Unverified Commit 69665c21 authored by Jacob Gissinger's avatar Jacob Gissinger Committed by GitHub
Browse files

Merge pull request #9 from lammps/master 

rebase
parents 020fc66a d5ec7629

cmake/CMakeLists.txt

+17 −3
Original line number Diff line number Diff line
@@ -240,8 +240,8 @@ if(ENABLE_LATTE) 
    message(STATUS "LATTE not found - we will build our own")

    include(ExternalProject)

    ExternalProject_Add(latte_build

      URL https://github.com/lanl/LATTE/archive/v1.0.1.tar.gz

      URL_MD5 5137e28cb1a64444bd571c98c98a6eee

      URL https://github.com/lanl/LATTE/archive/v1.1.1.tar.gz

      URL_MD5 cb86f1d2473ce00aa61ff6a023154b03

      SOURCE_SUBDIR cmake

      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE}

      )
@@ -290,7 +290,21 @@ if(ENABLE_USER-VTK) 
endif()



if(ENABLE_KIM)

  find_package(KIM REQUIRED)

  find_package(KIM QUIET)

  if(NOT KIM_FOUND)

    message(STATUS "KIM not found - we will build our own")

    include(ExternalProject)

    ExternalProject_Add(kim_build

      URL https://github.com/openkim/kim-api/archive/v1.9.4.tar.gz

      URL_MD5 f4d35a1705eed46d64c7c0ab448ff3e0

      BUILD_IN_SOURCE 1

      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>

      )

    ExternalProject_get_property(kim_build INSTALL_DIR)

    set(KIM_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v1)

    set(KIM_LIBRARIES ${INSTALL_DIR}/lib/libkim-api-v1.so)

    list(APPEND LAMMPS_DEPS kim_build)

  endif()

  list(APPEND LAMMPS_LINK_LIBS ${KIM_LIBRARIES})

  include_directories(${KIM_INCLUDE_DIRS})

endif()

doc/src/Developer/developer.tex

+16 −15
Original line number Diff line number Diff line
@@ -609,8 +609,9 @@ this situation there are several methods which should be implemented: 
\item \verb|double memory_usage| - return how much memory fix uses

\item \verb|void grow_arrays(int)| - do reallocation of the per particle arrays

  in your fix

\item \verb|void copy_arrays(int i, int j)| - copy i-th per-particle information 

  to j-th. Used when atoms sorting is performed

\item \verb|void copy_arrays(int i, int j, int delflag)| - copy i-th per-particle

  information to j-th. Used when atoms sorting is performed. if delflag is set

  and atom j owns a body, move the body information to atom i.

\item \verb|void set_arrays(int i)| - sets i-th particle related information to zero

\end{itemize}
@@ -654,7 +655,7 @@ void FixSavePos::grow_arrays(int nmax) 
    memory->grow(this->x, nmax, 3, "FixSavePos:x");

}



void FixSavePos::copy_arrays(int i, int j)

void FixSavePos::copy_arrays(int i, int j, int delflag)

{

    memcpy(this->x[j], this->x[i], sizeof(double) * 3);

}

doc/src/Manual.txt

+2 −2
Original line number Diff line number Diff line 
<!-- HTML_ONLY -->

<HEAD>

<TITLE>LAMMPS Users Manual</TITLE>

<META NAME="docnumber" CONTENT="30 Mar 2018 version">

<META NAME="docnumber" CONTENT="20 Apr 2018 version">

<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">

<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">

</HEAD>
@@ -19,7 +19,7 @@ 
:line



LAMMPS Documentation :c,h1

30 Mar 2018 version :c,h2

20 Apr 2018 version :c,h2



Version info: :h3

doc/src/Section_errors.txt

+0 −40
Original line number Diff line number Diff line
@@ -1565,15 +1565,6 @@ This operation is not allowed. :dd 


This operation is not allowed. :dd



{Cannot use -cuda on and -kokkos on together} :dt



This is not allowed since both packages can use GPUs. :dd



{Cannot use -cuda on without USER-CUDA installed} :dt



The USER-CUDA package must be installed via "make yes-user-cuda"

before LAMMPS is built. :dd



{Cannot use -kokkos on without KOKKOS installed} :dt



Self-explanatory. :dd
@@ -1597,11 +1588,6 @@ solver/pair style. :dd 


This is a current restriction of this command. :dd



{Cannot use GPU package with USER-CUDA package enabled} :dt



You cannot use both the GPU and USER-CUDA packages

together.  Use one or the other. :dd



{Cannot use Kokkos pair style with rRESPA inner/middle} :dt



Self-explanatory. :dd
@@ -8252,12 +8238,6 @@ Self-explanatory. :dd 
The package command cannot be used afer a read_data, read_restart, or

create_box command. :dd



{Package cuda command without USER-CUDA package enabled} :dt



The USER-CUDA package must be installed via "make yes-user-cuda"

before LAMMPS is built, and the "-c on" must be used to enable the

package. :dd



{Package gpu command without GPU package installed} :dt



The GPU package must be installed via "make yes-gpu" before LAMMPS is
@@ -10230,22 +10210,6 @@ it in different ways. :dd 


Self-explanatory. :dd



{USER-CUDA mode requires CUDA variant of min style} :dt



CUDA mode is enabled, so the min style must include a cuda suffix. :dd



{USER-CUDA mode requires CUDA variant of run style} :dt



CUDA mode is enabled, so the run style must include a cuda suffix. :dd



{USER-CUDA package does not yet support comm_style tiled} :dt



Self-explanatory. :dd



{USER-CUDA package requires a cuda enabled atom_style} :dt



Self-explanatory. :dd



{Unable to initialize accelerator for use} :dt



There was a problem initializing an accelerator for the gpu package :dd
@@ -10494,10 +10458,6 @@ Must use remap v option with fix deform with this pair style. :dd 


If fix deform is used, the remap v option is required. :dd



{Using suffix cuda without USER-CUDA package enabled} :dt



Self-explanatory. :dd



{Using suffix gpu without GPU package installed} :dt



Self-explanatory. :dd

doc/src/Section_intro.txt

+3 −3
Original line number Diff line number Diff line
@@ -526,14 +526,14 @@ and efforts. 
Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CGSDK, USER-OMP, USER-COLVARS, USER-MOLFILE, USER-QMMM, USER-TALLY, and COMPRESS packages

Roy Pollock (LLNL), Ewald and PPPM solvers

Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL package

Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential

Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential (superseded by USER-MEAMC)

Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics

Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion

Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling

Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD

Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA and KOKKOS packages

Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA (obsoleted by KOKKOS) and KOKKOS packages

Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field

Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling

Christoph Kloss (JKU), Christoph.Kloss at jku.at, LIGGGHTS fork for granular models and granular/fluid coupling

Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF

Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SMD and USER-SPH packages

Colin Denniston (U Western Ontario), cdennist at uwo.ca, USER-LB package :ul

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