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Merge pull request #3322 from akohlmey/collected-small-fixes

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Collected small fixes
This commit is contained in:
Axel Kohlmeyer
2022-06-29 18:03:08 -04:00
committed by GitHub
parent 0156efc70f 533a56404a
commit 0ae6f1c30e
7 changed files with 135 additions and 29 deletions
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11
cmake/Modules/LAMMPSInterfacePlugin.cmake
View File

@ -6,6 +6,9 @@ if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
"Please remove CMakeCache.txt and CMakeFiles first.")
endif()
set(LAMMPS_THIRDPARTY_URL "https://download.lammps.org/thirdparty"
CACHE STRING "URL for thirdparty package downloads")
# global LAMMPS/plugin build settings
set(LAMMPS_SOURCE_DIR "" CACHE PATH "Location of LAMMPS sources folder")
if(NOT LAMMPS_SOURCE_DIR)
@ -78,6 +81,13 @@ function(get_newest_file path variable)
set(${variable} ${_bestfile} PARENT_SCOPE)
endfunction()
# get LAMMPS version date
function(get_lammps_version version_header variable)
file(STRINGS ${version_header} line REGEX LAMMPS_VERSION)
string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\1\\2\\3" date "${line}")
set(${variable} "${date}" PARENT_SCOPE)
endfunction()
#################################################################################
# LAMMPS C++ interface. We only need the header related parts except on windows.
add_library(lammps INTERFACE)
@ -89,6 +99,7 @@ endif()
################################################################################
# MPI configuration
if(NOT CMAKE_CROSSCOMPILING)
set(MPI_CXX_SKIP_MPICXX TRUE)
find_package(MPI QUIET)
option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
else()

44
doc/src/dump.rst
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@ -27,6 +27,9 @@ dump command
:doc:`dump custom/adios <dump_adios>` command
=============================================
:doc:`dump cfg/uef <dump_cfg_uef>` command
==========================================
Syntax
""""""
@ -36,7 +39,7 @@ Syntax
* ID = user-assigned name for the dump
* group-ID = ID of the group of atoms to be dumped
* style = *atom* or *atom/gz* or *atom/zstd or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *dcd* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml*
* style = *atom* or *atom/gz* or *atom/zstd or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *dcd* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml*
* N = dump every this many timesteps
* file = name of file to write dump info to
* args = list of arguments for a particular style
@ -47,22 +50,23 @@ Syntax
*atom/gz* args = none
*atom/zstd* args = none
*atom/mpiio* args = none
*atom/adios* args = none, discussed on :doc:`dump atom/adios <dump_adios>` doc page
*atom/adios* args = none, discussed on :doc:`dump atom/adios <dump_adios>` page
*cfg* args = same as *custom* args, see below
*cfg/gz* args = same as *custom* args, see below
*cfg/zstd* args = same as *custom* args, see below
*cfg/mpiio* args = same as *custom* args, see below
*cfg/uef* args = same as *custom* args, discussed on :doc:`dump cfg/uef <dump_cfg_uef>` page
*custom*, *custom/gz*, *custom/zstd*, *custom/mpiio* args = see below
*custom/adios* args = same as *custom* args, discussed on :doc:`dump custom/adios <dump_adios>` doc page
*custom/adios* args = same as *custom* args, discussed on :doc:`dump custom/adios <dump_adios>` page
*dcd* args = none
*h5md* args = discussed on :doc:`dump h5md <dump_h5md>` doc page
*image* args = discussed on :doc:`dump image <dump_image>` doc page
*h5md* args = discussed on :doc:`dump h5md <dump_h5md>` page
*image* args = discussed on :doc:`dump image <dump_image>` page
*local*, *local/gz*, *local/zstd* args = see below
*molfile* args = discussed on :doc:`dump molfile <dump_molfile>` doc page
*movie* args = discussed on :doc:`dump image <dump_image>` doc page
*netcdf* args = discussed on :doc:`dump netcdf <dump_netcdf>` doc page
*netcdf/mpiio* args = discussed on :doc:`dump netcdf <dump_netcdf>` doc page
*vtk* args = same as *custom* args, see below, also :doc:`dump vtk <dump_vtk>` doc page
*molfile* args = discussed on :doc:`dump molfile <dump_molfile>` page
*movie* args = discussed on :doc:`dump image <dump_image>` page
*netcdf* args = discussed on :doc:`dump netcdf <dump_netcdf>` page
*netcdf/mpiio* args = discussed on :doc:`dump netcdf <dump_netcdf>` page
*vtk* args = same as *custom* args, see below, also :doc:`dump vtk <dump_vtk>` page
*xtc* args = none
*xyz* args = none
*xyz/gz* args = none
@ -155,7 +159,7 @@ timesteps in one of several styles. The *image* and *movie* styles are
the exception: the *image* style renders a JPG, PNG, or PPM image file
of the atom configuration every N timesteps while the *movie* style
combines and compresses them into a movie file; both are discussed in
detail on the :doc:`dump image <dump_image>` doc page. The timesteps on
detail on the :doc:`dump image <dump_image>` page. The timesteps on
which dump output is written can also be controlled by a variable.
See the :doc:`dump_modify every <dump_modify>` command.
@ -194,7 +198,7 @@ or multiple smaller files).
For the *atom*, *custom*, *cfg*, and *local* styles, sorting is off by
default. For the *dcd*, *xtc*, *xyz*, and *molfile* styles, sorting
by atom ID is on by default. See the :doc:`dump_modify <dump_modify>`
doc page for details.
page for details.
The *atom/gz*, *cfg/gz*, *custom/gz*, *local/gz*, and *xyz/gz* styles
are identical in command syntax to the corresponding styles without
@ -204,7 +208,7 @@ alternative approach to writing compressed files via a pipe, as done
by the regular dump styles, which may be required on clusters where
the interface to the high-speed network disallows using the fork()
library call (which is needed for a pipe). For the remainder of this
doc page, you should thus consider the *atom* and *atom/gz* styles
page, you should thus consider the *atom* and *atom/gz* styles
(etc) to be inter-changeable, with the exception of the required
filename suffix.
@ -218,7 +222,7 @@ As explained below, the *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and
*xyz/mpiio* styles are identical in command syntax and in the format
of the dump files they create, to the corresponding styles without
"mpiio", except the single dump file they produce is written in
parallel via the MPI-IO library. For the remainder of this doc page,
parallel via the MPI-IO library. For the remainder of this page,
you should thus consider the *atom* and *atom/mpiio* styles (etc) to
be inter-changeable. The one exception is how the filename is
specified for the MPI-IO styles, as explained below.
@ -664,7 +668,7 @@ so that each value is 0.0 to 1.0. If the simulation box is triclinic
(tilted), then all atom coords will still be between 0.0 and 1.0.
I.e. actual unscaled (x,y,z) = xs\*A + ys\*B + zs\*C, where (A,B,C) are
the non-orthogonal vectors of the simulation box edges, as discussed
on the :doc:`Howto triclinic <Howto_triclinic>` doc page.
on the :doc:`Howto triclinic <Howto_triclinic>` page.
Use *xu*, *yu*, *zu* if you want the coordinates "unwrapped" by the
image flags for each atom. Unwrapped means that if the atom has
@ -787,7 +791,7 @@ more info.
The *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and *xyz/mpiio* styles
are part of the MPIIO package. They are only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>`
doc page for more info.
page for more info.
The *xtc*, *dcd* and *yaml* styles are part of the EXTRA-DUMP package.
They are only enabled if LAMMPS was built with that package. See the
@ -797,12 +801,12 @@ Related commands
""""""""""""""""
:doc:`dump atom/adios <dump_adios>`, :doc:`dump custom/adios <dump_adios>`,
:doc:`dump h5md <dump_h5md>`, :doc:`dump image <dump_image>`,
:doc:`dump molfile <dump_molfile>`, :doc:`dump_modify <dump_modify>`,
:doc:`undump <undump>`
:doc:`dump cfg/uef <dump_cfg_uef>`, :doc:`dump h5md <dump_h5md>`,
:doc:`dump image <dump_image>`, :doc:`dump molfile <dump_molfile>`,
:doc:`dump_modify <dump_modify>`, :doc:`undump <undump>`, :doc:`write_dump <write_dump>`
Default
"""""""
The defaults for the *image* and *movie* styles are listed on the
:doc:`dump image <dump_image>` doc page.
:doc:`dump image <dump_image>` page.

17
examples/PACKAGES/pace/plugin/CMakeLists.txt
View File

@ -31,6 +31,23 @@ elseif(CMAKE_SYSTEM_NAME STREQUAL "Windows")
if(CMAKE_CROSSCOMPILING)
set_target_properties(paceplugin PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols")
endif()
get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION)
find_program(MAKENSIS_PATH makensis)
if(MAKENSIS_PATH)
execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_SOURCE_DIR}/lammps.ico
${CMAKE_SOURCE_DIR}/lammps-text-logo-wide.bmp ${CMAKE_SOURCE_DIR}/paceplugin.nsis ${CMAKE_BINARY_DIR})
if(BUILD_MPI)
add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION}-MPI paceplugin.nsis
DEPENDS paceplugin
BYPRODUCTS LAMMPS-ML-PACE-plugin-${LAMMPS_VERSION}-MPI.exe)
else()
add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION} paceplugin.nsis
COMMAND ${CMAKE_COMMAND} -E echo ${PWD}
DEPENDS paceplugin lammps.ico lammps-text-logo-wide.bmp paceplugin.nsis
BYPRODUCTS LAMMPS-ML-PACE-plugin-${LAMMPS_VERSION}.exe)
endif()
endif()
else()
set_target_properties(paceplugin PROPERTIES LINK_FLAGS "-rdynamic")
endif()

57
examples/plugins/LAMMPSInterfaceCXX.cmake
View File

@ -1,6 +1,9 @@
# Cmake script code to define the LAMMPS C++ interface
# settings required for building LAMMPS plugins
set(LAMMPS_THIRDPARTY_URL "https://download.lammps.org/thirdparty"
CACHE STRING "URL for thirdparty package downloads")
################################################################################
# helper function
function(validate_option name values)
@ -37,10 +40,56 @@ else()
endif()
if(BUILD_MPI)
find_package(MPI REQUIRED)
option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
if(LAMMPS_LONGLONG_TO_LONG)
target_compile_definitions(lammps INTERFACE -DLAMMPS_LONGLONG_TO_LONG)
# do not include the (obsolete) MPI C++ bindings which makes
# for leaner object files and avoids namespace conflicts
set(MPI_CXX_SKIP_MPICXX TRUE)
# We use a non-standard procedure to cross-compile with MPI on Windows
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
# Download and configure custom MPICH files for Windows
message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
else()
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN32_DEVEL_URL}
URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
else()
find_package(MPI REQUIRED)
option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
if(LAMMPS_LONGLONG_TO_LONG)
target_compile_definitions(lammps INTERFACE -DLAMMPS_LONGLONG_TO_LONG)
endif()
endif()
target_link_libraries(lammps INTERFACE MPI::MPI_CXX)
else()

1
src/variable.cpp
View File

@ -4803,6 +4803,7 @@ double Variable::evaluate_boolean(char *str)
} else if (opprevious == LT) {
if (flag1 || flag2)
error->all(FLERR,"If command boolean can only operate on numbers");
if (value1 < value2) argstack[nargstack].value = 1.0;
else argstack[nargstack].value = 0.0;
} else if (opprevious == LE) {
if (flag1 || flag2)

25
unittest/commands/test_variables.cpp
View File

@ -403,11 +403,36 @@ TEST_F(VariableTest, IfCommand)
text = END_CAPTURE_OUTPUT();
ASSERT_THAT(text, ContainsRegex(".*nope\?.*"));
BEGIN_CAPTURE_OUTPUT();
command("if 0<1 then 'print \"bingo!\"'");
text = END_CAPTURE_OUTPUT();
ASSERT_THAT(text, ContainsRegex(".*bingo!.*"));
BEGIN_CAPTURE_OUTPUT();
command("if 2<1 then 'print \"bingo!\"' else 'print \"nope?\"'");
text = END_CAPTURE_OUTPUT();
ASSERT_THAT(text, ContainsRegex(".*nope\?.*"));
BEGIN_CAPTURE_OUTPUT();
command("if (1<=0) then 'print \"bingo!\"' else 'print \"nope?\"'");
text = END_CAPTURE_OUTPUT();
ASSERT_THAT(text, ContainsRegex(".*nope\?.*"));
BEGIN_CAPTURE_OUTPUT();
command("if (0<=0) then 'print \"bingo!\"' else 'print \"nope?\"'");
text = END_CAPTURE_OUTPUT();
ASSERT_THAT(text, ContainsRegex(".*bingo!.*"));
BEGIN_CAPTURE_OUTPUT();
command("if (0>=1) then 'print \"bingo!\"' else 'print \"nope?\"'");
text = END_CAPTURE_OUTPUT();
ASSERT_THAT(text, ContainsRegex(".*nope\?.*"));
BEGIN_CAPTURE_OUTPUT();
command("if (1>=1) then 'print \"bingo!\"' else 'print \"nope?\"'");
text = END_CAPTURE_OUTPUT();
ASSERT_THAT(text, ContainsRegex(".*bingo!.*"));
BEGIN_CAPTURE_OUTPUT();
command("if (-1.0e-1<0.0E+0)|^(1<0) then 'print \"bingo!\"'");
text = END_CAPTURE_OUTPUT();

9
unittest/fortran/CMakeLists.txt
View File

@ -10,11 +10,6 @@ if(NOT CMAKE_Fortran_COMPILER_ID)
message(STATUS "Skipping Tests for the LAMMPS Fortran Module: cannot identify Fortran compiler")
return()
endif()
find_package(MPI QUIET)
if(BUILD_MPI AND NOT MPI_Fortran)
message(STATUS "Skipping Tests for the LAMMPS Fortran Module: no MPI support for Fortran")
return()
endif()
if(CMAKE_Fortran_COMPILER)
enable_language(C)
@ -22,6 +17,10 @@ if(CMAKE_Fortran_COMPILER)
get_filename_component(LAMMPS_FORTRAN_MODULE ${LAMMPS_SOURCE_DIR}/../fortran/lammps.f90 ABSOLUTE)
if(BUILD_MPI)
find_package(MPI REQUIRED)
if((NOT MPI_Fortran) OR (NOT MPI_Fortran_HAVE_F77_HEADER) OR (NOT MPI_Fortran_HAVE_F90_MODULE))
message(STATUS "Skipping Tests for the LAMMPS Fortran Module: no MPI support for Fortran")
return()
endif()
else()
add_library(fmpi_stubs STATIC mpi_stubs.f90)
add_library(MPI::MPI_Fortran ALIAS fmpi_stubs)