Loading doc/src/Build_cmake.rst +20 −14 Original line number Diff line number Diff line Loading @@ -22,27 +22,31 @@ Makefile(s). Example: cd lammps # change to the LAMMPS distribution directory mkdir build; cd build # create a new directory (folder) for build cmake [options ...] ../cmake # configuration with (command-line) cmake make # compilation make # compilation (or use "cmbuild" from "tools/cmake") The cmake command will detect available features, enable selected The ``cmake`` command will detect available features, enable selected packages and options, and will generate the build environment. By default this build environment will be created for "Unix Makefiles" on most platforms and particularly on Linux. However, alternate build tools (e.g. Ninja) and project files for Integrated Development Environments (IDEs) like Eclipse, CodeBlocks, or Kate can be generated, too. This is selected via the "-G" command line flag. For the rest of the documentation selected via the ``-G`` command line flag. For the rest of the documentation we will assume that the build environment is generated for makefiles and thus the make command will be used to compile and link LAMMPS as indicated above, producing (by default) an executable called "lmp" and a library called "liblammps.a" in the "build" folder. When generating and thus the ``make`` command will be used to compile and link LAMMPS as indicated above, producing (by default) an executable called ``lmp`` and a library called ``liblammps.a`` in the ``build`` folder. When generating a build environment for the "Ninja" build tool, the build command would be "ninja" instead of "make". be ``ninja`` instead of ``make``. Or you may copy the ``cmbuild`` script from the :ref:`tools/cmake folder <cmake>` somewhere in your path and use that, as it will indirectly call CMake with the configured tool. This is particularly, if you configured the build folder with a build tool in a non-standard location or name using ``-D CMAKE_MAKE_PROGRAM=<name>``. If your machine has multiple CPU cores (most do these days), using a command like "make -jN" (with N being the number of available local command like ``make -j N`` (with N being the number of available local CPU cores) can be much faster. If you plan to do development on LAMMPS or need to re-compile LAMMPS repeatedly, installation of the ccache (= Compiler Cache) software may speed up repeated compilation ``ccache`` (= Compiler Cache) software may speed up repeated compilation even more. After compilation, you may optionally install the LAMMPS executable into Loading @@ -60,9 +64,11 @@ to ${HOME}/.local ---------- .. _cmake_build: There are 3 variants of the CMake command itself: a command-line version (*cmake* or *cmake3*), a text mode UI version (*ccmake* or *ccmake3*), and a graphical GUI version (*cmake-gui*). You can use any of them (``cmake`` or ``cmake3``), a text mode UI version (``ccmake`` or ``ccmake3``), and a graphical GUI version (``cmake-gui``). You can use any of them interchangeably to configure and create the LAMMPS build environment. On Linux all the versions produce a Makefile as their output by default. See more details on each below. Loading @@ -75,7 +81,7 @@ the :doc:`Build <Build>` doc page. You must perform the CMake build system generation and compilation in a new directory you create. It can be anywhere on your local machine. In these Build pages we assume that you are building in a directory called "lammps/build". You can perform separate builds independently called ``lammps/build``. You can perform separate builds independently with different options, so long as you perform each of them in a separate directory you create. All the auxiliary files created by one build process (executable, object files, log files, etc) are stored in Loading @@ -84,10 +90,10 @@ this directory or sub-directories within it that CMake creates. .. note:: To perform a CMake build, no packages can be installed or a build been previously attempted in the LAMMPS src directory by using "make" been previously attempted in the LAMMPS src directory by using ``make`` commands to :doc:`perform a conventional LAMMPS build <Build_make>`. CMake detects if this is the case and generates an error, telling you to type "make no-all purge" in the src directory to un-install all to type ``make no-all purge`` in the src directory to un-install all packages. The purge removes all the \*.h files auto-generated by make. Loading doc/src/Tools.rst +71 −19 Original line number Diff line number Diff line Loading @@ -40,33 +40,61 @@ own sub-directories with their own Makefiles and/or README files. Pre-processing tools ==================== +-----------------------------+------------------------+----------------------+----------------------------------+----------------------------------+-----------------------------+ | :ref:`amber2lmp <amber>` | :ref:`ch2lmp <charmm>` | :ref:`chain <chain>` | :ref:`createatoms <createatoms>` | :ref:`drude <drude>` | :ref:`eam database <eamdb>` | +-----------------------------+------------------------+----------------------+----------------------------------+----------------------------------+-----------------------------+ | :ref:`eam generate <eamgn>` | :ref:`eff <eff>` | :ref:`ipp <ipp>` | :ref:`micelle2d <micelle>` | :ref:`moltemplate <moltemplate>` | :ref:`msi2lmp <msi>` | +-----------------------------+------------------------+----------------------+----------------------------------+----------------------------------+-----------------------------+ | :ref:`polybond <polybond>` | | | | | | +-----------------------------+------------------------+----------------------+----------------------------------+----------------------------------+-----------------------------+ .. table_from_list:: :columns: 6 * :ref:`amber2lmp <amber>` * :ref:`ch2lmp <charmm>` * :ref:`chain <chain>` * :ref:`createatoms <createatoms>` * :ref:`drude <drude>` * :ref:`eam database <eamdb>` * :ref:`eam generate <eamgn>` * :ref:`eff <eff>` * :ref:`ipp <ipp>` * :ref:`micelle2d <micelle>` * :ref:`moltemplate <moltemplate>` * :ref:`msi2lmp <msi>` * :ref:`polybond <polybond>` Post-processing tools ===================== +--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+ | :ref:`amber2lmp <amber>` | :ref:`binary2txt <binary>` | :ref:`ch2lmp <charmm>` | :ref:`colvars <colvars>` | :ref:`eff <eff>` | :ref:`fep <fep>` | +--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+ | :ref:`lmp2arc <arc>` | :ref:`lmp2cfg <cfg>` | :ref:`matlab <matlab>` | :ref:`phonon <phonon>` | :ref:`pymol_asphere <pymol>` | :ref:`python <pythontools>` | +--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+ | :ref:`reax <reax_tool>` | :ref:`replica <replica>` | :ref:`smd <smd>` | :ref:`spin <spin>` | :ref:`xmgrace <xmgrace>` | | +--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+ .. table_from_list:: :columns: 6 * :ref:`amber2lmp <amber>` * :ref:`binary2txt <binary>` * :ref:`ch2lmp <charmm>` * :ref:`colvars <colvars>` * :ref:`eff <eff>` * :ref:`fep <fep>` * :ref:`lmp2arc <arc>` * :ref:`lmp2cfg <cfg>` * :ref:`matlab <matlab>` * :ref:`phonon <phonon>` * :ref:`pymol_asphere <pymol>` * :ref:`python <pythontools>` * :ref:`reax <reax_tool>` * :ref:`replica <replica>` * :ref:`smd <smd>` * :ref:`spin <spin>` * :ref:`xmgrace <xmgrace>` Miscellaneous tools =================== +--------------------------+----------------------+-------------------+--------------------+---------------------------------------+ | :ref:`doxygen <doxygen>` | :ref:`emacs <emacs>` | :ref:`i-pi <ipi>` | :ref:`kate <kate>` | :ref:`singularity <singularity_tool>` | +--------------------------+----------------------+-------------------+--------------------+---------------------------------------+ | :ref:`vim <vim>` | | | | | +--------------------------+----------------------+-------------------+--------------------+---------------------------------------+ .. table_from_list:: :columns: 6 * :ref:`CMake <cmake>` * :ref:`doxygen <doxygen>` * :ref:`emacs <emacs>` * :ref:`i-pi <ipi>` * :ref:`kate <kate>` * :ref:`singularity <singularity_tool>` * :ref:`vim <vim>` ---------- Loading Loading @@ -157,6 +185,30 @@ See the def.chain or def.chain.ab files in the tools directory for examples of definition files. This tool was used to create the system for the :doc:`chain benchmark <Speed_bench>`. ---------- .. _cmake: CMake tools ----------- The ``cmbuild`` script is a wrapper around using ``cmake --build <dir> --target`` and allows compiling LAMMPS in a :ref:`CMake build folder <cmake_build>` with a make-like syntax regardless of the actual build tool and the specific name of the program used (e.g. ``ninja-v1.10`` or ``gmake``) when using ``-D CMAKE_MAKE_PROGRAM=<name>``. .. parsed-literal:: Usage: cmbuild [-v] [-h] [-C <dir>] [-j <num>] [<target1> [<target2>] ...] Options: -h print this message -j <NUM> allow processing of NUM concurrent tasks -C DIRECTORY execute build in folder DIRECTORY -v produce verbose output ---------- .. _colvars: Loading tools/README +23 −22 Original line number Diff line number Diff line Loading @@ -16,6 +16,7 @@ amber2lmp python scripts for using AMBER to setup LAMMPS input binary2txt convert a LAMMPS dump file from binary to ASCII text ch2lmp convert CHARMM files to LAMMPS input chain create a data file of bead-spring chains cmake tools and scripts for use with CMake colvars post-process output of the fix colvars command createatoms generate lattices of atoms within a geometry drude create Drude core/electron atom pairs in a data file Loading tools/cmake/cmbuild 0 → 100755 +69 −0 Original line number Diff line number Diff line #!/bin/bash # make like wrapper around "cmake --build" # (c) 2020 Axel Kohlmeyer <akohlmey@temple.edu> # This file is in the public domain WORKDIR="${PWD}" PARAMS="" MYARGS="" usage() { echo "Usage: cmbuild [-v] [-h] [-C <dir>] [-j <num>] [<target1> [<target2>] ...]" >&2 } help() { usage cat >&2 <<EOF Options: -h print this message -j <NUM> allow processing of NUM concurrent tasks -C DIRECTORY execute build in folder DIRECTORY -v produce verbose output EOF } while (( "$#" )); do case "$1" in -C) WORKDIR="$2" shift 2 ;; -v) MYARGS="${MYARGS} -v" shift ;; -h) help exit 2 ;; -j) MYARGS="${MYARGS} -j $2" shift 2 ;; --) shift break ;; -*) echo "Error: Unsupported flag $1" >&2 echo usage exit 1 ;; *) PARAMS="${PARAMS} $1" shift ;; esac done if [ ! -f "${WORKDIR}/CMakeCache.txt" ] ; then echo "Must execute in a CMake build directory or use -C flag to select one" >&2 exit 3 fi eval set -- "${PARAMS} $@" exec cmake --build "${WORKDIR}" ${MYARGS} --target "$@" Loading
doc/src/Build_cmake.rst +20 −14 Original line number Diff line number Diff line Loading @@ -22,27 +22,31 @@ Makefile(s). Example: cd lammps # change to the LAMMPS distribution directory mkdir build; cd build # create a new directory (folder) for build cmake [options ...] ../cmake # configuration with (command-line) cmake make # compilation make # compilation (or use "cmbuild" from "tools/cmake") The cmake command will detect available features, enable selected The ``cmake`` command will detect available features, enable selected packages and options, and will generate the build environment. By default this build environment will be created for "Unix Makefiles" on most platforms and particularly on Linux. However, alternate build tools (e.g. Ninja) and project files for Integrated Development Environments (IDEs) like Eclipse, CodeBlocks, or Kate can be generated, too. This is selected via the "-G" command line flag. For the rest of the documentation selected via the ``-G`` command line flag. For the rest of the documentation we will assume that the build environment is generated for makefiles and thus the make command will be used to compile and link LAMMPS as indicated above, producing (by default) an executable called "lmp" and a library called "liblammps.a" in the "build" folder. When generating and thus the ``make`` command will be used to compile and link LAMMPS as indicated above, producing (by default) an executable called ``lmp`` and a library called ``liblammps.a`` in the ``build`` folder. When generating a build environment for the "Ninja" build tool, the build command would be "ninja" instead of "make". be ``ninja`` instead of ``make``. Or you may copy the ``cmbuild`` script from the :ref:`tools/cmake folder <cmake>` somewhere in your path and use that, as it will indirectly call CMake with the configured tool. This is particularly, if you configured the build folder with a build tool in a non-standard location or name using ``-D CMAKE_MAKE_PROGRAM=<name>``. If your machine has multiple CPU cores (most do these days), using a command like "make -jN" (with N being the number of available local command like ``make -j N`` (with N being the number of available local CPU cores) can be much faster. If you plan to do development on LAMMPS or need to re-compile LAMMPS repeatedly, installation of the ccache (= Compiler Cache) software may speed up repeated compilation ``ccache`` (= Compiler Cache) software may speed up repeated compilation even more. After compilation, you may optionally install the LAMMPS executable into Loading @@ -60,9 +64,11 @@ to ${HOME}/.local ---------- .. _cmake_build: There are 3 variants of the CMake command itself: a command-line version (*cmake* or *cmake3*), a text mode UI version (*ccmake* or *ccmake3*), and a graphical GUI version (*cmake-gui*). You can use any of them (``cmake`` or ``cmake3``), a text mode UI version (``ccmake`` or ``ccmake3``), and a graphical GUI version (``cmake-gui``). You can use any of them interchangeably to configure and create the LAMMPS build environment. On Linux all the versions produce a Makefile as their output by default. See more details on each below. Loading @@ -75,7 +81,7 @@ the :doc:`Build <Build>` doc page. You must perform the CMake build system generation and compilation in a new directory you create. It can be anywhere on your local machine. In these Build pages we assume that you are building in a directory called "lammps/build". You can perform separate builds independently called ``lammps/build``. You can perform separate builds independently with different options, so long as you perform each of them in a separate directory you create. All the auxiliary files created by one build process (executable, object files, log files, etc) are stored in Loading @@ -84,10 +90,10 @@ this directory or sub-directories within it that CMake creates. .. note:: To perform a CMake build, no packages can be installed or a build been previously attempted in the LAMMPS src directory by using "make" been previously attempted in the LAMMPS src directory by using ``make`` commands to :doc:`perform a conventional LAMMPS build <Build_make>`. CMake detects if this is the case and generates an error, telling you to type "make no-all purge" in the src directory to un-install all to type ``make no-all purge`` in the src directory to un-install all packages. The purge removes all the \*.h files auto-generated by make. Loading
doc/src/Tools.rst +71 −19 Original line number Diff line number Diff line Loading @@ -40,33 +40,61 @@ own sub-directories with their own Makefiles and/or README files. Pre-processing tools ==================== +-----------------------------+------------------------+----------------------+----------------------------------+----------------------------------+-----------------------------+ | :ref:`amber2lmp <amber>` | :ref:`ch2lmp <charmm>` | :ref:`chain <chain>` | :ref:`createatoms <createatoms>` | :ref:`drude <drude>` | :ref:`eam database <eamdb>` | +-----------------------------+------------------------+----------------------+----------------------------------+----------------------------------+-----------------------------+ | :ref:`eam generate <eamgn>` | :ref:`eff <eff>` | :ref:`ipp <ipp>` | :ref:`micelle2d <micelle>` | :ref:`moltemplate <moltemplate>` | :ref:`msi2lmp <msi>` | +-----------------------------+------------------------+----------------------+----------------------------------+----------------------------------+-----------------------------+ | :ref:`polybond <polybond>` | | | | | | +-----------------------------+------------------------+----------------------+----------------------------------+----------------------------------+-----------------------------+ .. table_from_list:: :columns: 6 * :ref:`amber2lmp <amber>` * :ref:`ch2lmp <charmm>` * :ref:`chain <chain>` * :ref:`createatoms <createatoms>` * :ref:`drude <drude>` * :ref:`eam database <eamdb>` * :ref:`eam generate <eamgn>` * :ref:`eff <eff>` * :ref:`ipp <ipp>` * :ref:`micelle2d <micelle>` * :ref:`moltemplate <moltemplate>` * :ref:`msi2lmp <msi>` * :ref:`polybond <polybond>` Post-processing tools ===================== +--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+ | :ref:`amber2lmp <amber>` | :ref:`binary2txt <binary>` | :ref:`ch2lmp <charmm>` | :ref:`colvars <colvars>` | :ref:`eff <eff>` | :ref:`fep <fep>` | +--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+ | :ref:`lmp2arc <arc>` | :ref:`lmp2cfg <cfg>` | :ref:`matlab <matlab>` | :ref:`phonon <phonon>` | :ref:`pymol_asphere <pymol>` | :ref:`python <pythontools>` | +--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+ | :ref:`reax <reax_tool>` | :ref:`replica <replica>` | :ref:`smd <smd>` | :ref:`spin <spin>` | :ref:`xmgrace <xmgrace>` | | +--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+ .. table_from_list:: :columns: 6 * :ref:`amber2lmp <amber>` * :ref:`binary2txt <binary>` * :ref:`ch2lmp <charmm>` * :ref:`colvars <colvars>` * :ref:`eff <eff>` * :ref:`fep <fep>` * :ref:`lmp2arc <arc>` * :ref:`lmp2cfg <cfg>` * :ref:`matlab <matlab>` * :ref:`phonon <phonon>` * :ref:`pymol_asphere <pymol>` * :ref:`python <pythontools>` * :ref:`reax <reax_tool>` * :ref:`replica <replica>` * :ref:`smd <smd>` * :ref:`spin <spin>` * :ref:`xmgrace <xmgrace>` Miscellaneous tools =================== +--------------------------+----------------------+-------------------+--------------------+---------------------------------------+ | :ref:`doxygen <doxygen>` | :ref:`emacs <emacs>` | :ref:`i-pi <ipi>` | :ref:`kate <kate>` | :ref:`singularity <singularity_tool>` | +--------------------------+----------------------+-------------------+--------------------+---------------------------------------+ | :ref:`vim <vim>` | | | | | +--------------------------+----------------------+-------------------+--------------------+---------------------------------------+ .. table_from_list:: :columns: 6 * :ref:`CMake <cmake>` * :ref:`doxygen <doxygen>` * :ref:`emacs <emacs>` * :ref:`i-pi <ipi>` * :ref:`kate <kate>` * :ref:`singularity <singularity_tool>` * :ref:`vim <vim>` ---------- Loading Loading @@ -157,6 +185,30 @@ See the def.chain or def.chain.ab files in the tools directory for examples of definition files. This tool was used to create the system for the :doc:`chain benchmark <Speed_bench>`. ---------- .. _cmake: CMake tools ----------- The ``cmbuild`` script is a wrapper around using ``cmake --build <dir> --target`` and allows compiling LAMMPS in a :ref:`CMake build folder <cmake_build>` with a make-like syntax regardless of the actual build tool and the specific name of the program used (e.g. ``ninja-v1.10`` or ``gmake``) when using ``-D CMAKE_MAKE_PROGRAM=<name>``. .. parsed-literal:: Usage: cmbuild [-v] [-h] [-C <dir>] [-j <num>] [<target1> [<target2>] ...] Options: -h print this message -j <NUM> allow processing of NUM concurrent tasks -C DIRECTORY execute build in folder DIRECTORY -v produce verbose output ---------- .. _colvars: Loading
tools/README +23 −22 Original line number Diff line number Diff line Loading @@ -16,6 +16,7 @@ amber2lmp python scripts for using AMBER to setup LAMMPS input binary2txt convert a LAMMPS dump file from binary to ASCII text ch2lmp convert CHARMM files to LAMMPS input chain create a data file of bead-spring chains cmake tools and scripts for use with CMake colvars post-process output of the fix colvars command createatoms generate lattices of atoms within a geometry drude create Drude core/electron atom pairs in a data file Loading
tools/cmake/cmbuild 0 → 100755 +69 −0 Original line number Diff line number Diff line #!/bin/bash # make like wrapper around "cmake --build" # (c) 2020 Axel Kohlmeyer <akohlmey@temple.edu> # This file is in the public domain WORKDIR="${PWD}" PARAMS="" MYARGS="" usage() { echo "Usage: cmbuild [-v] [-h] [-C <dir>] [-j <num>] [<target1> [<target2>] ...]" >&2 } help() { usage cat >&2 <<EOF Options: -h print this message -j <NUM> allow processing of NUM concurrent tasks -C DIRECTORY execute build in folder DIRECTORY -v produce verbose output EOF } while (( "$#" )); do case "$1" in -C) WORKDIR="$2" shift 2 ;; -v) MYARGS="${MYARGS} -v" shift ;; -h) help exit 2 ;; -j) MYARGS="${MYARGS} -j $2" shift 2 ;; --) shift break ;; -*) echo "Error: Unsupported flag $1" >&2 echo usage exit 1 ;; *) PARAMS="${PARAMS} $1" shift ;; esac done if [ ! -f "${WORKDIR}/CMakeCache.txt" ] ; then echo "Must execute in a CMake build directory or use -C flag to select one" >&2 exit 3 fi eval set -- "${PARAMS} $@" exec cmake --build "${WORKDIR}" ${MYARGS} --target "$@"
