ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge pull request #4209 from akohlmey/plumed-plugin

Browse Source 
Add support to build the PLUMED package as a plugin
This commit is contained in:
Axel Kohlmeyer
2024-08-28 19:10:46 -04:00
committed by GitHub
parent 0ad64045f5 af5f437aeb
commit d48ca258fa
15 changed files with 306 additions and 6 deletions
Download Patch File Download Diff File Expand all files Collapse all files

5
cmake/CMakeLists.txt
View File

@ -12,6 +12,11 @@ endif()
if(POLICY CMP0075)
cmake_policy(SET CMP0075 NEW)
endif()
# set policy to silence warnings about requiring execute permission for find_program
# we use OLD because the python-config script for the Fedora MinGW cross-compiler requires it currently
if(POLICY CMP0109)
cmake_policy(SET CMP0109 OLD)
endif()
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)

8
cmake/Modules/Packages/ML-PACE.cmake
View File

@ -1,5 +1,11 @@
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
# PACE library support for ML-PACE package
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
endif()
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_MD5 "b45de9a633f42ed65422567e3ce56f9f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
mark_as_advanced(PACELIB_URL)
mark_as_advanced(PACELIB_MD5)

15
cmake/Modules/Packages/PLUMED.cmake
View File

@ -1,5 +1,10 @@
# Plumed2 support for PLUMED package
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
endif()
# for supporting multiple concurrent plumed2 installations for debugging and testing
set(PLUMED_SUFFIX "" CACHE STRING "Suffix for Plumed2 library")
mark_as_advanced(PLUMED_SUFFIX)
@ -81,6 +86,9 @@ if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
DEPENDS plumed_build
COMMENT "Copying Plumed files"
)
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps INTERFACE LAMMPS::PLUMED)
endif()
else()
@ -155,6 +163,9 @@ else()
endif()
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)
endif()
else()
find_package(PkgConfig REQUIRED)
pkg_check_modules(PLUMED REQUIRED plumed${PLUMED_SUFFIX})
@ -169,7 +180,9 @@ else()
endif()
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}")
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps PUBLIC LAMMPS::PLUMED)
endif()
endif()
endif()
target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)

10
doc/src/Build_extras.rst
View File

@ -1517,6 +1517,11 @@ in lib/pace or somewhere else, which must be done before building
LAMMPS with this package. The code for the library can be found
at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps-user-pace/>`_
Instead of including the ML-PACE package directly into LAMMPS, it
is also possible to skip this step and build the ML-PACE package as
a plugin using the CMake script files in the ``examples/PACKAGE/pace/plugin``
folder and then load this plugin at runtime with the :doc:`plugin command <plugin>`.
.. tabs::
.. tab:: CMake build
@ -1701,6 +1706,11 @@ try a different one, switch to a different build system, consider a
global PLUMED installation or consider downloading PLUMED during the
LAMMPS build.
Instead of including the PLUMED package directly into LAMMPS, it
is also possible to skip this step and build the PLUMED package as
a plugin using the CMake script files in the ``examples/PACKAGE/plumed/plugin``
folder and then load this plugin at runtime with the :doc:`plugin command <plugin>`.
.. tabs::
.. tab:: CMake build

2
doc/src/Developer_plugins.rst
View File

@ -283,7 +283,7 @@ in the ``examples/kim/plugin`` folder. No changes to the sources of the
KIM package themselves are needed; only the plugin interface and loader
code needs to be added. This example only supports building with CMake,
but is probably a more typical example. To compile you need to run CMake
with -DLAMMPS_SOURCE_DIR=<path/to/lammps/src/folder>. Other
with ``-DLAMMPS_SOURCE_DIR=<path/to/lammps/src/folder>``. Other
configuration setting are identical to those for compiling LAMMPS.
A second example for a plugin from a package is in the

7
doc/src/Packages_details.rst
View File

@ -1823,7 +1823,8 @@ Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1.
**Install:**
This package has :ref:`specific installation instructions <ml-pace>` on the
:doc:`Build extras <Build_extras>` page.
:doc:`Build extras <Build_extras>` page. This package may also be compiled
as a plugin to avoid licensing conflicts when distributing binaries.
**Supporting info:**
@ -2344,7 +2345,9 @@ and Gareth Tribello.
**Install:**
This package has :ref:`specific installation instructions <plumed>` on the :doc:`Build extras <Build_extras>` page.
This package has :ref:`specific installation instructions <plumed>` on the
:doc:`Build extras <Build_extras>` page. This package may also be compiled
as a plugin to avoid licensing conflicts when distributing binaries.
**Supporting info:**

2
examples/PACKAGES/pace/plugin/paceplugin.nsis
View File

@ -39,7 +39,7 @@ InstallDir "$LOCALAPPDATA\${PACEPLUGIN}"
ShowInstDetails show
ShowUninstDetails show
SetCompressor lzma
SetCompressor zlib
!define MUI_ABORTWARNING

59
examples/PACKAGES/plumed/plugin/CMakeLists.txt Normal file
View File

@ -0,0 +1,59 @@
# -*- CMake -*- build system for plugin examples.
# The is meant to be used as a template for plugins that are
# distributed independent from the LAMMPS package.
##########################################
cmake_minimum_required(VERSION 3.16)
project(plumedplugin VERSION 1.0 LANGUAGES CXX)
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR})
include(CheckIncludeFileCXX)
include(LAMMPSInterfacePlugin)
include(PLUMED)
##########################
# building the plugins
add_library(plumedplugin MODULE plumedplugin.cpp ${LAMMPS_SOURCE_DIR}/PLUMED/fix_plumed.cpp)
target_link_libraries(plumedplugin PRIVATE LAMMPS::PLUMED)
target_link_libraries(plumedplugin PRIVATE lammps)
target_include_directories(plumedplugin PRIVATE ${LAMMPS_SOURCE_DIR}/PLUMED)
set_target_properties(plumedplugin PROPERTIES PREFIX "" SUFFIX ".so")
# MacOS seems to need this
if(CMAKE_SYSTEM_NAME STREQUAL Darwin)
set_target_properties(plumedplugin PROPERTIES LINK_FLAGS "-Wl,-undefined,dynamic_lookup")
elseif(CMAKE_SYSTEM_NAME STREQUAL "Windows")
# tell CMake to export all symbols to a .dll on Windows with special case for MinGW cross-compilers
set_target_properties(plumedplugin PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
if(CMAKE_CROSSCOMPILING)
set_target_properties(plumedplugin PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols")
endif()
get_lammps_version(${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}/plumedplugin.nsis
${CMAKE_BINARY_DIR})
if(BUILD_MPI)
if(USE_MSMPI)
add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION}-MSMPI plumedplugin.nsis
DEPENDS plumedplugin plumed_copy lammps.ico lammps-text-logo-wide.bmp plumedplugin.nsis
BYPRODUCTS LAMMPS-PLUMED-plugin-${LAMMPS_VERSION}-MSMPI.exe)
else()
add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION}-MPI plumedplugin.nsis
DEPENDS plumedplugin plumed_copy lammps.ico lammps-text-logo-wide.bmp plumedplugin.nsis
BYPRODUCTS LAMMPS-PLUMED-plugin-${LAMMPS_VERSION}-MPI.exe)
endif()
else()
add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION} plumedplugin.nsis
COMMAND ${CMAKE_COMMAND} -E echo ${PWD}
DEPENDS plumedplugin plumed_copy lammps.ico lammps-text-logo-wide.bmp plumedplugin.nsis
BYPRODUCTS LAMMPS-PLUMED-plugin-${LAMMPS_VERSION}.exe)
endif()
endif()
else()
set_target_properties(plumedplugin PROPERTIES LINK_FLAGS "-rdynamic")
endif()

1
examples/PACKAGES/plumed/plugin/LAMMPSInterfacePlugin.cmake Symbolic link
View File

@ -0,0 +1 @@
../../../../cmake/Modules/LAMMPSInterfacePlugin.cmake

1
examples/PACKAGES/plumed/plugin/PLUMED.cmake Symbolic link
View File

@ -0,0 +1 @@
../../../../cmake/Modules/Packages/PLUMED.cmake

2
examples/PACKAGES/plumed/plugin/README.txt Normal file
View File

@ -0,0 +1,2 @@
This folder contains a loader and support files to build the PLUMED package as plugin.
For more information please see: https://docs.lammps.org/Developer_plugins.html

BIN
examples/PACKAGES/plumed/plugin/lammps-text-logo-wide.bmp Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 25 KiB

BIN
examples/PACKAGES/plumed/plugin/lammps.ico Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 204 KiB

28
examples/PACKAGES/plumed/plugin/plumedplugin.cpp Normal file
View File

@ -0,0 +1,28 @@
#include "lammpsplugin.h"
#include "version.h"
#include "fix_plumed.h"
using namespace LAMMPS_NS;
static Fix *fix_plumed_creator(LAMMPS *lmp, int argc, char **argv)
{
return new FixPlumed(lmp, argc, argv);
}
extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
{
lammpsplugin_t plugin;
lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
// register plumed fix style
plugin.version = LAMMPS_VERSION;
plugin.style = "fix";
plugin.name = "plumed";
plugin.info = "Plumed2 plugin fix style v1.0";
plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
plugin.creator.v1 = (lammpsplugin_factory1 *) &fix_plumed_creator;
plugin.handle = handle;
(*register_plugin)(&plugin, lmp);
}

172
examples/PACKAGES/plumed/plugin/plumedplugin.nsis Normal file
View File

@ -0,0 +1,172 @@
#!Nsis Installer Command Script
#
# The following external defines are recognized:
# ${VERSION} = YYYYMMDD
!include "MUI2.nsh"
!include "FileFunc.nsh"
!define MUI_ICON "lammps.ico"
!define MUI_UNICON "lammps.ico"
!define MUI_HEADERIMAGE
!define MUI_HEADERIMAGE_BITMAP "lammps-text-logo-wide.bmp"
!define MUI_HEADERIMAGE_RIGHT
Unicode true
XPStyle on
!include "LogicLib.nsh"
!addplugindir "envvar/Plugins/x86-unicode"
!include "x64.nsh"
RequestExecutionLevel user
!macro VerifyUserIsAdmin
UserInfo::GetAccountType
pop $0
${If} $0 != "admin"
messageBox mb_iconstop "Administrator rights required!"
setErrorLevel 740 ;ERROR_ELEVATION_REQUIRED
quit
${EndIf}
!macroend
!define PLUMEDPLUGIN "LAMMPS PLUMED Plugin ${VERSION}"
OutFile "LAMMPS-PLUMED-plugin-${VERSION}.exe"
Name "${PLUMEDPLUGIN}"
InstallDir "$LOCALAPPDATA\${PLUMEDPLUGIN}"
ShowInstDetails show
ShowUninstDetails show
SetCompressor zlib
!define MUI_ABORTWARNING
!insertmacro MUI_PAGE_DIRECTORY
!insertmacro MUI_PAGE_INSTFILES
!insertmacro MUI_UNPAGE_CONFIRM
!insertmacro MUI_UNPAGE_INSTFILES
!insertmacro MUI_LANGUAGE "English"
function .onInit
# Determine if LAMMPS was already installed and check whether it was in 32-bit
# or 64-bit. Then look up path to uninstaller and offer to uninstall or quit
SetRegView 32
ReadRegDWORD $0 HKCU "Software\LAMMPS-PLUMED" "Bits"
SetRegView LastUsed
${If} $0 == "32"
SetRegView 32
${ElseIf} $0 == "64"
SetRegView 64
${Else}
SetRegView 64
${EndIf}
ClearErrors
ReadRegStr $R0 HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" "UninstallString"
SetRegView LastUsed
${If} ${Errors}
DetailPrint "LAMMPS PLUMED plugin not (yet) installed"
${Else}
MessageBox MB_YESNO "LAMMPS PLUMED plugin ($0 bit) is already installed. Uninstall existing version?" /SD IDYES IDNO Quit
Pop $R1
StrCmp $R1 2 Quit +1
Exec $R0
Quit:
Quit
${EndIf}
setShellVarContext all
functionEnd
Section "${PLUMEDPLUGIN}" SecPlumedplugin
SectionIn RO
# Write LAMMPS installation bitness marker. Always use 32-bit registry view
SetRegView 32
IntFmt $0 "0x%08X" 64
WriteRegDWORD HKCU "Software\LAMMPS-PLUMED" "Bits" $0
# Switch to "native" registry view
SetRegView 64
SetShellVarContext current
SetOutPath "$INSTDIR"
CreateDirectory "$INSTDIR\patches"
CreateDirectory "$INSTDIR\bin"
File lammps.ico
File plumedplugin.so
SetOutPath "$INSTDIR\bin"
File plumed.exe
# Register Application and its uninstaller
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"DisplayName" "${PLUMEDPLUGIN}"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"Publisher" "The LAMMPS and PLUMED Developers"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"URLInfoAbout" "lammps.org"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"DisplayIcon" "$INSTDIR\lammps.ico"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"DisplayVersion" "${VERSION}"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"InstallLocation" "$INSTDIR"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"UninstallString" "$\"$INSTDIR\uninstall.exe$\""
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"QuietUninstallString" "$\"$INSTDIR\uninstall.exe$\" /S"
${GetSize} "$INSTDIR" "/S=0K" $0 $1 $2
IntFmt $0 "0x%08X" $0
WriteRegDWORD HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"EstimatedSize" "$0"
# update path variables
EnVar::SetHKCU
# add plumed executable path
EnVar::AddValue "PATH" "$INSTDIR\bin"
# add to LAMMPS plugin search path
EnVar::AddValue "LAMMPS_PLUGIN_PATH" "$INSTDIR"
# add plumed2 patch files
EnVar::AddValue "PLUMED_ROOT" "$INSTDIR"
WriteUninstaller "$INSTDIR\Uninstall.exe"
SectionEnd
function un.onInit
SetShellVarContext current
functionEnd
Section "Uninstall"
# remove LAMMPS bitness/installation indicator always in 32-bit registry view
SetRegView 32
DeleteRegKey HKCU "Software\LAMMPS-PLUMED"
# unregister extension, and uninstall info
SetRegView 64
SetShellVarContext current
# unregister installation
DeleteRegKey HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED"
# update path variables
EnVar::SetHKCU
# remove plumed executable path
EnVar::DeleteValue "PATH" "$INSTDIR\bin"
# remove entry from LAMMPS plugin search path
EnVar::DeleteValue "LAMMPS_PLUGIN_PATH" "$INSTDIR"
# remove plumed patch environment
EnVar::Delete "PLUMED_ROOT"
RMDir /r /REBOOTOK "$INSTDIR\patches"
RMDir /r /REBOOTOK "$INSTDIR\bin"
Delete /REBOOTOK "$INSTDIR\plumedplugin.so"
Delete /REBOOTOK "$INSTDIR\Uninstall.exe"
Delete /REBOOTOK "$INSTDIR\lammps.ico"
RMDir /REBOOTOK "$INSTDIR"
SectionEnd
# Local Variables:
# mode: sh
# End: