atom_swap.cpp +++ b/src/MC/fix_atom_swap.cpp @@ -16,14 +16,13 @@ Alexander Stukowski ------------------------------------------------------------------------- */ +#include "fix_atom_swap.h" +#include #include +#include #include -#include #include -#include "fix_atom_swap.h" #include "atom.h" -#include "atom_vec.h" -#include "atom_vec_hybrid.h" #include "update.h" #include "modify.h" #include "fix.h" @@ -40,18 +39,12 @@ #include "dihedral.h" #include "improper.h" #include "kspace.h" -#include "math_const.h" #include "memory.h" #include "error.h" -#include "thermo.h" -#include "output.h" #include "neighbor.h" -#include -using namespace std; using namespace LAMMPS_NS; using namespace FixConst; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/MC/fix_atom_swap.h b/src/MC/fix_atom_swap.h index 19895704f186dd87325acfcefc56d6ad902863ff..a5ce89b16b5f7e83fe72f267f4e96eb1f8acb770 100644 --- a/src/MC/fix_atom_swap.h +++ b/src/MC/fix_atom_swap.h @@ -20,7 +20,6 @@ FixStyle(atom/swap,FixAtomSwap) #ifndef LMP_FIX_MCSWAP_H #define LMP_FIX_MCSWAP_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp index 05edc0509ebca67a3e062d6a70ee012a0dd3376b..2ff0e4126ff069fff99ac6f591832fd4730d199b 100644 --- a/src/MC/fix_bond_break.cpp +++ b/src/MC/fix_bond_break.cpp @@ -11,19 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "fix_bond_break.h" #include #include -#include -#include "fix_bond_break.h" #include "update.h" #include "respa.h" #include "atom.h" -#include "atom_vec.h" #include "force.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "random_mars.h" #include "memory.h" #include "error.h" diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp index e1dd18cb5bebe868d21991498b304ce9a0246d80..3f63a22d605309101c162a83b814f1ef5e6546a3 100644 --- a/src/MC/fix_bond_create.cpp +++ b/src/MC/fix_bond_create.cpp @@ -11,15 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "fix_bond_create.h" #include #include -#include -#include "fix_bond_create.h" #include "update.h" #include "respa.h" #include "atom.h" -#include "atom_vec.h" #include "force.h" #include "pair.h" #include "comm.h" diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp index 9a726679077c22846740281bf2af1f2272bfb795..187c5524168385a0e611aac39f642f411416ec7a 100644 --- a/src/MC/fix_bond_swap.cpp +++ b/src/MC/fix_bond_swap.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_bond_swap.h" +#include #include -#include #include -#include "fix_bond_swap.h" #include "atom.h" #include "force.h" #include "pair.h" @@ -23,7 +23,6 @@ #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "group.h" #include "comm.h" #include "domain.h" #include "modify.h" diff --git a/src/MC/fix_bond_swap.h b/src/MC/fix_bond_swap.h index 0443144c239b4988bb622405357376b7bfd063dd..d24159d80711faaaefbdd93adf0e24ee00582966 100644 --- a/src/MC/fix_bond_swap.h +++ b/src/MC/fix_bond_swap.h @@ -21,7 +21,6 @@ FixStyle(bond/swap,FixBondSwap) #define LMP_FIX_BONDSWAP_H #include "fix.h" -#include "pair.h" namespace LAMMPS_NS { diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index 7ab087933517ae03a7a0794f3917e784ccde95e8..1050fd4712740c9bcee42e9e24b4a8fae24d2fad 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -15,13 +15,12 @@ Contributing author: Paul Crozier, Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "fix_gcmc.h" +#include #include -#include #include -#include "fix_gcmc.h" #include "atom.h" #include "atom_vec.h" -#include "atom_vec_hybrid.h" #include "molecule.h" #include "update.h" #include "modify.h" @@ -43,10 +42,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "thermo.h" -#include "output.h" #include "neighbor.h" -#include "utils.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -371,7 +367,7 @@ void FixGCMC::options(int narg, char **arg) ngrouptypesmax*sizeof(char *), "fix_gcmc:grouptypestrings"); } - grouptypes[ngrouptypes] = atoi(arg[iarg+1]); + grouptypes[ngrouptypes] = force->inumeric(FLERR,arg[iarg+1]); int n = strlen(arg[iarg+2]) + 1; grouptypestrings[ngrouptypes] = new char[n]; strcpy(grouptypestrings[ngrouptypes],arg[iarg+2]); diff --git a/src/MC/fix_gcmc.h b/src/MC/fix_gcmc.h index 5d0b7aab8fab5377f2ec065110b76fce99816851..da4232d19bb79f70c162f0969b5eeb65e57d32bd 100644 --- a/src/MC/fix_gcmc.h +++ b/src/MC/fix_gcmc.h @@ -20,7 +20,6 @@ FixStyle(gcmc,FixGCMC) #ifndef LMP_FIX_GCMC_H #define LMP_FIX_GCMC_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/MC/fix_tfmc.cpp b/src/MC/fix_tfmc.cpp index 46c5e592ae9e54b8e8dce22f4e70060c638295e8..e57f1cdf4a05afccfad4daad003c729b77e1ee2a 100644 --- a/src/MC/fix_tfmc.cpp +++ b/src/MC/fix_tfmc.cpp @@ -22,7 +22,6 @@ #include #include "atom.h" #include "force.h" -#include "update.h" #include "group.h" #include "random_mars.h" #include "comm.h" diff --git a/src/MC/pair_dsmc.cpp b/src/MC/pair_dsmc.cpp index c71eaa2295bd0460c16edb27aee9d5ff915ae955..43bffa7e8d467008e7b058c354416bd1124f1be1 100644 --- a/src/MC/pair_dsmc.cpp +++ b/src/MC/pair_dsmc.cpp @@ -15,12 +15,10 @@ Contributing authors: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_dsmc.h" +#include #include -#include -#include -#include #include -#include "pair_dsmc.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MESSAGE/fix_client_md.cpp b/src/MESSAGE/fix_client_md.cpp index 727481dcc0b6df765da08905c17f16ce1be00a9c..7d4ae13f0ff5279fedef4b069011a4aba045c750 100644 --- a/src/MESSAGE/fix_client_md.cpp +++ b/src/MESSAGE/fix_client_md.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_client_md.h" #include #include -#include "fix_client_md.h" #include "update.h" #include "atom.h" #include "comm.h" diff --git a/src/MESSAGE/message.cpp b/src/MESSAGE/message.cpp index 61221ca26e0b3b558deec55d836aa8f27269f54e..f8fc3497466c6e817f657db5d709bfa481259bdb 100644 --- a/src/MESSAGE/message.cpp +++ b/src/MESSAGE/message.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "message.h" +#include #include "error.h" // CSlib interface diff --git a/src/MESSAGE/server.cpp b/src/MESSAGE/server.cpp index f587fb76dfd6e488a56483edee9db6d56d74ff0e..dbcec0848856af3c93324185aa7e5a042213b042 100644 --- a/src/MESSAGE/server.cpp +++ b/src/MESSAGE/server.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "server.h" +#include #include "error.h" // customize by adding a new server protocol include and enum diff --git a/src/MESSAGE/server_md.cpp b/src/MESSAGE/server_md.cpp index bef327616ea4d7283a8b343efdea2f10fb3b6582..e16095ad4cb75013624c86ec0184de944ebdcf1e 100644 --- a/src/MESSAGE/server_md.cpp +++ b/src/MESSAGE/server_md.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "server_md.h" #include #include -#include "server_md.h" #include "atom.h" #include "atom_vec.h" #include "update.h" diff --git a/src/MISC/compute_msd_nongauss.cpp b/src/MISC/compute_msd_nongauss.cpp index f6291f4204e0633921c69f63c3f0709922e7fe24..6123bf49afec6f851fa9301769b537622063060d 100644 --- a/src/MISC/compute_msd_nongauss.cpp +++ b/src/MISC/compute_msd_nongauss.cpp @@ -15,14 +15,13 @@ Contributing authors: Rob Hoy ------------------------------------------------------------------------- */ -#include #include "compute_msd_nongauss.h" +#include #include "atom.h" #include "update.h" #include "group.h" #include "domain.h" #include "fix_store.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/MISC/compute_ti.cpp b/src/MISC/compute_ti.cpp index d2e43a9f69ffd417afd1668b983b2225960816b1..06188de238b6afa962817f31cb29d9961c1f1572 100644 --- a/src/MISC/compute_ti.cpp +++ b/src/MISC/compute_ti.cpp @@ -15,12 +15,11 @@ Contributing author: Sai Jayaraman (University of Notre Dame) ------------------------------------------------------------------------- */ +#include "compute_ti.h" #include -#include "atom.h" #include -#include "compute_ti.h" +#include "atom.h" #include "update.h" -#include "modify.h" #include "domain.h" #include "force.h" #include "pair.h" diff --git a/src/MISC/dump_xtc.cpp b/src/MISC/dump_xtc.cpp index a82cba20bde3fd4e1c05bac4525abe898d61fbae..1a2b71ab6dfadf6103b2bc4e07a21797452ff67f 100644 --- a/src/MISC/dump_xtc.cpp +++ b/src/MISC/dump_xtc.cpp @@ -22,12 +22,11 @@ support for groups ------------------------------------------------------------------------- */ +#include "dump_xtc.h" #include -#include #include #include #include -#include "dump_xtc.h" #include "domain.h" #include "atom.h" #include "update.h" diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp index 66aed348466d3f427f154a3eb85c54d43544b782..c9d4958594fb07eafdc53f4a8f4dd087ad30ce98 100644 --- a/src/MISC/fix_deposit.cpp +++ b/src/MISC/fix_deposit.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_deposit.h" +#include #include -#include #include -#include "fix_deposit.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" diff --git a/src/MISC/fix_deposit.h b/src/MISC/fix_deposit.h index 38958b80e7a2af9f0d2d088d5b716f4b575ebe19..e3104c890d2d8a9639b70e48b8e7cf0636b98303 100644 --- a/src/MISC/fix_deposit.h +++ b/src/MISC/fix_deposit.h @@ -20,7 +20,6 @@ FixStyle(deposit,FixDeposit) #ifndef LMP_FIX_DEPOSIT_H #define LMP_FIX_DEPOSIT_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/MISC/fix_efield.cpp b/src/MISC/fix_efield.cpp index 004c8ad7bc4ac254c884a44f32cdef7aa03c010a..5a13b93b91a72c42cd11609e6142a95122911a7d 100644 --- a/src/MISC/fix_efield.cpp +++ b/src/MISC/fix_efield.cpp @@ -16,10 +16,9 @@ Stan Moore (Sandia) for dipole terms ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_efield.h" +#include +#include #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/MISC/fix_evaporate.cpp b/src/MISC/fix_evaporate.cpp index 1bf7a15f1fe02372998cad59e425529e7470a822..d868254c50992f71ab6f4279d0e0cf11335ffb5f 100644 --- a/src/MISC/fix_evaporate.cpp +++ b/src/MISC/fix_evaporate.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_evaporate.h" +#include +#include #include "atom.h" #include "atom_vec.h" #include "molecule.h" @@ -25,7 +24,6 @@ #include "force.h" #include "group.h" #include "random_park.h" -#include "random_mars.h" #include "memory.h" #include "error.h" diff --git a/src/MISC/fix_gld.cpp b/src/MISC/fix_gld.cpp index 2bf02889a522a3639b7fd79bbe2c2661b169aea3..380c038e4a3794ada188fbdbd335c0272e7c9840 100644 --- a/src/MISC/fix_gld.cpp +++ b/src/MISC/fix_gld.cpp @@ -16,18 +16,15 @@ Andrew Baczewski (Michigan State/SNL) ------------------------------------------------------------------------- */ +#include "fix_gld.h" +#include #include -#include #include -#include "fix_gld.h" -#include "math_extra.h" #include "atom.h" #include "force.h" #include "update.h" #include "respa.h" #include "comm.h" -#include "input.h" -#include "variable.h" #include "random_mars.h" #include "memory.h" #include "error.h" diff --git a/src/MISC/fix_oneway.cpp b/src/MISC/fix_oneway.cpp index 73853775a30c2d8db9710101c366a6e714bd3903..68a27b68be4a7dfa365ace25146b538abd8b771e 100644 --- a/src/MISC/fix_oneway.cpp +++ b/src/MISC/fix_oneway.cpp @@ -15,14 +15,13 @@ Contributing author: Axel Kohlmeyer (ICTP, Italy) ------------------------------------------------------------------------- */ -#include #include "fix_oneway.h" +#include #include "atom.h" #include "domain.h" #include "error.h" #include "force.h" #include "region.h" -#include "error.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp index 02cce5a0140cf09ad595cfd575ee36b17b79fdb5..1453ceb31712ccdaa5ca566eb00efd9d4b4c2851 100644 --- a/src/MISC/fix_orient_bcc.cpp +++ b/src/MISC/fix_orient_bcc.cpp @@ -18,11 +18,11 @@ (https://dx.doi.org/10.6084/m9.figshare.1488628.v1 ------------------------------------------------------------------------- */ +#include "fix_orient_bcc.h" #include #include #include #include -#include "fix_orient_bcc.h" #include "atom.h" #include "update.h" #include "respa.h" @@ -30,7 +30,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "comm.h" -#include "output.h" #include "force.h" #include "math_const.h" #include "citeme.h" diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp index fc827ceb8f39ac30d1cd6c0b8e67a81154aa7031..082ecaf459663591b6f10867a4337310ffa412eb 100644 --- a/src/MISC/fix_orient_fcc.cpp +++ b/src/MISC/fix_orient_fcc.cpp @@ -15,11 +15,11 @@ Contributing authors: Koenraad Janssens and David Olmsted (SNL) ------------------------------------------------------------------------- */ +#include "fix_orient_fcc.h" #include #include #include #include -#include "fix_orient_fcc.h" #include "atom.h" #include "update.h" #include "respa.h" @@ -27,7 +27,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "comm.h" -#include "output.h" #include "force.h" #include "math_const.h" #include "citeme.h" diff --git a/src/MISC/fix_thermal_conductivity.cpp b/src/MISC/fix_thermal_conductivity.cpp index f1aec3ff6991a1adb129c54d90b0198dbee2831d..d0add6fecb46fddbca8de9ef9bcc7d05e2640b07 100644 --- a/src/MISC/fix_thermal_conductivity.cpp +++ b/src/MISC/fix_thermal_conductivity.cpp @@ -16,11 +16,9 @@ for swapping atoms of different masses ------------------------------------------------------------------------- */ -#include +#include "fix_thermal_conductivity.h" #include #include -#include -#include "fix_thermal_conductivity.h" #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/MISC/fix_ttm.cpp b/src/MISC/fix_ttm.cpp index 170103b0d0798772f15543069bd59b0619eb984a..eb9eb2620dc4ed2c20a9a57b2719ab39a5d75d4f 100644 --- a/src/MISC/fix_ttm.cpp +++ b/src/MISC/fix_ttm.cpp @@ -16,16 +16,14 @@ Carolyn Phillips (University of Michigan) ------------------------------------------------------------------------- */ +#include "fix_ttm.h" #include #include #include -#include -#include "fix_ttm.h" #include "atom.h" #include "force.h" #include "update.h" #include "domain.h" -#include "region.h" #include "respa.h" #include "comm.h" #include "random_mars.h" diff --git a/src/MISC/fix_viscosity.cpp b/src/MISC/fix_viscosity.cpp index 8e33c1c6148ec4ca20fab9219cf7348722b65ddb..d5a97cd4b0cfc998c5c8d2c7008f055117d10a97 100644 --- a/src/MISC/fix_viscosity.cpp +++ b/src/MISC/fix_viscosity.cpp @@ -16,11 +16,10 @@ for swapping atoms of different masses ------------------------------------------------------------------------- */ -#include +#include "fix_viscosity.h" #include +#include #include -#include -#include "fix_viscosity.h" #include "atom.h" #include "domain.h" #include "modify.h" diff --git a/src/MISC/pair_nm_cut.cpp b/src/MISC/pair_nm_cut.cpp index 124832b63eb6c12bd8d35d7b1856a13b7325875a..a084491a78990be8cec35d3606b721d79837a790 100644 --- a/src/MISC/pair_nm_cut.cpp +++ b/src/MISC/pair_nm_cut.cpp @@ -15,11 +15,10 @@ Contributing Author: Julien Devemy (ICCF) ------------------------------------------------------------------------- */ +#include "pair_nm_cut.h" +#include #include -#include -#include #include -#include "pair_nm_cut.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MISC/pair_nm_cut_coul_cut.cpp b/src/MISC/pair_nm_cut_coul_cut.cpp index a8428ab98025b9d99ffd3b5393a542114d3d38d5..df8a34062ad234d6eb76f74676739d8ac741f252 100644 --- a/src/MISC/pair_nm_cut_coul_cut.cpp +++ b/src/MISC/pair_nm_cut_coul_cut.cpp @@ -15,11 +15,10 @@ Contributing Author: Julien Devemy (ICCF) ------------------------------------------------------------------------- */ +#include "pair_nm_cut_coul_cut.h" +#include #include -#include -#include #include -#include "pair_nm_cut_coul_cut.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MISC/pair_nm_cut_coul_long.cpp b/src/MISC/pair_nm_cut_coul_long.cpp index af21f02881bebb5bd9afc73f0a94ce87cdceaa4e..4109fb0d9e23f63d919671c419bb3c403c580b7b 100644 --- a/src/MISC/pair_nm_cut_coul_long.cpp +++ b/src/MISC/pair_nm_cut_coul_long.cpp @@ -15,20 +15,16 @@ Contributing Author: Julien Devemy (ICCF) ------------------------------------------------------------------------- */ +#include "pair_nm_cut_coul_long.h" +#include #include -#include -#include #include -#include "pair_nm_cut_coul_long.h" #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" -#include "update.h" -#include "integrate.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/MISC/xdr_compat.cpp b/src/MISC/xdr_compat.cpp index 2d8d0ce7e5a86edecef5d09130bdc5bd8353fb56..9806b0bbd2ef71f35143f0b9f5a99000b56eb875 100644 --- a/src/MISC/xdr_compat.cpp +++ b/src/MISC/xdr_compat.cpp @@ -1,7 +1,6 @@ +#include "xdr_compat.h" #include -#include #include -#include "xdr_compat.h" /* This file is needed for systems, that do not provide XDR support * in their system libraries. It was written for windows, but will diff --git a/src/MISC/xdr_compat.h b/src/MISC/xdr_compat.h index 30622350807b7d871a9870e17b45cc4890e38646..5dfa01e0e81a180a2f07609dbfc54db7f1b5a10a 100644 --- a/src/MISC/xdr_compat.h +++ b/src/MISC/xdr_compat.h @@ -3,7 +3,6 @@ #include #include -#include #ifdef __cplusplus extern "C" { diff --git a/src/MOLECULE/angle_charmm.cpp b/src/MOLECULE/angle_charmm.cpp index efd1c682f7e52abf52db31773f98ec04932f682b..8a45f293681790410256182380594d743c5e9680 100644 --- a/src/MOLECULE/angle_charmm.cpp +++ b/src/MOLECULE/angle_charmm.cpp @@ -15,9 +15,9 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "angle_charmm.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/angle_charmm.h b/src/MOLECULE/angle_charmm.h index 2228ad8732d06fa47d65f7b3264467b0a0dad3df..444c833d37061a4f0f5508a705cda25667ad40c0 100644 --- a/src/MOLECULE/angle_charmm.h +++ b/src/MOLECULE/angle_charmm.h @@ -20,7 +20,6 @@ AngleStyle(charmm,AngleCharmm) #ifndef LMP_ANGLE_CHARMM_H #define LMP_ANGLE_CHARMM_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_cosine.cpp b/src/MOLECULE/angle_cosine.cpp index 6e1b9fa2fb44fea89300ca3545d24ece7ae880ab..645cf66ff28ab49f498b8ceeb3405abadd94a68c 100644 --- a/src/MOLECULE/angle_cosine.cpp +++ b/src/MOLECULE/angle_cosine.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "angle_cosine.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/angle_cosine.h b/src/MOLECULE/angle_cosine.h index f2406bc5ddf2126950b26f4fbd2bf3549f823ee5..ca1f4178f8addee57fbfba9be9f441e56db09339 100644 --- a/src/MOLECULE/angle_cosine.h +++ b/src/MOLECULE/angle_cosine.h @@ -20,7 +20,6 @@ AngleStyle(cosine,AngleCosine) #ifndef LMP_ANGLE_COSINE_H #define LMP_ANGLE_COSINE_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_cosine_delta.cpp b/src/MOLECULE/angle_cosine_delta.cpp index eca10970f2cc59db564543e52e3c39ca9c4b033c..679a8deb0e8bf08ece02503ffa092b070ac85baa 100644 --- a/src/MOLECULE/angle_cosine_delta.cpp +++ b/src/MOLECULE/angle_cosine_delta.cpp @@ -15,16 +15,12 @@ Contributing author: Axel Kohlmeyer (Temple U), akohlmey at gmail.com ------------------------------------------------------------------------- */ -#include -#include #include "angle_cosine_delta.h" +#include #include "atom.h" #include "neighbor.h" #include "domain.h" -#include "comm.h" #include "force.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/MOLECULE/angle_cosine_delta.h b/src/MOLECULE/angle_cosine_delta.h index 1e19ecaf7962e4883403a51e34d3707df5e1693e..70b574b234d5076a087f8bf32d2275bdae87408c 100644 --- a/src/MOLECULE/angle_cosine_delta.h +++ b/src/MOLECULE/angle_cosine_delta.h @@ -20,7 +20,6 @@ AngleStyle(cosine/delta,AngleCosineDelta) #ifndef LMP_ANGLE_COSINE_DELTA_H #define LMP_ANGLE_COSINE_DELTA_H -#include #include "angle_cosine_squared.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/MOLECULE/angle_cosine_periodic.cpp index cb0a26871ae44e105e94815890d880a5da881d3b..22c2f7ce8b957d1eb7f1882441b0231171f396cf 100644 --- a/src/MOLECULE/angle_cosine_periodic.cpp +++ b/src/MOLECULE/angle_cosine_periodic.cpp @@ -15,9 +15,9 @@ Contributing author: Tod A Pascal (Caltech) ------------------------------------------------------------------------- */ -#include -#include #include "angle_cosine_periodic.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/angle_cosine_periodic.h b/src/MOLECULE/angle_cosine_periodic.h index e131e85101e8d452bca29cc4389bd268baf5a8d2..f0188b6c171e811b74a02370b86fc0b2d34f4f06 100644 --- a/src/MOLECULE/angle_cosine_periodic.h +++ b/src/MOLECULE/angle_cosine_periodic.h @@ -20,7 +20,6 @@ AngleStyle(cosine/periodic, AngleCosinePeriodic) #ifndef LMP_ANGLE_PERIODIC_H #define LMP_ANGLE_PERIODIC_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_cosine_squared.cpp b/src/MOLECULE/angle_cosine_squared.cpp index 28d63344a49929f69a7d9fbcf1632b72658cc93f..56b3ee58cf45e46ee07cd3d361001651c9bb3bcd 100644 --- a/src/MOLECULE/angle_cosine_squared.cpp +++ b/src/MOLECULE/angle_cosine_squared.cpp @@ -15,9 +15,9 @@ Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U) ------------------------------------------------------------------------- */ -#include -#include #include "angle_cosine_squared.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/angle_cosine_squared.h b/src/MOLECULE/angle_cosine_squared.h index 8e8c84c0f99c98a107d8072cdfac53badf04c3b7..a19a9238509a0f4e00cce7230f27388555a2b411 100644 --- a/src/MOLECULE/angle_cosine_squared.h +++ b/src/MOLECULE/angle_cosine_squared.h @@ -20,7 +20,6 @@ AngleStyle(cosine/squared,AngleCosineSquared) #ifndef LMP_ANGLE_COSINE_SQUARED_H #define LMP_ANGLE_COSINE_SQUARED_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_harmonic.cpp b/src/MOLECULE/angle_harmonic.cpp index 48b493d9b2b7741d90bb7172a9e7bae27c0d74c3..2e96884c9da82e134b62da8fc28af6a093607366 100644 --- a/src/MOLECULE/angle_harmonic.cpp +++ b/src/MOLECULE/angle_harmonic.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "angle_harmonic.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/angle_harmonic.h b/src/MOLECULE/angle_harmonic.h index e0c067653bfec47c0e1ed4fb0455d191ea747cb7..f371178d58a64585c338f0f9378d142ad0766f02 100644 --- a/src/MOLECULE/angle_harmonic.h +++ b/src/MOLECULE/angle_harmonic.h @@ -20,7 +20,6 @@ AngleStyle(harmonic,AngleHarmonic) #ifndef LMP_ANGLE_HARMONIC_H #define LMP_ANGLE_HARMONIC_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp index 898ce49be7a627a0038eda0c95aa0b2ee4e924ef..54046c2ba8acad6c9ef3d48c8c53ae5577ca25b2 100644 --- a/src/MOLECULE/angle_table.cpp +++ b/src/MOLECULE/angle_table.cpp @@ -15,10 +15,11 @@ Contributing author: Chuanfu Luo (luochuanfu@gmail.com) ------------------------------------------------------------------------- */ +#include "angle_table.h" +#include #include #include #include -#include "angle_table.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/angle_table.h b/src/MOLECULE/angle_table.h index 81e6c2ed8999fc87a3db93db3a1d949a719227eb..8c854dc2e626cb9fdb45fc326f49f966b5787b37 100644 --- a/src/MOLECULE/angle_table.h +++ b/src/MOLECULE/angle_table.h @@ -20,7 +20,6 @@ AngleStyle(table,AngleTable) #ifndef LMP_ANGLE_TABLE_H #define LMP_ANGLE_TABLE_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/atom_vec_angle.cpp b/src/MOLECULE/atom_vec_angle.cpp index bdafdae148b04ee15ec647ba874d8005e8cebee2..4eba471b8f1bdb13fe841ebd93f14db6e875c1db 100644 --- a/src/MOLECULE/atom_vec_angle.cpp +++ b/src/MOLECULE/atom_vec_angle.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_angle.h" #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/MOLECULE/atom_vec_bond.cpp b/src/MOLECULE/atom_vec_bond.cpp index 275c42494177aef3ee3c07a69bcd316c8becb350..0bcd614f94b4e5e7fd9822223af9538e86ee5d07 100644 --- a/src/MOLECULE/atom_vec_bond.cpp +++ b/src/MOLECULE/atom_vec_bond.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_bond.h" #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/MOLECULE/atom_vec_full.cpp b/src/MOLECULE/atom_vec_full.cpp index 036324cb2cb864e4b4066b19f8823071ea04b091..76c60ba1219db6318d756e87a5a7eb9f49ec69a7 100644 --- a/src/MOLECULE/atom_vec_full.cpp +++ b/src/MOLECULE/atom_vec_full.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_full.h" #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/MOLECULE/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp index 49606f0a696f152b65bb96d3dc42359d8a28dc56..73cec704566560c0a13774280f4f6734e313ed86 100644 --- a/src/MOLECULE/atom_vec_molecular.cpp +++ b/src/MOLECULE/atom_vec_molecular.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_molecular.h" #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/MOLECULE/atom_vec_template.cpp b/src/MOLECULE/atom_vec_template.cpp index 14e7736b50da887368c741caf8c553beb90a7b0f..c9ccfc6d2b0fa93a3b48fabbb710149c53f3b376 100644 --- a/src/MOLECULE/atom_vec_template.cpp +++ b/src/MOLECULE/atom_vec_template.cpp @@ -11,12 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "atom_vec_template.h" #include "atom.h" #include "molecule.h" -#include "force.h" #include "comm.h" #include "domain.h" #include "modify.h" diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp index c023a7e81ed9633cbcb6a35aa70913f4e2f30f85..776291701b8d72f394f5057c71eea5784c2286ba 100644 --- a/src/MOLECULE/bond_fene.cpp +++ b/src/MOLECULE/bond_fene.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "bond_fene.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "update.h" #include "force.h" diff --git a/src/MOLECULE/bond_fene.h b/src/MOLECULE/bond_fene.h index 58cd6ce2894855ec390424f0ee8a9681833effcd..1963e3ca2286a642e63001330dfe895d7aef066e 100644 --- a/src/MOLECULE/bond_fene.h +++ b/src/MOLECULE/bond_fene.h @@ -20,7 +20,6 @@ BondStyle(fene,BondFENE) #ifndef LMP_BOND_FENE_H #define LMP_BOND_FENE_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp index b1bfdc6a1b9b5fac937a4d48eac66ee1c7e9535b..d03dfd912549e441fafbb6c2dc656332dfed6177 100644 --- a/src/MOLECULE/bond_fene_expand.cpp +++ b/src/MOLECULE/bond_fene_expand.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "bond_fene_expand.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "update.h" #include "force.h" diff --git a/src/MOLECULE/bond_fene_expand.h b/src/MOLECULE/bond_fene_expand.h index cb316ac5f2b366cd534e1429088eaffe6cce15e9..8cfc17dc686213dc0b56fe926bf45595143c78e6 100644 --- a/src/MOLECULE/bond_fene_expand.h +++ b/src/MOLECULE/bond_fene_expand.h @@ -20,7 +20,6 @@ BondStyle(fene/expand,BondFENEExpand) #ifndef LMP_BOND_FENE_EXPAND_H #define LMP_BOND_FENE_EXPAND_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_gromos.cpp b/src/MOLECULE/bond_gromos.cpp index f65adeb2cbffb551e07c42d4573d889af158c217..284c9202fd08612914e67a0cebdf9f141b13e2be 100644 --- a/src/MOLECULE/bond_gromos.cpp +++ b/src/MOLECULE/bond_gromos.cpp @@ -15,13 +15,11 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include #include "bond_gromos.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/MOLECULE/bond_gromos.h b/src/MOLECULE/bond_gromos.h index c26ad64b3d6ad5bcdeaaa3b8f94303299e7b0e82..966b914437bf9f4dfb36d0dc94fac73f375f440d 100644 --- a/src/MOLECULE/bond_gromos.h +++ b/src/MOLECULE/bond_gromos.h @@ -20,7 +20,6 @@ BondStyle(gromos,BondGromos) #ifndef LMP_BOND_GROMOS_H #define LMP_BOND_GROMOS_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_harmonic.cpp b/src/MOLECULE/bond_harmonic.cpp index cb8434ce6edfab9a22f3985abcc8e7e0561ac7dc..7b19034629827cae20edec4ab5b03cac64165caa 100644 --- a/src/MOLECULE/bond_harmonic.cpp +++ b/src/MOLECULE/bond_harmonic.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "bond_harmonic.h" +#include #include -#include #include -#include "bond_harmonic.h" #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/MOLECULE/bond_harmonic.h b/src/MOLECULE/bond_harmonic.h index 5c692b2a8e1add8419d7394649aa4021afd11985..576e63629bbb4cb727f0356179832cf4341c2f99 100644 --- a/src/MOLECULE/bond_harmonic.h +++ b/src/MOLECULE/bond_harmonic.h @@ -20,7 +20,6 @@ BondStyle(harmonic,BondHarmonic) #ifndef LMP_BOND_HARMONIC_H #define LMP_BOND_HARMONIC_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_morse.cpp b/src/MOLECULE/bond_morse.cpp index 91dd2dbc490bc55fd8760b7f786d52d3c5f73b7f..6e16070cae322dc23195a460e6a4e67d2154e0a5 100644 --- a/src/MOLECULE/bond_morse.cpp +++ b/src/MOLECULE/bond_morse.cpp @@ -15,12 +15,11 @@ Contributing author: Jeff Greathouse (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "bond_morse.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/MOLECULE/bond_morse.h b/src/MOLECULE/bond_morse.h index c4d60bc21768c1ffe3ddf806d26dfea6dd475a95..030a94a8da964c764d72d80167933076aeb362e2 100644 --- a/src/MOLECULE/bond_morse.h +++ b/src/MOLECULE/bond_morse.h @@ -20,7 +20,6 @@ BondStyle(morse,BondMorse) #ifndef LMP_BOND_MORSE_H #define LMP_BOND_MORSE_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_nonlinear.cpp b/src/MOLECULE/bond_nonlinear.cpp index 9999ead47f31985404774018564af752ed48f972..e06b1b9aac1b46b3b0eec342540158a37e601156 100644 --- a/src/MOLECULE/bond_nonlinear.cpp +++ b/src/MOLECULE/bond_nonlinear.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "bond_nonlinear.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/MOLECULE/bond_nonlinear.h b/src/MOLECULE/bond_nonlinear.h index 175421264b91e11b0f71453716bb11c774f00d34..7782b937784869bc62b4a674d64bf0a847ce1906 100644 --- a/src/MOLECULE/bond_nonlinear.h +++ b/src/MOLECULE/bond_nonlinear.h @@ -20,7 +20,6 @@ BondStyle(nonlinear,BondNonlinear) #ifndef LMP_BOND_NONLINEAR_H #define LMP_BOND_NONLINEAR_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_quartic.cpp b/src/MOLECULE/bond_quartic.cpp index 895202ff0079fcb15afa23578b0d570bd6ef9526..352b642bbec3d5880163232fbe22e40259315b24 100644 --- a/src/MOLECULE/bond_quartic.cpp +++ b/src/MOLECULE/bond_quartic.cpp @@ -15,14 +15,12 @@ Contributing authors: Chris Lorenz and Mark Stevens (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "bond_quartic.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" -#include "update.h" #include "force.h" #include "pair.h" #include "memory.h" diff --git a/src/MOLECULE/bond_quartic.h b/src/MOLECULE/bond_quartic.h index 2aaa76e2c374e531637455f612af56ab30bcc3d8..60ccf307b9380aa34e2b8cb57c80e4f62c7597c4 100644 --- a/src/MOLECULE/bond_quartic.h +++ b/src/MOLECULE/bond_quartic.h @@ -20,7 +20,6 @@ BondStyle(quartic,BondQuartic) #ifndef LMP_BOND_QUARTIC_H #define LMP_BOND_QUARTIC_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp index 170afc27f01f59b690fb0a2b46af2e1b9cb261f9..ce41303a7d4ec605cb3f8b7fd03622616b5dd1fb 100644 --- a/src/MOLECULE/bond_table.cpp +++ b/src/MOLECULE/bond_table.cpp @@ -15,13 +15,13 @@ Contributing author: Chuanfu Luo (luochuanfu@gmail.com) ------------------------------------------------------------------------- */ +#include "bond_table.h" +#include #include #include #include -#include "bond_table.h" #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/MOLECULE/bond_table.h b/src/MOLECULE/bond_table.h index 5d4f2e84934d2f45b0a528d7eccef3134903eadd..b08059415b345992801e0282f21a153707966fa1 100644 --- a/src/MOLECULE/bond_table.h +++ b/src/MOLECULE/bond_table.h @@ -20,7 +20,6 @@ BondStyle(table,BondTable) #ifndef LMP_BOND_TABLE_H #define LMP_BOND_TABLE_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp index 68c62eb4fd338a2ef73bf66c940915f85c9be05d..8cc071302466cda461449431d8374e81140fdb98 100644 --- a/src/MOLECULE/dihedral_charmm.cpp +++ b/src/MOLECULE/dihedral_charmm.cpp @@ -15,15 +15,13 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "dihedral_charmm.h" #include #include -#include #include -#include "dihedral_charmm.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "pair.h" #include "update.h" diff --git a/src/MOLECULE/dihedral_charmm.h b/src/MOLECULE/dihedral_charmm.h index 8f51b398dbfb57e5bf57788180dbc9cfab21bf9a..4be3925dad0a539a374c35a728b1c0679fcd4ddc 100644 --- a/src/MOLECULE/dihedral_charmm.h +++ b/src/MOLECULE/dihedral_charmm.h @@ -20,7 +20,6 @@ DihedralStyle(charmm,DihedralCharmm) #ifndef LMP_DIHEDRAL_CHARMM_H #define LMP_DIHEDRAL_CHARMM_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_charmmfsw.cpp b/src/MOLECULE/dihedral_charmmfsw.cpp index f65d01e9ed326c6cedd94bf1db607ec539864513..f384c4cd3650005afe34ff875c3fc82b2359f42f 100644 --- a/src/MOLECULE/dihedral_charmmfsw.cpp +++ b/src/MOLECULE/dihedral_charmmfsw.cpp @@ -18,15 +18,13 @@ with additional assistance from Robert A. Latour, Clemson University ------------------------------------------------------------------------- */ +#include "dihedral_charmmfsw.h" #include #include -#include #include -#include "dihedral_charmmfsw.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "pair.h" #include "update.h" diff --git a/src/MOLECULE/dihedral_charmmfsw.h b/src/MOLECULE/dihedral_charmmfsw.h index dd31067a8dba9bd39b01373fba5b3dc29da842d4..b33250004bc8bd14f2c0dee8bb58dd3ba05f6917 100644 --- a/src/MOLECULE/dihedral_charmmfsw.h +++ b/src/MOLECULE/dihedral_charmmfsw.h @@ -20,7 +20,6 @@ DihedralStyle(charmmfsw,DihedralCharmmfsw) #ifndef LMP_DIHEDRAL_CHARMMFSW_H #define LMP_DIHEDRAL_CHARMMFSW_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_harmonic.cpp b/src/MOLECULE/dihedral_harmonic.cpp index ddb94dc571aa591dc28fae710beda8b7ee23ee69..f1e5811a8499f0e0d5ad68a5ad6274b43b2d0f00 100644 --- a/src/MOLECULE/dihedral_harmonic.cpp +++ b/src/MOLECULE/dihedral_harmonic.cpp @@ -15,14 +15,12 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "dihedral_harmonic.h" #include #include -#include -#include "dihedral_harmonic.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "memory.h" diff --git a/src/MOLECULE/dihedral_harmonic.h b/src/MOLECULE/dihedral_harmonic.h index 20312612568ae92681d8a79649069e9496028896..938e59918bd5256dee97de73c93b05025df432ee 100644 --- a/src/MOLECULE/dihedral_harmonic.h +++ b/src/MOLECULE/dihedral_harmonic.h @@ -20,7 +20,6 @@ DihedralStyle(harmonic,DihedralHarmonic) #ifndef LMP_DIHEDRAL_HARMONIC_H #define LMP_DIHEDRAL_HARMONIC_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_helix.cpp b/src/MOLECULE/dihedral_helix.cpp index d19731c0970f91dfd06c6f34f7821bcd318f2457..56f7a3b5e8b79a05fcaaf9b4806c33401b0cf330 100644 --- a/src/MOLECULE/dihedral_helix.cpp +++ b/src/MOLECULE/dihedral_helix.cpp @@ -16,13 +16,11 @@ Mark Stevens (Sandia) ------------------------------------------------------------------------- */ +#include "dihedral_helix.h" #include #include -#include -#include "dihedral_helix.h" #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "update.h" diff --git a/src/MOLECULE/dihedral_helix.h b/src/MOLECULE/dihedral_helix.h index 745ab841156164e095c0ffbc55f93705d83f7662..0213c59e8a6854e09a1502668f6ca52f4aed08f1 100644 --- a/src/MOLECULE/dihedral_helix.h +++ b/src/MOLECULE/dihedral_helix.h @@ -20,7 +20,6 @@ DihedralStyle(helix,DihedralHelix) #ifndef LMP_DIHEDRAL_HELIX_H #define LMP_DIHEDRAL_HELIX_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_multi_harmonic.cpp b/src/MOLECULE/dihedral_multi_harmonic.cpp index 04e7bbb62754b9d1501819533aefcfca7e6a8a4d..eda7cede3e63b83a0fcabccad5ddbc09713f1ad0 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.cpp +++ b/src/MOLECULE/dihedral_multi_harmonic.cpp @@ -15,12 +15,11 @@ Contributing author: Mathias Puetz (SNL) and friends ------------------------------------------------------------------------- */ -#include -#include #include "dihedral_multi_harmonic.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "update.h" diff --git a/src/MOLECULE/dihedral_multi_harmonic.h b/src/MOLECULE/dihedral_multi_harmonic.h index 32f17e75ae4a79571a6cdca27e199405d25069c8..bb3d7183f72289cdfd6d12f10485dc6d4fe22d7d 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.h +++ b/src/MOLECULE/dihedral_multi_harmonic.h @@ -20,7 +20,6 @@ DihedralStyle(multi/harmonic,DihedralMultiHarmonic) #ifndef LMP_DIHEDRAL_MULTI_HARMONIC_H #define LMP_DIHEDRAL_MULTI_HARMONIC_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp index 293245e41145b7573a889b4b348c2c51005a0b99..556efd850a7d5eee0489bf9a2853d0cb46bce7ae 100644 --- a/src/MOLECULE/dihedral_opls.cpp +++ b/src/MOLECULE/dihedral_opls.cpp @@ -15,13 +15,12 @@ Contributing author: Mark Stevens (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "dihedral_opls.h" +#include +#include #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "memory.h" diff --git a/src/MOLECULE/dihedral_opls.h b/src/MOLECULE/dihedral_opls.h index c1e64ada1ee2bbc83e756ad6384605f6d6ea098d..01878173cdeb1371082bad4f1fefcab7c5fe7a7a 100644 --- a/src/MOLECULE/dihedral_opls.h +++ b/src/MOLECULE/dihedral_opls.h @@ -20,7 +20,6 @@ DihedralStyle(opls,DihedralOPLS) #ifndef LMP_DIHEDRAL_OPLS_H #define LMP_DIHEDRAL_OPLS_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp index 3395c7ef14a5e94e73e05c15ba99961641e63a80..fb0a550898c52b02e1300cb09d4f8b3f91ef5b38 100644 --- a/src/MOLECULE/fix_cmap.cpp +++ b/src/MOLECULE/fix_cmap.cpp @@ -27,20 +27,16 @@ - MacKerell et al., J. Comput. Chem. 25(2004):1400-1415. ------------------------------------------------------------------------- */ +#include "fix_cmap.h" #include #include #include #include -#include -#include "fix_cmap.h" #include "atom.h" -#include "atom_vec.h" #include "update.h" #include "respa.h" -#include "modify.h" #include "domain.h" #include "force.h" -#include "group.h" #include "comm.h" #include "math_const.h" #include "memory.h" diff --git a/src/MOLECULE/improper_cvff.cpp b/src/MOLECULE/improper_cvff.cpp index 01e9729e80c628e69fad9d67220c7259ba8936b7..abd2d4e11e98967de6c1c18808d35023eacde9bb 100644 --- a/src/MOLECULE/improper_cvff.cpp +++ b/src/MOLECULE/improper_cvff.cpp @@ -11,14 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "improper_cvff.h" #include #include -#include -#include "improper_cvff.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "memory.h" diff --git a/src/MOLECULE/improper_cvff.h b/src/MOLECULE/improper_cvff.h index d4c30cc2eead856bc70d8215add5d9a58b9942df..055d2ca9b83bc77440fc5f345e5f9c2b9c74802c 100644 --- a/src/MOLECULE/improper_cvff.h +++ b/src/MOLECULE/improper_cvff.h @@ -20,7 +20,6 @@ ImproperStyle(cvff,ImproperCvff) #ifndef LMP_IMPROPER_CVFF_H #define LMP_IMPROPER_CVFF_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/improper_harmonic.cpp b/src/MOLECULE/improper_harmonic.cpp index c5421fffdb4b61df2fd651e3588d4ed4ddf2be89..778fe646e16932327d8fc9e30b0b37b44ffbb9e1 100644 --- a/src/MOLECULE/improper_harmonic.cpp +++ b/src/MOLECULE/improper_harmonic.cpp @@ -11,14 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "improper_harmonic.h" #include #include -#include -#include "improper_harmonic.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "math_const.h" diff --git a/src/MOLECULE/improper_harmonic.h b/src/MOLECULE/improper_harmonic.h index fbbb8d33d6362ff934251ef1c90d665c669f7363..5949c6911e9f1dee7ac915288be0ae1acc59be56 100644 --- a/src/MOLECULE/improper_harmonic.h +++ b/src/MOLECULE/improper_harmonic.h @@ -20,7 +20,6 @@ ImproperStyle(harmonic,ImproperHarmonic) #ifndef LMP_IMPROPER_HARMONIC_H #define LMP_IMPROPER_HARMONIC_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp index 3de46df0f34e54842ae9de39f791d46c8567ca6b..d3adf199935746039992fe55a8934ec7e4b444ec 100644 --- a/src/MOLECULE/improper_umbrella.cpp +++ b/src/MOLECULE/improper_umbrella.cpp @@ -15,14 +15,12 @@ Contributing author: Tod A Pascal (Caltech) ------------------------------------------------------------------------- */ +#include "improper_umbrella.h" #include #include -#include -#include "improper_umbrella.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "math_const.h" diff --git a/src/MOLECULE/improper_umbrella.h b/src/MOLECULE/improper_umbrella.h index dc2262d01c31d48713c74bdcd1d347c7f8c98d15..da9d6c8f4bb7f6ab39a7be2eff335297bcd42a09 100644 --- a/src/MOLECULE/improper_umbrella.h +++ b/src/MOLECULE/improper_umbrella.h @@ -20,7 +20,6 @@ ImproperStyle(umbrella,ImproperUmbrella) #ifndef LMP_IMPROPER_UMBRELLA_H #define LMP_IMPROPER_UMBRELLA_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.cpp b/src/MOLECULE/pair_hbond_dreiding_lj.cpp index ddc11100819169035f3931e5eb92d1a3efb8d8fe..53c310170850aa348b837f329e8006f0dd397213 100644 --- a/src/MOLECULE/pair_hbond_dreiding_lj.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_lj.cpp @@ -15,15 +15,12 @@ Contributing author: Tod A Pascal (Caltech) ------------------------------------------------------------------------- */ +#include "pair_hbond_dreiding_lj.h" #include -#include -#include #include -#include "pair_hbond_dreiding_lj.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp index 055f0ed46b88128baaca7c045fcc903d5962a3f7..3039a662e6c98ce54202b4b0bfa05517f8f6cc98 100644 --- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp @@ -15,15 +15,12 @@ Contributing author: Tod A Pascal (Caltech) ------------------------------------------------------------------------- */ +#include "pair_hbond_dreiding_morse.h" #include -#include -#include #include -#include "pair_hbond_dreiding_morse.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp index af4611e0148517ffdb5c31f8ac42ee7491c6571c..5ebfe0a11082b4952260140df926776a2956dba7 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp @@ -15,11 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_charmm_coul_charmm.h" +#include #include -#include -#include #include -#include "pair_lj_charmm_coul_charmm.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp index d68d5e8f6d669d716a58b600a04b52fe052ed981..ff7dbb290b37fc5c6e7fd7e20d44cb4c62a8829f 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp @@ -11,8 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_lj_charmm_coul_charmm_implicit.h" #include "atom.h" #include "force.h" diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp index 0e1cbd85a5b91d11c9071d051c56fb6fc7dab0cc..4fb7cc522902b016c26b3cef6053d4747bb44346 100644 --- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp +++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp @@ -19,11 +19,10 @@ with additional assistance from Robert A. Latour, Clemson University ------------------------------------------------------------------------- */ +#include "pair_lj_charmmfsw_coul_charmmfsh.h" +#include #include -#include -#include #include -#include "pair_lj_charmmfsw_coul_charmmfsh.h" #include "atom.h" #include "update.h" #include "comm.h" diff --git a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp index 2b3d2c60f5d686c0706fb6efd09fc2ba72db01e6..e5f25a511b4805a1e105459589830315789156c4 100644 --- a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp +++ b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp @@ -15,10 +15,10 @@ Contributing author: Pavel Elkind (Gothenburg University) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_tip4p_cut.h" +#include #include -#include #include -#include "pair_lj_cut_tip4p_cut.h" #include "atom.h" #include "force.h" #include "neighbor.h" diff --git a/src/MOLECULE/pair_tip4p_cut.cpp b/src/MOLECULE/pair_tip4p_cut.cpp index e6fb9aab99e0eeb3c60f1dd0f7ecb376686f3a11..3a6702c9b26eefed68d0c927b0886d99901574ee 100644 --- a/src/MOLECULE/pair_tip4p_cut.cpp +++ b/src/MOLECULE/pair_tip4p_cut.cpp @@ -15,9 +15,9 @@ Contributing author: Pavel Elkind (Gothenburg University) ------------------------------------------------------------------------- */ -#include -#include #include "pair_tip4p_cut.h" +#include +#include #include "atom.h" #include "force.h" #include "neighbor.h" @@ -26,12 +26,10 @@ #include "angle.h" #include "bond.h" #include "comm.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/MPIIO/dump_atom_mpiio.cpp b/src/MPIIO/dump_atom_mpiio.cpp index f2f299144261d9d6035e49db8e1f30dedeea38ac..2b663554cc09621efd1524f4fad4994584d3ace3 100644 --- a/src/MPIIO/dump_atom_mpiio.cpp +++ b/src/MPIIO/dump_atom_mpiio.cpp @@ -15,12 +15,12 @@ Contributing author: Paul Coffman (IBM) ------------------------------------------------------------------------- */ -#include #include "dump_atom_mpiio.h" +#include +#include +#include #include "domain.h" -#include "atom.h" #include "update.h" -#include "group.h" #include "memory.h" #include "error.h" diff --git a/src/MPIIO/dump_atom_mpiio.h b/src/MPIIO/dump_atom_mpiio.h index ad49fa11823a21354c0340b335a01129e20fd97b..36b43e3f0867fcfc86594f3406828d02bf955848 100644 --- a/src/MPIIO/dump_atom_mpiio.h +++ b/src/MPIIO/dump_atom_mpiio.h @@ -21,7 +21,6 @@ DumpStyle(atom/mpiio,DumpAtomMPIIO) #define LMP_DUMP_ATOM_MPIIO_H #include "dump_atom.h" -#include namespace LAMMPS_NS { diff --git a/src/MPIIO/dump_cfg_mpiio.cpp b/src/MPIIO/dump_cfg_mpiio.cpp index c580d2e7af71cdb1b7ca037392e0e0656b6ac5b0..31848b550c253cd9a350e794a78c349477b6e0cb 100644 --- a/src/MPIIO/dump_cfg_mpiio.cpp +++ b/src/MPIIO/dump_cfg_mpiio.cpp @@ -15,18 +15,12 @@ Contributing author: Paul Coffman (IBM) ------------------------------------------------------------------------- */ +#include "dump_cfg_mpiio.h" #include #include #include -#include "dump_cfg_mpiio.h" #include "atom.h" #include "domain.h" -#include "comm.h" -#include "modify.h" -#include "compute.h" -#include "input.h" -#include "fix.h" -#include "variable.h" #include "update.h" #include "memory.h" #include "error.h" diff --git a/src/MPIIO/dump_custom_mpiio.cpp b/src/MPIIO/dump_custom_mpiio.cpp index 3650ca994e4d519d319ae0d182cb9b2011afd764..dca5833c5b885d65deb78eaf9ba93eb8ff35a746 100644 --- a/src/MPIIO/dump_custom_mpiio.cpp +++ b/src/MPIIO/dump_custom_mpiio.cpp @@ -15,20 +15,15 @@ Contributing author: Paul Coffman (IBM) ------------------------------------------------------------------------- */ +#include "dump_custom_mpiio.h" #include #include #include -#include "dump_custom_mpiio.h" -#include "atom.h" -#include "force.h" #include "domain.h" -#include "region.h" -#include "group.h" #include "input.h" #include "variable.h" #include "update.h" #include "modify.h" -#include "compute.h" #include "fix.h" #include "memory.h" #include "error.h" diff --git a/src/MPIIO/dump_xyz_mpiio.cpp b/src/MPIIO/dump_xyz_mpiio.cpp index f15d340cd14f3f470ac981e80d29c7428c2f6e09..f5caab3a9c56560795c949e7a6debe97be071e20 100644 --- a/src/MPIIO/dump_xyz_mpiio.cpp +++ b/src/MPIIO/dump_xyz_mpiio.cpp @@ -15,21 +15,13 @@ Contributing author: Paul Coffman (IBM) ------------------------------------------------------------------------- */ +#include "dump_xyz_mpiio.h" #include #include #include -#include "dump_xyz_mpiio.h" -#include "atom.h" -#include "force.h" #include "domain.h" -#include "region.h" -#include "group.h" -#include "input.h" -#include "variable.h" #include "update.h" -#include "modify.h" #include "compute.h" -#include "fix.h" #include "memory.h" #include "error.h" diff --git a/src/MPIIO/restart_mpiio.cpp b/src/MPIIO/restart_mpiio.cpp index 804df211dc4579957b14fa1b3e94b0bcf36c73f6..e8ef5c6c4ed1af306be93c7688e40084c4d9f615 100644 --- a/src/MPIIO/restart_mpiio.cpp +++ b/src/MPIIO/restart_mpiio.cpp @@ -15,9 +15,9 @@ Contributing author: Paul Coffman (IBM) ------------------------------------------------------------------------- */ +#include "restart_mpiio.h" #include #include -#include "restart_mpiio.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/MSCG/fix_mscg.cpp b/src/MSCG/fix_mscg.cpp index b28259524071672463f17051e5a388e0d89d133d..caa9a528a7875963e644f9df52a4b35f63ad1cb5 100644 --- a/src/MSCG/fix_mscg.cpp +++ b/src/MSCG/fix_mscg.cpp @@ -15,10 +15,10 @@ Contributing authors: Lauren Abbott (Sandia) ------------------------------------------------------------------------- */ +#include "fix_mscg.h" #include #include #include -#include "fix_mscg.h" #include "mscg.h" #include "atom.h" #include "comm.h" diff --git a/src/OPT/pair_eam_opt.cpp b/src/OPT/pair_eam_opt.cpp index fc2b6731ee8d455a4ffd2c71d22cd7bc8c06b87c..ad24aaee6380a004fc10431ca881146e6f795ef5 100644 --- a/src/OPT/pair_eam_opt.cpp +++ b/src/OPT/pair_eam_opt.cpp @@ -19,9 +19,9 @@ Vincent Natoli, Stone Ridge Technology ------------------------------------------------------------------------- */ +#include "pair_eam_opt.h" #include #include -#include "pair_eam_opt.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/OPT/pair_lj_charmm_coul_long_opt.cpp b/src/OPT/pair_lj_charmm_coul_long_opt.cpp index d80d3d1ec4462b8cb38ca81635c6d9cb1e214872..3dc6bdb6b4ea769309457f2d410e448be1f7af86 100644 --- a/src/OPT/pair_lj_charmm_coul_long_opt.cpp +++ b/src/OPT/pair_lj_charmm_coul_long_opt.cpp @@ -18,9 +18,9 @@ Vincent Natoli, Stone Ridge Technology ------------------------------------------------------------------------- */ +#include "pair_lj_charmm_coul_long_opt.h" #include #include -#include "pair_lj_charmm_coul_long_opt.h" #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_lj_cut_coul_long_opt.cpp b/src/OPT/pair_lj_cut_coul_long_opt.cpp index a25010cf1f740e2bce9d4737eee124f1af93f078..a1f97aaae9eb24f48df1bc18dd5df7aad5591276 100644 --- a/src/OPT/pair_lj_cut_coul_long_opt.cpp +++ b/src/OPT/pair_lj_cut_coul_long_opt.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "pair_lj_cut_coul_long_opt.h" +#include #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_lj_cut_opt.cpp b/src/OPT/pair_lj_cut_opt.cpp index c6684461bed36061526cfa3d446b5ee0778a77ba..3b3a19a9e8eff985f555fef08ffc908d77c1822c 100644 --- a/src/OPT/pair_lj_cut_opt.cpp +++ b/src/OPT/pair_lj_cut_opt.cpp @@ -18,8 +18,8 @@ Vincent Natoli, Stone Ridge Technology ------------------------------------------------------------------------- */ -#include #include "pair_lj_cut_opt.h" +#include #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_lj_cut_tip4p_long_opt.cpp b/src/OPT/pair_lj_cut_tip4p_long_opt.cpp index 92facca43ea308b00af24da966b598fea9ccc264..f8181d69a6973a80258f0d2270e346f5284567f6 100644 --- a/src/OPT/pair_lj_cut_tip4p_long_opt.cpp +++ b/src/OPT/pair_lj_cut_tip4p_long_opt.cpp @@ -15,8 +15,8 @@ OPT version: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_lj_cut_tip4p_long_opt.h" +#include #include "atom.h" #include "domain.h" #include "force.h" diff --git a/src/OPT/pair_lj_long_coul_long_opt.cpp b/src/OPT/pair_lj_long_coul_long_opt.cpp index 243b64391fe74cfd543222a24db9bf4574237dff..c323d078c4a565f895024860b19728b5ddd06ed8 100644 --- a/src/OPT/pair_lj_long_coul_long_opt.cpp +++ b/src/OPT/pair_lj_long_coul_long_opt.cpp @@ -15,8 +15,9 @@ OPT version: Wayne Mitchell (Loyola University New Orleans) ------------------------------------------------------------------------- */ -#include #include "pair_lj_long_coul_long_opt.h" +#include +#include #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_morse_opt.cpp b/src/OPT/pair_morse_opt.cpp index c9c6bba3554bb2b3c24cd6a8f771e23f8307857c..1d2e226777eb3b549d85602f7952690a48e0892f 100644 --- a/src/OPT/pair_morse_opt.cpp +++ b/src/OPT/pair_morse_opt.cpp @@ -18,9 +18,9 @@ Vincent Natoli, Stone Ridge Technology ------------------------------------------------------------------------- */ +#include "pair_morse_opt.h" #include #include -#include "pair_morse_opt.h" #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_ufm_opt.cpp b/src/OPT/pair_ufm_opt.cpp index f463dac3f1ebeccfef23b0adda63e212bcaaacf6..eabb093b186a9406198f8de0dc7541483ae5039b 100644 --- a/src/OPT/pair_ufm_opt.cpp +++ b/src/OPT/pair_ufm_opt.cpp @@ -17,9 +17,9 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ +#include "pair_ufm_opt.h" #include #include -#include "pair_ufm_opt.h" #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp index c4fa0bd43bd2fb335a900448123181883ca83f6c..3e3312bf01000aa7f9a1a887ed5a6e960f4265c2 100644 --- a/src/PERI/atom_vec_peri.cpp +++ b/src/PERI/atom_vec_peri.cpp @@ -15,14 +15,12 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ +#include "atom_vec_peri.h" #include -#include #include -#include "atom_vec_peri.h" #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "citeme.h" diff --git a/src/PERI/compute_damage_atom.cpp b/src/PERI/compute_damage_atom.cpp index 4bf8fa17a57fd7ff034a46a15f64c713d741fc01..230b766725f92b57eb2ebfd5417c6cdf540f088f 100644 --- a/src/PERI/compute_damage_atom.cpp +++ b/src/PERI/compute_damage_atom.cpp @@ -15,14 +15,12 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ -#include #include "compute_damage_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" -#include "pair_peri_pmb.h" #include "fix_peri_neigh.h" #include "memory.h" #include "error.h" diff --git a/src/PERI/compute_dilatation_atom.cpp b/src/PERI/compute_dilatation_atom.cpp index 990731a227d30865c2dbba4a2566217cd94913d7..095f61983888055385fc2a1c42c27ec69bf9b936 100644 --- a/src/PERI/compute_dilatation_atom.cpp +++ b/src/PERI/compute_dilatation_atom.cpp @@ -15,19 +15,17 @@ Contributing author: Rezwanur Rahman, John Foster (UTSA) ------------------------------------------------------------------------- */ -#include #include "compute_dilatation_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" +#include "fix.h" #include "force.h" -#include "pair.h" #include "pair_peri_lps.h" -#include "pair_peri_pmb.h" #include "pair_peri_ves.h" #include "pair_peri_eps.h" -#include "fix_peri_neigh.h" #include "memory.h" #include "error.h" diff --git a/src/PERI/compute_plasticity_atom.cpp b/src/PERI/compute_plasticity_atom.cpp index d08fb98e07b84d1c893c5d05588cb1db4e4622a6..e312630b6225c3ada14aa217d513af9b3cbb675e 100644 --- a/src/PERI/compute_plasticity_atom.cpp +++ b/src/PERI/compute_plasticity_atom.cpp @@ -15,15 +15,14 @@ Contributing author: Rezwanur Rahman, John Foster (UTSA) ------------------------------------------------------------------------- */ -#include #include "compute_plasticity_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" -#include "pair_peri_pmb.h" #include "fix_peri_neigh.h" +#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/PERI/fix_peri_neigh.cpp b/src/PERI/fix_peri_neigh.cpp index 66137e6a01445c5168f4a6a6cb3484f989954157..70f46dcdc1059b004a7809ea36a0998a584bbef1 100644 --- a/src/PERI/fix_peri_neigh.cpp +++ b/src/PERI/fix_peri_neigh.cpp @@ -15,9 +15,9 @@ Contributing authors: Mike Parks (SNL), Ezwanur Rahman, J.T. Foster (UTSA) ------------------------------------------------------------------------- */ -#include #include "fix_peri_neigh.h" -#include "pair_peri_pmb.h" +#include +#include #include "pair_peri_lps.h" #include "pair_peri_ves.h" #include "pair_peri_eps.h" @@ -25,7 +25,6 @@ #include "domain.h" #include "force.h" #include "comm.h" -#include "update.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp index c00495ba4df51d02103f55291aceaaf8e9a1897b..2579a9b75a56f09f3420837d56a6b532d15d45c8 100644 --- a/src/PERI/pair_peri_eps.cpp +++ b/src/PERI/pair_peri_eps.cpp @@ -15,15 +15,14 @@ Contributing author: Rezwanur Rahman, John Foster (UTSA) ------------------------------------------------------------------------- */ +#include "pair_peri_eps.h" +#include #include -#include #include -#include "pair_peri_eps.h" #include "atom.h" #include "domain.h" #include "lattice.h" #include "force.h" -#include "update.h" #include "modify.h" #include "fix.h" #include "fix_peri_neigh.h" @@ -32,7 +31,6 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "update.h" using namespace LAMMPS_NS; @@ -451,12 +449,12 @@ void PairPeriEPS::coeff(int narg, char **arg) force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); - double bulkmodulus_one = atof(arg[2]); - double shearmodulus_one = atof(arg[3]); - double cut_one = atof(arg[4]); - double s00_one = atof(arg[5]); - double alpha_one = atof(arg[6]); - double myieldstress_one = atof(arg[7]); + double bulkmodulus_one = force->numeric(FLERR,arg[2]); + double shearmodulus_one = force->numeric(FLERR,arg[3]); + double cut_one = force->numeric(FLERR,arg[4]); + double s00_one = force->numeric(FLERR,arg[5]); + double alpha_one = force->numeric(FLERR,arg[6]); + double myieldstress_one = force->numeric(FLERR,arg[7]); int count = 0; for (int i = ilo; i <= ihi; i++) { diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp index f0418c8c8d06aee51881e76f3d02c6d8036052fd..f32ce5fb1c1299224c0b842c17678a4e6250e503 100644 --- a/src/PERI/pair_peri_lps.cpp +++ b/src/PERI/pair_peri_lps.cpp @@ -15,15 +15,14 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ +#include "pair_peri_lps.h" +#include #include -#include #include -#include "pair_peri_lps.h" #include "atom.h" #include "domain.h" #include "lattice.h" #include "force.h" -#include "update.h" #include "modify.h" #include "fix.h" #include "fix_peri_neigh.h" @@ -32,7 +31,6 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "update.h" #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp index ad2f3fb7c7d17b5e3f94ff94ee071e578c50c9d1..ceab40d88d582bc61eedbc373ca3f6ca411d5fc2 100644 --- a/src/PERI/pair_peri_pmb.cpp +++ b/src/PERI/pair_peri_pmb.cpp @@ -15,23 +15,21 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ +#include "pair_peri_pmb.h" +#include #include #include -#include #include -#include "pair_peri_pmb.h" #include "atom.h" #include "domain.h" #include "lattice.h" #include "force.h" -#include "update.h" #include "modify.h" #include "fix.h" #include "fix_peri_neigh.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp index 24a9f92a974e1753e17e88e922a5dc147f9dd315..bd1eaa5fd25e236e7f5a0a573a073c032580c94b 100644 --- a/src/PERI/pair_peri_ves.cpp +++ b/src/PERI/pair_peri_ves.cpp @@ -15,15 +15,14 @@ Contributing authors: Rezwanur Rahman, J.T. Foster (UTSA) ------------------------------------------------------------------------- */ +#include "pair_peri_ves.h" +#include #include -#include #include -#include "pair_peri_ves.h" #include "atom.h" #include "domain.h" #include "lattice.h" #include "force.h" -#include "update.h" #include "modify.h" #include "fix.h" #include "fix_peri_neigh.h" @@ -428,13 +427,13 @@ void PairPeriVES::coeff(int narg, char **arg) force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); - double bulkmodulus_one = atof(arg[2]); - double shearmodulus_one = atof(arg[3]); - double cut_one = atof(arg[4]); - double s00_one = atof(arg[5]); - double alpha_one = atof(arg[6]); - double mlambdai_one = atof(arg[7]); - double mtaui_one = atof(arg[8]); + double bulkmodulus_one = force->numeric(FLERR,arg[2]); + double shearmodulus_one = force->numeric(FLERR,arg[3]); + double cut_one = force->numeric(FLERR,arg[4]); + double s00_one = force->numeric(FLERR,arg[5]); + double alpha_one = force->numeric(FLERR,arg[6]); + double mlambdai_one = force->numeric(FLERR,arg[7]); + double mtaui_one = force->numeric(FLERR,arg[8]); int count = 0; for (int i = ilo; i <= ihi; i++) { diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp index 41cfcede345357b2d9745f5365a39f1112df01eb..c8646f5b14811f7f28f8193ce8e0ea510ba8d226 100644 --- a/src/POEMS/fix_poems.cpp +++ b/src/POEMS/fix_poems.cpp @@ -17,20 +17,18 @@ Kurt Anderson (anderk5@rpi.edu) ------------------------------------------------------------------------- */ +#include "fix_poems.h" #include #include -#include #include #include #include "workspace.h" -#include "fix_poems.h" #include "atom.h" #include "domain.h" #include "update.h" #include "respa.h" #include "modify.h" #include "force.h" -#include "output.h" #include "group.h" #include "comm.h" #include "citeme.h" diff --git a/src/POEMS/fix_poems.h b/src/POEMS/fix_poems.h index 7b2c77a1bd78deec2d9ea0a62e3bc021d79b3e05..6892c51d7e542bf2c011e47e3400b911ecdebf75 100644 --- a/src/POEMS/fix_poems.h +++ b/src/POEMS/fix_poems.h @@ -22,6 +22,8 @@ FixStyle(poems,FixPOEMS) #include "fix.h" +class Workspace; + namespace LAMMPS_NS { class FixPOEMS : public Fix { @@ -94,7 +96,7 @@ class FixPOEMS : public Fix { // POEMS object - class Workspace *poems; + Workspace *poems; // internal class functions diff --git a/src/PYTHON/fix_python_invoke.cpp b/src/PYTHON/fix_python_invoke.cpp index 280c2d91e28e642a626700b6e5313a159a9304ff..57ea2e914870284828d957a504398b9d6c9e51a3 100644 --- a/src/PYTHON/fix_python_invoke.cpp +++ b/src/PYTHON/fix_python_invoke.cpp @@ -15,14 +15,11 @@ Contributing author: Richard Berger (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_python_invoke.h" -#include "atom.h" +#include // IWYU pragma: keep +#include #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" #include "lmppython.h" #include "python_compat.h" diff --git a/src/PYTHON/fix_python_move.cpp b/src/PYTHON/fix_python_move.cpp index ec21dbeadd77976e7beefbef80916dc8f75a2ce3..be63b851a2b62062d64689c611b21d75cdbb85a2 100644 --- a/src/PYTHON/fix_python_move.cpp +++ b/src/PYTHON/fix_python_move.cpp @@ -15,16 +15,9 @@ Contributing author: Richard Berger (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_python_move.h" -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "memory.h" -#include "neigh_list.h" +#include // IWYU pragma: keep +#include #include "lmppython.h" #include "error.h" #include "python_compat.h" diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp index 2148fc67b823b9361c219128e34421bcde1ee90e..0d79a319465ba8eddaaac6aeb2ec43406ac16c3f 100644 --- a/src/PYTHON/pair_python.cpp +++ b/src/PYTHON/pair_python.cpp @@ -15,13 +15,11 @@ Contributing authors: Axel Kohlmeyer and Richard Berger (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include "pair_python.h" +#include // IWYU pragma: keep #include #include -#include "pair_python.h" #include "atom.h" -#include "comm.h" #include "force.h" #include "memory.h" #include "update.h" diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp index aaa4f74c6962845cf9d1ff7f813878f44ebc0e4d..1188942e75905532e0dea89b5c5b76b290caf9ae 100644 --- a/src/PYTHON/python_impl.cpp +++ b/src/PYTHON/python_impl.cpp @@ -15,8 +15,10 @@ Contributing author: Richard Berger and Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include "lmppython.h" +#include "python_impl.h" +#include +#include +#include // IWYU pragma: keep #include "force.h" #include "input.h" #include "variable.h" diff --git a/src/PYTHON/python_impl.h b/src/PYTHON/python_impl.h index 2ccdda95c9c5bab311f6958866f14f200ebfef22..f890f54f3b272944cdbcd42dac55be5e8ee0d227 100644 --- a/src/PYTHON/python_impl.h +++ b/src/PYTHON/python_impl.h @@ -15,6 +15,7 @@ #define LMP_PYTHON_IMPL_H #include "pointers.h" +#include "lmppython.h" namespace LAMMPS_NS { diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp index 0ab010b7bbba2212fcdbb4e93fcb58a0cea9f3df..7768c01a41d45b8f43ec90f3800a22813341ef9f 100644 --- a/src/QEQ/fix_qeq.cpp +++ b/src/QEQ/fix_qeq.cpp @@ -16,29 +16,19 @@ Based on fix qeq/reax by H. Metin Aktulga ------------------------------------------------------------------------- */ +#include "fix_qeq.h" +#include #include -#include -#include #include -#include "fix_qeq.h" #include "atom.h" #include "comm.h" -#include "domain.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "update.h" #include "force.h" -#include "kspace.h" -#include "group.h" -#include "pair.h" -#include "respa.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace FixConst; #define MAXLINE 1024 diff --git a/src/QEQ/fix_qeq_dynamic.cpp b/src/QEQ/fix_qeq_dynamic.cpp index ba88f4f1c3496c2ab9ebfde454b84854d5c5a73c..a2cc683b564df03727a1f0a7f3b3c74162f3628e 100644 --- a/src/QEQ/fix_qeq_dynamic.cpp +++ b/src/QEQ/fix_qeq_dynamic.cpp @@ -15,24 +15,21 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ +#include "fix_qeq_dynamic.h" +#include #include -#include #include #include -#include "fix_qeq_dynamic.h" #include "atom.h" #include "comm.h" -#include "domain.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" #include "force.h" #include "group.h" -#include "pair.h" #include "kspace.h" #include "respa.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/QEQ/fix_qeq_fire.cpp b/src/QEQ/fix_qeq_fire.cpp index 1e3686f99ca39618d56fe7ec75b7a1b26fc12475..265528a089ca0ae72fe779c55ae2699bc4dbf14b 100644 --- a/src/QEQ/fix_qeq_fire.cpp +++ b/src/QEQ/fix_qeq_fire.cpp @@ -15,26 +15,23 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ +#include "fix_qeq_fire.h" +#include #include -#include #include #include -#include "fix_qeq_fire.h" #include "atom.h" #include "comm.h" -#include "domain.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" #include "force.h" #include "group.h" -#include "pair.h" #include "pair_comb.h" #include "pair_comb3.h" #include "kspace.h" #include "respa.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/QEQ/fix_qeq_point.cpp b/src/QEQ/fix_qeq_point.cpp index 9517343974c68e71b6a81c1cf977f20bc7903bd8..8fb9fd327321b462c4626a0b63ffefaa01273d1c 100644 --- a/src/QEQ/fix_qeq_point.cpp +++ b/src/QEQ/fix_qeq_point.cpp @@ -15,14 +15,11 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ +#include "fix_qeq_point.h" #include -#include -#include #include -#include "fix_qeq_point.h" #include "atom.h" #include "comm.h" -#include "domain.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp index 6367feacc584f2ec17c983627d7147df8ab6b349..37951adb1ad177f3aee2d1286a6ce3147878370f 100644 --- a/src/QEQ/fix_qeq_shielded.cpp +++ b/src/QEQ/fix_qeq_shielded.cpp @@ -15,14 +15,11 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ +#include "fix_qeq_shielded.h" #include -#include -#include #include -#include "fix_qeq_shielded.h" #include "atom.h" #include "comm.h" -#include "domain.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/QEQ/fix_qeq_slater.cpp b/src/QEQ/fix_qeq_slater.cpp index 3443a519a29ffdf586136e8d631f2d46b149e87b..4f5369eb877890cf4a36d9a72710f65fc276a481 100644 --- a/src/QEQ/fix_qeq_slater.cpp +++ b/src/QEQ/fix_qeq_slater.cpp @@ -15,14 +15,12 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ +#include "fix_qeq_slater.h" #include -#include #include #include -#include "fix_qeq_slater.h" #include "atom.h" #include "comm.h" -#include "domain.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" @@ -33,7 +31,6 @@ #include "kspace.h" #include "respa.h" #include "math_const.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/REPLICA/compute_event_displace.cpp b/src/REPLICA/compute_event_displace.cpp index df142215863e73e13ab3448d95ef29f95c427bc6..a6abcce85daf3ed103443cdb0be958cce5ccdf15 100644 --- a/src/REPLICA/compute_event_displace.cpp +++ b/src/REPLICA/compute_event_displace.cpp @@ -15,16 +15,13 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "compute_event_displace.h" #include -#include -#include #include -#include "compute_event_displace.h" #include "atom.h" #include "domain.h" #include "modify.h" #include "fix_event.h" -#include "memory.h" #include "error.h" #include "force.h" #include "update.h" diff --git a/src/REPLICA/fix_event.cpp b/src/REPLICA/fix_event.cpp index 8fc5de6b1600edf0fec80b3b71b3b83f0408461a..41f91332cb60d8aa96e5bd0f7315510bf36ec677 100644 --- a/src/REPLICA/fix_event.cpp +++ b/src/REPLICA/fix_event.cpp @@ -15,17 +15,11 @@ Contributing author: Mike Brown (SNL), Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "fix_event.h" #include "atom.h" -#include "update.h" #include "domain.h" -#include "neighbor.h" -#include "comm.h" -#include "universe.h" -#include "memory.h" #include "error.h" +#include "memory.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/REPLICA/fix_event_hyper.cpp b/src/REPLICA/fix_event_hyper.cpp index eae1ad021d31596573d43adedf2157009038a58b..0d32516deea208ccad97fdad7129fa2b4016d081 100644 --- a/src/REPLICA/fix_event_hyper.cpp +++ b/src/REPLICA/fix_event_hyper.cpp @@ -11,17 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_event_hyper.h" -#include "atom.h" -#include "update.h" -#include "domain.h" -#include "neighbor.h" #include "comm.h" -#include "universe.h" -#include "memory.h" #include "error.h" +#include "update.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/REPLICA/fix_event_prd.cpp b/src/REPLICA/fix_event_prd.cpp index a311a6444aad250d5b25454afabcf215a8be7fcc..19a89e988cb3137c3ab450d9314bd7b43c1f5e1e 100644 --- a/src/REPLICA/fix_event_prd.cpp +++ b/src/REPLICA/fix_event_prd.cpp @@ -15,17 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "fix_event_prd.h" -#include "atom.h" -#include "update.h" -#include "domain.h" -#include "neighbor.h" #include "comm.h" -#include "universe.h" -#include "memory.h" #include "error.h" +#include "update.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/REPLICA/fix_event_tad.cpp b/src/REPLICA/fix_event_tad.cpp index 0916fdf493748a842a6ad84783d5dfa0f9960075..d0b94a216bc237d13ba4a34cc2bbfa54f2b4eff5 100644 --- a/src/REPLICA/fix_event_tad.cpp +++ b/src/REPLICA/fix_event_tad.cpp @@ -15,17 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "fix_event_tad.h" -#include "atom.h" -#include "update.h" -#include "domain.h" -#include "neighbor.h" #include "comm.h" -#include "universe.h" -#include "memory.h" #include "error.h" +#include "update.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/REPLICA/fix_hyper.cpp b/src/REPLICA/fix_hyper.cpp index c86c00ad45306f53caacaf096c4afcb5f92aa465..21a4fde04d735097253f46656fd529ec7309ab5c 100644 --- a/src/REPLICA/fix_hyper.cpp +++ b/src/REPLICA/fix_hyper.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_hyper.h" +#include using namespace LAMMPS_NS; diff --git a/src/REPLICA/fix_hyper_global.cpp b/src/REPLICA/fix_hyper_global.cpp index 0c76b29911cfa8b2c23fcbe9d8f63c417f0afab6..5e9da0276837fbd315bd3a92e3d8a14800f51256 100644 --- a/src/REPLICA/fix_hyper_global.cpp +++ b/src/REPLICA/fix_hyper_global.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_hyper_global.h" #include #include -#include #include -#include "fix_hyper_global.h" #include "atom.h" #include "update.h" #include "force.h" @@ -24,7 +23,6 @@ #include "neighbor.h" #include "neigh_request.h" #include "neigh_list.h" -#include "modify.h" #include "math_extra.h" #include "memory.h" #include "error.h" diff --git a/src/REPLICA/fix_hyper_local.cpp b/src/REPLICA/fix_hyper_local.cpp index a6db4419f02d2cd974745360e3c1c2b61eb7d5b4..e8773095d152d115bda8346c526b0b3a9a4c2fed 100644 --- a/src/REPLICA/fix_hyper_local.cpp +++ b/src/REPLICA/fix_hyper_local.cpp @@ -11,21 +11,20 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_hyper_local.h" #include #include -#include #include -#include "fix_hyper_local.h" #include "atom.h" #include "update.h" #include "force.h" #include "pair.h" #include "domain.h" #include "comm.h" +#include "my_page.h" #include "neighbor.h" #include "neigh_request.h" #include "neigh_list.h" -#include "modify.h" #include "math_extra.h" #include "memory.h" #include "error.h" diff --git a/src/REPLICA/fix_hyper_local.h b/src/REPLICA/fix_hyper_local.h index 6f13acb60616710393673f38a042da84f220ffe3..8fb3a445c22b24c38e2be60db5ab6a4f23759ae4 100644 --- a/src/REPLICA/fix_hyper_local.h +++ b/src/REPLICA/fix_hyper_local.h @@ -21,7 +21,6 @@ FixStyle(hyper/local,FixHyperLocal) #define LMP_FIX_HYPER_LOCAL_H #include "fix_hyper.h" -#include "my_page.h" namespace LAMMPS_NS { diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp index e1b1e46a53f67fecd2fa65ef9b198a81317ea352..7b377ae9ecdc028b6051eca717940fb865f6338a 100644 --- a/src/REPLICA/fix_neb.cpp +++ b/src/REPLICA/fix_neb.cpp @@ -16,11 +16,10 @@ new options for inter-replica forces, first/last replica treatment ------------------------------------------------------------------------- */ +#include "fix_neb.h" #include #include -#include #include -#include "fix_neb.h" #include "universe.h" #include "update.h" #include "atom.h" diff --git a/src/REPLICA/hyper.cpp b/src/REPLICA/hyper.cpp index 00b91684e9e7476cf70d39e894bf71026841023e..af2a963616175e286a443a20a3b5b1e5d2c94d48 100644 --- a/src/REPLICA/hyper.cpp +++ b/src/REPLICA/hyper.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "hyper.h" +#include +#include #include "update.h" -#include "atom.h" #include "domain.h" #include "region.h" #include "integrate.h" diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp index 4061ec65415210fa5ded26ad3251cba26bda6c9c..dafc0c087585bb45b25f1f2423fe3516b0046824 100644 --- a/src/REPLICA/neb.cpp +++ b/src/REPLICA/neb.cpp @@ -11,16 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h -// due to OpenMPI bug which sets INT64_MAX via its mpi.h -// before lmptype.h can set flags to insure it is done correctly - -#include "lmptype.h" +#include "neb.h" #include #include #include #include -#include "neb.h" #include "universe.h" #include "atom.h" #include "update.h" diff --git a/src/REPLICA/neb.h b/src/REPLICA/neb.h index f585a0c8a74994d4e1059be924dfedbc7b8a679f..b53992711cc9845569b2a6a7f03d526c8d8d0264 100644 --- a/src/REPLICA/neb.h +++ b/src/REPLICA/neb.h @@ -20,7 +20,6 @@ CommandStyle(neb,NEB) #ifndef LMP_NEB_H #define LMP_NEB_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp index 6d450f48e3ed6bac08bcef47f5666e4e06a3f283..f631cc6a0a4592cdc8bdff9fe44f54a6e1c7a762 100644 --- a/src/REPLICA/prd.cpp +++ b/src/REPLICA/prd.cpp @@ -15,16 +15,9 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h -// due to OpenMPI bug which sets INT64_MAX via its mpi.h -// before lmptype.h can set flags to insure it is done correctly - -#include "lmptype.h" +#include "prd.h" #include -#include -#include #include -#include "prd.h" #include "universe.h" #include "update.h" #include "atom.h" @@ -40,11 +33,9 @@ #include "fix.h" #include "fix_event_prd.h" #include "force.h" -#include "pair.h" #include "random_park.h" #include "random_mars.h" #include "output.h" -#include "dump.h" #include "finish.h" #include "timer.h" #include "memory.h" diff --git a/src/REPLICA/tad.cpp b/src/REPLICA/tad.cpp index da42ba6faef97f44d513092b663434f4106f71f0..8a51f6d00e692c19e9b32d7e98453866446388e5 100644 --- a/src/REPLICA/tad.cpp +++ b/src/REPLICA/tad.cpp @@ -15,36 +15,24 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h -// due to OpenMPI bug which sets INT64_MAX via its mpi.h -// before lmptype.h can set flags to insure it is done correctly - -#include "lmptype.h" +#include "tad.h" #include #include -#include #include -#include "tad.h" #include "universe.h" #include "update.h" #include "atom.h" #include "domain.h" -#include "region.h" -#include "comm.h" -#include "velocity.h" #include "integrate.h" #include "min.h" #include "neighbor.h" #include "modify.h" #include "neb.h" #include "compute.h" -#include "fix.h" #include "fix_event_tad.h" #include "fix_store.h" #include "force.h" -#include "pair.h" #include "output.h" -#include "dump.h" #include "finish.h" #include "timer.h" #include "memory.h" diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp index fe3e3fb993d43e0d88c8eb2dcc777ea621a482ef..46fc3af6496379b85249ea31414ee61e045b48dc 100644 --- a/src/REPLICA/temper.cpp +++ b/src/REPLICA/temper.cpp @@ -15,10 +15,9 @@ Contributing author: Mark Sears (SNL) ------------------------------------------------------------------------- */ +#include "temper.h" #include -#include #include -#include "temper.h" #include "universe.h" #include "domain.h" #include "atom.h" @@ -27,13 +26,10 @@ #include "modify.h" #include "compute.h" #include "force.h" -#include "output.h" -#include "thermo.h" #include "fix.h" #include "random_park.h" #include "finish.h" #include "timer.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/REPLICA/verlet_split.cpp b/src/REPLICA/verlet_split.cpp index 7042fc6993abb8fc904043bbe62402a165f195ac..a5ed1a671db6fdf6f34d209cb39343ac41ee3c82 100644 --- a/src/REPLICA/verlet_split.cpp +++ b/src/REPLICA/verlet_split.cpp @@ -15,7 +15,6 @@ Contributing authors: Yuxing Peng and Chris Knight (U Chicago) ------------------------------------------------------------------------- */ -#include #include "verlet_split.h" #include "universe.h" #include "neighbor.h" diff --git a/src/RIGID/compute_erotate_rigid.cpp b/src/RIGID/compute_erotate_rigid.cpp index a3ddffd9abed86427c1d06da997e7d5344676795..e15c0deb82cb714cf81736d2c7d0311a44e6944f 100644 --- a/src/RIGID/compute_erotate_rigid.cpp +++ b/src/RIGID/compute_erotate_rigid.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_erotate_rigid.h" +#include #include "update.h" #include "force.h" #include "modify.h" diff --git a/src/RIGID/compute_ke_rigid.cpp b/src/RIGID/compute_ke_rigid.cpp index 4de13532b29856d7381f358d194d6554515983c6..031919b7a971350c675b3f6364f4c913f5af7362 100644 --- a/src/RIGID/compute_ke_rigid.cpp +++ b/src/RIGID/compute_ke_rigid.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_ke_rigid.h" +#include #include "update.h" #include "force.h" #include "modify.h" diff --git a/src/RIGID/compute_rigid_local.cpp b/src/RIGID/compute_rigid_local.cpp index ec2799b6bccaeb9f0aa0266801c28cb2c4b448e2..57f69a64e2f42e96e0afd0707a0bb8adf54a802c 100644 --- a/src/RIGID/compute_rigid_local.cpp +++ b/src/RIGID/compute_rigid_local.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_rigid_local.h" +#include #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/RIGID/fix_ehex.cpp b/src/RIGID/fix_ehex.cpp index 1476c71d3fa080912fbaa98ed44b09f410e43385..a5efc22d11b44b762a468e06418249dee7904f29 100644 --- a/src/RIGID/fix_ehex.cpp +++ b/src/RIGID/fix_ehex.cpp @@ -22,10 +22,10 @@ which implements the heat exchange (HEX) algorithm. ------------------------------------------------------------------------- */ +#include "fix_ehex.h" +#include #include -#include #include -#include "fix_ehex.h" #include "atom.h" #include "domain.h" #include "region.h" @@ -33,14 +33,9 @@ #include "force.h" #include "update.h" #include "modify.h" -#include "input.h" -#include "variable.h" #include "memory.h" #include "error.h" #include "fix_shake.h" -#include "neighbor.h" -#include "comm.h" -#include "timer.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/RIGID/fix_ehex.h b/src/RIGID/fix_ehex.h index e29ddac1352bc4119aca6b6ad1e92481b829c6c0..860ed3d1f36b7e17776464c763da5afa2955a563 100644 --- a/src/RIGID/fix_ehex.h +++ b/src/RIGID/fix_ehex.h @@ -22,8 +22,6 @@ FixStyle(ehex,FixEHEX) #define LMP_FIX_EHEX_H #include "fix.h" -#include "fix_shake.h" -#include "region.h" #define EHEX_DEBUG 0 namespace LAMMPS_NS { @@ -41,9 +39,9 @@ class FixEHEX : public Fix { double memory_usage(); void update_scalingmask(); void com_properties(double *, double *, double *, double*, double *, double*); - bool rescale_atom(int i, Region*region); + bool rescale_atom(int i, class Region *region); virtual void grow_arrays(int nmax); - bool check_cluster(tagint *shake_atom, int n, Region * region); + bool check_cluster(tagint *shake_atom, int n, class Region *region); private: int iregion; @@ -53,14 +51,14 @@ class FixEHEX : public Fix { char *idregion; int me; - double **x; // coordinates - double **f; // forces - double **v; // velocities - double *mass; // masses - double *rmass; // reduced masses - int *type; // atom types + double **x; // coordinates + double **f; // forces + double **v; // velocities + double *mass; // masses + double *rmass; // reduced masses + int *type; // atom types int nlocal; // number of local atoms - FixShake * fshake; // pointer to fix_shake/fix_rattle + class FixShake * fshake; // pointer to fix_shake/fix_rattle int constraints; // constraints (0/1) int cluster; // rescaling entire clusters (0/1) int hex; // HEX mode (0/1) diff --git a/src/RIGID/fix_rattle.cpp b/src/RIGID/fix_rattle.cpp index 403f3091c62d6a1941519f93b984cfe6637b8c76..93bf610e94d87d52d72ca77d0ac0ab6122191e54 100644 --- a/src/RIGID/fix_rattle.cpp +++ b/src/RIGID/fix_rattle.cpp @@ -15,33 +15,22 @@ Contributing author: Peter Wirnsberger (University of Cambridge) ------------------------------------------------------------------------- */ +#include "fix_rattle.h" #include #include -#include #include -#include -#include "fix_rattle.h" #include "atom.h" -#include "atom_vec.h" -#include "molecule.h" #include "update.h" -#include "respa.h" #include "modify.h" #include "domain.h" #include "force.h" -#include "bond.h" -#include "angle.h" #include "comm.h" -#include "group.h" -#include "fix_respa.h" -#include "math_const.h" #include "math_extra.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; using namespace FixConst; -using namespace MathConst; using namespace MathExtra; // set RATTLE_DEBUG 1 to check constraints at end of timestep diff --git a/src/RIGID/fix_rattle.h b/src/RIGID/fix_rattle.h index 48edaef37981a0df5d437f394f722eb825028545..cab148f10cba89786dddd5b25f2e1935bcc25075 100644 --- a/src/RIGID/fix_rattle.h +++ b/src/RIGID/fix_rattle.h @@ -20,7 +20,6 @@ FixStyle(rattle,FixRattle) #ifndef LMP_FIX_RATTLE_H #define LMP_FIX_RATTLE_H -#include "fix.h" #include "fix_shake.h" namespace LAMMPS_NS { diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index abb669bc026fc8c0285a6c630f484995f4087bf7..912f5294036a5535dde7246140fab15dd5ab4dcd 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_rigid.h" +#include #include -#include #include #include -#include "fix_rigid.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" @@ -31,7 +31,6 @@ #include "force.h" #include "input.h" #include "variable.h" -#include "output.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_nh.cpp b/src/RIGID/fix_rigid_nh.cpp index 4dceb1b8b4c214aab95999db1ff901df53341062..4738e253f6374cc65009fdde01d02c868c5b74bd 100644 --- a/src/RIGID/fix_rigid_nh.cpp +++ b/src/RIGID/fix_rigid_nh.cpp @@ -17,10 +17,9 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ +#include "fix_rigid_nh.h" #include -#include #include -#include "fix_rigid_nh.h" #include "math_extra.h" #include "atom.h" #include "compute.h" @@ -32,7 +31,6 @@ #include "comm.h" #include "force.h" #include "kspace.h" -#include "output.h" #include "memory.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp index 5016d3f1685eed9d809172de4d24344a056c5f75..1545e913c033e139d7c7edf2f2fb4c363559c50b 100644 --- a/src/RIGID/fix_rigid_nh_small.cpp +++ b/src/RIGID/fix_rigid_nh_small.cpp @@ -17,10 +17,10 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ +#include "fix_rigid_nh_small.h" +#include #include -#include #include -#include "fix_rigid_nh_small.h" #include "math_extra.h" #include "atom.h" #include "compute.h" @@ -32,7 +32,6 @@ #include "comm.h" #include "force.h" #include "kspace.h" -#include "output.h" #include "memory.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_nph.cpp b/src/RIGID/fix_rigid_nph.cpp index 45a4a8d09cd00dfa14abf23db64652a0ca5d4a12..706e08ec123c5364b5b7633ab1ddd9966afb2ced 100644 --- a/src/RIGID/fix_rigid_nph.cpp +++ b/src/RIGID/fix_rigid_nph.cpp @@ -17,9 +17,8 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include #include "fix_rigid_nph.h" -#include "domain.h" +#include #include "modify.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_nph_small.cpp b/src/RIGID/fix_rigid_nph_small.cpp index d32e3043f45451b7ef9a07856f918b5b3deb2bf8..32ac58220dbe8a81a594ea3d9e56516d14626fbe 100644 --- a/src/RIGID/fix_rigid_nph_small.cpp +++ b/src/RIGID/fix_rigid_nph_small.cpp @@ -17,9 +17,8 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include #include "fix_rigid_nph_small.h" -#include "domain.h" +#include #include "modify.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_npt.cpp b/src/RIGID/fix_rigid_npt.cpp index da5d5ffaa54837c0d54aa4830790ce98903a36cc..1f19fb4ec7d8226a803101fcabd5d62c908acde0 100644 --- a/src/RIGID/fix_rigid_npt.cpp +++ b/src/RIGID/fix_rigid_npt.cpp @@ -17,9 +17,8 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include #include "fix_rigid_npt.h" -#include "domain.h" +#include #include "modify.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_npt_small.cpp b/src/RIGID/fix_rigid_npt_small.cpp index f1fd5470da68dfd80bdc15644952dcfd649dc160..e8924be79fe8edca6d610905c0e43843c482fa1e 100644 --- a/src/RIGID/fix_rigid_npt_small.cpp +++ b/src/RIGID/fix_rigid_npt_small.cpp @@ -17,9 +17,8 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include #include "fix_rigid_npt_small.h" -#include "domain.h" +#include #include "modify.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index dedd71c98d1d0cc496a45193f4da07acb4b670d9..14e230ab9cc42c3912aed6dfa71a5d1406a43580 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -11,11 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_rigid_small.h" +#include #include -#include #include #include -#include "fix_rigid_small.h" +#include #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" @@ -31,7 +32,6 @@ #include "neighbor.h" #include "force.h" #include "input.h" -#include "output.h" #include "variable.h" #include "random_mars.h" #include "math_const.h" diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp index 23ced2d0e74b8bc3dcdfb2a8a0f4f088b991b5c3..48a08118c5f73648157ca9d317e6620dedf11e71 100644 --- a/src/RIGID/fix_shake.cpp +++ b/src/RIGID/fix_shake.cpp @@ -11,13 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_shake.h" #include #include -#include +#include #include -#include -#include "fix_shake.h" -#include "fix_rattle.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" diff --git a/src/SHOCK/fix_append_atoms.cpp b/src/SHOCK/fix_append_atoms.cpp index 2e515839c5ecb5d5100697e436eb17e493a7950a..5e85b390766fff17ec47e2725ee241aebcf29833 100644 --- a/src/SHOCK/fix_append_atoms.cpp +++ b/src/SHOCK/fix_append_atoms.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_append_atoms.h" +#include #include #include -#include -#include "fix_append_atoms.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/SHOCK/fix_msst.cpp b/src/SHOCK/fix_msst.cpp index c800e8a85da63b21eb245158986010e222dd442e..2e9f7518242def8dbe8a870c5d277fc8a4ffbcef 100644 --- a/src/SHOCK/fix_msst.cpp +++ b/src/SHOCK/fix_msst.cpp @@ -17,22 +17,19 @@ see Reed, Fried, Joannopoulos, Phys Rev Lett, 90, 235503 (2003) ------------------------------------------------------------------------- */ +#include "fix_msst.h" +#include #include -#include #include -#include "fix_msst.h" #include "atom.h" #include "force.h" #include "comm.h" -#include "output.h" #include "modify.h" #include "fix_external.h" #include "compute.h" #include "kspace.h" #include "update.h" -#include "respa.h" #include "domain.h" -#include "thermo.h" #include "memory.h" #include "error.h" diff --git a/src/SHOCK/fix_nphug.cpp b/src/SHOCK/fix_nphug.cpp index c6df6646cf44a436bc7f2622034add37c76d728e..8ad787d7593181271320c14f4e1d56b9b7b2a63f 100644 --- a/src/SHOCK/fix_nphug.cpp +++ b/src/SHOCK/fix_nphug.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_nphug.h" #include -#include #include -#include "fix_nphug.h" #include "modify.h" #include "error.h" #include "update.h" @@ -22,8 +21,6 @@ #include "force.h" #include "domain.h" #include "group.h" -#include "memory.h" -#include "comm.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/SHOCK/fix_wall_piston.cpp b/src/SHOCK/fix_wall_piston.cpp index eb89e19517d5b02ed2db08dbb4824c52615cf037..5a359d9f6f4e31354d3c08f3b45968aac09e4602 100644 --- a/src/SHOCK/fix_wall_piston.cpp +++ b/src/SHOCK/fix_wall_piston.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_wall_piston.h" #include #include -#include -#include "fix_wall_piston.h" #include "atom.h" -#include "modify.h" #include "domain.h" #include "lattice.h" #include "update.h" diff --git a/src/SNAP/compute_sna_atom.cpp b/src/SNAP/compute_sna_atom.cpp index cc7a84281e4c6c3cf07dec3abb9673b3a07bf5fc..7ca9d5246726c31b5b1f1fcd4a3968096163f850 100644 --- a/src/SNAP/compute_sna_atom.cpp +++ b/src/SNAP/compute_sna_atom.cpp @@ -10,10 +10,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "sna.h" + +#include "compute_sna_atom.h" #include #include -#include "compute_sna_atom.h" +#include "sna.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/SNAP/compute_snad_atom.cpp b/src/SNAP/compute_snad_atom.cpp index 0a82cdeb0033422bc86e24a0e07bd58ba8ffb63e..7744a23612d0877c4d38228b93dc07df3b3cb9e7 100644 --- a/src/SNAP/compute_snad_atom.cpp +++ b/src/SNAP/compute_snad_atom.cpp @@ -10,10 +10,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "sna.h" + +#include "compute_snad_atom.h" #include #include -#include "compute_snad_atom.h" +#include "sna.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/SNAP/compute_snav_atom.cpp b/src/SNAP/compute_snav_atom.cpp index 374bf32298b95c7a06f7d7400de3186bd9719b6a..c26edf36e0269f5f3c1285c5ba76e7ceb1992b06 100644 --- a/src/SNAP/compute_snav_atom.cpp +++ b/src/SNAP/compute_snav_atom.cpp @@ -10,10 +10,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "sna.h" + +#include "compute_snav_atom.h" #include #include -#include "compute_snav_atom.h" +#include "sna.h" #include "atom.h" #include "update.h" #include "modify.h" @@ -21,7 +22,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "force.h" -#include "pair.h" #include "comm.h" #include "memory.h" #include "error.h" diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp index 4dce39361f38952c84681a849f807ef73bfe5025..59b333fa31737f917313bf33b9c60685433ff9ad 100644 --- a/src/SNAP/pair_snap.cpp +++ b/src/SNAP/pair_snap.cpp @@ -11,24 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_snap.h" +#include #include #include #include -#include "pair_snap.h" #include "atom.h" -#include "atom_vec.h" #include "force.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "sna.h" -#include "domain.h" #include "memory.h" #include "error.h" -#include - using namespace LAMMPS_NS; #define MAXLINE 1024 diff --git a/src/SNAP/sna.cpp b/src/SNAP/sna.cpp index 985110bdee3747f6d86ab95536ed9c1c2dca8ab0..01d2d12b8f5085678c59f35d7c367a50801a9205 100644 --- a/src/SNAP/sna.cpp +++ b/src/SNAP/sna.cpp @@ -18,14 +18,8 @@ #include "sna.h" #include #include "math_const.h" -#include "math_extra.h" -#include -#include - #include "memory.h" #include "error.h" -#include "comm.h" -#include "atom.h" using namespace std; using namespace LAMMPS_NS; diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp index 8cc38dbc15fbbc9c89e0e3c3df1395886bcfd583..ad1384ffd2e3a18fbd7b1755fc1fd0ddf6ca07fb 100644 --- a/src/SPIN/atom_vec_spin.cpp +++ b/src/SPIN/atom_vec_spin.cpp @@ -23,16 +23,14 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include "atom_vec_spin.h" #include -#include #include #include "atom.h" -#include "atom_vec_spin.h" #include "comm.h" #include "domain.h" #include "error.h" #include "fix.h" -#include "force.h" #include "memory.h" #include "modify.h" #include "utils.h" diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp index 501b708c88d229bfef404af155267945c6849776..1f808eb1bdcb739297201eb1309696991ad789cd 100644 --- a/src/SPIN/compute_spin.cpp +++ b/src/SPIN/compute_spin.cpp @@ -21,21 +21,17 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include "compute_spin.h" #include -#include +#include #include "atom.h" -#include "compute_spin.h" -#include "domain.h" #include "error.h" #include "force.h" -#include "math_special.h" #include "math_const.h" #include "memory.h" -#include "modify.h" #include "update.h" using namespace LAMMPS_NS; -using namespace MathSpecial; using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp index ec6f719a77b535689ba563b5fb2f1212e9ecf141..ec9c98c4f8f5192e1b9e97829a82b320b6a04513 100644 --- a/src/SPIN/fix_langevin_spin.cpp +++ b/src/SPIN/fix_langevin_spin.cpp @@ -21,31 +21,19 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ -#include +#include "fix_langevin_spin.h" #include #include -#include - -#include "atom.h" -#include "atom_vec_ellipsoid.h" #include "comm.h" -#include "compute.h" -#include "domain.h" #include "error.h" -#include "fix_langevin_spin.h" #include "force.h" -#include "group.h" -#include "input.h" #include "math_const.h" -#include "math_extra.h" #include "memory.h" #include "modify.h" -#include "random_mars.h" #include "random_park.h" -#include "region.h" #include "respa.h" #include "update.h" -#include "variable.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -142,13 +130,11 @@ void FixLangevinSpin::init() void FixLangevinSpin::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) - post_force(vflag); - else { + if (utils::strmatch(update->integrate_style,"^respa")) { ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1); post_force_respa(vflag,nlevels_respa-1,0); ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1); - } + } else post_force(vflag); } /* ---------------------------------------------------------------------- */ diff --git a/src/SPIN/fix_neb_spin.cpp b/src/SPIN/fix_neb_spin.cpp index a8cb0cd2ca5f85f13d7d2d7dadd0714338effe52..5acbbf59e8f012109ca3cbdcc91bf70fb72b54b0 100644 --- a/src/SPIN/fix_neb_spin.cpp +++ b/src/SPIN/fix_neb_spin.cpp @@ -21,15 +21,13 @@ Computer Physics Communications, 196, 335-347. ------------------------------------------------------------------------- */ +#include "fix_neb_spin.h" #include #include -#include #include -#include "fix_neb_spin.h" #include "universe.h" #include "update.h" #include "atom.h" -#include "domain.h" #include "comm.h" #include "modify.h" #include "compute.h" @@ -37,11 +35,9 @@ #include "memory.h" #include "error.h" #include "force.h" -#include "math_const.h" using namespace LAMMPS_NS; using namespace FixConst; -using namespace MathConst; enum{SINGLE_PROC_DIRECT,SINGLE_PROC_MAP,MULTI_PROC}; diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index b992f17cc3a0dc45406d5718b0fdb5bd4dc07ccf..b1b466b5a47dcd9a539c862093bce109636627eb 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -21,38 +21,24 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ -#include -#include +#include "fix_nve_spin.h" #include - #include "atom.h" -#include "atom_vec.h" #include "citeme.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "fix_nve_spin.h" #include "fix_precession_spin.h" #include "fix_langevin_spin.h" #include "fix_setforce_spin.h" #include "force.h" -#include "math_vector.h" -#include "math_extra.h" -#include "math_const.h" #include "memory.h" #include "modify.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "pair.h" -#include "pair_hybrid.h" #include "pair_spin.h" -#include "respa.h" #include "update.h" using namespace LAMMPS_NS; using namespace FixConst; -using namespace MathConst; -using namespace MathExtra; static const char cite_fix_nve_spin[] = "fix nve/spin command:\n\n" diff --git a/src/SPIN/fix_nve_spin.h b/src/SPIN/fix_nve_spin.h index 4800575c064116f932be8c38b5fb162f56ddef9c..1e3b87c1fb82b79cd1302077ed0ec1bcb20be595 100644 --- a/src/SPIN/fix_nve_spin.h +++ b/src/SPIN/fix_nve_spin.h @@ -21,8 +21,6 @@ FixStyle(nve/spin,FixNVESpin) #define LMP_FIX_NVE_SPIN_H #include "fix.h" -#include "pair.h" -#include "pair_spin.h" namespace LAMMPS_NS { diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp index 1ea134d36721a0b21b180a9ef9a1377224be540f..3296b282281035e80030759d26ea0348b53bf94e 100644 --- a/src/SPIN/fix_precession_spin.cpp +++ b/src/SPIN/fix_precession_spin.cpp @@ -21,21 +21,16 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include "fix_precession_spin.h" +#include #include -#include -#include #include #include "atom.h" #include "error.h" -#include "domain.h" -#include "error.h" -#include "fix_precession_spin.h" #include "force.h" #include "input.h" #include "math_const.h" -#include "memory.h" #include "modify.h" -#include "neigh_list.h" #include "respa.h" #include "update.h" #include "variable.h" diff --git a/src/SPIN/fix_setforce_spin.cpp b/src/SPIN/fix_setforce_spin.cpp index c2807418ecf0f314a67095426aa4e13a1191b49a..e36a9d260d488c6cd09ccc4e72221a6be1a14796 100644 --- a/src/SPIN/fix_setforce_spin.cpp +++ b/src/SPIN/fix_setforce_spin.cpp @@ -21,20 +21,15 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ -#include -#include #include "fix_setforce_spin.h" #include "atom.h" #include "update.h" #include "modify.h" #include "domain.h" #include "region.h" -#include "respa.h" #include "input.h" #include "variable.h" #include "memory.h" -#include "error.h" -#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/SPIN/min_spin.cpp b/src/SPIN/min_spin.cpp index dda414ff9759fbc5c2d4ce2fa9f6f4748980aa79..553526ea8e9460da515e411dd67adcc2cce949cf 100644 --- a/src/SPIN/min_spin.cpp +++ b/src/SPIN/min_spin.cpp @@ -17,11 +17,10 @@ Please cite the related publication: ------------------------------------------------------------------------- */ +#include "min_spin.h" #include #include -#include #include -#include "min_spin.h" #include "universe.h" #include "atom.h" #include "force.h" @@ -29,8 +28,6 @@ #include "output.h" #include "timer.h" #include "error.h" -#include "modify.h" -#include "math_special.h" #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/SPIN/neb_spin.cpp b/src/SPIN/neb_spin.cpp index 46a0541488acb9e9aaab9e0ad100c10135172d8b..2bcfe6573af1b62b1b7d81a7f10381d73b2e8f52 100644 --- a/src/SPIN/neb_spin.cpp +++ b/src/SPIN/neb_spin.cpp @@ -21,18 +21,12 @@ Computer Physics Communications, 196, 335-347. ------------------------------------------------------------------------- */ -// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h -// due to OpenMPI bug which sets INT64_MAX via its mpi.h -// before lmptype.h can set flags to insure it is done correctly - -#include "lmptype.h" +#include "neb_spin.h" #include #include #include #include -#include "neb_spin.h" #include "citeme.h" -#include "compute.h" #include "force.h" #include "universe.h" #include "atom.h" @@ -49,10 +43,8 @@ #include "timer.h" #include "memory.h" #include "error.h" -#include "math_const.h" using namespace LAMMPS_NS; -using namespace MathConst; static const char cite_neb_spin[] = "neb/spin command:\n\n" diff --git a/src/SPIN/neb_spin.h b/src/SPIN/neb_spin.h index c128eaffa414bc52c5952fab28969c9a7dcf7716..568eca09579f3ae14b9e41fa3ca93b61e03159fb 100644 --- a/src/SPIN/neb_spin.h +++ b/src/SPIN/neb_spin.h @@ -20,7 +20,6 @@ CommandStyle(neb/spin,NEBSpin) #ifndef LMP_NEB_SPIN_H #define LMP_NEB_SPIN_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/SPIN/pair_spin.cpp b/src/SPIN/pair_spin.cpp index 929b79bef3feccd319649caf54cbb014c2084899..fef247c09b973077d4fa1cc46879c879801b6b9b 100644 --- a/src/SPIN/pair_spin.cpp +++ b/src/SPIN/pair_spin.cpp @@ -21,26 +21,15 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ -#include -#include +#include "pair_spin.h" #include - #include "atom.h" -#include "comm.h" #include "error.h" #include "fix.h" -#include "fix_nve_spin.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "math_const.h" -#include "memory.h" #include "modify.h" #include "pair.h" -#include "pair_hybrid.h" -#include "pair_hybrid_overlay.h" -#include "pair_spin.h" #include "update.h" using namespace LAMMPS_NS; diff --git a/src/SPIN/pair_spin.h b/src/SPIN/pair_spin.h index 1be8550c653a379edc8e393516975c6c74ed8112..3a909e1d1305bc4bed4ad8b92d28cd3384509fc1 100644 --- a/src/SPIN/pair_spin.h +++ b/src/SPIN/pair_spin.h @@ -14,7 +14,7 @@ #ifndef LMP_PAIR_SPIN_H #define LMP_PAIR_SPIN_H -#include "pair.h" +#include "pair.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/SPIN/pair_spin_dipole_cut.cpp b/src/SPIN/pair_spin_dipole_cut.cpp index 4ff198488ad4c809e47e563d4f4a2000b207f493..fb0ec8bb20bbbe91fec92918694674cc0f26685e 100644 --- a/src/SPIN/pair_spin_dipole_cut.cpp +++ b/src/SPIN/pair_spin_dipole_cut.cpp @@ -21,16 +21,16 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include "pair_spin_dipole_cut.h" +#include #include -#include -#include #include -#include "pair_spin_dipole_cut.h" #include "atom.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" +#include "fix.h" #include "fix_nve_spin.h" #include "force.h" #include "math_const.h" diff --git a/src/SPIN/pair_spin_dipole_long.cpp b/src/SPIN/pair_spin_dipole_long.cpp index e3575a6a07b5d600b1f89f2f8b57e1e5398f54e9..670fccfce28c0a698bb162d18d973e69583470da 100644 --- a/src/SPIN/pair_spin_dipole_long.cpp +++ b/src/SPIN/pair_spin_dipole_long.cpp @@ -13,20 +13,19 @@ /* ------------------------------------------------------------------------ Contributing authors: Julien Tranchida (SNL) - Stan Moore (SNL) + Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pair_spin_dipole_long.h" +#include #include -#include -#include #include - -#include "pair_spin_dipole_long.h" #include "atom.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" +#include "fix.h" #include "fix_nve_spin.h" #include "force.h" #include "kspace.h" @@ -59,12 +58,12 @@ lockfixnvespin(NULL) no_virial_fdotr_compute = 1; lattice_flag = 0; - hbar = force->hplanck/MY_2PI; // eV/(rad.THz) + hbar = force->hplanck/MY_2PI; // eV/(rad.THz) mub = 9.274e-4; // in A.Ang^2 mu_0 = 785.15; // in eV/Ang/A^2 mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI); // in eV.Ang^3 - //mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI); // in eV - mub2mu0hbinv = mub2mu0 / hbar; // in rad.THz + //mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI); // in eV + mub2mu0hbinv = mub2mu0 / hbar; // in rad.THz } @@ -243,7 +242,7 @@ void PairSpinDipoleLong::compute(int eflag, int vflag) double **x = atom->x; double **f = atom->f; double **fm = atom->fm; - double **sp = atom->sp; + double **sp = atom->sp; int *type = atom->type; int nlocal = atom->nlocal; int newton_pair = force->newton_pair; @@ -314,36 +313,36 @@ void PairSpinDipoleLong::compute(int eflag, int vflag) bij[2] = (3.0*bij[1] + pre2*expm2) * r2inv; bij[3] = (5.0*bij[2] + pre3*expm2) * r2inv; - compute_long(i,j,eij,bij,fmi,spi,spj); - compute_long_mech(i,j,eij,bij,fmi,spi,spj); + compute_long(i,j,eij,bij,fmi,spi,spj); + compute_long_mech(i,j,eij,bij,fmi,spi,spj); } // force accumulation - f[i][0] += fi[0]; - f[i][1] += fi[1]; + f[i][0] += fi[0]; + f[i][1] += fi[1]; f[i][2] += fi[2]; - fm[i][0] += fmi[0]; - fm[i][1] += fmi[1]; + fm[i][0] += fmi[0]; + fm[i][1] += fmi[1]; fm[i][2] += fmi[2]; if (newton_pair || j < nlocal) { - f[j][0] -= fi[0]; - f[j][1] -= fi[1]; + f[j][0] -= fi[0]; + f[j][1] -= fi[1]; f[j][2] -= fi[2]; } if (eflag) { - if (rsq <= local_cut2) { - evdwl -= spi[0]*fmi[0] + spi[1]*fmi[1] + - spi[2]*fmi[2]; - evdwl *= hbar; - } + if (rsq <= local_cut2) { + evdwl -= spi[0]*fmi[0] + spi[1]*fmi[1] + + spi[2]*fmi[2]; + evdwl *= hbar; + } } else evdwl = 0.0; if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, - evdwl,ecoul,fi[0],fi[1],fi[2],rij[0],rij[1],rij[2]); + evdwl,ecoul,fi[0],fi[1],fi[2],rij[0],rij[1],rij[2]); } } @@ -365,7 +364,7 @@ void PairSpinDipoleLong::compute_single_pair(int ii, double fmi[3]) int *type = atom->type; double **x = atom->x; - double **sp = atom->sp; + double **sp = atom->sp; double **fm_long = atom->fm_long; ilist = list->ilist; @@ -550,7 +549,7 @@ void PairSpinDipoleLong::write_restart(FILE *fp) for (j = i; j <= atom->ntypes; j++) { fwrite(&setflag[i][j],sizeof(int),1,fp); if (setflag[i][j]) { - fwrite(&cut_spin_long[i][j],sizeof(int),1,fp); + fwrite(&cut_spin_long[i][j],sizeof(int),1,fp); } } } @@ -573,10 +572,10 @@ void PairSpinDipoleLong::read_restart(FILE *fp) if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { - if (me == 0) { - fread(&cut_spin_long[i][j],sizeof(int),1,fp); - } - MPI_Bcast(&cut_spin_long[i][j],1,MPI_INT,0,world); + if (me == 0) { + fread(&cut_spin_long[i][j],sizeof(int),1,fp); + } + MPI_Bcast(&cut_spin_long[i][j],1,MPI_INT,0,world); } } } diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp index 41430d230f40c9506bd749f909ba4bf417e9fdda..afd2deaa6a30d3677765a60050048cdc37b700c4 100644 --- a/src/SPIN/pair_spin_dmi.cpp +++ b/src/SPIN/pair_spin_dmi.cpp @@ -21,28 +21,24 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include "pair_spin_dmi.h" +#include #include -#include #include - #include "atom.h" #include "comm.h" #include "error.h" #include "force.h" #include "fix.h" #include "fix_nve_spin.h" -#include "pair_hybrid.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "math_const.h" #include "memory.h" #include "modify.h" -#include "pair_spin_dmi.h" #include "update.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp index 93b6d9501e5f668d68cdf6c88607332d0a52248e..cc28018ad0ea145f13ae9f9266fece49c867aaf5 100644 --- a/src/SPIN/pair_spin_exchange.cpp +++ b/src/SPIN/pair_spin_exchange.cpp @@ -21,28 +21,24 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include "pair_spin_exchange.h" +#include #include -#include #include - #include "atom.h" #include "comm.h" #include "error.h" #include "fix.h" #include "fix_nve_spin.h" #include "force.h" -#include "pair_hybrid.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "math_const.h" #include "memory.h" #include "modify.h" -#include "pair_spin_exchange.h" #include "update.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp index 1f1488b93cfdefc9631aefc6db179b35424d660e..6756ebc3ccddf2c2c3a298a0f284dbea75e85962 100644 --- a/src/SPIN/pair_spin_magelec.cpp +++ b/src/SPIN/pair_spin_magelec.cpp @@ -21,28 +21,24 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include "pair_spin_magelec.h" +#include #include -#include #include - #include "atom.h" #include "comm.h" #include "error.h" #include "fix.h" #include "fix_nve_spin.h" #include "force.h" -#include "pair_hybrid.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "math_const.h" #include "memory.h" #include "modify.h" -#include "pair_spin_magelec.h" #include "update.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/SPIN/pair_spin_neel.cpp b/src/SPIN/pair_spin_neel.cpp index 03041da17fc65570504beaff1f58aa734791f92e..355ba20f398405726fde38d9fc23c348909a5507 100644 --- a/src/SPIN/pair_spin_neel.cpp +++ b/src/SPIN/pair_spin_neel.cpp @@ -21,29 +21,24 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include "pair_spin_neel.h" +#include #include -#include #include - #include "atom.h" #include "comm.h" #include "error.h" -#include "force.h" #include "fix.h" #include "fix_nve_spin.h" #include "force.h" -#include "pair_hybrid.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "math_const.h" #include "memory.h" #include "modify.h" -#include "pair_spin_neel.h" #include "update.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp index d87d2b5e56bfc8a786b3a6d8d63e7a9d1e7eb88e..d5eec91f501af52c09c225ad23f9466bced58667 100644 --- a/src/SRD/fix_srd.cpp +++ b/src/SRD/fix_srd.cpp @@ -15,10 +15,10 @@ Contributing authors: Jeremy Lechman (SNL), Pieter in 't Veld (BASF) ------------------------------------------------------------------------- */ +#include "fix_srd.h" +#include #include #include -#include -#include "fix_srd.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" @@ -27,7 +27,6 @@ #include "group.h" #include "update.h" #include "force.h" -#include "pair.h" #include "domain.h" #include "neighbor.h" #include "comm.h" diff --git a/src/SRD/fix_wall_srd.cpp b/src/SRD/fix_wall_srd.cpp index 24b0c3cec5c2d5210ed21a39450649ac16464485..ab113df28af60f82968986db2a569a35e7ee8f88 100644 --- a/src/SRD/fix_wall_srd.cpp +++ b/src/SRD/fix_wall_srd.cpp @@ -11,11 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_wall_srd.h" -#include "atom.h" -#include "modify.h" +#include +#include #include "fix.h" #include "domain.h" #include "lattice.h" diff --git a/src/USER-ADIOS/dump_atom_adios.cpp b/src/USER-ADIOS/dump_atom_adios.cpp index 55d6c5fbf9e36f2f2c6bfac350ca93c7af4098b0..e711b8a583b3341b7eb3d22ceb575e4e6e1d8871 100644 --- a/src/USER-ADIOS/dump_atom_adios.cpp +++ b/src/USER-ADIOS/dump_atom_adios.cpp @@ -16,6 +16,7 @@ ------------------------------------------------------------------------- */ #include "dump_atom_adios.h" +#include #include "atom.h" #include "domain.h" #include "error.h" @@ -23,7 +24,6 @@ #include "memory.h" #include "universe.h" #include "update.h" -#include #include "adios2.h" diff --git a/src/USER-ADIOS/dump_custom_adios.cpp b/src/USER-ADIOS/dump_custom_adios.cpp index 67f3deeb645f1c4eb00dd48757d89dc8cbe805ae..ee6d7d7e490d2f36fa035912e4315f74bf34e7b8 100644 --- a/src/USER-ADIOS/dump_custom_adios.cpp +++ b/src/USER-ADIOS/dump_custom_adios.cpp @@ -16,6 +16,8 @@ ------------------------------------------------------------------------- */ #include "dump_custom_adios.h" +#include +#include #include "atom.h" #include "compute.h" #include "domain.h" @@ -30,8 +32,6 @@ #include "universe.h" #include "update.h" #include "variable.h" -#include -#include #include "adios2.h" diff --git a/src/USER-ATC/fix_atc.cpp b/src/USER-ATC/fix_atc.cpp index f53343ced1380ce59fe9a6b273e14fda3035335f..e2a1768f55c9b356f78f0272d301bc64fabb4196 100644 --- a/src/USER-ATC/fix_atc.cpp +++ b/src/USER-ATC/fix_atc.cpp @@ -11,8 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -// LAMMPS #include "fix_atc.h" +#include +#include +#include #include "fix_nve.h" #include "atom.h" #include "force.h" @@ -24,7 +26,7 @@ #include "pointers.h" #include "comm.h" #include "group.h" -// ATC + #include "ATC_Method.h" #include "ATC_Transfer.h" #include "ATC_TransferKernel.h" @@ -34,10 +36,6 @@ #include "ATC_CouplingMass.h" #include "ATC_CouplingMomentumEnergy.h" #include "LammpsInterface.h" -// other -#include -#include -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-AWPMD/atom_vec_wavepacket.cpp b/src/USER-AWPMD/atom_vec_wavepacket.cpp index bffe49e6c52ccd8bf8d4e878d5d1589fc7d984da..bce334a7b340aab4d054bc6debc0213c2bb2779c 100644 --- a/src/USER-AWPMD/atom_vec_wavepacket.cpp +++ b/src/USER-AWPMD/atom_vec_wavepacket.cpp @@ -15,15 +15,12 @@ Contributing author: Ilya Valuev (JIHT, Moscow, Russia) ------------------------------------------------------------------------- */ -#include -#include -#include #include "atom_vec_wavepacket.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" #include "memory.h" #include "error.h" diff --git a/src/USER-AWPMD/fix_nve_awpmd.cpp b/src/USER-AWPMD/fix_nve_awpmd.cpp index 7722c931218f3cc56c1a8acbf6fd0d4bcec97e78..a147a11081f18e37b94461e0a0e6f402ffc3da6c 100644 --- a/src/USER-AWPMD/fix_nve_awpmd.cpp +++ b/src/USER-AWPMD/fix_nve_awpmd.cpp @@ -15,15 +15,14 @@ Contributing author: Ilya Valuev (JIHT, Moscow, Russia) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nve_awpmd.h" +#include "pair_awpmd_cut.h" #include "atom.h" #include "force.h" #include "update.h" #include "respa.h" #include "error.h" +#include "utils.h" #include "TCP/wpmd_split.h" @@ -62,7 +61,7 @@ void FixNVEAwpmd::init() dtv = update->dt; dtf = 0.5 * update->dt * force->ftm2v; - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) step_respa = ((Respa *) update->integrate)->step; awpmd_pair=(PairAWPMDCut *)force->pair; diff --git a/src/USER-AWPMD/fix_nve_awpmd.h b/src/USER-AWPMD/fix_nve_awpmd.h index 140d2343087c087744ef484bc56835316b6f2474..832f5821a3684ba7f85963c3ffc75a015541d035 100644 --- a/src/USER-AWPMD/fix_nve_awpmd.h +++ b/src/USER-AWPMD/fix_nve_awpmd.h @@ -25,7 +25,6 @@ FixStyle(nve/awpmd,FixNVEAwpmd) #define LMP_FIX_NVE_awpmd_H #include "fix.h" -#include "pair_awpmd_cut.h" namespace LAMMPS_NS { @@ -45,7 +44,7 @@ class FixNVEAwpmd : public Fix { double *step_respa; int mass_require; - PairAWPMDCut *awpmd_pair; + class PairAWPMDCut *awpmd_pair; }; } diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/USER-AWPMD/pair_awpmd_cut.cpp index 1b7bf35c28d5dc2672b2aa9f076714faa8baa7fb..75ebb0e2515653fff5f0768f6373041fd54b49b7 100644 --- a/src/USER-AWPMD/pair_awpmd_cut.cpp +++ b/src/USER-AWPMD/pair_awpmd_cut.cpp @@ -15,11 +15,12 @@ Contributing author: Ilya Valuev (JIHT, Moscow, Russia) ------------------------------------------------------------------------- */ +#include "pair_awpmd_cut.h" +#include #include -#include -#include #include -#include "pair_awpmd_cut.h" +#include +#include #include "atom.h" #include "update.h" #include "min.h" @@ -32,6 +33,9 @@ #include "memory.h" #include "error.h" +#include "logexc.h" +#include "vector_3.h" +#include "TCP/wpmd.h" #include "TCP/wpmd_split.h" using namespace LAMMPS_NS; diff --git a/src/USER-BOCS/compute_pressure_bocs.cpp b/src/USER-BOCS/compute_pressure_bocs.cpp index c43910ec6d9382b36be3db1be51b93973018f45d..d0a24b99a392a07f60371439eb224e1c64f87fc7 100644 --- a/src/USER-BOCS/compute_pressure_bocs.cpp +++ b/src/USER-BOCS/compute_pressure_bocs.cpp @@ -14,10 +14,11 @@ from The Pennsylvania State University ------------------------------------------------------------------------- */ +#include "compute_pressure_bocs.h" #include +#include #include #include -#include "compute_pressure_bocs.h" #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp index 7bdb8933e3d4e47893949731cd949833a65c0d48..936e5ff58e4b9906c415f2f10ecf569df8af5774 100644 --- a/src/USER-BOCS/fix_bocs.cpp +++ b/src/USER-BOCS/fix_bocs.cpp @@ -14,11 +14,10 @@ from The Pennsylvania State University ------------------------------------------------------------------------- */ +#include "fix_bocs.h" #include #include #include -#include "fix_bocs.h" -#include "math_extra.h" #include "atom.h" #include "force.h" #include "group.h" diff --git a/src/USER-CGDNA/bond_oxdna2_fene.cpp b/src/USER-CGDNA/bond_oxdna2_fene.cpp index 557d62aac6e79621ce4dbccf64361e6158981ec4..682f3253452f17dc22c1140706b6ec7d136bc7e7 100644 --- a/src/USER-CGDNA/bond_oxdna2_fene.cpp +++ b/src/USER-CGDNA/bond_oxdna2_fene.cpp @@ -14,8 +14,6 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include #include "bond_oxdna2_fene.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/USER-CGDNA/bond_oxdna_fene.cpp index 9d6453f5a8b87df264c69db4ffa9c2d9d8d49c0c..f549fc423d34ced167a98ee0e93b97355dc6aa55 100644 --- a/src/USER-CGDNA/bond_oxdna_fene.cpp +++ b/src/USER-CGDNA/bond_oxdna_fene.cpp @@ -14,12 +14,11 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include #include "bond_oxdna_fene.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "update.h" #include "force.h" diff --git a/src/USER-CGDNA/fix_nve_dot.cpp b/src/USER-CGDNA/fix_nve_dot.cpp index 72b33887936daf62d25f9ad2f5d479db3f4800f8..ff8e1c0ee20c215bccbf423e33f763a304673cc6 100644 --- a/src/USER-CGDNA/fix_nve_dot.cpp +++ b/src/USER-CGDNA/fix_nve_dot.cpp @@ -14,16 +14,11 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nve_dot.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" -#include "force.h" #include "update.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp index c73801c97aeb2962377b59f6d562430c2c850b46..59def4c812df66878e92cf421d997c4b72452a93 100644 --- a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp +++ b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp @@ -15,10 +15,9 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ +#include "fix_nve_dotc_langevin.h" #include -#include #include -#include "fix_nve_dotc_langevin.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" @@ -26,7 +25,6 @@ #include "update.h" #include "comm.h" #include "random_mars.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/mf_oxdna.h b/src/USER-CGDNA/mf_oxdna.h index c63a37cde2ab4b8a9fa07e6b556181e947e4c997..e4ed1bbd032d73855418dc9cc9b3377f83a309b8 100644 --- a/src/USER-CGDNA/mf_oxdna.h +++ b/src/USER-CGDNA/mf_oxdna.h @@ -14,7 +14,6 @@ #ifndef MF_OXDNA_H #define MF_OXDNA_H -#include #include "math_extra.h" namespace MFOxdna { diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp index 4fde5e37b4484bd1879286392e397ae37578997d..609b63e27f35919daaa1a7a6868fc2d95025a0e0 100644 --- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp @@ -14,20 +14,16 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ +#include "pair_oxdna2_coaxstk.h" +#include #include -#include -#include #include -#include "pair_oxdna2_coaxstk.h" #include "mf_oxdna.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp index ca5f44b815367ea2bdf69422fe7152d58ccff58a..630dd7a55920efaf364614e3e11093ef5729b4b9 100644 --- a/src/USER-CGDNA/pair_oxdna2_dh.cpp +++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp @@ -14,29 +14,21 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ +#include "pair_oxdna2_dh.h" +#include #include -#include -#include #include -#include "pair_oxdna2_dh.h" -#include "mf_oxdna.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "math_const.h" #include "memory.h" #include "error.h" #include "atom_vec_ellipsoid.h" #include "math_extra.h" using namespace LAMMPS_NS; -using namespace MathConst; -using namespace MFOxdna; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-CGDNA/pair_oxdna2_excv.cpp b/src/USER-CGDNA/pair_oxdna2_excv.cpp index f2fb77b3b2e1e201b06fc45d6f143773ad81e07e..d8a263676f181ee64bf1f17e744f166994d9372b 100644 --- a/src/USER-CGDNA/pair_oxdna2_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna2_excv.cpp @@ -14,10 +14,6 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_oxdna2_excv.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp index 6b10117f91d05a1c054e00cf0fdc8716346765f3..d71acc2029f34f0d0e56aca88a60db54897b6f08 100644 --- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp @@ -14,20 +14,16 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ +#include "pair_oxdna_coaxstk.h" +#include #include -#include -#include #include -#include "pair_oxdna_coaxstk.h" #include "mf_oxdna.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/USER-CGDNA/pair_oxdna_excv.cpp index ddfe32946cd3d5413d4f474bdbbb6d4875cdb76a..f187fc7403af849370e817c1712ff2037f537ef9 100644 --- a/src/USER-CGDNA/pair_oxdna_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna_excv.cpp @@ -14,28 +14,22 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ +#include "pair_oxdna_excv.h" +#include #include -#include -#include #include -#include "pair_oxdna_excv.h" #include "mf_oxdna.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "math_const.h" #include "memory.h" #include "error.h" #include "atom_vec_ellipsoid.h" #include "math_extra.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace MFOxdna; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp index 03e83e1324ea858f0792d19c043f404351d80e96..e9852d0e3880cd11215f545056b8d0f08c4cac97 100644 --- a/src/USER-CGDNA/pair_oxdna_hbond.cpp +++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp @@ -14,28 +14,22 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ +#include "pair_oxdna_hbond.h" +#include #include -#include -#include #include -#include "pair_oxdna_hbond.h" #include "mf_oxdna.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "math_const.h" #include "memory.h" #include "error.h" #include "atom_vec_ellipsoid.h" #include "math_extra.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace MFOxdna; // sequence-specific base-pairing strength diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/USER-CGDNA/pair_oxdna_stk.cpp index 3c7a3f05bcd220ca38d77c3c27de9546bf090bf8..3d0c4e9136bf31485c38a08fe51b441876d94123 100644 --- a/src/USER-CGDNA/pair_oxdna_stk.cpp +++ b/src/USER-CGDNA/pair_oxdna_stk.cpp @@ -14,28 +14,22 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ +#include "pair_oxdna_stk.h" +#include #include -#include -#include #include -#include "pair_oxdna_stk.h" +#include #include "mf_oxdna.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "math_const.h" #include "memory.h" #include "error.h" #include "atom_vec_ellipsoid.h" #include "math_extra.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace MFOxdna; // sequence-specific stacking strength diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp index d5248937caaff07b97b714aa2168341bd4770855..95f569481836f225c185a0f96990d61db91e9b9f 100644 --- a/src/USER-CGDNA/pair_oxdna_xstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp @@ -14,20 +14,16 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ +#include "pair_oxdna_xstk.h" +#include #include -#include -#include #include -#include "pair_oxdna_xstk.h" #include "mf_oxdna.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/USER-CGSDK/angle_sdk.cpp b/src/USER-CGSDK/angle_sdk.cpp index 823c725e077e18266dd8a81ede2d72b3c9b4b1ea..862c165bbd06511a23685112d8cd4b5d718c3d0b 100644 --- a/src/USER-CGSDK/angle_sdk.cpp +++ b/src/USER-CGSDK/angle_sdk.cpp @@ -18,9 +18,9 @@ lj/sdk potential for coarse grained MD simulations. ------------------------------------------------------------------------- */ -#include -#include #include "angle_sdk.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "pair.h" diff --git a/src/USER-CGSDK/angle_sdk.h b/src/USER-CGSDK/angle_sdk.h index 293004ad4d51b4e159dce696cd8d7aea89caf063..2e94b444702628580979f0159fb0ea24dfa3189e 100644 --- a/src/USER-CGSDK/angle_sdk.h +++ b/src/USER-CGSDK/angle_sdk.h @@ -20,7 +20,6 @@ AngleStyle(sdk,AngleSDK) #ifndef LMP_ANGLE_SDK_H #define LMP_ANGLE_SDK_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-CGSDK/pair_lj_sdk.cpp b/src/USER-CGSDK/pair_lj_sdk.cpp index 7dd6c04436f0130d031f4cca399a2866d4f645d3..1301dc41551fa79921ef9cbfd2dd951e80852bfd 100644 --- a/src/USER-CGSDK/pair_lj_sdk.cpp +++ b/src/USER-CGSDK/pair_lj_sdk.cpp @@ -16,20 +16,14 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ +#include "pair_lj_sdk.h" +#include #include -#include -#include #include -#include "pair_lj_sdk.h" #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "math_const.h" #include "memory.h" #include "error.h" @@ -37,7 +31,6 @@ #include "lj_sdk_common.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace LJSDKParms; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp index 33a1659df986f62aab1311013091fff96fea9777..62acf00d279893259ef6563ad05d68202c93b7bd 100644 --- a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp +++ b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp @@ -16,21 +16,16 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ +#include "pair_lj_sdk_coul_long.h" +#include #include -#include -#include #include -#include "pair_lj_sdk_coul_long.h" #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "math_const.h" #include "memory.h" #include "error.h" @@ -38,7 +33,6 @@ #include "lj_sdk_common.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace LJSDKParms; #define EWALD_F 1.12837917 diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp index d26f8efcdc05856b30df557177d4c416813ed5e7..f168089fae7f2098c539755e48f8ce41832542b2 100644 --- a/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp +++ b/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp @@ -16,28 +16,18 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ +#include "pair_lj_sdk_coul_msm.h" #include -#include -#include #include -#include "pair_lj_sdk_coul_msm.h" #include "atom.h" -#include "comm.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "math_const.h" -#include "memory.h" #include "error.h" #include "lj_sdk_common.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace LJSDKParms; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-COLVARS/colvarproxy_lammps.cpp b/src/USER-COLVARS/colvarproxy_lammps.cpp index 651999f79c121f77f8d86b306f99a49cff3df580..2c43a3fb265215de8feedd0932e411be74e463b1 100644 --- a/src/USER-COLVARS/colvarproxy_lammps.cpp +++ b/src/USER-COLVARS/colvarproxy_lammps.cpp @@ -8,33 +8,22 @@ // Colvars repository at GitHub. +#include "colvarproxy_lammps.h" #include +#include +#include +#include +#include +#include +#include + #include "lammps.h" -#include "atom.h" #include "error.h" #include "output.h" #include "random_park.h" -#include "fix_colvars.h" - #include "colvarmodule.h" -#include "colvar.h" -#include "colvarbias.h" -#include "colvaratoms.h" #include "colvarproxy.h" -#include "colvarproxy_lammps.h" - -#include -#include -#include - -#include -#include -#include - -#include -#include -#include #define HASH_FAIL -1 diff --git a/src/USER-COLVARS/colvarproxy_lammps.h b/src/USER-COLVARS/colvarproxy_lammps.h index c3d9dbb35fb4b3eb0f16808386c5d12e9a2ad248..8ed03309a348d8eddb3fbef69d60845484334538 100644 --- a/src/USER-COLVARS/colvarproxy_lammps.h +++ b/src/USER-COLVARS/colvarproxy_lammps.h @@ -10,33 +10,22 @@ #ifndef COLVARPROXY_LAMMPS_H #define COLVARPROXY_LAMMPS_H -#include "colvarproxy_lammps_version.h" - -#include "colvarmodule.h" -#include "colvarproxy.h" -#include "colvarvalue.h" - -#include "lammps.h" -#include "domain.h" -#include "force.h" -#include "update.h" +#include "colvarproxy_lammps_version.h" // IWYU pragma: export +#include +#include #include #include -#include -/* struct for packed data communication of coordinates and forces. */ -struct commdata { - int tag,type; - double x,y,z,m,q; -}; +#include "colvarmodule.h" +#include "colvarproxy.h" +#include "colvartypes.h" -inline std::ostream & operator<< (std::ostream &out, const commdata &cd) -{ - out << " (" << cd.tag << "/" << cd.type << ": " - << cd.x << ", " << cd.y << ", " << cd.z << ") "; - return out; -} +#include "random_park.h" +#include "lammps.h" // IWYU pragma: keep +#include "domain.h" // IWYU pragma: keep +#include "force.h" // IWYU pragma: keep +#include "update.h" // IWYU pragma: keep /// \brief Communication between colvars and LAMMPS /// (implementation of \link colvarproxy \endlink) @@ -46,8 +35,8 @@ class colvarproxy_lammps : public colvarproxy { protected: // pointers to LAMMPS class instances - class LAMMPS_NS::LAMMPS *_lmp; - class LAMMPS_NS::RanPark *_random; + LAMMPS_NS::LAMMPS *_lmp; + LAMMPS_NS::RanPark *_random; // state of LAMMPS properties double t_target, my_timestep, my_boltzmann, my_angstrom; diff --git a/src/USER-COLVARS/fix_colvars.cpp b/src/USER-COLVARS/fix_colvars.cpp index ff0e8fb3347d7727c80f6b0cf8993cd300009f0a..4a57e59fbd11ed099ecc1b15b1131047e322f8a1 100644 --- a/src/USER-COLVARS/fix_colvars.cpp +++ b/src/USER-COLVARS/fix_colvars.cpp @@ -24,27 +24,29 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include "fix_colvars.h" +#include #include #include -#include +#include +#include +#include +#include -#include "fix_colvars.h" #include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "group.h" +#include "force.h" #include "memory.h" #include "modify.h" -#include "random_park.h" #include "respa.h" #include "universe.h" #include "update.h" #include "citeme.h" #include "colvarproxy_lammps.h" +#include "colvarmodule.h" static const char colvars_pub[] = "fix colvars command:\n\n" @@ -57,6 +59,19 @@ static const char colvars_pub[] = " note = {doi: 10.1080/00268976.2013.813594}\n" "}\n\n"; +/* struct for packed data communication of coordinates and forces. */ +struct LAMMPS_NS::commdata { + int tag,type; + double x,y,z,m,q; +}; + +inline std::ostream & operator<< (std::ostream &out, const LAMMPS_NS::commdata &cd) +{ + out << " (" << cd.tag << "/" << cd.type << ": " + << cd.x << ", " << cd.y << ", " << cd.z << ") "; + return out; +} + /* re-usable integer hash table code with static linkage. */ /** hash table top level data structure */ diff --git a/src/USER-COLVARS/fix_colvars.h b/src/USER-COLVARS/fix_colvars.h index a0c197fca4446e55f0c437ecc49c7666f8e7110c..985457e7462190275072b0ba4922b2aebb04a550 100644 --- a/src/USER-COLVARS/fix_colvars.h +++ b/src/USER-COLVARS/fix_colvars.h @@ -34,10 +34,9 @@ FixStyle(colvars,FixColvars) #define LMP_FIX_COLVARS_H #include "fix.h" +#include -// forward declaration class colvarproxy_lammps; -struct commdata; namespace LAMMPS_NS { @@ -64,7 +63,7 @@ class FixColvars : public Fix { virtual void restart(char *); protected: - class colvarproxy_lammps *proxy; // pointer to the colvars proxy class + colvarproxy_lammps *proxy; // pointer to the colvars proxy class char *conf_file; // name of colvars config file char *inp_name; // name/prefix of colvars restart file char *out_name; // prefix string for all output files diff --git a/src/USER-COLVARS/group_ndx.cpp b/src/USER-COLVARS/group_ndx.cpp index 858336c9d505d460377dac00d4ce488abad818fc..1e37e2de9c9d7be83da409b65d0500acb86eed85 100644 --- a/src/USER-COLVARS/group_ndx.cpp +++ b/src/USER-COLVARS/group_ndx.cpp @@ -17,15 +17,13 @@ ------------------------------------------------------------------------- */ #include "group_ndx.h" +#include +#include #include "atom.h" #include "comm.h" #include "group.h" -#include "memory.h" #include "error.h" -#include -#include - using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- diff --git a/src/USER-COLVARS/ndx_group.cpp b/src/USER-COLVARS/ndx_group.cpp index 7b46364f189cc1e9ebef74bb965c8670affadbd2..a1369df2fb3f90dd117b276dde349b4ecd00093f 100644 --- a/src/USER-COLVARS/ndx_group.cpp +++ b/src/USER-COLVARS/ndx_group.cpp @@ -17,17 +17,14 @@ ------------------------------------------------------------------------- */ #include "ndx_group.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "group.h" -#include "memory.h" -#include "force.h" #include "error.h" -#include -#include -#include - using namespace LAMMPS_NS; #define BUFLEN 4096 #define DELTA 16384 diff --git a/src/USER-DIFFRACTION/compute_saed.cpp b/src/USER-DIFFRACTION/compute_saed.cpp index dcafe57ba80f0d6b7f59602750eed317cae6c363..971d9bd380b6a7bebcf3149616222402ab294b0c 100644 --- a/src/USER-DIFFRACTION/compute_saed.cpp +++ b/src/USER-DIFFRACTION/compute_saed.cpp @@ -15,13 +15,12 @@ Contributing authors: Shawn Coleman & Douglas Spearot (Arkansas) ------------------------------------------------------------------------- */ +#include "compute_saed.h" #include #include #include -#include #include #include "math_const.h" -#include "compute_saed.h" #include "compute_saed_consts.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-DIFFRACTION/compute_xrd.cpp b/src/USER-DIFFRACTION/compute_xrd.cpp index d6b7549272a0ac1dd9a3b8a25d7cf3e5d6330a28..f48951f1ff7cfeb00066df13b8b28dc9a3ded1f7 100644 --- a/src/USER-DIFFRACTION/compute_xrd.cpp +++ b/src/USER-DIFFRACTION/compute_xrd.cpp @@ -16,13 +16,12 @@ Updated: 06/17/2015-2 ------------------------------------------------------------------------- */ +#include "compute_xrd.h" #include #include #include -#include #include #include "math_const.h" -#include "compute_xrd.h" #include "compute_xrd_consts.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/USER-DIFFRACTION/fix_saed_vtk.cpp index 4d9af6681852ee88e25f200aae8ad55303ce51c6..c3a72e494bfbcc9c539b6e46ea4bfa8b36a1e4bd 100644 --- a/src/USER-DIFFRACTION/fix_saed_vtk.cpp +++ b/src/USER-DIFFRACTION/fix_saed_vtk.cpp @@ -16,17 +16,14 @@ Incorporating SAED: Shawn Coleman (Arkansas) ------------------------------------------------------------------------- */ +#include "fix_saed_vtk.h" #include #include #include -#include "fix_saed_vtk.h" #include "update.h" #include "modify.h" #include "compute.h" #include "compute_saed.h" -#include "group.h" -#include "input.h" -#include "variable.h" #include "memory.h" #include "error.h" #include "force.h" diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.h b/src/USER-DIFFRACTION/fix_saed_vtk.h index 2fc09c781c8da9644959fd5ddba30588556cf162..94abbf01943022e16d6d786345b2b01e0187c36c 100644 --- a/src/USER-DIFFRACTION/fix_saed_vtk.h +++ b/src/USER-DIFFRACTION/fix_saed_vtk.h @@ -20,7 +20,6 @@ FixStyle(saed/vtk,FixSAEDVTK) #ifndef LMP_FIX_SAED_VTK_H #define LMP_FIX_SAED_VTK_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/USER-DPD/atom_vec_dpd.cpp b/src/USER-DPD/atom_vec_dpd.cpp index de673caec0268b845886d92b02760da0a1b227f5..d1768d473ef50be5306038fc824cf1182a3fddae 100644 --- a/src/USER-DPD/atom_vec_dpd.cpp +++ b/src/USER-DPD/atom_vec_dpd.cpp @@ -15,12 +15,10 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include #include "atom_vec_dpd.h" #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/USER-DPD/compute_dpd.cpp b/src/USER-DPD/compute_dpd.cpp index 08aa19bcdfcffed106ff2d1836473840a4546525..0ef78681646d61578e76df265788d413f454b6f3 100644 --- a/src/USER-DPD/compute_dpd.cpp +++ b/src/USER-DPD/compute_dpd.cpp @@ -15,13 +15,10 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include #include "compute_dpd.h" +#include #include "atom.h" #include "update.h" -#include "force.h" -#include "domain.h" -#include "group.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-DPD/compute_dpd_atom.cpp b/src/USER-DPD/compute_dpd_atom.cpp index 78f842a68f2f2b351c672ba68bf4dbd6f4628057..0fd732f669d30e7b482b9402b9cf1ca2f4520ccf 100644 --- a/src/USER-DPD/compute_dpd_atom.cpp +++ b/src/USER-DPD/compute_dpd_atom.cpp @@ -15,21 +15,15 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_dpd_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" -#include "domain.h" -#include "group.h" #include "memory.h" #include "error.h" #include "comm.h" -#include - using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-DPD/fix_dpd_energy.cpp b/src/USER-DPD/fix_dpd_energy.cpp index 5759a164f5cbec2bef1102c1380e3c01c222f9af..6ee88ea88a2c130abc08f6d052fc12d4ad35b9f9 100644 --- a/src/USER-DPD/fix_dpd_energy.cpp +++ b/src/USER-DPD/fix_dpd_energy.cpp @@ -11,14 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_dpd_energy.h" #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" -#include "modify.h" #include "error.h" #include "pair_dpd_fdt_energy.h" diff --git a/src/USER-DPD/fix_eos_cv.cpp b/src/USER-DPD/fix_eos_cv.cpp index 919e6829f30fd91d5a8d2580ac64c0b276f44ea0..5b25519a401d2e2ce073bd2903f2064b6ccd94ea 100644 --- a/src/USER-DPD/fix_eos_cv.cpp +++ b/src/USER-DPD/fix_eos_cv.cpp @@ -15,8 +15,6 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include -#include #include "fix_eos_cv.h" #include "atom.h" #include "error.h" diff --git a/src/USER-DPD/fix_eos_table.cpp b/src/USER-DPD/fix_eos_table.cpp index 7d701f5fb8ed17c7e600a9a405096aa4f1df14d6..ff9a186c47a4e8ebd61d28e530a713b42cf1cc14 100644 --- a/src/USER-DPD/fix_eos_table.cpp +++ b/src/USER-DPD/fix_eos_table.cpp @@ -15,9 +15,10 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ +#include "fix_eos_table.h" +#include #include #include -#include "fix_eos_table.h" #include "atom.h" #include "error.h" #include "force.h" diff --git a/src/USER-DPD/fix_eos_table_rx.cpp b/src/USER-DPD/fix_eos_table_rx.cpp index 779cee0e8bf02f763d681ebcc65980c5faebafa3..9f1bd6a3bbcaaca743fa8c39ae5490ea2f438ede 100644 --- a/src/USER-DPD/fix_eos_table_rx.cpp +++ b/src/USER-DPD/fix_eos_table_rx.cpp @@ -15,10 +15,11 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ +#include "fix_eos_table_rx.h" +#include #include #include #include -#include "fix_eos_table_rx.h" #include "atom.h" #include "error.h" #include "force.h" diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp index cb8349786f324e8e0fcd86fa27bd30c114d468b8..03e8ae49a4718eff0aef7b977c361da82f112a10 100644 --- a/src/USER-DPD/fix_rx.cpp +++ b/src/USER-DPD/fix_rx.cpp @@ -11,12 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "fix_rx.h" +#include #include #include #include #include // DBL_EPSILON -#include "fix_rx.h" #include "atom.h" #include "error.h" #include "group.h" diff --git a/src/USER-DPD/fix_shardlow.cpp b/src/USER-DPD/fix_shardlow.cpp index 4e133480ad4d97cbd830cd962bcb971c2ac9df9d..b0efeb634d207238e5737fedcc1eb28e0ed98b54 100644 --- a/src/USER-DPD/fix_shardlow.cpp +++ b/src/USER-DPD/fix_shardlow.cpp @@ -33,27 +33,25 @@ 135, 204105. ------------------------------------------------------------------------- */ -#include +#include "fix_shardlow.h" #include #include #include -#include "fix_shardlow.h" +#include #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" -#include "atom_vec.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" +#include "npair.h" #include "memory.h" #include "domain.h" #include "modify.h" #include "pair_dpd_fdt.h" #include "pair_dpd_fdt_energy.h" -#include "pair.h" #include "npair_half_bin_newton_ssa.h" #include "citeme.h" diff --git a/src/USER-DPD/nbin_ssa.cpp b/src/USER-DPD/nbin_ssa.cpp index dcd434cb4a40511ba1f1015b64931bbed770ccb2..e3fa71aedfd1e3faf3d8f04fa1f31367f4f59e84 100644 --- a/src/USER-DPD/nbin_ssa.cpp +++ b/src/USER-DPD/nbin_ssa.cpp @@ -21,8 +21,6 @@ #include "update.h" #include "group.h" #include "domain.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-DPD/npair_half_bin_newton_ssa.cpp b/src/USER-DPD/npair_half_bin_newton_ssa.cpp index ba90ebc465228992237b008e6e28e54a3bbd44c4..2139173d4717b285ed75a7429c39f85fff520ad1 100644 --- a/src/USER-DPD/npair_half_bin_newton_ssa.cpp +++ b/src/USER-DPD/npair_half_bin_newton_ssa.cpp @@ -17,7 +17,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_newton_ssa.h" -#include "neighbor.h" #include "nstencil_ssa.h" #include "nbin_ssa.h" #include "neigh_list.h" @@ -25,7 +24,6 @@ #include "atom_vec.h" #include "molecule.h" #include "domain.h" -#include "group.h" #include "memory.h" #include "my_page.h" #include "error.h" diff --git a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp b/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp index 451381c1049242ac8cd3fe8efdb6599f71672897..9953fca62c4de87ee466a373c3e18fda3fb55057 100644 --- a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp +++ b/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp @@ -17,8 +17,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_2d_newton_ssa.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp b/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp index cdd3b8856f682ec9535a7c9e694dabe751b84ffa..4dd3c4a5fe27c35fbddd148a75d2c1d5c45332c3 100644 --- a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp +++ b/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp @@ -17,8 +17,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_3d_newton_ssa.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_dpd_fdt.cpp b/src/USER-DPD/pair_dpd_fdt.cpp index 07ef8190f04fbe74ea3cbc235ca751d900decc64..1cb9d68d063b0c9d275e90927979b0a3824fdbe4 100644 --- a/src/USER-DPD/pair_dpd_fdt.cpp +++ b/src/USER-DPD/pair_dpd_fdt.cpp @@ -15,23 +15,20 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ +#include "pair_dpd_fdt.h" +#include #include -#include -#include #include #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "update.h" #include "fix.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "random_mars.h" #include "memory.h" #include "modify.h" -#include "pair_dpd_fdt.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_dpd_fdt_energy.cpp b/src/USER-DPD/pair_dpd_fdt_energy.cpp index 12e6989c00692d53b25152f207ce63c1c37298ed..22741a055d5124a0fd3924f1f19f069dc76c6356 100644 --- a/src/USER-DPD/pair_dpd_fdt_energy.cpp +++ b/src/USER-DPD/pair_dpd_fdt_energy.cpp @@ -15,23 +15,20 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ +#include "pair_dpd_fdt_energy.h" +#include #include -#include -#include #include #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "update.h" #include "fix.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "random_mars.h" #include "memory.h" #include "modify.h" -#include "pair_dpd_fdt_energy.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/USER-DPD/pair_exp6_rx.cpp index 13521b52b18ae5d63328bdadd68c695704d06395..5cf2859ae3914dd852968ebcfe2492bcb6d71118 100644 --- a/src/USER-DPD/pair_exp6_rx.cpp +++ b/src/USER-DPD/pair_exp6_rx.cpp @@ -11,17 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_exp6_rx.h" +#include #include -#include #include #include #include -#include "pair_exp6_rx.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "math_const.h" #include "math_special.h" #include "memory.h" #include "error.h" @@ -29,7 +28,6 @@ #include "fix.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace MathSpecial; #define MAXLINE 1024 diff --git a/src/USER-DPD/pair_table_rx.cpp b/src/USER-DPD/pair_table_rx.cpp index f2d0d7b1fbd1ed5d6179a5d27a92ddfc23065182..e767f93367073bacf2e5f9e909eba12e9893ffb4 100644 --- a/src/USER-DPD/pair_table_rx.cpp +++ b/src/USER-DPD/pair_table_rx.cpp @@ -15,14 +15,12 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_table_rx.h" #include #include -#include #include -#include "pair_table_rx.h" #include "atom.h" #include "force.h" -#include "comm.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/USER-DRUDE/compute_temp_drude.cpp b/src/USER-DRUDE/compute_temp_drude.cpp index 4830e950d0c3c07cdf0fae375db9e21ff1858207..a12c248680593046b1f3dca27fd5595484248268 100644 --- a/src/USER-DRUDE/compute_temp_drude.cpp +++ b/src/USER-DRUDE/compute_temp_drude.cpp @@ -11,19 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_temp_drude.h" #include -#include #include -#include "compute_temp_drude.h" #include "atom.h" #include "update.h" #include "force.h" -#include "group.h" #include "modify.h" -#include "fix.h" +#include "fix_drude.h" #include "domain.h" -#include "lattice.h" -#include "memory.h" #include "error.h" #include "comm.h" diff --git a/src/USER-DRUDE/compute_temp_drude.h b/src/USER-DRUDE/compute_temp_drude.h index 88d767f8b75eac00b5b3dc847bf5d1344301692c..530c84ce3d347b4ffdbb2e8c898f05890200adb1 100644 --- a/src/USER-DRUDE/compute_temp_drude.h +++ b/src/USER-DRUDE/compute_temp_drude.h @@ -21,7 +21,6 @@ ComputeStyle(temp/drude,ComputeTempDrude) #define LMP_COMPUTE_TEMP_DRUDE_H #include "compute.h" -#include "fix_drude.h" namespace LAMMPS_NS { @@ -37,7 +36,7 @@ class ComputeTempDrude : public Compute { private: int fix_dof; - FixDrude * fix_drude; + class FixDrude * fix_drude; char *id_temp; class Compute *temperature; bigint dof_core, dof_drude; diff --git a/src/USER-DRUDE/fix_drude.cpp b/src/USER-DRUDE/fix_drude.cpp index 7800efe7ff74aa5174a041853557f7b2ce5dbf32..080408459c754863f6f9054a18e98f2791a05a2d 100644 --- a/src/USER-DRUDE/fix_drude.cpp +++ b/src/USER-DRUDE/fix_drude.cpp @@ -11,9 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_drude.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "modify.h" diff --git a/src/USER-DRUDE/fix_drude_transform.cpp b/src/USER-DRUDE/fix_drude_transform.cpp index 34742a0683311a8e1286b4e122897434d845209b..4128c508d69fd75a94a793c916f20587a99eb9be 100644 --- a/src/USER-DRUDE/fix_drude_transform.cpp +++ b/src/USER-DRUDE/fix_drude_transform.cpp @@ -12,15 +12,16 @@ ------------------------------------------------------------------------- */ /** Fix Drude Transform ******************************************************/ +#include "fix_drude_transform.h" +#include #include #include -#include "fix_drude_transform.h" +#include "fix_drude.h" #include "atom.h" #include "domain.h" #include "comm.h" #include "error.h" #include "modify.h" -#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-DRUDE/fix_drude_transform.h b/src/USER-DRUDE/fix_drude_transform.h index 41f4e147ed3209accc8536b9fc71da22d4468105..b74a500c95276642d6e1e7df6fb8aab5872f9692 100644 --- a/src/USER-DRUDE/fix_drude_transform.h +++ b/src/USER-DRUDE/fix_drude_transform.h @@ -22,7 +22,6 @@ FixStyle(drude/transform/inverse,FixDrudeTransform) #define LMP_FIX_DRUDE_TRANSFORM_H #include "fix.h" -#include "fix_drude.h" namespace LAMMPS_NS { @@ -42,7 +41,7 @@ class FixDrudeTransform : public Fix { void unpack_forward_comm(int n, int first, double *buf); protected: double * mcoeff; - FixDrude * fix_drude; + class FixDrude * fix_drude; }; } diff --git a/src/USER-DRUDE/fix_langevin_drude.cpp b/src/USER-DRUDE/fix_langevin_drude.cpp index b9d1139f83df65d20644bc9356733c0c2e48701c..d413c31bd71892fc95a8b04fbd460b486a6210ad 100644 --- a/src/USER-DRUDE/fix_langevin_drude.cpp +++ b/src/USER-DRUDE/fix_langevin_drude.cpp @@ -11,17 +11,17 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_langevin_drude.h" +#include #include -#include #include -#include "fix_langevin_drude.h" +#include "fix_drude.h" #include "atom.h" #include "force.h" #include "comm.h" #include "input.h" #include "variable.h" #include "random_mars.h" -#include "group.h" #include "update.h" #include "modify.h" #include "compute.h" diff --git a/src/USER-DRUDE/fix_langevin_drude.h b/src/USER-DRUDE/fix_langevin_drude.h index d65440582c6b9ebf56b79131312c29c51888f1a2..9437883ba348bb382b8930e21707fbf6a20f2c27 100644 --- a/src/USER-DRUDE/fix_langevin_drude.h +++ b/src/USER-DRUDE/fix_langevin_drude.h @@ -21,7 +21,6 @@ FixStyle(langevin/drude,FixLangevinDrude) #define LMP_FIX_LANGEVIN_DRUDE_H #include "fix.h" -#include "fix_drude.h" namespace LAMMPS_NS { @@ -51,7 +50,7 @@ class FixLangevinDrude : public Fix { class RanMars *random_core, *random_drude; int zero; bigint ncore; - FixDrude * fix_drude; + class FixDrude * fix_drude; class Compute *temperature; char *id_temp; }; diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp index 1ebe4a4c2d6ea8e6d0c4873bd8496a1da7e714c1..851effd89c8fc5229ca1684d8e3e5df0bf6ef65c 100644 --- a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp +++ b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp @@ -15,20 +15,17 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_thole_long.h" +#include #include -#include -#include #include -#include "pair_lj_cut_thole_long.h" +#include "fix_drude.h" #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" -#include "update.h" -#include "integrate.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.h b/src/USER-DRUDE/pair_lj_cut_thole_long.h index 27a917c7375a5c58c49baf037c9bfb65bea5eb84..4c3a88306418614a0f42b876e709fefe8b0c73bf 100644 --- a/src/USER-DRUDE/pair_lj_cut_thole_long.h +++ b/src/USER-DRUDE/pair_lj_cut_thole_long.h @@ -21,7 +21,6 @@ PairStyle(lj/cut/thole/long,PairLJCutTholeLong) #define LMP_PAIR_LJ_CUT_THOLE_LONG_H #include "pair.h" -#include "fix_drude.h" namespace LAMMPS_NS { @@ -58,7 +57,7 @@ class PairLJCutTholeLong : public Pair { double cut_global; double **cut,**scale; double **polar,**thole,**ascreen; - FixDrude *fix_drude; + class FixDrude *fix_drude; virtual void allocate(); }; diff --git a/src/USER-DRUDE/pair_thole.cpp b/src/USER-DRUDE/pair_thole.cpp index 1bb75af825e12039e2d0825213abcfde518bc9a4..1f81263e95b72e3838d60238e08ea669602d3956 100644 --- a/src/USER-DRUDE/pair_thole.cpp +++ b/src/USER-DRUDE/pair_thole.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_thole.h" +#include #include -#include -#include #include -#include "pair_thole.h" #include "atom.h" #include "comm.h" #include "force.h" @@ -24,7 +23,7 @@ #include "memory.h" #include "error.h" #include "fix.h" -#include "fix_store.h" +#include "fix_drude.h" #include "domain.h" #include "modify.h" diff --git a/src/USER-DRUDE/pair_thole.h b/src/USER-DRUDE/pair_thole.h index 2c462b431a7db297bf3bf6f15945becc1410da90..88c00b6d208580f164f0b75e50a631ec919a8513 100644 --- a/src/USER-DRUDE/pair_thole.h +++ b/src/USER-DRUDE/pair_thole.h @@ -21,7 +21,6 @@ PairStyle(thole,PairThole) #define LMP_PAIR_THOLE_H #include "pair.h" -#include "fix_drude.h" namespace LAMMPS_NS { @@ -46,7 +45,7 @@ class PairThole : public Pair { double cut_global; double **cut,**scale; double **polar,**thole,**ascreen; - FixDrude * fix_drude; + class FixDrude * fix_drude; virtual void allocate(); }; diff --git a/src/USER-EFF/atom_vec_electron.cpp b/src/USER-EFF/atom_vec_electron.cpp index cf4555f02e5efec46ce78ce5fbe257ecdf4e3ad0..552a89c04aaf74b36c7a858946d04d411a06e97e 100644 --- a/src/USER-EFF/atom_vec_electron.cpp +++ b/src/USER-EFF/atom_vec_electron.cpp @@ -15,15 +15,12 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include -#include -#include #include "atom_vec_electron.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" #include "citeme.h" #include "memory.h" diff --git a/src/USER-EFF/compute_ke_atom_eff.cpp b/src/USER-EFF/compute_ke_atom_eff.cpp index b1b87cd3df18d10d9dd1e366d1ed8fc849fd7909..c943366f1b3f414cc2ff5575347a32cacacdb01e 100644 --- a/src/USER-EFF/compute_ke_atom_eff.cpp +++ b/src/USER-EFF/compute_ke_atom_eff.cpp @@ -15,7 +15,6 @@ Contributing author: Andres Jaramillo-Botero ------------------------------------------------------------------------- */ -#include #include #include #include "compute_ke_atom_eff.h" diff --git a/src/USER-EFF/compute_ke_eff.cpp b/src/USER-EFF/compute_ke_eff.cpp index b4f571cb63718e8e425820961fb1ae62c4bea93c..3e277fc66c4b7e0d2e4ee8acb47bf56f3dc496a9 100644 --- a/src/USER-EFF/compute_ke_eff.cpp +++ b/src/USER-EFF/compute_ke_eff.cpp @@ -16,14 +16,12 @@ ------------------------------------------------------------------------- */ #include -#include #include #include "compute_ke_eff.h" #include "atom.h" #include "update.h" #include "force.h" #include "domain.h" -#include "group.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-EFF/compute_temp_deform_eff.cpp b/src/USER-EFF/compute_temp_deform_eff.cpp index 621eff210f39f61172957c40c5702087dce7f802..dcf7e8623451bf8d5f0e12b185551df394cc45ec 100644 --- a/src/USER-EFF/compute_temp_deform_eff.cpp +++ b/src/USER-EFF/compute_temp_deform_eff.cpp @@ -16,7 +16,6 @@ ------------------------------------------------------------------------- */ #include -#include #include #include #include "compute_temp_deform_eff.h" diff --git a/src/USER-EFF/compute_temp_eff.cpp b/src/USER-EFF/compute_temp_eff.cpp index 956461adf19489df4ad25c3c56812726c5a0a111..e9295ea6804606a692aad3b363c16f3724882128 100644 --- a/src/USER-EFF/compute_temp_eff.cpp +++ b/src/USER-EFF/compute_temp_eff.cpp @@ -15,11 +15,9 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ +#include "compute_temp_eff.h" #include -#include -#include #include -#include "compute_temp_eff.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/USER-EFF/compute_temp_region_eff.cpp b/src/USER-EFF/compute_temp_region_eff.cpp index 8cab69036761a45b321bc7aa524ad7b3bb207964..b27699cde94b6e655ffd6987e6d62ed5d9d45048 100644 --- a/src/USER-EFF/compute_temp_region_eff.cpp +++ b/src/USER-EFF/compute_temp_region_eff.cpp @@ -16,14 +16,12 @@ ------------------------------------------------------------------------- */ #include -#include #include #include #include "compute_temp_region_eff.h" #include "atom.h" #include "update.h" #include "force.h" -#include "modify.h" #include "domain.h" #include "region.h" #include "group.h" diff --git a/src/USER-EFF/fix_langevin_eff.cpp b/src/USER-EFF/fix_langevin_eff.cpp index d362113997fde58d193cb318968f86da02950410..5158d7c68122c0ef55357df370f287818256ef2f 100644 --- a/src/USER-EFF/fix_langevin_eff.cpp +++ b/src/USER-EFF/fix_langevin_eff.cpp @@ -17,19 +17,13 @@ #include #include -#include #include #include "fix_langevin_eff.h" -#include "math_extra.h" #include "atom.h" -#include "force.h" #include "update.h" #include "modify.h" #include "compute.h" #include "domain.h" -#include "region.h" -#include "respa.h" -#include "comm.h" #include "input.h" #include "variable.h" #include "random_mars.h" diff --git a/src/USER-EFF/fix_nh_eff.cpp b/src/USER-EFF/fix_nh_eff.cpp index 3e0a59612c2d0ccf4af8e64dd98f76e4dbfaa82c..034233732ec7b415adbf1fcc44b7a1fa40f13788 100644 --- a/src/USER-EFF/fix_nh_eff.cpp +++ b/src/USER-EFF/fix_nh_eff.cpp @@ -15,12 +15,10 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include #include #include "fix_nh_eff.h" #include "atom.h" #include "atom_vec.h" -#include "group.h" #include "error.h" #include "domain.h" diff --git a/src/USER-EFF/fix_nve_eff.cpp b/src/USER-EFF/fix_nve_eff.cpp index 699dd9f9497e1433e9b22202fd5b714df87ff174..ea719c91c02f6592bd445cff4f17818ecc85e0ee 100644 --- a/src/USER-EFF/fix_nve_eff.cpp +++ b/src/USER-EFF/fix_nve_eff.cpp @@ -15,8 +15,6 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include -#include #include #include #include "fix_nve_eff.h" diff --git a/src/USER-EFF/fix_nvt_eff.cpp b/src/USER-EFF/fix_nvt_eff.cpp index 9e23ee023be8702180190bae0bdf3d9e9f0e5ac2..8516accd31ffbff93145f8e692e28d7c40635138 100644 --- a/src/USER-EFF/fix_nvt_eff.cpp +++ b/src/USER-EFF/fix_nvt_eff.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include -#include #include "fix_nvt_eff.h" #include "group.h" #include "modify.h" diff --git a/src/USER-EFF/fix_nvt_sllod_eff.cpp b/src/USER-EFF/fix_nvt_sllod_eff.cpp index ed2274dcf91af6a937273cedea0cb921f00d0029..0ebbf04d642a93fe82cf54319c5a87a649728848 100644 --- a/src/USER-EFF/fix_nvt_sllod_eff.cpp +++ b/src/USER-EFF/fix_nvt_sllod_eff.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include +#include #include #include "fix_nvt_sllod_eff.h" #include "math_extra.h" diff --git a/src/USER-EFF/fix_temp_rescale_eff.cpp b/src/USER-EFF/fix_temp_rescale_eff.cpp index 37f45b3c28ad45142262121a957787b5e8e43a8c..4a8f4b0372dbcdbd37f12bcaaf38c6683210b27a 100644 --- a/src/USER-EFF/fix_temp_rescale_eff.cpp +++ b/src/USER-EFF/fix_temp_rescale_eff.cpp @@ -23,8 +23,6 @@ #include "force.h" #include "group.h" #include "update.h" -#include "domain.h" -#include "region.h" #include "comm.h" #include "modify.h" #include "compute.h" diff --git a/src/USER-EFF/pair_eff_cut.cpp b/src/USER-EFF/pair_eff_cut.cpp index f566922ef7977b9f4e04b867c6f43ff6ae436e52..a4c0557620588fa45ea4b42cb7bd2176a6abd810 100644 --- a/src/USER-EFF/pair_eff_cut.cpp +++ b/src/USER-EFF/pair_eff_cut.cpp @@ -15,8 +15,8 @@ Contributing author: Andres Jaramillo-Botero ------------------------------------------------------------------------- */ +#include #include -#include #include #include #include "pair_eff_cut.h" @@ -31,7 +31,6 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "atom_vec_electron.h" using namespace LAMMPS_NS; diff --git a/src/USER-FEP/compute_fep.cpp b/src/USER-FEP/compute_fep.cpp index dc0b71e71be05340263e2724871bbc47764cc1fe..1853828db3679a66684aa69a5959ab5a430ffae7 100644 --- a/src/USER-FEP/compute_fep.cpp +++ b/src/USER-FEP/compute_fep.cpp @@ -15,7 +15,7 @@ Contributing author: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include +#include "compute_fep.h" #include #include #include @@ -34,7 +34,6 @@ #include "timer.h" #include "memory.h" #include "error.h" -#include "compute_fep.h" using namespace LAMMPS_NS; diff --git a/src/USER-FEP/fix_adapt_fep.cpp b/src/USER-FEP/fix_adapt_fep.cpp index 7304bc4ef6f36496200c950f9541407838b315d3..46cf32cf0bca97c210d7108ca9bc06cf32177239 100644 --- a/src/USER-FEP/fix_adapt_fep.cpp +++ b/src/USER-FEP/fix_adapt_fep.cpp @@ -15,10 +15,8 @@ Charges by type and after option: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_adapt_fep.h" +#include #include "atom.h" #include "update.h" #include "group.h" diff --git a/src/USER-FEP/pair_coul_cut_soft.cpp b/src/USER-FEP/pair_coul_cut_soft.cpp index 86a6d02819e9952aef1949de80c5d0cfb13b01fd..a4ff3ca846cc79fc492ca7b614cea4e727fb62a1 100644 --- a/src/USER-FEP/pair_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_coul_cut_soft.cpp @@ -15,11 +15,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ +#include "pair_coul_cut_soft.h" +#include #include -#include -#include #include -#include "pair_coul_cut_soft.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-FEP/pair_coul_long_soft.cpp b/src/USER-FEP/pair_coul_long_soft.cpp index 9d3ffc0da18b636f68310fdb3e9bfa1aced26ec6..c0030f89358d53e04619356e3932a5f80e37826c 100644 --- a/src/USER-FEP/pair_coul_long_soft.cpp +++ b/src/USER-FEP/pair_coul_long_soft.cpp @@ -16,19 +16,16 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ +#include "pair_coul_long_soft.h" +#include #include -#include -#include #include -#include "pair_coul_long_soft.h" #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "neighbor.h" #include "neigh_list.h" -#include "update.h" -#include "integrate.h" #include "memory.h" #include "error.h" diff --git a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp index ac6f1e63844365315889018e7a9a2ab5774f318b..4c3be6addbefa64152cd45e5587ec913ac2ea892 100644 --- a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp @@ -16,17 +16,15 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ +#include "pair_lj_charmm_coul_long_soft.h" +#include #include -#include -#include #include -#include "pair_lj_charmm_coul_long_soft.h" #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp index ae79515488e0d38d7e06a9af5249b8ca2d88faea..bbe67e4ff3e50eaaf5b9b83c4cbb35c5c6a993c4 100644 --- a/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_class2_coul_cut_soft.h" +#include #include -#include -#include #include -#include "pair_lj_class2_coul_cut_soft.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp b/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp index 275486d1e2196d0b80c8b89503a4ce109e20cda5..a3e0f732a22cef32aa79d3f1271635d1a4b6f2a4 100644 --- a/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_class2_coul_long_soft.h" +#include #include -#include -#include #include -#include "pair_lj_class2_coul_long_soft.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-FEP/pair_lj_class2_soft.cpp b/src/USER-FEP/pair_lj_class2_soft.cpp index d22cd538832d968d0573354a536cc9b084454016..d98a5db5f397252ce32ff04cd98dab80dee18c00 100644 --- a/src/USER-FEP/pair_lj_class2_soft.cpp +++ b/src/USER-FEP/pair_lj_class2_soft.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_class2_soft.h" +#include #include -#include -#include #include -#include "pair_lj_class2_soft.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp index 35c9162dbc9eae267609eaca7d5e1c3b7b591706..38fcb6fc07446cb9aa262ef091c0be081128aa06 100644 --- a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp @@ -15,11 +15,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_cut_soft.h" +#include #include -#include -#include #include -#include "pair_lj_cut_coul_cut_soft.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp index 79253d2b9c7544db3c509bdb62aa069b1e951fa1..740daabf627489f73b953bafcbb6b6198cee1b62 100644 --- a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp @@ -16,17 +16,15 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_long_soft.h" +#include #include -#include -#include #include -#include "pair_lj_cut_coul_long_soft.h" #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-FEP/pair_lj_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_soft.cpp index 4192d6546b4dd70f433836e76168468e15628f91..5e9a77877e85f9456bc4f87903be81b369baeb77 100644 --- a/src/USER-FEP/pair_lj_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_soft.cpp @@ -16,11 +16,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_soft.h" +#include #include -#include -#include #include -#include "pair_lj_cut_soft.h" #include "atom.h" #include "comm.h" #include "force.h" @@ -28,7 +27,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory.h" diff --git a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp index 8ac28f9fa9a508646302f0200c84c6d4ee7052fc..d4f6dcb91093ccb2e1dc3a8f13b33d8f1b045ff1 100644 --- a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp @@ -17,23 +17,18 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_tip4p_long_soft.h" +#include #include -#include -#include #include -#include "pair_lj_cut_tip4p_long_soft.h" #include "angle.h" #include "atom.h" #include "bond.h" #include "comm.h" #include "domain.h" #include "force.h" -#include "kspace.h" -#include "update.h" -#include "respa.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" diff --git a/src/USER-FEP/pair_morse_soft.cpp b/src/USER-FEP/pair_morse_soft.cpp index 21f616a082959bc1758d845f572ccb4470632ba4..2803e7df49e69e5f86e598c000f4af854d8572dc 100644 --- a/src/USER-FEP/pair_morse_soft.cpp +++ b/src/USER-FEP/pair_morse_soft.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_morse_soft.h" +#include #include -#include -#include #include -#include "pair_morse_soft.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-FEP/pair_tip4p_long_soft.cpp b/src/USER-FEP/pair_tip4p_long_soft.cpp index 9b6a6841fe66f363e95287da63a9b18ff6e31a52..9cea5b54c5d129c8a4dd631c34f8f19658589aec 100644 --- a/src/USER-FEP/pair_tip4p_long_soft.cpp +++ b/src/USER-FEP/pair_tip4p_long_soft.cpp @@ -17,23 +17,18 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ +#include "pair_tip4p_long_soft.h" +#include #include -#include -#include #include -#include "pair_tip4p_long_soft.h" #include "angle.h" #include "atom.h" #include "bond.h" #include "comm.h" #include "domain.h" #include "force.h" -#include "kspace.h" -#include "update.h" -#include "respa.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" diff --git a/src/USER-INTEL/angle_charmm_intel.h b/src/USER-INTEL/angle_charmm_intel.h index 5d173ee6a982e834587d5d7bc908854ec3a538d8..155ecfaff9855f979b043616641a6632f75a90e8 100644 --- a/src/USER-INTEL/angle_charmm_intel.h +++ b/src/USER-INTEL/angle_charmm_intel.h @@ -24,7 +24,6 @@ AngleStyle(charmm/intel,AngleCharmmIntel) #ifndef LMP_ANGLE_CHARMM_INTEL_H #define LMP_ANGLE_CHARMM_INTEL_H -#include #include "angle_charmm.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/angle_harmonic_intel.h b/src/USER-INTEL/angle_harmonic_intel.h index e7768542a1f1fbcb90692cf7f8afbad7f31d4ded..c00292f7ce5d78ad51eaac80b2669254429dd830 100644 --- a/src/USER-INTEL/angle_harmonic_intel.h +++ b/src/USER-INTEL/angle_harmonic_intel.h @@ -24,7 +24,6 @@ AngleStyle(harmonic/intel,AngleHarmonicIntel) #ifndef LMP_ANGLE_HARMONIC_INTEL_H #define LMP_ANGLE_HARMONIC_INTEL_H -#include #include "angle_harmonic.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/bond_fene_intel.h b/src/USER-INTEL/bond_fene_intel.h index afe3b85470d6d81b0639a57a3ce7ade9a1ff0467..58fcdb866928db932e1924b0d8e51ad0872efaac 100644 --- a/src/USER-INTEL/bond_fene_intel.h +++ b/src/USER-INTEL/bond_fene_intel.h @@ -24,7 +24,6 @@ BondStyle(fene/intel,BondFENEIntel) #ifndef LMP_BOND_FENE_INTEL_H #define LMP_BOND_FENE_INTEL_H -#include #include "bond_fene.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/bond_harmonic_intel.h b/src/USER-INTEL/bond_harmonic_intel.h index b86a560d6e167e592aaee3cdfdc97b13fe906879..3c1d050a3bb159f04eb4fbaae60885152b09bf47 100644 --- a/src/USER-INTEL/bond_harmonic_intel.h +++ b/src/USER-INTEL/bond_harmonic_intel.h @@ -24,7 +24,6 @@ BondStyle(harmonic/intel,BondHarmonicIntel) #ifndef LMP_BOND_HARMONIC_INTEL_H #define LMP_BOND_HARMONIC_INTEL_H -#include #include "bond_harmonic.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/improper_cvff_intel.h b/src/USER-INTEL/improper_cvff_intel.h index e815fa75c904e678f375af053c82ed2ea5a2a2b4..812b49d50c3006914f4c88afc084e8dbd9a57422 100644 --- a/src/USER-INTEL/improper_cvff_intel.h +++ b/src/USER-INTEL/improper_cvff_intel.h @@ -24,7 +24,6 @@ ImproperStyle(cvff/intel,ImproperCvffIntel) #ifndef LMP_IMPROPER_CVFF_INTEL_H #define LMP_IMPROPER_CVFF_INTEL_H -#include #include "improper_cvff.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/improper_harmonic_intel.h b/src/USER-INTEL/improper_harmonic_intel.h index ce38e8fc317ed5dc996de47387baec910c40f71c..6d7c829961fe4ccf20961cf87aa946300d49838d 100644 --- a/src/USER-INTEL/improper_harmonic_intel.h +++ b/src/USER-INTEL/improper_harmonic_intel.h @@ -24,7 +24,6 @@ ImproperStyle(harmonic/intel,ImproperHarmonicIntel) #ifndef LMP_IMPROPER_HARMONIC_INTEL_H #define LMP_IMPROPER_HARMONIC_INTEL_H -#include #include "improper_harmonic.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/intel_simd.h b/src/USER-INTEL/intel_simd.h index 75fc9828b96f0f99cfcfac86ce384c9f535efe73..9022f439c40806dcab29d72df51f74412e12d058 100644 --- a/src/USER-INTEL/intel_simd.h +++ b/src/USER-INTEL/intel_simd.h @@ -29,7 +29,6 @@ authors for more details. #ifndef INTEL_SIMD_H #define INTEL_SIMD_H -#include #include "intel_preprocess.h" #include "immintrin.h" diff --git a/src/USER-INTEL/pair_eam_intel.h b/src/USER-INTEL/pair_eam_intel.h index 83b1fbf6a13e76cffcd55e574cac81d4c4ac1d8a..a9590f6b3db09f1fde150a814beb7a26e987a6ce 100644 --- a/src/USER-INTEL/pair_eam_intel.h +++ b/src/USER-INTEL/pair_eam_intel.h @@ -20,7 +20,6 @@ PairStyle(eam/intel,PairEAMIntel) #ifndef LMP_PAIR_EAM_INTEL_H #define LMP_PAIR_EAM_INTEL_H -#include #include "pair_eam.h" #include "fix_intel.h" diff --git a/src/USER-LB/fix_lb_fluid.cpp b/src/USER-LB/fix_lb_fluid.cpp index 31c54aee76505938170bcc13235fb6e64d883b80..8ad3dbe33e64619fc61579eb735edad7f9e45b0e 100644 --- a/src/USER-LB/fix_lb_fluid.cpp +++ b/src/USER-LB/fix_lb_fluid.cpp @@ -20,15 +20,14 @@ #include #include #include -#include #include +#include +#include #include "comm.h" #include "memory.h" #include "error.h" #include "domain.h" #include "atom.h" -#include -#include #include "group.h" #include "random_mars.h" #include "update.h" diff --git a/src/USER-LB/fix_lb_momentum.cpp b/src/USER-LB/fix_lb_momentum.cpp index df17561380e993e86470c0be3abad33adf7d5ca9..10fffed0189c833dab7e106a0bd92cfd32a392bd 100644 --- a/src/USER-LB/fix_lb_momentum.cpp +++ b/src/USER-LB/fix_lb_momentum.cpp @@ -18,16 +18,15 @@ Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U) ------------------------------------------------------------------------- */ +#include "fix_lb_momentum.h" +#include #include #include -#include "fix_lb_momentum.h" #include "atom.h" -#include "domain.h" #include "group.h" #include "error.h" #include "fix_lb_fluid.h" #include "modify.h" -#include "comm.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-LB/fix_lb_pc.cpp b/src/USER-LB/fix_lb_pc.cpp index ce6ca0c9a1ff67ffe9a2b02c22060b79830345f3..d61692419a1bd3ef51512c661d2783adb13a04af 100644 --- a/src/USER-LB/fix_lb_pc.cpp +++ b/src/USER-LB/fix_lb_pc.cpp @@ -15,17 +15,14 @@ Contributing authors: Frances Mackay, Santtu Ollila, Colin Denniston (UWO) ------------------------------------------------------------------------- */ +#include "fix_lb_pc.h" #include -#include #include -#include "fix_lb_pc.h" #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" #include "memory.h" -#include "comm.h" #include "domain.h" #include "fix_lb_fluid.h" #include "modify.h" diff --git a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp index 83dc7516311fdcbc8c2b90b41ea73d2fb815b2eb..af1b01043d0b9bb787c719b26bec207a4da62b97 100644 --- a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp +++ b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp @@ -16,21 +16,18 @@ Based on fix_rigid (version from 2008). ------------------------------------------------------------------------- */ +#include "fix_lb_rigid_pc_sphere.h" +#include #include -#include #include #include -#include "fix_lb_rigid_pc_sphere.h" #include "atom.h" -#include "atom_vec.h" #include "domain.h" #include "update.h" -#include "respa.h" #include "modify.h" #include "group.h" #include "comm.h" #include "force.h" -#include "output.h" #include "memory.h" #include "error.h" #include "fix_lb_fluid.h" diff --git a/src/USER-LB/fix_lb_viscous.cpp b/src/USER-LB/fix_lb_viscous.cpp index afe23477be49fee5025294712ea6ee226c61f40b..59fddebd6751093034ccb91bdda992526556322c 100644 --- a/src/USER-LB/fix_lb_viscous.cpp +++ b/src/USER-LB/fix_lb_viscous.cpp @@ -15,10 +15,8 @@ Contributing authors: Frances Mackay, Santtu Ollila, Colin Denniston (UWO) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_lb_viscous.h" +#include #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp index 00293bfec7d553f0000bde951acd1e9c3de35992..74a9a1833fd9f66fe8761cc44df05b0fb42f7d99 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.cpp +++ b/src/USER-MANIFOLD/fix_manifoldforce.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "fix_manifoldforce.h" // For stuff +#include #include -#include #include "atom.h" #include "update.h" #include "respa.h" @@ -21,7 +21,6 @@ #include "force.h" #include "manifold.h" -#include "fix_manifoldforce.h" // For stuff #include "manifold_factory.h" // For constructing manifold diff --git a/src/USER-MANIFOLD/fix_manifoldforce.h b/src/USER-MANIFOLD/fix_manifoldforce.h index 527bee3f86d33a976a20007b09470d318575e185..1d5afc7afc3ae826ff31f2ded17c98ef8861a4d5 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.h +++ b/src/USER-MANIFOLD/fix_manifoldforce.h @@ -43,9 +43,9 @@ FixStyle(manifoldforce,FixManifoldForce) #define LMP_FIX_MANIFOLDFORCE_H #include "fix.h" -#include "manifold.h" namespace LAMMPS_NS { +namespace user_manifold { class manifold; } class FixManifoldForce : public Fix { public: diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp index de134e32edbd24653b3e467d9f533c62a9d82a1f..7f8d9d567568b5015c936ec63a903f006193b4eb 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp @@ -32,24 +32,18 @@ ------------------------------------------------------------------------- */ -#include -#include +#include "fix_nve_manifold_rattle.h" +#include #include #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" -#include "group.h" -#include #include "input.h" #include "variable.h" #include "citeme.h" -#include "memory.h" #include "comm.h" - -#include "fix_nve_manifold_rattle.h" #include "manifold_factory.h" #include "manifold.h" diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.h b/src/USER-MANIFOLD/fix_nve_manifold_rattle.h index 2bc821ab04fc37e2ad7f275954fae78f161bf4ba..581ecf36d32e043b5a0fb978d9fb230d7010ef80 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.h +++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.h @@ -42,12 +42,10 @@ FixStyle(nve/manifold/rattle,FixNVEManifoldRattle) #define LMP_FIX_NVE_MANIFOLD_RATTLE_H #include "fix.h" -#include "manifold.h" - namespace LAMMPS_NS { -// namespace user_manifold { +namespace user_manifold { class manifold; } class FixNVEManifoldRattle : public Fix { public: @@ -98,9 +96,7 @@ namespace LAMMPS_NS { user_manifold::manifold *ptr_m; - void print_stats( const char * ); - int was_var( const char * ); virtual void update_var_params(); diff --git a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp index a4eed663367f44ca4f75cdfd18ecf9dbc81d02d3..2789f8738a1584b593016d96ae422b69970e226a 100644 --- a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp @@ -32,25 +32,18 @@ ------------------------------------------------------------------------- */ -#include -#include +#include "fix_nvt_manifold_rattle.h" #include #include #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" #include "group.h" -#include "input.h" -#include "variable.h" #include "citeme.h" -#include "memory.h" -#include "comm.h" #include "modify.h" #include "compute.h" -#include "fix_nvt_manifold_rattle.h" #include "manifold.h" diff --git a/src/USER-MANIFOLD/manifold_factory.h b/src/USER-MANIFOLD/manifold_factory.h index cc3e1245bfd11f0a4c46cdb55948f40c3810bffd..ac2aee8a26623044b580072d996e3c7141d9f309 100644 --- a/src/USER-MANIFOLD/manifold_factory.h +++ b/src/USER-MANIFOLD/manifold_factory.h @@ -35,8 +35,7 @@ #ifndef LMP_MANIFOLD_FACTORY_H #define LMP_MANIFOLD_FACTORY_H - -#include "manifold.h" +#include #include /* @@ -79,14 +78,16 @@ static FILE *screen = fopen("/dev/stdout","w"); #define FLERR __FILE__,__LINE__ // Equivalent to definition in pointers.h #endif // USE_PHONY_LAMMPS - - /* Here the actual implementation of LAMMPS-related functions begins. */ namespace LAMMPS_NS { +class LAMMPS; namespace user_manifold { +// forward declaration +class manifold; + // Templated, so needs to be in header. template void make_manifold_if( manifold **man_ptr, const char *name, @@ -103,8 +104,6 @@ namespace user_manifold { int , char ** ); } // namespace user_manifold - } // namespace LAMMPS_NS - #endif // LMP_MANIFOLD_FACTORY_H diff --git a/src/USER-MANIFOLD/manifold_thylakoid.cpp b/src/USER-MANIFOLD/manifold_thylakoid.cpp index 530e0a876dcb40a005e66d2d5701d91facf06a52..e4ef039832b9aae0b4bf72f725b886b06e069703 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid.cpp +++ b/src/USER-MANIFOLD/manifold_thylakoid.cpp @@ -1,6 +1,6 @@ #include "manifold_thylakoid.h" #include - +#include "manifold_thylakoid_shared.h" #include "comm.h" #include "domain.h" // For some checks regarding the simulation box. #include "error.h" diff --git a/src/USER-MANIFOLD/manifold_thylakoid.h b/src/USER-MANIFOLD/manifold_thylakoid.h index 5e5d3b9c4192a9c622c06da6daeee0722bf3cdff..35ad4dfd9c9881b76adcebcf7e6c44472c0e4aeb 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid.h +++ b/src/USER-MANIFOLD/manifold_thylakoid.h @@ -3,14 +3,11 @@ #include "manifold.h" #include -#include - -#include "manifold_thylakoid_shared.h" namespace LAMMPS_NS { namespace user_manifold { - + struct thyla_part; class manifold_thylakoid : public manifold { public: diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h index ff9027dfb33a4d9bfb95966d2eb309208c85e1af..da558057901639df60f13e15331a9ece34de0f2f 100644 --- a/src/USER-MEAMC/meam.h +++ b/src/USER-MEAMC/meam.h @@ -1,13 +1,12 @@ #ifndef LMP_MEAM_H #define LMP_MEAM_H -#include "memory.h" #include -#include #define maxelt 5 namespace LAMMPS_NS { +class Memory; typedef enum { FCC, BCC, HCP, DIM, DIA, B1, C11, L12, B2 } lattice_t; diff --git a/src/USER-MEAMC/meam_dens_final.cpp b/src/USER-MEAMC/meam_dens_final.cpp index c55b1b45c44633cb9b0cb9f45199ee29c52214b5..867106df88339a71136faca301fcd15f7e9cb531 100644 --- a/src/USER-MEAMC/meam_dens_final.cpp +++ b/src/USER-MEAMC/meam_dens_final.cpp @@ -1,5 +1,4 @@ #include "meam.h" -#include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_dens_init.cpp b/src/USER-MEAMC/meam_dens_init.cpp index 3bb9328142034c475d41ec974412d370e14e7589..155941422cb5697cf6a758854b4083c4c92d2822 100644 --- a/src/USER-MEAMC/meam_dens_init.cpp +++ b/src/USER-MEAMC/meam_dens_init.cpp @@ -1,4 +1,6 @@ #include "meam.h" +#include +#include "memory.h" #include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_force.cpp b/src/USER-MEAMC/meam_force.cpp index 06fbb57adb11a778d088c1fc166ffe231ff23ade..09aad9011177309189ac8bb71ccb33c4a9af02b1 100644 --- a/src/USER-MEAMC/meam_force.cpp +++ b/src/USER-MEAMC/meam_force.cpp @@ -1,6 +1,7 @@ #include "meam.h" -#include "math_special.h" +#include #include +#include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_impl.cpp b/src/USER-MEAMC/meam_impl.cpp index b099ead8d5b3677a1f543577bad33e9e51d8c20c..74e8af1cde49f73b12f47b096ddf0180cb7cd1a2 100644 --- a/src/USER-MEAMC/meam_impl.cpp +++ b/src/USER-MEAMC/meam_impl.cpp @@ -16,6 +16,7 @@ ------------------------------------------------------------------------- */ #include "meam.h" +#include #include "memory.h" using namespace LAMMPS_NS; @@ -43,7 +44,7 @@ MEAM::MEAM(Memory* mem) rho_ref_meam[i] = ibar_meam[i] = ielt_meam[i] = 0.0; for (int j = 0; j < maxelt; j++) { lattce_meam[i][j] = FCC; - Ec_meam[i][j] = re_meam[i][j] = alpha_meam[i][j] = delta_meam[i][j] = Ec_meam[i][j] = ebound_meam[i][j] = attrac_meam[i][j] = repuls_meam[i][j] = 0.0; + Ec_meam[i][j] = re_meam[i][j] = alpha_meam[i][j] = delta_meam[i][j] = ebound_meam[i][j] = attrac_meam[i][j] = repuls_meam[i][j] = 0.0; nn2_meam[i][j] = zbl_meam[i][j] = eltind[i][j] = 0; } } diff --git a/src/USER-MEAMC/meam_setup_done.cpp b/src/USER-MEAMC/meam_setup_done.cpp index 2a762d12047f52de5aad2e4ea71ff9be3dc0896a..7000eac6ae49a944ed47c2bfd4a7bb1d33aa254c 100644 --- a/src/USER-MEAMC/meam_setup_done.cpp +++ b/src/USER-MEAMC/meam_setup_done.cpp @@ -1,6 +1,10 @@ #include "meam.h" -#include "math_special.h" +#include +#include #include +#include "math_special.h" +#include "memory.h" + using namespace LAMMPS_NS; void diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp index 7c96fadb44d11f909fdbccf39293a3f970b1923c..a9034a1af35806ca1f27d49e079ab6ad1852cae2 100644 --- a/src/USER-MEAMC/pair_meamc.cpp +++ b/src/USER-MEAMC/pair_meamc.cpp @@ -15,16 +15,14 @@ Contributing author: Greg Wagner (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include "pair_meamc.h" +#include #include #include #include "meam.h" -#include "pair_meamc.h" #include "atom.h" #include "force.h" #include "comm.h" -#include "memory.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/USER-MEAMC/pair_meamc.h b/src/USER-MEAMC/pair_meamc.h index a006e70bdbc9ba94034eac294f537de547894ad8..31dd8ba02243de8c0857ca24e272bade7f6a1fdd 100644 --- a/src/USER-MEAMC/pair_meamc.h +++ b/src/USER-MEAMC/pair_meamc.h @@ -24,7 +24,6 @@ PairStyle(meam,PairMEAMC) #include "pair.h" namespace LAMMPS_NS { -class MEAM; class PairMEAMC : public Pair { public: diff --git a/src/USER-MESO/atom_vec_edpd.cpp b/src/USER-MESO/atom_vec_edpd.cpp index eee8ae25b03a5e72696625beb4bc668c97cdfb6e..edc7a3433190bf5b35e2baef669becad07684aa6 100644 --- a/src/USER-MESO/atom_vec_edpd.cpp +++ b/src/USER-MESO/atom_vec_edpd.cpp @@ -10,13 +10,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "atom_vec_edpd.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "update.h" diff --git a/src/USER-MESO/atom_vec_mdpd.cpp b/src/USER-MESO/atom_vec_mdpd.cpp index fd3c01f0c64371d2efbb32b2c0bf0e4b9555dfbd..4c9db36645028e4ab224b359e636430f396c2539 100644 --- a/src/USER-MESO/atom_vec_mdpd.cpp +++ b/src/USER-MESO/atom_vec_mdpd.cpp @@ -11,13 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "atom_vec_mdpd.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "update.h" diff --git a/src/USER-MESO/atom_vec_tdpd.cpp b/src/USER-MESO/atom_vec_tdpd.cpp index f91731f8acbd42d033f94a0b296eb2914b11a80b..74ac47066b297c8994401cb976778a6ca9d2ae6d 100644 --- a/src/USER-MESO/atom_vec_tdpd.cpp +++ b/src/USER-MESO/atom_vec_tdpd.cpp @@ -11,19 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "atom_vec_tdpd.h" +#include #include "atom.h" #include "comm.h" -#include "force.h" #include "domain.h" #include "modify.h" #include "fix.h" #include "update.h" #include "memory.h" #include "error.h" -#include "input.h" #include "utils.h" using namespace LAMMPS_NS; @@ -66,7 +63,7 @@ void AtomVecTDPD::process_args(int narg, char **arg) { if (narg < 1) error->all(FLERR,"Invalid atom_style tdpd command"); - atom->cc_species = force->inumeric(FLERR,arg[0]); + atom->cc_species = utils::inumeric(FLERR,arg[0],false,lmp); cc_species = atom->cc_species; // reset sizes that depend on cc_species @@ -802,7 +799,7 @@ void AtomVecTDPD::data_atom(double *coord, imageint imagetmp, char **values) x[nlocal][2] = coord[2]; for(int k = 0; k < cc_species; k++) - cc[nlocal][k] = atof( values[5+k] ); + cc[nlocal][k] = utils::numeric(FLERR,values[5+k],true,lmp); image[nlocal] = imagetmp; diff --git a/src/USER-MESO/compute_edpd_temp_atom.cpp b/src/USER-MESO/compute_edpd_temp_atom.cpp index 119e0079d133dc50ba146952967cd99eb3dd3876..9eb6e9752b09743be825c682e74f040c369aee39 100644 --- a/src/USER-MESO/compute_edpd_temp_atom.cpp +++ b/src/USER-MESO/compute_edpd_temp_atom.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_edpd_temp_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MESO/fix_edpd_source.cpp b/src/USER-MESO/fix_edpd_source.cpp index 24bef2b1f72fdfe4c1f06b21175b5d9b90ef6eff..e62d9a8a79053e4e1d597b4c65b1c70088bacb04 100644 --- a/src/USER-MESO/fix_edpd_source.cpp +++ b/src/USER-MESO/fix_edpd_source.cpp @@ -11,17 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_edpd_source.h" +#include +#include #include "atom.h" -#include "comm.h" -#include "update.h" -#include "modify.h" -#include "domain.h" -#include "lattice.h" -#include "input.h" -#include "variable.h" #include "error.h" #include "force.h" diff --git a/src/USER-MESO/fix_mvv_dpd.cpp b/src/USER-MESO/fix_mvv_dpd.cpp index f663165f78d834d4aec55b51bb23e9f0e63a7c5f..116bbf506ab259671d90f869fa2785ec7dea14df 100644 --- a/src/USER-MESO/fix_mvv_dpd.cpp +++ b/src/USER-MESO/fix_mvv_dpd.cpp @@ -20,13 +20,11 @@ Email: zhen_li@brown.edu ------------------------------------------------------------------------- */ -#include -#include #include "fix_mvv_dpd.h" +#include #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-MESO/fix_mvv_edpd.cpp b/src/USER-MESO/fix_mvv_edpd.cpp index 8719d0d262d35e3f20eb0e0d57f031141ed69981..bd9cd9cc2a33ff922f8fa92fbb5c490f306aae02 100644 --- a/src/USER-MESO/fix_mvv_edpd.cpp +++ b/src/USER-MESO/fix_mvv_edpd.cpp @@ -29,13 +29,11 @@ Communications, 2015, 51: 11038-11040. ------------------------------------------------------------------------- */ -#include -#include #include "fix_mvv_edpd.h" +#include #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-MESO/fix_mvv_tdpd.cpp b/src/USER-MESO/fix_mvv_tdpd.cpp index 24b1bbcf48bc2ed85d27fbf8e80893794689bdfc..b7fe37d7ee649ca1d166cc4b5d6c5072c8c4b805 100644 --- a/src/USER-MESO/fix_mvv_tdpd.cpp +++ b/src/USER-MESO/fix_mvv_tdpd.cpp @@ -25,13 +25,11 @@ -reaction problems". The Journal of Chemical Physics, 2015, 143: 014101. ------------------------------------------------------------------------- */ -#include -#include #include "fix_mvv_tdpd.h" +#include #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-MESO/fix_tdpd_source.cpp b/src/USER-MESO/fix_tdpd_source.cpp index 89e8005b43500bedefeee55078c3fe5b914ebec3..990f6a5b78c3b8c6656efcc5e26b048a9798b7c7 100644 --- a/src/USER-MESO/fix_tdpd_source.cpp +++ b/src/USER-MESO/fix_tdpd_source.cpp @@ -11,17 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_tdpd_source.h" +#include +#include #include "atom.h" -#include "comm.h" -#include "update.h" -#include "modify.h" -#include "domain.h" -#include "lattice.h" -#include "input.h" -#include "variable.h" #include "error.h" #include "force.h" diff --git a/src/USER-MESO/pair_edpd.cpp b/src/USER-MESO/pair_edpd.cpp index e428b028223b2221c5629316290838517b88df07..f72b6d6b93243a81e7be514f922953e94208b687 100644 --- a/src/USER-MESO/pair_edpd.cpp +++ b/src/USER-MESO/pair_edpd.cpp @@ -16,14 +16,12 @@ Email: zhen_li@brown.edu ------------------------------------------------------------------------- */ +#include "pair_edpd.h" +#include #include -#include -#include #include #include -#include "pair_edpd.h" #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "update.h" #include "force.h" diff --git a/src/USER-MESO/pair_mdpd.cpp b/src/USER-MESO/pair_mdpd.cpp index 4102499d468e24e3f0b95d58b161e82a42d08802..56adad26ce86719f817639d0551c7ab1e5190fbb 100644 --- a/src/USER-MESO/pair_mdpd.cpp +++ b/src/USER-MESO/pair_mdpd.cpp @@ -16,13 +16,11 @@ Email: zhen_li@brown.edu ------------------------------------------------------------------------- */ +#include "pair_mdpd.h" +#include #include -#include -#include #include -#include "pair_mdpd.h" #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "update.h" #include "force.h" diff --git a/src/USER-MESO/pair_mdpd_rhosum.cpp b/src/USER-MESO/pair_mdpd_rhosum.cpp index 2fd238088c92d9e07d8291455e8abfbafba1f359..05cb123f61e8db934f74e82d93c48181974c3695 100644 --- a/src/USER-MESO/pair_mdpd_rhosum.cpp +++ b/src/USER-MESO/pair_mdpd_rhosum.cpp @@ -19,9 +19,8 @@ Contributing author: Zhen Li (Brown University) ------------------------------------------------------------------------- */ -#include -#include #include "pair_mdpd_rhosum.h" +#include #include "atom.h" #include "force.h" #include "comm.h" @@ -30,8 +29,6 @@ #include "memory.h" #include "error.h" #include "neighbor.h" -#include "update.h" -#include "domain.h" using namespace LAMMPS_NS; diff --git a/src/USER-MESO/pair_tdpd.cpp b/src/USER-MESO/pair_tdpd.cpp index 7df9d6d163e677f27307f6c8d1b760ebe4ce6ad6..346401b1ba576e7444809e8e5c45ac0993860cb3 100644 --- a/src/USER-MESO/pair_tdpd.cpp +++ b/src/USER-MESO/pair_tdpd.cpp @@ -16,13 +16,10 @@ Email: zhen_li@brown.edu ------------------------------------------------------------------------- */ +#include "pair_tdpd.h" #include -#include -#include #include -#include "pair_tdpd.h" #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "update.h" #include "force.h" diff --git a/src/USER-MGPT/mgpt_linalg.cpp b/src/USER-MGPT/mgpt_linalg.cpp index 68701037f4a52bbdfeba238004f67d7900d2cb72..bc158737391f7757915dd27c482fbdce989f4a0e 100644 --- a/src/USER-MGPT/mgpt_linalg.cpp +++ b/src/USER-MGPT/mgpt_linalg.cpp @@ -20,8 +20,6 @@ #include #include -#include -#include #define restrict __restrict__ diff --git a/src/USER-MGPT/mgpt_readpot.h b/src/USER-MGPT/mgpt_readpot.h index c19ea40774c7cb80ff893e510cd2689dfd809ab0..8f46592e8a56028ebc37f174eca7927cbe68270c 100644 --- a/src/USER-MGPT/mgpt_readpot.h +++ b/src/USER-MGPT/mgpt_readpot.h @@ -20,7 +20,8 @@ #define READPOT__ #include - +#include +#include #include "mgpt_splinetab.h" struct potdata { diff --git a/src/USER-MGPT/pair_mgpt.cpp b/src/USER-MGPT/pair_mgpt.cpp index 91c624eec5c5017308aefe7903c290b84b43a61d..0634872c70b129362af22b22d11d55d90b8a31ca 100644 --- a/src/USER-MGPT/pair_mgpt.cpp +++ b/src/USER-MGPT/pair_mgpt.cpp @@ -21,17 +21,16 @@ (2011). See LLNL copyright notice at bottom of this file. ------------------------------------------------------------------------- */ +#include "pair_mgpt.h" +#include #include -#include #include #include #include -#include "pair_mgpt.h" #include "atom.h" #include "force.h" #include "comm.h" -#include "memory.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/USER-MGPT/pair_mgpt.h b/src/USER-MGPT/pair_mgpt.h index 94c66fb6038f8d7fcc2cca4711230abe65df56ce..ff71edc9f3dee4fe9ad7d3cc1e63c7bdeea75b85 100644 --- a/src/USER-MGPT/pair_mgpt.h +++ b/src/USER-MGPT/pair_mgpt.h @@ -30,9 +30,7 @@ PairStyle(mgpt,PairMGPT) #ifndef LMP_PAIR_MGPT_H #define LMP_PAIR_MGPT_H -#include -#include -#include +#include #include #include "pair.h" @@ -78,29 +76,29 @@ public: Link(const K &k,Link *n) : next(n),key(k),hits(1) {} static void *operator new(std::size_t sz) { - const size_t align = 32; - size_t x = (size_t) (void *) ::operator new(sz+align); - size_t y = (x + align) - ((x+align)&(align-1)); - assert(sizeof(void *) <= align); - assert((x & (sizeof(void *)-1)) == 0); - ((void **) y)[-1] = (void *) x; - return (void *) y; + const size_t align = 32; + size_t x = (size_t) (void *) ::operator new(sz+align); + size_t y = (x + align) - ((x+align)&(align-1)); + assert(sizeof(void *) <= align); + assert((x & (sizeof(void *)-1)) == 0); + ((void **) y)[-1] = (void *) x; + return (void *) y; } static void operator delete(void *ptr) { - ::operator delete(((void **) ptr)[-1]); + ::operator delete(((void **) ptr)[-1]); } }; int isprime(int x) { if(x%2 == 0) - return 0; + return 0; else { - int k = 3; - while(k*k <= x) { - if(x%k == 0) return 0; - k = k+2; - } - return 1; + int k = 3; + while(k*k <= x) { + if(x%k == 0) return 0; + k = k+2; + } + return 1; } } @@ -118,25 +116,25 @@ public: Iterator(Hash &HH) : H(HH),idx(-1),p(0) { next(); } Iterator(Hash &HH,int iidx,Link *pp) : H(HH),idx(iidx),p(pp) {} void next() { - if(idx >= H.Size()) return; - if(p != 0) p = p->next; - if(p == 0) { - do { - idx = idx+1; - if(idx >= H.Size()) return; - p = H.table[idx]; - } while(p == 0); - } + if(idx >= H.Size()) return; + if(p != 0) p = p->next; + if(p == 0) { + do { + idx = idx+1; + if(idx >= H.Size()) return; + p = H.table[idx]; + } while(p == 0); + } } K *key() { return &p->key; } T *data() { return &p->data; } Link *link() { return p; } int operator==(const Iterator &a) { - return idx==a.idx && p==a.p; + return idx==a.idx && p==a.p; } int operator!=(const Iterator &a) { - return !(*this == a); + return !(*this == a); } }; @@ -148,7 +146,7 @@ public: table = new Link *[size]; for(int i = 0; inext; - delete p; - p = q; - } + Link *p = table[i]; + while(p != 0) { + Link *q = p->next; + delete p; + p = q; + } } delete[] table; } @@ -180,24 +178,24 @@ public: int idx = key.hash() % size; if(idx < 0) idx = idx + size; if(idx >= size || idx < 0) { - printf("(1) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size); - exit(1); + printf("(1) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size); + exit(1); } used = used + 1; if(1) { - table[idx] = new Link(key,table[idx]); - return &table[idx]->data; + table[idx] = new Link(key,table[idx]); + return &table[idx]->data; } else { /* This is for threading... and incomplete */ - typedef Link *LinkPtr; - LinkPtr ptr = table[idx],last = 0,dataptr = new Link(key,0); - - while(ptr != 0) { - last = ptr; - ptr = ptr->next; - } - *((volatile LinkPtr *) &(last->next)) = dataptr; - return &(dataptr->data); + typedef Link *LinkPtr; + LinkPtr ptr = table[idx],last = 0,dataptr = new Link(key,0); + + while(ptr != 0) { + last = ptr; + ptr = ptr->next; + } + *((volatile LinkPtr *) &(last->next)) = dataptr; + return &(dataptr->data); } } void Remove(const K &key) { @@ -206,28 +204,28 @@ public: int count = 1; if(idx < 0) idx = idx + size; if(idx >= size || idx < 0) { - printf("(2) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size); - exit(1); + printf("(2) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size); + exit(1); } p = table[idx]; while(p != 0 && !(p->key == key)) { - last = p; - p = p->next; - count = count + 1; + last = p; + p = p->next; + count = count + 1; } if(p != 0) { - used = used - 1; - if(last == 0) - table[idx] = p->next; - else - last->next = p->next; - delete p; + used = used - 1; + if(last == 0) + table[idx] = p->next; + else + last->next = p->next; + delete p; } if(count > maxlength) - maxlength = count; + maxlength = count; nsearch = nsearch + 1; nstep = nstep + count; } @@ -237,19 +235,19 @@ public: int count = 1; if(idx < 0) idx = idx + size; if(idx >= size || idx < 0) { - printf("(3) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size); - exit(1); + printf("(3) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size); + exit(1); } p = table[idx]; while(p != 0 && !(p->key == key)) { - p = p->next; - count = count + 1; + p = p->next; + count = count + 1; } if(count > maxlength) - maxlength = count; + maxlength = count; nsearch = nsearch + 1; nstep = nstep + count; @@ -284,46 +282,46 @@ public: } void zero() { for(int i = 0; i<8; i++) - for(int j = 0; j<8; j++) - m[i][j] = 0.0; + for(int j = 0; j<8; j++) + m[i][j] = 0.0; } void operator=(const Matrix &A) { for(int i = 1; i<=sz; i++) - for(int j = 1; j<=sz; j++) - m[i][j] = A.m[i][j]; + for(int j = 1; j<=sz; j++) + m[i][j] = A.m[i][j]; } void operator=(double x) { for(int i = 1; i<=sz; i++) - for(int j = 1; j<=sz; j++) - m[i][j] = x; + for(int j = 1; j<=sz; j++) + m[i][j] = x; } Matrix operator+(const Matrix &B) const { Matrix s; for(int i = 1; i<=sz; i++) - for(int j = 1; j<=sz; j++) - s.m[i][j] = m[i][j] + B.m[i][j]; + for(int j = 1; j<=sz; j++) + s.m[i][j] = m[i][j] + B.m[i][j]; return s; } Matrix operator-(const Matrix &B) const { Matrix s; for(int i = 1; i<=sz; i++) - for(int j = 1; j<=sz; j++) - s.m[i][j] = m[i][j] - B.m[i][j]; + for(int j = 1; j<=sz; j++) + s.m[i][j] = m[i][j] - B.m[i][j]; return s; } Matrix operator-() const { Matrix s; for(int i = 1; i<=sz; i++) - for(int j = 1; j<=sz; j++) - s.m[i][j] = -m[i][j]; + for(int j = 1; j<=sz; j++) + s.m[i][j] = -m[i][j]; return s; } Matrix operator*(double x) const { Matrix P; for(int i = 1; i<=sz; i++) - for(int j = 0; j<=sz; j++) - P.m[i][j] = m[i][j] * x; + for(int j = 0; j<=sz; j++) + P.m[i][j] = m[i][j] * x; return P; } Matrix operator/(double x) const { @@ -332,8 +330,8 @@ public: Matrix transpose() const { Matrix T; for(int i = 1; i<=sz; i++) - for(int j = 1; j<=sz; j++) - T.m[j][i] = m[i][j]; + for(int j = 1; j<=sz; j++) + T.m[j][i] = m[i][j]; return T; } }; @@ -375,13 +373,13 @@ public: int align_check() { return - (H1H2.align_check() << 0) | - (H1xH2.align_check() << 1) | - (H1yH2.align_check() << 2) | - (H1zH2.align_check() << 3) | - (H1H2x.align_check() << 4) | - (H1H2y.align_check() << 5) | - (H1H2z.align_check() << 6) ; + (H1H2.align_check() << 0) | + (H1xH2.align_check() << 1) | + (H1yH2.align_check() << 2) | + (H1zH2.align_check() << 3) | + (H1H2x.align_check() << 4) | + (H1H2y.align_check() << 5) | + (H1H2z.align_check() << 6) ; } void zero() { @@ -397,18 +395,18 @@ public: void make_bond(const double xx[][3],int i,int j,bond_data *bptr); void make_triplet(bond_data *ij_bond,bond_data *ik_bond,triplet_data *triptr); triplet_data *get_triplet(const double xx[][3],int i,int j,int k, - Hash *bhash,triplet_data *twork, - double *dvir_ij_p,double *dvir_ik_p); + Hash *bhash,triplet_data *twork, + double *dvir_ij_p,double *dvir_ik_p); int c1_outside(const double a[3], - int triclinic,const double alpha[3]) { + int triclinic,const double alpha[3]) { const double stol = 1e-5; if(triclinic) { for(int p = 0; p<3; p++) { - double cog = a[p]; - if(cog < domain->sublo_lamda[p]-0.5*rmax*alpha[p]-stol) return 1; - if(cog > domain->subhi_lamda[p]+0.5*rmax*alpha[p]+stol) return 1; + double cog = a[p]; + if(cog < domain->sublo_lamda[p]-0.5*rmax*alpha[p]-stol) return 1; + if(cog > domain->subhi_lamda[p]+0.5*rmax*alpha[p]+stol) return 1; } } else { @@ -416,63 +414,63 @@ public: for(int p = 0; p<3; p++) { - double cog = a[p]; - if(cog < domain->sublo[p]-0.5*rmax-stol) return 1; - if(cog > domain->subhi[p]+0.5*rmax+stol) return 1; - - if(cog < domain->sublo[p]-stol) { - double t = cog - (domain->sublo[p]-stol); - rout = rout + t*t; - } else if(cog > domain->subhi[p]+stol) { - double t = cog - (domain->subhi[p]+stol); - rout = rout + t*t; - } + double cog = a[p]; + if(cog < domain->sublo[p]-0.5*rmax-stol) return 1; + if(cog > domain->subhi[p]+0.5*rmax+stol) return 1; + + if(cog < domain->sublo[p]-stol) { + double t = cog - (domain->sublo[p]-stol); + rout = rout + t*t; + } else if(cog > domain->subhi[p]+stol) { + double t = cog - (domain->subhi[p]+stol); + rout = rout + t*t; + } } if(rout > 0.25*rmax*rmax) - return 1; + return 1; } return 0; } int c2_outside(const double a[3],const double b[3], - int triclinic,const double alpha[3]) { + int triclinic,const double alpha[3]) { const double stol = 1e-5; if(triclinic) { for(int p = 0; p<3; p++) { - double cog = 0.5*(a[p] + b[p]); - if(cog < domain->sublo_lamda[p]-0.5*rcrit*alpha[p]-stol) return 1; - if(cog > domain->subhi_lamda[p]+0.5*rcrit*alpha[p]+stol) return 1; + double cog = 0.5*(a[p] + b[p]); + if(cog < domain->sublo_lamda[p]-0.5*rcrit*alpha[p]-stol) return 1; + if(cog > domain->subhi_lamda[p]+0.5*rcrit*alpha[p]+stol) return 1; } } else { double rout = 0.0; for(int p = 0; p<3; p++) { - double cog = 0.5*(a[p] + b[p]); - if(cog < domain->sublo[p]-0.5*rcrit-stol) return 1; - if(cog > domain->subhi[p]+0.5*rcrit+stol) return 1; - - if(cog < domain->sublo[p]-stol) { - double t = cog - (domain->sublo[p]-stol); - rout = rout + t*t; - } else if(cog > domain->subhi[p]+stol) { - double t = cog - (domain->subhi[p]+stol); - rout = rout + t*t; - } + double cog = 0.5*(a[p] + b[p]); + if(cog < domain->sublo[p]-0.5*rcrit-stol) return 1; + if(cog > domain->subhi[p]+0.5*rcrit+stol) return 1; + + if(cog < domain->sublo[p]-stol) { + double t = cog - (domain->sublo[p]-stol); + rout = rout + t*t; + } else if(cog > domain->subhi[p]+stol) { + double t = cog - (domain->subhi[p]+stol); + rout = rout + t*t; + } } if(rout > 0.25*rcrit*rcrit) - return 1; + return 1; } return 0; } double get_weight(const int triclinic, - const double a[3] = 0,const double b[3] = 0, - const double c[3] = 0,const double d[3] = 0) { + const double a[3] = 0,const double b[3] = 0, + const double c[3] = 0,const double d[3] = 0) { const double *s0 = triclinic ? domain->sublo_lamda : domain->sublo, *s1 = triclinic ? domain->subhi_lamda : domain->subhi; @@ -499,46 +497,46 @@ public: } void force_debug_3t(double xx[][3], - int i0,int j0,int k0, - int i ,int j ,int k , - double dfix,double dfiy,double dfiz, - double dfjx,double dfjy,double dfjz, - double dfkx,double dfky,double dfkz); + int i0,int j0,int k0, + int i ,int j ,int k , + double dfix,double dfiy,double dfiz, + double dfjx,double dfjy,double dfjz, + double dfkx,double dfky,double dfkz); void force_debug_3v(double xx[][3], - int i0,int j0,int k0, - int i ,int j ,int k , - double dfix,double dfiy,double dfiz, - double dfjx,double dfjy,double dfjz, - double dfkx,double dfky,double dfkz); + int i0,int j0,int k0, + int i ,int j ,int k , + double dfix,double dfiy,double dfiz, + double dfjx,double dfjy,double dfjz, + double dfkx,double dfky,double dfkz); void force_debug_4(double xx[][3], - int i0,int j0,int k0,int m0, - int i ,int j ,int k ,int m , - double dfix,double dfiy,double dfiz, - double dfjx,double dfjy,double dfjz, - double dfkx,double dfky,double dfkz, - double dfmx,double dfmy,double dfmz); + int i0,int j0,int k0,int m0, + int i ,int j ,int k ,int m , + double dfix,double dfiy,double dfiz, + double dfjx,double dfjy,double dfjz, + double dfkx,double dfky,double dfkz, + double dfmx,double dfmy,double dfmz); double numderiv3t(double xx[][3],int i,int j,int k,int p); double numderiv3v(double xx[][3],int i,int j,int k,int p,int ipert); double numderiv4(double xx[][3],int i,int j,int k,int m,int p); void compute_x(const int *nnei,const int * const *nlist, - double *e_s,double *e_p,double *e_t,double *e_q, - int evflag,int newton_pair); + double *e_s,double *e_p,double *e_t,double *e_q, + int evflag,int newton_pair); /* Reimplementation of bond matrix computation */ void fl_deriv_new(double r,double ri,double xhat,double yhat,double zhat, - double &fl_0,double &fl_x,double &fl_y,double &fl_z, - double &fl_rp,double &fl_p1,double &fl_r0,double &fl_al); + double &fl_0,double &fl_x,double &fl_y,double &fl_z, + double &fl_rp,double &fl_p1,double &fl_r0,double &fl_al); void hamltn_5_raw(const double xin,const double yin,const double zin, - double M [8][8],double Mx[8][8], - double My[8][8],double Mz[8][8], - double *fl_deriv_sum_p); + double M [8][8],double Mx[8][8], + double My[8][8],double Mz[8][8], + double *fl_deriv_sum_p); void hamltn_7_raw(const double xin,const double yin,const double zin, - double M [8][8],double Mx[8][8], - double My[8][8],double Mz[8][8], - double *fl_deriv_sum_p); + double M [8][8],double Mx[8][8], + double My[8][8],double Mz[8][8], + double *fl_deriv_sum_p); /* * */ // Old matrix routines, only used in force debug routines. @@ -547,9 +545,9 @@ public: Matrix h; for(int l = 1; l <= lmax; l++) { for(int n = 1; n <= lmax; n++) { - h.m[l][n] = 0.0; - for(int m = 1; m <= lmax; m++) - h.m[l][n] += ha.m[l][m] * hb.m[m][n]; + h.m[l][n] = 0.0; + for(int m = 1; m <= lmax; m++) + h.m[l][n] += ha.m[l][m] * hb.m[m][n]; } } return h; @@ -561,7 +559,7 @@ public: for(int n = 1; n <= lmax; n++) { double cquan = 0.0; for(int m = 1; m <= lmax; m++) - cquan += ha.m[n][m] * hb.m[m][n]; + cquan += ha.m[n][m] * hb.m[m][n]; zquan += cquan; } return zquan; @@ -573,32 +571,32 @@ public: int i,j,k; if(lmax == 5) { - const int n = 5; - for(i = 1; i<=n; i++) - for(j = 1; j<=n; j++) { - double s = 0.0; - for(k = 1; k<=n; k++) - s = s + a.m[i][k]*b.m[j][k]; - c.m[i][j] = s; - } + const int n = 5; + for(i = 1; i<=n; i++) + for(j = 1; j<=n; j++) { + double s = 0.0; + for(k = 1; k<=n; k++) + s = s + a.m[i][k]*b.m[j][k]; + c.m[i][j] = s; + } } else if(lmax == 7) { - const int n = 7; - for(i = 1; i<=n; i++) - for(j = 1; j<=n; j++) { - double s = 0.0; - for(k = 1; k<=n; k++) - s = s + a.m[i][k]*b.m[j][k]; - c.m[i][j] = s; - } + const int n = 7; + for(i = 1; i<=n; i++) + for(j = 1; j<=n; j++) { + double s = 0.0; + for(k = 1; k<=n; k++) + s = s + a.m[i][k]*b.m[j][k]; + c.m[i][j] = s; + } } else { - const int n = lmax; - for(i = 1; i<=n; i++) - for(j = 1; j<=n; j++) { - double s = 0.0; - for(k = 1; k<=n; k++) - s = s + a.m[i][k]*b.m[j][k]; - c.m[i][j] = s; - } + const int n = lmax; + for(i = 1; i<=n; i++) + for(j = 1; j<=n; j++) { + double s = 0.0; + for(k = 1; k<=n; k++) + s = s + a.m[i][k]*b.m[j][k]; + c.m[i][j] = s; + } } } @@ -609,7 +607,7 @@ public: for(i = 0; i -#include #include "angle_cosine_shift.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-MISC/angle_cosine_shift.h b/src/USER-MISC/angle_cosine_shift.h index 030709a0e20ba90a8a168fe11fcd1b53a33f72da..febabcc0907fff93406cc373f202f91e947a8438 100644 --- a/src/USER-MISC/angle_cosine_shift.h +++ b/src/USER-MISC/angle_cosine_shift.h @@ -20,7 +20,6 @@ AngleStyle(cosine/shift,AngleCosineShift) #ifndef LMP_ANGLE_COSINE_SHIFT_H #define LMP_ANGLE_COSINE_SHIFT_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_cosine_shift_exp.cpp b/src/USER-MISC/angle_cosine_shift_exp.cpp index 8c6282de206202b3d4dd94aeb920545ea1ff9c3e..79cb0fea7ca71c8facff410ec53b36b9e689561e 100644 --- a/src/USER-MISC/angle_cosine_shift_exp.cpp +++ b/src/USER-MISC/angle_cosine_shift_exp.cpp @@ -15,9 +15,9 @@ Contributing author: Carsten Svaneborg, science@zqex.dk ------------------------------------------------------------------------- */ -#include -#include #include "angle_cosine_shift_exp.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-MISC/angle_cosine_shift_exp.h b/src/USER-MISC/angle_cosine_shift_exp.h index 8b8e389380b7af7be8f1a2ce4816827c19000d29..9614ddcc195c2c91797f23ad120db3b219f42bb2 100644 --- a/src/USER-MISC/angle_cosine_shift_exp.h +++ b/src/USER-MISC/angle_cosine_shift_exp.h @@ -18,7 +18,6 @@ AngleStyle(cosine/shift/exp,AngleCosineShiftExp) #ifndef LMP_ANGLE_COSINE_SHIFT_EXP_H #define LMP_ANGLE_COSINE_SHIFT_EXP_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_dipole.cpp b/src/USER-MISC/angle_dipole.cpp index 781da46869ebdcbd6c4e656223e92619075496ea..0956ba3b8f31fcdbb266d7f2399d3c7f9b203ba7 100644 --- a/src/USER-MISC/angle_dipole.cpp +++ b/src/USER-MISC/angle_dipole.cpp @@ -15,9 +15,9 @@ Contributing authors: Mario Orsi & Wei Ding (QMUL), m.orsi@qmul.ac.uk ------------------------------------------------------------------------- */ -#include -#include #include "angle_dipole.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-MISC/angle_dipole.h b/src/USER-MISC/angle_dipole.h index 6c5dccb803677b274c7cd903549389b80befb986..187822d0d4673891890fa1e3ef68fd136d5ae7ec 100644 --- a/src/USER-MISC/angle_dipole.h +++ b/src/USER-MISC/angle_dipole.h @@ -20,7 +20,6 @@ AngleStyle(dipole,AngleDipole) #ifndef LMP_ANGLE_DIPOLE_H #define LMP_ANGLE_DIPOLE_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_fourier.cpp b/src/USER-MISC/angle_fourier.cpp index 8f5074ff5d85fbf4a1412280e109e6f077b31087..dcf5080431cb383374abc902542d5ebddf83b834 100644 --- a/src/USER-MISC/angle_fourier.cpp +++ b/src/USER-MISC/angle_fourier.cpp @@ -16,9 +16,9 @@ [ based on angle_cosine_squared.cpp Naveen Michaud-Agrawal (Johns Hopkins U)] ------------------------------------------------------------------------- */ -#include -#include #include "angle_fourier.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-MISC/angle_fourier.h b/src/USER-MISC/angle_fourier.h index 14b4eedf57be4bee470b70243a9b30a5ec7e6554..53eeea98da48a3384c6d0b95d98dc8e39dbcd5e0 100644 --- a/src/USER-MISC/angle_fourier.h +++ b/src/USER-MISC/angle_fourier.h @@ -20,7 +20,6 @@ AngleStyle(fourier,AngleFourier) #ifndef ANGLE_FOURIER_H #define ANGLE_FOURIER_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_fourier_simple.cpp b/src/USER-MISC/angle_fourier_simple.cpp index 615556bbe7cc3ded511c3fb045d7288cf72ce70a..bbe3f8520b45c064edec0f0a5ef615e83d970366 100644 --- a/src/USER-MISC/angle_fourier_simple.cpp +++ b/src/USER-MISC/angle_fourier_simple.cpp @@ -16,9 +16,9 @@ [ based on angle_cosine_squared.cpp Naveen Michaud-Agrawal (Johns Hopkins U)] ------------------------------------------------------------------------- */ -#include -#include #include "angle_fourier_simple.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-MISC/angle_fourier_simple.h b/src/USER-MISC/angle_fourier_simple.h index 3a7bd37750a93b029f0917a95dd5a7374c2a2e12..df2253317fcf2c0483d1523cc83a3f97960e7c16 100644 --- a/src/USER-MISC/angle_fourier_simple.h +++ b/src/USER-MISC/angle_fourier_simple.h @@ -20,7 +20,6 @@ AngleStyle(fourier/simple,AngleFourierSimple) #ifndef ANGLE_FOURIER_SIMPLE_H #define ANGLE_FOURIER_SIMPLE_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_quartic.cpp b/src/USER-MISC/angle_quartic.cpp index 21a96100aa9c9e3abc1bcf86c016ec2ad1e0dada..5c5f3411e423bcce0c458c418299a8561cbc297d 100644 --- a/src/USER-MISC/angle_quartic.cpp +++ b/src/USER-MISC/angle_quartic.cpp @@ -16,9 +16,9 @@ [ based on angle_harmonic.cpp] ------------------------------------------------------------------------- */ -#include -#include #include "angle_quartic.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-MISC/angle_quartic.h b/src/USER-MISC/angle_quartic.h index 7043cab06413dda4da43caa8baac0aa3a762cf6c..b916a5f89f28798b88aaf575a84f1c9d972f7882 100644 --- a/src/USER-MISC/angle_quartic.h +++ b/src/USER-MISC/angle_quartic.h @@ -20,7 +20,6 @@ AngleStyle(quartic,AngleQuartic) #ifndef LMP_ANGLE_QUARTIC_H #define LMP_ANGLE_QUARTIC_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/bond_harmonic_shift.cpp b/src/USER-MISC/bond_harmonic_shift.cpp index c7e4444ccefa565918a7b2d8e3b6dd111b37874c..fdd31117831fed94b6d98c042503061e5987cae1 100644 --- a/src/USER-MISC/bond_harmonic_shift.cpp +++ b/src/USER-MISC/bond_harmonic_shift.cpp @@ -15,12 +15,11 @@ Contributing author: Carsten Svaneborg, science@zqex.dk ------------------------------------------------------------------------- */ -#include -#include #include "bond_harmonic_shift.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/USER-MISC/bond_harmonic_shift.h b/src/USER-MISC/bond_harmonic_shift.h index ff0d358243a832c36e43333ce5707a4321fa9fcc..b77cefb4af9d7f939965da1a372d74a6e0dd333d 100644 --- a/src/USER-MISC/bond_harmonic_shift.h +++ b/src/USER-MISC/bond_harmonic_shift.h @@ -20,7 +20,6 @@ BondStyle(harmonic/shift,BondHarmonicShift) #ifndef LMP_BOND_HARMONIC_SHIFT_H #define LMP_BOND_HARMONIC_SHIFT_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/bond_harmonic_shift_cut.cpp b/src/USER-MISC/bond_harmonic_shift_cut.cpp index 5b396f5d725047c07927af0f2fe250ccda85403e..0688cb428a75b63357e8d29c86bda7469107513e 100644 --- a/src/USER-MISC/bond_harmonic_shift_cut.cpp +++ b/src/USER-MISC/bond_harmonic_shift_cut.cpp @@ -15,12 +15,11 @@ Contributing author: Carsten Svaneborg, science@zqex.dk ------------------------------------------------------------------------- */ -#include -#include #include "bond_harmonic_shift_cut.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/USER-MISC/bond_harmonic_shift_cut.h b/src/USER-MISC/bond_harmonic_shift_cut.h index 5db76d51aa5fbde88bc2061a4b34c506bcd239c3..ad2bcd61adfd6ba72ef1e4fd0c3e974340fa2b17 100644 --- a/src/USER-MISC/bond_harmonic_shift_cut.h +++ b/src/USER-MISC/bond_harmonic_shift_cut.h @@ -20,7 +20,6 @@ BondStyle(harmonic/shift/cut,BondHarmonicShiftCut) #ifndef LMP_BOND_HARMONIC_SHIFT_CUT_H #define LMP_BOND_HARMONIC_SHIFT_CUT_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/compute_cnp_atom.cpp b/src/USER-MISC/compute_cnp_atom.cpp index 6fa16f1a9ac5b6f82a35eac3a9d792c9dedabe30..ba97be25d407a87f02e7d9a67915b94d1159a4de 100644 --- a/src/USER-MISC/compute_cnp_atom.cpp +++ b/src/USER-MISC/compute_cnp_atom.cpp @@ -21,11 +21,10 @@ branicio@usc.edu ------------------------------------------------------------------------- */ +#include "compute_cnp_atom.h" +#include #include -#include #include - -#include "compute_cnp_atom.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/USER-MISC/compute_entropy_atom.cpp b/src/USER-MISC/compute_entropy_atom.cpp index 0367d7fe6d9e7605186e79fe0cdac4c05352f2c6..00f7e6dc8b7e1c90e8128d277a9b75c50fd6d590 100644 --- a/src/USER-MISC/compute_entropy_atom.cpp +++ b/src/USER-MISC/compute_entropy_atom.cpp @@ -15,10 +15,9 @@ Contributing author: Pablo Piaggi (EPFL Lausanne) ------------------------------------------------------------------------- */ +#include "compute_entropy_atom.h" #include #include -#include -#include "compute_entropy_atom.h" #include "atom.h" #include "update.h" #include "modify.h" @@ -28,13 +27,11 @@ #include "force.h" #include "pair.h" #include "comm.h" -#include "math_extra.h" #include "math_const.h" #include "memory.h" #include "error.h" #include "domain.h" - using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/compute_gyration_shape.cpp b/src/USER-MISC/compute_gyration_shape.cpp new file mode 100644 index 0000000000000000000000000000000000000000..a0ee6089b70d90acfd928ce5440b15fbc15cca21 --- /dev/null +++ b/src/USER-MISC/compute_gyration_shape.cpp @@ -0,0 +1,130 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + * Contributing author: Evangelos Voyiatzis (Royal DSM) + * ------------------------------------------------------------------------- */ + + +#include "compute_gyration_shape.h" +#include +#include +#include "error.h" +#include "math_extra.h" +#include "math_special.h" +#include "modify.h" +#include "update.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeGyrationShape::ComputeGyrationShape(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg), id_gyration(NULL) +{ + if (narg != 4) error->all(FLERR,"Illegal compute gyration/shape command"); + + vector_flag = 1; + size_vector = 6; + extscalar = 0; + extvector = 0; + + // ID of compute gyration + int n = strlen(arg[3]) + 1; + id_gyration = new char[n]; + strcpy(id_gyration,arg[3]); + + init(); + + vector = new double[6]; +} + +/* ---------------------------------------------------------------------- */ + +ComputeGyrationShape::~ComputeGyrationShape() +{ + delete [] id_gyration; + delete [] vector; +} + +/* ---------------------------------------------------------------------- */ + +void ComputeGyrationShape::init() +{ + // check that the compute gyration command exist + int icompute = modify->find_compute(id_gyration); + if (icompute < 0) + error->all(FLERR,"Compute gyration ID does not exist for " + "compute gyration/shape"); + + // check the id_gyration corresponds really to a compute gyration command + c_gyration = (Compute *) modify->compute[icompute]; + if (strcmp(c_gyration->style,"gyration") != 0) + error->all(FLERR,"Compute gyration compute ID does not point to " + "gyration compute for compute gyration/shape"); +} + +/* ---------------------------------------------------------------------- + compute shape parameters based on the eigenvalues of the + gyration tensor of group of atoms +------------------------------------------------------------------------- */ + +void ComputeGyrationShape::compute_vector() +{ + invoked_vector = update->ntimestep; + c_gyration->compute_vector(); + double *gyration_tensor = c_gyration->vector; + + // call the function for the calculation of the eigenvalues + double ione[3][3], evalues[3], evectors[3][3]; + + ione[0][0] = gyration_tensor[0]; + ione[1][1] = gyration_tensor[1]; + ione[2][2] = gyration_tensor[2]; + ione[0][1] = ione[1][0] = gyration_tensor[3]; + ione[1][2] = ione[2][1] = gyration_tensor[4]; + ione[0][2] = ione[2][0] = gyration_tensor[5]; + + int ierror = MathExtra::jacobi(ione,evalues,evectors); + if (ierror) error->all(FLERR, "Insufficient Jacobi rotations " + "for gyration/shape"); + + // sort the eigenvalues according to their size with bubble sort + double t; + for (int i = 0; i < 3; i++) { + for (int j = 0; j < 2-i; j++) { + if (fabs(evalues[j]) < fabs(evalues[j+1])) { + t = evalues[j]; + evalues[j] = evalues[j+1]; + evalues[j+1] = t; + } + } + } + + // compute the shape parameters of the gyration tensor + double sq_eigen_x = MathSpecial::square(evalues[0]); + double sq_eigen_y = MathSpecial::square(evalues[1]); + double sq_eigen_z = MathSpecial::square(evalues[2]); + + double nominator = MathSpecial::square(sq_eigen_x) + + MathSpecial::square(sq_eigen_y) + + MathSpecial::square(sq_eigen_z); + double denominator = MathSpecial::square(sq_eigen_x+sq_eigen_y+sq_eigen_z); + + vector[0] = evalues[0]; + vector[1] = evalues[1]; + vector[2] = evalues[2]; + vector[3] = sq_eigen_z - 0.5*(sq_eigen_x + sq_eigen_y); + vector[4] = sq_eigen_y - sq_eigen_x; + vector[5] = 0.5*(3*nominator/denominator - 1.0); +} diff --git a/src/USER-MISC/compute_gyration_shape.h b/src/USER-MISC/compute_gyration_shape.h new file mode 100644 index 0000000000000000000000000000000000000000..1d58f000dd0e325050b4df6f7d390da6a19ff762 --- /dev/null +++ b/src/USER-MISC/compute_gyration_shape.h @@ -0,0 +1,60 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(gyration/shape,ComputeGyrationShape) + +#else + +#ifndef LMP_COMPUTE_GYRATION_SHAPE_H +#define LMP_COMPUTE_GYRATION_SHAPE_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeGyrationShape : public Compute { + public: + char *id_gyration; // fields accessed by other classes + + ComputeGyrationShape(class LAMMPS *, int, char **); + ~ComputeGyrationShape(); + void init(); + void compute_vector(); + + private: + class Compute *c_gyration; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Compute gyration ID does not exist for compute gyration/shape + +Self-explanatory. Provide a valid compute ID + +E: Compute gyration/shape compute ID does not point to a gyration compute + +Self-explanatory. Provide an ID of a compute gyration command. +*/ diff --git a/src/USER-MISC/compute_momentum.cpp b/src/USER-MISC/compute_momentum.cpp new file mode 100644 index 0000000000000000000000000000000000000000..541b52d9c04014ca81771d61caeaa7df4de69d8e --- /dev/null +++ b/src/USER-MISC/compute_momentum.cpp @@ -0,0 +1,56 @@ + +#include "compute_momentum.h" +#include +#include "atom.h" +#include "error.h" +#include "update.h" + +using namespace LAMMPS_NS; + +ComputeMomentum::ComputeMomentum(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (narg != 3) error->all(FLERR,"Illegal compute momentum command"); + + vector_flag = 1; + size_vector = 3; + extvector = 1; + vector = new double[size_vector]; +} + +ComputeMomentum::~ComputeMomentum() { + delete[] vector; +} + +void ComputeMomentum::init() +{ +} + +void ComputeMomentum::compute_vector() +{ + invoked_vector = update->ntimestep; + + double **v = atom->v; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *mask = atom->mask; + int *type = atom->type; + int nlocal = atom->nlocal; + + double mom[3] = {0.0, 0.0, 0.0}; + + if (rmass) { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + for(int j = 0; j < 3; ++j) + mom[j] += rmass[i] * v[i][j]; + } + } else { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) + for(int j = 0; j < 3; ++j) + mom[j] += mass[type[i]] * v[i][j]; + } + + MPI_Allreduce(&mom, vector, 3, MPI_DOUBLE, MPI_SUM, world); +} diff --git a/src/USER-MISC/compute_momentum.h b/src/USER-MISC/compute_momentum.h new file mode 100644 index 0000000000000000000000000000000000000000..1e0c52c0458b5b9bfe0f8b8324d19eb94abe56be --- /dev/null +++ b/src/USER-MISC/compute_momentum.h @@ -0,0 +1,36 @@ +#ifdef COMPUTE_CLASS + +ComputeStyle(momentum,ComputeMomentum) + +#else + +#ifndef LMP_COMPUTE_MOMENTUM_H +#define LMP_COMPUTE_MOMENTUM_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeMomentum : public Compute { + public: + ComputeMomentum(class LAMMPS *, int, char **); + virtual ~ComputeMomentum(); + + virtual void init(); + virtual void compute_vector(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +*/ diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp index c250eaf677ccd2b7fa2491c5302bc12ae2a18e98..6d2509d685402f4147698e457fddcf91278a2095 100644 --- a/src/USER-MISC/compute_pressure_cylinder.cpp +++ b/src/USER-MISC/compute_pressure_cylinder.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_pressure_cylinder.h" +#include +#include #include "atom.h" #include "update.h" #include "force.h" @@ -22,7 +21,6 @@ #include "neighbor.h" #include "neigh_request.h" #include "neigh_list.h" -#include "group.h" #include "memory.h" #include "error.h" #include "citeme.h" diff --git a/src/USER-MISC/compute_pressure_grem.cpp b/src/USER-MISC/compute_pressure_grem.cpp index 087c01bd8e2ad8da526bf213609c8f7241377b0d..ba949727b010b0da0e992243ea9dd2b2f45b7a89 100644 --- a/src/USER-MISC/compute_pressure_grem.cpp +++ b/src/USER-MISC/compute_pressure_grem.cpp @@ -11,17 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_pressure_grem.h" -#include "atom.h" +#include #include "update.h" #include "domain.h" #include "modify.h" #include "fix.h" #include "force.h" -#include "pair.h" #include "kspace.h" #include "error.h" diff --git a/src/USER-MISC/compute_stress_mop.cpp b/src/USER-MISC/compute_stress_mop.cpp index cb2a0b97136476145d8c82207e8599f5e3c3ae9b..2f932321e1d109493dfa00898559630ace89613f 100644 --- a/src/USER-MISC/compute_stress_mop.cpp +++ b/src/USER-MISC/compute_stress_mop.cpp @@ -15,18 +15,14 @@ Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon) --------------------------------------------------------------------------*/ +#include "compute_stress_mop.h" #include #include #include -#include -#include "compute_stress_mop.h" #include "atom.h" #include "update.h" #include "domain.h" -#include "group.h" -#include "modify.h" -#include "fix.h" #include "neighbor.h" #include "force.h" #include "pair.h" diff --git a/src/USER-MISC/compute_stress_mop_profile.cpp b/src/USER-MISC/compute_stress_mop_profile.cpp index 5499a37a4669063244ce677302f0354ad95474b7..5f6d0a36b227a5c12a469745217829ff707dd45c 100644 --- a/src/USER-MISC/compute_stress_mop_profile.cpp +++ b/src/USER-MISC/compute_stress_mop_profile.cpp @@ -15,18 +15,14 @@ Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon) --------------------------------------------------------------------------*/ +#include "compute_stress_mop_profile.h" #include #include #include -#include -#include "compute_stress_mop_profile.h" #include "atom.h" #include "update.h" #include "domain.h" -#include "group.h" -#include "modify.h" -#include "fix.h" #include "neighbor.h" #include "force.h" #include "pair.h" diff --git a/src/USER-MISC/compute_temp_rotate.cpp b/src/USER-MISC/compute_temp_rotate.cpp index 36093bd1e1f181ad11e790cc383280d6206a3c3e..94c6115186176b84ba035b874327e5990611ef02 100644 --- a/src/USER-MISC/compute_temp_rotate.cpp +++ b/src/USER-MISC/compute_temp_rotate.cpp @@ -15,16 +15,13 @@ Contributing author: Laurent Joly (U Lyon, France), ljoly.ulyon@gmail.com ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_temp_rotate.h" +#include #include "atom.h" #include "update.h" #include "force.h" #include "group.h" #include "domain.h" -#include "lattice.h" #include "error.h" #include "memory.h" diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.cpp b/src/USER-MISC/dihedral_cosine_shift_exp.cpp index c411ea815007587c93baf53b283dc38d06e4ebf1..820dfabdeb6dc48ab97e97698778d3b5ac9c0555 100644 --- a/src/USER-MISC/dihedral_cosine_shift_exp.cpp +++ b/src/USER-MISC/dihedral_cosine_shift_exp.cpp @@ -15,14 +15,12 @@ Contributing author: Carsten Svaneborg, science@zqex.dk ------------------------------------------------------------------------- */ +#include "dihedral_cosine_shift_exp.h" #include #include -#include -#include "dihedral_cosine_shift_exp.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "memory.h" diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.h b/src/USER-MISC/dihedral_cosine_shift_exp.h index fc4be5049b49c920d40d4fe83995a3b89f2b87db..4d180f42de5e492e714b3b0cd670018ce74f8798 100644 --- a/src/USER-MISC/dihedral_cosine_shift_exp.h +++ b/src/USER-MISC/dihedral_cosine_shift_exp.h @@ -20,7 +20,6 @@ DihedralStyle(cosine/shift/exp,DihedralCosineShiftExp) #ifndef LMP_DIHEDRAL_COSINE_SHIFT_EXP_H #define LMP_DIHEDRAL_COSINE_SHIFT_EXP_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/dihedral_fourier.cpp b/src/USER-MISC/dihedral_fourier.cpp index af86259c01e5fde04d509faecd4583d72497f518..7cc250b1a882f80daf94b85f72e22ee7fbfe8e3d 100644 --- a/src/USER-MISC/dihedral_fourier.cpp +++ b/src/USER-MISC/dihedral_fourier.cpp @@ -16,16 +16,13 @@ [ based on dihedral_charmm.cpp Paul Crozier (SNL) ] ------------------------------------------------------------------------- */ +#include "dihedral_fourier.h" #include #include -#include -#include "dihedral_fourier.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" -#include "pair.h" #include "update.h" #include "math_const.h" #include "memory.h" diff --git a/src/USER-MISC/dihedral_fourier.h b/src/USER-MISC/dihedral_fourier.h index c1ed843c3486348cd90d364f2d46453838f6d1fc..8b6291fc4ca9651f624e09b548fef09f3a351f5f 100644 --- a/src/USER-MISC/dihedral_fourier.h +++ b/src/USER-MISC/dihedral_fourier.h @@ -20,7 +20,6 @@ DihedralStyle(fourier,DihedralFourier) #ifndef LMP_DIHEDRAL_FOURIER_H #define LMP_DIHEDRAL_FOURIER_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/dihedral_nharmonic.cpp b/src/USER-MISC/dihedral_nharmonic.cpp index ea2b76f4152b6af03b555e9c3e6b6c60deebf4c1..f1e0018689cf3fa85134049dea750fd95ed254c7 100644 --- a/src/USER-MISC/dihedral_nharmonic.cpp +++ b/src/USER-MISC/dihedral_nharmonic.cpp @@ -16,12 +16,11 @@ [ based on dihedral_multi_harmonic.cpp Mathias Puetz (SNL) and friends ] ------------------------------------------------------------------------- */ -#include -#include #include "dihedral_nharmonic.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "update.h" diff --git a/src/USER-MISC/dihedral_nharmonic.h b/src/USER-MISC/dihedral_nharmonic.h index 7c6a35b200a3a6a8bb91cb21b9a5d9babc3cdfd8..6fd1da3b8b76bf4be159b7042b3655816d0c0177 100644 --- a/src/USER-MISC/dihedral_nharmonic.h +++ b/src/USER-MISC/dihedral_nharmonic.h @@ -20,7 +20,6 @@ DihedralStyle(nharmonic,DihedralNHarmonic) #ifndef DIHEDRAL_NHARMONIC_H #define DIHEDRAL_NHARMONIC_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/dihedral_quadratic.cpp b/src/USER-MISC/dihedral_quadratic.cpp index 8436e73c5c3ecbee0be18d4982841546377d254e..02effc2f4fd5425eaf4c767fc47563823531a592 100644 --- a/src/USER-MISC/dihedral_quadratic.cpp +++ b/src/USER-MISC/dihedral_quadratic.cpp @@ -16,12 +16,11 @@ [ based on dihedral_helix.cpp Paul Crozier (SNL) ] ------------------------------------------------------------------------- */ -#include -#include #include "dihedral_quadratic.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "update.h" diff --git a/src/USER-MISC/dihedral_quadratic.h b/src/USER-MISC/dihedral_quadratic.h index edc29c3cf8b5b87a84d291450dacdeb359d05ac1..0b99cbc4f79cc3919a452f38da4ffcfd8856116c 100644 --- a/src/USER-MISC/dihedral_quadratic.h +++ b/src/USER-MISC/dihedral_quadratic.h @@ -20,7 +20,6 @@ DihedralStyle(quadratic,DihedralQuadratic) #ifndef LMP_DIHEDRAL_QUADRATIC_H #define LMP_DIHEDRAL_QUADRATIC_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/dihedral_spherical.cpp b/src/USER-MISC/dihedral_spherical.cpp index 3b30121551be6b1e9dda04b62734440e6477c254..78d45f923d12683deb4dec3d9e748d0a20810b4a 100644 --- a/src/USER-MISC/dihedral_spherical.cpp +++ b/src/USER-MISC/dihedral_spherical.cpp @@ -17,22 +17,19 @@ and Paul Crozier (SNL) ] ------------------------------------------------------------------------- */ +#include "dihedral_spherical.h" #include #include -#include #include #include "atom.h" #include "comm.h" #include "neighbor.h" #include "domain.h" #include "force.h" -#include "pair.h" -#include "update.h" #include "math_const.h" #include "math_extra.h" #include "memory.h" #include "error.h" -#include "dihedral_spherical.h" using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-MISC/dihedral_spherical.h b/src/USER-MISC/dihedral_spherical.h index ae0ece189a69118853c35b54ba74a00d7800a634..472db36f33478721b4052f2498e1c3f4af799d22 100644 --- a/src/USER-MISC/dihedral_spherical.h +++ b/src/USER-MISC/dihedral_spherical.h @@ -20,7 +20,6 @@ DihedralStyle(spherical,DihedralSpherical) #ifndef LMP_DIHEDRAL_SPHERICAL_H #define LMP_DIHEDRAL_SPHERICAL_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/dihedral_table.cpp b/src/USER-MISC/dihedral_table.cpp index ce5a32b603929669d178ca86048eed2acb163b02..59a16f376fa8a7d6a02c6be64c6647214ca7c6f1 100644 --- a/src/USER-MISC/dihedral_table.cpp +++ b/src/USER-MISC/dihedral_table.cpp @@ -17,21 +17,20 @@ the "tridiag.c" written by Gerard Jungman for GSL ------------------------------------------------------------------------- */ +#include +#include #include #include #include -#include #include -#include -#include -#include +#include // IWYU pragma: keep +#include // IWYU pragma: keep #include "atom.h" #include "comm.h" #include "neighbor.h" #include "domain.h" #include "force.h" -#include "update.h" #include "memory.h" #include "error.h" #include "dihedral_table.h" diff --git a/src/USER-MISC/dihedral_table_cut.cpp b/src/USER-MISC/dihedral_table_cut.cpp index f5c85cc52baba93ac4a4166b9fc867e908ecb420..87f0c9bf665d2878632ab1bbcaa8ece598d93680 100644 --- a/src/USER-MISC/dihedral_table_cut.cpp +++ b/src/USER-MISC/dihedral_table_cut.cpp @@ -16,25 +16,23 @@ Based on tabulated dihedral (dihedral_table.cpp) by Andrew Jewett ------------------------------------------------------------------------- */ +#include "dihedral_table_cut.h" +#include +#include #include #include #include -#include #include -#include -#include -#include +#include // IWYU pragma: keep +#include // IWYU pragma: keep -#include "dihedral_table_cut.h" #include "atom.h" #include "neighbor.h" #include "update.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "citeme.h" #include "math_const.h" -#include "math_extra.h" #include "memory.h" #include "error.h" #include "utils.h" @@ -42,8 +40,6 @@ using namespace LAMMPS_NS; using namespace MathConst; using namespace std; -using namespace MathExtra; - static const char cite_dihedral_tablecut[] = "dihedral_style table/cut command:\n\n" diff --git a/src/USER-MISC/fix_addtorque.cpp b/src/USER-MISC/fix_addtorque.cpp index 2cd1ac7527f063fb28dc9080000321126f7a00e4..665f1d4a60f58364647b101a1771278c525c4d94 100644 --- a/src/USER-MISC/fix_addtorque.cpp +++ b/src/USER-MISC/fix_addtorque.cpp @@ -15,9 +15,9 @@ Contributing author: Laurent Joly (U Lyon, France), ljoly.ulyon@gmail.com ------------------------------------------------------------------------- */ -#include -#include #include "fix_addtorque.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" @@ -25,7 +25,6 @@ #include "respa.h" #include "input.h" #include "variable.h" -#include "memory.h" #include "error.h" #include "group.h" #include "force.h" diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/USER-MISC/fix_ave_correlate_long.cpp index dc52d94b141264c5348600a61445e3612dad1b26..b1bcc07fa781cf2b266b80911705df959a9e9571 100644 --- a/src/USER-MISC/fix_ave_correlate_long.cpp +++ b/src/USER-MISC/fix_ave_correlate_long.cpp @@ -21,11 +21,12 @@ see J. Chem. Phys. 133, 154103 (2010) ------------------------------------------------------------------------- */ +#include "fix_ave_correlate_long.h" +#include #include #include #include #include -#include "fix_ave_correlate_long.h" #include "update.h" #include "modify.h" #include "compute.h" diff --git a/src/USER-MISC/fix_ave_correlate_long.h b/src/USER-MISC/fix_ave_correlate_long.h index 548a0e7183a0abbbeb1a5952d25659990fe5c1c2..a0c5863e991989ac3f3c839a15aa6eb06830f0d2 100644 --- a/src/USER-MISC/fix_ave_correlate_long.h +++ b/src/USER-MISC/fix_ave_correlate_long.h @@ -20,7 +20,6 @@ FixStyle(ave/correlate/long,FixAveCorrelateLong) #ifndef LMP_FIX_AVE_CORRELATE_LONG_H #define LMP_FIX_AVE_CORRELATE_LONG_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp index c641912db61cf01ab2b261e30f0e35d283fdf724..05dc54c57e3ec71f6a8b8681f6f5c9e87bb433f7 100644 --- a/src/USER-MISC/fix_bond_react.cpp +++ b/src/USER-MISC/fix_bond_react.cpp @@ -15,11 +15,10 @@ See the README file in the top-level LAMMPS directory. Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu) ------------------------------------------------------------------------- */ +#include "fix_bond_react.h" #include #include #include -#include -#include "fix_bond_react.h" #include "update.h" #include "modify.h" #include "respa.h" @@ -1286,7 +1285,7 @@ void FixBondReact::make_a_guess() for (int i = 0; i < nxspecial[atom->map(glove[pion][1])][0]; i++) { if (atom->map(xspecial[atom->map(glove[pion][1])][i]) < 0) { - error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away1"); // parallel issues. + error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away"); // parallel issues. } if (i_limit_tags[(int)atom->map(xspecial[atom->map(glove[pion][1])][i])] != 0) { status = GUESSFAIL; @@ -1397,7 +1396,7 @@ void FixBondReact::check_a_neighbor() //another check for ghost atoms. perhaps remove the one in make_a_guess if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) { - error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away2"); + error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away"); } for (int j = 0; j < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; j++) { @@ -1449,7 +1448,7 @@ void FixBondReact::check_a_neighbor() //another check for ghost atoms. perhaps remove the one in make_a_guess if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) { - error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away3"); + error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away"); } for (int ii = 0; ii < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; ii++) { @@ -1560,7 +1559,7 @@ void FixBondReact::inner_crosscheck_loop() //another check for ghost atoms. perhaps remove the one in make_a_guess if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) { - error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away4"); + error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away"); } if (guess_branch[avail_guesses-1] == 0) avail_guesses--; diff --git a/src/USER-MISC/fix_electron_stopping.cpp b/src/USER-MISC/fix_electron_stopping.cpp index 0831ebcf898e1ec214f62ea27c47d18c9cb702f3..2130f0742079fce2d44847bc6f6604253809c99f 100644 --- a/src/USER-MISC/fix_electron_stopping.cpp +++ b/src/USER-MISC/fix_electron_stopping.cpp @@ -16,16 +16,14 @@ Information: k.avchachov@gmail.com ------------------------------------------------------------------------- */ +#include "fix_electron_stopping.h" #include -#include #include -#include "fix_electron_stopping.h" #include "mpi.h" #include "atom.h" #include "update.h" #include "domain.h" #include "region.h" -#include "group.h" #include "force.h" #include "fix.h" #include "memory.h" diff --git a/src/USER-MISC/fix_ffl.cpp b/src/USER-MISC/fix_ffl.cpp index 9ab113aeaa3d99d6556f28088390dc358e909078..a245b6b4e5140306aa070d92af786a4901c44b76 100644 --- a/src/USER-MISC/fix_ffl.cpp +++ b/src/USER-MISC/fix_ffl.cpp @@ -18,31 +18,21 @@ /* ---------------------------------------------------------------------- Contributing authors: Lionel Constantin (EPFL), David M. Wilkins (EPFL), - Michele Ceriotti (EPFL) + Michele Ceriotti (EPFL) ------------------------------------------------------------------------- */ +#include "fix_ffl.h" #include #include #include -#include -#include "fix_ffl.h" -#include "math_extra.h" #include "atom.h" -#include "atom_vec_ellipsoid.h" #include "force.h" #include "update.h" -#include "modify.h" -#include "compute.h" -#include "domain.h" -#include "region.h" #include "respa.h" #include "comm.h" -#include "input.h" -#include "variable.h" #include "random_mars.h" #include "memory.h" #include "error.h" -#include "group.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_filter_corotate.cpp b/src/USER-MISC/fix_filter_corotate.cpp index f6cc1c435fb56e5f6c0e850bf352b3a7ad878b73..bfc5f58f931e2791e02264371b1c9e177c67dd72 100644 --- a/src/USER-MISC/fix_filter_corotate.cpp +++ b/src/USER-MISC/fix_filter_corotate.cpp @@ -16,30 +16,25 @@ some subroutines are from fix_shake.cpp ------------------------------------------------------------------------- */ +#include "fix_filter_corotate.h" #include +#include +#include #include #include -#include "fix_filter_corotate.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "bond.h" +#include "comm.h" +#include "domain.h" #include "angle.h" +#include "bond.h" #include "math_const.h" #include "update.h" #include "modify.h" -#include "domain.h" -#include "region.h" #include "memory.h" #include "error.h" #include "force.h" -#include "comm.h" -#include "error.h" -#include "memory.h" -#include "domain.h" -#include "integrate.h" #include "respa.h" -#include "neighbor.h" #include "citeme.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/fix_flow_gauss.cpp b/src/USER-MISC/fix_flow_gauss.cpp index b6366ec509cd356990aff55b10d19c9ebb1baefe..70be1f1e45f316c317febdb2a6c4b5fa14a0eec9 100644 --- a/src/USER-MISC/fix_flow_gauss.cpp +++ b/src/USER-MISC/fix_flow_gauss.cpp @@ -16,13 +16,12 @@ Joel.Eaves@Colorado.edu ------------------------------------------------------------------------- */ -#include -#include #include "fix_flow_gauss.h" +#include +#include #include "atom.h" #include "force.h" #include "group.h" -#include "comm.h" #include "update.h" #include "domain.h" #include "error.h" diff --git a/src/USER-MISC/fix_gle.cpp b/src/USER-MISC/fix_gle.cpp index 01da7f87cf97c9cddd391844a1c3edfcae575f8d..b8bdc66d08525747f7aef83bc9fe411539722a44 100644 --- a/src/USER-MISC/fix_gle.cpp +++ b/src/USER-MISC/fix_gle.cpp @@ -16,28 +16,19 @@ Axel Kohylmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "fix_gle.h" #include #include #include #include -#include "fix_gle.h" -#include "math_extra.h" #include "atom.h" -#include "atom_vec_ellipsoid.h" #include "force.h" #include "update.h" -#include "modify.h" -#include "compute.h" -#include "domain.h" -#include "region.h" #include "respa.h" #include "comm.h" -#include "input.h" -#include "variable.h" #include "random_mars.h" #include "memory.h" #include "error.h" -#include "group.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_grem.cpp b/src/USER-MISC/fix_grem.cpp index 635acf705c93bfc758bde45dc14b1e77276ae22a..42727400683eaffe2b584156a383c1bc35867054 100644 --- a/src/USER-MISC/fix_grem.cpp +++ b/src/USER-MISC/fix_grem.cpp @@ -22,19 +22,14 @@ Tom Keyes (Boston University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include "comm.h" #include "fix_grem.h" +#include #include "atom.h" #include "force.h" #include "update.h" #include "modify.h" #include "domain.h" -#include "input.h" #include "compute.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/fix_imd.cpp b/src/USER-MISC/fix_imd.cpp index 1c3eafdc46cf1ca42b451bd33e5b2e8f3e058890..10aaa285a540c76cb76a5b128e157a636d0341bf 100644 --- a/src/USER-MISC/fix_imd.cpp +++ b/src/USER-MISC/fix_imd.cpp @@ -58,8 +58,6 @@ negotiate an appropriate license for such distribution." #include "group.h" #include "memory.h" -#include -#include #include #include diff --git a/src/USER-MISC/fix_ipi.cpp b/src/USER-MISC/fix_ipi.cpp index 32892d87a8edd81945e7b613567b3998a5eb03cd..08b39ee89b0ad713a60c83309fdb11bcc6c2f425 100644 --- a/src/USER-MISC/fix_ipi.cpp +++ b/src/USER-MISC/fix_ipi.cpp @@ -15,15 +15,12 @@ Contributing author: Michele Ceriotti (EPFL), Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "fix_ipi.h" #include -#include #include -#include -#include "fix_ipi.h" #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" #include "kspace.h" #include "modify.h" @@ -32,8 +29,6 @@ #include "neighbor.h" #include "irregular.h" #include "domain.h" -#include "compute_pressure.h" -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_nvk.cpp b/src/USER-MISC/fix_nvk.cpp index 2ac2a7c9fca3ad1b2218ab6127def276a8cca14d..410a269f8cec30eed5258111cbc2c16ddd4e1871 100644 --- a/src/USER-MISC/fix_nvk.cpp +++ b/src/USER-MISC/fix_nvk.cpp @@ -15,18 +15,16 @@ Contributing author: Efrem Braun (UC Berkeley) ------------------------------------------------------------------------- */ +#include "fix_nvk.h" +#include #include -#include #include -#include "fix_nvk.h" #include "atom.h" #include "force.h" #include "update.h" #include "respa.h" #include "error.h" -#include "compute.h" #include "math_extra.h" -#include "domain.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_pimd.cpp b/src/USER-MISC/fix_pimd.cpp index 3929d47d6b0fb627c6cb6332ac6f406286474a61..8f790f0a59b7ad161becdc8ab292aa6d0cbcc3ad 100644 --- a/src/USER-MISC/fix_pimd.cpp +++ b/src/USER-MISC/fix_pimd.cpp @@ -21,10 +21,11 @@ Version 1.0 ------------------------------------------------------------------------- */ +#include "fix_pimd.h" +#include #include #include #include -#include "fix_pimd.h" #include "universe.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/fix_rhok.cpp b/src/USER-MISC/fix_rhok.cpp index 6a6e71ebaaf63b254c79d3e40d7bd706c94d1498..c638adf6a40883d1044466ab2af44c2f2a495252 100644 --- a/src/USER-MISC/fix_rhok.cpp +++ b/src/USER-MISC/fix_rhok.cpp @@ -13,12 +13,11 @@ Contributing author: Ulf R. Pedersen, ulf@urp.dk ------------------------------------------------------------------------- */ -#include -#include +#include "fix_rhok.h" +#include #include #include -#include "fix_rhok.h" #include "atom.h" #include "domain.h" #include "error.h" diff --git a/src/USER-MISC/fix_smd.cpp b/src/USER-MISC/fix_smd.cpp index cbebdebdbf920bce5ba705ff4630f24892f32b23..32c040c2b4b1d2391179e3f7e897bc6c7440bb06 100644 --- a/src/USER-MISC/fix_smd.cpp +++ b/src/USER-MISC/fix_smd.cpp @@ -16,10 +16,10 @@ based on fix spring by: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "fix_smd.h" +#include #include -#include #include -#include "fix_smd.h" #include "atom.h" #include "comm.h" #include "update.h" diff --git a/src/USER-MISC/fix_srp.cpp b/src/USER-MISC/fix_srp.cpp index ebc161ff99b31c32431df6cfbf21f478f3276014..c0db252db483786e55e8462818e1966e36694d7f 100644 --- a/src/USER-MISC/fix_srp.cpp +++ b/src/USER-MISC/fix_srp.cpp @@ -15,9 +15,10 @@ Contributing authors: Timothy Sirk (ARL), Pieter in't Veld (BASF) ------------------------------------------------------------------------- */ -#include -#include #include "fix_srp.h" +#include +#include +#include #include "atom.h" #include "force.h" #include "domain.h" @@ -635,11 +636,11 @@ void FixSRP::restart(char *buf) int FixSRP::modify_param(int /*narg*/, char **arg) { if (strcmp(arg[0],"btype") == 0) { - btype = atoi(arg[1]); + btype = force->inumeric(FLERR,arg[1]); return 2; } if (strcmp(arg[0],"bptype") == 0) { - bptype = atoi(arg[1]); + bptype = force->inumeric(FLERR,arg[1]); return 2; } return 0; diff --git a/src/USER-MISC/fix_srp.h b/src/USER-MISC/fix_srp.h index 7dbf044bdadcd14562d99ecd0b56d1f046cc9aed..f8343df8a66fd2e2f1c76af5fa91c1c0cccac48f 100644 --- a/src/USER-MISC/fix_srp.h +++ b/src/USER-MISC/fix_srp.h @@ -20,7 +20,6 @@ FixStyle(SRP,FixSRP) #ifndef LMP_FIX_SRP_H #define LMP_FIX_SRP_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/fix_ti_spring.cpp b/src/USER-MISC/fix_ti_spring.cpp index 305e29e0339ea754984caa3977b07ccf32ea9732..8481b34a6b84fd835dbf963d3438426b4a2d8ba6 100644 --- a/src/USER-MISC/fix_ti_spring.cpp +++ b/src/USER-MISC/fix_ti_spring.cpp @@ -18,9 +18,9 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ -#include -#include #include "fix_ti_spring.h" +#include +#include #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp index a34c2eb42ff5468efd59f22e33d7e718e088f711..55526a914940099a2c9995053c6622c60c178d96 100644 --- a/src/USER-MISC/fix_ttm_mod.cpp +++ b/src/USER-MISC/fix_ttm_mod.cpp @@ -17,17 +17,14 @@ Vasily Pisarev (Joint Institute for High Temperatures of RAS) ------------------------------------------------------------------------- */ -#include "lmptype.h" +#include "fix_ttm_mod.h" #include #include #include -#include -#include "fix_ttm_mod.h" #include "atom.h" #include "force.h" #include "update.h" #include "domain.h" -#include "region.h" #include "respa.h" #include "comm.h" #include "random_mars.h" diff --git a/src/USER-MISC/fix_wall_ees.cpp b/src/USER-MISC/fix_wall_ees.cpp index 5ca16ebdadd26706a3cdbcdb26d6ed3f4def9b0f..bd7e23047240c3d7161ab8555cc14f8f7b9b31db 100644 --- a/src/USER-MISC/fix_wall_ees.cpp +++ b/src/USER-MISC/fix_wall_ees.cpp @@ -15,21 +15,13 @@ Contributing author: Abdoreza Ershadinia, a.ershadinia at gmail.com ------------------------------------------------------------------------- */ +#include "fix_wall_ees.h" #include #include "math_extra.h" -#include "fix_wall_ees.h" #include "atom.h" #include "atom_vec.h" #include "atom_vec_ellipsoid.h" -#include "domain.h" -#include "region.h" -#include "force.h" -#include "lattice.h" -#include "update.h" -#include "output.h" -#include "respa.h" #include "error.h" -#include "math_extra.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_wall_region_ees.cpp b/src/USER-MISC/fix_wall_region_ees.cpp index 33bf636e640e2aa81c795fbeb417a7341b044b50..5c6bb1874b43f33e40a10750d6f20dfe9e5a4585 100644 --- a/src/USER-MISC/fix_wall_region_ees.cpp +++ b/src/USER-MISC/fix_wall_region_ees.cpp @@ -15,19 +15,16 @@ Contributing author: Abdoreza Ershadinia, a.ershadinia at gmail.com ------------------------------------------------------------------------- */ +#include "fix_wall_region_ees.h" +#include #include -#include #include -#include "fix_wall_region_ees.h" #include "atom.h" -#include "atom_vec.h" #include "atom_vec_ellipsoid.h" #include "domain.h" #include "region.h" #include "force.h" -#include "lattice.h" #include "update.h" -#include "output.h" #include "respa.h" #include "error.h" #include "math_extra.h" diff --git a/src/USER-MISC/improper_cossq.cpp b/src/USER-MISC/improper_cossq.cpp index c8eb0808fb3c759f21514b65ca9c283b210de4e8..2ea804b95d8754cdea78bf8425a52b5bb4f87543 100644 --- a/src/USER-MISC/improper_cossq.cpp +++ b/src/USER-MISC/improper_cossq.cpp @@ -16,14 +16,12 @@ gvog@chemeng.ntua.gr ------------------------------------------------------------------------- */ +#include "improper_cossq.h" #include #include -#include -#include "improper_cossq.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "memory.h" diff --git a/src/USER-MISC/improper_cossq.h b/src/USER-MISC/improper_cossq.h index ea880adfaf40845d301893abeb63849fb13a93e6..9e430bfa1ad8df72569d01887ce0fa6408c53e57 100644 --- a/src/USER-MISC/improper_cossq.h +++ b/src/USER-MISC/improper_cossq.h @@ -20,7 +20,6 @@ ImproperStyle(cossq,ImproperCossq) #ifndef LMP_IMPROPER_COSSQ_H #define LMP_IMPROPER_COSSQ_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/improper_distance.cpp b/src/USER-MISC/improper_distance.cpp index 50babcc84eb0e6f537dca30e8cdac17650c8ada7..2efab8b5f81e5f5ba30638896b7de3165c7b9909 100644 --- a/src/USER-MISC/improper_distance.cpp +++ b/src/USER-MISC/improper_distance.cpp @@ -15,16 +15,14 @@ Contributing author: Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ +#include "improper_distance.h" #include #include -#include -#include "improper_distance.h" #include "atom.h" #include "comm.h" #include "neighbor.h" #include "domain.h" #include "force.h" -#include "update.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MISC/improper_distance.h b/src/USER-MISC/improper_distance.h index 57e4d671e94320503bd1497ed18849366cd983b3..d7575c358518a5f43007824f92674be0299ae1e2 100644 --- a/src/USER-MISC/improper_distance.h +++ b/src/USER-MISC/improper_distance.h @@ -20,7 +20,6 @@ ImproperStyle(distance,ImproperDistance) #ifndef LMP_IMPROPER_DISTANCE_H #define LMP_IMPROPER_DISTANCE_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/improper_fourier.cpp b/src/USER-MISC/improper_fourier.cpp index 288d888d122104d949bd45b3e86ab3351698c491..a0ef3a205859d72434c010b8eaeffd628191e22f 100644 --- a/src/USER-MISC/improper_fourier.cpp +++ b/src/USER-MISC/improper_fourier.cpp @@ -16,15 +16,12 @@ [ based on improper_umbrella.cpp Tod A Pascal (Caltech) ] ------------------------------------------------------------------------- */ +#include "improper_fourier.h" #include #include -#include -#include -#include "improper_fourier.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "memory.h" diff --git a/src/USER-MISC/improper_fourier.h b/src/USER-MISC/improper_fourier.h index 0525c45494b56741b100d2e545c21364f5e8955a..91dfacfd8e2f67a1939380ca8ea474837a3f565a 100644 --- a/src/USER-MISC/improper_fourier.h +++ b/src/USER-MISC/improper_fourier.h @@ -20,7 +20,6 @@ ImproperStyle(fourier,ImproperFourier) #ifndef LMP_IMPROPER_FOURIER_H #define LMP_IMPROPER_FOURIER_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/improper_ring.cpp b/src/USER-MISC/improper_ring.cpp index 36ba73af0f818f62d4fa179c4e4540e5780ce8f4..48db5a41e9e22d6fa85612888b726fd781887994 100644 --- a/src/USER-MISC/improper_ring.cpp +++ b/src/USER-MISC/improper_ring.cpp @@ -36,16 +36,13 @@ of j. ------------------------------------------------------------------------- */ +#include "improper_ring.h" #include #include -#include -#include "improper_ring.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" -#include "update.h" #include "math_const.h" #include "math_special.h" #include "memory.h" diff --git a/src/USER-MISC/improper_ring.h b/src/USER-MISC/improper_ring.h index c31329816f806f573a044f77962eeab0c1cd418d..7c53c6f59f1caedbef699e34a712ffcd5d3ead59 100644 --- a/src/USER-MISC/improper_ring.h +++ b/src/USER-MISC/improper_ring.h @@ -20,7 +20,6 @@ ImproperStyle(ring,ImproperRing) #ifndef LMP_IMPROPER_RING_H #define LMP_IMPROPER_RING_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp index 21a6f1deee85c6c1ee7cd9b8b5a5a0c0da8aa6f8..b3abc647ef302cedce534098777162ef3c349770 100644 --- a/src/USER-MISC/pair_agni.cpp +++ b/src/USER-MISC/pair_agni.cpp @@ -15,18 +15,16 @@ Contributing authors: Axel Kohlmeyer (Temple U), Venkatesh Botu ------------------------------------------------------------------------- */ +#include "pair_agni.h" +#include #include -#include #include #include -#include "pair_agni.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" #include "force.h" #include "comm.h" -#include "memory.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MISC/pair_buck_mdf.cpp b/src/USER-MISC/pair_buck_mdf.cpp index afd15d7fdb1ab40beb0382786b95bafdfab337de..e9771975229074650df22b72a45dd7fb9242a5a1 100644 --- a/src/USER-MISC/pair_buck_mdf.cpp +++ b/src/USER-MISC/pair_buck_mdf.cpp @@ -15,21 +15,18 @@ Contributing author: Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ +#include "pair_buck_mdf.h" +#include #include -#include -#include #include -#include "pair_buck_mdf.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/pair_coul_diel.cpp b/src/USER-MISC/pair_coul_diel.cpp index a86921d2961fee2a06670cc12a13d5c1307572ab..a375901ecde082219428823a80ced918223b0823 100644 --- a/src/USER-MISC/pair_coul_diel.cpp +++ b/src/USER-MISC/pair_coul_diel.cpp @@ -14,11 +14,9 @@ Contributiong authors: Arben Jusufi, Axel Kohlmeyer (Temple U.) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_diel.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_coul_shield.cpp b/src/USER-MISC/pair_coul_shield.cpp index f74dcfe7d866270b21c4adc73f6dfd51891da18a..9264e51287f745523dfeeb06399ea2291a14e259 100644 --- a/src/USER-MISC/pair_coul_shield.cpp +++ b/src/USER-MISC/pair_coul_shield.cpp @@ -18,11 +18,8 @@ [Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017)] ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_shield.h" +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_drip.cpp b/src/USER-MISC/pair_drip.cpp index 118c033b5cfc3f63203eb6850fe109785972075a..20ec3abcf91f268610e07acbcb2c51d90aeb91df 100644 --- a/src/USER-MISC/pair_drip.cpp +++ b/src/USER-MISC/pair_drip.cpp @@ -20,19 +20,17 @@ Phys. Rev. B, 98, 235404 (2018). ------------------------------------------------------------------------- */ +#include "pair_drip.h" +#include #include -#include #include #include -#include -#include "pair_drip.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "my_page.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MISC/pair_drip.h b/src/USER-MISC/pair_drip.h index 0a8f90dfc2fd54f8096748843c9e9b05e1f8610c..3ea6c735a63b373672f199cafee0ad745cd69597 100644 --- a/src/USER-MISC/pair_drip.h +++ b/src/USER-MISC/pair_drip.h @@ -31,8 +31,6 @@ PairStyle(drip, PairDRIP) #define LMP_PAIR_DRIP_H #include "pair.h" -#include "my_page.h" -#include namespace LAMMPS_NS { diff --git a/src/USER-MISC/pair_e3b.cpp b/src/USER-MISC/pair_e3b.cpp index 43b472594a16907a188973fd774fe0fe2d4098ea..aa19849baa6a361d83346f1c717720105979085d 100644 --- a/src/USER-MISC/pair_e3b.cpp +++ b/src/USER-MISC/pair_e3b.cpp @@ -14,16 +14,14 @@ contact: stevene.strong at gmail dot com ------------------------------------------------------------------------- */ +#include "pair_e3b.h" +#include #include -#include -#include #include - -#include "pair_e3b.h" +#include #include "atom.h" #include "neighbor.h" -#include "neigh_request.h" #include "neigh_list.h" #include "force.h" #include "comm.h" diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp index 0b5220fdfd055ab07b0dea4ff13bd4ae58a306ed..8dee4a606b3002efa3ecf6ebed5609cc8321f0e0 100644 --- a/src/USER-MISC/pair_edip.cpp +++ b/src/USER-MISC/pair_edip.cpp @@ -21,12 +21,12 @@ Phys. Rev. B 58, 2539 (1998) ------------------------------------------------------------------------- */ +#include "pair_edip.h" +#include #include #include -#include #include #include -#include "pair_edip.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-MISC/pair_edip_multi.cpp b/src/USER-MISC/pair_edip_multi.cpp index ab48fbaa73fa49b166907f04cd8aa96363dcbd43..9f953610de618957ea0ebfdba59e2087f4f00007 100644 --- a/src/USER-MISC/pair_edip_multi.cpp +++ b/src/USER-MISC/pair_edip_multi.cpp @@ -17,12 +17,11 @@ Contributing author: Chao Jiang ------------------------------------------------------------------------- */ +#include "pair_edip_multi.h" +#include #include -#include -#include #include #include -#include "pair_edip_multi.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-MISC/pair_extep.cpp b/src/USER-MISC/pair_extep.cpp index bd5da71f4ab88345a72683e2536d5332670c43fc..8507fd49f675e5770d9887c5c2223948d518cc77 100644 --- a/src/USER-MISC/pair_extep.cpp +++ b/src/USER-MISC/pair_extep.cpp @@ -15,12 +15,12 @@ Contributing author: Jan Los ------------------------------------------------------------------------- */ +#include "pair_extep.h" +#include #include -#include #include #include #include -#include "pair_extep.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-MISC/pair_extep.h b/src/USER-MISC/pair_extep.h index 535e7261e392913ca75011aae5342ecfcd7de34b..1f127b71e0d7e34f83bb8cbdeeb60ac8684d16f8 100644 --- a/src/USER-MISC/pair_extep.h +++ b/src/USER-MISC/pair_extep.h @@ -21,7 +21,6 @@ PairStyle(extep,PairExTeP) #define LMP_PAIR_EXTEP_H #include "pair.h" -#include "my_page.h" #define MAXTYPES 8 #define NSPLINE 5 diff --git a/src/USER-MISC/pair_gauss_cut.cpp b/src/USER-MISC/pair_gauss_cut.cpp index 24d0b191d86b5109699d08968fe58ccd1732f950..e6cfc02f631125eeb98698544601c707af2706a0 100644 --- a/src/USER-MISC/pair_gauss_cut.cpp +++ b/src/USER-MISC/pair_gauss_cut.cpp @@ -15,18 +15,13 @@ Contributing authors: Arben Jusufi, Axel Kohlmeyer (Temple U.) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_gauss_cut.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" -#include "update.h" -#include "integrate.h" #include "memory.h" #include "error.h" #include "math_const.h" diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp index a41c660b7b9e8f5aed17ba27553e3f82ab24cb32..b94db6a87140d27ea65eac23beba73592659db15 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp +++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp @@ -20,12 +20,11 @@ [Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)] ------------------------------------------------------------------------- */ +#include "pair_ilp_graphene_hbn.h" #include #include -#include #include #include -#include "pair_ilp_graphene_hbn.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.h b/src/USER-MISC/pair_ilp_graphene_hbn.h index 07c3b2e97b12c39224656eca4fa69cad6cc9a3dc..ae4662cdc55037a79e67d3e68d14c20f150c446d 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.h +++ b/src/USER-MISC/pair_ilp_graphene_hbn.h @@ -21,8 +21,6 @@ PairStyle(ilp/graphene/hbn,PairILPGrapheneHBN) #define LMP_PAIR_ILP_GRAPHENE_HBN_H #include "pair.h" -#include "my_page.h" -#include namespace LAMMPS_NS { diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp index e73278968d66a1b87ff8510d7bf11a897853cc7f..0009531ca8dec847e10df2cd4d4ced830f2adf11 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp @@ -20,12 +20,11 @@ [Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)] ------------------------------------------------------------------------- */ +#include "pair_kolmogorov_crespi_full.h" #include -#include #include #include #include -#include "pair_kolmogorov_crespi_full.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.h b/src/USER-MISC/pair_kolmogorov_crespi_full.h index 9923b409a7de490ce2717bf80aebfe010d34110d..68dede0dd51f31a413ab67d23e7bbc8618fadd07 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.h +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.h @@ -21,8 +21,6 @@ PairStyle(kolmogorov/crespi/full,PairKolmogorovCrespiFull) #define LMP_PAIR_KolmogorovCrespi_FULL_H #include "pair.h" -#include "my_page.h" -#include namespace LAMMPS_NS { diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp index 79d6aa3daf465a916ac868621a98d101bec760a3..61c326ac879c9164320cb631b3b98412aa28f841 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp @@ -21,11 +21,11 @@ The simplification is that all normals are taken along the z-direction ------------------------------------------------------------------------- */ +#include "pair_kolmogorov_crespi_z.h" +#include #include -#include #include #include -#include "pair_kolmogorov_crespi_z.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_lebedeva_z.cpp b/src/USER-MISC/pair_lebedeva_z.cpp index c9d90e2850cfba58b7f9031d03fc1833d1cf9870..8930042cef76b15ac18cc2e86a004e0413c6e702 100644 --- a/src/USER-MISC/pair_lebedeva_z.cpp +++ b/src/USER-MISC/pair_lebedeva_z.cpp @@ -22,11 +22,11 @@ [Lebedeva et al., Physica E, 44(6), 949-954, 2012.] ------------------------------------------------------------------------- */ +#include "pair_lebedeva_z.h" +#include #include -#include #include #include -#include "pair_lebedeva_z.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_lennard_mdf.cpp b/src/USER-MISC/pair_lennard_mdf.cpp index e2e81e49438babcf3a7368f74d22868c234dcdca..50f59107a0b7d3b0280b5f2999cfc6c4dca16319 100644 --- a/src/USER-MISC/pair_lennard_mdf.cpp +++ b/src/USER-MISC/pair_lennard_mdf.cpp @@ -16,15 +16,13 @@ Contributing author: Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ +#include "pair_lennard_mdf.h" +#include #include -#include -#include #include -#include "pair_lennard_mdf.h" #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MISC/pair_list.cpp b/src/USER-MISC/pair_list.cpp index 562a60aa9939d4c8b92197fb2df91bbee37f8218..2f4e886a616f01eb28a4b9df818ea9b78aac2f1b 100644 --- a/src/USER-MISC/pair_list.cpp +++ b/src/USER-MISC/pair_list.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "pair_list.h" +#include +#include +#include #include "atom.h" #include "comm.h" -#include "domain.h" #include "force.h" #include "memory.h" - #include "error.h" -#include -#include -#include -#include - using namespace LAMMPS_NS; static const char * const stylename[] = { diff --git a/src/USER-MISC/pair_lj_expand_coul_long.cpp b/src/USER-MISC/pair_lj_expand_coul_long.cpp index fe21538f2dfcc8c2d2e0098312ea671be1443190..ffa828826f4d38bd3c43ba3c4d98c095309c5ede 100644 --- a/src/USER-MISC/pair_lj_expand_coul_long.cpp +++ b/src/USER-MISC/pair_lj_expand_coul_long.cpp @@ -15,17 +15,15 @@ Contributing author: Trung Nguyen (Northwestern) ------------------------------------------------------------------------- */ +#include "pair_lj_expand_coul_long.h" +#include #include -#include -#include #include -#include "pair_lj_expand_coul_long.h" #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-MISC/pair_lj_mdf.cpp b/src/USER-MISC/pair_lj_mdf.cpp index cfe125f21fa8eeab6aabc723dd1aae0004a7f744..3fe0fa6bf9c04f4c70d4fb8fae6ea0b6283d0331 100644 --- a/src/USER-MISC/pair_lj_mdf.cpp +++ b/src/USER-MISC/pair_lj_mdf.cpp @@ -16,15 +16,13 @@ Contributing author: Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ +#include "pair_lj_mdf.h" +#include #include -#include -#include #include -#include "pair_lj_mdf.h" #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp index af7d23370d162107a4dea8c3455d64dabe575008..758962ce297096378dcd981627a2606b60713c54 100644 --- a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp +++ b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp @@ -16,10 +16,10 @@ Samuel Genheden (University of Southampton) ------------------------------------------------------------------------- */ +#include "pair_lj_sf_dipole_sf.h" +#include #include -#include #include -#include "pair_lj_sf_dipole_sf.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp index f09919ce0f14984a1825648d935950c9e0d63634..79e7ac7e092f1cc33de4962e3178234d3a3ed9e1 100644 --- a/src/USER-MISC/pair_meam_spline.cpp +++ b/src/USER-MISC/pair_meam_spline.cpp @@ -31,15 +31,13 @@ conform with pairing, updated to LAMMPS style ------------------------------------------------------------------------- */ +#include "pair_meam_spline.h" #include -#include #include #include -#include "pair_meam_spline.h" #include "atom.h" #include "force.h" #include "comm.h" -#include "memory.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp index af1e8788bddcebfa709b894d255eaf05739fac65..eeadacf33a81e6c209eaa44d51100a162d255469 100644 --- a/src/USER-MISC/pair_meam_sw_spline.cpp +++ b/src/USER-MISC/pair_meam_sw_spline.cpp @@ -23,15 +23,13 @@ * 01-Aug-12 - RER: First code version. ------------------------------------------------------------------------- */ +#include "pair_meam_sw_spline.h" #include -#include #include #include -#include "pair_meam_sw_spline.h" #include "atom.h" #include "force.h" #include "comm.h" -#include "memory.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/USER-MISC/pair_momb.cpp b/src/USER-MISC/pair_momb.cpp index 1716149a986cefbdc744ab817597117fcd986a7e..29d5715302c14863d75d2ab02f621ba45cfd58d4 100644 --- a/src/USER-MISC/pair_momb.cpp +++ b/src/USER-MISC/pair_momb.cpp @@ -16,10 +16,9 @@ Ya Zhou (Penn State University) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_momb.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/USER-MISC/pair_morse_smooth_linear.cpp index 7c7973f830f954b30ff3ab8283ae8bc7ede409f7..c3cbe39db70596ab9c270524ce3897e5529493dc 100644 --- a/src/USER-MISC/pair_morse_smooth_linear.cpp +++ b/src/USER-MISC/pair_morse_smooth_linear.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_morse_smooth_linear.h" +#include #include -#include -#include #include -#include "pair_morse_smooth_linear.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_srp.cpp b/src/USER-MISC/pair_srp.cpp index 01deaf0fbe01d20fdafcf3232ccc58cbcd267239..416ace81321f12ef6859cfaab3b0fa3211f47485 100644 --- a/src/USER-MISC/pair_srp.cpp +++ b/src/USER-MISC/pair_srp.cpp @@ -25,9 +25,11 @@ There is an example script for this package in examples/USER/srp. Please contact Timothy Sirk for questions (tim.sirk@us.army.mil). ------------------------------------------------------------------------- */ +#include "pair_srp.h" +#include +#include #include #include -#include "pair_srp.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/USER-MISC/pair_tersoff_table.cpp index e0985d1dce00e6e4b0f6db5af13d2fef813d0d39..5c4f60f354382a8bd313c3bab71c6863c0de100a 100644 --- a/src/USER-MISC/pair_tersoff_table.cpp +++ b/src/USER-MISC/pair_tersoff_table.cpp @@ -20,11 +20,11 @@ 1) Tersoff, Phys. Rev. B 39, 5566 (1988) ------------------------------------------------------------------------- */ +#include "pair_tersoff_table.h" +#include #include -#include #include #include -#include "pair_tersoff_table.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-MISC/temper_grem.cpp b/src/USER-MISC/temper_grem.cpp index 031a449689150ffe24d6413213d2183dd5ac5521..d0e2fa56064ce2f53b3ff9b42e80d0d1a46d48b5 100644 --- a/src/USER-MISC/temper_grem.cpp +++ b/src/USER-MISC/temper_grem.cpp @@ -15,26 +15,21 @@ Contributing author: David Stelter (BU) ------------------------------------------------------------------------- */ +#include "temper_grem.h" #include -#include #include -#include "temper_grem.h" #include "fix_grem.h" #include "universe.h" #include "domain.h" -#include "atom.h" #include "update.h" #include "integrate.h" #include "modify.h" #include "compute.h" #include "force.h" -#include "output.h" -#include "thermo.h" #include "fix.h" #include "random_park.h" #include "finish.h" #include "timer.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/temper_npt.cpp b/src/USER-MISC/temper_npt.cpp index 7cf8fbab9b76d86e46c54ebfd9c17b77fc873d0e..9fd4bd6d067a377d558efc8c1989ea5825194265 100644 --- a/src/USER-MISC/temper_npt.cpp +++ b/src/USER-MISC/temper_npt.cpp @@ -17,10 +17,9 @@ Contact Email: amulyapervaje@gmail.com ------------------------------------------------------------------------- */ +#include "temper_npt.h" #include -#include #include -#include "temper_npt.h" #include "universe.h" #include "domain.h" #include "atom.h" @@ -29,13 +28,10 @@ #include "modify.h" #include "compute.h" #include "force.h" -#include "output.h" -#include "thermo.h" #include "fix.h" #include "random_park.h" #include "finish.h" #include "timer.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-MOFFF/angle_class2_p6.cpp b/src/USER-MOFFF/angle_class2_p6.cpp index e8e6f279def7751d890acf08055cd8886f178f39..bb0a01d546548830f271b2229128243bf5e9df07 100644 --- a/src/USER-MOFFF/angle_class2_p6.cpp +++ b/src/USER-MOFFF/angle_class2_p6.cpp @@ -16,10 +16,10 @@ and Rochus Schmid (Ruhr-Universitaet Bochum) ------------------------------------------------------------------------- */ +#include "angle_class2_p6.h" +#include #include #include -#include -#include "angle_class2_p6.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-MOFFF/angle_class2_p6.h b/src/USER-MOFFF/angle_class2_p6.h index b583a45b191d17b79f3f7537967331635c757c09..f2f324c0c6da40d997f041c90c5e652a7a9f3316 100644 --- a/src/USER-MOFFF/angle_class2_p6.h +++ b/src/USER-MOFFF/angle_class2_p6.h @@ -20,7 +20,6 @@ AngleStyle(class2/p6,AngleClass2P6) #ifndef LMP_ANGLE_CLASS2_P6_H #define LMP_ANGLE_CLASS2_P6_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MOFFF/angle_cosine_buck6d.cpp b/src/USER-MOFFF/angle_cosine_buck6d.cpp index 3829d2b8dc3aa577302f50726c8f9be3f7bce6f8..c17b2a1dba6469af89197cf09147a4022908f3ca 100644 --- a/src/USER-MOFFF/angle_cosine_buck6d.cpp +++ b/src/USER-MOFFF/angle_cosine_buck6d.cpp @@ -16,9 +16,9 @@ and Rochus Schmid (Ruhr-Universitaet Bochum) ------------------------------------------------------------------------- */ -#include -#include #include "angle_cosine_buck6d.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" @@ -26,13 +26,11 @@ #include "force.h" #include "pair.h" #include "math_const.h" -#include "math_special.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; using namespace MathConst; -using namespace MathSpecial; #define SMALL 0.001 diff --git a/src/USER-MOFFF/angle_cosine_buck6d.h b/src/USER-MOFFF/angle_cosine_buck6d.h index 689b1634e02c935c126380682fcbcbea0f573633..1d0df1022815cc47138dbff815c1f9582dbb8678 100644 --- a/src/USER-MOFFF/angle_cosine_buck6d.h +++ b/src/USER-MOFFF/angle_cosine_buck6d.h @@ -20,7 +20,6 @@ AngleStyle(cosine/buck6d, AngleCosineBuck6d) #ifndef LMP_ANGLE_COSINE_BUCK6D_H #define LMP_ANGLE_COSINE_BUCK6D_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MOFFF/improper_inversion_harmonic.cpp b/src/USER-MOFFF/improper_inversion_harmonic.cpp index 3f1e61e54a16d45d25e964b1c32f6a0d931ba3b7..12f7062ccc9eca3ab385ad1e35a9d094013aa1cc 100644 --- a/src/USER-MOFFF/improper_inversion_harmonic.cpp +++ b/src/USER-MOFFF/improper_inversion_harmonic.cpp @@ -19,17 +19,13 @@ [ abbreviated from and verified via DLPOLY2.0 ] ------------------------------------------------------------------------- */ +#include "improper_inversion_harmonic.h" #include #include -#include -#include -#include "improper_inversion_harmonic.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" -#include "update.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MOFFF/improper_inversion_harmonic.h b/src/USER-MOFFF/improper_inversion_harmonic.h index 201c9e358d3d2d392dd856c9468595d2c9d53090..206b40aebfd1ba60e2b20bcb4f47d8e4de7dc367 100644 --- a/src/USER-MOFFF/improper_inversion_harmonic.h +++ b/src/USER-MOFFF/improper_inversion_harmonic.h @@ -20,7 +20,6 @@ ImproperStyle(inversion/harmonic,ImproperInversionHarmonic) #ifndef LMP_IMPROPER_INVERSION_HARMONIC_H #define LMP_IMPROPER_INVERSION_HARMONIC_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp index 282bb0c58f4aa60111ac2ee0677a06a3823fdc9d..9c917d1c191ed97a925fdf1437f7a77adf009633 100644 --- a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp +++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp @@ -18,11 +18,9 @@ Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ +#include "pair_buck6d_coul_gauss_dsf.h" #include -#include -#include #include -#include "pair_buck6d_coul_gauss_dsf.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp index d6a4121d21015d9ed39b2b2af2bea7118957b555..953507ce21396eca7e76292b957fffe5db9faf57 100644 --- a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp +++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp @@ -17,11 +17,10 @@ References: Bureekaew and Schmid, Phys. Status Solidi B 250, 1128 (2013) ------------------------------------------------------------------------- */ +#include "pair_buck6d_coul_gauss_long.h" +#include #include -#include -#include #include -#include "pair_buck6d_coul_gauss_long.h" #include "atom.h" #include "comm.h" #include "force.h" @@ -29,12 +28,10 @@ #include "neighbor.h" #include "neigh_list.h" #include "memory.h" -#include "math_const.h" #include "error.h" #include "math_special.h" using namespace LAMMPS_NS; -using namespace MathConst; #define EWALD_F 1.12837917 diff --git a/src/USER-MOLFILE/dump_molfile.cpp b/src/USER-MOLFILE/dump_molfile.cpp index 732fea74bde61ae3a3fd4ba5bd6779cbeb1711db..d9d8ec3c97aaa9de218508454c6c38cdfda663bd 100644 --- a/src/USER-MOLFILE/dump_molfile.cpp +++ b/src/USER-MOLFILE/dump_molfile.cpp @@ -15,15 +15,14 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include "dump_molfile.h" +#include #include #include -#include "dump_molfile.h" #include "domain.h" #include "atom.h" #include "comm.h" #include "update.h" -#include "output.h" #include "group.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MOLFILE/reader_molfile.cpp b/src/USER-MOLFILE/reader_molfile.cpp index ca1a61850c91e7789e36c48d4cec4ee39926ec84..5cff56753b2bbc951d75806eb7a945a7051ea5c6 100644 --- a/src/USER-MOLFILE/reader_molfile.cpp +++ b/src/USER-MOLFILE/reader_molfile.cpp @@ -15,11 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include "reader_molfile.h" #include #include -#include "reader_molfile.h" -#include "atom.h" #include "comm.h" #include "memory.h" #include "error.h" diff --git a/src/USER-OMP/angle_charmm_omp.cpp b/src/USER-OMP/angle_charmm_omp.cpp index 118ba00226ae8f81ebacad7b63cbfff89587ae11..f135446915a998d219fb2b410e2ecc31e1b51f82 100644 --- a/src/USER-OMP/angle_charmm_omp.cpp +++ b/src/USER-OMP/angle_charmm_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_charmm_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_class2_omp.cpp b/src/USER-OMP/angle_class2_omp.cpp index e072d136e19f02ac31b851992288d07fa419b358..0cf54896630d19fb946015b59a5eef51069582db 100644 --- a/src/USER-OMP/angle_class2_omp.cpp +++ b/src/USER-OMP/angle_class2_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_class2_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_cosine_delta_omp.cpp b/src/USER-OMP/angle_cosine_delta_omp.cpp index a6dfb20433f9b6723c8d914ffe7c0626c49ec7dc..7f4d994c4fe2c61b05014ad88a661a60a855c626 100644 --- a/src/USER-OMP/angle_cosine_delta_omp.cpp +++ b/src/USER-OMP/angle_cosine_delta_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_delta_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_cosine_omp.cpp b/src/USER-OMP/angle_cosine_omp.cpp index 9097c8569c3c013136c37df68696c73fbacb4794..0543c947995e2bdb5a9e7b9cdb2a5cceccf3950f 100644 --- a/src/USER-OMP/angle_cosine_omp.cpp +++ b/src/USER-OMP/angle_cosine_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_cosine_periodic_omp.cpp b/src/USER-OMP/angle_cosine_periodic_omp.cpp index 3fcea7ad1d1023cc5415c49e9067455e372c0ae0..907315f83bbd5945fd7e4be709c6aaffda57adbb 100644 --- a/src/USER-OMP/angle_cosine_periodic_omp.cpp +++ b/src/USER-OMP/angle_cosine_periodic_omp.cpp @@ -16,20 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_periodic_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" +#include "timer.h" #include "math_special.h" -#include - #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace MathSpecial; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp index 6bd2feb023b008840b352b5066dfb692e6a56850..6c42319905f36bb161e13200459863846ac9b52e 100644 --- a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp +++ b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_shift_exp_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_cosine_shift_omp.cpp b/src/USER-OMP/angle_cosine_shift_omp.cpp index 56486faac1dd7362ce285a02f779999cfc6be03e..5c0afcf316f16930a26345e0dddc00806db658fa 100644 --- a/src/USER-OMP/angle_cosine_shift_omp.cpp +++ b/src/USER-OMP/angle_cosine_shift_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_shift_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_cosine_squared_omp.cpp b/src/USER-OMP/angle_cosine_squared_omp.cpp index 6dd2a3bb3b8217167f5e61045de48857771a2b97..27c47b90d8186324682c59d253593887cfbca27a 100644 --- a/src/USER-OMP/angle_cosine_squared_omp.cpp +++ b/src/USER-OMP/angle_cosine_squared_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_squared_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_dipole_omp.cpp b/src/USER-OMP/angle_dipole_omp.cpp index da2e819ee2ef22754d6741d72cd69cfb3263a5f0..6af5b44a033bcfd7e2ee7c300a6184f1bd108fc3 100644 --- a/src/USER-OMP/angle_dipole_omp.cpp +++ b/src/USER-OMP/angle_dipole_omp.cpp @@ -16,20 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_dipole_omp.h" +#include #include "atom.h" #include "comm.h" #include "error.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_fourier_omp.cpp b/src/USER-OMP/angle_fourier_omp.cpp index b2f9b47e05446564b342f3e1a5b04b310a45dc9e..98527c202809cc9afe4c1f8603d6d8c1e807521a 100644 --- a/src/USER-OMP/angle_fourier_omp.cpp +++ b/src/USER-OMP/angle_fourier_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_fourier_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_fourier_simple_omp.cpp b/src/USER-OMP/angle_fourier_simple_omp.cpp index 93532a30e560c78de51cf0c4998e3494c52ef2a6..71d0197b725a6b0fd29bcce8695c5554d2ba2168 100644 --- a/src/USER-OMP/angle_fourier_simple_omp.cpp +++ b/src/USER-OMP/angle_fourier_simple_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_fourier_simple_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_harmonic_omp.cpp b/src/USER-OMP/angle_harmonic_omp.cpp index 824b25428730a8deb9c1fd34a2c5ba6de9a0a236..ee08bbd8adfc553e9a198bca93175a43be2dc299 100644 --- a/src/USER-OMP/angle_harmonic_omp.cpp +++ b/src/USER-OMP/angle_harmonic_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_harmonic_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_quartic_omp.cpp b/src/USER-OMP/angle_quartic_omp.cpp index fff08ddb3993e9a8ab82fdc3a824eea91fab8c7d..57459482228304c9ef646455bb87233e667bc0f9 100644 --- a/src/USER-OMP/angle_quartic_omp.cpp +++ b/src/USER-OMP/angle_quartic_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_quartic_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_sdk_omp.cpp b/src/USER-OMP/angle_sdk_omp.cpp index e8c762092ceefd89ff642a3d57eb00b6c446cad4..e0b1da0baf7579d69b9f83310f2e363a16ab81fa 100644 --- a/src/USER-OMP/angle_sdk_omp.cpp +++ b/src/USER-OMP/angle_sdk_omp.cpp @@ -16,20 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_sdk_omp.h" +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "comm.h" #include "force.h" -#include "math_const.h" - -#include - #include "lj_sdk_common.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace LJSDKParms; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_table_omp.cpp b/src/USER-OMP/angle_table_omp.cpp index d9d80b744d3bf56a3874250ad8098726864a47b5..4f6edf2073956e1c689027637b9e3ebdecc72b18 100644 --- a/src/USER-OMP/angle_table_omp.cpp +++ b/src/USER-OMP/angle_table_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_table_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/bond_class2_omp.cpp b/src/USER-OMP/bond_class2_omp.cpp index fdd73c20b003605ce33e337de78a8daa84b79ce2..7d1b693faf7f51d494550f0358ac1b0f9d328532 100644 --- a/src/USER-OMP/bond_class2_omp.cpp +++ b/src/USER-OMP/bond_class2_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_fene_expand_omp.cpp b/src/USER-OMP/bond_fene_expand_omp.cpp index a8eec117608adc6f99ce73232d9143200311e472..aefae6dcf70a7668bc29dfd3dda91b2bed722b49 100644 --- a/src/USER-OMP/bond_fene_expand_omp.cpp +++ b/src/USER-OMP/bond_fene_expand_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "error.h" #include "update.h" diff --git a/src/USER-OMP/bond_fene_omp.cpp b/src/USER-OMP/bond_fene_omp.cpp index be7dcd4b49c6cc0907999c56655f5a315cb829b5..2b579114ba48258c2a87025024aa6e284ddc85ed 100644 --- a/src/USER-OMP/bond_fene_omp.cpp +++ b/src/USER-OMP/bond_fene_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "error.h" #include "update.h" diff --git a/src/USER-OMP/bond_gromos_omp.cpp b/src/USER-OMP/bond_gromos_omp.cpp index 8f0926c0e96b5d9145f4228f73ce1abdda0a71f3..ba23217a1f47856af9294ca80aafbbf17bad506f 100644 --- a/src/USER-OMP/bond_gromos_omp.cpp +++ b/src/USER-OMP/bond_gromos_omp.cpp @@ -20,9 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_harmonic_omp.cpp b/src/USER-OMP/bond_harmonic_omp.cpp index a3bb69c53c2d6ab84bce3fe99cffa0104c2cdf82..5515284f9a39d9dc053a1a99d691b150f14c0e60 100644 --- a/src/USER-OMP/bond_harmonic_omp.cpp +++ b/src/USER-OMP/bond_harmonic_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp index 5c16e27a32fffd14f967777f198cad1e76beb27f..a871fa8c0471f5eefcdb8bade0a19d908fc71552 100644 --- a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp +++ b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_harmonic_shift_omp.cpp b/src/USER-OMP/bond_harmonic_shift_omp.cpp index 39e957c137d5d190c313207faf54865350efadca..4117da9159b85ca603605a91e380baa9c8762c36 100644 --- a/src/USER-OMP/bond_harmonic_shift_omp.cpp +++ b/src/USER-OMP/bond_harmonic_shift_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_morse_omp.cpp b/src/USER-OMP/bond_morse_omp.cpp index c0203de0d6e71e33ea4dac17c39528d5ac2b63d5..e6526dc8dc598f07fca411578d9080d6559c0304 100644 --- a/src/USER-OMP/bond_morse_omp.cpp +++ b/src/USER-OMP/bond_morse_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_nonlinear_omp.cpp b/src/USER-OMP/bond_nonlinear_omp.cpp index 8fa3daf8abd77a69e3467c34b0f86884a2662cd3..0d1a6484156538dca62791d1fbf1bec4fbb33005 100644 --- a/src/USER-OMP/bond_nonlinear_omp.cpp +++ b/src/USER-OMP/bond_nonlinear_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_quartic_omp.cpp b/src/USER-OMP/bond_quartic_omp.cpp index fd0ccaf79d3e921599583ff33bb962ef9f931f67..60d3a5601c71c4d34737ca27aafdd8108090de6e 100644 --- a/src/USER-OMP/bond_quartic_omp.cpp +++ b/src/USER-OMP/bond_quartic_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "pair.h" #include diff --git a/src/USER-OMP/bond_table_omp.cpp b/src/USER-OMP/bond_table_omp.cpp index 1616988385a0861272c9749b7344c8993ef9ce1d..8e1e792c7377d242a8d93fed2e68c2c03890ed74 100644 --- a/src/USER-OMP/bond_table_omp.cpp +++ b/src/USER-OMP/bond_table_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/dihedral_charmm_omp.cpp b/src/USER-OMP/dihedral_charmm_omp.cpp index b09863613ed6a367953744d9ebb876e793bdeef9..95ad9af6a62bba294ecf682d05649bc10ab4f580 100644 --- a/src/USER-OMP/dihedral_charmm_omp.cpp +++ b/src/USER-OMP/dihedral_charmm_omp.cpp @@ -15,13 +15,12 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include #include "dihedral_charmm_omp.h" +#include #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "pair.h" #include "update.h" diff --git a/src/USER-OMP/dihedral_class2_omp.cpp b/src/USER-OMP/dihedral_class2_omp.cpp index 03ac9d9babbdd50662579cf6b9cb7e085f71260f..6c2bc02ff405fc1f129e9d94ee795237553f9c4e 100644 --- a/src/USER-OMP/dihedral_class2_omp.cpp +++ b/src/USER-OMP/dihedral_class2_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp index c64cad9fc3c61a36274dee57124c6a3eff187607..d77e9d6b3e0518fcf8034f9c082041327cb92f2a 100644 --- a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp +++ b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_fourier_omp.cpp b/src/USER-OMP/dihedral_fourier_omp.cpp index 94bdae3795c104a7ddaa952cc133586f6efc2a73..93dbd773cad07b16de20e5439c163292ff57f4ba 100644 --- a/src/USER-OMP/dihedral_fourier_omp.cpp +++ b/src/USER-OMP/dihedral_fourier_omp.cpp @@ -15,20 +15,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "dihedral_fourier_omp.h" +#include #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" -#include "math_const.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define TOLERANCE 0.05 diff --git a/src/USER-OMP/dihedral_harmonic_omp.cpp b/src/USER-OMP/dihedral_harmonic_omp.cpp index 10ccbd3d9f67d2b9fe14018f8cc9e6f068e6b752..84aa584d9ebb44bffaae9b73b1b5728a949e6747 100644 --- a/src/USER-OMP/dihedral_harmonic_omp.cpp +++ b/src/USER-OMP/dihedral_harmonic_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_helix_omp.cpp b/src/USER-OMP/dihedral_helix_omp.cpp index 8c8e29cac0e6f6b9002b2919d5bd59984b5e2136..51b07754e2ff4d3b338be7599cd39146709be159 100644 --- a/src/USER-OMP/dihedral_helix_omp.cpp +++ b/src/USER-OMP/dihedral_helix_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "math_const.h" diff --git a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp index 38961e1746b197e55617c41ec207297fc89d4857..4cb6919a961c330ee45d5bc97dbf09be2c120ea7 100644 --- a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp +++ b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_nharmonic_omp.cpp b/src/USER-OMP/dihedral_nharmonic_omp.cpp index e74238265ddb65b8f3c787c5a08e8dd35788c808..203884531bf3fc2f9dd8f8d537bd7d2975042ea7 100644 --- a/src/USER-OMP/dihedral_nharmonic_omp.cpp +++ b/src/USER-OMP/dihedral_nharmonic_omp.cpp @@ -20,10 +20,10 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "error.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/dihedral_opls_omp.cpp b/src/USER-OMP/dihedral_opls_omp.cpp index 64eaffe6fe00753804fe592929bd6352401387f9..af12bb866eabc1875e49c263c2be7288439c863c 100644 --- a/src/USER-OMP/dihedral_opls_omp.cpp +++ b/src/USER-OMP/dihedral_opls_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_quadratic_omp.cpp b/src/USER-OMP/dihedral_quadratic_omp.cpp index 8df622b8475792d6d1e44de4c3f4baa9a10b76a0..8cea62aaea7515d5ed6c3c00836cf99626d2f3f3 100644 --- a/src/USER-OMP/dihedral_quadratic_omp.cpp +++ b/src/USER-OMP/dihedral_quadratic_omp.cpp @@ -20,10 +20,10 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "error.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/dihedral_table_omp.cpp b/src/USER-OMP/dihedral_table_omp.cpp index 792ee90c261394b5717cae06c2ca65b1af4226a9..6b10027b9deca0479f1fe0a7ed346be14fc96c25 100644 --- a/src/USER-OMP/dihedral_table_omp.cpp +++ b/src/USER-OMP/dihedral_table_omp.cpp @@ -15,19 +15,14 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include - #include "dihedral_table_omp.h" +#include #include "atom.h" #include "comm.h" -#include "neighbor.h" #include "domain.h" +#include "neighbor.h" #include "force.h" -#include "update.h" -#include "error.h" - +#include "timer.h" #include "math_const.h" #include "math_extra.h" diff --git a/src/USER-OMP/domain_omp.cpp b/src/USER-OMP/domain_omp.cpp index 584e56b1f0e6995bad4258a7e9eefd31dc8ca780..a18931c551fb39714f7bc2bebfcf0c4ff91cd6fc 100644 --- a/src/USER-OMP/domain_omp.cpp +++ b/src/USER-OMP/domain_omp.cpp @@ -15,7 +15,6 @@ Contributing author : Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "domain.h" #include "accelerator_omp.h" #include "atom.h" diff --git a/src/USER-OMP/ewald_omp.cpp b/src/USER-OMP/ewald_omp.cpp index b56fc25142d45ebf7e6b8cf6d1bc5f91fd44bcf2..aadf63741d8a41fdbe4af83814075017b9570857 100644 --- a/src/USER-OMP/ewald_omp.cpp +++ b/src/USER-OMP/ewald_omp.cpp @@ -15,15 +15,14 @@ Contributing authors: Roy Pollock (LLNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include #include "ewald_omp.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" - -#include - +#include "timer.h" #include "math_const.h" #include "suffix.h" diff --git a/src/USER-OMP/fix_gravity_omp.cpp b/src/USER-OMP/fix_gravity_omp.cpp index eae918ec5250c905053f42c8ea850d2345ba7f7e..fa6b698821aeb11690b7035eec43a440728dd065 100644 --- a/src/USER-OMP/fix_gravity_omp.cpp +++ b/src/USER-OMP/fix_gravity_omp.cpp @@ -15,19 +15,12 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_gravity_omp.h" #include "atom.h" #include "update.h" -#include "domain.h" #include "input.h" #include "modify.h" -#include "respa.h" #include "variable.h" -#include "error.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_neigh_history_omp.cpp b/src/USER-OMP/fix_neigh_history_omp.cpp index efa7f5a3f1697499824d93a1b62a74b251b46bdc..c2bc8af5e07364f9afeca1b2de2edb31551a8d3a 100644 --- a/src/USER-OMP/fix_neigh_history_omp.cpp +++ b/src/USER-OMP/fix_neigh_history_omp.cpp @@ -11,18 +11,14 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_neigh_history_omp.h" +#include +#include "my_page.h" #include "atom.h" #include "comm.h" -#include "neighbor.h" #include "neigh_list.h" -#include "force.h" #include "pair.h" -#include "update.h" #include "memory.h" -#include "modify.h" #include "error.h" #if defined(_OPENMP) diff --git a/src/USER-OMP/fix_nh_omp.cpp b/src/USER-OMP/fix_nh_omp.cpp index 76a47b71fdf7c86b0ead410c639e82050523ef44..2abd739f717368165c6d7371dc30f73af0abc71b 100644 --- a/src/USER-OMP/fix_nh_omp.cpp +++ b/src/USER-OMP/fix_nh_omp.cpp @@ -16,15 +16,13 @@ ------------------------------------------------------------------------- */ #include "fix_nh_omp.h" +#include #include "atom.h" #include "compute.h" #include "domain.h" #include "error.h" #include "modify.h" -#include -#include - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_nh_sphere_omp.cpp b/src/USER-OMP/fix_nh_sphere_omp.cpp index a32f0f8b51e3d4a91e3d866cd04afbe5e1520223..64bc536bb0e3ac792eecf00276d53b1173b76b3b 100644 --- a/src/USER-OMP/fix_nh_sphere_omp.cpp +++ b/src/USER-OMP/fix_nh_sphere_omp.cpp @@ -15,12 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "fix_nh_sphere_omp.h" #include "atom.h" -#include "atom_vec.h" #include "compute.h" -#include "group.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/fix_nve_omp.cpp b/src/USER-OMP/fix_nve_omp.cpp index c61ad7155c10194d242719cd4895c4a8dd52ee23..61ed82b16fbc1b918fede4c5632617c9137c9b11 100644 --- a/src/USER-OMP/fix_nve_omp.cpp +++ b/src/USER-OMP/fix_nve_omp.cpp @@ -13,7 +13,6 @@ #include "fix_nve_omp.h" #include "atom.h" -#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_nve_sphere_omp.cpp b/src/USER-OMP/fix_nve_sphere_omp.cpp index 2286120bee01328de42d248d195c868985925441..ccdd65487445d3ee9735a78ca02386a2f6a6c4a2 100644 --- a/src/USER-OMP/fix_nve_sphere_omp.cpp +++ b/src/USER-OMP/fix_nve_sphere_omp.cpp @@ -11,16 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nve_sphere_omp.h" +#include #include "atom.h" -#include "atom_vec.h" -#include "update.h" -#include "respa.h" #include "force.h" -#include "error.h" #include "math_vector.h" #include "math_extra.h" diff --git a/src/USER-OMP/fix_nvt_sllod_omp.cpp b/src/USER-OMP/fix_nvt_sllod_omp.cpp index e439647c12ed563312f40aa8351f2b92591696d2..208dfb943202389da052d1bac6fcd4191f1e755d 100644 --- a/src/USER-OMP/fix_nvt_sllod_omp.cpp +++ b/src/USER-OMP/fix_nvt_sllod_omp.cpp @@ -15,18 +15,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include #include "fix_nvt_sllod_omp.h" +#include #include "math_extra.h" #include "atom.h" -#include "domain.h" #include "group.h" #include "modify.h" #include "fix.h" #include "fix_deform.h" #include "compute.h" #include "error.h" +#include "domain.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_omp.cpp b/src/USER-OMP/fix_omp.cpp index a4587b1c145555607b0cd9bfe9ddade6c78f3e09..1fca1e739bb24e0f8767044e5d736f42c92e2a75 100644 --- a/src/USER-OMP/fix_omp.cpp +++ b/src/USER-OMP/fix_omp.cpp @@ -24,13 +24,10 @@ #include "neigh_request.h" #include "universe.h" #include "update.h" -#include "integrate.h" -#include "min.h" #include "timer.h" #include "fix_omp.h" #include "thr_data.h" -#include "thr_omp.h" #include "pair_hybrid.h" #include "bond_hybrid.h" @@ -40,8 +37,11 @@ #include "kspace.h" #include -#include -#include + +#if defined(_OPENMP) +#include +#endif + #include "suffix.h" diff --git a/src/USER-OMP/fix_qeq_comb_omp.cpp b/src/USER-OMP/fix_qeq_comb_omp.cpp index 2f0a90a790efe9002c08a154b7786c7405d0b2ec..b0573dfa971151ce4aa05d2c3ef56dcf2f0f7e84 100644 --- a/src/USER-OMP/fix_qeq_comb_omp.cpp +++ b/src/USER-OMP/fix_qeq_comb_omp.cpp @@ -15,24 +15,20 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "fix_qeq_comb_omp.h" #include #include #include -#include "fix_qeq_comb_omp.h" -#include "fix_omp.h" +#include "pair_comb.h" #include "atom.h" #include "comm.h" #include "force.h" #include "group.h" #include "memory.h" -#include "modify.h" #include "error.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "respa.h" #include "update.h" -#include "pair_comb_omp.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_qeq_reax_omp.cpp b/src/USER-OMP/fix_qeq_reax_omp.cpp index 45da91305d7d8059ecf0b688731c73d54ef6a981..f7945b55793ffea910aad4c4e97ef6715ca12efd 100644 --- a/src/USER-OMP/fix_qeq_reax_omp.cpp +++ b/src/USER-OMP/fix_qeq_reax_omp.cpp @@ -31,26 +31,22 @@ High Performance Computing Applications, to appear. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_qeq_reax_omp.h" -#include "pair_reaxc_omp.h" +#include +#include +#include "pair_reaxc.h" #include "atom.h" #include "comm.h" -#include "domain.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "update.h" -#include "force.h" -#include "group.h" -#include "pair.h" -#include "respa.h" #include "memory.h" #include "error.h" #include "reaxc_defs.h" +#include "reaxc_types.h" + +#if defined(_OPENMP) +#include +#endif using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp index 53d013474104725d33b9f5ad8a4e83d33cd0d140..74b2a9277541dcabddf1786b1f57259506737bbc 100644 --- a/src/USER-OMP/fix_rigid_nh_omp.cpp +++ b/src/USER-OMP/fix_rigid_nh_omp.cpp @@ -16,7 +16,8 @@ ------------------------------------------------------------------------- */ #include "fix_rigid_nh_omp.h" - +#include +#include #include "atom.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" @@ -24,12 +25,12 @@ #include "comm.h" #include "compute.h" #include "domain.h" +#include "error.h" #include "force.h" #include "kspace.h" #include "modify.h" #include "update.h" - -#include +#include "timer.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/fix_rigid_nph_omp.cpp b/src/USER-OMP/fix_rigid_nph_omp.cpp index 7db45ed9bf414a4b0c417a47b08945c8f9ba1a91..31d53868c8155f68af26e4b22014c98ccb0a7ffc 100644 --- a/src/USER-OMP/fix_rigid_nph_omp.cpp +++ b/src/USER-OMP/fix_rigid_nph_omp.cpp @@ -17,9 +17,8 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include #include "fix_rigid_nph_omp.h" -#include "domain.h" +#include #include "modify.h" #include "error.h" diff --git a/src/USER-OMP/fix_rigid_npt_omp.cpp b/src/USER-OMP/fix_rigid_npt_omp.cpp index a041706f388890decd8c834021553e9eb18ddec2..1e7c139d522aef83ffbf55c791915a79edea9937 100644 --- a/src/USER-OMP/fix_rigid_npt_omp.cpp +++ b/src/USER-OMP/fix_rigid_npt_omp.cpp @@ -17,9 +17,8 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include #include "fix_rigid_npt_omp.h" -#include "domain.h" +#include #include "modify.h" #include "error.h" diff --git a/src/USER-OMP/fix_rigid_omp.cpp b/src/USER-OMP/fix_rigid_omp.cpp index 12c6362ed8bd4803e76e07c1b8e54dec5a74f8d5..b807ddba7c0432edf7b37d69bc342f32783c556a 100644 --- a/src/USER-OMP/fix_rigid_omp.cpp +++ b/src/USER-OMP/fix_rigid_omp.cpp @@ -16,16 +16,17 @@ ------------------------------------------------------------------------- */ #include "fix_rigid_omp.h" - +#include +#include +#include #include "atom.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" #include "comm.h" +#include "error.h" #include "domain.h" -#include - #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/fix_rigid_small_omp.cpp b/src/USER-OMP/fix_rigid_small_omp.cpp index a0495b3b933a4fa5a852b079dfd5936cb8b10088..41f6c53e40bcdf366bb01ee85f23adac692b08e6 100644 --- a/src/USER-OMP/fix_rigid_small_omp.cpp +++ b/src/USER-OMP/fix_rigid_small_omp.cpp @@ -16,15 +16,14 @@ ------------------------------------------------------------------------- */ #include "fix_rigid_small_omp.h" - +#include #include "atom.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" #include "comm.h" #include "domain.h" - -#include +#include "timer.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/improper_class2_omp.cpp b/src/USER-OMP/improper_class2_omp.cpp index c2b493f425b0df8a116b1d803f6f0b994d1eabcc..3bff179b4482207ff04c44e944cfbefc97875bf1 100644 --- a/src/USER-OMP/improper_class2_omp.cpp +++ b/src/USER-OMP/improper_class2_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_cossq_omp.cpp b/src/USER-OMP/improper_cossq_omp.cpp index 3b328e5b78a054d9141658efccf303976147fd77..0f99f2732fb005369184d223a76450dc1f8c36a0 100644 --- a/src/USER-OMP/improper_cossq_omp.cpp +++ b/src/USER-OMP/improper_cossq_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_cvff_omp.cpp b/src/USER-OMP/improper_cvff_omp.cpp index fe1fc45bec8179f1c7c8bde19bcac4e469e99d44..fdc29c74b10734e523b18085eddca2120d625500 100644 --- a/src/USER-OMP/improper_cvff_omp.cpp +++ b/src/USER-OMP/improper_cvff_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_fourier_omp.cpp b/src/USER-OMP/improper_fourier_omp.cpp index b5af428cb97caa9c3a9fa885752b0e810f55eafe..b49b895c78f892b962a0cc23ae559879248f2fc7 100644 --- a/src/USER-OMP/improper_fourier_omp.cpp +++ b/src/USER-OMP/improper_fourier_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_harmonic_omp.cpp b/src/USER-OMP/improper_harmonic_omp.cpp index 6e02d0968e832068ef8a344cdc11641f9216946d..32e837fdfe3e14f32c47c4dce6ef42017041a72d 100644 --- a/src/USER-OMP/improper_harmonic_omp.cpp +++ b/src/USER-OMP/improper_harmonic_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_ring_omp.cpp b/src/USER-OMP/improper_ring_omp.cpp index e198b993376154dacf288635517f9884eb45919d..c8fe685faa5b1168bd5c4dbeb82b37955236e1cc 100644 --- a/src/USER-OMP/improper_ring_omp.cpp +++ b/src/USER-OMP/improper_ring_omp.cpp @@ -15,15 +15,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "improper_ring_omp.h" +#include #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" -#include "update.h" -#include "error.h" #include "math_special.h" #include "suffix.h" diff --git a/src/USER-OMP/improper_umbrella_omp.cpp b/src/USER-OMP/improper_umbrella_omp.cpp index ceaca3507472fe91770ac93301abd17560b98a91..f3fdf4570f36e59d6351c514864809f22f48a991 100644 --- a/src/USER-OMP/improper_umbrella_omp.cpp +++ b/src/USER-OMP/improper_umbrella_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/msm_cg_omp.cpp b/src/USER-OMP/msm_cg_omp.cpp index 8a920e05d57f5a4927f8c40e4f56e648b5ae1be0..3c5439db5d93cc341c0f1b102131fc48868e58b8 100644 --- a/src/USER-OMP/msm_cg_omp.cpp +++ b/src/USER-OMP/msm_cg_omp.cpp @@ -16,10 +16,10 @@ Original MSM class by: Paul Crozier, Stan Moore, Stephen Bond, (all SNL) ------------------------------------------------------------------------- */ +#include "msm_cg_omp.h" #include #include #include -#include #include #include "atom.h" @@ -29,12 +29,14 @@ #include "force.h" #include "neighbor.h" #include "memory.h" -#include "msm_cg_omp.h" +#include "thr_omp.h" +#include "timer.h" -#include "math_const.h" +#if defined(_OPENMP) +#include +#endif using namespace LAMMPS_NS; -using namespace MathConst; #define OFFSET 16384 #define SMALLQ 0.00001 diff --git a/src/USER-OMP/msm_omp.cpp b/src/USER-OMP/msm_omp.cpp index 74cbb56be7f27f957aa50e800521ef86eee584b2..81f84e8f6f8ce1d992698b10fe07c4c3b98c3ddb 100644 --- a/src/USER-OMP/msm_omp.cpp +++ b/src/USER-OMP/msm_omp.cpp @@ -16,15 +16,11 @@ ------------------------------------------------------------------------- */ #include "msm_omp.h" -#include "atom.h" +#include #include "comm.h" #include "domain.h" #include "error.h" -#include "force.h" -#include "memory.h" -#include "math_const.h" - -#include +#include "timer.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/npair_full_bin_atomonly_omp.cpp b/src/USER-OMP/npair_full_bin_atomonly_omp.cpp index d9e0fb9297287a87fadcb5b614099a1326453fb5..3bda2e4c5a822982f7c08425cfe39f6e165cf0ae 100644 --- a/src/USER-OMP/npair_full_bin_atomonly_omp.cpp +++ b/src/USER-OMP/npair_full_bin_atomonly_omp.cpp @@ -13,16 +13,13 @@ #include "npair_full_bin_atomonly_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "domain.h" #include "my_page.h" #include "error.h" using namespace LAMMPS_NS; -using namespace NeighConst; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/npair_full_bin_ghost_omp.cpp b/src/USER-OMP/npair_full_bin_ghost_omp.cpp index b915aca002a68ee7893aa18269a8128349b97a89..b0b0070df59e9a03478f2326ef6e28fdf3141e29 100644 --- a/src/USER-OMP/npair_full_bin_ghost_omp.cpp +++ b/src/USER-OMP/npair_full_bin_ghost_omp.cpp @@ -13,7 +13,6 @@ #include "npair_full_bin_ghost_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -23,7 +22,6 @@ #include "error.h" using namespace LAMMPS_NS; -using namespace NeighConst; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/npair_full_bin_omp.cpp b/src/USER-OMP/npair_full_bin_omp.cpp index e1f75c06e2a8f36d245cfa7b6589b2628eb6a159..d3e30b49324c9379e291f4cb78e1320e46c748f1 100644 --- a/src/USER-OMP/npair_full_bin_omp.cpp +++ b/src/USER-OMP/npair_full_bin_omp.cpp @@ -13,7 +13,6 @@ #include "npair_full_bin_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -23,7 +22,6 @@ #include "error.h" using namespace LAMMPS_NS; -using namespace NeighConst; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/npair_full_multi_omp.cpp b/src/USER-OMP/npair_full_multi_omp.cpp index 9bc196e17a1a39cda046bd1fe6b7327c64dd345c..707db2edcfc0fa4cd4bed94283a748071f98fbdf 100644 --- a/src/USER-OMP/npair_full_multi_omp.cpp +++ b/src/USER-OMP/npair_full_multi_omp.cpp @@ -13,7 +13,6 @@ #include "npair_full_multi_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -23,7 +22,6 @@ #include "error.h" using namespace LAMMPS_NS; -using namespace NeighConst; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/npair_full_nsq_ghost_omp.cpp b/src/USER-OMP/npair_full_nsq_ghost_omp.cpp index b33f76bb22fef32feae0d98be04c5f5bb3f96234..527df58fd66ba60414758bdc7ebfbbabb6a31c4b 100644 --- a/src/USER-OMP/npair_full_nsq_ghost_omp.cpp +++ b/src/USER-OMP/npair_full_nsq_ghost_omp.cpp @@ -13,7 +13,6 @@ #include "npair_full_nsq_ghost_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -23,7 +22,6 @@ #include "error.h" using namespace LAMMPS_NS; -using namespace NeighConst; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/npair_full_nsq_omp.cpp b/src/USER-OMP/npair_full_nsq_omp.cpp index 1d0f26d6388f9af0b92520d8e4aa7d5a62eaca29..2719f5dc2c075d9051c5dcac7f63b90b36681dfd 100644 --- a/src/USER-OMP/npair_full_nsq_omp.cpp +++ b/src/USER-OMP/npair_full_nsq_omp.cpp @@ -13,7 +13,6 @@ #include "npair_full_nsq_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -24,7 +23,6 @@ #include "error.h" using namespace LAMMPS_NS; -using namespace NeighConst; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp b/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp index 02d98ff6ab46691ba77643d7a812ad42f410b72d..a69779d96d6c86a7bbcb4cb10ca4bca26ba26c27 100644 --- a/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp +++ b/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp @@ -13,12 +13,9 @@ #include "npair_half_bin_atomonly_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp b/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp index 24fe75ec5576ae1021a7a2fc919cf62d6be38d52..5f8ffdab29ac4ee23aa0986383bda518e42b71da 100644 --- a/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp +++ b/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_bin_newtoff_ghost_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_bin_newtoff_omp.cpp index ff74b54d7d68dd258fc6be84b9b3e4c35852ad53..35807645cfe622f5d10dc5a7441e11839231464d 100644 --- a/src/USER-OMP/npair_half_bin_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_bin_newtoff_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_bin_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_bin_newton_omp.cpp b/src/USER-OMP/npair_half_bin_newton_omp.cpp index f7d969ba271a110edf8b83a631a48394ddb0ea63..2700d6863bfd47be498f29207eead212946f4d5b 100644 --- a/src/USER-OMP/npair_half_bin_newton_omp.cpp +++ b/src/USER-OMP/npair_half_bin_newton_omp.cpp @@ -13,11 +13,9 @@ #include "npair_half_bin_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "group.h" #include "molecule.h" #include "domain.h" #include "my_page.h" diff --git a/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp b/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp index c843d623cd44960b8f8ebaaf68142f8896e10acb..d94845898c2b7442b2926f7b9283c69bcfc5c7ae 100644 --- a/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_bin_newton_tri_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp index 705d1b8d9ff1ec53e44c240f6a9ab02b647f2f25..c06737dc1cb753f4110ceb08f88e7f88ae418935 100644 --- a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_multi_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_multi_newton_omp.cpp b/src/USER-OMP/npair_half_multi_newton_omp.cpp index f16dd027a0c26552494726af0b8e53730beffeb9..50df756be4857f3e8be95935deb31ec77cf85e76 100644 --- a/src/USER-OMP/npair_half_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_multi_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp index ce93e854855febab09e54f763311b3432b04788c..8b78b311dd917f38298b4bd0efe2809483ac7882 100644 --- a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_multi_newton_tri_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp b/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp index add4c44d9eb3ed13897f0786f9bf97447271ce9f..f0eb211425361736c144546d1d74e24f32311abc 100644 --- a/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp +++ b/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_nsq_newtoff_ghost_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp b/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp index 01da73cf1eb1365671eaea577d9cce2e95c0d62b..55b9f9e51260b4d8f22a3a3a4449bc396659e405 100644 --- a/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_nsq_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_nsq_newton_omp.cpp b/src/USER-OMP/npair_half_nsq_newton_omp.cpp index 3815b1b85bc77ff1828c702b4bd8f67c8d341b09..223da622e86d09b71f8bc7b614c998e94be33d0f 100644 --- a/src/USER-OMP/npair_half_nsq_newton_omp.cpp +++ b/src/USER-OMP/npair_half_nsq_newton_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_nsq_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp index f094691b71da6e7dc291bde662a88251f79e796a..9bb4d277fe02249ef08711522778571dae4f7485 100644 --- a/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_respa_bin_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp b/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp index de7ef5f7d52b4b04d11dde4a16212de34dee8941..9ed0ae482dab3ac8d1ed009bacd88c5e33364616 100644 --- a/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp +++ b/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_respa_bin_newton_omp.h" -#include "neighbor.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" diff --git a/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp b/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp index f20d101bc9dbc1f131e5a7435751ed471626266a..cd036849400e3cac72314419b93d67ae71ace78e 100644 --- a/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_respa_bin_newton_tri_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp b/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp index 0f726cdd7f322dafa176884f1510134a2ce5e6a3..b1e7467ec7ded49c4a5c56f063849e5c43235580 100644 --- a/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_respa_nsq_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp b/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp index 2783e1255eb1147a15c5ebc04a41905c0a6ac27f..c22965895da5b35e192e146c6a3a4a0d491feb55 100644 --- a/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp +++ b/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_respa_nsq_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp index dff2a762d51dd71b96fc84d98aa26d618acd2750..1b437482c4ae3a8b7731553e8e1d37d1aaf15de5 100644 --- a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_bin_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp index 3053b815946f59ffa07b2943da022374083f1c14..8e0581d4ce184f4258e31c5f91078f7e6ec65af9 100644 --- a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_bin_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp index b02bfa345e8b1b9ccceae4e55ba0c482df8e46a2..38a2c0d61ffe1bdb36f191861cf39df82f48d703 100644 --- a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_size_bin_newton_tri_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp index 717012b226e3dfb08292b40e029bdb65592450ce..d1505e1b2ef6f8d4f4cefe57850099c3a2192500 100644 --- a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_nsq_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp b/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp index 5a55029d30fd77e50349f2aa6214a38009588a86..9027b0728d7d9e35c3b56cfea08b303db218abd0 100644 --- a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_nsq_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_halffull_newtoff_omp.cpp b/src/USER-OMP/npair_halffull_newtoff_omp.cpp index 947e4e1ad2a3dca86e90858e206a705c1923e666..7d2fe4f109e3d49d8f4daeef88788c621ee76cec 100644 --- a/src/USER-OMP/npair_halffull_newtoff_omp.cpp +++ b/src/USER-OMP/npair_halffull_newtoff_omp.cpp @@ -13,12 +13,8 @@ #include "npair_halffull_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" -#include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/USER-OMP/npair_halffull_newton_omp.cpp b/src/USER-OMP/npair_halffull_newton_omp.cpp index 6e158d372d7967f363f06772feba7a230ad15940..3fcc8c2e9868a293dd99a2d68ab9b3560fccd1d5 100644 --- a/src/USER-OMP/npair_halffull_newton_omp.cpp +++ b/src/USER-OMP/npair_halffull_newton_omp.cpp @@ -13,12 +13,9 @@ #include "npair_halffull_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/USER-OMP/pair_beck_omp.cpp b/src/USER-OMP/pair_beck_omp.cpp index 90c37779329a65c90bf4604bb43a59b2c9eb8547..8d0605fae9f5b94452cde3f07ce5ec20685d29a2 100644 --- a/src/USER-OMP/pair_beck_omp.cpp +++ b/src/USER-OMP/pair_beck_omp.cpp @@ -12,14 +12,14 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_beck_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_special.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_born_coul_wolf_omp.cpp b/src/USER-OMP/pair_born_coul_wolf_omp.cpp index 567eddc9cb5e830e1ceefbeaf596f4e28b3c6e3d..55da972c4efc32292aef6231e0816f4826bdcd18 100644 --- a/src/USER-OMP/pair_born_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_born_coul_wolf_omp.cpp @@ -12,14 +12,14 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_born_coul_wolf_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_const.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_born_omp.cpp b/src/USER-OMP/pair_born_omp.cpp index fce2013745f4b241777f1c47a27473689249f6f3..35ad4fcb4868cf872b086451c6a1ba8be36bf3cd 100644 --- a/src/USER-OMP/pair_born_omp.cpp +++ b/src/USER-OMP/pair_born_omp.cpp @@ -12,13 +12,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_born_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_brownian_omp.cpp b/src/USER-OMP/pair_brownian_omp.cpp index cef9fb0955c7f313a572fdb8525b174be5c28cf2..6367976c7d2372715343fe576da1af66b73c845e 100644 --- a/src/USER-OMP/pair_brownian_omp.cpp +++ b/src/USER-OMP/pair_brownian_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_brownian_omp.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" @@ -26,6 +26,7 @@ #include "random_mars.h" #include "math_const.h" #include "math_special.h" +#include "timer.h" #include "fix_wall.h" diff --git a/src/USER-OMP/pair_brownian_poly_omp.cpp b/src/USER-OMP/pair_brownian_poly_omp.cpp index 239a82024272cb5e60b92596df10280dc5db8c52..dcb412463487a7e2d2f49ffa6d982e2b1399f533 100644 --- a/src/USER-OMP/pair_brownian_poly_omp.cpp +++ b/src/USER-OMP/pair_brownian_poly_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_brownian_poly_omp.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/USER-OMP/pair_buck_omp.cpp b/src/USER-OMP/pair_buck_omp.cpp index cc7e81b9c5084ed5c4145ef0d889197f73007ebf..8d5c80513a0a4862603fd8555152e1ac57d58425 100644 --- a/src/USER-OMP/pair_buck_omp.cpp +++ b/src/USER-OMP/pair_buck_omp.cpp @@ -12,13 +12,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_buck_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_coul_cut_omp.cpp b/src/USER-OMP/pair_coul_cut_omp.cpp index 056daf210a5ce678620777ceff3f672df4fe95ff..267beeecbd300b65914a2fe0228429bf5a865f95 100644 --- a/src/USER-OMP/pair_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_coul_cut_omp.cpp @@ -12,13 +12,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_coul_cut_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_coul_debye_omp.cpp b/src/USER-OMP/pair_coul_debye_omp.cpp index d202e314bfa65888960ccb19939abb89b3026734..4d3f92c495e34586bcb5e9ccdf5a2d7bacf71613 100644 --- a/src/USER-OMP/pair_coul_debye_omp.cpp +++ b/src/USER-OMP/pair_coul_debye_omp.cpp @@ -12,13 +12,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_coul_debye_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_coul_dsf_omp.cpp b/src/USER-OMP/pair_coul_dsf_omp.cpp index 217fb844c3f5d6e4466e34d336569bc0417e85a6..bd7f5cfed2f5f253f2f1b52a295c7833fa864abb 100644 --- a/src/USER-OMP/pair_coul_dsf_omp.cpp +++ b/src/USER-OMP/pair_coul_dsf_omp.cpp @@ -12,14 +12,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_coul_dsf_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - +#include "timer.h" #include "suffix.h" #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_coul_wolf_omp.cpp b/src/USER-OMP/pair_coul_wolf_omp.cpp index 0913a2b188a8f62fbc2fd8110d563449509b7f38..92d5bd7b159f13a39465899d2dc2eab79a4fd562 100644 --- a/src/USER-OMP/pair_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_coul_wolf_omp.cpp @@ -12,14 +12,14 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_coul_wolf_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_const.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_dpd_omp.cpp b/src/USER-OMP/pair_dpd_omp.cpp index 77db3d9183b9fd03537d7ad01b71b7e813c84214..b7f3a7f4d43751dccdf2ddd8b76d4760f0ea11dd 100644 --- a/src/USER-OMP/pair_dpd_omp.cpp +++ b/src/USER-OMP/pair_dpd_omp.cpp @@ -12,15 +12,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_dpd_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "update.h" #include "random_mars.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp index 85cab4fe7b2ad4dd029b014f19e6d73ed4d9eb0e..87d637e80d452c7f43cdaace25d046fae89cb9ed 100644 --- a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp @@ -15,13 +15,15 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_thole_long_omp.h" #include #include #include #include -#include "pair_lj_cut_thole_long_omp.h" #include "atom.h" #include "comm.h" +#include "domain.h" +#include "fix_drude.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" @@ -29,7 +31,7 @@ #include "math_const.h" #include "error.h" #include "suffix.h" -#include "domain.h" +#include "timer.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp b/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp index e2c1da1a89f249a8b99d0d8f62312cacf87e8101..18fc20701575b57a31e151fd91f1955592b682b8 100644 --- a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_lj_cut_tip4p_long_omp.h" +#include #include "atom.h" #include "domain.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lubricate_poly_omp.cpp b/src/USER-OMP/pair_lubricate_poly_omp.cpp index 3a5f03364de4f61ce807459bc8078e85e61e2c18..04ac59b121a8af3517d11e9d3aa8353b740de4eb 100644 --- a/src/USER-OMP/pair_lubricate_poly_omp.cpp +++ b/src/USER-OMP/pair_lubricate_poly_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_lubricate_poly_omp.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/USER-OMP/pair_reaxc_omp.cpp b/src/USER-OMP/pair_reaxc_omp.cpp index 2f175151307fc6197a0e853aa70b1c16a806fd13..aedd4380661c4d2946d057aa01f3cd0d79502fcc 100644 --- a/src/USER-OMP/pair_reaxc_omp.cpp +++ b/src/USER-OMP/pair_reaxc_omp.cpp @@ -34,6 +34,8 @@ ------------------------------------------------------------------------- */ #include "pair_reaxc_omp.h" +#include +#include #include "atom.h" #include "update.h" #include "force.h" @@ -42,32 +44,27 @@ #include "neigh_list.h" #include "neigh_request.h" #include "modify.h" -#include "fix.h" #include "fix_reaxc.h" #include "citeme.h" #include "memory.h" #include "error.h" #include "timer.h" +#include "reaxc_defs.h" #include "reaxc_types.h" #include "reaxc_allocate.h" -#include "reaxc_control.h" -#include "reaxc_ffield.h" #include "reaxc_forces_omp.h" #include "reaxc_init_md_omp.h" #include "reaxc_io_tools.h" #include "reaxc_list.h" -#include "reaxc_lookup.h" #include "reaxc_reset_tools.h" #include "reaxc_tool_box.h" -#include "reaxc_traj.h" -#include "reaxc_vector.h" -#include "fix_reaxc_bonds.h" #if defined(_OPENMP) #include #endif +#include "suffix.h" using namespace LAMMPS_NS; #ifdef OMP_TIMING diff --git a/src/USER-OMP/pair_reaxc_omp.h b/src/USER-OMP/pair_reaxc_omp.h index ad8c368aaf95be118bca70a8fefa45981c9feb18..0cae28f56b5cf44675fb9ec0968ffa09a8c55a5b 100644 --- a/src/USER-OMP/pair_reaxc_omp.h +++ b/src/USER-OMP/pair_reaxc_omp.h @@ -22,7 +22,6 @@ PairStyle(reax/c/omp,PairReaxCOMP) #include "pair_reaxc.h" #include "thr_omp.h" -#include "suffix.h" namespace LAMMPS_NS { diff --git a/src/USER-OMP/pppm_cg_omp.cpp b/src/USER-OMP/pppm_cg_omp.cpp index 2b4619f685e2b53304c0f39db6fdaca7ec3de9d1..1117979f1f33765369dd6ce4015cbf663087f41c 100644 --- a/src/USER-OMP/pppm_cg_omp.cpp +++ b/src/USER-OMP/pppm_cg_omp.cpp @@ -15,20 +15,20 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "pppm_cg_omp.h" +#include #include #include -#include "pppm_cg_omp.h" #include "atom.h" #include "comm.h" #include "domain.h" -#include "error.h" -#include "fix_omp.h" #include "force.h" -#include "neighbor.h" -#include "memory.h" #include "math_const.h" #include "math_special.h" - +#include "timer.h" +#if defined(_OPENMP) +#include +#endif #include "suffix.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pppm_disp_omp.cpp b/src/USER-OMP/pppm_disp_omp.cpp index 435341a31ca421e957b407b907833c0339140381..de902b1a57289343b61ae0785d36f86593d49869 100644 --- a/src/USER-OMP/pppm_disp_omp.cpp +++ b/src/USER-OMP/pppm_disp_omp.cpp @@ -16,15 +16,20 @@ Rolf Isele-Holder (RWTH Aachen University) ------------------------------------------------------------------------- */ +#include "pppm_disp_omp.h" +#include #include #include -#include "pppm_disp_omp.h" #include "atom.h" #include "comm.h" #include "domain.h" +#include "error.h" #include "force.h" -#include "memory.h" #include "math_const.h" +#include "timer.h" +#if defined(_OPENMP) +#include +#endif #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pppm_disp_tip4p_omp.cpp b/src/USER-OMP/pppm_disp_tip4p_omp.cpp index a53c5b2ac5a911c5aa8cc6a5ba3dbb8e4421b842..fc9466e395ab333627e0fc8f1b41a12fcac1471a 100644 --- a/src/USER-OMP/pppm_disp_tip4p_omp.cpp +++ b/src/USER-OMP/pppm_disp_tip4p_omp.cpp @@ -15,23 +15,22 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "pppm_disp_tip4p_omp.h" +#include #include #include -#include "pppm_disp_tip4p_omp.h" #include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "fix_omp.h" #include "force.h" -#include "memory.h" #include "math_const.h" -#include "math_special.h" - +#if defined(_OPENMP) +#include +#endif #include "suffix.h" using namespace LAMMPS_NS; using namespace MathConst; -using namespace MathSpecial; #ifdef FFT_SINGLE #define ZEROF 0.0f diff --git a/src/USER-OMP/pppm_omp.cpp b/src/USER-OMP/pppm_omp.cpp index 66190b3f510a2b39f1e9070c2f159a8f00173a72..3ef3de1ab7aec2ce22bd22367f068e93ea1c29aa 100644 --- a/src/USER-OMP/pppm_omp.cpp +++ b/src/USER-OMP/pppm_omp.cpp @@ -15,18 +15,21 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "pppm_omp.h" +#include #include #include -#include "pppm_omp.h" #include "atom.h" #include "comm.h" #include "domain.h" -#include "error.h" -#include "fix_omp.h" #include "force.h" -#include "memory.h" #include "math_const.h" #include "math_special.h" +#include "timer.h" + +#if defined(_OPENMP) +#include +#endif #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pppm_tip4p_omp.cpp b/src/USER-OMP/pppm_tip4p_omp.cpp index 5fe44d2b71d05b0a2e5f59cc45c7a220a588aa7e..d7c12613d96660ecf2610687f04a1318056ba318 100644 --- a/src/USER-OMP/pppm_tip4p_omp.cpp +++ b/src/USER-OMP/pppm_tip4p_omp.cpp @@ -15,18 +15,21 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "pppm_tip4p_omp.h" +#include #include #include -#include "pppm_tip4p_omp.h" #include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "fix_omp.h" #include "force.h" -#include "memory.h" #include "math_const.h" #include "math_special.h" +#include "timer.h" +#if defined(_OPENMP) +#include +#endif #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/reaxc_bond_orders_omp.cpp b/src/USER-OMP/reaxc_bond_orders_omp.cpp index 33780f5e3f6d4dc74ab89a247e39098ac2093ee9..d581819e00bb8e1dc4f054e2fb6e05d65e7d5c60 100644 --- a/src/USER-OMP/reaxc_bond_orders_omp.cpp +++ b/src/USER-OMP/reaxc_bond_orders_omp.cpp @@ -26,9 +26,13 @@ . ----------------------------------------------------------------------*/ +#include "reaxc_bond_orders_omp.h" +#include +#include +#include "fix_omp.h" +#include "reaxc_defs.h" #include "pair_reaxc_omp.h" #include "reaxc_types.h" -#include "reaxc_bond_orders_omp.h" #include "reaxc_list.h" #include "reaxc_vector.h" diff --git a/src/USER-OMP/reaxc_bonds_omp.cpp b/src/USER-OMP/reaxc_bonds_omp.cpp index 5160c6f55df1c66aa11728423caa2d35b58d2bd0..b6a76b3f3a18dad7972e63afd891b691f40e81d0 100644 --- a/src/USER-OMP/reaxc_bonds_omp.cpp +++ b/src/USER-OMP/reaxc_bonds_omp.cpp @@ -26,13 +26,13 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc_omp.h" - #include "reaxc_bonds_omp.h" -#include "reaxc_bond_orders_omp.h" +#include +#include +#include "fix_omp.h" +#include "reaxc_defs.h" +#include "pair_reaxc_omp.h" #include "reaxc_list.h" -#include "reaxc_tool_box.h" -#include "reaxc_vector.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/reaxc_forces_omp.cpp b/src/USER-OMP/reaxc_forces_omp.cpp index 0a08bd6a465c682621e3a2d9a80f4882ad01b6c3..971667cc2db889cedc1482c9ceacfd073f4a7c8b 100644 --- a/src/USER-OMP/reaxc_forces_omp.cpp +++ b/src/USER-OMP/reaxc_forces_omp.cpp @@ -26,19 +26,19 @@ . ----------------------------------------------------------------------*/ +#include "reaxc_forces_omp.h" +#include +#include +#include "fix_omp.h" +#include "reaxc_defs.h" #include "pair_reaxc_omp.h" -#include "thr_data.h" -#include "reaxc_forces_omp.h" #include "reaxc_bond_orders_omp.h" #include "reaxc_bonds_omp.h" #include "reaxc_hydrogen_bonds_omp.h" -#include "reaxc_io_tools.h" #include "reaxc_list.h" -#include "reaxc_lookup.h" #include "reaxc_multi_body_omp.h" #include "reaxc_nonbonded_omp.h" -#include "reaxc_tool_box.h" #include "reaxc_torsion_angles_omp.h" #include "reaxc_valence_angles_omp.h" #include "reaxc_vector.h" diff --git a/src/USER-OMP/reaxc_forces_omp.h b/src/USER-OMP/reaxc_forces_omp.h index d1e2a5c65a99bbe53e28a75fd002302cf7696c9d..6df0288656a3420ad3dbaa13f2dfc659dfcfdc9d 100644 --- a/src/USER-OMP/reaxc_forces_omp.h +++ b/src/USER-OMP/reaxc_forces_omp.h @@ -30,7 +30,6 @@ #define __FORCES_OMP_H_ #include "reaxc_types.h" -#include "reaxc_defs.h" void Init_Force_FunctionsOMP( control_params* ); void Compute_ForcesOMP( reax_system*, control_params*, simulation_data*, diff --git a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp index 7acf26262ead651a7320dbe79583395b55ec8179..d06966a92d8e62ba535585d7f216440b2efefbda 100644 --- a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp +++ b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp @@ -26,10 +26,12 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc_omp.h" - #include "reaxc_hydrogen_bonds_omp.h" -#include "reaxc_bond_orders_omp.h" +#include +#include +#include "fix_omp.h" +#include "pair_reaxc_omp.h" +#include "reaxc_defs.h" #include "reaxc_list.h" #include "reaxc_valence_angles.h" // To access Calculate_Theta() #include "reaxc_valence_angles_omp.h" // To access Calculate_dCos_ThetaOMP() diff --git a/src/USER-OMP/reaxc_init_md_omp.cpp b/src/USER-OMP/reaxc_init_md_omp.cpp index fe7682d0358ace6e0a57c1af091b0e955f53788f..9d40479ddfce64312b5f6f673bae55d72f72d954 100644 --- a/src/USER-OMP/reaxc_init_md_omp.cpp +++ b/src/USER-OMP/reaxc_init_md_omp.cpp @@ -26,18 +26,16 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc_omp.h" #include "reaxc_init_md_omp.h" -#include "reaxc_allocate.h" +#include +#include "reaxc_defs.h" #include "reaxc_forces.h" #include "reaxc_forces_omp.h" #include "reaxc_io_tools.h" #include "reaxc_list.h" #include "reaxc_lookup.h" -#include "reaxc_reset_tools.h" -#include "reaxc_system_props.h" #include "reaxc_tool_box.h" -#include "reaxc_vector.h" +#include "error.h" // Functions defined in reaxc_init_md.cpp extern int Init_MPI_Datatypes(reax_system*, storage*, mpi_datatypes*, MPI_Comm, char*); diff --git a/src/USER-OMP/reaxc_multi_body_omp.cpp b/src/USER-OMP/reaxc_multi_body_omp.cpp index 7552e7a7333d47088962ddd56acebe25be1b334f..5f4b6d4eb05f292e666806e5a5a45fccdd656809 100644 --- a/src/USER-OMP/reaxc_multi_body_omp.cpp +++ b/src/USER-OMP/reaxc_multi_body_omp.cpp @@ -26,13 +26,14 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc_omp.h" -#include "thr_data.h" - #include "reaxc_multi_body_omp.h" -#include "reaxc_bond_orders_omp.h" +#include +#include +#include "fix_omp.h" +#include +#include "pair_reaxc_omp.h" +#include "reaxc_defs.h" #include "reaxc_list.h" -#include "reaxc_vector.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/reaxc_nonbonded_omp.cpp b/src/USER-OMP/reaxc_nonbonded_omp.cpp index ea92e0c2107a7820d0b4887aab10142eecd36d61..564088880ad6bec5d3ad5c4aa3419a76f822cb9f 100644 --- a/src/USER-OMP/reaxc_nonbonded_omp.cpp +++ b/src/USER-OMP/reaxc_nonbonded_omp.cpp @@ -29,6 +29,7 @@ #include "pair_reaxc_omp.h" #include "thr_data.h" +#include "reaxc_defs.h" #include "reaxc_types.h" #include "reaxc_nonbonded.h" diff --git a/src/USER-OMP/reaxc_torsion_angles_omp.cpp b/src/USER-OMP/reaxc_torsion_angles_omp.cpp index d290dc264f2dfe3af9eb5e9a2fdcae97a751dabf..68bacb72027f8717c97fbcc2c3580020edbcbfc4 100644 --- a/src/USER-OMP/reaxc_torsion_angles_omp.cpp +++ b/src/USER-OMP/reaxc_torsion_angles_omp.cpp @@ -26,14 +26,14 @@ . ----------------------------------------------------------------------*/ +#include "reaxc_torsion_angles_omp.h" +#include +#include "fix_omp.h" #include "pair_reaxc_omp.h" -#include "thr_data.h" +#include "reaxc_defs.h" #include "reaxc_types.h" -#include "reaxc_torsion_angles_omp.h" -#include "reaxc_bond_orders_omp.h" #include "reaxc_list.h" -#include "reaxc_tool_box.h" #include "reaxc_vector.h" #if defined(_OPENMP) diff --git a/src/USER-OMP/reaxc_valence_angles_omp.cpp b/src/USER-OMP/reaxc_valence_angles_omp.cpp index 195f16a75d07a1475bab2480dcd28dfd126524ef..104fadbbae19be5b827f9da14c04731b37f62c7f 100644 --- a/src/USER-OMP/reaxc_valence_angles_omp.cpp +++ b/src/USER-OMP/reaxc_valence_angles_omp.cpp @@ -26,13 +26,16 @@ . ----------------------------------------------------------------------*/ +#include "reaxc_valence_angles_omp.h" +#include +#include #include "pair_reaxc_omp.h" -#include "thr_data.h" +#include "fix_omp.h" +#include "error.h" +#include "reaxc_defs.h" #include "reaxc_types.h" #include "reaxc_valence_angles.h" -#include "reaxc_valence_angles_omp.h" -#include "reaxc_bond_orders_omp.h" #include "reaxc_list.h" #include "reaxc_vector.h" diff --git a/src/USER-OMP/respa_omp.cpp b/src/USER-OMP/respa_omp.cpp index 9c8555c66d6d12dfe2c0ca448d3b90a19bc5b332..5add419253a2763a00461111604411166f235665 100644 --- a/src/USER-OMP/respa_omp.cpp +++ b/src/USER-OMP/respa_omp.cpp @@ -15,13 +15,11 @@ Contributing authors: Mark Stevens (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "respa_omp.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "atom.h" +#include "domain.h" #include "force.h" #include "pair.h" #include "bond.h" @@ -32,11 +30,8 @@ #include "output.h" #include "update.h" #include "modify.h" -#include "compute.h" -#include "fix_respa.h" -#include "timer.h" -#include "memory.h" #include "error.h" +#include "timer.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/thr_data.h b/src/USER-OMP/thr_data.h index 3cea1b0018df5e76ce12f87149529128f1dfd7d4..edff17cad3c582739765910cee6082f10805d15d 100644 --- a/src/USER-OMP/thr_data.h +++ b/src/USER-OMP/thr_data.h @@ -18,10 +18,6 @@ #ifndef LMP_THR_DATA_H #define LMP_THR_DATA_H -#if defined(_OPENMP) -#include -#endif - #include "timer.h" namespace LAMMPS_NS { @@ -35,7 +31,7 @@ class ThrData { public: ThrData(int tid, class Timer *t); - ~ThrData() { delete _timer; _timer = NULL; }; + ~ThrData() { delete _timer; _timer = nullptr; }; void check_tid(int); // thread id consistency check int get_tid() const { return _tid; }; // our thread id. @@ -140,7 +136,7 @@ class ThrData { // disabled default methods private: - ThrData() : _tid(-1), _timer(NULL) {}; + ThrData() : _tid(-1), _timer(nullptr) {}; }; //////////////////////////////////////////////////////////////////////// diff --git a/src/USER-OMP/thr_omp.cpp b/src/USER-OMP/thr_omp.cpp index 22f751e6c0f99fb839632e25e8b72f08d60aacfb..51030358d3b8c9b0bcfac5fca13872839a533165 100644 --- a/src/USER-OMP/thr_omp.cpp +++ b/src/USER-OMP/thr_omp.cpp @@ -22,7 +22,6 @@ #include "comm.h" #include "error.h" #include "force.h" -#include "memory.h" #include "modify.h" #include "neighbor.h" #include "timer.h" @@ -34,7 +33,6 @@ #include "angle.h" #include "dihedral.h" #include "improper.h" -#include "kspace.h" #include "compute.h" #include "math_const.h" diff --git a/src/USER-OMP/thr_omp.h b/src/USER-OMP/thr_omp.h index 87d921290efd93e5ed14d158188617e5ca0bf50c..062d77bc0ecfa191466fdda04a056b64b4493b94 100644 --- a/src/USER-OMP/thr_omp.h +++ b/src/USER-OMP/thr_omp.h @@ -18,10 +18,13 @@ #ifndef LMP_THR_OMP_H #define LMP_THR_OMP_H +#if defined(_OPENMP) +#include +#endif #include "pointers.h" #include "error.h" -#include "fix_omp.h" -#include "thr_data.h" +#include "fix_omp.h" // IWYU pragma: export +#include "thr_data.h" // IWYU pragma: export namespace LAMMPS_NS { @@ -31,8 +34,6 @@ class Bond; class Angle; class Dihedral; class Improper; -class KSpace; -class Fix; class ThrOMP { diff --git a/src/USER-PHONON/dynamical_matrix.cpp b/src/USER-PHONON/dynamical_matrix.cpp index d94bd11a80530708957993b36c0a30222518b993..559ef4c36f5378500a6f0f3b7afe605aee4ee166 100644 --- a/src/USER-PHONON/dynamical_matrix.cpp +++ b/src/USER-PHONON/dynamical_matrix.cpp @@ -3,15 +3,15 @@ // #include -#include +#include +#include #include "dynamical_matrix.h" #include "atom.h" -#include "modify.h" #include "domain.h" #include "comm.h" +#include "error.h" #include "group.h" #include "force.h" -#include "math_extra.h" #include "memory.h" #include "bond.h" #include "angle.h" @@ -25,7 +25,6 @@ #include "finish.h" #include - using namespace LAMMPS_NS; enum{REGULAR,ESKM}; diff --git a/src/USER-PHONON/fix_phonon.cpp b/src/USER-PHONON/fix_phonon.cpp index cdbe4068bc9d96de79e52b02c4f6a09bacf5d23d..9b663ce3838b414bfe040d7f9adc0968b48e5fb4 100644 --- a/src/USER-PHONON/fix_phonon.cpp +++ b/src/USER-PHONON/fix_phonon.cpp @@ -23,8 +23,8 @@ konglt@sjtu.edu.cn; konglt@gmail.com ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include #include "fix_phonon.h" #include "fft3d_wrap.h" @@ -33,7 +33,6 @@ #include "domain.h" #include "force.h" #include "group.h" -#include "lattice.h" #include "modify.h" #include "update.h" #include "citeme.h" diff --git a/src/USER-PTM/compute_ptm_atom.cpp b/src/USER-PTM/compute_ptm_atom.cpp index 41e6540b975a73dc16ae64abc758759870a09e62..ad3d3facdb86fe43ef1872cdcf2ef372b3ce891a 100644 --- a/src/USER-PTM/compute_ptm_atom.cpp +++ b/src/USER-PTM/compute_ptm_atom.cpp @@ -16,15 +16,14 @@ under Contributing author: PM Larsen (MIT) ------------------------------------------------------------------------- */ +#include "compute_ptm_atom.h" #include #include -#include #include #include #include "atom.h" #include "comm.h" -#include "compute_ptm_atom.h" #include "error.h" #include "force.h" #include "memory.h" @@ -32,7 +31,6 @@ under #include "neigh_list.h" #include "neigh_request.h" #include "neighbor.h" -#include "pair.h" #include "update.h" #include "ptm_functions.h" diff --git a/src/USER-PTM/ptm_convex_hull_incremental.cpp b/src/USER-PTM/ptm_convex_hull_incremental.cpp index 45643ec515d490183ceedbf14c09d5a5a1e7314a..8dd06e8168cb6b7b0b5a6b27166ba80e6a0bdc6d 100644 --- a/src/USER-PTM/ptm_convex_hull_incremental.cpp +++ b/src/USER-PTM/ptm_convex_hull_incremental.cpp @@ -11,7 +11,6 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI #include #include #include -#include #include "ptm_convex_hull_incremental.h" #include "ptm_constants.h" diff --git a/src/USER-PTM/ptm_index.cpp b/src/USER-PTM/ptm_index.cpp index 3068e7a7f634381aab4d4a5afcbcbe20f2024486..cedd35126d7398882183d2a2b759db6042cfaaf6 100644 --- a/src/USER-PTM/ptm_index.cpp +++ b/src/USER-PTM/ptm_index.cpp @@ -12,20 +12,17 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI #include "ptm_convex_hull_incremental.h" #include "ptm_deformation_gradient.h" #include "ptm_functions.h" -#include "ptm_graph_data.h" #include "ptm_initialize_data.h" #include "ptm_neighbour_ordering.h" #include "ptm_normalize_vertices.h" #include "ptm_polar.h" #include "ptm_quat.h" #include "ptm_structure_matcher.h" -#include #include -#include #include #include -#include #include +#include static double calculate_interatomic_distance(int type, double scale) { assert(type >= 1 && type <= 8); diff --git a/src/USER-PTM/ptm_initialize_data.cpp b/src/USER-PTM/ptm_initialize_data.cpp index 49dc6f232379e5e895d29dc2deba1471c12c4477..ff8245fe4476bc9c5990cccbb471483526c1b8da 100644 --- a/src/USER-PTM/ptm_initialize_data.cpp +++ b/src/USER-PTM/ptm_initialize_data.cpp @@ -7,14 +7,12 @@ The above copyright notice and this permission notice shall be included in all c THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -#include -#include -#include -#include -#include -#include -#include #include "ptm_initialize_data.h" +#include "ptm_canonical_coloured.h" +#include "ptm_convex_hull_incremental.h" +#include "ptm_graph_tools.h" +#include "ptm_neighbour_ordering.h" +#include static void make_facets_clockwise(int num_facets, int8_t (*facets)[3], const double (*points)[3]) diff --git a/src/USER-PTM/ptm_initialize_data.h b/src/USER-PTM/ptm_initialize_data.h index 20c9921962b6522c424165899570580c69225ce4..4e7f3e8f0a31bb2a8b70f5a7bf6c461d08a3e3bb 100644 --- a/src/USER-PTM/ptm_initialize_data.h +++ b/src/USER-PTM/ptm_initialize_data.h @@ -12,12 +12,8 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI #include "ptm_graph_data.h" -#include "ptm_graph_tools.h" #include "ptm_deformation_gradient.h" #include "ptm_fundamental_mappings.h" -#include "ptm_neighbour_ordering.h" -#include "ptm_canonical_coloured.h" -#include "ptm_convex_hull_incremental.h" #include "ptm_alt_templates.h" diff --git a/src/USER-PTM/ptm_neighbour_ordering.cpp b/src/USER-PTM/ptm_neighbour_ordering.cpp index cb72a43711a7952b47f30de10f893f72f7a0c2f6..1332b8819bd51d5d2acf7d2545edd16285d6c11e 100644 --- a/src/USER-PTM/ptm_neighbour_ordering.cpp +++ b/src/USER-PTM/ptm_neighbour_ordering.cpp @@ -9,16 +9,15 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI //todo: normalize vertices -#include +#include "ptm_neighbour_ordering.h" #include #include #include #include #include +#include #include "ptm_constants.h" #include "ptm_voronoi_cell.h" -#include "ptm_neighbour_ordering.h" -#include "ptm_normalize_vertices.h" namespace ptm { diff --git a/src/USER-PTM/ptm_polar.h b/src/USER-PTM/ptm_polar.h index e03963048b4c1225a5904dbc3cc031026264b0cb..f11dd98ee92846d5af7a259fd366acaa50555052 100644 --- a/src/USER-PTM/ptm_polar.h +++ b/src/USER-PTM/ptm_polar.h @@ -11,7 +11,6 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI #define PTM_POLAR_H #include -#include namespace ptm { diff --git a/src/USER-PTM/ptm_quat.cpp b/src/USER-PTM/ptm_quat.cpp index 4a93499b3a1db1f0926cf64ff4209cc8729d7081..527f4d111696e5b9e5086187567fcdfe4bbd0a2c 100644 --- a/src/USER-PTM/ptm_quat.cpp +++ b/src/USER-PTM/ptm_quat.cpp @@ -7,9 +7,9 @@ The above copyright notice and this permission notice shall be included in all c THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ +#include "ptm_quat.h" #include #include -#include #include diff --git a/src/USER-PTM/ptm_structure_matcher.cpp b/src/USER-PTM/ptm_structure_matcher.cpp index d50676a3c174d590d135be829bdab207f40828c0..b587ad225f0b48aa76f13ef736966de54d7875b8 100644 --- a/src/USER-PTM/ptm_structure_matcher.cpp +++ b/src/USER-PTM/ptm_structure_matcher.cpp @@ -7,20 +7,16 @@ The above copyright notice and this permission notice shall be included in all c THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -#include -#include +#include "ptm_structure_matcher.h" #include #include -#include -#include -#include +#include #include "ptm_convex_hull_incremental.h" #include "ptm_canonical_coloured.h" #include "ptm_graph_data.h" #include "ptm_graph_tools.h" #include "ptm_normalize_vertices.h" #include "ptm_polar.h" -#include "ptm_structure_matcher.h" #include "ptm_constants.h" diff --git a/src/USER-PTM/ptm_structure_matcher.h b/src/USER-PTM/ptm_structure_matcher.h index e75892f8cbf0933fee84579640edcc7cce40fd27..63bc5ed1fef4d5830eda29045dc40ea89e0839b5 100644 --- a/src/USER-PTM/ptm_structure_matcher.h +++ b/src/USER-PTM/ptm_structure_matcher.h @@ -12,7 +12,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI #include "ptm_initialize_data.h" #include "ptm_constants.h" - +#include "ptm_convex_hull_incremental.h" namespace ptm { diff --git a/src/USER-PTM/ptm_voronoi_cell.cpp b/src/USER-PTM/ptm_voronoi_cell.cpp index dfe61eb24f1d8f0aebd3e9672f858ab61d285bc8..dc4ce4e747a8b0c3e16a079f8a95c15cccd1ae09 100644 --- a/src/USER-PTM/ptm_voronoi_cell.cpp +++ b/src/USER-PTM/ptm_voronoi_cell.cpp @@ -52,7 +52,7 @@ such enhancements or derivative works thereof, in binary and source code form. * \brief Function implementations for the voronoicell and related classes. */ #include -#include +#include #include #include "ptm_voronoi_config.h" #include "ptm_voronoi_cell.h" diff --git a/src/USER-PTM/ptm_voronoi_cell.h b/src/USER-PTM/ptm_voronoi_cell.h index eb091dd36b2c02d2a31820ca003beb7c60b404c0..69e3b5bdc4ff49517766224831546fa764620de1 100644 --- a/src/USER-PTM/ptm_voronoi_cell.h +++ b/src/USER-PTM/ptm_voronoi_cell.h @@ -56,9 +56,6 @@ such enhancements or derivative works thereof, in binary and source code form. #define PTM_VOROPP_CELL_HH #include -#include - -#include "ptm_voronoi_config.h" namespace ptm_voro { diff --git a/src/USER-QTB/fix_qbmsst.cpp b/src/USER-QTB/fix_qbmsst.cpp index b9b07664d2c0e0249571f7f2aa00f74139c54f29..abbf1701b84865fd6240ca56211b518817a4e87b 100644 --- a/src/USER-QTB/fix_qbmsst.cpp +++ b/src/USER-QTB/fix_qbmsst.cpp @@ -16,31 +16,22 @@ Implementation of the Multi-Scale Shock Method with quantum nuclear effects ------------------------------------------------------------------------- */ +#include "fix_qbmsst.h" #include #include #include #include -#include "fix_qbmsst.h" -#include "math_extra.h" #include "atom.h" -#include "atom_vec_ellipsoid.h" #include "force.h" #include "update.h" #include "modify.h" #include "compute.h" #include "domain.h" -#include "region.h" -#include "respa.h" #include "comm.h" -#include "input.h" -#include "output.h" -#include "variable.h" #include "random_mars.h" #include "memory.h" #include "error.h" -#include "group.h" #include "kspace.h" -#include "thermo.h" #include "utils.h" using namespace LAMMPS_NS; diff --git a/src/USER-QTB/fix_qtb.cpp b/src/USER-QTB/fix_qtb.cpp index 015f953b8e1438682d39c9df6f7cbfaf677e0adf..593ca310068ac9d83471b3fd5738b8bdcbc7e7d1 100644 --- a/src/USER-QTB/fix_qtb.cpp +++ b/src/USER-QTB/fix_qtb.cpp @@ -16,28 +16,21 @@ Implementation of the colored thermostat for quantum nuclear effects ------------------------------------------------------------------------- */ +#include "fix_qtb.h" #include #include #include #include -#include "fix_qtb.h" -#include "math_extra.h" #include "atom.h" -#include "atom_vec_ellipsoid.h" #include "force.h" #include "update.h" #include "modify.h" #include "compute.h" -#include "domain.h" -#include "region.h" #include "respa.h" #include "comm.h" -#include "input.h" -#include "variable.h" #include "random_mars.h" #include "memory.h" #include "error.h" -#include "group.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-REAXC/compute_spec_atom.cpp b/src/USER-REAXC/compute_spec_atom.cpp index 77b82b3e5514cf75a7e15f3a26f9a01ba2b63a85..bc5b26b69907040779d1dd2553bb7080cf67ee29 100644 --- a/src/USER-REAXC/compute_spec_atom.cpp +++ b/src/USER-REAXC/compute_spec_atom.cpp @@ -11,19 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_spec_atom.h" -#include "math_extra.h" +#include #include "atom.h" #include "update.h" #include "force.h" -#include "domain.h" #include "memory.h" #include "error.h" - -#include "reaxc_defs.h" -#include "reaxc_types.h" #include "pair_reaxc.h" using namespace LAMMPS_NS; diff --git a/src/USER-REAXC/compute_spec_atom.h b/src/USER-REAXC/compute_spec_atom.h index 4d5cb86d71f42c5e9a14c3d3d56b3df3113d9ec1..cf0aa0215d1159efb4717691e6e10cbc84301cd2 100644 --- a/src/USER-REAXC/compute_spec_atom.h +++ b/src/USER-REAXC/compute_spec_atom.h @@ -21,7 +21,6 @@ ComputeStyle(SPEC/ATOM,ComputeSpecAtom) #define LMP_COMPUTE_SPEC_ATOM_H #include "compute.h" -#include "pointers.h" namespace LAMMPS_NS { diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp index 6c0da278c28ba07171086969ba33c31f05be1fc9..924b6806de08fe9691ccc5801f1994c9160910e4 100644 --- a/src/USER-REAXC/fix_qeq_reax.cpp +++ b/src/USER-REAXC/fix_qeq_reax.cpp @@ -18,15 +18,13 @@ Hybrid and sub-group capabilities: Ray Shan (Sandia) ------------------------------------------------------------------------- */ +#include "fix_qeq_reax.h" +#include #include -#include -#include #include -#include "fix_qeq_reax.h" #include "pair_reaxc.h" #include "atom.h" #include "comm.h" -#include "domain.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" @@ -39,6 +37,7 @@ #include "citeme.h" #include "error.h" #include "reaxc_defs.h" +#include "reaxc_types.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-REAXC/fix_reaxc.cpp b/src/USER-REAXC/fix_reaxc.cpp index dc67ad6ffb0199c861f7cc3d179575281fe6edc2..c98adf5b45e082872a7320c2c65f8713f844c832 100644 --- a/src/USER-REAXC/fix_reaxc.cpp +++ b/src/USER-REAXC/fix_reaxc.cpp @@ -23,8 +23,6 @@ #include "fix_reaxc.h" #include "atom.h" -#include "pair.h" -#include "comm.h" #include "memory.h" using namespace LAMMPS_NS; diff --git a/src/USER-REAXC/fix_reaxc_bonds.cpp b/src/USER-REAXC/fix_reaxc_bonds.cpp index 9dc347826f626ac819593db18bbc450e7ce0635c..f7ad7ed6d4b4d0c4ef26e82a690ce9789d45dc72 100644 --- a/src/USER-REAXC/fix_reaxc_bonds.cpp +++ b/src/USER-REAXC/fix_reaxc_bonds.cpp @@ -15,22 +15,14 @@ Contributing author: Ray Shan (Sandia, tnshan@sandia.gov) ------------------------------------------------------------------------- */ -#include -#include -#include "fix_ave_atom.h" #include "fix_reaxc_bonds.h" +#include +#include #include "atom.h" #include "update.h" #include "pair_reaxc.h" -#include "modify.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "comm.h" #include "force.h" -#include "compute.h" -#include "input.h" -#include "variable.h" #include "memory.h" #include "error.h" #include "reaxc_list.h" diff --git a/src/USER-REAXC/fix_reaxc_bonds.h b/src/USER-REAXC/fix_reaxc_bonds.h index d72f5446b5141a7c701f527cc0f67c1e32524a8e..e83e01f1d5254417cf08ac39bcdcfa1faa9d9ba9 100644 --- a/src/USER-REAXC/fix_reaxc_bonds.h +++ b/src/USER-REAXC/fix_reaxc_bonds.h @@ -20,9 +20,7 @@ FixStyle(reax/c/bonds,FixReaxCBonds) #ifndef LMP_FIX_REAXC_BONDS_H #define LMP_FIX_REAXC_BONDS_H -#include #include "fix.h" -#include "pointers.h" namespace LAMMPS_NS { diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp index 46426d484ae89c6f8d1a631e5d7061ac16ac3668..74692f1c9b6f0d291664a58f7096db8544e4f2d4 100644 --- a/src/USER-REAXC/fix_reaxc_species.cpp +++ b/src/USER-REAXC/fix_reaxc_species.cpp @@ -16,27 +16,23 @@ Oleg Sergeev (VNIIA, sergeev@vniia.ru) ------------------------------------------------------------------------- */ +#include "fix_reaxc_species.h" +#include #include -#include #include #include "fix_ave_atom.h" -#include "fix_reaxc_species.h" #include "atom.h" #include "domain.h" #include "update.h" -#include "pair_reaxc.h" #include "modify.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "comm.h" #include "force.h" -#include "compute.h" -#include "input.h" -#include "variable.h" #include "memory.h" #include "error.h" -#include "reaxc_list.h" +#include "pair_reaxc.h" +#include "reaxc_defs.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-REAXC/fix_reaxc_species.h b/src/USER-REAXC/fix_reaxc_species.h index 23a470fd0ac63a37862bd032d51e953c261db3f9..937af98527acf1873405701b4c9ed9decfb07709 100644 --- a/src/USER-REAXC/fix_reaxc_species.h +++ b/src/USER-REAXC/fix_reaxc_species.h @@ -21,11 +21,6 @@ FixStyle(reax/c/species,FixReaxCSpecies) #define LMP_FIX_REAXC_SPECIES_H #include "fix.h" -#include "pointers.h" - -#include "pair_reaxc.h" -#include "reaxc_types.h" -#include "reaxc_defs.h" #define BUFLEN 1000 diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp index 8f8dcfb8fc3439ad1be98c2ad8c8d2464ca02dc5..959405576e97bf145bed1436e6174da2f7510385 100644 --- a/src/USER-REAXC/pair_reaxc.cpp +++ b/src/USER-REAXC/pair_reaxc.cpp @@ -21,6 +21,11 @@ ------------------------------------------------------------------------- */ #include "pair_reaxc.h" +#include +#include +#include +#include +#include #include "atom.h" #include "update.h" #include "force.h" @@ -35,6 +40,7 @@ #include "memory.h" #include "error.h" +#include "reaxc_defs.h" #include "reaxc_types.h" #include "reaxc_allocate.h" #include "reaxc_control.h" @@ -45,9 +51,7 @@ #include "reaxc_list.h" #include "reaxc_lookup.h" #include "reaxc_reset_tools.h" -#include "reaxc_traj.h" #include "reaxc_vector.h" -#include "fix_reaxc_bonds.h" using namespace LAMMPS_NS; diff --git a/src/USER-REAXC/reaxc_allocate.cpp b/src/USER-REAXC/reaxc_allocate.cpp index 460f8aeb6a77fb1754059af169ec5a6c8ac2dd58..6303db5619da816b796db4dd26cfd6aa819c4782 100644 --- a/src/USER-REAXC/reaxc_allocate.cpp +++ b/src/USER-REAXC/reaxc_allocate.cpp @@ -24,14 +24,13 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_allocate.h" +#include +#include "reaxc_defs.h" #include "reaxc_list.h" -#include "reaxc_reset_tools.h" #include "reaxc_tool_box.h" -#include "reaxc_vector.h" -#if defined(_OPENMP) +#if defined(LMP_USER_OMP) && defined(_OPENMP) #include #endif diff --git a/src/USER-REAXC/reaxc_bond_orders.cpp b/src/USER-REAXC/reaxc_bond_orders.cpp index 1ed58a0bfd234905c50fc3ee8d5dc111d52406ac..869e796661490b7ba3025e420583427fc5908e2d 100644 --- a/src/USER-REAXC/reaxc_bond_orders.cpp +++ b/src/USER-REAXC/reaxc_bond_orders.cpp @@ -24,9 +24,11 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" -#include "reaxc_types.h" #include "reaxc_bond_orders.h" +#include +#include "pair.h" +#include "reaxc_defs.h" +#include "reaxc_types.h" #include "reaxc_list.h" #include "reaxc_vector.h" diff --git a/src/USER-REAXC/reaxc_bonds.cpp b/src/USER-REAXC/reaxc_bonds.cpp index 48fb872324695ef3f9288e32e3f78f752127b9da..4cfd2a3c3aa3fb5c8773ec0eacf0b1d5cfeea5d1 100644 --- a/src/USER-REAXC/reaxc_bonds.cpp +++ b/src/USER-REAXC/reaxc_bonds.cpp @@ -24,12 +24,11 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_bonds.h" -#include "reaxc_bond_orders.h" +#include +#include "pair.h" +#include "reaxc_defs.h" #include "reaxc_list.h" -#include "reaxc_tool_box.h" -#include "reaxc_vector.h" void Bonds( reax_system *system, control_params * /*control*/, simulation_data *data, storage *workspace, reax_list **lists, diff --git a/src/USER-REAXC/reaxc_control.cpp b/src/USER-REAXC/reaxc_control.cpp index 535226fff8935ea1f4977f299f3ba72285d4b4be..12aa989fa211ee101bef0252600ef946474dbab5 100644 --- a/src/USER-REAXC/reaxc_control.cpp +++ b/src/USER-REAXC/reaxc_control.cpp @@ -24,8 +24,10 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_control.h" +#include +#include +#include "reaxc_defs.h" #include "reaxc_tool_box.h" #include "error.h" diff --git a/src/USER-REAXC/reaxc_ffield.cpp b/src/USER-REAXC/reaxc_ffield.cpp index 9534637645f0a055839339d53c4c626b5a194bbc..e3a6645fc2c09d5e3009490ddcd5f327460ee202 100644 --- a/src/USER-REAXC/reaxc_ffield.cpp +++ b/src/USER-REAXC/reaxc_ffield.cpp @@ -24,12 +24,16 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" -#include "error.h" #include "reaxc_ffield.h" +#include +#include +#include +#include +#include +#include "reaxc_defs.h" +#include "error.h" #include "reaxc_tool_box.h" - char Read_Force_Field( FILE *fp, reax_interaction *reax, control_params *control ) { diff --git a/src/USER-REAXC/reaxc_ffield.h b/src/USER-REAXC/reaxc_ffield.h index 7cef730f91f26ece468fff9e551df9ca04e9bcfd..b6fe1c9ea91582a125b74d64a8c5c5a42fe01acd 100644 --- a/src/USER-REAXC/reaxc_ffield.h +++ b/src/USER-REAXC/reaxc_ffield.h @@ -28,6 +28,7 @@ #define __FFIELD_H_ #include "reaxc_types.h" +#include char Read_Force_Field( FILE*, reax_interaction*, control_params* ); diff --git a/src/USER-REAXC/reaxc_forces.cpp b/src/USER-REAXC/reaxc_forces.cpp index 186cde681a3841c35b62ec2698c18e268f549dd0..6cd627f05dca93eec0123a13b1cfda5076ba0400 100644 --- a/src/USER-REAXC/reaxc_forces.cpp +++ b/src/USER-REAXC/reaxc_forces.cpp @@ -24,24 +24,22 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_forces.h" +#include +#include +#include #include "reaxc_bond_orders.h" #include "reaxc_bonds.h" #include "reaxc_hydrogen_bonds.h" -#include "reaxc_io_tools.h" #include "reaxc_list.h" -#include "reaxc_lookup.h" #include "reaxc_multi_body.h" #include "reaxc_nonbonded.h" -#include "reaxc_tool_box.h" #include "reaxc_torsion_angles.h" #include "reaxc_valence_angles.h" #include "reaxc_vector.h" #include "error.h" - interaction_function Interaction_Functions[NUM_INTRS]; void Dummy_Interaction( reax_system * /*system*/, control_params * /*control*/, diff --git a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp index be34df75718d824e196aff40d652ce66ec1f9506..5929703bad7ab138003ded99d9d7cc495a3b5ab3 100644 --- a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp +++ b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp @@ -24,9 +24,10 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_hydrogen_bonds.h" -#include "reaxc_bond_orders.h" +#include +#include "pair.h" +#include "reaxc_defs.h" #include "reaxc_list.h" #include "reaxc_valence_angles.h" #include "reaxc_vector.h" diff --git a/src/USER-REAXC/reaxc_init_md.cpp b/src/USER-REAXC/reaxc_init_md.cpp index df5de49034b9e1400e72cc48e4815d8a53351ed0..966ad78c34b70c953baaf832edc4e91f98842a31 100644 --- a/src/USER-REAXC/reaxc_init_md.cpp +++ b/src/USER-REAXC/reaxc_init_md.cpp @@ -24,17 +24,19 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_init_md.h" +#include +#include +#include +#include +#include "reaxc_defs.h" #include "reaxc_allocate.h" #include "reaxc_forces.h" #include "reaxc_io_tools.h" #include "reaxc_list.h" #include "reaxc_lookup.h" #include "reaxc_reset_tools.h" -#include "reaxc_system_props.h" #include "reaxc_tool_box.h" -#include "reaxc_vector.h" #include "error.h" diff --git a/src/USER-REAXC/reaxc_init_md.h b/src/USER-REAXC/reaxc_init_md.h index ab519a4c7230e3496f11e0d998780d1eee715231..5d593f50eafe968c24b04c4e0b25d142c6d57424 100644 --- a/src/USER-REAXC/reaxc_init_md.h +++ b/src/USER-REAXC/reaxc_init_md.h @@ -28,7 +28,7 @@ #define __INIT_MD_H_ #include "reaxc_types.h" - +#include void Initialize( reax_system*, control_params*, simulation_data*, storage*, reax_list**, output_controls*, mpi_datatypes*, MPI_Comm ); diff --git a/src/USER-REAXC/reaxc_io_tools.cpp b/src/USER-REAXC/reaxc_io_tools.cpp index 51aa8bca0fad8f048a635e13d6531b63f62c8cf5..f68a2a2abbc1aefbc26d0a491efe7a32aaa96b4c 100644 --- a/src/USER-REAXC/reaxc_io_tools.cpp +++ b/src/USER-REAXC/reaxc_io_tools.cpp @@ -24,15 +24,12 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" -#include "update.h" #include "reaxc_io_tools.h" -#include "reaxc_list.h" -#include "reaxc_reset_tools.h" +#include +#include +#include "reaxc_defs.h" #include "reaxc_system_props.h" -#include "reaxc_tool_box.h" #include "reaxc_traj.h" -#include "reaxc_vector.h" int Init_Output_Files( reax_system *system, control_params *control, output_controls *out_control, mpi_datatypes *mpi_data, @@ -85,7 +82,7 @@ int Init_Output_Files( reax_system *system, control_params *control, /************************ close output files ************************/ -int Close_Output_Files( reax_system *system, control_params *control, +int Close_Output_Files( reax_system *system, control_params * /* control */, output_controls *out_control, mpi_datatypes * /*mpi_data*/ ) { if (out_control->write_steps > 0) diff --git a/src/USER-REAXC/reaxc_list.cpp b/src/USER-REAXC/reaxc_list.cpp index cd4f815286341f2ed80c88b5a08121d68a0940d4..53bd05bc8d424ef2c63f4954967ba4598197536a 100644 --- a/src/USER-REAXC/reaxc_list.cpp +++ b/src/USER-REAXC/reaxc_list.cpp @@ -24,8 +24,8 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_list.h" +#include "reaxc_defs.h" #include "reaxc_tool_box.h" #include "error.h" diff --git a/src/USER-REAXC/reaxc_lookup.cpp b/src/USER-REAXC/reaxc_lookup.cpp index 8d33a33fba3a4f1b039a54d04b2b543cf2f4851a..622483fdc9ad4ea43d05504ab6ff6741be669ccf 100644 --- a/src/USER-REAXC/reaxc_lookup.cpp +++ b/src/USER-REAXC/reaxc_lookup.cpp @@ -24,12 +24,13 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_lookup.h" +#include +#include +#include "reaxc_defs.h" #include "reaxc_nonbonded.h" #include "reaxc_tool_box.h" - void Tridiagonal_Solve( const double *a, const double *b, double *c, double *d, double *x, unsigned int n){ int i; diff --git a/src/USER-REAXC/reaxc_lookup.h b/src/USER-REAXC/reaxc_lookup.h index 3fd0c2581a87170bd784229d23e2275039d71990..3aae7e0b631841513320421edc38be9fd04fd144 100644 --- a/src/USER-REAXC/reaxc_lookup.h +++ b/src/USER-REAXC/reaxc_lookup.h @@ -28,6 +28,7 @@ #define __LOOKUP_H_ #include "reaxc_types.h" +namespace LAMMPS_NS { class Error; } void Tridiagonal_Solve( const double *a, const double *b, double *c, double *d, double *x, unsigned int n); @@ -35,8 +36,9 @@ void Tridiagonal_Solve( const double *a, const double *b, void Natural_Cubic_Spline( LAMMPS_NS::Error*, const double *h, const double *f, cubic_spline_coef *coef, unsigned int n ); -void Complete_Cubic_Spline( LAMMPS_NS::Error*, const double *h, const double *f, double v0, double vlast, - cubic_spline_coef *coef, unsigned int n ); +void Complete_Cubic_Spline( LAMMPS_NS::Error*, const double *h, const double *f, + double v0, double vlast, cubic_spline_coef *coef, + unsigned int n ); int Init_Lookup_Tables( reax_system*, control_params*, storage*, mpi_datatypes*, char* ); diff --git a/src/USER-REAXC/reaxc_multi_body.cpp b/src/USER-REAXC/reaxc_multi_body.cpp index f7d72a2678ed61090c07a199662518a8a69717ae..ed1a3d5ac1e0190e33ec81a878ea5459236f88da 100644 --- a/src/USER-REAXC/reaxc_multi_body.cpp +++ b/src/USER-REAXC/reaxc_multi_body.cpp @@ -24,11 +24,12 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_multi_body.h" -#include "reaxc_bond_orders.h" +#include +#include +#include "pair.h" +#include "reaxc_defs.h" #include "reaxc_list.h" -#include "reaxc_vector.h" void Atom_Energy( reax_system *system, control_params *control, simulation_data *data, storage *workspace, reax_list **lists, diff --git a/src/USER-REAXC/reaxc_nonbonded.cpp b/src/USER-REAXC/reaxc_nonbonded.cpp index b0fea8c1b9cb965dc36f0e8aee7a18734e832f01..497a1a0ebecd5eaa348cfad4e0ffbeaf0d070f56 100644 --- a/src/USER-REAXC/reaxc_nonbonded.cpp +++ b/src/USER-REAXC/reaxc_nonbonded.cpp @@ -24,10 +24,11 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" -#include "reaxc_types.h" #include "reaxc_nonbonded.h" -#include "reaxc_bond_orders.h" +#include +#include "pair.h" +#include "reaxc_defs.h" +#include "reaxc_types.h" #include "reaxc_list.h" #include "reaxc_vector.h" diff --git a/src/USER-REAXC/reaxc_reset_tools.cpp b/src/USER-REAXC/reaxc_reset_tools.cpp index e00656694c66b268162fee5f5a942766539f0a22..91b1a9e14f940d45e52cf9c8d8b44a0dd534ec7a 100644 --- a/src/USER-REAXC/reaxc_reset_tools.cpp +++ b/src/USER-REAXC/reaxc_reset_tools.cpp @@ -24,8 +24,9 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_reset_tools.h" +#include +#include "reaxc_defs.h" #include "reaxc_list.h" #include "reaxc_tool_box.h" #include "reaxc_vector.h" diff --git a/src/USER-REAXC/reaxc_system_props.cpp b/src/USER-REAXC/reaxc_system_props.cpp index 5024feffcf0c8fe8056a5286ce485a6e090ecee6..166f070be6ae5a80556c1370a662cfacbbc34039 100644 --- a/src/USER-REAXC/reaxc_system_props.cpp +++ b/src/USER-REAXC/reaxc_system_props.cpp @@ -24,11 +24,9 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_system_props.h" -#include "reaxc_tool_box.h" -#include "reaxc_vector.h" - +#include +#include "reaxc_defs.h" void Compute_System_Energy( reax_system *system, simulation_data *data, MPI_Comm comm ) diff --git a/src/USER-REAXC/reaxc_system_props.h b/src/USER-REAXC/reaxc_system_props.h index 161060e1849222f7bff553db18ffe8adb9cd75b0..4d80e229664f72aff562629d7cc9ba0e4317acf8 100644 --- a/src/USER-REAXC/reaxc_system_props.h +++ b/src/USER-REAXC/reaxc_system_props.h @@ -28,6 +28,7 @@ #define __SYSTEM_PROP_H_ #include "reaxc_types.h" +#include void Compute_System_Energy( reax_system*, simulation_data*, MPI_Comm ); diff --git a/src/USER-REAXC/reaxc_tool_box.cpp b/src/USER-REAXC/reaxc_tool_box.cpp index ffe42e37bbf668bd3069071b4704f9b746e92e5b..811c2ed0eee6e158281088a3cfc86d9ebcf99e11 100644 --- a/src/USER-REAXC/reaxc_tool_box.cpp +++ b/src/USER-REAXC/reaxc_tool_box.cpp @@ -24,8 +24,15 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_tool_box.h" +#include +#include +#include +#include "reaxc_defs.h" + +#if !defined(_MSC_VER) +#include +#endif #include "error.h" diff --git a/src/USER-REAXC/reaxc_tool_box.h b/src/USER-REAXC/reaxc_tool_box.h index 0465376dba76af1d2c6daa87a1f78dffdbea1df1..b3258192652463e2446e72dfeb35177f779e2a47 100644 --- a/src/USER-REAXC/reaxc_tool_box.h +++ b/src/USER-REAXC/reaxc_tool_box.h @@ -28,7 +28,7 @@ #define __TOOL_BOX_H_ #include "reaxc_types.h" -#include "reaxc_defs.h" +namespace LAMMPS_NS { class Error; } /* from system_props.h */ double Get_Time( ); diff --git a/src/USER-REAXC/reaxc_torsion_angles.cpp b/src/USER-REAXC/reaxc_torsion_angles.cpp index ed76368d68379f87c626c6b66328a2a83ba78e28..ce944b217f709aea7247c29a55079e4cf42a799e 100644 --- a/src/USER-REAXC/reaxc_torsion_angles.cpp +++ b/src/USER-REAXC/reaxc_torsion_angles.cpp @@ -24,11 +24,11 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_torsion_angles.h" -#include "reaxc_bond_orders.h" +#include +#include "pair.h" +#include "reaxc_defs.h" #include "reaxc_list.h" -#include "reaxc_tool_box.h" #include "reaxc_vector.h" #define MIN_SINE 1e-10 diff --git a/src/USER-REAXC/reaxc_traj.cpp b/src/USER-REAXC/reaxc_traj.cpp index 356d7b6eeb0bb3d180d70e69de145c6bf974be02..fb493feae52c1f1671468b4a43469ac6108a096f 100644 --- a/src/USER-REAXC/reaxc_traj.cpp +++ b/src/USER-REAXC/reaxc_traj.cpp @@ -24,10 +24,13 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_traj.h" +#include +#include +#include +#include +#include "reaxc_defs.h" #include "reaxc_list.h" -#include "reaxc_tool_box.h" #include "error.h" diff --git a/src/USER-REAXC/reaxc_types.h b/src/USER-REAXC/reaxc_types.h index 0821c065cc55525f21d8ac9b5706f6d4581ca953..319c37392789af4a7b1b1698d1c934d8e2972022 100644 --- a/src/USER-REAXC/reaxc_types.h +++ b/src/USER-REAXC/reaxc_types.h @@ -27,19 +27,11 @@ #ifndef __REAX_TYPES_H_ #define __REAX_TYPES_H_ -#include #include "lmptype.h" - -#include -#include +#include #include -#include -#include -#include -#include #include "accelerator_kokkos.h" - namespace LAMMPS_NS { class Error;} #if defined LMP_USER_OMP diff --git a/src/USER-REAXC/reaxc_valence_angles.cpp b/src/USER-REAXC/reaxc_valence_angles.cpp index 4ba870b6d9140abc7d3b84ae95edf9e94bba2f3e..560955fa9d32f35887eaf86efbd42fad744424bb 100644 --- a/src/USER-REAXC/reaxc_valence_angles.cpp +++ b/src/USER-REAXC/reaxc_valence_angles.cpp @@ -24,9 +24,10 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_valence_angles.h" -#include "reaxc_bond_orders.h" +#include +#include "pair.h" +#include "reaxc_defs.h" #include "reaxc_list.h" #include "reaxc_vector.h" diff --git a/src/USER-REAXC/reaxc_vector.cpp b/src/USER-REAXC/reaxc_vector.cpp index b54d329ce9b40c7c5238ed510a4e014bcee02baf..207d745df3bb7a2d1e6a0b04830627be658566d4 100644 --- a/src/USER-REAXC/reaxc_vector.cpp +++ b/src/USER-REAXC/reaxc_vector.cpp @@ -24,9 +24,9 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_vector.h" - +#include +#include "reaxc_defs.h" void rvec_Copy( rvec dest, rvec src ) { diff --git a/src/USER-REAXC/reaxc_vector.h b/src/USER-REAXC/reaxc_vector.h index 906b200dc9358b0ad7f825af4ac5fce7c3060346..549c1f927c7448c9b0e6d3045a414dd51a9ed04b 100644 --- a/src/USER-REAXC/reaxc_vector.h +++ b/src/USER-REAXC/reaxc_vector.h @@ -27,9 +27,7 @@ #ifndef __VECTOR_H_ #define __VECTOR_H_ -#include "pair.h" #include "reaxc_types.h" -#include "reaxc_defs.h" void rvec_Copy( rvec, rvec ); void rvec_Scale( rvec, double, rvec ); diff --git a/src/USER-SDPD/fix_meso_move.cpp b/src/USER-SDPD/fix_meso_move.cpp index 85b08a2af7833df21b0cf7e4be1007e97ece435a..176cd8b8954a1973487d8e606f849b483abb73b6 100644 --- a/src/USER-SDPD/fix_meso_move.cpp +++ b/src/USER-SDPD/fix_meso_move.cpp @@ -16,11 +16,10 @@ Morteza Jalalvand (IASBS) jalalvand.m AT gmail.com ------------------------------------------------------------------------- */ +#include "fix_meso_move.h" #include #include -#include "fix_meso_move.h" #include "atom.h" -#include "group.h" #include "update.h" #include "modify.h" #include "force.h" diff --git a/src/USER-SDPD/fix_rigid_meso.cpp b/src/USER-SDPD/fix_rigid_meso.cpp index 49c9ca86146e420ee814288f92b90e344fa1b279..e93c543e726b72e9b543b76522a063a2f58fcb9e 100644 --- a/src/USER-SDPD/fix_rigid_meso.cpp +++ b/src/USER-SDPD/fix_rigid_meso.cpp @@ -27,17 +27,10 @@ and all codes relevant to that has been removed ------------------------------------------------------------------------- */ -#include #include "fix_rigid_meso.h" #include "math_extra.h" #include "atom.h" -#include "compute.h" #include "domain.h" -#include "update.h" -#include "modify.h" -#include "group.h" -#include "force.h" -#include "output.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp index db80debe51b863da4fc15625c4a510427a13d0e1..d799869db3e3a954e4f17425cc4494dfa5c4b5b9 100644 --- a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp +++ b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp @@ -18,9 +18,8 @@ references: Espanol and Revenga, Phys Rev E 67, 026705 (2003) ------------------------------------------------------------------------- */ -#include -#include #include "pair_sdpd_taitwater_isothermal.h" +#include #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp index 9c634be091a40f1cb6016414e7aa9ae8e8ca4251..604504c5a79564bfa9c3da94d46de06e82066179 100644 --- a/src/USER-SMD/atom_vec_smd.cpp +++ b/src/USER-SMD/atom_vec_smd.cpp @@ -22,24 +22,19 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "atom_vec_smd.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" -#include "fix_adapt.h" -#include "math_const.h" #include "memory.h" #include "error.h" #include "utils.h" using namespace LAMMPS_NS; -using namespace MathConst; + #define NMAT_FULL 9 #define NMAT_SYMM 6 diff --git a/src/USER-SMD/compute_smd_contact_radius.cpp b/src/USER-SMD/compute_smd_contact_radius.cpp index 8193ad6ccf4cf1e92c3875ed8276e1ad0cfb010b..46cbc602f2792d56250ce7ac2cee977f45c83f77 100644 --- a/src/USER-SMD/compute_smd_contact_radius.cpp +++ b/src/USER-SMD/compute_smd_contact_radius.cpp @@ -23,13 +23,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_smd_contact_radius.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SMD/compute_smd_damage.cpp b/src/USER-SMD/compute_smd_damage.cpp index 9603fd5c64c299ef1c89a48e66da913913328d2e..96a936cd82b7dc83128278115ddc6af7fe189271 100644 --- a/src/USER-SMD/compute_smd_damage.cpp +++ b/src/USER-SMD/compute_smd_damage.cpp @@ -23,13 +23,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_smd_damage.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SMD/compute_smd_internal_energy.cpp b/src/USER-SMD/compute_smd_internal_energy.cpp index d937aa98a42a1d3e1079fd54b9bfe36ec5a98ec4..f88da8bc33411950599dd276507aa540d1bb88a7 100644 --- a/src/USER-SMD/compute_smd_internal_energy.cpp +++ b/src/USER-SMD/compute_smd_internal_energy.cpp @@ -29,7 +29,6 @@ #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SMD/compute_smd_plastic_strain.cpp b/src/USER-SMD/compute_smd_plastic_strain.cpp index 67466ebb72cd97ea1769d81849fdc56de5457c88..c1c001a5dd79a106f32c5e0c81cd90cd207b1385 100644 --- a/src/USER-SMD/compute_smd_plastic_strain.cpp +++ b/src/USER-SMD/compute_smd_plastic_strain.cpp @@ -23,13 +23,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_smd_plastic_strain.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SMD/compute_smd_plastic_strain_rate.cpp b/src/USER-SMD/compute_smd_plastic_strain_rate.cpp index 20dfa64edd2c3762c067c54799a70746d5727354..272a2c59e5adedb984ae542ab418c09e4846542d 100644 --- a/src/USER-SMD/compute_smd_plastic_strain_rate.cpp +++ b/src/USER-SMD/compute_smd_plastic_strain_rate.cpp @@ -23,13 +23,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_smd_plastic_strain_rate.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SMD/compute_smd_rho.cpp b/src/USER-SMD/compute_smd_rho.cpp index 5c78e604b6639428ca6d088a19e661ac28c6d5a1..d9c0a99b070b65b680350580c4de285f1ef468f5 100644 --- a/src/USER-SMD/compute_smd_rho.cpp +++ b/src/USER-SMD/compute_smd_rho.cpp @@ -22,13 +22,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_smd_rho.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp index 37ad78dcea2a532af82fc097307328a585e3366d..09aeeea74aa65d755be7a69c69d7cf88b86829d2 100644 --- a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp +++ b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp @@ -22,20 +22,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include "compute_smd_tlsph_defgrad.h" #include -#include #include -#include "compute_smd_tlsph_defgrad.h" #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" -#include "pair.h" + using namespace Eigen; using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_tlsph_shape.cpp b/src/USER-SMD/compute_smd_tlsph_shape.cpp index bbab274b5cca0dd4d785ea0be2044df1e6c2cef9..ba1a9306ef6ba4401a0e58cd80365ff2140cd9be 100644 --- a/src/USER-SMD/compute_smd_tlsph_shape.cpp +++ b/src/USER-SMD/compute_smd_tlsph_shape.cpp @@ -22,13 +22,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include "compute_smd_tlsph_shape.h" #include -#include #include -#include -#include "compute_smd_tlsph_shape.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/USER-SMD/compute_smd_tlsph_strain.cpp b/src/USER-SMD/compute_smd_tlsph_strain.cpp index a94a3cd51158defab103323d007c7662efafbeac..f0061bf7a1cbd699ef8c91f67b8620963d648870 100644 --- a/src/USER-SMD/compute_smd_tlsph_strain.cpp +++ b/src/USER-SMD/compute_smd_tlsph_strain.cpp @@ -23,12 +23,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include "compute_smd_tlsph_strain.h" #include -#include #include -#include "compute_smd_tlsph_strain.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/USER-SMD/compute_smd_tlsph_stress.cpp b/src/USER-SMD/compute_smd_tlsph_stress.cpp index a54b07dd1ef5b007c9f7d9ede03bd6b8b6583c67..9c78b192ce3fb9a4e7ce7fa78f2d377a9690ccde 100644 --- a/src/USER-SMD/compute_smd_tlsph_stress.cpp +++ b/src/USER-SMD/compute_smd_tlsph_stress.cpp @@ -22,9 +22,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_smd_tlsph_stress.h" +#include #include #include -#include "compute_smd_tlsph_stress.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/USER-SMD/compute_smd_triangle_vertices.cpp b/src/USER-SMD/compute_smd_triangle_vertices.cpp index b24223b8b5f20030f4d00f59d14eb190ffefd6f3..06706a85ad6a075509c8faaaeec2b1a396fc3150 100644 --- a/src/USER-SMD/compute_smd_triangle_vertices.cpp +++ b/src/USER-SMD/compute_smd_triangle_vertices.cpp @@ -23,22 +23,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include #include "compute_smd_triangle_vertices.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" -#include "pair.h" -using namespace Eigen; using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_ulsph_strain.cpp b/src/USER-SMD/compute_smd_ulsph_strain.cpp index 89b85f7bc1cafc299fc45b55a5c88f5757b3d616..cf1535759c7635c6bc51fc42ef85f7306d0b5828 100644 --- a/src/USER-SMD/compute_smd_ulsph_strain.cpp +++ b/src/USER-SMD/compute_smd_ulsph_strain.cpp @@ -23,22 +23,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include #include "compute_smd_ulsph_strain.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" -#include "pair.h" -using namespace Eigen; using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_ulsph_stress.cpp b/src/USER-SMD/compute_smd_ulsph_stress.cpp index 7f1bbc4c29fadf300623ae243ae0ed97047ec220..ea477375ce95a49addccd5308d8992d888a730b5 100644 --- a/src/USER-SMD/compute_smd_ulsph_stress.cpp +++ b/src/USER-SMD/compute_smd_ulsph_stress.cpp @@ -22,9 +22,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_smd_ulsph_stress.h" +#include #include #include -#include "compute_smd_ulsph_stress.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/USER-SMD/compute_smd_vol.cpp b/src/USER-SMD/compute_smd_vol.cpp index 17a6b556e8ac352eab0703e4d19744d51933905d..eb1f144275406effe900d1cef15d645b969d0d33 100644 --- a/src/USER-SMD/compute_smd_vol.cpp +++ b/src/USER-SMD/compute_smd_vol.cpp @@ -22,13 +22,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_smd_vol.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SMD/fix_smd_adjust_dt.cpp b/src/USER-SMD/fix_smd_adjust_dt.cpp index f015c6c4dfdbe4357e1714bdcd4bfc10e6017630..ab6dd5ef5c50b5c97c5eb552b305ae6a34c3df57 100644 --- a/src/USER-SMD/fix_smd_adjust_dt.cpp +++ b/src/USER-SMD/fix_smd_adjust_dt.cpp @@ -22,21 +22,14 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_smd_adjust_dt.h" -#include "atom.h" +#include +#include #include "update.h" -#include "integrate.h" -#include "domain.h" -#include "lattice.h" #include "force.h" #include "pair.h" #include "modify.h" #include "fix.h" -#include "output.h" -#include "dump.h" #include "comm.h" #include "error.h" diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.cpp b/src/USER-SMD/fix_smd_integrate_tlsph.cpp index f931ae94ffcaca9f599d3ad26d67b92ee224cf5a..8464bed60909067cb7ae620fa672bff62f59190f 100644 --- a/src/USER-SMD/fix_smd_integrate_tlsph.cpp +++ b/src/USER-SMD/fix_smd_integrate_tlsph.cpp @@ -22,22 +22,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include "fix_smd_integrate_tlsph.h" +#include #include -#include #include -#include "fix_smd_integrate_tlsph.h" #include "atom.h" #include "force.h" #include "update.h" #include "error.h" #include "pair.h" -#include "neigh_list.h" -#include "domain.h" -#include "neighbor.h" #include "comm.h" -#include "modify.h" using namespace Eigen; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.cpp b/src/USER-SMD/fix_smd_integrate_ulsph.cpp index 6c4705eb96ef45424522f418376d1de1911f294d..0f0d224f95c3ad0e2b883e3d97a11d179726efd3 100644 --- a/src/USER-SMD/fix_smd_integrate_ulsph.cpp +++ b/src/USER-SMD/fix_smd_integrate_ulsph.cpp @@ -22,25 +22,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "fix_smd_integrate_ulsph.h" #include -#include #include #include -#include "fix_smd_integrate_ulsph.h" #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "update.h" -#include "integrate.h" -#include "respa.h" -#include "memory.h" #include "error.h" #include "pair.h" -#include "domain.h" using namespace Eigen; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp index fe8695b23ec341b39e80af441eaf5250e8435952..cbaad9ac4cf62e39ccfb0b7d66ea0ad18a900146 100644 --- a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp +++ b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp @@ -22,25 +22,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include "fix_smd_move_triangulated_surface.h" #include -#include +#include #include -#include "fix_smd_move_triangulated_surface.h" #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "update.h" -#include "integrate.h" -#include "respa.h" -#include "memory.h" #include "error.h" -#include "pair.h" -#include "domain.h" #include "math_const.h" using namespace Eigen; diff --git a/src/USER-SMD/fix_smd_setvel.cpp b/src/USER-SMD/fix_smd_setvel.cpp index 4bc8b5127b07251a8f5492f4e919ca3077445074..2964ded5445e27ceaa7d98ac830918d4c7bb75b3 100644 --- a/src/USER-SMD/fix_smd_setvel.cpp +++ b/src/USER-SMD/fix_smd_setvel.cpp @@ -23,9 +23,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_smd_setvel.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp index a2813cc3cae52d8a7b3bd1f09fec1ef333823d1d..6aa23fe3b2f7be3b588b5cb174d7ccc8091cff33 100644 --- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp +++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp @@ -24,20 +24,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_smd_tlsph_reference_configuration.h" #include -#include -#include #include -#include "fix_smd_tlsph_reference_configuration.h" #include "atom.h" #include "comm.h" -#include "neighbor.h" #include "neigh_list.h" #include "lattice.h" #include "force.h" #include "pair.h" #include "update.h" -#include "modify.h" #include "memory.h" #include "error.h" #include "domain.h" diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.h b/src/USER-SMD/fix_smd_tlsph_reference_configuration.h index 8549621c2f9765f5f8813bdc7d2c4f17ba0d43d0..5f952bde934ad4e628b63446e3de45fdaa1531e0 100644 --- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.h +++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.h @@ -35,7 +35,6 @@ FixStyle(SMD_TLSPH_NEIGHBORS,FixSMD_TLSPH_ReferenceConfiguration) #define LMP_FIX_SMD_TLSPH_REFERENCE_H #include "fix.h" -#include "my_page.h" namespace LAMMPS_NS { diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp index a37ba67a800c56eb8f30e510fca8e4915c293431..9183bcd9eafd5fa8efb1c7003462fc76559abafc 100644 --- a/src/USER-SMD/fix_smd_wall_surface.cpp +++ b/src/USER-SMD/fix_smd_wall_surface.cpp @@ -15,21 +15,15 @@ Contributing authors: Mike Parks (SNL), Ezwanur Rahman, J.T. Foster (UTSA) ------------------------------------------------------------------------- */ -#include +#include "fix_smd_wall_surface.h" +#include #include -#include +#include #include -#include "fix_smd_wall_surface.h" #include "atom.h" #include "domain.h" #include "force.h" #include "comm.h" -#include "update.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "pair.h" -#include "lattice.h" #include "memory.h" #include "error.h" #include "atom_vec.h" diff --git a/src/USER-SMD/pair_smd_hertz.cpp b/src/USER-SMD/pair_smd_hertz.cpp index 541be9f05cb16c8c7134c1f84221e6e8729ea29b..97be94d83319b38b131301fe57adb7de12aff27b 100644 --- a/src/USER-SMD/pair_smd_hertz.cpp +++ b/src/USER-SMD/pair_smd_hertz.cpp @@ -26,17 +26,14 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ +#include "pair_smd_hertz.h" +#include #include -#include #include #include -#include "pair_smd_hertz.h" #include "atom.h" #include "domain.h" #include "force.h" -#include "update.h" -#include "modify.h" -#include "fix.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp index 1d7bbca780bbd0a104458d2f697b5f7c17a26b6d..82b7c8ff9d94f11e6b7e6738a3d9331c4a694f6f 100644 --- a/src/USER-SMD/pair_smd_tlsph.cpp +++ b/src/USER-SMD/pair_smd_tlsph.cpp @@ -22,15 +22,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_smd_tlsph.h" +#include #include -#include -#include #include -#include +#include #include -#include #include -#include "pair_smd_tlsph.h" #include "fix_smd_tlsph_reference_configuration.h" #include "atom.h" #include "domain.h" @@ -41,12 +39,9 @@ #include "fix.h" #include "comm.h" #include "neighbor.h" -#include "neigh_list.h" #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "math_special.h" -#include "update.h" #include "smd_material_models.h" #include "smd_kernels.h" #include "smd_math.h" @@ -1781,9 +1776,8 @@ void PairTlsph::init_style() { optional granular history list ------------------------------------------------------------------------- */ -void PairTlsph::init_list(int id, NeighList *ptr) { - if (id == 0) - list = ptr; +void PairTlsph::init_list(int id, class NeighList *ptr) { + if (id == 0) list = ptr; } /* ---------------------------------------------------------------------- @@ -1791,8 +1785,7 @@ void PairTlsph::init_list(int id, NeighList *ptr) { ------------------------------------------------------------------------- */ double PairTlsph::memory_usage() { - - return 118 * nmax * sizeof(double); + return 118.0 * nmax * sizeof(double); } /* ---------------------------------------------------------------------- diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/USER-SMD/pair_smd_triangulated_surface.cpp index d3a498337950f1c354ee1042c2c6373a761f3bca..f9052be08714e7246631b533f3c10b6e67593f20 100644 --- a/src/USER-SMD/pair_smd_triangulated_surface.cpp +++ b/src/USER-SMD/pair_smd_triangulated_surface.cpp @@ -26,20 +26,15 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ +#include "pair_smd_triangulated_surface.h" +#include #include -#include #include #include -#include -#include #include -#include "pair_smd_triangulated_surface.h" #include "atom.h" #include "domain.h" #include "force.h" -#include "update.h" -#include "modify.h" -#include "fix.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp index 2c4a2de989a1511054b2335d6ed47332e162d45d..b53eb779de6dd1dc8ba38ec88554581d41736aee 100644 --- a/src/USER-SMD/pair_smd_ulsph.cpp +++ b/src/USER-SMD/pair_smd_ulsph.cpp @@ -22,19 +22,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_smd_ulsph.h" +#include #include -#include -#include #include -#include -#include -#include "pair_smd_ulsph.h" +#include +#include #include "atom.h" #include "domain.h" #include "force.h" #include "update.h" -#include "modify.h" -#include "fix.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-SMD/smd_material_models.cpp b/src/USER-SMD/smd_material_models.cpp index 42134288720406df76ebabdce03393bdfe6df019..5ee67fbb4e2f89a3aaf8c138c40c1b07d9b86c99 100644 --- a/src/USER-SMD/smd_material_models.cpp +++ b/src/USER-SMD/smd_material_models.cpp @@ -21,6 +21,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "smd_material_models.h" +#include +#include +#include #include #include #include "math_special.h" diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/USER-SMTBQ/pair_smtbq.cpp index ba7f8eb88c345ec5c9add0de10a88e00d172a413..f61fc1a72ee1d058daf0d3b805928d95e9809c0d 100644 --- a/src/USER-SMTBQ/pair_smtbq.cpp +++ b/src/USER-SMTBQ/pair_smtbq.cpp @@ -38,25 +38,24 @@ . ------------------------------------------------------------------------- */ +#include "pair_smtbq.h" +#include #include -#include #include #include +#include #include -#include "pair_smtbq.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "group.h" #include "update.h" #include "math_const.h" #include "math_special.h" #include "memory.h" #include "error.h" -#include "domain.h" #include #include diff --git a/src/USER-SPH/atom_vec_meso.cpp b/src/USER-SPH/atom_vec_meso.cpp index aa3e680c61b600ccad3bbbcac1cbe6eeeb002c6e..cd7c2251ab031726afa92f98cc14c9e52416a2f0 100644 --- a/src/USER-SPH/atom_vec_meso.cpp +++ b/src/USER-SPH/atom_vec_meso.cpp @@ -11,13 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "atom_vec_meso.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/USER-SPH/compute_meso_e_atom.cpp b/src/USER-SPH/compute_meso_e_atom.cpp index e39dee2b5fb83e883e1bb8e4e8ff02892399d29a..c56243e5ed7c8be217b0e4c1d4220b27e37d2222 100644 --- a/src/USER-SPH/compute_meso_e_atom.cpp +++ b/src/USER-SPH/compute_meso_e_atom.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_meso_e_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SPH/compute_meso_rho_atom.cpp b/src/USER-SPH/compute_meso_rho_atom.cpp index eeb3f987bc7d82aad15a09a11b7cb3532e0ce8c3..b2fbd2d70a9d818033e21dfaf27ff604e927e0a3 100644 --- a/src/USER-SPH/compute_meso_rho_atom.cpp +++ b/src/USER-SPH/compute_meso_rho_atom.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_meso_rho_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SPH/compute_meso_t_atom.cpp b/src/USER-SPH/compute_meso_t_atom.cpp index dc4f3407f143ff7c75acdcee7ea7290aacf41503..bab96468dd9dc7afb8fb72342f1850d94b325c95 100644 --- a/src/USER-SPH/compute_meso_t_atom.cpp +++ b/src/USER-SPH/compute_meso_t_atom.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_meso_t_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SPH/fix_meso.cpp b/src/USER-SPH/fix_meso.cpp index b688eccfea4bff3003db9db77d77d15db7349abe..4f4e532291aac29f36bd81494e57c581414ae9f9 100644 --- a/src/USER-SPH/fix_meso.cpp +++ b/src/USER-SPH/fix_meso.cpp @@ -11,23 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_meso.h" #include "atom.h" -#include "comm.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "update.h" -#include "integrate.h" -#include "respa.h" -#include "memory.h" #include "error.h" -#include "pair.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-SPH/fix_meso_stationary.cpp b/src/USER-SPH/fix_meso_stationary.cpp index 29e8a1554c7abcb08175a27763e8846865d8e99c..b7f0675ef8b6bcdd8c467c2301fd97108b61b966 100644 --- a/src/USER-SPH/fix_meso_stationary.cpp +++ b/src/USER-SPH/fix_meso_stationary.cpp @@ -11,23 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_meso_stationary.h" #include "atom.h" -#include "comm.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "update.h" -#include "integrate.h" -#include "respa.h" -#include "memory.h" #include "error.h" -#include "pair.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-SPH/pair_sph_heatconduction.cpp b/src/USER-SPH/pair_sph_heatconduction.cpp index bafa26be89d47ef2f09c5d94ea9847c77451f91d..cff90090151eba9295b033518a44b1e359d4623a 100644 --- a/src/USER-SPH/pair_sph_heatconduction.cpp +++ b/src/USER-SPH/pair_sph_heatconduction.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_sph_heatconduction.h" +#include #include "atom.h" #include "force.h" -#include "comm.h" #include "memory.h" #include "error.h" #include "neigh_list.h" diff --git a/src/USER-SPH/pair_sph_idealgas.cpp b/src/USER-SPH/pair_sph_idealgas.cpp index db5ec964bc35da427bc312f7889b022256205882..f206bf68f561a642e273a0c41880632dda581beb 100644 --- a/src/USER-SPH/pair_sph_idealgas.cpp +++ b/src/USER-SPH/pair_sph_idealgas.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_sph_idealgas.h" +#include #include "atom.h" #include "force.h" -#include "comm.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SPH/pair_sph_lj.cpp b/src/USER-SPH/pair_sph_lj.cpp index 7d315c975cb29708171dfc411665935b6376bb5a..3173e2a47d56f05cb802c6165f93b14d1d2bc97d 100644 --- a/src/USER-SPH/pair_sph_lj.cpp +++ b/src/USER-SPH/pair_sph_lj.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_sph_lj.h" +#include #include "atom.h" #include "force.h" -#include "comm.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SPH/pair_sph_rhosum.cpp b/src/USER-SPH/pair_sph_rhosum.cpp index 842dddc7448e6e08ea6a803ee181d363bb05e92d..fa51dc37816357aedbe305ffb484b0c7a6198403 100644 --- a/src/USER-SPH/pair_sph_rhosum.cpp +++ b/src/USER-SPH/pair_sph_rhosum.cpp @@ -11,8 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_sph_rhosum.h" #include "atom.h" #include "force.h" diff --git a/src/USER-SPH/pair_sph_taitwater.cpp b/src/USER-SPH/pair_sph_taitwater.cpp index cf3c0e914bb425e69d5085f295336eda4a7ce33e..f2a34d4edd65ed4e5397eeaa82d8fb6f9cc23e3c 100644 --- a/src/USER-SPH/pair_sph_taitwater.cpp +++ b/src/USER-SPH/pair_sph_taitwater.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_sph_taitwater.h" +#include #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/USER-SPH/pair_sph_taitwater_morris.cpp b/src/USER-SPH/pair_sph_taitwater_morris.cpp index 5cbaa5959f42acfad8e28b84c7ac0274294aa3ae..9ca03e3476c746618f544d52985ca4d7b7907352 100644 --- a/src/USER-SPH/pair_sph_taitwater_morris.cpp +++ b/src/USER-SPH/pair_sph_taitwater_morris.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_sph_taitwater_morris.h" +#include #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/USER-TALLY/compute_force_tally.cpp b/src/USER-TALLY/compute_force_tally.cpp index 3339e0555b27afd0b6aae8da1a3b1e07ac06ad8e..9d15fbc44139c50cf456bb1e5a9f1302916447cd 100644 --- a/src/USER-TALLY/compute_force_tally.cpp +++ b/src/USER-TALLY/compute_force_tally.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_force_tally.h" +#include +#include #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-TALLY/compute_heat_flux_tally.cpp b/src/USER-TALLY/compute_heat_flux_tally.cpp index 2a5f724953ba9004a23473806f40323e19c63230..350bc4b4b6b75989218ef23b83dc4b3a5b33ebe2 100644 --- a/src/USER-TALLY/compute_heat_flux_tally.cpp +++ b/src/USER-TALLY/compute_heat_flux_tally.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_heat_flux_tally.h" +#include #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-TALLY/compute_pe_mol_tally.cpp b/src/USER-TALLY/compute_pe_mol_tally.cpp index 5fabd4a77b2026bf50d2d7465cb6569aa059a8b5..ce647a04c3fc966f003e945973dbd8cc03de26da 100644 --- a/src/USER-TALLY/compute_pe_mol_tally.cpp +++ b/src/USER-TALLY/compute_pe_mol_tally.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_pe_mol_tally.h" +#include #include "atom.h" #include "group.h" #include "pair.h" #include "update.h" -#include "memory.h" #include "error.h" #include "force.h" #include "comm.h" diff --git a/src/USER-TALLY/compute_pe_tally.cpp b/src/USER-TALLY/compute_pe_tally.cpp index 8e6703bde124b18d1f0952f1c0f6cc394a4bdf1d..edfa49b1b1e2a6857e950614ed9f1bb415d4fae0 100644 --- a/src/USER-TALLY/compute_pe_tally.cpp +++ b/src/USER-TALLY/compute_pe_tally.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_pe_tally.h" +#include #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-TALLY/compute_stress_tally.cpp b/src/USER-TALLY/compute_stress_tally.cpp index 07d685a9c207fddcbc58069d44bc0a04ee8c32c7..1ea096e2865592a0cc46fdef0bf72d73e9c6a968 100644 --- a/src/USER-TALLY/compute_stress_tally.cpp +++ b/src/USER-TALLY/compute_stress_tally.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_stress_tally.h" +#include #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-UEF/compute_pressure_uef.cpp b/src/USER-UEF/compute_pressure_uef.cpp index 8b6285304228970aaceb014bee9446990703ecad..adb9970c12ee1afea5316cd2891d549f15a846d0 100644 --- a/src/USER-UEF/compute_pressure_uef.cpp +++ b/src/USER-UEF/compute_pressure_uef.cpp @@ -13,21 +13,14 @@ Contributing author: David Nicholson (MIT) ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_pressure_uef.h" +#include #include "fix_nh_uef.h" #include "update.h" #include "domain.h" #include "modify.h" #include "fix.h" #include "force.h" -#include "pair.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" -#include "improper.h" #include "kspace.h" #include "error.h" diff --git a/src/USER-UEF/compute_temp_uef.cpp b/src/USER-UEF/compute_temp_uef.cpp index 999296ec7e73f54bcb664cd6bc1492826ed4ce0c..698c4452c26bcba8b42e64f32cc56e10a73d2e08 100644 --- a/src/USER-UEF/compute_temp_uef.cpp +++ b/src/USER-UEF/compute_temp_uef.cpp @@ -13,11 +13,9 @@ Contributing author: David Nicholson (MIT) ------------------------------------------------------------------------- */ -#include -#include #include "compute_temp_uef.h" +#include #include "fix_nh_uef.h" -#include "update.h" #include "modify.h" #include "fix.h" #include "error.h" diff --git a/src/USER-UEF/dump_cfg_uef.cpp b/src/USER-UEF/dump_cfg_uef.cpp index 58b3ec5a1fb8715c900bd61be9dcb037c66b73dd..8e6268eee69daab3d7bba962eeae023e08f20dce 100644 --- a/src/USER-UEF/dump_cfg_uef.cpp +++ b/src/USER-UEF/dump_cfg_uef.cpp @@ -13,15 +13,10 @@ Contributing Author: David Nicholson (MIT) ------------------------------------------------------------------------- */ - -#include -#include -#include #include "dump_cfg.h" +#include #include "atom.h" -#include "domain.h" #include "modify.h" -#include "compute.h" #include "fix.h" #include "error.h" #include "uef_utils.h" diff --git a/src/USER-UEF/fix_nh_uef.cpp b/src/USER-UEF/fix_nh_uef.cpp index bffcd7849f7535ae9f486fb7664b1722718b79b3..8873688eb794ebb96a8676ccef91ef2700e112e1 100644 --- a/src/USER-UEF/fix_nh_uef.cpp +++ b/src/USER-UEF/fix_nh_uef.cpp @@ -13,19 +13,16 @@ Contributing author: David Nicholson (MIT) ------------------------------------------------------------------------- */ +#include "fix_nh_uef.h" #include -#include #include -#include "fix_nh_uef.h" #include "atom.h" #include "force.h" -#include "group.h" #include "comm.h" #include "citeme.h" #include "irregular.h" #include "modify.h" #include "compute.h" -#include "kspace.h" #include "update.h" #include "domain.h" #include "error.h" diff --git a/src/USER-YAFF/angle_cross.cpp b/src/USER-YAFF/angle_cross.cpp index 2e6731f4943b7d3cafbe4a717e566de1ca8e6ba6..0f8861cdf5efbe6eaa341400ba21fa6ef7a95c78 100644 --- a/src/USER-YAFF/angle_cross.cpp +++ b/src/USER-YAFF/angle_cross.cpp @@ -15,10 +15,9 @@ Contributing author: Steven Vandenbrande ------------------------------------------------------------------------- */ -#include -#include -#include #include "angle_cross.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-YAFF/angle_cross.h b/src/USER-YAFF/angle_cross.h index 7709c104145a4ebad853814dcadf792e9e0f5c3e..ba958f98ec410940283e98d4f157a80461e8ad5b 100644 --- a/src/USER-YAFF/angle_cross.h +++ b/src/USER-YAFF/angle_cross.h @@ -20,7 +20,6 @@ AngleStyle(cross,AngleCross) #ifndef LMP_ANGLE_CROSS_H #define LMP_ANGLE_CROSS_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-YAFF/angle_mm3.cpp b/src/USER-YAFF/angle_mm3.cpp index 53cb11b5df6f96fb4e442799d7c42477c64ba018..b90db37afac4069fe2bc232aca7cbc24fbe8e34d 100644 --- a/src/USER-YAFF/angle_mm3.cpp +++ b/src/USER-YAFF/angle_mm3.cpp @@ -15,10 +15,9 @@ Contributing author: Steven Vandenbrande ------------------------------------------------------------------------- */ -#include -#include -#include #include "angle_mm3.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-YAFF/angle_mm3.h b/src/USER-YAFF/angle_mm3.h index 2d19b4d1b464e6e534dcfa9e0a0acafc0b563581..985c4bb9b4744d2df3d8d19120dca9f9395fd857 100644 --- a/src/USER-YAFF/angle_mm3.h +++ b/src/USER-YAFF/angle_mm3.h @@ -20,7 +20,6 @@ AngleStyle(mm3,AngleMM3) #ifndef LMP_ANGLE_MM3_H #define LMP_ANGLE_MM3_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-YAFF/bond_mm3.cpp b/src/USER-YAFF/bond_mm3.cpp index ee1ebcdd6123c2304e7e788c663a2b60de1ae2d6..2a7d5d184305f810a6d83f56d5fd680a29bcd65c 100644 --- a/src/USER-YAFF/bond_mm3.cpp +++ b/src/USER-YAFF/bond_mm3.cpp @@ -15,12 +15,11 @@ Contributing author: Steven Vandenbrande ------------------------------------------------------------------------- */ -#include -#include #include "bond_mm3.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/USER-YAFF/bond_mm3.h b/src/USER-YAFF/bond_mm3.h index 9711d895290e18aa40a4cfb6e35695673e176f44..56f3136ea81a5376d21f67c3e3cee136ad956f02 100644 --- a/src/USER-YAFF/bond_mm3.h +++ b/src/USER-YAFF/bond_mm3.h @@ -20,7 +20,6 @@ BondStyle(mm3,BondMM3) #ifndef LMP_BOND_MM3_H #define LMP_BOND_MM3_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/USER-YAFF/improper_distharm.cpp b/src/USER-YAFF/improper_distharm.cpp index b45087a9ab8a99d94e00469c1f3682ad757ebf6d..2b62f827e771afd38c0f1b769275e748d0370505 100644 --- a/src/USER-YAFF/improper_distharm.cpp +++ b/src/USER-YAFF/improper_distharm.cpp @@ -16,16 +16,14 @@ improper_distance code by Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ -#include -#include -#include #include "improper_distharm.h" +#include +#include #include "atom.h" #include "comm.h" #include "neighbor.h" #include "domain.h" #include "force.h" -#include "update.h" #include "memory.h" #include "error.h" diff --git a/src/USER-YAFF/improper_distharm.h b/src/USER-YAFF/improper_distharm.h index b8b9ae780e06d592f10a0e7b27926b4ce916a5b6..0a8d34ac444b22acbfe028c856e78d642476f955 100644 --- a/src/USER-YAFF/improper_distharm.h +++ b/src/USER-YAFF/improper_distharm.h @@ -20,7 +20,6 @@ ImproperStyle(distharm,ImproperDistHarm) #ifndef LMP_IMPROPER_DISTHARM_H #define LMP_IMPROPER_DISTHARM_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/USER-YAFF/improper_sqdistharm.cpp b/src/USER-YAFF/improper_sqdistharm.cpp index ae702820cb9b200af6ec2e60e178959b31f9b701..bcc0549f7ec4ca58fcdd1423c83a6f3bed4dc59a 100644 --- a/src/USER-YAFF/improper_sqdistharm.cpp +++ b/src/USER-YAFF/improper_sqdistharm.cpp @@ -16,16 +16,14 @@ improper_distance code by Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ -#include -#include -#include #include "improper_sqdistharm.h" +#include +#include #include "atom.h" #include "comm.h" #include "neighbor.h" #include "domain.h" #include "force.h" -#include "update.h" #include "memory.h" #include "error.h" diff --git a/src/USER-YAFF/improper_sqdistharm.h b/src/USER-YAFF/improper_sqdistharm.h index 301b5066cbabc4d8a877dd0b56caf603634ac450..3aceb01a037e01df50e10eee387477789b4b8920 100644 --- a/src/USER-YAFF/improper_sqdistharm.h +++ b/src/USER-YAFF/improper_sqdistharm.h @@ -20,7 +20,6 @@ ImproperStyle(sqdistharm,ImproperSQDistHarm) #ifndef LMP_IMPROPER_SQDISTHARM_H #define LMP_IMPROPER_SQDISTHARM_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp index f37dcc3ed1ad78be4275b28d9642f3a47650307f..ab983a78bca0fa1cfd2e78fe18b0d4d0d5de40bd 100644 --- a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp @@ -15,17 +15,15 @@ Contributing author: Steven Vandenbrande ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_switch3_coulgauss_long.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp index 931ed1d116616a6b603c40a4dbc90cead2e438d1..4175ef915d5cf3d421f7f30c3d804c80b5ff69a1 100644 --- a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp @@ -15,17 +15,15 @@ Contributing author: Steven Vandenbrande ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_mm3_switch3_coulgauss_long.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/VORONOI/compute_voronoi_atom.cpp b/src/VORONOI/compute_voronoi_atom.cpp index 860126fa7736b95e3f65ae788298a321ded554dd..d5976f85d3cd02d71ba169b6f98a25188f27282b 100644 --- a/src/VORONOI/compute_voronoi_atom.cpp +++ b/src/VORONOI/compute_voronoi_atom.cpp @@ -15,16 +15,14 @@ Contributing author: Daniel Schwen ------------------------------------------------------------------------- */ +#include "compute_voronoi_atom.h" #include #include #include -#include -#include "voro++.hh" -#include "compute_voronoi_atom.h" +#include #include "atom.h" #include "group.h" #include "update.h" -#include "modify.h" #include "domain.h" #include "memory.h" #include "error.h" diff --git a/src/accelerator_kokkos.h b/src/accelerator_kokkos.h index 74bd470572b252a6169ee3d76c098b9ef4034d9e..a3fff2fe164cf0c2aeb514a8f248ef33520c9cd9 100644 --- a/src/accelerator_kokkos.h +++ b/src/accelerator_kokkos.h @@ -19,14 +19,14 @@ #ifdef LMP_KOKKOS -#include "kokkos.h" -#include "atom_kokkos.h" -#include "comm_kokkos.h" -#include "comm_tiled_kokkos.h" -#include "domain_kokkos.h" -#include "neighbor_kokkos.h" -#include "memory_kokkos.h" -#include "modify_kokkos.h" +#include "kokkos.h" // IWYU pragma: export +#include "atom_kokkos.h" // IWYU pragma: export +#include "comm_kokkos.h" // IWYU pragma: export +#include "comm_tiled_kokkos.h" // IWYU pragma: export +#include "domain_kokkos.h" // IWYU pragma: export +#include "neighbor_kokkos.h" // IWYU pragma: export +#include "memory_kokkos.h" // IWYU pragma: export +#include "modify_kokkos.h" // IWYU pragma: export #define LAMMPS_INLINE KOKKOS_INLINE_FUNCTION diff --git a/src/angle.cpp b/src/angle.cpp index 2a297990ac83046595212b2819d621bfa6ab2b1a..1b9532ea32205c243cde8eea3d2c10952f71588c 100644 --- a/src/angle.cpp +++ b/src/angle.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "angle.h" #include "atom.h" #include "comm.h" diff --git a/src/angle.h b/src/angle.h index ddd12ab7b809bde44846e8e192b677670f9788d4..c0d1199dcdf6562aeecf5e16b18a5a419f48d6f6 100644 --- a/src/angle.h +++ b/src/angle.h @@ -14,8 +14,7 @@ #ifndef LMP_ANGLE_H #define LMP_ANGLE_H -#include -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/angle_deprecated.cpp b/src/angle_deprecated.cpp index b5af217b7b00c12d64de91354dc3c9f1994f2ac1..cc29c9978e62657e2bf8c2c19b218afaeeabe8d5 100644 --- a/src/angle_deprecated.cpp +++ b/src/angle_deprecated.cpp @@ -15,12 +15,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "angle_deprecated.h" +#include #include "angle_hybrid.h" #include "comm.h" #include "force.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -43,7 +44,7 @@ void AngleDeprecated::settings(int, char **) // hybrid substyles are created in AngleHybrid::settings(), so when this is // called, our style was just added at the end of the list of substyles - if (strncmp(my_style,"hybrid",6) == 0) { + if (utils::strmatch(my_style,"^hybrid")) { AngleHybrid *hybrid = (AngleHybrid *)force->angle; my_style = hybrid->keywords[hybrid->nstyles]; } diff --git a/src/angle_hybrid.cpp b/src/angle_hybrid.cpp index d6c616fae409e46ce3241252211e4b8396906ba7..6ffbc19d08eae3814e634982e8dc3d4639e41ed4 100644 --- a/src/angle_hybrid.cpp +++ b/src/angle_hybrid.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "angle_hybrid.h" +#include #include #include -#include "angle_hybrid.h" #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/angle_hybrid.h b/src/angle_hybrid.h index 4fde71e43f1251822355823dab06e941d8f33f31..730d55b0e20b7b330393e24e83cc14ca5ac4c560 100644 --- a/src/angle_hybrid.h +++ b/src/angle_hybrid.h @@ -20,7 +20,6 @@ AngleStyle(hybrid,AngleHybrid) #ifndef LMP_ANGLE_HYBRID_H #define LMP_ANGLE_HYBRID_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/angle_zero.cpp b/src/angle_zero.cpp index 6eb127fa581bec6db9dc5ef5c73e24421d5802b1..3c92b852b39b54abfd2fb47431eebf65daed68be 100644 --- a/src/angle_zero.cpp +++ b/src/angle_zero.cpp @@ -15,10 +15,9 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include -#include #include "angle_zero.h" +#include +#include #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/angle_zero.h b/src/angle_zero.h index b91be5c8d72a5330cabd8b3dca8d0cb8c450ab69..bc1ce0725f0efd2a7e8b2ac84e991163510faaea 100644 --- a/src/angle_zero.h +++ b/src/angle_zero.h @@ -20,7 +20,6 @@ AngleStyle(zero,AngleZero) #ifndef LMP_ANGLE_ZERO_H #define LMP_ANGLE_ZERO_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/atom.cpp b/src/atom.cpp index e5a982d6204dba49ab2cc7f826eec09e655b73f0..24ad2d40da26e547200483b3b9c829aa5a468177 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -11,13 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "atom.h" #include -#include -#include +#include #include #include -#include -#include "atom.h" #include "style_atom.h" #include "atom_vec.h" #include "atom_vec_ellipsoid.h" @@ -27,15 +25,12 @@ #include "modify.h" #include "fix.h" #include "compute.h" -#include "output.h" -#include "thermo.h" #include "update.h" #include "domain.h" #include "group.h" #include "input.h" #include "variable.h" #include "molecule.h" -#include "atom_masks.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/atom_map.cpp b/src/atom_map.cpp index e9cd590624c2ded25b55bdbb15af6a9cfb4d4e39..7949e327a910d107c417cc0d73eaed0654668075 100644 --- a/src/atom_map.cpp +++ b/src/atom_map.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom.h" +#include +#include #include "comm.h" #include "memory.h" #include "error.h" diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index d4bea15d0b0300ad3e20ac823f63969437b55d85..1ea085b869c081357f0226a3b8bc51284b939366 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "atom_vec.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/atom_vec.h b/src/atom_vec.h index 87fb35d9c72042e478d8cb8dde75549fddd70b17..26c181be1e8ae5c9cfba244bd6936431b0d49969 100644 --- a/src/atom_vec.h +++ b/src/atom_vec.h @@ -14,8 +14,7 @@ #ifndef LMP_ATOM_VEC_H #define LMP_ATOM_VEC_H -#include -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/atom_vec_atomic.cpp b/src/atom_vec_atomic.cpp index af4b4e617de633a88bdab758f3fee874e35227eb..25a28f16686a7ae634e55ad8bded40c00efc9114 100644 --- a/src/atom_vec_atomic.cpp +++ b/src/atom_vec_atomic.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_atomic.h" #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index 96cf0ec90928e54f324f9ba846823a54d8c416bb..5e83946078d4d161873b090ab097fa40b2f61f9f 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -11,17 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "atom_vec_body.h" +#include +#include +#include "my_pool_chunk.h" #include "style_body.h" #include "body.h" #include "atom.h" #include "comm.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" #include "memory.h" #include "error.h" diff --git a/src/atom_vec_body.h b/src/atom_vec_body.h index 4d02c4b3e05455d933626989a5763c4c3079022e..38309648fb94744e8e0089f952aaa031a3d90ce5 100644 --- a/src/atom_vec_body.h +++ b/src/atom_vec_body.h @@ -21,7 +21,6 @@ AtomStyle(body,AtomVecBody) #define LMP_ATOM_VEC_BODY_H #include "atom_vec.h" -#include "my_pool_chunk.h" namespace LAMMPS_NS { @@ -112,7 +111,6 @@ class AtomVecBody : public AtomVec { void grow_bonus(); void copy_bonus(int, int); - //void check(int); }; } diff --git a/src/atom_vec_charge.cpp b/src/atom_vec_charge.cpp index fa3c99ca346e60dc80f42fcb2f9d6c03a12625c9..9f35d16ff0b7f9b0b35506a560f7ee9fa556936b 100644 --- a/src/atom_vec_charge.cpp +++ b/src/atom_vec_charge.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_charge.h" #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp index 7bb29bd6bc30779eb54b9f9b46595a0175081fb9..5565b82a100e72825f18136d2249e709b5a35756 100644 --- a/src/atom_vec_ellipsoid.cpp +++ b/src/atom_vec_ellipsoid.cpp @@ -15,12 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include #include "atom_vec_ellipsoid.h" +#include #include "math_extra.h" #include "atom.h" #include "comm.h" -#include "force.h" #include "domain.h" #include "modify.h" #include "fix.h" diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp index 18f6fb567d247364c70203d7b817f4e236d2b6b0..9e9dbc95f0f9dc6092ef0ba0abe5272917f0bbe0 100644 --- a/src/atom_vec_hybrid.cpp +++ b/src/atom_vec_hybrid.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "atom_vec_hybrid.h" +#include #include "atom.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/atom_vec_hybrid.h b/src/atom_vec_hybrid.h index a027923a1717a0385943e2885122f25c677e1430..8129baccba4682ed2134f4edd79be99a886bde7f 100644 --- a/src/atom_vec_hybrid.h +++ b/src/atom_vec_hybrid.h @@ -20,7 +20,6 @@ AtomStyle(hybrid,AtomVecHybrid) #ifndef LMP_ATOM_VEC_HYBRID_H #define LMP_ATOM_VEC_HYBRID_H -#include #include "atom_vec.h" namespace LAMMPS_NS { diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp index ba59b3d17a05a11ae9ccdd796d4585985142025a..695ced13fd74588e60aafb3027f8e59611f4dd96 100644 --- a/src/atom_vec_line.cpp +++ b/src/atom_vec_line.cpp @@ -11,15 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "atom_vec_line.h" #include -#include #include -#include "atom_vec_line.h" #include "atom.h" #include "comm.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" #include "math_const.h" #include "memory.h" diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp index 2a77ec418b8eac0979bb99f022bdaa7c51b50e62..75136503eae0950d974dbab480cb8557ecd4ece1 100644 --- a/src/atom_vec_sphere.cpp +++ b/src/atom_vec_sphere.cpp @@ -11,15 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "atom_vec_sphere.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" #include "fix_adapt.h" #include "math_const.h" diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp index 45418b35fd87447a14eb5e851fecf9bb9f41cff5..3b7bfe53775c5aeff584da7761d49a7839b99744 100644 --- a/src/atom_vec_tri.cpp +++ b/src/atom_vec_tri.cpp @@ -11,16 +11,14 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "atom_vec_tri.h" #include -#include #include -#include "atom_vec_tri.h" #include "math_extra.h" #include "atom.h" #include "comm.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" #include "math_const.h" #include "memory.h" diff --git a/src/balance.cpp b/src/balance.cpp index 61ac895467609d705cb4985f113df3cf5028d284..c3b6f7d3bfedd9c7f3da7193181ecfe75a13bbfb 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -18,11 +18,10 @@ //#define BALANCE_DEBUG 1 +#include "balance.h" #include #include -#include #include -#include "balance.h" #include "atom.h" #include "comm.h" #include "rcb.h" @@ -30,7 +29,6 @@ #include "domain.h" #include "force.h" #include "update.h" -#include "group.h" #include "modify.h" #include "fix_store.h" #include "imbalance.h" @@ -39,7 +37,6 @@ #include "imbalance_neigh.h" #include "imbalance_store.h" #include "imbalance_var.h" -#include "timer.h" #include "memory.h" #include "error.h" diff --git a/src/balance.h b/src/balance.h index 420031502a8f826a636c8d63e1a3a421beb37de6..424da33757974e6a582047c504ecb8620a85305a 100644 --- a/src/balance.h +++ b/src/balance.h @@ -20,7 +20,6 @@ CommandStyle(balance,Balance) #ifndef LMP_BALANCE_H #define LMP_BALANCE_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/body.cpp b/src/body.cpp index 78e2f5d71b3637db3a71a0176325bf6ef4b2b969..c0e58d3f4c0525c2854e4fcbde7e8273a6c6cf60 100644 --- a/src/body.cpp +++ b/src/body.cpp @@ -11,11 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "body.h" -#include "error.h" +#include using namespace LAMMPS_NS; diff --git a/src/body.h b/src/body.h index 59001620f8965b5941c354b43fa2192762f8ee07..44581b75f6ffcb943da07dd2b056d94463e4ed0d 100644 --- a/src/body.h +++ b/src/body.h @@ -16,7 +16,6 @@ #include "pointers.h" #include "atom_vec_body.h" -#include "my_pool_chunk.h" namespace LAMMPS_NS { diff --git a/src/bond.cpp b/src/bond.cpp index edcd869425bd0d7444915d6e1f16dd1f71cb1a17..bb5430628083906b8ad7295cdf501e86d8bd8865 100644 --- a/src/bond.cpp +++ b/src/bond.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "bond.h" +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/bond.h b/src/bond.h index cce94e33a01c6441ad032d2051279861fe13ba89..b558a2a35e5d8bf6e1ac352d2af530e48244d7c8 100644 --- a/src/bond.h +++ b/src/bond.h @@ -14,8 +14,7 @@ #ifndef LMP_BOND_H #define LMP_BOND_H -#include -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/bond_deprecated.cpp b/src/bond_deprecated.cpp index 567b1a4d0070fec0087fd15b04c545aa3690c710..3e20553cacfdac24416f4361f317fff75ad6c355 100644 --- a/src/bond_deprecated.cpp +++ b/src/bond_deprecated.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "bond_deprecated.h" +#include #include "bond_hybrid.h" #include "comm.h" #include "force.h" diff --git a/src/bond_hybrid.cpp b/src/bond_hybrid.cpp index 1527943dc7e57333dfb1c0cb70e2538376b0465b..2b365014cfb2e88aa37c02872e5adf121c88133b 100644 --- a/src/bond_hybrid.cpp +++ b/src/bond_hybrid.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "bond_hybrid.h" +#include #include #include -#include "bond_hybrid.h" #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/bond_hybrid.h b/src/bond_hybrid.h index e51d467ac14391962770f6060ecfcfd3131cffb4..19e4debfed98b1b5175f570b44e7592bad03336a 100644 --- a/src/bond_hybrid.h +++ b/src/bond_hybrid.h @@ -20,7 +20,6 @@ BondStyle(hybrid,BondHybrid) #ifndef LMP_BOND_HYBRID_H #define LMP_BOND_HYBRID_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/bond_zero.cpp b/src/bond_zero.cpp index 0847cf9e6b5367a254856510fc0d27cef716e368..9be37c13be8bfded37bcfc6d28b89f95fd558f02 100644 --- a/src/bond_zero.cpp +++ b/src/bond_zero.cpp @@ -15,10 +15,9 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include -#include #include "bond_zero.h" +#include +#include #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/bond_zero.h b/src/bond_zero.h index 9443ff0784c64bba76ca5079ae79d90f31b8b1f8..7cbd2b9a96f78d68686b73a50cb49e7d27da16bb 100644 --- a/src/bond_zero.h +++ b/src/bond_zero.h @@ -20,7 +20,6 @@ BondStyle(zero,BondZero) #ifndef LMP_BOND_ZERO_H #define LMP_BOND_ZERO_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/change_box.cpp b/src/change_box.cpp index b7d3cb245fc479aba50080b710a5976d171e9985..98119fb3bf0d9972e763c0f804fa1d4c7de9ff75 100644 --- a/src/change_box.cpp +++ b/src/change_box.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "change_box.h" #include #include -#include #include -#include "change_box.h" #include "atom.h" #include "modify.h" #include "fix.h" diff --git a/src/citeme.cpp b/src/citeme.cpp index d0217226716b23dc5ba031626aefffba916f4012..c8745891cfbc2213be07dcaac14440d55728bf2c 100644 --- a/src/citeme.cpp +++ b/src/citeme.cpp @@ -12,9 +12,7 @@ ------------------------------------------------------------------------- */ #include "citeme.h" -#include "version.h" #include "universe.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/citeme.h b/src/citeme.h index 262b284337a12dfca5f5c81bffcec5cc0c248eeb..c383ec2227ce328d513ec759c67b1de308881102 100644 --- a/src/citeme.h +++ b/src/citeme.h @@ -15,7 +15,6 @@ #define LMP_CITEME_H #include "pointers.h" -#include #include namespace LAMMPS_NS { @@ -29,7 +28,7 @@ class CiteMe : protected Pointers { private: FILE *fp; // opaque pointer to log.cite file object typedef std::set citeset; - citeset *cs; // registered set of publications + citeset *cs; // registered set of publications }; } diff --git a/src/comm.cpp b/src/comm.cpp index 052de937935a669d04e2b747ad8fc01b02536370..3f2138aacc8ba793f6dc351a0365e7a19d9f169b 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -11,16 +11,18 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "comm.h" #include #include #include -#include "comm.h" #include "universe.h" #include "atom.h" #include "atom_vec.h" #include "force.h" #include "pair.h" +#include "bond.h" #include "modify.h" +#include "neighbor.h" #include "fix.h" #include "compute.h" #include "domain.h" @@ -585,6 +587,82 @@ void Comm::set_proc_grid(int outflag) } } +/* ---------------------------------------------------------------------- + determine suitable communication cutoff. + this uses three inputs: 1) maximum neighborlist cutoff, 2) an estimate + based on bond lengths and bonded interaction styles present, and 3) a + user supplied communication cutoff. + the neighbor list cutoff (1) is *always* used, since it is a requirement + for neighborlists working correctly. the bond length based cutoff is + *only* used, if no pair style is defined and no user cutoff is provided. + otherwise, a warning is printed. if the bond length based estimate is + larger than what is used. + print a warning, if a user specified communication cutoff is overridden. +------------------------------------------------------------------------- */ + +double Comm::get_comm_cutoff() +{ + double maxcommcutoff, maxbondcutoff = 0.0; + + if (force->bond) { + int n = atom->nbondtypes; + for (int i = 1; i <= n; ++i) + maxbondcutoff = MAX(maxbondcutoff,force->bond->equilibrium_distance(i)); + + // apply bond length based heuristics. + + if (force->newton_bond) { + if (force->dihedral || force->improper) { + maxbondcutoff *= 2.25; + } else { + maxbondcutoff *=1.5; + } + } else { + if (force->dihedral || force->improper) { + maxbondcutoff *= 3.125; + } else if (force->angle) { + maxbondcutoff *= 2.25; + } else { + maxbondcutoff *=1.5; + } + } + maxbondcutoff += neighbor->skin; + } + + // always take the larger of max neighbor list and user specified cutoff + + maxcommcutoff = MAX(cutghostuser,neighbor->cutneighmax); + + // use cutoff estimate from bond length only if no user specified + // cutoff was given and no pair style present. Otherwise print a + // warning, if the estimated bond based cutoff is larger than what + // is currently used. + + if (!force->pair && (cutghostuser == 0.0)) { + maxcommcutoff = MAX(maxcommcutoff,maxbondcutoff); + } else { + if ((me == 0) && (maxbondcutoff > maxcommcutoff)) { + char mesg[256]; + snprintf(mesg,256,"Communication cutoff %g is shorter than a bond " + "length based estimate of %g. This may lead to errors.", + maxcommcutoff,maxbondcutoff); + error->warning(FLERR,mesg); + } + } + + // print warning if neighborlist cutoff overrides user cutoff + + if (me == 0) { + if ((cutghostuser > 0.0) && (maxcommcutoff > cutghostuser)) { + char mesg[128]; + snprintf(mesg,128,"Communication cutoff adjusted to %g",maxcommcutoff); + error->warning(FLERR,mesg); + } + } + + return maxcommcutoff; +} + /* ---------------------------------------------------------------------- determine which proc owns atom with coord x[3] based on current decomp x will be in box (orthogonal) or lamda coords (triclinic) @@ -963,11 +1041,6 @@ rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs, return 0; // all nout_rvous are 0, no 2nd irregular } - - - - - // create procs and outbuf for All2all if necesary if (!outorder) { diff --git a/src/comm.h b/src/comm.h index 30360b1059be7e87743a0a25baddc38395719a33..5978836da7583cca4091bff6a923ad07604110a5 100644 --- a/src/comm.h +++ b/src/comm.h @@ -14,7 +14,7 @@ #ifndef LMP_COMM_H #define LMP_COMM_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { @@ -70,6 +70,8 @@ class Comm : protected Pointers { void set_processors(int, char **); // set 3d processor grid attributes virtual void set_proc_grid(int outflag = 1); // setup 3d grid of procs + double get_comm_cutoff(); // determine communication cutoff + virtual void setup() = 0; // setup 3d comm pattern virtual void forward_comm(int dummy = 0) = 0; // forward comm of atom coords virtual void reverse_comm() = 0; // reverse comm of forces @@ -237,6 +239,15 @@ Self-explanatory. E: Cannot put data on ring from NULL pointer +W: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. + +The communication cutoff defaults to the maximum of what is inferred from pair and +bond styles (will be zero, if none are defined) and what is specified via +"comm_modify cutoff" (defaults to 0.0). If this results to 0.0, no ghost atoms will +be generated and LAMMPS may lose atoms or use incorrect periodic images of atoms in +interaction lists. To avoid, either define pair style zero with a suitable cutoff +or use comm_modify cutoff. + UNDOCUMENTED U: OMP_NUM_THREADS environment is not set. diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 330551aaed74ff5b0861606aaa99038d9a67f79a..324e6dd7bf2cd64d344c32237b872865092391f8 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -15,27 +15,18 @@ Contributing author (triclinic) : Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "comm_brick.h" #include #include #include -#include -#include -#include "comm_brick.h" -#include "comm_tiled.h" -#include "universe.h" #include "atom.h" #include "atom_vec.h" -#include "force.h" #include "pair.h" #include "domain.h" #include "neighbor.h" -#include "group.h" -#include "modify.h" #include "fix.h" #include "compute.h" -#include "output.h" #include "dump.h" -#include "math_extra.h" #include "error.h" #include "memory.h" @@ -175,7 +166,10 @@ void CommBrick::setup() int ntypes = atom->ntypes; double *prd,*sublo,*subhi; - double cut = MAX(neighbor->cutneighmax,cutghostuser); + double cut = get_comm_cutoff(); + if ((cut == 0.0) && (me == 0)) + error->warning(FLERR,"Communication cutoff is 0.0. No ghost atoms " + "will be generated. Atoms may get lost."); if (triclinic == 0) { prd = domain->prd; diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index d1d625445a0d9539eb1b220630316ed5449d65b3..b3b77584a910bcdb6542186474ca1909dfef91bd 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -11,19 +11,17 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "comm_tiled.h" -#include "comm_brick.h" +#include +#include +#include #include "atom.h" #include "atom_vec.h" #include "domain.h" -#include "force.h" #include "pair.h" #include "neighbor.h" -#include "modify.h" #include "fix.h" #include "compute.h" -#include "output.h" #include "dump.h" #include "memory.h" #include "error.h" @@ -157,7 +155,11 @@ void CommTiled::setup() // set cutoff for comm forward and comm reverse // check that cutoff < any periodic box length - double cut = MAX(neighbor->cutneighmax,cutghostuser); + double cut = get_comm_cutoff(); + if ((cut == 0.0) && (me == 0)) + error->warning(FLERR,"Communication cutoff is 0.0. No ghost atoms " + "will be generated. Atoms may get lost."); + cutghost[0] = cutghost[1] = cutghost[2] = cut; if ((periodicity[0] && cut > prd[0]) || diff --git a/src/comm_tiled.h b/src/comm_tiled.h index 13ecbc4b01bde46b2728127e0f7b029834da8d01..5a9beb28f73ae31958b826a816956e7aa985e0f0 100644 --- a/src/comm_tiled.h +++ b/src/comm_tiled.h @@ -14,6 +14,7 @@ #ifndef LMP_COMM_TILED_H #define LMP_COMM_TILED_H +#include #include "comm.h" namespace LAMMPS_NS { diff --git a/src/compute.cpp b/src/compute.cpp index 207f825ec850b2118ce7dff45668045a295c40fd..cc92d2b5d32e34c9dc334599c3d9cd5c7628ce4f 100644 --- a/src/compute.cpp +++ b/src/compute.cpp @@ -11,15 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include "compute.h" #include #include -#include "compute.h" -#include "atom.h" #include "domain.h" #include "force.h" -#include "comm.h" #include "group.h" #include "modify.h" #include "fix.h" diff --git a/src/compute.h b/src/compute.h index a0238343687d5eb045a851e36a6df501ed639cad..38d001db6fadde04b248196cc7dadf69ceb23e3b 100644 --- a/src/compute.h +++ b/src/compute.h @@ -14,7 +14,7 @@ #ifndef LMP_COMPUTE_H #define LMP_COMPUTE_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/compute_adf.cpp b/src/compute_adf.cpp index e9f9ba2b6fe25b7e216d8de65d6b4f0b5449dcb9..dee5fb214f152a29e755fcb318544be4ee69b7d9 100644 --- a/src/compute_adf.cpp +++ b/src/compute_adf.cpp @@ -15,20 +15,17 @@ Contributing authors: Aidan P. Thompson (SNL) ------------------------------------------------------------------------- */ +#include "compute_adf.h" #include #include -#include #include -#include "compute_adf.h" #include "atom.h" #include "update.h" #include "force.h" #include "pair.h" -#include "domain.h" #include "neighbor.h" #include "neigh_request.h" #include "neigh_list.h" -#include "group.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/compute_adf.h b/src/compute_adf.h index a7983b71734392a8812b788f380ebfe1a3984f8e..f76801320795634eca1c9b6f20167e62f042b855 100644 --- a/src/compute_adf.h +++ b/src/compute_adf.h @@ -20,7 +20,6 @@ ComputeStyle(adf,ComputeADF) #ifndef LMP_COMPUTE_ADF_H #define LMP_COMPUTE_ADF_H -#include #include "compute.h" namespace LAMMPS_NS { diff --git a/src/compute_aggregate_atom.cpp b/src/compute_aggregate_atom.cpp index 6c8c8e5d9ad0aac6b2fdfc34777b13a87361aa24..e495ac689926b75a15c262f7f7364e58bffe95d4 100644 --- a/src/compute_aggregate_atom.cpp +++ b/src/compute_aggregate_atom.cpp @@ -15,9 +15,10 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "compute_aggregate_atom.h" +#include #include #include -#include "compute_aggregate_atom.h" #include "atom.h" #include "atom_vec.h" #include "update.h" diff --git a/src/compute_angle.cpp b/src/compute_angle.cpp index 59945f5832c3f78a7b32d8f6526f40c16da573c3..fc72a584531d28126881f253d95b09fbdda521b3 100644 --- a/src/compute_angle.cpp +++ b/src/compute_angle.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_angle.h" +#include +#include "angle.h" #include "update.h" #include "force.h" #include "angle_hybrid.h" diff --git a/src/compute_angle_local.cpp b/src/compute_angle_local.cpp index 11962116651b5fd1bd7a99ac78b5aeea414cc6e4..b100824ea9780f3116ff360c5238e8fd6c3c430c 100644 --- a/src/compute_angle_local.cpp +++ b/src/compute_angle_local.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_angle_local.h" #include #include -#include "compute_angle_local.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" diff --git a/src/compute_angmom_chunk.cpp b/src/compute_angmom_chunk.cpp index a70eaaf49f3d334b87067a20f9f27b6560ee7829..05ea963b82515ce0454a864e28b7a6541117eb2f 100644 --- a/src/compute_angmom_chunk.cpp +++ b/src/compute_angmom_chunk.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_angmom_chunk.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_bond.cpp b/src/compute_bond.cpp index 896aaec9bdfa97c1c84d4fc22244f40396e4ebc3..5cc947c7646cb0523659d7176a3b0374fed3474b 100644 --- a/src/compute_bond.cpp +++ b/src/compute_bond.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_bond.h" +#include +#include "bond.h" #include "update.h" #include "force.h" #include "bond_hybrid.h" diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp index ccdd3ee77c9cd9a43c73ff08b4292f7ccc6df625..d579772384333cb178d8a87e2aecf0b01fc7ed8b 100644 --- a/src/compute_bond_local.cpp +++ b/src/compute_bond_local.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_bond_local.h" #include #include -#include "compute_bond_local.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" diff --git a/src/compute_centro_atom.cpp b/src/compute_centro_atom.cpp index 5096879b32bbeebd8cfc8392e0cbcb01a71b3d09..18fc31390feba5025b0244909557bd2ec8d03c10 100644 --- a/src/compute_centro_atom.cpp +++ b/src/compute_centro_atom.cpp @@ -15,9 +15,8 @@ Contributing author: Michel Perez (U Lyon) for non-fcc lattices ------------------------------------------------------------------------- */ -#include -#include #include "compute_centro_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp index 61b653b3750ab75b184f30803136c7c85c5b47af..92567101dea5b75ae18bb3e64937fbd5776a8ed7 100644 --- a/src/compute_chunk_atom.cpp +++ b/src/compute_chunk_atom.cpp @@ -13,10 +13,13 @@ // NOTE: allow for bin center to be variables for sphere/cylinder +#include "compute_chunk_atom.h" #include +#include #include #include -#include "compute_chunk_atom.h" +#include +#include #include "atom.h" #include "update.h" #include "force.h" @@ -24,6 +27,7 @@ #include "region.h" #include "lattice.h" #include "modify.h" +#include "fix.h" #include "fix_store.h" #include "comm.h" #include "group.h" @@ -33,8 +37,6 @@ #include "memory.h" #include "error.h" -#include - using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/compute_chunk_spread_atom.cpp b/src/compute_chunk_spread_atom.cpp index a58c52d8e8fcedf1e08e0aad668e989b9ab61c72..41dbf2d5cb2af0d74955a7028f95277ad901686d 100644 --- a/src/compute_chunk_spread_atom.cpp +++ b/src/compute_chunk_spread_atom.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_chunk_spread_atom.h" #include #include -#include "compute_chunk_spread_atom.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_cluster_atom.cpp b/src/compute_cluster_atom.cpp index 0c34b426719ddaa0446b82cd3ad95a1eb4b69a54..ff227b35908e7cd3e8ae684f13b992225ca87499 100644 --- a/src/compute_cluster_atom.cpp +++ b/src/compute_cluster_atom.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_cluster_atom.h" +#include #include #include -#include -#include "compute_cluster_atom.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_cna_atom.cpp b/src/compute_cna_atom.cpp index b8ad3f0f644eb3a7bd11d32d45808e9fabcb919e..054798f63729c271b561048fbb2f97bdc503cb0b 100644 --- a/src/compute_cna_atom.cpp +++ b/src/compute_cna_atom.cpp @@ -15,10 +15,10 @@ Contributing author: Wan Liang (Chinese Academy of Sciences) ------------------------------------------------------------------------- */ +#include "compute_cna_atom.h" +#include #include -#include #include -#include "compute_cna_atom.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_com_chunk.cpp b/src/compute_com_chunk.cpp index ec667672454d66436276b94c64dd9d5f47355279..c39911214c02d1e846156d1864bea1b33c625789 100644 --- a/src/compute_com_chunk.cpp +++ b/src/compute_com_chunk.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_com_chunk.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_contact_atom.cpp b/src/compute_contact_atom.cpp index e60a51832a063e78c4ec22b3d8cf36765565716e..7a288afb438382e359d76b33fe601c97ffd73eca 100644 --- a/src/compute_contact_atom.cpp +++ b/src/compute_contact_atom.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_contact_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" @@ -22,7 +20,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "force.h" -#include "pair.h" #include "comm.h" #include "memory.h" #include "error.h" diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp index 54f4c70c7116c27ab9f95febe14a3d5e4ebdf6e4..30747c13140d1c2ffff8d8eaf36951ab98cc5a67 100644 --- a/src/compute_coord_atom.cpp +++ b/src/compute_coord_atom.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_coord_atom.h" #include #include -#include -#include "compute_coord_atom.h" #include "compute_orientorder_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_deprecated.cpp b/src/compute_deprecated.cpp index 069fa734376aeb02d32c3a737f7fe07f4c561518..1db78b6bdf72ae0e2997664be5f34f38f97bc9df 100644 --- a/src/compute_deprecated.cpp +++ b/src/compute_deprecated.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_deprecated.h" +#include #include "comm.h" #include "error.h" diff --git a/src/compute_dihedral.cpp b/src/compute_dihedral.cpp index 3595b2eda32f24e02287753dc04a8f8d9f1714e8..e50903104ab49b9b8dae84961acfc188040f5dce 100644 --- a/src/compute_dihedral.cpp +++ b/src/compute_dihedral.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_dihedral.h" +#include #include "update.h" #include "force.h" +#include "dihedral.h" #include "dihedral_hybrid.h" #include "error.h" diff --git a/src/compute_dihedral_local.cpp b/src/compute_dihedral_local.cpp index 9efdd61cb85791599fe977a49478a9c6730ece48..ac2c884c3f4b6a54bb21db55eb9c3125c8957a13 100644 --- a/src/compute_dihedral_local.cpp +++ b/src/compute_dihedral_local.cpp @@ -11,19 +11,17 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_dihedral_local.h" #include #include -#include "compute_dihedral_local.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" #include "update.h" #include "domain.h" #include "force.h" -#include "dihedral.h" #include "input.h" #include "variable.h" - #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/compute_dipole_chunk.cpp b/src/compute_dipole_chunk.cpp index b0474b6359c7a654a8ec97ced8121ac0d3da2b1f..3790da2035216bf555931af0c4e740f2311f8472 100644 --- a/src/compute_dipole_chunk.cpp +++ b/src/compute_dipole_chunk.cpp @@ -11,8 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_dipole_chunk.h" +#include +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_displace_atom.cpp b/src/compute_displace_atom.cpp index d8f279058e140b93e7383a348025a28aa3fb7065..41db4db1d654fe47f8f854686991050a3adb2c25 100644 --- a/src/compute_displace_atom.cpp +++ b/src/compute_displace_atom.cpp @@ -11,15 +11,14 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_displace_atom.h" #include #include -#include "compute_displace_atom.h" #include "atom.h" #include "update.h" #include "group.h" #include "domain.h" #include "modify.h" -#include "fix.h" #include "fix_store.h" #include "input.h" #include "variable.h" diff --git a/src/compute_erotate_sphere.cpp b/src/compute_erotate_sphere.cpp index 31ed0aaba5b4f194fe366e2267daa0fc03f12a1c..2a8588f06176ae985cc4b61e070c851cd0e2ff2a 100644 --- a/src/compute_erotate_sphere.cpp +++ b/src/compute_erotate_sphere.cpp @@ -11,14 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_erotate_sphere.h" +#include #include "atom.h" -#include "atom_vec.h" #include "update.h" #include "force.h" -#include "domain.h" -#include "group.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/compute_erotate_sphere_atom.cpp b/src/compute_erotate_sphere_atom.cpp index 999bc062c57406292cf7b0d469c9f5f1133e0f66..78664a912f8ca4be54ee211417508731dc9112e0 100644 --- a/src/compute_erotate_sphere_atom.cpp +++ b/src/compute_erotate_sphere_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_erotate_sphere_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_fragment_atom.cpp b/src/compute_fragment_atom.cpp index bb273f3bdb11d6262d7f465851fc9144b956ade5..f9b68dd217c91d017e533f1b743e46c067192cb0 100644 --- a/src/compute_fragment_atom.cpp +++ b/src/compute_fragment_atom.cpp @@ -15,8 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "compute_fragment_atom.h" +#include +#include #include "atom.h" #include "atom_vec.h" #include "update.h" diff --git a/src/compute_global_atom.cpp b/src/compute_global_atom.cpp index dc9ab52f4978268a7fe51dcbd03b5afbeff51a54..15f8a8f1aabd5491f8f935cd8d68282ab1c9e226 100644 --- a/src/compute_global_atom.cpp +++ b/src/compute_global_atom.cpp @@ -11,17 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_global_atom.h" #include #include -#include "compute_global_atom.h" #include "atom.h" #include "update.h" -#include "domain.h" #include "modify.h" #include "fix.h" -#include "force.h" -#include "comm.h" -#include "group.h" #include "input.h" #include "variable.h" #include "memory.h" diff --git a/src/compute_group_group.cpp b/src/compute_group_group.cpp index 17e8737350dff5c97d32da81fda70ca030b5c508..c64db19fc1a861fbb3f6b1c9d82137806a0719ea 100644 --- a/src/compute_group_group.cpp +++ b/src/compute_group_group.cpp @@ -16,10 +16,10 @@ K-space terms added by Stan Moore (BYU) ------------------------------------------------------------------------- */ +#include "compute_group_group.h" #include #include #include -#include "compute_group_group.h" #include "atom.h" #include "update.h" #include "force.h" @@ -33,7 +33,6 @@ #include "comm.h" #include "domain.h" #include "math_const.h" -#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/compute_gyration.cpp b/src/compute_gyration.cpp index 0e29c0d6670534240c686d00f9d9f3e99ccdb871..bce0c0de85fff660f24daf5947e21f89a8bf9076 100644 --- a/src/compute_gyration.cpp +++ b/src/compute_gyration.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_gyration.h" +#include #include "update.h" #include "atom.h" #include "group.h" diff --git a/src/compute_gyration_chunk.cpp b/src/compute_gyration_chunk.cpp index 6a23398aca3151533a39c317aafc73f1a5dc650e..5677ce4b6a37f4f17bbd16df1a4317930307593f 100644 --- a/src/compute_gyration_chunk.cpp +++ b/src/compute_gyration_chunk.cpp @@ -11,9 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_gyration_chunk.h" +#include #include #include -#include "compute_gyration_chunk.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_heat_flux.cpp b/src/compute_heat_flux.cpp index 0b378650343edad6b08909bc07b7b72c9309d8c2..c465a2ab02dd5f2b3dd5c72876bcca25f1c6d681 100644 --- a/src/compute_heat_flux.cpp +++ b/src/compute_heat_flux.cpp @@ -16,14 +16,13 @@ Mario Pinto (Computational Research Lab, Pune, India) ------------------------------------------------------------------------- */ -#include -#include #include "compute_heat_flux.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" #include "force.h" -#include "group.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/compute_hexorder_atom.cpp b/src/compute_hexorder_atom.cpp index 6d17ae15bd5eaf1ea29f503d469181c5511b4cb0..96d4c476786844327edd7e05055261a9133cac40 100644 --- a/src/compute_hexorder_atom.cpp +++ b/src/compute_hexorder_atom.cpp @@ -15,10 +15,10 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_hexorder_atom.h" +#include +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_improper.cpp b/src/compute_improper.cpp index ac2a23e727cc87bb65e23063b4e105c87fa61afe..181771dcfb75f5d064f6e0d9babab24c65979f50 100644 --- a/src/compute_improper.cpp +++ b/src/compute_improper.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_improper.h" +#include #include "update.h" #include "force.h" +#include "improper.h" #include "improper_hybrid.h" #include "error.h" diff --git a/src/compute_improper_local.cpp b/src/compute_improper_local.cpp index 2861850c7972147e04d755f7cf35a9ff5b57cb89..e363749b677130a5792bb2b458897435356cda07 100644 --- a/src/compute_improper_local.cpp +++ b/src/compute_improper_local.cpp @@ -11,16 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_improper_local.h" #include #include -#include "compute_improper_local.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" #include "update.h" #include "domain.h" #include "force.h" -#include "improper.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/compute_inertia_chunk.cpp b/src/compute_inertia_chunk.cpp index a33073c35a8194f61302f2e7831d424f40aae1e7..be980a08ee3c2fbf817d24842b96b69cf7ff2f35 100644 --- a/src/compute_inertia_chunk.cpp +++ b/src/compute_inertia_chunk.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_inertia_chunk.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_ke.cpp b/src/compute_ke.cpp index fb3c5a96959525b2e6db63e5bda4fc7f715ac026..c6ba478dcb4568d019f8a4127f61c89a7a053ab3 100644 --- a/src/compute_ke.cpp +++ b/src/compute_ke.cpp @@ -11,13 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_ke.h" +#include #include "atom.h" #include "update.h" #include "force.h" -#include "domain.h" -#include "group.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/compute_ke_atom.cpp b/src/compute_ke_atom.cpp index c5506996dab5843e97260d51f7342088f77ae727..102d6364ffd730d66a1fd750265da4f3e4b28be3 100644 --- a/src/compute_ke_atom.cpp +++ b/src/compute_ke_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_ke_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_msd.cpp b/src/compute_msd.cpp index 608d3e6b3346499c24471a99881f8383d32f2d8d..b15bb8e875423b1dcab8c54f1a55d5f2c72cdf83 100644 --- a/src/compute_msd.cpp +++ b/src/compute_msd.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_msd.h" +#include +#include #include "atom.h" #include "update.h" #include "group.h" diff --git a/src/compute_msd_chunk.cpp b/src/compute_msd_chunk.cpp index 1f974cc06cd0163c7dfc511370bb55e5afe96df2..8039a4fcd59e72467ab8197710f8a5b6925da838 100644 --- a/src/compute_msd_chunk.cpp +++ b/src/compute_msd_chunk.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_msd_chunk.h" +#include +#include #include "atom.h" #include "group.h" #include "update.h" diff --git a/src/compute_omega_chunk.cpp b/src/compute_omega_chunk.cpp index 23447da602d492a6ad97924891f6cb56a6e8ce15..327c64493fe041cc960bd5ddb1f77fd1ca09e8f1 100644 --- a/src/compute_omega_chunk.cpp +++ b/src/compute_omega_chunk.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_omega_chunk.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp index 8a0a525fdc7a133cfc513cdc2e02b7ecad0dfae0..266df575f91c2cbbc25413704889824cb4554072 100644 --- a/src/compute_orientorder_atom.cpp +++ b/src/compute_orientorder_atom.cpp @@ -16,10 +16,10 @@ Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "compute_orientorder_atom.h" #include #include #include -#include "compute_orientorder_atom.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_pair.cpp b/src/compute_pair.cpp index df4f3a1ddb79f272c5527cccdb76df093c394b3e..e9a3faf723d966c7634efcb282760c18534d5dfb 100644 --- a/src/compute_pair.cpp +++ b/src/compute_pair.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_pair.h" #include #include #include -#include "compute_pair.h" #include "update.h" #include "force.h" #include "pair.h" diff --git a/src/compute_pair_local.cpp b/src/compute_pair_local.cpp index c356a08be9ee8d62fc180e189dbd69d0c2d877e6..2018d929f345709806c8eee356aa62e4ebce7e36 100644 --- a/src/compute_pair_local.cpp +++ b/src/compute_pair_local.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_pair_local.h" #include #include #include -#include "compute_pair_local.h" #include "atom.h" #include "update.h" #include "force.h" @@ -22,7 +22,6 @@ #include "neighbor.h" #include "neigh_request.h" #include "neigh_list.h" -#include "group.h" #include "memory.h" #include "error.h" diff --git a/src/compute_pe.cpp b/src/compute_pe.cpp index 5839ec209599834366af029d48f37d03c2d2a6eb..fd7b74b43a9db3420c4411f92f43af88a4ae0173 100644 --- a/src/compute_pe.cpp +++ b/src/compute_pe.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_pe.h" #include #include -#include "compute_pe.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_pe_atom.cpp b/src/compute_pe_atom.cpp index 2f1dc5650eb5b7f507efece1cd7ac065547812d0..274e1b05a6dc299c39877ac4d846c8d7aa54ac6b 100644 --- a/src/compute_pe_atom.cpp +++ b/src/compute_pe_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_pe_atom.h" +#include #include "atom.h" #include "update.h" #include "comm.h" @@ -24,7 +24,6 @@ #include "improper.h" #include "kspace.h" #include "modify.h" -#include "fix.h" #include "memory.h" #include "error.h" diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp index 978cad0cad0c618173a6da0f1b038f21b23b5b5a..cb0743a7d6e5c7a99db313a5ae85a1ab2b9ad0ef 100644 --- a/src/compute_pressure.cpp +++ b/src/compute_pressure.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_pressure.h" #include #include -#include -#include "compute_pressure.h" #include "atom.h" #include "update.h" #include "domain.h" @@ -22,6 +21,7 @@ #include "fix.h" #include "force.h" #include "pair.h" +#include "pair_hybrid.h" #include "bond.h" #include "angle.h" #include "dihedral.h" @@ -66,6 +66,7 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) : // process optional args + pairhybridflag = 0; if (narg == 4) { keflag = 1; pairflag = 1; @@ -79,6 +80,37 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) : int iarg = 4; while (iarg < narg) { if (strcmp(arg[iarg],"ke") == 0) keflag = 1; + else if (strcmp(arg[iarg],"pair/hybrid") == 0) { + int n = strlen(arg[++iarg]) + 1; + if (lmp->suffix) n += strlen(lmp->suffix) + 1; + pstyle = new char[n]; + strcpy(pstyle,arg[iarg++]); + + nsub = 0; + + if (narg > iarg) { + if (isdigit(arg[iarg][0])) { + nsub = force->inumeric(FLERR,arg[iarg]); + ++iarg; + if (nsub <= 0) + error->all(FLERR,"Illegal compute pressure command"); + } + } + + // check if pair style with and without suffix exists + + pairhybrid = (Pair *) force->pair_match(pstyle,1,nsub); + if (!pairhybrid && lmp->suffix) { + strcat(pstyle,"/"); + strcat(pstyle,lmp->suffix); + pairhybrid = (Pair *) force->pair_match(pstyle,1,nsub); + } + + if (!pairhybrid) + error->all(FLERR,"Unrecognized pair style in compute pressure command"); + + pairhybridflag = 1; + } else if (strcmp(arg[iarg],"pair") == 0) pairflag = 1; else if (strcmp(arg[iarg],"bond") == 0) bondflag = 1; else if (strcmp(arg[iarg],"angle") == 0) angleflag = 1; @@ -133,6 +165,20 @@ void ComputePressure::init() temperature = modify->compute[icompute]; } + // recheck if pair style with and without suffix exists + + if (pairhybridflag) { + pairhybrid = (Pair *) force->pair_match(pstyle,1,nsub); + if (!pairhybrid && lmp->suffix) { + strcat(pstyle,"/"); + strcat(pstyle,lmp->suffix); + pairhybrid = (Pair *) force->pair_match(pstyle,1,nsub); + } + + if (!pairhybrid) + error->all(FLERR,"Unrecognized pair style in compute pressure command"); + } + // detect contributions to virial // vptr points to all virial[6] contributions @@ -140,6 +186,7 @@ void ComputePressure::init() nvirial = 0; vptr = NULL; + if (pairhybridflag && force->pair) nvirial++; if (pairflag && force->pair) nvirial++; if (bondflag && atom->molecular && force->bond) nvirial++; if (angleflag && atom->molecular && force->angle) nvirial++; @@ -152,6 +199,11 @@ void ComputePressure::init() if (nvirial) { vptr = new double*[nvirial]; nvirial = 0; + if (pairhybridflag && force->pair) { + PairHybrid *ph = (PairHybrid *) force->pair; + ph->no_virial_fdotr_compute = 1; + vptr[nvirial++] = pairhybrid->virial; + } if (pairflag && force->pair) vptr[nvirial++] = force->pair->virial; if (bondflag && force->bond) vptr[nvirial++] = force->bond->virial; if (angleflag && force->angle) vptr[nvirial++] = force->angle->virial; diff --git a/src/compute_pressure.h b/src/compute_pressure.h index a59a64e634fbd5ed5c7194e5ca6703949e7dcb05..8d0ec4aa04ad81e009fb86d3796daa4472a396af 100644 --- a/src/compute_pressure.h +++ b/src/compute_pressure.h @@ -41,10 +41,16 @@ class ComputePressure : public Compute { Compute *temperature; char *id_temp; double virial[6]; + int pairhybridflag; + class Pair *pairhybrid; int keflag,pairflag,bondflag,angleflag,dihedralflag,improperflag; int fixflag,kspaceflag; void virial_compute(int, int); + + private: + char *pstyle; + int nsub; }; } diff --git a/src/compute_property_atom.cpp b/src/compute_property_atom.cpp index 0b57840696bae1261c223ab1616986aea117a153..065e3eeb826a7ab581b7138fdbfee1c8afaf8abc 100644 --- a/src/compute_property_atom.cpp +++ b/src/compute_property_atom.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_property_atom.h" #include #include -#include "compute_property_atom.h" #include "math_extra.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/compute_property_chunk.cpp b/src/compute_property_chunk.cpp index 489890e1cc4608f4fd7c54a33bef3ec33db0e843..579c7cae3fa85e7c458145b66deed9bf01d4b74b 100644 --- a/src/compute_property_chunk.cpp +++ b/src/compute_property_chunk.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_property_chunk.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp index ddcf5913ca003bd9938974d196625d4de3381b8d..651e1190b1fe0dada3698d2b435f8988f0d50940 100644 --- a/src/compute_property_local.cpp +++ b/src/compute_property_local.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_property_local.h" +#include #include "atom.h" #include "atom_vec.h" #include "update.h" diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp index d49485b4ea411ce3cc2b850d49fa95a543a216d6..501a506c98b31161d3dd99d19e91b2a67aaecee1 100644 --- a/src/compute_rdf.cpp +++ b/src/compute_rdf.cpp @@ -15,11 +15,10 @@ Contributing authors: Paul Crozier (SNL), Jeff Greathouse (SNL) ------------------------------------------------------------------------- */ +#include "compute_rdf.h" #include #include -#include #include -#include "compute_rdf.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_rdf.h b/src/compute_rdf.h index 52a93a38dd78deac22423ef8930b4f3371dc5fa9..85f6ce6ad23dda63b925b118b36284c387142a61 100644 --- a/src/compute_rdf.h +++ b/src/compute_rdf.h @@ -20,7 +20,6 @@ ComputeStyle(rdf,ComputeRDF) #ifndef LMP_COMPUTE_RDF_H #define LMP_COMPUTE_RDF_H -#include #include "compute.h" namespace LAMMPS_NS { diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp index 16dc84628a1dfb135d5af20ec2bc47af00070d9f..8467554faaa17bca4f16df31fada0856e438d4d2 100644 --- a/src/compute_reduce.cpp +++ b/src/compute_reduce.cpp @@ -11,17 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_reduce.h" #include #include #include -#include "compute_reduce.h" #include "atom.h" #include "update.h" #include "domain.h" #include "modify.h" #include "fix.h" -#include "force.h" -#include "comm.h" #include "group.h" #include "input.h" #include "variable.h" diff --git a/src/compute_reduce_chunk.cpp b/src/compute_reduce_chunk.cpp index f31672ef745fe4d3a723f91fd625a451b5eb8f6b..3b68e20fcb08f2480431f9989ba2dd4a2b79f57d 100644 --- a/src/compute_reduce_chunk.cpp +++ b/src/compute_reduce_chunk.cpp @@ -11,9 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_reduce_chunk.h" +#include +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_reduce_region.cpp b/src/compute_reduce_region.cpp index 8e91a299e88025807b611f4317b496d585dd3eb9..9074124a6111ba93893e6b3810f739382ac6d05d 100644 --- a/src/compute_reduce_region.cpp +++ b/src/compute_reduce_region.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_reduce_region.h" +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_slice.cpp b/src/compute_slice.cpp index ac70e7dd15803751674ffaf9ee3fc25e5f674c06..67b60882f689a94d04119c5a5114469e3eab56cf 100644 --- a/src/compute_slice.cpp +++ b/src/compute_slice.cpp @@ -11,13 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_slice.h" +#include #include #include -#include "compute_slice.h" #include "update.h" #include "modify.h" #include "fix.h" -#include "group.h" #include "input.h" #include "variable.h" #include "memory.h" diff --git a/src/compute_stress_atom.cpp b/src/compute_stress_atom.cpp index 5211f015abd19054f39552fa49f20f2fec68ebcb..7c0ed9ef1707ba7908769f35eea20690ce0b53a1 100644 --- a/src/compute_stress_atom.cpp +++ b/src/compute_stress_atom.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_stress_atom.h" +#include #include "atom.h" #include "update.h" #include "comm.h" diff --git a/src/compute_temp.cpp b/src/compute_temp.cpp index 70a77345930e1a611b2481ac31e4ea3ec68e005f..402b84bb4b2a72124832430f35d315e7a0330a2b 100644 --- a/src/compute_temp.cpp +++ b/src/compute_temp.cpp @@ -11,14 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_temp.h" +#include #include "atom.h" #include "update.h" #include "force.h" #include "domain.h" -#include "comm.h" #include "group.h" #include "error.h" diff --git a/src/compute_temp_chunk.cpp b/src/compute_temp_chunk.cpp index 396492e18d9538e30f053ee84dfa0a501271f496..0fa5bbbb8af3b4e27d5816433f3f00c18e4aed38 100644 --- a/src/compute_temp_chunk.cpp +++ b/src/compute_temp_chunk.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_temp_chunk.h" +#include +#include #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_temp_com.cpp b/src/compute_temp_com.cpp index c46a17497f730919b46567740bc55e0b831c5856..dc12e8f6db003deb49454c3c8cb12542d02c5142 100644 --- a/src/compute_temp_com.cpp +++ b/src/compute_temp_com.cpp @@ -11,16 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_temp_com.h" +#include #include "atom.h" #include "update.h" #include "force.h" #include "group.h" #include "domain.h" -#include "lattice.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/compute_temp_deform.cpp b/src/compute_temp_deform.cpp index 280c17dd083a4a164047c6d9ee6e6e442b637ed0..7d81a84bc41a9cf0079e4559937dd6796a9cf40f 100644 --- a/src/compute_temp_deform.cpp +++ b/src/compute_temp_deform.cpp @@ -15,9 +15,9 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "compute_temp_deform.h" #include #include -#include "compute_temp_deform.h" #include "domain.h" #include "atom.h" #include "update.h" diff --git a/src/compute_temp_partial.cpp b/src/compute_temp_partial.cpp index ee72ba3e74fc6036e12b7c5831bb155a8f3e8984..f5f29d9dc03e25b3190f6c2da09ebcfb284cd555 100644 --- a/src/compute_temp_partial.cpp +++ b/src/compute_temp_partial.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_temp_partial.h" +#include #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_temp_profile.cpp b/src/compute_temp_profile.cpp index c7f0b28a6cb096184ad2f3b2cdd269df7af2664f..fce145848ebd9130df4f5ce1d049cc91827c1055 100644 --- a/src/compute_temp_profile.cpp +++ b/src/compute_temp_profile.cpp @@ -11,15 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_temp_profile.h" #include -#include #include -#include "compute_temp_profile.h" #include "atom.h" #include "update.h" #include "force.h" #include "group.h" -#include "fix.h" #include "domain.h" #include "memory.h" #include "error.h" diff --git a/src/compute_temp_ramp.cpp b/src/compute_temp_ramp.cpp index 36e7f51ce43d0129f90fffdf3b42ad895e97171b..30f6701fcd16644caa1d458c839622b270757a14 100644 --- a/src/compute_temp_ramp.cpp +++ b/src/compute_temp_ramp.cpp @@ -11,15 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_temp_ramp.h" #include -#include #include -#include "compute_temp_ramp.h" #include "atom.h" #include "update.h" #include "force.h" #include "group.h" -#include "fix.h" #include "domain.h" #include "lattice.h" #include "memory.h" diff --git a/src/compute_temp_region.cpp b/src/compute_temp_region.cpp index 0c54aeb63cfa03ee6dea74cd0871ae9328ef3fb4..4c0b925eb678eb3a3fdddce8f5d97d04779fca24 100644 --- a/src/compute_temp_region.cpp +++ b/src/compute_temp_region.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_temp_region.h" #include #include -#include "compute_temp_region.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_temp_sphere.cpp b/src/compute_temp_sphere.cpp index 23e74634b5e0cf179468760f0520a6ba6e4b89ee..786ef523ad8ebe51db6c552cccb04e34d495a5fe 100644 --- a/src/compute_temp_sphere.cpp +++ b/src/compute_temp_sphere.cpp @@ -11,16 +11,14 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_temp_sphere.h" #include #include -#include "compute_temp_sphere.h" #include "atom.h" -#include "atom_vec.h" #include "update.h" #include "force.h" #include "domain.h" #include "modify.h" -#include "comm.h" #include "group.h" #include "error.h" diff --git a/src/compute_torque_chunk.cpp b/src/compute_torque_chunk.cpp index d9de99bcb2589e4c8bfcb6fc63bf43163efe0761..35eef8fe10a2577ceb6b15393402b7fef1b5b1f7 100644 --- a/src/compute_torque_chunk.cpp +++ b/src/compute_torque_chunk.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_torque_chunk.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_vacf.cpp b/src/compute_vacf.cpp index d46b8b5fa01f69c36a934cb69dc01520cc62928c..5123e3aab4374a740912dd300858108e54aeacbb 100644 --- a/src/compute_vacf.cpp +++ b/src/compute_vacf.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_vacf.h" +#include +#include #include "atom.h" #include "update.h" #include "group.h" diff --git a/src/compute_vcm_chunk.cpp b/src/compute_vcm_chunk.cpp index a6dd796c63c7e71db984e60550ef4918d777cb83..b0a8dbeee7b5efce1b967bf8b67109fffee16222 100644 --- a/src/compute_vcm_chunk.cpp +++ b/src/compute_vcm_chunk.cpp @@ -11,13 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_vcm_chunk.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" #include "compute_chunk_atom.h" -#include "domain.h" #include "memory.h" #include "error.h" diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index 52e4256fca0e51fdc7dec8c719491f8b225056d4..8a091ef2ef88561f02462f5b3b505a6a6942ce6b 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "create_atoms.h" +#include +#include #include "atom.h" #include "atom_vec.h" #include "molecule.h" @@ -23,8 +22,6 @@ #include "modify.h" #include "force.h" #include "special.h" -#include "fix.h" -#include "compute.h" #include "domain.h" #include "lattice.h" #include "region.h" @@ -176,8 +173,6 @@ void CreateAtoms::command(int narg, char **arg) } else error->all(FLERR,"Illegal create_atoms command"); iarg += 3; } else if (strcmp(arg[iarg],"rotate") == 0) { - if (style != SINGLE) - error->all(FLERR,"Cannot use create_atoms rotate unless single style"); if (iarg+5 > narg) error->all(FLERR,"Illegal create_atoms command"); double thetaone; double axisone[3]; @@ -678,7 +673,9 @@ void CreateAtoms::add_random() coord[1] >= sublo[1] && coord[1] < subhi[1] && coord[2] >= sublo[2] && coord[2] < subhi[2]) { if (mode == ATOM) atom->avec->create_atom(ntype,xone); - else add_molecule(xone); + else if (quatone[0] == 0 && quatone[1] == 0 && quatone[2] == 0) + add_molecule(xone); + else add_molecule(xone, quatone); } } @@ -832,7 +829,9 @@ void CreateAtoms::add_lattice() // add the atom or entire molecule to my list of atoms if (mode == ATOM) atom->avec->create_atom(basistype[m],x); - else add_molecule(x); + else if (quatone[0] == 0 && quatone[1] == 0 && quatone[2] == 0) + add_molecule(x); + else add_molecule(x,quatone); } } } diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp index e19b56555420e907c192d29c8c3ca7b59ec66113..5b7c354595e47feb68e8cb597964707abdfa0334 100644 --- a/src/create_bonds.cpp +++ b/src/create_bonds.cpp @@ -15,9 +15,9 @@ Contributing authors: Mike Salerno (NRL) added single methods ------------------------------------------------------------------------- */ -#include -#include #include "create_bonds.h" +#include +#include #include "atom.h" #include "domain.h" #include "force.h" diff --git a/src/create_box.cpp b/src/create_box.cpp index b5e37b759ca0bd4b6ec0cd7c49aeacf859450bde..4a826cb6912ae738d28f0dcff679267c41ba0771 100644 --- a/src/create_box.cpp +++ b/src/create_box.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "create_box.h" +#include #include "atom.h" #include "atom_vec.h" -#include "force.h" #include "domain.h" #include "region.h" #include "region_prism.h" diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp index 41df167f0795113661d07eda0ab8989c5582f332..e8d9c5d53b1f9bd5cb8ce6f2db7d0eee83339efc 100644 --- a/src/delete_atoms.cpp +++ b/src/delete_atoms.cpp @@ -11,9 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "delete_atoms.h" +#include +#include +#include #include "atom.h" #include "atom_vec.h" #include "atom_vec_ellipsoid.h" diff --git a/src/delete_bonds.cpp b/src/delete_bonds.cpp index fe32bca87977d92ac7c8b3a8f64509117cb1e619..c450f77ee73711ae656efb8d0ace09fc51a73a2d 100644 --- a/src/delete_bonds.cpp +++ b/src/delete_bonds.cpp @@ -11,14 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "delete_bonds.h" #include #include #include -#include "delete_bonds.h" #include "atom.h" #include "atom_vec.h" #include "domain.h" -#include "neighbor.h" #include "comm.h" #include "force.h" #include "group.h" diff --git a/src/deprecated.cpp b/src/deprecated.cpp index b937482669d3f37fd676c835277440c4155a8621..86af54fbfdce5e3842c8dc28575b0f0b5169dca2 100644 --- a/src/deprecated.cpp +++ b/src/deprecated.cpp @@ -15,10 +15,9 @@ Contributing authors: Axel Kohlmeyer (Temple U), ------------------------------------------------------------------------- */ -#include #include "deprecated.h" +#include #include "comm.h" -#include "force.h" #include "error.h" #include "input.h" diff --git a/src/dihedral.cpp b/src/dihedral.cpp index adccf2a490b32d90828b69110bbb97e512934b09..d2de841dd0e4e3eeaa48fef258ab88f364deb207 100644 --- a/src/dihedral.cpp +++ b/src/dihedral.cpp @@ -11,13 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "dihedral.h" #include "atom.h" #include "comm.h" #include "force.h" -#include "pair.h" -#include "suffix.h" #include "atom_masks.h" #include "memory.h" #include "error.h" diff --git a/src/dihedral.h b/src/dihedral.h index ac3786c40e19bfb83d5b92b9fc0ba14c1541cb5a..f7b0ad1c71a2dbbc8714584e220b0b6a741f4719 100644 --- a/src/dihedral.h +++ b/src/dihedral.h @@ -14,8 +14,7 @@ #ifndef LMP_DIHEDRAL_H #define LMP_DIHEDRAL_H -#include -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/dihedral_deprecated.cpp b/src/dihedral_deprecated.cpp index 70888ca76db0cf507293dcc1a7857356c131b7e2..0205b1b88796ccaf3d3dfcc1236f45d59e42e812 100644 --- a/src/dihedral_deprecated.cpp +++ b/src/dihedral_deprecated.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "dihedral_deprecated.h" +#include #include "dihedral_hybrid.h" #include "comm.h" #include "force.h" diff --git a/src/dihedral_hybrid.cpp b/src/dihedral_hybrid.cpp index 8908139bdc7292a38ade4d9fd56f59833b4125db..6c0a4338ae4ebc15dd37ceb5ecb0bf5a7de87c36 100644 --- a/src/dihedral_hybrid.cpp +++ b/src/dihedral_hybrid.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "dihedral_hybrid.h" +#include #include #include -#include "dihedral_hybrid.h" #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/dihedral_hybrid.h b/src/dihedral_hybrid.h index 0839fdfc61a8f6cdb9c45589d5cfbe6495d79167..2804060af451e9d4bd03be38cb7125e38ec206b0 100644 --- a/src/dihedral_hybrid.h +++ b/src/dihedral_hybrid.h @@ -20,7 +20,6 @@ DihedralStyle(hybrid,DihedralHybrid) #ifndef LMP_DIHEDRAL_HYBRID_H #define LMP_DIHEDRAL_HYBRID_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/dihedral_zero.cpp b/src/dihedral_zero.cpp index 8145d5f32d0e18341550d92b0f4dbc27b390ec8b..daf46fe79aa7b52b0c13aa351861ae5d15301a30 100644 --- a/src/dihedral_zero.cpp +++ b/src/dihedral_zero.cpp @@ -15,13 +15,10 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include -#include #include "dihedral_zero.h" +#include #include "atom.h" #include "force.h" -#include "comm.h" #include "memory.h" #include "error.h" diff --git a/src/dihedral_zero.h b/src/dihedral_zero.h index e7dbb0d3a53a9dae1f675db394b6755f68efa42d..e97f8f66416121bcc24e65a9ae079c84c280e75c 100644 --- a/src/dihedral_zero.h +++ b/src/dihedral_zero.h @@ -24,7 +24,6 @@ DihedralStyle(zero,DihedralZero) #ifndef LMP_DIHEDRAL_ZERO_H #define LMP_DIHEDRAL_ZERO_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp index 7b29b1d3d51e0c4877b31b00fd9431c91c3a8a27..dc94c3ed358f06880b8c797c09774f735cc3c882 100644 --- a/src/displace_atoms.cpp +++ b/src/displace_atoms.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "displace_atoms.h" #include -#include +#include #include -#include "displace_atoms.h" #include "atom.h" #include "modify.h" #include "domain.h" diff --git a/src/domain.cpp b/src/domain.cpp index 74d7560c3114417a9c2283622f53a4c457728d07..372b264013ff0620b4eb7b8ea287be8e8893e368 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -15,12 +15,10 @@ Contributing author (triclinic) : Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "domain.h" #include -#include #include -#include #include -#include "domain.h" #include "style_region.h" #include "atom.h" #include "atom_vec.h" @@ -37,13 +35,11 @@ #include "output.h" #include "thermo.h" #include "universe.h" -#include "math_const.h" #include "memory.h" #include "error.h" #include "utils.h" using namespace LAMMPS_NS; -using namespace MathConst; #define BIG 1.0e20 #define SMALL 1.0e-4 diff --git a/src/domain.h b/src/domain.h index e131d07a1b8c42bfbc06b1cf163ebf8fd034f2e0..a0bda8ae720e379384006cd27aefd04f48ffc595 100644 --- a/src/domain.h +++ b/src/domain.h @@ -15,9 +15,9 @@ #define LMP_DOMAIN_H #include -#include "pointers.h" #include #include +#include "pointers.h" namespace LAMMPS_NS { diff --git a/src/dump.cpp b/src/dump.cpp index 8fa07a9cb257714fdb2412ddfaf4cfdbb6e3d771..57a8decbb0dccf28dda89a7b658ee082b3e75040 100644 --- a/src/dump.cpp +++ b/src/dump.cpp @@ -11,11 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "dump.h" #include -#include #include -#include -#include "dump.h" #include "atom.h" #include "irregular.h" #include "update.h" diff --git a/src/dump.h b/src/dump.h index 1c6a131f76088e060cf5cb697e7ef744d660d95e..bc7fd2d5a50a56e59a877cf74f52b62d9ef94fa2 100644 --- a/src/dump.h +++ b/src/dump.h @@ -14,9 +14,7 @@ #ifndef LMP_DUMP_H #define LMP_DUMP_H -#include -#include -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp index 74583f40131cead43003e76838ddeeac204555fd..e2e77cfb770fa93b4ad37a949163e66f1dd3b012 100644 --- a/src/dump_atom.cpp +++ b/src/dump_atom.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "dump_atom.h" +#include #include "domain.h" #include "atom.h" #include "update.h" -#include "group.h" #include "memory.h" #include "error.h" diff --git a/src/dump_cfg.cpp b/src/dump_cfg.cpp index ddd662c8a65c3ae0365672ed3e82f27c7587be52..3430720b8c489b3ab844c884f81be464e80bd4d7 100644 --- a/src/dump_cfg.cpp +++ b/src/dump_cfg.cpp @@ -16,18 +16,10 @@ Memory efficiency improved by Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include #include "dump_cfg.h" +#include #include "atom.h" #include "domain.h" -#include "comm.h" -#include "modify.h" -#include "compute.h" -#include "input.h" -#include "fix.h" -#include "variable.h" #include "memory.h" #include "error.h" diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index 17ad4b89ef2a1eec6782165f024426173d70f1ad..ce83e442c9e296ac8b3bbdc7adc7d4845e5b0095 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "dump_custom.h" #include #include -#include "dump_custom.h" #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/dump_dcd.cpp b/src/dump_dcd.cpp index 384e9089c0a1781bfaaaf2eb87137a823382367b..254b371e2251a289c10973160f73363c1326be78 100644 --- a/src/dump_dcd.cpp +++ b/src/dump_dcd.cpp @@ -16,12 +16,10 @@ Axel Kohlmeyer (Temple U), support for groups ------------------------------------------------------------------------- */ +#include "dump_dcd.h" #include -#include // requires C++-11 -#include #include #include -#include "dump_dcd.h" #include "domain.h" #include "atom.h" #include "update.h" diff --git a/src/dump_deprecated.cpp b/src/dump_deprecated.cpp index f0999f42769db5a2c3e1a5a9d6b32d95c4475ead..4263b9801f59ce61b7214edd0b751fa4f7c1a60d 100644 --- a/src/dump_deprecated.cpp +++ b/src/dump_deprecated.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "dump_deprecated.h" +#include #include "comm.h" #include "error.h" diff --git a/src/dump_image.cpp b/src/dump_image.cpp index 0d63d2e4cba5b45b7b464d611c55b2d5f608eee4..7e6bc0c44c1ce059116c85f9106c7ea2a9fd7553 100644 --- a/src/dump_image.cpp +++ b/src/dump_image.cpp @@ -11,20 +11,20 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "dump_image.h" +#include #include #include -#include #include -#include "dump_image.h" #include "image.h" #include "atom.h" +#include "atom_vec.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" #include "atom_vec_body.h" #include "body.h" #include "molecule.h" #include "domain.h" -#include "group.h" #include "force.h" #include "comm.h" #include "modify.h" diff --git a/src/dump_local.cpp b/src/dump_local.cpp index 8dc055469064c4751a5d3b1a0b7586de417c5a95..9f021a7b6aa373c552a876b3cd2855b4c481a711 100644 --- a/src/dump_local.cpp +++ b/src/dump_local.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "dump_local.h" #include #include #include -#include "dump_local.h" -#include "atom.h" #include "modify.h" #include "fix.h" #include "compute.h" diff --git a/src/dump_movie.cpp b/src/dump_movie.cpp index 59dfdc3d6e9e579ee49d851577182bbde622700a..ea67320d4a41cb03e9730925686d916a1bd36793 100644 --- a/src/dump_movie.cpp +++ b/src/dump_movie.cpp @@ -15,13 +15,10 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include #include "dump_movie.h" +#include #include "comm.h" #include "force.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/dump_xyz.cpp b/src/dump_xyz.cpp index fd52671d8140056f8fce6995d5f8e7e4680e6410..10ba10f9951d4a2b12e08c1ee0d76607ab9204a5 100644 --- a/src/dump_xyz.cpp +++ b/src/dump_xyz.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "dump_xyz.h" +#include #include "atom.h" -#include "group.h" #include "error.h" #include "memory.h" #include "update.h" diff --git a/src/error.cpp b/src/error.cpp index cc80dcb4d8073c42831894df390fb8e9208eed89..656c957ee20f04fb8404bafc2813e39abfa7cadb 100644 --- a/src/error.cpp +++ b/src/error.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "error.h" #include #include #include -#include "error.h" #include "universe.h" -#include "update.h" #include "output.h" #include "input.h" diff --git a/src/finish.cpp b/src/finish.cpp index 1baa6d6fda65767c8f9aec34f49a989a8ea8cc63..9ab97ae410c4490d5231689987387a5755455bba 100644 --- a/src/finish.cpp +++ b/src/finish.cpp @@ -11,16 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "finish.h" #include #include #include #include -#include -#include "finish.h" -#include "timer.h" -#include "universe.h" #include "accelerator_kokkos.h" -#include "accelerator_omp.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" @@ -32,10 +28,10 @@ #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "output.h" #include "memory.h" #include "error.h" -#include "utils.h" +#include "timer.h" +#include "universe.h" #ifdef LMP_USER_OMP #include "modify.h" diff --git a/src/fix.cpp b/src/fix.cpp index 634bc2393dc71dab874972c9f474d4991d54de12..e0cfeca1a941d5db7b1a79af4c4a4a02a814203a 100644 --- a/src/fix.cpp +++ b/src/fix.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix.h" #include #include -#include "fix.h" #include "atom.h" #include "group.h" #include "force.h" -#include "comm.h" #include "atom_masks.h" #include "memory.h" #include "error.h" diff --git a/src/fix.h b/src/fix.h index 7eaff38bd3aa48030152c02012a75e07ef16be98..7e55e96269d287dbc060f0124eab7cce2462620f 100644 --- a/src/fix.h +++ b/src/fix.h @@ -14,7 +14,7 @@ #ifndef LMP_FIX_H #define LMP_FIX_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp index 9a5b528747bf2165266b6e5d46e5c7c2f796fb6e..8668690e1db821d6ebe4ddea34cc416bd272a15c 100644 --- a/src/fix_adapt.cpp +++ b/src/fix_adapt.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_adapt.h" +#include #include "atom.h" #include "bond.h" #include "update.h" diff --git a/src/fix_addforce.cpp b/src/fix_addforce.cpp index d66457a1f19ef1a903d22c87099d6c5cb75d01bb..275ec2c846d849e4a1a4e85f4d75b43f9aeea343 100644 --- a/src/fix_addforce.cpp +++ b/src/fix_addforce.cpp @@ -11,9 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_addforce.h" +#include #include #include -#include "fix_addforce.h" #include "atom.h" #include "atom_masks.h" #include "update.h" diff --git a/src/fix_ave_atom.cpp b/src/fix_ave_atom.cpp index c8cbad75c969adc32517e122f6da84e5ba3236f6..694df2bcf7392cfe777adb772211172b6fd1fbd4 100644 --- a/src/fix_ave_atom.cpp +++ b/src/fix_ave_atom.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_ave_atom.h" #include #include -#include "fix_ave_atom.h" #include "atom.h" -#include "domain.h" #include "update.h" #include "modify.h" #include "compute.h" diff --git a/src/fix_ave_atom.h b/src/fix_ave_atom.h index e4baf6bda14bfc8672e1ae1818117826a1028ddd..42aa282d5396969215c3a69f6b5bf4e8e4282ec8 100644 --- a/src/fix_ave_atom.h +++ b/src/fix_ave_atom.h @@ -20,7 +20,6 @@ FixStyle(ave/atom,FixAveAtom) #ifndef LMP_FIX_AVE_ATOM_H #define LMP_FIX_AVE_ATOM_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp index 7aed4dcbe7b6844742f4fb03462e16bb4d060d4a..45eb38f5c2625e8e3ade8238260eab5ccfd496bd 100644 --- a/src/fix_ave_chunk.cpp +++ b/src/fix_ave_chunk.cpp @@ -11,10 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_ave_chunk.h" +#include #include #include #include -#include "fix_ave_chunk.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/fix_ave_chunk.h b/src/fix_ave_chunk.h index 4dc1c1c24602e8947a027866222f7b6e843cab69..dac5761ae85f9ee35bceb1b8a67d61ca9838766b 100644 --- a/src/fix_ave_chunk.h +++ b/src/fix_ave_chunk.h @@ -20,7 +20,6 @@ FixStyle(ave/chunk,FixAveChunk) #ifndef LMP_FIX_AVE_CHUNK_H #define LMP_FIX_AVE_CHUNK_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp index 5c95f20ec2eec92658465585f4dbce83eda498a7..f65b53efc8111dc05656d8090321d895414677df 100644 --- a/src/fix_ave_correlate.cpp +++ b/src/fix_ave_correlate.cpp @@ -17,10 +17,11 @@ Reese Jones (Sandia) ------------------------------------------------------------------------- */ +#include "fix_ave_correlate.h" +#include #include #include #include -#include "fix_ave_correlate.h" #include "update.h" #include "modify.h" #include "compute.h" diff --git a/src/fix_ave_correlate.h b/src/fix_ave_correlate.h index ff20e8ba94c2e54ec8c98cb735b734d0fb8a943f..05fd6b6576ad3bee7bfc2b04481743232afb162d 100644 --- a/src/fix_ave_correlate.h +++ b/src/fix_ave_correlate.h @@ -20,7 +20,6 @@ FixStyle(ave/correlate,FixAveCorrelate) #ifndef LMP_FIX_AVE_CORRELATE_H #define LMP_FIX_AVE_CORRELATE_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp index 87da5222f02341a5b0b7be3aee0ccfdb34480c4b..5a5de6d0b62068a40bf3273e15c2c55c6bef3af8 100644 --- a/src/fix_ave_histo.cpp +++ b/src/fix_ave_histo.cpp @@ -11,15 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_ave_histo.h" +#include #include #include #include -#include "fix_ave_histo.h" #include "atom.h" #include "update.h" #include "modify.h" #include "compute.h" -#include "group.h" #include "input.h" #include "variable.h" #include "memory.h" diff --git a/src/fix_ave_histo.h b/src/fix_ave_histo.h index 3616959c612a0e66760eaa21b588ddc4728a4bb7..35bdfcfa7f9020ee2ecb5e6cf3b02a4bd6835fe8 100644 --- a/src/fix_ave_histo.h +++ b/src/fix_ave_histo.h @@ -20,7 +20,6 @@ FixStyle(ave/histo,FixAveHisto) #ifndef LMP_FIX_AVE_HISTO_H #define LMP_FIX_AVE_HISTO_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_histo_weight.cpp b/src/fix_ave_histo_weight.cpp index c78f4fa1e38765c2e150c59f840d00bc535deee4..1f0d282e5de5b8d3da1fe9959615661897f81825 100644 --- a/src/fix_ave_histo_weight.cpp +++ b/src/fix_ave_histo_weight.cpp @@ -14,21 +14,18 @@ /* ---------------------------------------------------------------------- Contributing author: Shawn Coleman (ARL) ------------------------------------------------------------------------- */ - -#include -#include -#include #include "fix_ave_histo_weight.h" +#include +#include +#include "fix.h" #include "atom.h" #include "update.h" #include "modify.h" #include "compute.h" -#include "group.h" #include "input.h" #include "variable.h" #include "memory.h" #include "error.h" -#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_histo_weight.h b/src/fix_ave_histo_weight.h index e5638e121569cd5e328ad7760a3ea6b957af8938..6ec3ba5721b1db204fc12b5d33c691bcb0b4a795 100644 --- a/src/fix_ave_histo_weight.h +++ b/src/fix_ave_histo_weight.h @@ -20,7 +20,6 @@ FixStyle(ave/histo/weight,FixAveHistoWeight) #ifndef LMP_FIX_AVE_HISTO_WEIGHT_H #define LMP_FIX_AVE_HISTO_WEIGHT_H -#include #include "fix_ave_histo.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp index 50654b6561a04027c695fa6e3e0a913064bd0950..05d556d0c81aae5c2433f67660a84b3d7c8e90f6 100644 --- a/src/fix_ave_time.cpp +++ b/src/fix_ave_time.cpp @@ -15,10 +15,11 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "fix_ave_time.h" +#include #include #include #include -#include "fix_ave_time.h" #include "update.h" #include "force.h" #include "modify.h" diff --git a/src/fix_ave_time.h b/src/fix_ave_time.h index 62dfbad2963e90b29679929dbfaf3b488df6d06c..01228f9e55f333a34b4d91e5b4decc3384a61aea 100644 --- a/src/fix_ave_time.h +++ b/src/fix_ave_time.h @@ -20,7 +20,6 @@ FixStyle(ave/time,FixAveTime) #ifndef LMP_FIX_AVE_TIME_H #define LMP_FIX_AVE_TIME_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_aveforce.cpp b/src/fix_aveforce.cpp index 1c87ba57851a0e5de4864b1ba3be8d6f845aae8e..8ad07780a96bdae619755972729832cefcdd41bc 100644 --- a/src/fix_aveforce.cpp +++ b/src/fix_aveforce.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_aveforce.h" #include #include -#include -#include "fix_aveforce.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/fix_balance.cpp b/src/fix_balance.cpp index ddaf42b49da872d1d2337c94b622ba59191a2983..5ca1ec124ae7f465d14fcd841110333acb0ea019 100644 --- a/src/fix_balance.cpp +++ b/src/fix_balance.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_balance.h" +#include #include "balance.h" #include "update.h" #include "atom.h" @@ -26,7 +25,6 @@ #include "modify.h" #include "fix_store.h" #include "rcb.h" -#include "timer.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/fix_balance.h b/src/fix_balance.h index 64383b59508bce2ded60e67a7311a28cd164a9bc..76cbea258a8191e4cdd5283a91f35e3b5d904f7a 100644 --- a/src/fix_balance.h +++ b/src/fix_balance.h @@ -20,7 +20,6 @@ FixStyle(balance,FixBalance) #ifndef LMP_FIX_BALANCE_H #define LMP_FIX_BALANCE_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_box_relax.cpp b/src/fix_box_relax.cpp index a315330d149eb40f0f5fb7f4446f6495d8738149..c19ea918b4617de95a79571b712e9af09b6e4b6f 100644 --- a/src/fix_box_relax.cpp +++ b/src/fix_box_relax.cpp @@ -15,10 +15,9 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "fix_box_relax.h" #include #include -#include -#include "fix_box_relax.h" #include "atom.h" #include "domain.h" #include "update.h" diff --git a/src/fix_controller.cpp b/src/fix_controller.cpp index eb7a79496253bd787e7baa1a33b59301cfa83773..855869a574d35c126cfe02805788d5f9c4c33a5a 100644 --- a/src/fix_controller.cpp +++ b/src/fix_controller.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_controller.h" #include #include -#include "fix_controller.h" #include "force.h" #include "update.h" #include "modify.h" diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp index 909ead3e2a9052ba27ecc3405d47074344ad5bf0..9d84c4bb62e5af11cfa7c8d58978bdce33ba1e2d 100644 --- a/src/fix_deform.cpp +++ b/src/fix_deform.cpp @@ -15,10 +15,9 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "fix_deform.h" #include -#include #include -#include "fix_deform.h" #include "atom.h" #include "update.h" #include "comm.h" diff --git a/src/fix_deprecated.cpp b/src/fix_deprecated.cpp index 7db27152ba9fdc5cc79de59231182835679baced..0c212668b3caf91b775c035a1624ceacd3b0549d 100644 --- a/src/fix_deprecated.cpp +++ b/src/fix_deprecated.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_deprecated.h" +#include #include "comm.h" #include "error.h" diff --git a/src/fix_drag.cpp b/src/fix_drag.cpp index e4cf12d1ffcc2215ece204d559aa4ab943b5b23f..9af5a376757b95c65b37f50d7ff90de6d5257a8a 100644 --- a/src/fix_drag.cpp +++ b/src/fix_drag.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_drag.h" +#include #include -#include #include -#include "fix_drag.h" #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/fix_dt_reset.cpp b/src/fix_dt_reset.cpp index 7566094b48050d21cd6f281e9b8582706d8a7de2..da4bdad827a51088a6f10314abe3e02bf4d31532 100644 --- a/src/fix_dt_reset.cpp +++ b/src/fix_dt_reset.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_dt_reset.h" +#include #include -#include #include -#include "fix_dt_reset.h" #include "atom.h" #include "update.h" #include "integrate.h" diff --git a/src/fix_enforce2d.cpp b/src/fix_enforce2d.cpp index 986ded5d16d10f859f10acd41cefcdc61fe33985..3edd24e9afda763d660e44d8cbe7e5033e336c88 100644 --- a/src/fix_enforce2d.cpp +++ b/src/fix_enforce2d.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_enforce2d.h" +#include #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/fix_external.cpp b/src/fix_external.cpp index b1ffa65e492ecd021d76224de0f32827bbd9618d..afb420df93bde80c55116ce4a71af59504327ab1 100644 --- a/src/fix_external.cpp +++ b/src/fix_external.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_external.h" +#include #include "atom.h" #include "update.h" #include "memory.h" diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp index bc10eb280782bf83023b24a1202336e4b3e5ddf8..14ba913c010420a3c5ab0cd0a0442e520f3d95fc 100644 --- a/src/fix_gravity.cpp +++ b/src/fix_gravity.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_gravity.h" +#include #include -#include -#include #include -#include "fix_gravity.h" #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/fix_group.cpp b/src/fix_group.cpp index 8a332bed959babb89cf3cc360ba157092c80f642..d2eea9f7811831c9c117483f8d261149f6c68355 100644 --- a/src/fix_group.cpp +++ b/src/fix_group.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_group.h" +#include #include "group.h" #include "update.h" #include "atom.h" diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp index 5fda4c30d685a54e2bf2c232e0c63967a46e2a31..8ebb39f0e900e68a58dc888b7b33dc01b4beb930 100644 --- a/src/fix_halt.cpp +++ b/src/fix_halt.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_halt.h" +#include #include -#include #include -#include "fix_halt.h" #include "update.h" #include "force.h" -#include "update.h" #include "input.h" #include "variable.h" #include "atom.h" diff --git a/src/fix_halt.h b/src/fix_halt.h index 372c915a7fb958e2f994b354c4964e4dc2ebb5bf..93c5e95078038c4f9113a0e0364db378cb355ce7 100644 --- a/src/fix_halt.h +++ b/src/fix_halt.h @@ -20,7 +20,6 @@ FixStyle(halt,FixHalt) #ifndef LMP_FIX_HALT_H #define LMP_FIX_HALT_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_heat.cpp b/src/fix_heat.cpp index f34845785c03b583e508ddd671d97023c4dd3e9a..67d445df9252a857c681f35880cd4274a4b63e65 100644 --- a/src/fix_heat.cpp +++ b/src/fix_heat.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "fix_heat.h" +#include #include -#include #include -#include "fix_heat.h" #include "atom.h" #include "domain.h" #include "region.h" diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp index b8e07dfd53f358cdf1f305ab3a16864e0ed8c8f5..04837ff39b48ddfaac4c4a6503f1d69c9a86aa91 100644 --- a/src/fix_indent.cpp +++ b/src/fix_indent.cpp @@ -15,10 +15,10 @@ Contributing author: Ravi Agrawal (Northwestern U) ------------------------------------------------------------------------- */ +#include "fix_indent.h" +#include #include #include -#include -#include "fix_indent.h" #include "atom.h" #include "input.h" #include "variable.h" @@ -26,7 +26,6 @@ #include "lattice.h" #include "update.h" #include "modify.h" -#include "output.h" #include "respa.h" #include "error.h" #include "force.h" diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp index 3f2ec20db06588bb641ec52c5cb67a77230893b1..a050e5a13a2d4d51c9a8f104e1117d6588833eca 100644 --- a/src/fix_langevin.cpp +++ b/src/fix_langevin.cpp @@ -16,11 +16,10 @@ Aidan Thompson (SNL) GJF formulation ------------------------------------------------------------------------- */ +#include "fix_langevin.h" #include #include #include -#include -#include "fix_langevin.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" @@ -28,8 +27,6 @@ #include "update.h" #include "modify.h" #include "compute.h" -#include "domain.h" -#include "region.h" #include "respa.h" #include "comm.h" #include "input.h" diff --git a/src/fix_lineforce.cpp b/src/fix_lineforce.cpp index aea1a2a25bc3c4b54ca6428ed17dec3baca36a49..c153ee65ddf7ad5cb26eb728ead7d2a2009c2b77 100644 --- a/src/fix_lineforce.cpp +++ b/src/fix_lineforce.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_lineforce.h" #include #include -#include -#include "fix_lineforce.h" #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/fix_minimize.cpp b/src/fix_minimize.cpp index fa39643a1bc9beba894349396b1e325ec59a208d..df2dfb02a777dc22ed51786966a42364d2416c7b 100644 --- a/src/fix_minimize.cpp +++ b/src/fix_minimize.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_minimize.h" #include "atom.h" #include "domain.h" #include "memory.h" -#include "error.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_momentum.cpp b/src/fix_momentum.cpp index 680251e670a44330782eaab69619a55119a2c7de..a363cb8eacfce0a2de1667cba90c068fd2114c4e 100644 --- a/src/fix_momentum.cpp +++ b/src/fix_momentum.cpp @@ -11,9 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_momentum.h" +#include +#include +#include #include "atom.h" #include "domain.h" #include "group.h" diff --git a/src/fix_move.cpp b/src/fix_move.cpp index 0a5f506ab265ff14b6070b6c537b9ae4bd180f56..770c0fca6b3f7cd2e6063b619429e1908c4bf033 100644 --- a/src/fix_move.cpp +++ b/src/fix_move.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_move.h" #include -#include #include -#include "fix_move.h" #include "atom.h" -#include "group.h" #include "update.h" #include "modify.h" #include "force.h" diff --git a/src/fix_move.h b/src/fix_move.h index 5993d7d6e808f0e57b3427660c8d58e6bea6daeb..740b051be0083ac3cfae6499bbf176d61d4075c6 100644 --- a/src/fix_move.h +++ b/src/fix_move.h @@ -20,7 +20,6 @@ FixStyle(move,FixMove) #ifndef LMP_FIX_MOVE_H #define LMP_FIX_MOVE_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_neigh_history.cpp b/src/fix_neigh_history.cpp index 207c409596a7994c9bff40d419041f8eaff714f2..5c740ae6492ab8a428b5909c2b7ce8fb4c408b8d 100644 --- a/src/fix_neigh_history.cpp +++ b/src/fix_neigh_history.cpp @@ -11,18 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_neigh_history.h" #include #include -#include -#include "fix_neigh_history.h" +#include "my_page.h" #include "atom.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" #include "force.h" #include "pair.h" -#include "update.h" -#include "modify.h" #include "memory.h" #include "error.h" diff --git a/src/fix_neigh_history.h b/src/fix_neigh_history.h index 601e8a55a2bf5f4cbdc3903d4aadd06665bc7f81..51d03f5b125f8390ffc05b255d4cf08e4ba8a955 100644 --- a/src/fix_neigh_history.h +++ b/src/fix_neigh_history.h @@ -21,7 +21,6 @@ FixStyle(NEIGH_HISTORY,FixNeighHistory) #define LMP_FIX_NEIGH_HISTORY_H #include "fix.h" -#include "my_page.h" namespace LAMMPS_NS { diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index deca0ad83d09bf2215776ec7b1f54e5977b9a0c0..bb3fe7559cbe960599dbc30556c840942032cce4 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -15,11 +15,9 @@ Contributing authors: Mark Stevens (SNL), Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "fix_nh.h" #include -#include #include -#include "fix_nh.h" -#include "math_extra.h" #include "atom.h" #include "force.h" #include "group.h" diff --git a/src/fix_nh_sphere.cpp b/src/fix_nh_sphere.cpp index f1764932429c84c80f9660a777153eff82470060..1ff3fc2d4d90824fb78aa4e710d0c73f43b6bf36 100644 --- a/src/fix_nh_sphere.cpp +++ b/src/fix_nh_sphere.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include #include "fix_nh_sphere.h" +#include +#include #include "atom.h" #include "atom_vec.h" -#include "group.h" #include "error.h" #include "force.h" #include "domain.h" diff --git a/src/fix_nph.cpp b/src/fix_nph.cpp index 40265ef57c6e278a5260a5a007d3a1597d758c44..7148b024de9c3dc2fbf50989771678c54142ad00 100644 --- a/src/fix_nph.cpp +++ b/src/fix_nph.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nph.h" +#include #include "modify.h" #include "error.h" diff --git a/src/fix_nph_sphere.cpp b/src/fix_nph_sphere.cpp index 3fcbe5e9c686e7801156570b42021c03ab60e9fa..f64f144f344244e8d4d038ce535f9f6a27ef59f5 100644 --- a/src/fix_nph_sphere.cpp +++ b/src/fix_nph_sphere.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nph_sphere.h" +#include #include "modify.h" #include "error.h" diff --git a/src/fix_npt.cpp b/src/fix_npt.cpp index d17577d68d7c1e751f3d19a43eb4f5d1da9ac497..e856fafe2d6d32beef16034422970c5adb12cfc1 100644 --- a/src/fix_npt.cpp +++ b/src/fix_npt.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_npt.h" +#include #include "modify.h" #include "error.h" diff --git a/src/fix_npt_sphere.cpp b/src/fix_npt_sphere.cpp index 50ac990dafc0ad3295ff6821472611e9b3011e76..9cbb17b0ca2dfbb9019172c61ec9be81eee49df2 100644 --- a/src/fix_npt_sphere.cpp +++ b/src/fix_npt_sphere.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_npt_sphere.h" +#include #include "modify.h" #include "error.h" diff --git a/src/fix_nve.cpp b/src/fix_nve.cpp index 959483230e5753b43c802c0755605e4789803c85..863ce5404ddb0b1472dc60e2f9763048504f2fa8 100644 --- a/src/fix_nve.cpp +++ b/src/fix_nve.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_nve.h" +#include #include "atom.h" #include "force.h" #include "update.h" diff --git a/src/fix_nve_limit.cpp b/src/fix_nve_limit.cpp index 68ff0665a18f63be1ffad76a4362cc3a38ca5513..d63c736e73806621dd89de2c8305e823ef52c107 100644 --- a/src/fix_nve_limit.cpp +++ b/src/fix_nve_limit.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_nve_limit.h" +#include #include -#include -#include #include -#include "fix_nve_limit.h" #include "atom.h" #include "force.h" #include "update.h" diff --git a/src/fix_nve_noforce.cpp b/src/fix_nve_noforce.cpp index d4fca9e6760444e23db32386a7d181e08e742e3f..022e8abe74ec0f79cd133bcb7b7a533dc084b56a 100644 --- a/src/fix_nve_noforce.cpp +++ b/src/fix_nve_noforce.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_nve_noforce.h" +#include #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/fix_nve_sphere.cpp b/src/fix_nve_sphere.cpp index 0bee8b868538ccf11f9c92e556e38dd009ad3c06..c0fea17c2bb7f41e41d9da44dff0addca7875918 100644 --- a/src/fix_nve_sphere.cpp +++ b/src/fix_nve_sphere.cpp @@ -11,15 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_nve_sphere.h" #include -#include #include -#include "fix_nve_sphere.h" #include "atom.h" #include "domain.h" #include "atom_vec.h" -#include "update.h" -#include "respa.h" #include "force.h" #include "error.h" #include "math_vector.h" diff --git a/src/fix_nvt.cpp b/src/fix_nvt.cpp index 7247612dd470bc71ce513e2ae2c1aef042508572..6f0d4c6c5041d0061879e95eeeb48b9fb0c474ac 100644 --- a/src/fix_nvt.cpp +++ b/src/fix_nvt.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nvt.h" +#include #include "group.h" #include "modify.h" #include "error.h" diff --git a/src/fix_nvt_sllod.cpp b/src/fix_nvt_sllod.cpp index c7d23364a77df40d72c80bad8bbd5575071e0ddf..138794862ae41085a1f80e07d8d7e5791415351e 100644 --- a/src/fix_nvt_sllod.cpp +++ b/src/fix_nvt_sllod.cpp @@ -15,9 +15,8 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "fix_nvt_sllod.h" +#include #include "math_extra.h" #include "atom.h" #include "domain.h" diff --git a/src/fix_nvt_sphere.cpp b/src/fix_nvt_sphere.cpp index 44046699ba96e16da7a787695a35bd49a00e7c67..fed37990113c83c1dd8e2034529ddd559cf21a35 100644 --- a/src/fix_nvt_sphere.cpp +++ b/src/fix_nvt_sphere.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nvt_sphere.h" +#include #include "group.h" #include "modify.h" #include "error.h" diff --git a/src/fix_planeforce.cpp b/src/fix_planeforce.cpp index 45dc782fcf086da5fd4bf8c586a04f7ec383d58f..a3f27277bd5563790b7ce87f245dbc08270b0fcf 100644 --- a/src/fix_planeforce.cpp +++ b/src/fix_planeforce.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_planeforce.h" #include #include -#include -#include "fix_planeforce.h" #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/fix_press_berendsen.cpp b/src/fix_press_berendsen.cpp index 95db004436a512a5d00f5a8aa506202d53084907..c090c554e2b6d19305dcffc9facab9ae84e4cd4e 100644 --- a/src/fix_press_berendsen.cpp +++ b/src/fix_press_berendsen.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_press_berendsen.h" #include -#include #include -#include "fix_press_berendsen.h" #include "atom.h" #include "force.h" #include "comm.h" @@ -23,7 +22,6 @@ #include "compute.h" #include "kspace.h" #include "update.h" -#include "respa.h" #include "domain.h" #include "error.h" diff --git a/src/fix_print.cpp b/src/fix_print.cpp index f6db88114a8ba59555858ebdd5355aa59a92e246..dc76fc39f94f883d0910e9e5ff755c773f4007b4 100644 --- a/src/fix_print.cpp +++ b/src/fix_print.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_print.h" +#include +#include #include "update.h" #include "input.h" #include "modify.h" diff --git a/src/fix_print.h b/src/fix_print.h index 37b6680aee9405326b7461cd82aa6cda89be5bd4..56441602204f8a8f09aa794d67b8f9eb154f25b5 100644 --- a/src/fix_print.h +++ b/src/fix_print.h @@ -20,7 +20,6 @@ FixStyle(print,FixPrint) #ifndef LMP_FIX_PRINT_H #define LMP_FIX_PRINT_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp index c89419f85014de0b089c2823b0b0730abf8d5fa9..555114e4f9d80ecfcbce38c5a04cb6b0925a4b03 100644 --- a/src/fix_property_atom.cpp +++ b/src/fix_property_atom.cpp @@ -11,16 +11,14 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_property_atom.h" #include #include -#include "fix_property_atom.h" #include "atom.h" #include "comm.h" #include "memory.h" #include "error.h" -#include "update.h" - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_read_restart.cpp b/src/fix_read_restart.cpp index 3c3178f4af3e6d05866eea3e1ce3d81108100618..afedf9c12c452d1b853e405dcc78bfdd75fc2a16 100644 --- a/src/fix_read_restart.cpp +++ b/src/fix_read_restart.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_read_restart.h" #include "atom.h" #include "memory.h" diff --git a/src/fix_recenter.cpp b/src/fix_recenter.cpp index 75b383d67a2f46ef99e7d721c70964c9d47b654b..f461e0fa52237e11f965fd0d08934315370613fe 100644 --- a/src/fix_recenter.cpp +++ b/src/fix_recenter.cpp @@ -15,9 +15,9 @@ Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U) ------------------------------------------------------------------------- */ -#include -#include #include "fix_recenter.h" +#include +#include #include "atom.h" #include "group.h" #include "update.h" diff --git a/src/fix_respa.cpp b/src/fix_respa.cpp index 64461ba7ca2044277ab86fc5ccc83a7fbcbf2f6a..742dd5c58bde57c229f2a1c2a259f278d925cd9b 100644 --- a/src/fix_respa.cpp +++ b/src/fix_respa.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_respa.h" +#include #include "atom.h" #include "force.h" #include "memory.h" diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp index 08485d65b388f2d17e385881b86a348608a80ccb..5a0d4fb66241f4c955139e9eb976f7ea3b267921 100644 --- a/src/fix_restrain.cpp +++ b/src/fix_restrain.cpp @@ -16,17 +16,16 @@ support for bond and angle restraints by Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ +#include "fix_restrain.h" +#include #include #include -#include -#include "fix_restrain.h" #include "atom.h" #include "force.h" #include "update.h" #include "domain.h" #include "comm.h" #include "respa.h" -#include "input.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/fix_setforce.cpp b/src/fix_setforce.cpp index fc8b7aeb59862fb78860b507f31f9477fa3888a0..77c4bfbddce05de32687ecf92762c1a329d14484 100644 --- a/src/fix_setforce.cpp +++ b/src/fix_setforce.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_setforce.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp index 328a0eeafda12cf3f71efffb8d8168b6e27fe9ae..510b194ab7d0d53ff3def0b45788b48e6589cd67 100644 --- a/src/fix_spring.cpp +++ b/src/fix_spring.cpp @@ -15,14 +15,12 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "fix_spring.h" #include -#include #include -#include "fix_spring.h" #include "atom.h" #include "update.h" #include "respa.h" -#include "domain.h" #include "force.h" #include "group.h" #include "error.h" diff --git a/src/fix_spring_chunk.cpp b/src/fix_spring_chunk.cpp index 5b5d95b111b5d7eb8eb8b3049217be5272be3d3a..e14936a9767d5b72f7d5f1e633187af6692c65fc 100644 --- a/src/fix_spring_chunk.cpp +++ b/src/fix_spring_chunk.cpp @@ -11,15 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_spring_chunk.h" #include -#include #include -#include "fix_spring_chunk.h" #include "atom.h" #include "update.h" #include "force.h" #include "respa.h" -#include "domain.h" #include "modify.h" #include "compute_chunk_atom.h" #include "compute_com_chunk.h" diff --git a/src/fix_spring_rg.cpp b/src/fix_spring_rg.cpp index 28c89690061eb2c92c3a6b587e9833f052b0be3f..f1e68bffa487debab806c0c27d76afcdeba0b456 100644 --- a/src/fix_spring_rg.cpp +++ b/src/fix_spring_rg.cpp @@ -16,10 +16,8 @@ Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_spring_rg.h" +#include #include "atom.h" #include "update.h" #include "group.h" diff --git a/src/fix_spring_self.cpp b/src/fix_spring_self.cpp index 670883af41b3bc29f865789e0d57a0b7decc5de2..c94f21b492cc6b8ed1562790d19415891683b7e4 100644 --- a/src/fix_spring_self.cpp +++ b/src/fix_spring_self.cpp @@ -15,9 +15,9 @@ Contributing author: Naveen Michaud-Agrawal (Johns Hopkins University) ------------------------------------------------------------------------- */ -#include -#include #include "fix_spring_self.h" +#include +#include #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/fix_store.cpp b/src/fix_store.cpp index 9db65d0987be99c813071c5a827ec8361e98fba8..94c62c18506a2738c590f1ed4dda21be33f19d3b 100644 --- a/src/fix_store.cpp +++ b/src/fix_store.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_store.h" +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/fix_store.h b/src/fix_store.h index 5524770a9700be426df90671e5be2336c499b6f9..437c14f0f7a86df27ea31cc6f9cd5f5bfb85c180 100644 --- a/src/fix_store.h +++ b/src/fix_store.h @@ -20,7 +20,6 @@ FixStyle(STORE,FixStore) #ifndef LMP_FIX_STORE_H #define LMP_FIX_STORE_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_store_force.cpp b/src/fix_store_force.cpp index a841714098e1f808217afcf13d7335a7a4fd3199..5c25f0e162870357939ee12de4e18916a4cf7a10 100644 --- a/src/fix_store_force.cpp +++ b/src/fix_store_force.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_store_force.h" +#include #include "atom.h" #include "update.h" -#include "group.h" #include "respa.h" #include "memory.h" #include "error.h" diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp index da899a173cc22fe837d9e177064b343159d901a5..18dfa026d9de686fbd7eee280b2fda749184781a 100644 --- a/src/fix_store_state.cpp +++ b/src/fix_store_state.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_store_state.h" #include #include -#include "fix_store_state.h" #include "atom.h" #include "domain.h" #include "update.h" diff --git a/src/fix_temp_berendsen.cpp b/src/fix_temp_berendsen.cpp index 55518015c4a1a5bfd743e369d7b92a500ee1e2ed..be8922be4e44bed37277f33b026f75e70a725b38 100644 --- a/src/fix_temp_berendsen.cpp +++ b/src/fix_temp_berendsen.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_temp_berendsen.h" #include -#include #include -#include "fix_temp_berendsen.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/fix_temp_csld.cpp b/src/fix_temp_csld.cpp index 7bdf7763555c56841348040e0f4f78bd246cd9b1..f827c88f51fd378e39cec3c5838c363752bb54f1 100644 --- a/src/fix_temp_csld.cpp +++ b/src/fix_temp_csld.cpp @@ -15,10 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "fix_temp_csld.h" #include -#include #include -#include "fix_temp_csld.h" #include "atom.h" #include "force.h" #include "memory.h" diff --git a/src/fix_temp_csvr.cpp b/src/fix_temp_csvr.cpp index 495a1551135f48c37fb5c29d1a132434e5ed1f71..55cbb60407b880de6d8bf00cbab453568712ef1c 100644 --- a/src/fix_temp_csvr.cpp +++ b/src/fix_temp_csvr.cpp @@ -16,13 +16,12 @@ Based on code by Paolo Raiteri (Curtin U) and Giovanni Bussi (SISSA) ------------------------------------------------------------------------- */ +#include "fix_temp_csvr.h" +#include #include -#include #include -#include "fix_temp_csvr.h" #include "atom.h" #include "force.h" -#include "memory.h" #include "comm.h" #include "input.h" #include "variable.h" diff --git a/src/fix_temp_rescale.cpp b/src/fix_temp_rescale.cpp index 11dfa6a5fcdf05c4e75a459f3bc5d74503616e83..a9d605d5ba850da278bdcf8a2fc80a9a901c9be9 100644 --- a/src/fix_temp_rescale.cpp +++ b/src/fix_temp_rescale.cpp @@ -11,16 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_temp_rescale.h" #include -#include #include -#include "fix_temp_rescale.h" #include "atom.h" #include "force.h" #include "group.h" #include "update.h" -#include "domain.h" -#include "region.h" #include "comm.h" #include "input.h" #include "variable.h" diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp index 10315a750d767ed9d291d153115fe5e8ddffe48f..cfe9a9572e635b47a61728d3be64a4fa83f54489 100644 --- a/src/fix_tmd.cpp +++ b/src/fix_tmd.cpp @@ -16,11 +16,10 @@ Christian Burisch (Bochum Univeristy, Germany) ------------------------------------------------------------------------- */ +#include "fix_tmd.h" #include #include -#include #include -#include "fix_tmd.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/fix_tmd.h b/src/fix_tmd.h index b6db41dd5a158361be5d000fd416c0afc9b216c3..f23a64a0274a815cc0da513b69c3c8ff6e060f66 100644 --- a/src/fix_tmd.h +++ b/src/fix_tmd.h @@ -20,7 +20,6 @@ FixStyle(tmd,FixTMD) #ifndef LMP_FIX_TMD_H #define LMP_FIX_TMD_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp index 6387af767606cac35b701410c5a4cbf8fabdf50d..53093acbf6773b219f09ebfec7377cc346f5fae5 100644 --- a/src/fix_vector.cpp +++ b/src/fix_vector.cpp @@ -11,13 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_vector.h" +#include +#include #include "update.h" #include "force.h" #include "modify.h" #include "compute.h" -#include "group.h" #include "input.h" #include "variable.h" #include "memory.h" diff --git a/src/fix_viscous.cpp b/src/fix_viscous.cpp index e8451423227decc258780ff3b65a76a66e11f9eb..bdd1e19976d808dc80202fc4e7ce785f0e45e323 100644 --- a/src/fix_viscous.cpp +++ b/src/fix_viscous.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_viscous.h" +#include #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp index e84d01191d43bc800b115e89cfb2ae9636461635..8ceafb4bfc28f875d5c29ca9a232acbd748eec39 100644 --- a/src/fix_wall.cpp +++ b/src/fix_wall.cpp @@ -11,11 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_wall.h" -#include "atom.h" +#include +#include #include "input.h" #include "variable.h" #include "domain.h" diff --git a/src/fix_wall_harmonic.cpp b/src/fix_wall_harmonic.cpp index 4dc067178ad5d42da7f4f6c0eb580adff908df1e..6c6d5ec40279bb5c26829021db5d0de2b62e6934 100644 --- a/src/fix_wall_harmonic.cpp +++ b/src/fix_wall_harmonic.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_wall_harmonic.h" #include "atom.h" #include "error.h" diff --git a/src/fix_wall_lj1043.cpp b/src/fix_wall_lj1043.cpp index a93f4dd699c6424cfdc2d918aba8ab862df13cd9..5656cf113d3b4c5e283b57e341c0abe24dc187e0 100644 --- a/src/fix_wall_lj1043.cpp +++ b/src/fix_wall_lj1043.cpp @@ -15,8 +15,8 @@ Contributing author: Jonathan Lee (Sandia) ------------------------------------------------------------------------- */ -#include #include "fix_wall_lj1043.h" +#include #include "atom.h" #include "math_const.h" diff --git a/src/fix_wall_lj126.cpp b/src/fix_wall_lj126.cpp index 369ef78c97875ee693c2e0151e8527270068cfeb..e748e2ef13485d2fa37875662d11faee2912306e 100644 --- a/src/fix_wall_lj126.cpp +++ b/src/fix_wall_lj126.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_wall_lj126.h" +#include #include "atom.h" #include "error.h" diff --git a/src/fix_wall_lj93.cpp b/src/fix_wall_lj93.cpp index ce5a06c81b956fbafe3570c73903a7a52afdc802..c0e81b60eede35d0c40daa940bbefac715a26718 100644 --- a/src/fix_wall_lj93.cpp +++ b/src/fix_wall_lj93.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_wall_lj93.h" +#include #include "atom.h" #include "error.h" diff --git a/src/fix_wall_reflect.cpp b/src/fix_wall_reflect.cpp index 8acba720352dc38030263f29486b55c77be4e539..bc3414d650b85835490c9ba322f74bd0a3c3a22e 100644 --- a/src/fix_wall_reflect.cpp +++ b/src/fix_wall_reflect.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_wall_reflect.h" +#include #include "atom.h" #include "comm.h" #include "update.h" diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp index ff147d74463827b410f6c7bb9b92a90eb83bc93d..c1a689d90aa89c103900c420b078bf9546c3b9f6 100644 --- a/src/fix_wall_region.cpp +++ b/src/fix_wall_region.cpp @@ -11,18 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_wall_region.h" +#include #include -#include #include -#include "fix_wall_region.h" #include "atom.h" -#include "atom_vec.h" #include "domain.h" #include "region.h" #include "force.h" -#include "lattice.h" #include "update.h" -#include "output.h" #include "respa.h" #include "error.h" #include "math_const.h" diff --git a/src/force.cpp b/src/force.cpp index 26483589324437776f769830501ecd1e7c4a55b8..1a826b2843269d99647247e2ef97ef99c74ff853 100644 --- a/src/force.cpp +++ b/src/force.cpp @@ -11,17 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "force.h" #include #include #include -#include "force.h" #include "style_bond.h" #include "style_angle.h" #include "style_dihedral.h" #include "style_improper.h" #include "style_pair.h" #include "style_kspace.h" -#include "atom.h" #include "comm.h" #include "pair.h" #include "pair_hybrid.h" @@ -32,8 +31,6 @@ #include "dihedral.h" #include "improper.h" #include "kspace.h" -#include "group.h" -#include "memory.h" #include "error.h" #include "utils.h" diff --git a/src/force.h b/src/force.h index 227b9427c0edfa491c9b757fb84ce37380f28371..26a3ecdfb837239077169b4ad43f7188be52ddbb 100644 --- a/src/force.h +++ b/src/force.h @@ -15,7 +15,6 @@ #define LMP_FORCE_H #include "pointers.h" -#include #include #include diff --git a/src/group.cpp b/src/group.cpp index 256bab77780c98c2e967317f3df36b177c24eac1..d119964ea17d1df3cb0565213dced5deb1f2b1a0 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "group.h" #include #include -#include #include -#include -#include "group.h" +#include #include "domain.h" #include "atom.h" #include "force.h" diff --git a/src/group.h b/src/group.h index 962d37b32ad53538dba1fa36f31e1338d79f6b37..ec913f98bcfabb8b2550962c087886101cf444ba 100644 --- a/src/group.h +++ b/src/group.h @@ -14,7 +14,6 @@ #ifndef LMP_GROUP_H #define LMP_GROUP_H -#include #include "pointers.h" #include diff --git a/src/hashlittle.cpp b/src/hashlittle.cpp index f612be9eeb0e947b3052137d1583b70815f47dda..c3824b71fe28f49bca68e766db280a162944e0f4 100644 --- a/src/hashlittle.cpp +++ b/src/hashlittle.cpp @@ -2,9 +2,7 @@ // from lookup3.c, by Bob Jenkins, May 2006, Public Domain // bob_jenkins@burtleburtle.net -#include -#include -#include +#include "hashlittle.h" // if the system defines the __BYTE_ORDER__ define, // we use it instead of guessing the platform @@ -142,7 +140,7 @@ acceptable. Do NOT use for cryptographic purposes. ------------------------------------------------------------------------------- */ -uint32_t hashlittle( const void *key, size_t length, uint32_t initval) +uint32_t LAMMPS_NS::hashlittle(const void *key, size_t length, uint32_t initval) { #ifndef PURIFY_HATES_HASHLITTLE diff --git a/src/hashlittle.h b/src/hashlittle.h index 7b57a35c80a52e8411388f56583e236790541d00..75380d366b0783f770ef5e6bed932e9f3222b6f4 100644 --- a/src/hashlittle.h +++ b/src/hashlittle.h @@ -2,4 +2,13 @@ // from lookup3.c, by Bob Jenkins, May 2006, Public Domain // bob_jenkins@burtleburtle.net -uint32_t hashlittle(const void *key, size_t length, uint32_t); +#ifndef LMP_HASHLITTLE_H +#define LMP_HASHLITTLE_H + +#include +#include + +namespace LAMMPS_NS { + uint32_t hashlittle(const void *key, size_t length, uint32_t); +} +#endif diff --git a/src/image.cpp b/src/image.cpp index 3df167bbf60b519184a128d9bceb0ba258ab0a72..4a5009b8ed20a673298324ad15e370ac14dc6c3f 100644 --- a/src/image.cpp +++ b/src/image.cpp @@ -15,12 +15,11 @@ Contributing author: Nathan Fabian (Sandia) ------------------------------------------------------------------------- */ +#include "image.h" #include #include #include -#include #include -#include "image.h" #include "math_extra.h" #include "random_mars.h" #include "math_const.h" @@ -29,7 +28,7 @@ #include "memory.h" #ifdef LAMMPS_JPEG -#include "jpeglib.h" +#include #endif #ifdef LAMMPS_PNG diff --git a/src/image.h b/src/image.h index 5672bf85c571d801876d37ebe889fefb12c1707c..7df81425d90ec8dce7998bf188f96b841a461218 100644 --- a/src/image.h +++ b/src/image.h @@ -15,7 +15,6 @@ #define LMP_IMAGE_H #include -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/imbalance.h b/src/imbalance.h index d3c3b9a64262c4dbd0aca56f83798a85db6b14b5..0cc4ac844efe8304c347d5205ccff92f7bf6e06c 100644 --- a/src/imbalance.h +++ b/src/imbalance.h @@ -14,8 +14,7 @@ #ifndef LMP_IMBALANCE_H #define LMP_IMBALANCE_H -#include -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/imbalance_neigh.cpp b/src/imbalance_neigh.cpp index 2a55754da8205cd7421aa9705d0f47b9c104a585..19f3915a11b15c37ec397fbdb455d64b83ccbbfc 100644 --- a/src/imbalance_neigh.cpp +++ b/src/imbalance_neigh.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "imbalance_neigh.h" +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/imbalance_store.cpp b/src/imbalance_store.cpp index 6b69caf785c964e831236c65a2b545ca4ec85ec6..343d47b18989c239e7469a71f6a78e65e09f847b 100644 --- a/src/imbalance_store.cpp +++ b/src/imbalance_store.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "imbalance_store.h" +#include #include "atom.h" -#include "input.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/imbalance_time.cpp b/src/imbalance_time.cpp index a5fe538b8f70f2de226c11d93b6c61c6659638b6..0831713204c715ef9ab8f144b3164bf6b353386c 100644 --- a/src/imbalance_time.cpp +++ b/src/imbalance_time.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "imbalance_time.h" +#include #include "atom.h" -#include "comm.h" #include "force.h" #include "timer.h" #include "error.h" diff --git a/src/imbalance_var.cpp b/src/imbalance_var.cpp index e089b1df0ce3e522dbd518b128cd1a867e429668..ba84ef01efe901494e018e097cf52ab93ccf46a0 100644 --- a/src/imbalance_var.cpp +++ b/src/imbalance_var.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "imbalance_var.h" +#include +#include #include "atom.h" #include "group.h" #include "input.h" @@ -20,9 +21,6 @@ #include "memory.h" #include "error.h" -// DEBUG -#include "update.h" - using namespace LAMMPS_NS; /* -------------------------------------------------------------------- */ diff --git a/src/improper.cpp b/src/improper.cpp index 17e2df4e590e65fe61000c948d129163173f0b97..eefe3222eeda1823c3accc3f85a41a6f1c748bf7 100644 --- a/src/improper.cpp +++ b/src/improper.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "improper.h" #include "atom.h" #include "comm.h" diff --git a/src/improper.h b/src/improper.h index 876c928d7ebc0c4feec20225fd0a884030c50fdb..c30079bb5ec755806f54d926ba1d8750979d338a 100644 --- a/src/improper.h +++ b/src/improper.h @@ -14,8 +14,7 @@ #ifndef LMP_IMPROPER_H #define LMP_IMPROPER_H -#include -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/improper_deprecated.cpp b/src/improper_deprecated.cpp index 6f4d08764fe85bd779406c5d5218011898cba748..62a688527a78f8e5c62e05437188d333f18f8337 100644 --- a/src/improper_deprecated.cpp +++ b/src/improper_deprecated.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "improper_deprecated.h" +#include #include "improper_hybrid.h" #include "comm.h" #include "force.h" diff --git a/src/improper_hybrid.cpp b/src/improper_hybrid.cpp index 174f54907ef26140128dda69ac0de8ad8f81e1b2..730a75766c81e8884a13fd43315cf9a97fc387f0 100644 --- a/src/improper_hybrid.cpp +++ b/src/improper_hybrid.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "improper_hybrid.h" +#include #include #include -#include "improper_hybrid.h" #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/improper_hybrid.h b/src/improper_hybrid.h index 89595ccfc44ff6f07ecfac4641b9440769a1f7fd..3e5423b173c2b053b995d809e79b894d735f2eed 100644 --- a/src/improper_hybrid.h +++ b/src/improper_hybrid.h @@ -20,7 +20,6 @@ ImproperStyle(hybrid,ImproperHybrid) #ifndef LMP_IMPROPER_HYBRID_H #define LMP_IMPROPER_HYBRID_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/improper_zero.cpp b/src/improper_zero.cpp index 747dd579191f591988569853279c8829e2e787cf..efa70c8ff52e501be34adb19a9cb44f65654f1ec 100644 --- a/src/improper_zero.cpp +++ b/src/improper_zero.cpp @@ -15,13 +15,10 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include -#include #include "improper_zero.h" +#include #include "atom.h" #include "force.h" -#include "comm.h" #include "memory.h" #include "error.h" diff --git a/src/improper_zero.h b/src/improper_zero.h index 0a2290b6f747a45013639005239284fe59c548fe..1a70059070a7e1f4fa9f7568c401dda41eecb542 100644 --- a/src/improper_zero.h +++ b/src/improper_zero.h @@ -20,7 +20,6 @@ ImproperStyle(zero,ImproperZero) #ifndef LMP_IMPROPER_ZERO_H #define LMP_IMPROPER_ZERO_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/info.cpp b/src/info.cpp index 6241877c8226898725970569de774ec291f23b23..0d54c6d0017c71467fc254f589e42d2a600fd705 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -16,8 +16,14 @@ Richard Berger (Temple U) ------------------------------------------------------------------------- */ -#include #include "info.h" +#include +#include +#include +#include +#include +#include +#include #include "accelerator_kokkos.h" #include "atom.h" #include "comm.h" @@ -44,18 +50,12 @@ #include "error.h" #include "utils.h" -#include -#include -#include -#include - #ifdef _WIN32 #define PSAPI_VERSION 1 #include #include // requires C++-11 #include #else -#include #include #include #endif @@ -374,7 +374,7 @@ void Info::command(int narg, char **arg) if (comm->mode == 0) { fprintf(out,"Communication mode = single\n"); fprintf(out,"Communication cutoff = %g\n", - MAX(comm->cutghostuser,neighbor->cutneighmax)); + comm->get_comm_cutoff()); } if (comm->mode == 1) { diff --git a/src/input.cpp b/src/input.cpp index 08e3655437fe07e8247834f05eb94e7011a66290..6871ee23f5396fcffe556b48a1fdbd108d0b8a17 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -11,15 +11,14 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "input.h" #include -#include #include #include #include #include #include #include -#include "input.h" #include "style_command.h" #include "universe.h" #include "atom.h" @@ -52,10 +51,6 @@ #include "memory.h" #include "utils.h" -#ifdef _OPENMP -#include -#endif - #ifdef _WIN32 #include #endif @@ -314,6 +309,17 @@ char *Input::one(const char *single) return command; } +/* ---------------------------------------------------------------------- + Send text to active echo file pointers +------------------------------------------------------------------------- */ +void Input::write_echo(const char *txt) +{ + if (me == 0) { + if (echo_screen && screen) fputs(txt,screen); + if (echo_log && logfile) fputs(txt,logfile); + } +} + /* ---------------------------------------------------------------------- parse copy of command line by inserting string terminators strip comment = all chars from # on diff --git a/src/input.h b/src/input.h index 7b6e55c2ba735b2b93efccc0068cd42d7cc52277..4b274c17a99bbbd723bb9a5d186af7d849975ed3 100644 --- a/src/input.h +++ b/src/input.h @@ -14,7 +14,6 @@ #ifndef LMP_INPUT_H #define LMP_INPUT_H -#include #include "pointers.h" #include #include @@ -39,17 +38,18 @@ class Input : protected Pointers { void substitute(char *&, char *&, int &, int &, int); // substitute for variables in a string int expand_args(int, char **, int, char **&); // expand args due to wildcard - + void write_echo(const char *); // send text to active echo file pointers + protected: char *command; // ptr to current command + int echo_screen; // 0 = no, 1 = yes + int echo_log; // 0 = no, 1 = yes private: int me; // proc ID int maxarg; // max # of args in arg char *line,*copy,*work; // input line & copy and work string int maxline,maxcopy,maxwork; // max lengths of char strings - int echo_screen; // 0 = no, 1 = yes - int echo_log; // 0 = no, 1 = yes int nfile,maxfile; // current # and max # of open input files int label_active; // 0 = no label, 1 = looking for label char *labelstr; // label string being looked for diff --git a/src/integrate.cpp b/src/integrate.cpp index d6b27e042d2ee7042d10d0af4bf4376423efc054..545de849d51bf0180f58a0d9f677cb73ce1cd49f 100644 --- a/src/integrate.cpp +++ b/src/integrate.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "integrate.h" #include "update.h" #include "force.h" diff --git a/src/irregular.cpp b/src/irregular.cpp index 1865f9cbf63454e897cd71c083615454a597b8d1..b67214df25b57b4442fed07b016fef8bb0ef46d7 100644 --- a/src/irregular.cpp +++ b/src/irregular.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "irregular.h" #include -#include #include -#include "irregular.h" #include "atom.h" #include "atom_vec.h" #include "domain.h" diff --git a/src/irregular.h b/src/irregular.h index d56bcb253d6b6ab72d8fa9960fdd1d8406a76408..3fdfe20b3636e07941ec61c64f505ce4b901446b 100644 --- a/src/irregular.h +++ b/src/irregular.h @@ -14,6 +14,7 @@ #ifndef LMP_IRREGULAR_H #define LMP_IRREGULAR_H +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/kspace.cpp b/src/kspace.cpp index 643cf22113357ed55d449572d4b6a51a16010a46..f9020416bfd10840352a7b6cfef3f680324112e0 100644 --- a/src/kspace.cpp +++ b/src/kspace.cpp @@ -11,9 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "kspace.h" +#include +#include #include #include -#include "kspace.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/kspace.h b/src/kspace.h index 69f4ccb433e8e2cb7d6822b0c1ac46bc597ab06a..c04a0db989308d7894bac0acec59d9bf58763966 100644 --- a/src/kspace.h +++ b/src/kspace.h @@ -14,7 +14,7 @@ #ifndef LMP_KSPACE_H #define LMP_KSPACE_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export #ifdef FFT_SINGLE typedef float FFT_SCALAR; diff --git a/src/kspace_deprecated.cpp b/src/kspace_deprecated.cpp index 1d62de269203a0641946fc73790e466343ba64d0..0b6490b4cfbc298e613233d55341729ae28b5986 100644 --- a/src/kspace_deprecated.cpp +++ b/src/kspace_deprecated.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "kspace_deprecated.h" +#include #include "comm.h" #include "force.h" #include "error.h" diff --git a/src/lammps.cpp b/src/lammps.cpp index f8d04c9323c78659b7e28a31700c47cbb0635082..5ddc1600a4145f36ca6e953a643a85bfce59aedb 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -11,26 +11,28 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "lammps.h" #include +#include #include +#include #include #include #include -#include "lammps.h" -#include "style_angle.h" -#include "style_atom.h" -#include "style_bond.h" -#include "style_command.h" -#include "style_compute.h" -#include "style_dihedral.h" -#include "style_dump.h" -#include "style_fix.h" -#include "style_improper.h" -#include "style_integrate.h" -#include "style_kspace.h" -#include "style_minimize.h" -#include "style_pair.h" -#include "style_region.h" +#include "style_angle.h" // IWYU pragma: keep +#include "style_atom.h" // IWYU pragma: keep +#include "style_bond.h" // IWYU pragma: keep +#include "style_command.h" // IWYU pragma: keep +#include "style_compute.h" // IWYU pragma: keep +#include "style_dihedral.h" // IWYU pragma: keep +#include "style_dump.h" // IWYU pragma: keep +#include "style_fix.h" // IWYU pragma: keep +#include "style_improper.h" // IWYU pragma: keep +#include "style_integrate.h" // IWYU pragma: keep +#include "style_kspace.h" // IWYU pragma: keep +#include "style_minimize.h" // IWYU pragma: keep +#include "style_pair.h" // IWYU pragma: keep +#include "style_region.h" // IWYU pragma: keep #include "universe.h" #include "input.h" #include "info.h" @@ -46,7 +48,7 @@ #include "output.h" #include "citeme.h" #include "accelerator_kokkos.h" -#include "accelerator_omp.h" +#include "accelerator_omp.h" // IWYU pragma: keep #include "timer.h" #include "lmppython.h" #include "version.h" diff --git a/src/lammps.h b/src/lammps.h index e02d0c764a82cf67e1f64466ffea30abce99dd28..dc2916f214c1e9b64d077f7ecd23b6af6aa5c3a7 100644 --- a/src/lammps.h +++ b/src/lammps.h @@ -14,6 +14,7 @@ #ifndef LMP_LAMMPS_H #define LMP_LAMMPS_H +#include #include namespace LAMMPS_NS { diff --git a/src/lattice.cpp b/src/lattice.cpp index ee2fea2a758dca955bb4a8841ff481d99974dac9..98faf680e831c2e33d27bc2150f2865acd79d7c2 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "lattice.h" #include #include #include -#include "lattice.h" #include "update.h" #include "domain.h" #include "comm.h" diff --git a/src/library.cpp b/src/library.cpp index a653b83adba7beba21eba6849010d3fe1a0538c5..eabe5fd17971ad8ed49762158c243fdcade85f32 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -14,14 +14,12 @@ // C or Fortran style library interface to LAMMPS // customize by adding new LAMMPS-specific functions +#include "library.h" #include +#include #include #include -#include "library.h" -#include "lmptype.h" -#include "lammps.h" #include "universe.h" -#include "input.h" #include "atom_vec.h" #include "atom.h" #include "domain.h" diff --git a/src/library.h b/src/library.h index f6f8d9d75c2922deef37c5d8182dbaac5666c8e1..8b03bb36216937168f56faf4c01cc3cc2c63283e 100644 --- a/src/library.h +++ b/src/library.h @@ -17,7 +17,9 @@ */ #include +#ifdef LAMMPS_BIGBIG #include /* for int64_t */ +#endif /* ifdefs allow this file to be included in a C program */ diff --git a/src/lmppython.cpp b/src/lmppython.cpp index 7c6a490c24fcae06b298d453b30a00bd28e3c1f1..52abd93f1083b3e9a1045a3eb7843dddb7216fff 100644 --- a/src/lmppython.cpp +++ b/src/lmppython.cpp @@ -12,7 +12,11 @@ ------------------------------------------------------------------------- */ #include "lmppython.h" +#if LMP_PYTHON +#include "python_impl.h" +#else #include "error.h" +#endif using namespace LAMMPS_NS; diff --git a/src/lmppython.h b/src/lmppython.h index afc21037fb1752d94d96ad1a68580c346811a711..3d55c4827b87ccfea06a3cc3d219098e219894a3 100644 --- a/src/lmppython.h +++ b/src/lmppython.h @@ -51,11 +51,6 @@ private: }; } - -#endif - -#if LMP_PYTHON -#include "python_impl.h" #endif /* ERROR/WARNING messages: diff --git a/src/lmptype.h b/src/lmptype.h index ad00df6c633c3f5ec4a4f9dac45d0cdbb777a196..65e46535fc489ccdd8ee6b48692b61c80e6d8895 100644 --- a/src/lmptype.h +++ b/src/lmptype.h @@ -49,10 +49,6 @@ namespace LAMMPS_NS { -// enum used for KOKKOS host/device flags - -enum ExecutionSpace{Host,Device}; - // reserve 2 hi bits in molecular system neigh list for special bonds flag // max local + ghost atoms per processor = 2^30 - 1 diff --git a/src/main.cpp b/src/main.cpp index 8eb5e4e5433da594017958784de1de0790b37b82..b7f6adbddae87b05c8392d6cde4d1123369a7465 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -11,12 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "lammps.h" +#include #include "input.h" -#include "error.h" -#include -#include #if defined(LAMMPS_TRAP_FPE) && defined(_GNU_SOURCE) #include diff --git a/src/math_extra.cpp b/src/math_extra.cpp index f7e5bb646b0a7fa8a9e6f3bbb30313879b0c87f1..797d210d0e056238fc53c3bbbb8dff2df287d788 100644 --- a/src/math_extra.cpp +++ b/src/math_extra.cpp @@ -15,9 +15,9 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "math_extra.h" #include #include -#include "math_extra.h" #define MAXJACOBI 50 diff --git a/src/math_extra.h b/src/math_extra.h index 85f57224cfb97a3f6a7bde21dddbae18409dae93..09b135c64130da96075aa1da5a0a291830c745b3 100644 --- a/src/math_extra.h +++ b/src/math_extra.h @@ -19,9 +19,6 @@ #define LMP_MATH_EXTRA_H #include -#include -#include -#include "error.h" namespace MathExtra { diff --git a/src/math_special.cpp b/src/math_special.cpp index 31567bdc77fa90bab58d307356d3a9b67aa109ba..bf11a1ad45720cd2cf88663522e44cb617d8349c 100644 --- a/src/math_special.cpp +++ b/src/math_special.cpp @@ -1,6 +1,6 @@ -#include -#include // requires C++-11 #include "math_special.h" +#include +#include // IWYU pragma: keep using namespace LAMMPS_NS; diff --git a/src/memory.cpp b/src/memory.cpp index b2f8a95b17a83c5b5f5ddec188f4e72c38c6d97e..a513dde6c2e82590226aec8e16cb3affdc0f5c58 100644 --- a/src/memory.cpp +++ b/src/memory.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "memory.h" +#include #include "error.h" #if defined(LMP_USER_INTEL) && defined(__INTEL_COMPILER) diff --git a/src/memory.h b/src/memory.h index c5eddc7fe709137e7ce9847b30a02a9b96636d0a..42c9bf6aba617d67790786f88f55a3f095336661 100644 --- a/src/memory.h +++ b/src/memory.h @@ -14,7 +14,6 @@ #ifndef LMP_MEMORY_H #define LMP_MEMORY_H -#include "lmptype.h" #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/min.cpp b/src/min.cpp index 2a42a444a035f985fda5c63a72ca1eb0a707b70b..408954edb8d37c3ba1a5c3c8c2e7e84e5fd50221 100644 --- a/src/min.cpp +++ b/src/min.cpp @@ -19,10 +19,10 @@ JR Shewchuk, http://www-2.cs.cmu.edu/~jrs/jrspapers.html#cg ------------------------------------------------------------------------- */ +#include "min.h" +#include #include -#include #include -#include "min.h" #include "atom.h" #include "atom_vec.h" #include "domain.h" diff --git a/src/min_cg.cpp b/src/min_cg.cpp index 20e8cc30dd35f05355eb44869f48a2dc914a7c90..ff318d23da689109fd97cbe84e476a461ed93bfd 100644 --- a/src/min_cg.cpp +++ b/src/min_cg.cpp @@ -11,11 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "min_cg.h" #include #include -#include -#include "min_cg.h" -#include "atom.h" #include "update.h" #include "output.h" #include "timer.h" diff --git a/src/min_fire.cpp b/src/min_fire.cpp index a50071d56204e197a9a4d321640ec50c7d897b99..b7f853afd27681ebfc368608a474bf40e2dff6e5 100644 --- a/src/min_fire.cpp +++ b/src/min_fire.cpp @@ -11,15 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "min_fire.h" +#include +#include #include "universe.h" #include "atom.h" #include "force.h" #include "update.h" #include "output.h" #include "timer.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/min_hftn.cpp b/src/min_hftn.cpp index 0c834fbeb442e71e5227989de328dbe252339ae8..dcfed10fefae11b47e1bb2d143746d84ee9ad83e 100644 --- a/src/min_hftn.cpp +++ b/src/min_hftn.cpp @@ -17,11 +17,12 @@ "Parallel Unconstrained Min", Plantenga, SAND98-8201 ------------------------------------------------------------------------- */ +#include "min_hftn.h" +#include #include #include #include "atom.h" #include "fix_minimize.h" -#include "min_hftn.h" #include "modify.h" #include "output.h" #include "pair.h" diff --git a/src/min_linesearch.cpp b/src/min_linesearch.cpp index f93a56b09d93895dddd0770a377629b50e0b8412..a7a10dcd5172fd39e49e300906b6c59e01964a7d 100644 --- a/src/min_linesearch.cpp +++ b/src/min_linesearch.cpp @@ -21,19 +21,15 @@ JR Shewchuk, http://www-2.cs.cmu.edu/~jrs/jrspapers.html#cg ------------------------------------------------------------------------- */ -#include #include "min_linesearch.h" +#include +#include #include "atom.h" -#include "update.h" -#include "neighbor.h" -#include "domain.h" #include "modify.h" #include "fix_minimize.h" #include "pair.h" #include "output.h" #include "thermo.h" -#include "timer.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/min_quickmin.cpp b/src/min_quickmin.cpp index 8b48816355b0a5b64db0a77fd3c11a9fccff1886..04e72b046d15d258e089d69454f7967067f92873 100644 --- a/src/min_quickmin.cpp +++ b/src/min_quickmin.cpp @@ -11,16 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "min_quickmin.h" #include #include -#include "min_quickmin.h" #include "universe.h" #include "atom.h" #include "force.h" #include "update.h" #include "output.h" #include "timer.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/min_sd.cpp b/src/min_sd.cpp index 5d44437ca07e6ca372068e5ae2516cc32d05a045..e4e159003f46df61b794b4f7bbc8ee04c3f957ff 100644 --- a/src/min_sd.cpp +++ b/src/min_sd.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "min_sd.h" -#include "atom.h" +#include #include "update.h" #include "output.h" #include "timer.h" diff --git a/src/minimize.cpp b/src/minimize.cpp index e27fffd74bb15c1e005052a3669e09a8b20d13d7..e1af92401941ebda6dac402ca54e715886137da7 100644 --- a/src/minimize.cpp +++ b/src/minimize.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "minimize.h" #include "domain.h" #include "update.h" diff --git a/src/modify.cpp b/src/modify.cpp index 3f034bf034d35756a7f25e5051533f83e0f9f875..109571d531a5d86a60df8f97ec70289725aaa16c 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "modify.h" +#include #include "style_compute.h" #include "style_fix.h" #include "atom.h" @@ -798,7 +797,7 @@ void Modify::add_fix(int narg, char **arg, int trysuffix) const char *exceptions[] = {"GPU", "OMP", "INTEL", "property/atom", "cmap", "cmap3", "rx", - "deprecated", NULL}; + "deprecated", "STORE/KIM", NULL}; if (domain->box_exist == 0) { int m; diff --git a/src/modify.h b/src/modify.h index 5ff81855feda2fd5477ccabac73e52516de30807..b7364851968810c12483ed23fc9ce0c344a0925a 100644 --- a/src/modify.h +++ b/src/modify.h @@ -14,7 +14,6 @@ #ifndef LMP_MODIFY_H #define LMP_MODIFY_H -#include #include "pointers.h" #include #include diff --git a/src/molecule.cpp b/src/molecule.cpp index 454459084a70aceca4a09ad9b8972e2c1167a4a7..38887ebb0c82095bf00f83bf2423c3f8b0449916 100644 --- a/src/molecule.cpp +++ b/src/molecule.cpp @@ -11,9 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "molecule.h" +#include +#include +#include +#include #include "atom.h" #include "atom_vec.h" #include "atom_vec_body.h" @@ -21,12 +23,10 @@ #include "comm.h" #include "domain.h" #include "math_extra.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; #define MAXLINE 256 #define EPSILON 1.0e-7 diff --git a/src/mpiio.h b/src/mpiio.h index 4953ade1859520e07d0cc05ec32fa00f861c2b9d..0098fca0e11b96e4d8a0004448cc5ae6c1e58618 100644 --- a/src/mpiio.h +++ b/src/mpiio.h @@ -23,7 +23,7 @@ #error "The MPIIO package cannot be compiled in serial with MPI STUBS" #endif -#include "restart_mpiio.h" +#include "restart_mpiio.h" // IWYU pragma: export #else diff --git a/src/my_pool_chunk.h b/src/my_pool_chunk.h index 8bf88d35bbe425c67193daeba0d309aff73eb78c..a313e45f05fd4400886a4c8b381a715708d26309 100644 --- a/src/my_pool_chunk.h +++ b/src/my_pool_chunk.h @@ -43,6 +43,10 @@ public variables: #ifndef LAMMPS_MY_POOL_CHUNK_H #define LAMMPS_MY_POOL_CHUNK_H +#if defined(LMP_USER_INTEL) && !defined(LAMMPS_MEMALIGN) && !defined(_WIN32) +#define LAMMPS_MEMALIGN 64 +#endif + #include namespace LAMMPS_NS { @@ -190,9 +194,17 @@ class MyPoolChunk { for (int i = oldpage; i < npage; i++) { whichbin[i] = ibin; +#if defined(LAMMPS_MEMALIGN) + void *ptr; + if (posix_memalign(&ptr, LAMMPS_MEMALIGN, + chunkperpage*chunksize[ibin]*sizeof(T))) + errorflag = 2; + pages[i] = (T *) ptr; +#else pages[i] = (T *) malloc(chunkperpage*chunksize[ibin]*sizeof(T)); size += chunkperpage*chunksize[ibin]; if (!pages[i]) errorflag = 2; +#endif } // reset free list for unused chunks on new pages diff --git a/src/nbin.cpp b/src/nbin.cpp index 3e50148a0498dcaab8582a6aeec4881d316d54b7..4838d1d63dd54e467b08eb749dfbe3eac7c83d37 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include "nbin.h" +#include #include "neighbor.h" #include "neigh_request.h" #include "domain.h" -#include "update.h" #include "memory.h" #include "error.h" diff --git a/src/neigh_list.cpp b/src/neigh_list.cpp index 6bdb9beae62e6924b201af00b3c60bb5086dcc9a..31720cc78c18775b41ee09d1e93fb5526f7751bd 100644 --- a/src/neigh_list.cpp +++ b/src/neigh_list.cpp @@ -12,15 +12,13 @@ ------------------------------------------------------------------------- */ #include "neigh_list.h" +#include "my_page.h" // IWYU pragma: keep #include "atom.h" #include "comm.h" -#include "update.h" -#include "pair.h" #include "neighbor.h" #include "neigh_request.h" #include "my_page.h" #include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/neigh_list.h b/src/neigh_list.h index 755a1bf13415c4cdd7d428f3000c2039047ed081..aca11cd9212280458b5b19bf79635b281223b7bf 100644 --- a/src/neigh_list.h +++ b/src/neigh_list.h @@ -15,7 +15,6 @@ #define LMP_NEIGH_LIST_H #include "pointers.h" -#include "my_page.h" namespace LAMMPS_NS { diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 038262419857afbf770eab3c090f1afd8bc4a14e..d38aed08c0dd1eb7e8712e0b0212e2f074a3b189 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -15,11 +15,10 @@ Contributing author (triclinic and multi-neigh) : Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "neighbor.h" #include #include -#include #include -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "nbin.h" @@ -48,8 +47,6 @@ #include "error.h" #include "utils.h" -#include - using namespace LAMMPS_NS; using namespace NeighConst; diff --git a/src/neighbor.h b/src/neighbor.h index 3466dd426a3f5245631655c8a7b91f6867e52218..50de4b4c98fffc1dffdedcbf173882b60a2a97e5 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -15,7 +15,6 @@ #define LMP_NEIGHBOR_H #include "pointers.h" -#include namespace LAMMPS_NS { diff --git a/src/npair.cpp b/src/npair.cpp index 24cdc7750af504f1f510fdd0e29a5ba0b0b9355a..b63135fad6baeb8081bdcb899f9bfdf1469f46cb 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair.h" +#include #include "neighbor.h" #include "neigh_request.h" #include "nbin.h" diff --git a/src/npair_copy.cpp b/src/npair_copy.cpp index 9426d22ed3595dd2157d20adbf56265d3f3bb42b..0a522c628d8e7e5b3e3a38601c96cc648947364e 100644 --- a/src/npair_copy.cpp +++ b/src/npair_copy.cpp @@ -12,14 +12,7 @@ ------------------------------------------------------------------------- */ #include "npair_copy.h" -#include "neighbor.h" #include "neigh_list.h" -#include "atom.h" -#include "atom_vec.h" -#include "molecule.h" -#include "domain.h" -#include "my_page.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/npair_full_bin.cpp b/src/npair_full_bin.cpp index 94a6af129cbed7b448d0bab554f6fd433a9483bc..464dca92519ae73a9bb641a73a85f6343d306df9 100644 --- a/src/npair_full_bin.cpp +++ b/src/npair_full_bin.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_full_bin.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_full_bin_atomonly.cpp b/src/npair_full_bin_atomonly.cpp index db84733f1c584201d8d15c6e0bb01cd0bb8111ee..758fc7e42ba2acd73b765336ebb60e2e15214761 100644 --- a/src/npair_full_bin_atomonly.cpp +++ b/src/npair_full_bin_atomonly.cpp @@ -12,11 +12,9 @@ ------------------------------------------------------------------------- */ #include "npair_full_bin_atomonly.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/npair_full_bin_ghost.cpp b/src/npair_full_bin_ghost.cpp index 2edd03cc9e5a48fa91c985613213d1e5f05f8674..61b27dd99d32a61c4209bebcba3507f4a952a290 100644 --- a/src/npair_full_bin_ghost.cpp +++ b/src/npair_full_bin_ghost.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_full_bin_ghost.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_full_multi.cpp b/src/npair_full_multi.cpp index 9a2490ac5d18acb07375675da9b4b1e795053abd..40ed2275bec800fe91a9f7ff56572f4d9b6d7f84 100644 --- a/src/npair_full_multi.cpp +++ b/src/npair_full_multi.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_full_multi.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_full_nsq.cpp b/src/npair_full_nsq.cpp index 1b404ffc947bb767b4cbb7c34c0a8de0236640cb..76b66fd004a8cbc05ade92477f38005c35752288 100644 --- a/src/npair_full_nsq.cpp +++ b/src/npair_full_nsq.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_full_nsq.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_full_nsq_ghost.cpp b/src/npair_full_nsq_ghost.cpp index 1727b2905e0152d473c8bb03b0e98a571a24ce4f..b20fa9b8cef4885c2ced5abe898ed43c9e9e0e2e 100644 --- a/src/npair_full_nsq_ghost.cpp +++ b/src/npair_full_nsq_ghost.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_full_nsq_ghost.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_bin_atomonly_newton.cpp b/src/npair_half_bin_atomonly_newton.cpp index 6da44b4a5cfc252ab8c449fd12ed36d282dfbb36..a7fa3985ef140453230caee76e76faedc4a70674 100644 --- a/src/npair_half_bin_atomonly_newton.cpp +++ b/src/npair_half_bin_atomonly_newton.cpp @@ -12,12 +12,9 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_atomonly_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/npair_half_bin_newtoff.cpp b/src/npair_half_bin_newtoff.cpp index 4c44741ffed9a19ab258223b7f2d2ea6c5b652b3..65768918c9e4c99ef72ec0e5927f87e4e9f9edf9 100644 --- a/src/npair_half_bin_newtoff.cpp +++ b/src/npair_half_bin_newtoff.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_bin_newtoff_ghost.cpp b/src/npair_half_bin_newtoff_ghost.cpp index 72ec15e66a733424d918250f8e52553f5f257be1..91fbf049cbafa5dd87e617f17d2e8d624a195554 100644 --- a/src/npair_half_bin_newtoff_ghost.cpp +++ b/src/npair_half_bin_newtoff_ghost.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_newtoff_ghost.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_bin_newton.cpp b/src/npair_half_bin_newton.cpp index 3a387870e3c48c8104813a5eae8576744c58ff2c..fe388e114426fce180bef1a7e15580031ee53e9d 100644 --- a/src/npair_half_bin_newton.cpp +++ b/src/npair_half_bin_newton.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_bin_newton_tri.cpp b/src/npair_half_bin_newton_tri.cpp index 169e710e0e5e18779d88aa4e039619c620351e1c..1f0e3c1187dddae3d53cba65634f4908cbc03a12 100644 --- a/src/npair_half_bin_newton_tri.cpp +++ b/src/npair_half_bin_newton_tri.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_newton_tri.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_multi_newtoff.cpp b/src/npair_half_multi_newtoff.cpp index 07b5c87a6cfb85b6c399597fdac9da27e3ff800b..57dcf29cc765f8f3e791e55ca6dd001235093a60 100644 --- a/src/npair_half_multi_newtoff.cpp +++ b/src/npair_half_multi_newtoff.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_multi_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_multi_newton.cpp b/src/npair_half_multi_newton.cpp index 3d909793291cae7fedab4eed4420fa09a0c11242..a9293d3d6416e6b48511c114f57c8ca59abacbc0 100644 --- a/src/npair_half_multi_newton.cpp +++ b/src/npair_half_multi_newton.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_multi_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_multi_newton_tri.cpp b/src/npair_half_multi_newton_tri.cpp index 909c69246b7e9c481ce97576400cbd7481d9f6aa..c1d845cb388c1ea48396e4a0442d15fddd921d58 100644 --- a/src/npair_half_multi_newton_tri.cpp +++ b/src/npair_half_multi_newton_tri.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_multi_newton_tri.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_nsq_newtoff.cpp b/src/npair_half_nsq_newtoff.cpp index 06e8344332101ad5a5d7bdc22035cb35bd236eca..db369687d024c852c7ee6cc84df663820b7d2f0b 100644 --- a/src/npair_half_nsq_newtoff.cpp +++ b/src/npair_half_nsq_newtoff.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_nsq_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_nsq_newtoff_ghost.cpp b/src/npair_half_nsq_newtoff_ghost.cpp index 1865061a8b46f38ef53d9a0a06e8988c0c452e7a..0a9b6d0f45d31df4d77d69a9297736fb6e6497ed 100644 --- a/src/npair_half_nsq_newtoff_ghost.cpp +++ b/src/npair_half_nsq_newtoff_ghost.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_nsq_newtoff_ghost.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_nsq_newton.cpp b/src/npair_half_nsq_newton.cpp index 11c71d5609c2985f804cc583dc19b2e735b268a5..69489915b2b57db90185e9601eb6d7d9fe2fd893 100644 --- a/src/npair_half_nsq_newton.cpp +++ b/src/npair_half_nsq_newton.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_nsq_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_respa_bin_newtoff.cpp b/src/npair_half_respa_bin_newtoff.cpp index 0145771f4aafa11a3083c70466bb9476ad771b29..8c1d8d684f64f129225aafa1f8fa83ebc7cf2e95 100644 --- a/src/npair_half_respa_bin_newtoff.cpp +++ b/src/npair_half_respa_bin_newtoff.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_respa_bin_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_respa_bin_newton.cpp b/src/npair_half_respa_bin_newton.cpp index 72a613204d889c8d7c5873d424aa8d9491b69f48..d2598fa1a4ed6e6317c35a3c592dd899236908ed 100644 --- a/src/npair_half_respa_bin_newton.cpp +++ b/src/npair_half_respa_bin_newton.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_respa_bin_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_respa_bin_newton_tri.cpp b/src/npair_half_respa_bin_newton_tri.cpp index add1cf6e5cb50b36fed9dc0d30b8fff7e554ecbe..efe48d48e1aae1790d252c1ddc2416f526bc5fcc 100644 --- a/src/npair_half_respa_bin_newton_tri.cpp +++ b/src/npair_half_respa_bin_newton_tri.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_respa_bin_newton_tri.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_respa_nsq_newtoff.cpp b/src/npair_half_respa_nsq_newtoff.cpp index c0e932f0aeededae43300ff794cd5508fc8eb2b5..334ebb5ca80f956a5f870c88fbbc54da51045e40 100644 --- a/src/npair_half_respa_nsq_newtoff.cpp +++ b/src/npair_half_respa_nsq_newtoff.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_respa_nsq_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_respa_nsq_newton.cpp b/src/npair_half_respa_nsq_newton.cpp index f7d161896d47bc520278b68fd0674ef5fa2eae82..7ecd02b0c55770db5359a4deff3ca23e23d950c9 100644 --- a/src/npair_half_respa_nsq_newton.cpp +++ b/src/npair_half_respa_nsq_newton.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_respa_nsq_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_size_bin_newtoff.cpp b/src/npair_half_size_bin_newtoff.cpp index 021452028b3802f68c759707dbd9f00d4bb6c320..b9e44675acd8ffae228876e3f61c2e967a99c88b 100644 --- a/src/npair_half_size_bin_newtoff.cpp +++ b/src/npair_half_size_bin_newtoff.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_bin_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_size_bin_newton.cpp b/src/npair_half_size_bin_newton.cpp index 760c09570a0dcad90ae2e66ec1d3e3a2480f93df..93bcc2537314dde0dfcabdda9a42634531938ba2 100644 --- a/src/npair_half_size_bin_newton.cpp +++ b/src/npair_half_size_bin_newton.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_bin_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_size_bin_newton_tri.cpp b/src/npair_half_size_bin_newton_tri.cpp index d831982ed6033842b85cbdf677ca5e59b1a40a66..39068c02bcaa3f08b86cf06ce33833add7afbfb7 100644 --- a/src/npair_half_size_bin_newton_tri.cpp +++ b/src/npair_half_size_bin_newton_tri.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_bin_newton_tri.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_size_nsq_newtoff.cpp b/src/npair_half_size_nsq_newtoff.cpp index 1c2fe5f3d57b4666a0807c7765bb380bce935204..6f169d0b6c81a08e8994e0db3a6dae1d389ba790 100644 --- a/src/npair_half_size_nsq_newtoff.cpp +++ b/src/npair_half_size_nsq_newtoff.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_nsq_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_size_nsq_newton.cpp b/src/npair_half_size_nsq_newton.cpp index ce9f8ec18631876d99d0b5bb1d2641aabee72da4..d427c14809fd41650b08afd2081ff6c284cfb1d9 100644 --- a/src/npair_half_size_nsq_newton.cpp +++ b/src/npair_half_size_nsq_newton.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_nsq_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_halffull_newtoff.cpp b/src/npair_halffull_newtoff.cpp index 84816f07b25da9825aec2b663bfa7855d292ac4b..6ff5433e8888f747c7a570e8236f785e9670d6a3 100644 --- a/src/npair_halffull_newtoff.cpp +++ b/src/npair_halffull_newtoff.cpp @@ -12,12 +12,8 @@ ------------------------------------------------------------------------- */ #include "npair_halffull_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" -#include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/npair_halffull_newton.cpp b/src/npair_halffull_newton.cpp index 371bbd33a85cd6c73c3b20a03e3251a4c1c3f7e9..0912cfe12fe65a94e17d1f76a954dbfadf5a0572 100644 --- a/src/npair_halffull_newton.cpp +++ b/src/npair_halffull_newton.cpp @@ -12,12 +12,9 @@ ------------------------------------------------------------------------- */ #include "npair_halffull_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/npair_skip.cpp b/src/npair_skip.cpp index 1fe202537a84ce1b9a5c36dcc9770bb377ff23a5..028041a9477a6c04afb33263551bcff6cb0e052f 100644 --- a/src/npair_skip.cpp +++ b/src/npair_skip.cpp @@ -12,12 +12,9 @@ ------------------------------------------------------------------------- */ #include "npair_skip.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/npair_skip_respa.cpp b/src/npair_skip_respa.cpp index 1d4eda53549f9ec180dd7e9d2c66c0999a2fd88f..68436654b26689547d01c106d1047f186a3f23e9 100644 --- a/src/npair_skip_respa.cpp +++ b/src/npair_skip_respa.cpp @@ -12,12 +12,9 @@ ------------------------------------------------------------------------- */ #include "npair_skip_respa.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/npair_skip_size.cpp b/src/npair_skip_size.cpp index 67717ae57660ca11e71685c7c445bab8eff6602b..436d21f76fa226add3c1ee5e44d363a4af729ec6 100644 --- a/src/npair_skip_size.cpp +++ b/src/npair_skip_size.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_skip_size.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_skip_size_off2on.cpp b/src/npair_skip_size_off2on.cpp index 74a80e6d3d3e2da207aaa1c424069bac4148020a..cd674ff7774566dd0358575ea5830e3c77d4c0ec 100644 --- a/src/npair_skip_size_off2on.cpp +++ b/src/npair_skip_size_off2on.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_skip_size_off2on.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_skip_size_off2on_oneside.cpp b/src/npair_skip_size_off2on_oneside.cpp index a042acd1c6bb034d4a84e568487c48170c1dfbca..0540592cba468fbb87ec72e428c6c3de6510436d 100644 --- a/src/npair_skip_size_off2on_oneside.cpp +++ b/src/npair_skip_size_off2on_oneside.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_skip_size_off2on_oneside.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/nstencil_full_bin_2d.cpp b/src/nstencil_full_bin_2d.cpp index 0986c40dd442176d63056eea3eeeae9b2f16990d..b18d990bbadc8e793ca880db13879676c9803200 100644 --- a/src/nstencil_full_bin_2d.cpp +++ b/src/nstencil_full_bin_2d.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_full_bin_2d.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_full_bin_3d.cpp b/src/nstencil_full_bin_3d.cpp index b6a21981328726e3036c77e75ad6034ec1f23c3e..46ec073ddd718e21d063d072c461fe7021ed6af1 100644 --- a/src/nstencil_full_bin_3d.cpp +++ b/src/nstencil_full_bin_3d.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_full_bin_3d.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_full_ghost_bin_2d.cpp b/src/nstencil_full_ghost_bin_2d.cpp index bbbf1a4466b5be805af706a805b80e3e2af75de3..5ac19569c5aa3ad9ba5b30763caaf981b34921fc 100644 --- a/src/nstencil_full_ghost_bin_2d.cpp +++ b/src/nstencil_full_ghost_bin_2d.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_full_ghost_bin_2d.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_full_ghost_bin_3d.cpp b/src/nstencil_full_ghost_bin_3d.cpp index e9abca21745101cd122b3fe0c7aa6f344b6caf05..6ee56516dc6da7d57324b7f140cad158ced639bd 100644 --- a/src/nstencil_full_ghost_bin_3d.cpp +++ b/src/nstencil_full_ghost_bin_3d.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_full_ghost_bin_3d.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_full_multi_2d.cpp b/src/nstencil_full_multi_2d.cpp index ed2ffe11dc8bac72220c2803b03e34a155428ec8..c69c53a761a894706ba7b52e774bd41a6fc73e55 100644 --- a/src/nstencil_full_multi_2d.cpp +++ b/src/nstencil_full_multi_2d.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_full_multi_2d.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_full_multi_3d.cpp b/src/nstencil_full_multi_3d.cpp index c171bfadc53be32726b3f55428c7728b349ddd5c..df47c1e7e92afecf399acf77db88c761b5eef881 100644 --- a/src/nstencil_full_multi_3d.cpp +++ b/src/nstencil_full_multi_3d.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_full_multi_3d.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_bin_2d_newtoff.cpp b/src/nstencil_half_bin_2d_newtoff.cpp index e51db6fe7a4161b4db8e7b1f1ef784687299544b..f3a6c5d08b7442106e7414fb57df0d0518d1124d 100644 --- a/src/nstencil_half_bin_2d_newtoff.cpp +++ b/src/nstencil_half_bin_2d_newtoff.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_2d_newtoff.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_bin_2d_newton.cpp b/src/nstencil_half_bin_2d_newton.cpp index 9479bbf0c83cb326d85f17f3a7a0e733d68f9383..8fdc8f1aa9ef3f57a2d95c965c65c8473d64608d 100644 --- a/src/nstencil_half_bin_2d_newton.cpp +++ b/src/nstencil_half_bin_2d_newton.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_2d_newton.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_bin_2d_newton_tri.cpp b/src/nstencil_half_bin_2d_newton_tri.cpp index 4f89b1c326661b428e11af25b063b2961076c540..30d064fb2929d69c499323a898dbd5221adef2ca 100644 --- a/src/nstencil_half_bin_2d_newton_tri.cpp +++ b/src/nstencil_half_bin_2d_newton_tri.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_2d_newton_tri.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_bin_3d_newtoff.cpp b/src/nstencil_half_bin_3d_newtoff.cpp index 433de400c20d63793e356647c951d86d4f21eca9..e44a93d47d184890e0a57e399a781360d0c69df9 100644 --- a/src/nstencil_half_bin_3d_newtoff.cpp +++ b/src/nstencil_half_bin_3d_newtoff.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_3d_newtoff.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_bin_3d_newton.cpp b/src/nstencil_half_bin_3d_newton.cpp index 24c234c00419d14f84dccb748a98360432646065..998ed28afedc80b1ca0d918c0060f8c133185fc1 100644 --- a/src/nstencil_half_bin_3d_newton.cpp +++ b/src/nstencil_half_bin_3d_newton.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_3d_newton.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_bin_3d_newton_tri.cpp b/src/nstencil_half_bin_3d_newton_tri.cpp index 691ce0bb8095dca0db721a5bc04f350aaa9cc63f..2aae44ceaf088cb69cd4ede27bf13ee4e22d2ada 100644 --- a/src/nstencil_half_bin_3d_newton_tri.cpp +++ b/src/nstencil_half_bin_3d_newton_tri.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_3d_newton_tri.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_ghost_bin_2d_newtoff.cpp b/src/nstencil_half_ghost_bin_2d_newtoff.cpp index 4bb0ecafe2cff123112e4e9f11393c8450b33fde..6f9a7585fef0cb23bd7be9ebc8d3f26fce13eca7 100644 --- a/src/nstencil_half_ghost_bin_2d_newtoff.cpp +++ b/src/nstencil_half_ghost_bin_2d_newtoff.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_ghost_bin_2d_newtoff.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_ghost_bin_3d_newtoff.cpp b/src/nstencil_half_ghost_bin_3d_newtoff.cpp index 1026b11542779a6a14079e7a8d10f6f313f0d467..6492fe4a4e4991e312fb971b8ecb01f8b447a94b 100644 --- a/src/nstencil_half_ghost_bin_3d_newtoff.cpp +++ b/src/nstencil_half_ghost_bin_3d_newtoff.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_ghost_bin_3d_newtoff.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_multi_2d_newtoff.cpp b/src/nstencil_half_multi_2d_newtoff.cpp index 567abe2878a5134ed5d25dfb28f4c510d7a154ad..63cd3fd5245182db2199a39b746ae47cac7e4554 100644 --- a/src/nstencil_half_multi_2d_newtoff.cpp +++ b/src/nstencil_half_multi_2d_newtoff.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_multi_2d_newtoff.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_multi_2d_newton.cpp b/src/nstencil_half_multi_2d_newton.cpp index 5dc2c371481186746f728f95d4478f0a0635139f..f6f6c488a5442a7679c21d9ed2433c37d8691022 100644 --- a/src/nstencil_half_multi_2d_newton.cpp +++ b/src/nstencil_half_multi_2d_newton.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_multi_2d_newton.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_multi_2d_newton_tri.cpp b/src/nstencil_half_multi_2d_newton_tri.cpp index 59a5a1d19ec7d88741f74ba9f8899b2fcd2f4f6c..b44ab36ea09b8fdc7ed3a377cdeebd40df78183a 100644 --- a/src/nstencil_half_multi_2d_newton_tri.cpp +++ b/src/nstencil_half_multi_2d_newton_tri.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_multi_2d_newton_tri.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_multi_3d_newtoff.cpp b/src/nstencil_half_multi_3d_newtoff.cpp index 72b882dddcc552009a5a6a9c09b6a1ddf40b9fcd..5a83c4e0026b3548cb1cb641a8e6e693efd36dfe 100644 --- a/src/nstencil_half_multi_3d_newtoff.cpp +++ b/src/nstencil_half_multi_3d_newtoff.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_multi_3d_newtoff.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_multi_3d_newton.cpp b/src/nstencil_half_multi_3d_newton.cpp index 9a5d5cab653d6706e7c24dfdcbeb8dc4b2359165..5b0c7f9f63605e88171f44d51f87684e118b2057 100644 --- a/src/nstencil_half_multi_3d_newton.cpp +++ b/src/nstencil_half_multi_3d_newton.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_multi_3d_newton.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_multi_3d_newton_tri.cpp b/src/nstencil_half_multi_3d_newton_tri.cpp index 953beb3211ff053261ada587b69fbc5b0ae896df..b25a0d0bdb3ec8f881858256db2afead812bbfd1 100644 --- a/src/nstencil_half_multi_3d_newton_tri.cpp +++ b/src/nstencil_half_multi_3d_newton_tri.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_multi_3d_newton_tri.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/ntopo.cpp b/src/ntopo.cpp index 8a87a5d6e5fa9003e78a7e5be6ce9d744ee1ca89..ca63b8532818f102ae0699c64d76f7edc5bb6cb5 100644 --- a/src/ntopo.cpp +++ b/src/ntopo.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo.h" +#include #include "atom.h" #include "neighbor.h" #include "comm.h" diff --git a/src/ntopo_angle_all.cpp b/src/ntopo_angle_all.cpp index 2a358c8ce574e4291ec8a492e7904402d7622a90..e0c20609a1da1bdd35639ab6f3254527debf1a29 100644 --- a/src/ntopo_angle_all.cpp +++ b/src/ntopo_angle_all.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_angle_all.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_angle_partial.cpp b/src/ntopo_angle_partial.cpp index c82110cda5309f01f3a223c1c4eabc6d3e615051..a6fd900825c6be26ab5da615b2ae8177d4878e05 100644 --- a/src/ntopo_angle_partial.cpp +++ b/src/ntopo_angle_partial.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_angle_partial.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_angle_template.cpp b/src/ntopo_angle_template.cpp index 15a8b658f328357e0a27368a22d888bc6b9f9387..8cbcf8bcbd98b1458f0961cdb80c5a193e328606 100644 --- a/src/ntopo_angle_template.cpp +++ b/src/ntopo_angle_template.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_angle_template.h" +#include #include "atom.h" #include "atom_vec.h" #include "force.h" diff --git a/src/ntopo_bond_all.cpp b/src/ntopo_bond_all.cpp index 42e9e2303d7af91b2bf3086f14defc3465bf48b0..5309754554f2ac0caa14db5598143266dd5e799a 100644 --- a/src/ntopo_bond_all.cpp +++ b/src/ntopo_bond_all.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_bond_all.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_bond_partial.cpp b/src/ntopo_bond_partial.cpp index 5a1acd9191b7a1485d435382fcc1c909622d336d..1cbf5eed1162cb10c58ae24cde7e1c5bfb399fca 100644 --- a/src/ntopo_bond_partial.cpp +++ b/src/ntopo_bond_partial.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_bond_partial.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_bond_template.cpp b/src/ntopo_bond_template.cpp index fa98658ad0d640023e80149bdd2b878906120930..cd7b85aa19b246681f6564d6aad63de94ccaf206 100644 --- a/src/ntopo_bond_template.cpp +++ b/src/ntopo_bond_template.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_bond_template.h" +#include #include "atom.h" #include "atom_vec.h" #include "force.h" diff --git a/src/ntopo_dihedral_all.cpp b/src/ntopo_dihedral_all.cpp index 9c94fb10f959e93a9f56db10474039f62feb39b1..5af2d526e0acc2493f0e5139cf05260f4a248837 100644 --- a/src/ntopo_dihedral_all.cpp +++ b/src/ntopo_dihedral_all.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_dihedral_all.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_dihedral_partial.cpp b/src/ntopo_dihedral_partial.cpp index 14749e6511d74d26fc09ee55cedfab9b272c0443..faac57aa51e2f8a8a65a81c375fc437885f43e78 100644 --- a/src/ntopo_dihedral_partial.cpp +++ b/src/ntopo_dihedral_partial.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_dihedral_partial.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_dihedral_template.cpp b/src/ntopo_dihedral_template.cpp index 8ea860c2e21fdb9b5ee4bc548866b13c2d91a6c0..bce8ecf4bc510758900bf1a23bf6408769dd5405 100644 --- a/src/ntopo_dihedral_template.cpp +++ b/src/ntopo_dihedral_template.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_dihedral_template.h" +#include #include "atom.h" #include "atom_vec.h" #include "force.h" diff --git a/src/ntopo_improper_all.cpp b/src/ntopo_improper_all.cpp index 6c478dec527c8e3d75e6c1bdfe0a3dfe5c7396a6..0cbecbf962aa205c2e7d74b48d3c0c2fb08e03e5 100644 --- a/src/ntopo_improper_all.cpp +++ b/src/ntopo_improper_all.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_improper_all.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_improper_partial.cpp b/src/ntopo_improper_partial.cpp index 2c37668ca850eb80bcb661ad7857c89bdc185162..17e5d4cf62a8bb244d461c9e05ba0328991245a7 100644 --- a/src/ntopo_improper_partial.cpp +++ b/src/ntopo_improper_partial.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_improper_partial.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_improper_template.cpp b/src/ntopo_improper_template.cpp index 953e010d89a0bd5f1e2f862349216edfdaf97a91..a80fe60e1d29080062850b05e255a734e687efa1 100644 --- a/src/ntopo_improper_template.cpp +++ b/src/ntopo_improper_template.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_improper_template.h" +#include #include "atom.h" #include "atom_vec.h" #include "force.h" diff --git a/src/output.cpp b/src/output.cpp index 6253d7de3710a4491801f7878c1caef804b703ba..193db9ae2a4c12a4061aeaa459c22c85e11d0093 100644 --- a/src/output.cpp +++ b/src/output.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "output.h" +#include +#include #include "style_dump.h" #include "atom.h" #include "neighbor.h" @@ -26,7 +25,6 @@ #include "domain.h" #include "thermo.h" #include "modify.h" -#include "compute.h" #include "force.h" #include "dump.h" #include "write_restart.h" diff --git a/src/pair.cpp b/src/pair.cpp index 2b4863a54c6e9a5ac8d9a2d78b0de9e7fdccadc3..36194aec9bc57bde84f9b6ffd6b5e303a791072d 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -15,24 +15,18 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair.h" #include -#include -#include -#include +#include // IWYU pragma: keep +#include // IWYU pragma: keep #include -#include -#include #include -#include "pair.h" #include "atom.h" #include "neighbor.h" -#include "neigh_list.h" #include "domain.h" #include "comm.h" #include "force.h" #include "kspace.h" -#include "update.h" -#include "modify.h" #include "compute.h" #include "suffix.h" #include "atom_masks.h" diff --git a/src/pair.h b/src/pair.h index bad2b83c747508e9fbe9d01960df762de6871ca8..9ced2fa1c7030bd69e8c0f57738846b752b8d1e9 100644 --- a/src/pair.h +++ b/src/pair.h @@ -14,7 +14,7 @@ #ifndef LMP_PAIR_H #define LMP_PAIR_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/pair_beck.cpp b/src/pair_beck.cpp index 17731ebf0b0fe1d2f83b15c3bd584b004038b178..b94436b696e750550333d7d8b1c79c85fe2fac7a 100644 --- a/src/pair_beck.cpp +++ b/src/pair_beck.cpp @@ -15,10 +15,9 @@ Contributing author: Jonathan Zimmerman (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_beck.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_born.cpp b/src/pair_born.cpp index 78434c91f84b190141ac93b8cffb5beeef4422fc..bd993acb569b5e3a5d93266ff6e0ccfd1b199d72 100644 --- a/src/pair_born.cpp +++ b/src/pair_born.cpp @@ -15,11 +15,10 @@ Contributing Author: Sai Jayaraman (Sandia) ------------------------------------------------------------------------- */ +#include "pair_born.h" +#include #include -#include -#include #include -#include "pair_born.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_born_coul_dsf.cpp b/src/pair_born_coul_dsf.cpp index 2e565897b5e9f2a8026efd8ba666b1d67ecf61f6..f7e139c750e5455038a21d7a38248a00bd33bb12 100644 --- a/src/pair_born_coul_dsf.cpp +++ b/src/pair_born_coul_dsf.cpp @@ -16,11 +16,9 @@ References: Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_born_coul_dsf.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_born_coul_wolf.cpp b/src/pair_born_coul_wolf.cpp index 3bb0e39e5753ee64fa65798fe612565addf432b5..f4d533bdb029b806229cd10ec9b2e968c68ed281 100644 --- a/src/pair_born_coul_wolf.cpp +++ b/src/pair_born_coul_wolf.cpp @@ -15,11 +15,9 @@ Contributing author: Yongfeng Zhang (INL), yongfeng.zhang@inl.gov ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_born_coul_wolf.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_buck.cpp b/src/pair_buck.cpp index a3cf1a38d629fce282f414b5a85e6c7c3eff2072..a94ce87891c5c4d95f42259a6fd489460351e344 100644 --- a/src/pair_buck.cpp +++ b/src/pair_buck.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_buck.h" +#include #include -#include -#include #include -#include "pair_buck.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_buck_coul_cut.cpp b/src/pair_buck_coul_cut.cpp index 094797694ce996a3f4d9747cb5e1b064bf9d90ff..d05c139f7188e6b3907d26c88b2f5d7e0331bdaf 100644 --- a/src/pair_buck_coul_cut.cpp +++ b/src/pair_buck_coul_cut.cpp @@ -15,10 +15,9 @@ Contributing author: Eduardo Bringa (LLNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_buck_coul_cut.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp index 196e06421921fc33334d03c2350de86ae6824801..9e6f238ebaf5c4cae72ea47d6755c160f666682b 100644 --- a/src/pair_coul_cut.cpp +++ b/src/pair_coul_cut.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_coul_cut.h" +#include #include -#include -#include #include -#include "pair_coul_cut.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_coul_debye.cpp b/src/pair_coul_debye.cpp index c8afdabb939e092121f971ed9078d0dd71adfb5f..1b87a9370118cf26a38174261589ac3cc40b5364 100644 --- a/src/pair_coul_debye.cpp +++ b/src/pair_coul_debye.cpp @@ -11,17 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_debye.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/pair_coul_dsf.cpp b/src/pair_coul_dsf.cpp index e487ff171cc14c389a13b795f39c911fee82f985..22230182b05e144af209015402b348e2ebb47f7b 100644 --- a/src/pair_coul_dsf.cpp +++ b/src/pair_coul_dsf.cpp @@ -16,11 +16,10 @@ References: Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ +#include "pair_coul_dsf.h" +#include #include -#include -#include #include -#include "pair_coul_dsf.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_coul_streitz.cpp b/src/pair_coul_streitz.cpp index 282c855249f03099795441457732331ba786b533..628f6a6b367872f4da85614a10bb401d46640054 100644 --- a/src/pair_coul_streitz.cpp +++ b/src/pair_coul_streitz.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ +#include "pair_coul_streitz.h" +#include #include -#include #include #include -#include "pair_coul_streitz.h" #include "atom.h" #include "comm.h" #include "force.h" @@ -27,8 +27,6 @@ #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "group.h" -#include "update.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/pair_coul_wolf.cpp b/src/pair_coul_wolf.cpp index dbf21b8bee3365ac88063f8f95058e65253b5ccf..15c7839fc6981bd8238ebe85248ca267bdc9048c 100644 --- a/src/pair_coul_wolf.cpp +++ b/src/pair_coul_wolf.cpp @@ -15,11 +15,9 @@ Contributing author: Yongfeng Zhang (INL), yongfeng.zhang@inl.gov ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_wolf.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_deprecated.cpp b/src/pair_deprecated.cpp index 0b1342fb2d4137b192d7cad031cfe7da1e3ed05a..058809eb800e252a9d752e82bf593aac6f0a4955 100644 --- a/src/pair_deprecated.cpp +++ b/src/pair_deprecated.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_deprecated.h" +#include #include "pair_hybrid.h" #include "comm.h" #include "force.h" diff --git a/src/pair_dpd.cpp b/src/pair_dpd.cpp index 914b4aee17f767bd79c957f17960fc28fb1d73d3..ec65eaafd6ba35a659ed95b17f588baf359e094f 100644 --- a/src/pair_dpd.cpp +++ b/src/pair_dpd.cpp @@ -15,12 +15,10 @@ Contributing author: Kurt Smith (U Pittsburgh) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_dpd.h" +#include +#include #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "update.h" #include "force.h" diff --git a/src/pair_dpd_tstat.cpp b/src/pair_dpd_tstat.cpp index 1207c954eb92eeecf1883c1a96cc72a642b114e9..15d7c90b277148f02d861f574034649b8b33d4b7 100644 --- a/src/pair_dpd_tstat.cpp +++ b/src/pair_dpd_tstat.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "pair_dpd_tstat.h" +#include +#include #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/pair_gauss.cpp b/src/pair_gauss.cpp index 2d157d6cac6018f70fa7502577cedd7469f776f5..7fd3233f4c4b0ddbee64f1d89de4ee64c17392cb 100644 --- a/src/pair_gauss.cpp +++ b/src/pair_gauss.cpp @@ -15,15 +15,13 @@ Contributing author: Sai Jayaraman (Sandia) ------------------------------------------------------------------------- */ +#include "pair_gauss.h" +#include #include -#include -#include #include -#include "pair_gauss.h" #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index 9aff8a387ad7494fa6118955868fbca034988ccc..762b9fe8fc6ab2aa646a99fa70969209fde568b3 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -12,11 +12,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include "pair_hybrid.h" +#include #include #include -#include "pair_hybrid.h" #include "atom.h" #include "force.h" #include "pair.h" diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h index e313e16f18e39c26169b82200bdd137da8cce0e7..074517a85902bc18304ca7baa93477ce385fcca7 100644 --- a/src/pair_hybrid.h +++ b/src/pair_hybrid.h @@ -20,7 +20,6 @@ PairStyle(hybrid,PairHybrid) #ifndef LMP_PAIR_HYBRID_H #define LMP_PAIR_HYBRID_H -#include #include "pair.h" namespace LAMMPS_NS { diff --git a/src/pair_hybrid_overlay.cpp b/src/pair_hybrid_overlay.cpp index 717c0de1d1a19d7c9aa264e14d3134ccfceb42a9..e67cb677afbfbe7f39d07d03ad708722060823d9 100644 --- a/src/pair_hybrid_overlay.cpp +++ b/src/pair_hybrid_overlay.cpp @@ -11,14 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "pair_hybrid_overlay.h" #include #include -#include "pair_hybrid_overlay.h" #include "atom.h" #include "force.h" -#include "neighbor.h" -#include "neigh_request.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/pair_lj96_cut.cpp b/src/pair_lj96_cut.cpp index cefe9b87e0dbed27f4033b0fe28c9bf49460464a..c27038900d0ae6a0024a012b330f90d14268f57f 100644 --- a/src/pair_lj96_cut.cpp +++ b/src/pair_lj96_cut.cpp @@ -15,11 +15,10 @@ Contributing author: Chuanfu Luo (luochuanfu@gmail.com) ------------------------------------------------------------------------- */ +#include "pair_lj96_cut.h" +#include #include -#include -#include #include -#include "pair_lj96_cut.h" #include "atom.h" #include "comm.h" #include "force.h" @@ -27,7 +26,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory.h" diff --git a/src/pair_lj_cubic.cpp b/src/pair_lj_cubic.cpp index fdbfca608f7ce1be3202bc85ac77f3e5ff446f5c..79909524945ad9a724ec9b66b69f8f05f1c0d878 100644 --- a/src/pair_lj_cubic.cpp +++ b/src/pair_lj_cubic.cpp @@ -16,15 +16,12 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cubic.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp index 2a0fcde3a5b8add7f66be081664d2e622c208c13..0302858adbe3e26f61e905e95c94acf71ff6eeec 100644 --- a/src/pair_lj_cut.cpp +++ b/src/pair_lj_cut.cpp @@ -15,11 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut.h" +#include #include -#include -#include #include -#include "pair_lj_cut.h" #include "atom.h" #include "comm.h" #include "force.h" @@ -27,7 +26,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory.h" diff --git a/src/pair_lj_cut_coul_cut.cpp b/src/pair_lj_cut_coul_cut.cpp index 38a6e2c431e84d2b2ae9725e478f63bb1051c018..d4640bee3a009b299b771ea7897f66f51647d055 100644 --- a/src/pair_lj_cut_coul_cut.cpp +++ b/src/pair_lj_cut_coul_cut.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_cut.h" +#include #include -#include -#include #include -#include "pair_lj_cut_coul_cut.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_lj_cut_coul_debye.cpp b/src/pair_lj_cut_coul_debye.cpp index cc6e92b2e358fe5caa3cc4a171321a491257f336..4ef533a7432157451206c3cd3b075b251d726477 100644 --- a/src/pair_lj_cut_coul_debye.cpp +++ b/src/pair_lj_cut_coul_debye.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_lj_cut_coul_debye.h" +#include +#include #include "atom.h" #include "neigh_list.h" #include "force.h" diff --git a/src/pair_lj_cut_coul_dsf.cpp b/src/pair_lj_cut_coul_dsf.cpp index f114a5851f161593174de0963640345df6537b62..778f9f2fb4cf5e6de17dc2227f94357ff8a9a2d0 100644 --- a/src/pair_lj_cut_coul_dsf.cpp +++ b/src/pair_lj_cut_coul_dsf.cpp @@ -16,11 +16,10 @@ References: Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_dsf.h" +#include #include -#include -#include #include -#include "pair_lj_cut_coul_dsf.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_lj_cut_coul_wolf.cpp b/src/pair_lj_cut_coul_wolf.cpp index 55aff0d7c5ab0e2515c36b070c9d124117b3d5b2..00a58325292ca620f3769f8381a9d21071a1cde5 100644 --- a/src/pair_lj_cut_coul_wolf.cpp +++ b/src/pair_lj_cut_coul_wolf.cpp @@ -15,19 +15,14 @@ Contributing author: Vishal Boddu (FAU) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_cut_coul_wolf.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp index d5c0a40f2d52609296084a060e4cbde5709beea1..a5184bc2f5f049a81ce6f5dbd65c376842c48695 100644 --- a/src/pair_lj_expand.cpp +++ b/src/pair_lj_expand.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_expand.h" +#include #include -#include -#include #include -#include "pair_lj_expand.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_lj_gromacs.cpp b/src/pair_lj_gromacs.cpp index 1fdaefebe984f7ef6692ed9ee00a79a642843f1b..baef482ef9262abdc6ab42c038266bf0199da2f3 100644 --- a/src/pair_lj_gromacs.cpp +++ b/src/pair_lj_gromacs.cpp @@ -15,15 +15,12 @@ Contributing author: Mark Stevens (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_gromacs.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/pair_lj_gromacs_coul_gromacs.cpp b/src/pair_lj_gromacs_coul_gromacs.cpp index 28dc8ec79b5dd823de071dce626f8b47b2895e4a..c62944b6a11feecfdec84880e62f9441b9b48425 100644 --- a/src/pair_lj_gromacs_coul_gromacs.cpp +++ b/src/pair_lj_gromacs_coul_gromacs.cpp @@ -15,11 +15,9 @@ Contributing author: Mark Stevens (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_gromacs_coul_gromacs.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_lj_smooth.cpp b/src/pair_lj_smooth.cpp index ecacadbffaca7d1a6e63c3f18c2cefdf195eb019..7c7eb51b5349f727d85460307fcf13ea3d329f3c 100644 --- a/src/pair_lj_smooth.cpp +++ b/src/pair_lj_smooth.cpp @@ -15,10 +15,9 @@ Contributing author: Craig Maloney (UCSB) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_lj_smooth.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp index 265828c4cf63325055c0951ae490faec6ba6d6e5..a3e4aed2fe388ae46d69a6633a50aab7a7ff7462 100644 --- a/src/pair_lj_smooth_linear.cpp +++ b/src/pair_lj_smooth_linear.cpp @@ -15,10 +15,9 @@ Contributing author: Jonathan Zimmerman (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_lj_smooth_linear.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_mie_cut.cpp b/src/pair_mie_cut.cpp index 231832dc489663c8d4c2e8191b4962d810e01f1a..46657687f67d4a7bbe287bd2b12e74d3fa6eb446 100644 --- a/src/pair_mie_cut.cpp +++ b/src/pair_mie_cut.cpp @@ -15,11 +15,10 @@ Contributing author: Cassiano Aimoli (aimoli@gmail.com) ------------------------------------------------------------------------- */ +#include "pair_mie_cut.h" +#include #include -#include -#include #include -#include "pair_mie_cut.h" #include "atom.h" #include "comm.h" #include "force.h" @@ -27,7 +26,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory.h" diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp index dca1834c14c5163c9937245a0759cb71504546a0..d088f98bf42221f21fbadc0f71afbdfada398f90 100644 --- a/src/pair_morse.cpp +++ b/src/pair_morse.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_morse.h" +#include #include -#include -#include #include -#include "pair_morse.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp index 7602f7b925d640da1d6d6e15f1828c5ed27b2784..6f821e684bc6d219a49af05281b3d64b75bcd444 100644 --- a/src/pair_soft.cpp +++ b/src/pair_soft.cpp @@ -11,15 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_soft.h" +#include #include -#include -#include #include -#include "pair_soft.h" #include "atom.h" #include "comm.h" #include "force.h" -#include "update.h" #include "neigh_list.h" #include "math_const.h" #include "memory.h" diff --git a/src/pair_table.cpp b/src/pair_table.cpp index b1b6f45edadec7dfd1e2d2deab660dc9ddf29852..9fcbc3ee9f7549ecc46cac21e1fd76c05e2a46cf 100644 --- a/src/pair_table.cpp +++ b/src/pair_table.cpp @@ -15,11 +15,12 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_table.h" #include #include #include #include -#include "pair_table.h" +#include #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/pair_ufm.cpp b/src/pair_ufm.cpp index 226fb6e7d92cb8bb9a1e9b72d5bfdd9e231d4885..8cc4d2796f267261e3643103935af7b3188a95bc 100644 --- a/src/pair_ufm.cpp +++ b/src/pair_ufm.cpp @@ -17,26 +17,18 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ +#include "pair_ufm.h" +#include #include -#include -#include #include -#include "pair_ufm.h" #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp index 913afbd5a118dc5f0425b9886305ea56b816f22c..e8775c96688f0d9dde43e27fc4f8893987b139b0 100644 --- a/src/pair_yukawa.cpp +++ b/src/pair_yukawa.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_yukawa.h" +#include +#include #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/pair_zbl.cpp b/src/pair_zbl.cpp index 254a82ea647db64b20033ee302a5cbd3db179c7a..199e4f0907dac19ae24fbd47996940b66a0f806f 100644 --- a/src/pair_zbl.cpp +++ b/src/pair_zbl.cpp @@ -15,21 +15,12 @@ Contributing authors: Stephen Foiles, Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_zbl.h" +#include #include "atom.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" -#include "math_const.h" #include "memory.h" #include "error.h" @@ -37,7 +28,6 @@ // "The Stopping and Range of Ions in Matter" volume 1, Pergamon, 1985. using namespace LAMMPS_NS; -using namespace MathConst; using namespace PairZBLConstants; /* ---------------------------------------------------------------------- */ diff --git a/src/pair_zero.cpp b/src/pair_zero.cpp index 143808f598c802069d0149ada09e01e6b5cf3887..403bd73944c42b73cea6cddbeac249ac870457dc 100644 --- a/src/pair_zero.cpp +++ b/src/pair_zero.cpp @@ -15,11 +15,9 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_zero.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pointers.h b/src/pointers.h index 44967f51359a28067fee329362a65c8b3a8920dd..2d528db392a2abd4e145f3a8e02f98d1df3396e4 100644 --- a/src/pointers.h +++ b/src/pointers.h @@ -21,9 +21,11 @@ #ifndef LMP_POINTERS_H #define LMP_POINTERS_H -#include "lmptype.h" -#include -#include "lammps.h" +#include "lmptype.h" // IWYU pragma: export +#include // IWYU pragma: export +#include // IWYU pragme: export +#include // IWYU pragma: export +#include "lammps.h" // IWYU pragma: export namespace LAMMPS_NS { @@ -34,6 +36,15 @@ namespace LAMMPS_NS { #define MIN(A,B) ((A) < (B) ? (A) : (B)) #define MAX(A,B) ((A) > (B) ? (A) : (B)) +// enum used for KOKKOS host/device flags + +enum ExecutionSpace{Host,Device}; + +// global forward declarations + +template class MyPoolChunk; +template class MyPage; + class Pointers { public: Pointers(LAMMPS *ptr) : diff --git a/src/procmap.cpp b/src/procmap.cpp index 8207b61f4cf978715056208ea7ff2d1d241f947b..1741e351fe12a2fc9d79b62235cad5ecfc909647 100644 --- a/src/procmap.cpp +++ b/src/procmap.cpp @@ -16,6 +16,12 @@ ------------------------------------------------------------------------- */ #include "procmap.h" +#include +#include +#include +#include +#include +#include #include "universe.h" #include "comm.h" #include "domain.h" @@ -23,9 +29,6 @@ #include "memory.h" #include "error.h" -#include -#include - using namespace LAMMPS_NS; #define MAXLINE 128 diff --git a/src/random_mars.cpp b/src/random_mars.cpp index 464e640eab5b73489d4216467de4e848da23e293..9de5290d29a21e4e86b13dc3f55da42521dcd212 100644 --- a/src/random_mars.cpp +++ b/src/random_mars.cpp @@ -14,8 +14,8 @@ // Marsaglia random number generator // see RANMAR in F James, Comp Phys Comm, 60, 329 (1990) -#include #include "random_mars.h" +#include #include "error.h" using namespace LAMMPS_NS; diff --git a/src/random_park.cpp b/src/random_park.cpp index fc00939bd471f4f07f863141a4f22da586f564cc..e12e8a3a104b3bfa1d0120a3f8a59a77f90c2fcd 100644 --- a/src/random_park.cpp +++ b/src/random_park.cpp @@ -13,8 +13,8 @@ // Park/Miller RNG -#include #include "random_park.h" +#include #include "error.h" using namespace LAMMPS_NS; diff --git a/src/rcb.cpp b/src/rcb.cpp index 83cdccdf80cf99296ec812f2c930a8d3a1ae30a3..2cc70a2de9530730a48e23228b7a07e902752f42 100644 --- a/src/rcb.cpp +++ b/src/rcb.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "rcb.h" #include #include -#include "rcb.h" #include "irregular.h" #include "memory.h" -#include "error.h" using namespace LAMMPS_NS; @@ -473,6 +472,24 @@ void RCB::compute(int dimension, int n, double **x, double *wt, valuehalf = valuehalf_select; if (ndot > 0) memcpy(dotmark,dotmark_select,ndot*sizeof(int)); + // special case for zero box width + // can occur when all dots are on corner vertices of this sub-box + // split box on longest dimension + // reset dotmark for that cut + + if (largest == 0.0) { + dim = 0; + if (hi[1]-lo[1] > hi[0]-lo[0]) dim = 1; + if (dimension == 3 && hi[2]-lo[2] > hi[dim]-lo[dim]) dim = 2; + valuehalf = 0.5* (lo[dim] + hi[dim]); + + for (j = 0; j < nlist; j++) { + i = dotlist[j]; + if (dots[i].x[dim] <= valuehalf) dotmark[i] = 0; + else dotmark[i] = 1; + } + } + // found median // store cut info only if I am procmid diff --git a/src/read_data.cpp b/src/read_data.cpp index 989f98926969fd848eb2b8ed6373e038802a29db..1208ab4b439f99f5727419918f3c51890220a285 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -15,19 +15,15 @@ // due to OpenMPI bug which sets INT64_MAX via its mpi.h // before lmptype.h can set flags to insure it is done correctly -#include "lmptype.h" +#include "read_data.h" #include -#include #include -#include #include -#include "read_data.h" #include "atom.h" #include "atom_vec.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" -#include "force.h" #include "molecule.h" #include "group.h" #include "comm.h" diff --git a/src/read_data.h b/src/read_data.h index 26ab6ff3816c1e0490c13dff72138c2c8bd5144f..98de607f6bbe34257c0a4ff66fa5dcc3f13de749 100644 --- a/src/read_data.h +++ b/src/read_data.h @@ -20,7 +20,6 @@ CommandStyle(read_data,ReadData) #ifndef LMP_READ_DATA_H #define LMP_READ_DATA_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/read_dump.cpp b/src/read_dump.cpp index 85e2312a427ab6217a0ebe7cc3ab61573b2857e3..7316a2f5cd7f1771996be8fbd42943e98cbc4591 100644 --- a/src/read_dump.cpp +++ b/src/read_dump.cpp @@ -19,25 +19,19 @@ // due to OpenMPI bug which sets INT64_MAX via its mpi.h // before lmptype.h can set flags to insure it is done correctly -#include "lmptype.h" +#include "read_dump.h" #include #include -#include -#include "read_dump.h" +#include #include "reader.h" #include "style_reader.h" #include "atom.h" #include "atom_vec.h" #include "update.h" -#include "modify.h" -#include "fix.h" -#include "compute.h" #include "domain.h" #include "comm.h" #include "force.h" #include "irregular.h" -#include "input.h" -#include "variable.h" #include "error.h" #include "memory.h" #include "utils.h" diff --git a/src/read_dump.h b/src/read_dump.h index 3ee13f779cd40703d17e4b0952764ccb9a10b937..6fb4f11ed146e0d4fea2118aab51c82acdee5969 100644 --- a/src/read_dump.h +++ b/src/read_dump.h @@ -23,7 +23,6 @@ CommandStyle(read_dump,ReadDump) #define LMP_READ_DUMP_H #include -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 6e156da837c7ae3c0e5cb9d46ebc0c532304630a..3d2e2b6592d4921ce7f69d062b1e9a32278c453d 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "read_restart.h" #include #include -#include #include -#include "read_restart.h" #include "atom.h" #include "atom_vec.h" #include "domain.h" @@ -23,7 +22,6 @@ #include "irregular.h" #include "update.h" #include "modify.h" -#include "fix.h" #include "fix_read_restart.h" #include "group.h" #include "force.h" diff --git a/src/read_restart.h b/src/read_restart.h index 23d6ec3fba0bf0599f966797999bd2ff21d14cd5..63adf37b2288eff2449088562a2f7493808ef471 100644 --- a/src/read_restart.h +++ b/src/read_restart.h @@ -20,7 +20,6 @@ CommandStyle(read_restart,ReadRestart) #ifndef LMP_READ_RESTART_H #define LMP_READ_RESTART_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/reader.cpp b/src/reader.cpp index 5292c9c992cd3a8fd97bdb52a0f32c3bc24194be..ee032dc822b07d3f8ab061b7d5fc84c2fae438e2 100644 --- a/src/reader.cpp +++ b/src/reader.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "reader.h" +#include #include "error.h" using namespace LAMMPS_NS; diff --git a/src/reader_native.cpp b/src/reader_native.cpp index 60b7ecd76495643f05c1cf0d6315eb6a7900e097..fba613bdd36b90e743be431a3cdae2f116090cb1 100644 --- a/src/reader_native.cpp +++ b/src/reader_native.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "reader_native.h" #include #include -#include "reader_native.h" #include "atom.h" #include "memory.h" #include "error.h" diff --git a/src/reader_xyz.cpp b/src/reader_xyz.cpp index 19f0ff21355abdaa099a15b3caba85a6ca8db524..a5209956b9cce6165a5e9185c2108b7dcaa755ce 100644 --- a/src/reader_xyz.cpp +++ b/src/reader_xyz.cpp @@ -15,10 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include #include "reader_xyz.h" -#include "atom.h" +#include #include "memory.h" #include "error.h" #include "force.h" diff --git a/src/region.cpp b/src/region.cpp index 6b49a2819b5f88bf30829e2ee9322c3544bbde88..7a676de1afe1f155ab6d6a16cea64fccd2d89250 100644 --- a/src/region.cpp +++ b/src/region.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "region.h" #include -#include #include -#include "region.h" #include "update.h" #include "domain.h" #include "lattice.h" diff --git a/src/region.h b/src/region.h index 6a3806fed79cb37da1e270924b0d8d88df062f3f..0dce004a5bdc5c0aed737dda33fba9fd9091cbe5 100644 --- a/src/region.h +++ b/src/region.h @@ -14,7 +14,7 @@ #ifndef LMP_REGION_H #define LMP_REGION_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/region_block.cpp b/src/region_block.cpp index e55c4811898f0b084b8bf52c6615ab9e81526ee9..8ea8b3f20245aa90b0844df6ddb1160b40adf9ca 100644 --- a/src/region_block.cpp +++ b/src/region_block.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "region_block.h" +#include #include "force.h" #include "domain.h" #include "math_extra.h" diff --git a/src/region_cone.cpp b/src/region_cone.cpp index 72f56a268fe4ece8ce5771c6bda9ad5bd56a7523..3c7d0a29d82dd690a22f9b30d363c84d04437870 100644 --- a/src/region_cone.cpp +++ b/src/region_cone.cpp @@ -15,10 +15,9 @@ Contributing author: Pim Schravendijk ------------------------------------------------------------------------- */ +#include "region_cone.h" #include -#include #include -#include "region_cone.h" #include "domain.h" #include "error.h" #include "force.h" diff --git a/src/region_cylinder.cpp b/src/region_cylinder.cpp index 7709c57aab296a9c97bf037f8d111c7d1c8db686..b2c06270d07991536938ff6819952ec0fb5fa916 100644 --- a/src/region_cylinder.cpp +++ b/src/region_cylinder.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "region_cylinder.h" #include -#include #include -#include "region_cylinder.h" #include "update.h" #include "domain.h" #include "input.h" diff --git a/src/region_deprecated.cpp b/src/region_deprecated.cpp index 87225959fa5255b1cfde0f4343b2a6376adab4af..a2e4e88393fbd6c9891397a4fcac108285ed7ce1 100644 --- a/src/region_deprecated.cpp +++ b/src/region_deprecated.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "region_deprecated.h" +#include #include "comm.h" #include "error.h" diff --git a/src/region_intersect.cpp b/src/region_intersect.cpp index 96d3bed16c319657aa20c10e6d6eff2f21f44179..fe074a6b4c2c6328e63934989a80cd52fc2e2521 100644 --- a/src/region_intersect.cpp +++ b/src/region_intersect.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "region_intersect.h" +#include #include "domain.h" #include "error.h" #include "force.h" diff --git a/src/region_plane.cpp b/src/region_plane.cpp index e67a2c85bd8d7e7bf6aa842171c20d05df893279..85671357ef4edb2b62c33c25ce564ccb1c43d5bf 100644 --- a/src/region_plane.cpp +++ b/src/region_plane.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "region_plane.h" +#include #include "error.h" #include "force.h" diff --git a/src/region_prism.cpp b/src/region_prism.cpp index 22fc504c37537b14e2370ef822ba4c17a4547d09..b6c54c2fb998e929331b2f767863a6e2e4f2a7b3 100644 --- a/src/region_prism.cpp +++ b/src/region_prism.cpp @@ -15,10 +15,8 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "region_prism.h" +#include #include "domain.h" #include "force.h" #include "math_extra.h" diff --git a/src/region_sphere.cpp b/src/region_sphere.cpp index 8080ef5882e5798da884c4fa135ac8e863e8ff21..bf874ad3112192215990de675fe910d07f22100d 100644 --- a/src/region_sphere.cpp +++ b/src/region_sphere.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "region_sphere.h" #include -#include #include -#include "region_sphere.h" #include "update.h" #include "input.h" #include "variable.h" diff --git a/src/region_union.cpp b/src/region_union.cpp index 33ac6fedd709acf0f6b06d99fb095e6facd799c6..be1fe6eeff61a086c650f00352cb22b32f5c6305 100644 --- a/src/region_union.cpp +++ b/src/region_union.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "region_union.h" +#include #include "domain.h" #include "error.h" #include "force.h" diff --git a/src/replicate.cpp b/src/replicate.cpp index 3c8f4a8aeea283e9664aa99d8c30bc5f0c6a6b31..1617ab031389276eaaad666d08c735dd0b20f16a 100644 --- a/src/replicate.cpp +++ b/src/replicate.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "replicate.h" +#include +#include #include "atom.h" #include "atom_vec.h" -#include "atom_vec_hybrid.h" #include "force.h" #include "domain.h" #include "comm.h" diff --git a/src/rerun.cpp b/src/rerun.cpp index 063ea882c23691ed439235550a02f20bcebcb655..3cd1c5362819903d284a2249e57462e2a5f87785 100644 --- a/src/rerun.cpp +++ b/src/rerun.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "rerun.h" +#include #include "read_dump.h" #include "domain.h" #include "update.h" diff --git a/src/reset_ids.cpp b/src/reset_ids.cpp index b2cf7a9bbce2a5286c5415a8e34148bef37d9aad..857738e8412b87b2398fbdf21d8cb21a789d314f 100644 --- a/src/reset_ids.cpp +++ b/src/reset_ids.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "reset_ids.h" +#include #include "atom.h" #include "atom_vec.h" #include "domain.h" @@ -28,7 +29,7 @@ ResetIDs::ResetIDs(LAMMPS *lmp) : Pointers(lmp) {} /* ---------------------------------------------------------------------- */ -void ResetIDs::command(int narg, char **/*arg*/) +void ResetIDs::command(int narg, char ** /* arg */) { if (domain->box_exist == 0) error->all(FLERR,"Reset_ids command before simulation box is defined"); diff --git a/src/respa.cpp b/src/respa.cpp index 6fa9959d785c3d688e3f41c2a6d0172cd30c025a..a184756335d9c78e40f8c92182d51863836ee975 100644 --- a/src/respa.cpp +++ b/src/respa.cpp @@ -15,14 +15,14 @@ Contributing authors: Mark Stevens (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "respa.h" +#include #include "neighbor.h" #include "atom.h" #include "atom_vec.h" #include "domain.h" #include "comm.h" +#include "fix.h" #include "force.h" #include "pair.h" #include "bond.h" @@ -33,10 +33,8 @@ #include "output.h" #include "update.h" #include "modify.h" -#include "compute.h" #include "fix_respa.h" #include "timer.h" -#include "memory.h" #include "error.h" #include "utils.h" #include "pair_hybrid.h" diff --git a/src/run.cpp b/src/run.cpp index beb71be52c1faafeecfb8b3e4fd6c6cb2315e2fc..2c2f00a7a8d0a005514b1bffd212cd6291cc89e0 100644 --- a/src/run.cpp +++ b/src/run.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "run.h" +#include #include "domain.h" #include "update.h" #include "force.h" diff --git a/src/set.cpp b/src/set.cpp index 00b2d8a9b0be28265de356a2d479c2e6ac9884a6..3bf00063c56de6a9a48d5b770c23528612a2751b 100644 --- a/src/set.cpp +++ b/src/set.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "set.h" #include #include -#include #include -#include "set.h" +#include #include "atom.h" #include "atom_vec.h" #include "atom_vec_ellipsoid.h" @@ -26,9 +26,7 @@ #include "region.h" #include "group.h" #include "comm.h" -#include "neighbor.h" #include "force.h" -#include "pair.h" #include "input.h" #include "variable.h" #include "random_park.h" diff --git a/src/special.cpp b/src/special.cpp index 903794c0f6cb2984f15ad472fa0c5f75a511cd13..3dd817bc7f0e5ffa6930922c6edc0a7c1eed3c6c 100644 --- a/src/special.cpp +++ b/src/special.cpp @@ -11,19 +11,17 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "special.h" +#include #include "atom.h" #include "atom_vec.h" #include "force.h" #include "comm.h" #include "modify.h" #include "fix.h" -#include "accelerator_kokkos.h" +#include "accelerator_kokkos.h" // IWYU pragma: export #include "atom_masks.h" #include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/thermo.cpp b/src/thermo.cpp index bba867d195b0aa5572eb2ab10dcab82f699e721c..3748ee77fe7a41a239a8e1e82c7e1cd858e1d322 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -15,12 +15,10 @@ // due to OpenMPI bug which sets INT64_MAX via its mpi.h // before lmptype.h can set flags to insure it is done correctly -#include "lmptype.h" +#include "thermo.h" #include #include -#include #include -#include "thermo.h" #include "atom.h" #include "update.h" #include "comm.h" @@ -43,11 +41,8 @@ #include "kspace.h" #include "output.h" #include "timer.h" -#include "math_const.h" #include "memory.h" #include "error.h" -#include "universe.h" - #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/thermo.h b/src/thermo.h index 8c32f24d3c2142f4953126e97dbd6bdd38921928..f2384e0ac3a022b76582a5906a5e43b36bd0cfef 100644 --- a/src/thermo.h +++ b/src/thermo.h @@ -18,9 +18,6 @@ namespace LAMMPS_NS { -class DumpNetCDF; -class DumpNetCDFMPIIO; - class Thermo : protected Pointers { friend class MinCG; // accesses compute_pe friend class DumpNetCDF; // accesses thermo properties diff --git a/src/timer.cpp b/src/timer.cpp index 65cb6ab5d8fef698784258a1c80220848f96d9bb..0a5e56ab35b1c6e6932f1f994e6144ef9dc5d766 100644 --- a/src/timer.cpp +++ b/src/timer.cpp @@ -11,14 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "timer.h" #include #include #include -#include "timer.h" #include "comm.h" #include "error.h" #include "force.h" -#include "memory.h" #ifdef _WIN32 #include diff --git a/src/universe.cpp b/src/universe.cpp index dba31f8b76d4e19915fffb379d42c21f7b02a839..036b3a7e6609918ea4d846febe2d8009fdd33d4d 100644 --- a/src/universe.cpp +++ b/src/universe.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "universe.h" #include #include #include #include -#include -#include "universe.h" #include "version.h" #include "error.h" #include "force.h" diff --git a/src/universe.h b/src/universe.h index 3073409b8677a41a1c0326e4c965591170aa3403..fd6655c749bf118046b8d31f6522314b8654c3b7 100644 --- a/src/universe.h +++ b/src/universe.h @@ -14,7 +14,6 @@ #ifndef LMP_UNIVERSE_H #define LMP_UNIVERSE_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/update.cpp b/src/update.cpp index f5e706e3543e0493ebd5189821483379780e4c72..8a3e6f0d1df9104294df68610e2d9f8b57b477ad 100644 --- a/src/update.cpp +++ b/src/update.cpp @@ -11,23 +11,18 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "update.h" +#include #include "integrate.h" #include "min.h" #include "style_integrate.h" #include "style_minimize.h" #include "neighbor.h" -#include "neigh_list.h" #include "force.h" #include "modify.h" #include "fix.h" -#include "domain.h" -#include "region.h" #include "compute.h" #include "output.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/utils.cpp b/src/utils.cpp index 4e39187f778c20391b71cca3d07296449dee2b97..5e53a3a09dda065b62e44c892b39091611d26434 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "utils.h" #include #include -#include "utils.h" #include "lammps.h" #include "error.h" diff --git a/src/variable.cpp b/src/variable.cpp index 63a425bcf5bc5c08538c06a2c389f8142dbd1733..3fffa11d5e29782304e60a13eb84bd18bf376590 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -11,12 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "variable.h" +#include #include #include #include #include #include -#include "variable.h" #include "universe.h" #include "atom.h" #include "update.h" @@ -26,6 +27,7 @@ #include "region.h" #include "modify.h" #include "compute.h" +#include "input.h" #include "fix.h" #include "fix_store.h" #include "force.h" @@ -33,7 +35,6 @@ #include "thermo.h" #include "random_mars.h" #include "math_const.h" -#include "atom_masks.h" #include "lmppython.h" #include "memory.h" #include "info.h" diff --git a/src/variable.h b/src/variable.h index 512195bd142cadb6486e94b0195f0f12382760e7..a504da14ec28de9255241cedade10b7b81a95abe 100644 --- a/src/variable.h +++ b/src/variable.h @@ -14,9 +14,7 @@ #ifndef LMP_VARIABLE_H #define LMP_VARIABLE_H -#include #include "pointers.h" -#include "input.h" namespace LAMMPS_NS { diff --git a/src/velocity.cpp b/src/velocity.cpp index 95d820cc22829f51a7ed30f5a8bc685aeffb2b49..e5985884f8f9878c595b2e973bd3889091924dcf 100644 --- a/src/velocity.cpp +++ b/src/velocity.cpp @@ -11,14 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "velocity.h" #include -#include -#include #include -#include "velocity.h" #include "atom.h" -#include "update.h" #include "domain.h" #include "lattice.h" #include "input.h" diff --git a/src/verlet.cpp b/src/verlet.cpp index fcba248d5f8ddcc1e46cd0d8ec8a4ae2e04351a4..8cd6fe940d444cc8847eac41176193e8925a76af 100644 --- a/src/verlet.cpp +++ b/src/verlet.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "verlet.h" +#include #include "neighbor.h" #include "domain.h" #include "comm.h" @@ -28,10 +28,7 @@ #include "output.h" #include "update.h" #include "modify.h" -#include "compute.h" -#include "fix.h" #include "timer.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/write_coeff.cpp b/src/write_coeff.cpp index 9bf54b3c08d36557d13af5913b97952ef2a74a46..8e5b4fcb71ddff25597862ab9ddec8ed8f8f2873 100644 --- a/src/write_coeff.cpp +++ b/src/write_coeff.cpp @@ -11,10 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "write_coeff.h" #include #include +#include #include -#include "write_coeff.h" #include "pair.h" #include "bond.h" #include "angle.h" diff --git a/src/write_coeff.h b/src/write_coeff.h index 569a615e6e577f06386fd0accb394971a7ab1edc..b995e60d6341b91c81fbbf96ffa65623f64ac9f5 100644 --- a/src/write_coeff.h +++ b/src/write_coeff.h @@ -20,7 +20,6 @@ CommandStyle(write_coeff,WriteCoeff) #ifndef LMP_WRITE_COEFF_H #define LMP_WRITE_COEFF_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/write_data.cpp b/src/write_data.cpp index decc92ea8c9593bb4031588d28169f0562ae2935..3d788b96659c13897ab087f0b597febff5a656aa 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "write_data.h" #include #include -#include "write_data.h" #include "atom.h" #include "atom_vec.h" -#include "group.h" #include "force.h" #include "pair.h" #include "bond.h" diff --git a/src/write_data.h b/src/write_data.h index 6f1bb2ec47f9a609c7a6bf1823a7869561480942..1c0f6b2a7c72c828184666fd7318eda43ea01445 100644 --- a/src/write_data.h +++ b/src/write_data.h @@ -20,7 +20,6 @@ CommandStyle(write_data,WriteData) #ifndef LMP_WRITE_DATA_H #define LMP_WRITE_DATA_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/write_dump.cpp b/src/write_dump.cpp index 072680a8a51d368e8caed42fc056d21e5c1a7998..31ceb4cbbf8ff25369adfec74a8f26ef22697c64 100644 --- a/src/write_dump.cpp +++ b/src/write_dump.cpp @@ -15,15 +15,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "write_dump.h" +#include +#include #include "style_dump.h" #include "dump.h" #include "dump_image.h" -#include "atom.h" #include "comm.h" -#include "group.h" -#include "input.h" #include "update.h" #include "error.h" #include "utils.h" diff --git a/src/write_restart.cpp b/src/write_restart.cpp index e0e17cd2928c149ca610802d691cd53d3ea91ba6..4b84e790b8c322e134960d799c4c79423517f781 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "write_restart.h" #include #include -#include "write_restart.h" #include "atom.h" #include "atom_vec.h" -#include "atom_vec_hybrid.h" #include "group.h" #include "force.h" #include "pair.h" diff --git a/src/write_restart.h b/src/write_restart.h index c6202acbfd1bf08f47baacb33ebb3832f35b2f89..e7cdc6a501c9911a0235ec1e9b3c450943960964 100644 --- a/src/write_restart.h +++ b/src/write_restart.h @@ -20,7 +20,6 @@ CommandStyle(write_restart,WriteRestart) #ifndef LMP_WRITE_RESTART_H #define LMP_WRITE_RESTART_H -#include #include "pointers.h" namespace LAMMPS_NS {