Merge branch 'develop' into quick-regression

examples/COUPLE/plugin/liblammpsplugin.c

@@ -41,7 +41,6 @@
 
 #include <stdlib.h>
 
-
 liblammpsplugin_t *liblammpsplugin_load(const char *lib)
 {
   liblammpsplugin_t *lmp;
@@ -191,6 +190,9 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
   ADDSYM(is_running);
   ADDSYM(force_timeout);
 
+  // symbol not present
+  if (!lmp->config_has_exceptions) return NULL;
+
   lmp->has_exceptions = lmp->config_has_exceptions();
   if (lmp->has_exceptions) {
     ADDSYM(has_error);

examples/PACKAGES/pace/plugin/paceplugin.nsis

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

examples/PACKAGES/plumed/plugin/CMakeLists.txt

@@ -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()

examples/PACKAGES/plumed/plugin/LAMMPSInterfacePlugin.cmake

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

examples/PACKAGES/plumed/plugin/PLUMED.cmake

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

examples/PACKAGES/plumed/plugin/README.txt

@@ -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

examples/PACKAGES/plumed/plugin/plumedplugin.cpp

@@ -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);
+}

examples/PACKAGES/plumed/plugin/plumedplugin.nsis

@@ -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:

examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized

@@ -44,6 +44,7 @@ thermo 50
 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
+  react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map rescale_charges yes
 
 fix 1 statted_grp_REACT nvt temp 300 300 100
 

examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability

@@ -47,7 +47,7 @@ thermo 50
 
 fix myrxns all bond/react stabilization yes statted_grp .03 &
   react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 &
-  react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234
+  react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234 rescale_charges yes
 
 fix 1 statted_grp_REACT nvt temp 300 300 100
 

examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized

@@ -44,7 +44,7 @@ thermo 50
 
 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
+  react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map rescale_charges yes
 
 fix 1 all nve/limit .03
 

examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_reacted.molecule_template

@@ -48,27 +48,6 @@ Types
      17 hc
      18 hc
 
-Charges
-
-      1 -0.300000
-      2  0.000000
-      3  0.000000
-      4  0.000000
-      5  0.000000
-      6  0.000000
-      7  0.000000
-      8  0.000000
-      9  0.000000
-     10  0.300000
-     11  0.000000
-     12  0.000000
-     13  0.000000
-     14  0.000000
-     15  0.000000
-     16  0.000000
-     17  0.000000
-     18  0.000000
-
 Molecules
 
       1      1

examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_reacted.molecule_template

@@ -44,21 +44,21 @@ Types
 
 Charges
 
-      1 -0.300000
-      2  0.000000
-      3  0.000000
-      4  0.410000
-      5  0.000000
-      6  0.000000
-      7  0.000000
-      8  0.000000
-      9  0.000000
-     10  0.300000
-     11  0.000000
-     12 -0.820000
-     13  0.000000
-     14  0.000000
-     15  0.410000
+      1 -0.60533
+      2 -0.01149
+      3 -0.76306
+      4 0.38
+      5 0.29346
+      6 0.18360
+      7 0.15396
+      8 -0.72636
+      9 -0.27437
+     10 0.40603
+     11 -0.65530
+     12 -0.76
+     13 0.21423
+     14 0.18949
+     15 0.38
 
 Molecules