convert plugin functionality into a package

cmake/CMakeLists.txt

@@ -113,7 +113,7 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
 
 set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
   GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS
-  QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
+  PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
   USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK
   USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
   USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
@@ -240,11 +240,6 @@ if(BUILD_OMP)
   target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
 endif()
 
-# link with -ldl or equivalent for plugin loading; except on Windows
-if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
-  target_link_libraries(lammps PRIVATE ${CMAKE_DL_LIBS})
-endif()
-
 # Compiler specific features for testing
 if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
   option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
@@ -538,6 +533,18 @@ foreach(PKG_WITH_INCL CORESHELL QEQ USER-OMP USER-SDPD KOKKOS OPT USER-INTEL GPU
   endif()
 endforeach()
 
+if(PKG_PLUGIN)
+  if(BUILD_SHARED_LIBS)
+    target_compile_definitions(lammps PRIVATE -DLMP_PLUGIN)
+  else()
+    message(WARNING "Plugin loading will not work unless BUILD_SHARED_LIBS is enabled")
+  endif()
+  # link with -ldl or equivalent for plugin loading; except on Windows
+  if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+    target_link_libraries(lammps PRIVATE ${CMAKE_DL_LIBS})
+  endif()
+endif()
+
 ######################################################################
 # the windows version of LAMMPS requires a couple extra libraries
 # and the MPI library - if use - has to be linked right before those

cmake/presets/most.cmake

@@ -4,7 +4,7 @@
 
 set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
         GRANULAR KSPACE MANYBODY MC MISC MLIAP MOLECULE OPT PERI
-        POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
+        PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
         USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
         USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC USER-MESODPD
         USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION

lib/README

@@ -19,39 +19,41 @@ atc           atomistic-to-continuum methods, USER-ATC package
                 from Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia)
 awpmd         antisymmetrized wave packet molecular dynamics, AWPMD package
                 from Ilya Valuev (JIHT RAS)
-colvars	      collective variable module (Metadynamics, ABF and more)
+colvars       collective variable module (Metadynamics, ABF and more)
                 from Giacomo Fiorin and Jerome Henin (ICMS, Temple U)
 compress      hook to system lib for performing I/O compression, COMPRESS pkg
-	        from Axel Kohlmeyer (Temple U)
-gpu	      general GPU routines, GPU package
-	        from Mike Brown (ORNL)
+                from Axel Kohlmeyer (Temple U)
+gpu           general GPU routines, GPU package
+                from Mike Brown (ORNL)
 h5md          ch5md library for output of MD data in HDF5 format
                 from Pierre de Buyl (KU Leuven)
 kim           hooks to the KIM library, used by KIM package
                 from Ryan Elliott and Ellad Tadmor (U Minn)
 kokkos        Kokkos package for GPU and many-core acceleration
                 from Kokkos development team (Sandia)
 linalg        set of BLAS and LAPACK routines needed by USER-ATC package
-	        from Axel Kohlmeyer (Temple U)
+                from Axel Kohlmeyer (Temple U)
 message       client/server communication library via MPI, sockets, files
-	        from Steve Plimpton (Sandia)
+                from Steve Plimpton (Sandia)
 molfile       hooks to VMD molfile plugins, used by the USER-MOLFILE package
                 from Axel Kohlmeyer (Temple U) and the VMD development team
 mscg          hooks to the MSCG library, used by fix_mscg command
                 from Jacob Wagner and Greg Voth group (U Chicago)
 netcdf        hooks to a NetCDF library installed on your system
                 from Lars Pastewka (Karlsruhe Institute of Technology)
-poems	      POEMS rigid-body integration package, POEMS package
+plugin        settings to load styles into LAMMPS from plugins
+                from Axel Kohlmeyer (Temple U)
+poems         POEMS rigid-body integration package, POEMS package
                 from Rudranarayan Mukherjee (RPI)
 python        hooks to the system Python library, used by the PYTHON package
                 from the LAMMPS development team
-qmmm	      quantum mechanics/molecular mechanics coupling interface
+qmmm          quantum mechanics/molecular mechanics coupling interface
                 from Axel Kohlmeyer (Temple U)
 quip          interface to QUIP/libAtoms framework, USER-QUIP package
                 from Albert Bartok-Partay and Gabor Csanyi (U Cambridge)
 smd           hooks to Eigen library, used by USER-SMD package
                 from Georg Ganzenmueller (Ernst Mach Institute, Germany)
 voronoi       hooks to the Voro++ library, used by compute voronoi/atom command
-	        from Daniel Schwen (LANL)
+                from Daniel Schwen (LANL)
 vtk           hooks to the VTK library, used by dump custom/vtk command
                 from Richard Berger (JKU)

lib/plugin/README

@@ -0,0 +1,16 @@
+This directory has a Makefile.lammps file with settings that allows
+LAMMPS to dynamically link LAMMPS plugins. More details about this
+are in the manual.
+
+In order to be able to dynamically load and execute the plugins from
+inside LAMMPS, you need to link with a system library containing functions
+like dlopen(), dlsym() and so on for dynamic linking of executable code
+into an executable.  This library is defined by setting the plugin_SYSLIB
+variable in the Makefile.lammps file in this dir.  For this mechanism
+to work, LAMMPS must be built as a shared library (i.e. with mode=shared).
+
+For Linux and most current unix-like operating systems, this can be
+kept at the default setting of "-ldl" (on some platforms this library
+is called "-ldld").  The Windows platform is currently not supported.
+
+See the header of Makefile.lammps for more info.

src/.gitignore

@@ -172,6 +172,10 @@
 /pair_lj_charmmfsw_coul_long.cpp
 /pair_lj_charmmfsw_coul_long.h
 
+/plugin.cpp
+/plugin.h
+/lammpsplugin.h
+
 /atom_vec_spin.cpp
 /atom_vec_spin.h
 /compute_spin.cpp

src/MAKE/Makefile.mpi

@@ -13,7 +13,7 @@ DEPFLAGS =	-M
 
 LINK =		mpicxx
 LINKFLAGS =	-g -O3
-LIB = -ldl
+LIB =
 SIZE =		size
 
 ARCHIVE =	ar

src/MAKE/Makefile.serial

@@ -13,7 +13,7 @@ DEPFLAGS =	-M
 
 LINK =		g++
 LINKFLAGS =	-g -O
-LIB = -ldl
+LIB =
 SIZE =		size
 
 ARCHIVE =	ar

src/Makefile

@@ -48,7 +48,7 @@ endif
 
 PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
 	  granular kim kokkos kspace latte manybody mc message misc \
-	  mliap molecule mpiio mscg opt peri poems \
+	  mliap molecule mpiio mscg opt peri plugin poems \
 	  python qeq replica rigid shock snap spin srd voronoi
 
 PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \

src/PLUGIN/Install.sh

@@ -0,0 +1,64 @@
+# Install/unInstall package files in LAMMPS
+# mode = 0/1/2 for uninstall/install/update
+
+mode=$1
+
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
+# arg1 = file, arg2 = file it depends on
+
+action () {
+  if (test $mode = 0) then
+    rm -f ../$1
+  elif (! cmp -s $1 ../$1) then
+    if (test -z "$2" || test -e ../$2) then
+      cp $1 ..
+      if (test $mode = 2) then
+        echo "  updating src/$1"
+      fi
+    fi
+  elif (test -n "$2") then
+    if (test ! -e ../$2) then
+      rm -f ../$1
+    fi
+  fi
+}
+
+# all package files with no dependencies
+
+for file in *.cpp *.h; do
+  test -f ${file} && action $file
+done
+
+# edit 2 Makefile.package files to include/exclude package info
+
+if (test $1 = 1) then
+
+  if (test -e ../Makefile.package) then
+    sed -i -e 's/[^ \t]*plugin[^ \t]* //' ../Makefile.package
+    sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(plugin_SYSINC) |' ../Makefile.package
+    sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(plugin_SYSLIB) |' ../Makefile.package
+    sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(plugin_SYSPATH) |' ../Makefile.package
+  fi
+
+  if (test -e ../Makefile.package.settings) then
+    sed -i -e '/^include.*plugin.*$/d' ../Makefile.package.settings
+    # multiline form needed for BSD sed on Macs
+    sed -i -e '4 i \
+include ..\/..\/lib\/plugin\/Makefile.lammps
+' ../Makefile.package.settings
+  fi
+
+elif (test $1 = 0) then
+
+  if (test -e ../Makefile.package) then
+    sed -i -e 's/[^ \t]*plugin[^ \t]* //' ../Makefile.package
+  fi
+
+  if (test -e ../Makefile.package.settings) then
+    sed -i -e '/^include.*plugin.*$/d' ../Makefile.package.settings
+  fi
+
+fi

src/PLUGIN/README

@@ -0,0 +1,12 @@
+This package provides a plugin command that can load LAMMPS
+styles linked into shared object files into a LAMMPS binary
+at run time without having to recompile and relink LAMMPS.
+For more details please see the LAMMPS manual.
+
+To be able to dynamically load and execute the plugins from inside
+LAMMPS, you need to link with an appropriate system library, which
+is done using the settings in lib/plugin/Makefile.lammps.  See
+that file and the lib/plugin/README file for more details.
+
+The person who created this package is Axel Kohlmeyer at Temple U
+(akohlmey at gmail.com).  Contact him directly if you have questions.

src/plugin.cpp → src/PLUGIN/plugin.cpp

@@ -38,9 +38,53 @@ namespace LAMMPS_NS
   // map for counting references to dso handles
   static std::map<void *, int> dso_refcounter;
 
+
+/* ---------------------------------------------------------------------- */
+
+  Plugin::Plugin(LAMMPS *lmp) : Pointers(lmp) {}
+
+/* ---------------------------------------------------------------------- */
+
+  void Plugin::command(int narg, char **arg)
+  {
+    if (narg < 1) error->all(FLERR,"Illegal plugin command");
+
+#if defined(LMP_PLUGIN)
+    std::string cmd = arg[0];
+    if (cmd == "load") {
+      if (narg < 2) error->all(FLERR,"Illegal plugin load command");
+      for (int i=1; i < narg; ++i)
+        plugin_load(arg[i],lmp);
+
+    } else if (cmd == "unload") {
+      if (narg != 3) error->all(FLERR,"Illegal plugin unload command");
+      plugin_unload(arg[1],arg[2],lmp);
+
+    } else if (cmd == "clear") {
+      plugin_clear(lmp);
+
+    } else if (cmd == "list") {
+      if (comm->me == 0) {
+        int num = plugin_get_num_plugins();
+        utils::logmesg(lmp,"Currently loaded plugins\n");
+        for (int i=0; i < num; ++i) {
+          auto entry = plugin_get_info(i);
+          utils::logmesg(lmp,fmt::format("{:4}: {} style plugin {}\n",
+                                         i+1,entry->style,entry->name));
+        }
+      }
+    } else error->all(FLERR,"Illegal plugin command");
+#else
+    if (comm->me == 0)
+      error->warning(FLERR,"Ignoring plugin command. LAMMPS must be built as "
+                     "a shared library for it to work.");
+#endif
+  }
+
   // load DSO and call included registration function
   void plugin_load(const char *file, LAMMPS *lmp)
   {
+#if defined(LMP_PLUGIN)
     int me = lmp->comm->me;
 #if defined(WIN32)
     lmp->error->all(FLERR,"Loading of plugins on Windows is not supported\n");
@@ -77,6 +121,7 @@ namespace LAMMPS_NS
 
     (*(lammpsplugin_initfunc)(initfunc))((void *)lmp, dso,
                                          (void *)&plugin_register);
+#endif
 #endif
   }
 
@@ -89,6 +134,7 @@ namespace LAMMPS_NS
 
   void plugin_register(lammpsplugin_t *plugin, void *ptr)
   {
+#if defined(LMP_PLUGIN)
     LAMMPS *lmp = (LAMMPS *)ptr;
     int me = lmp->comm->me;
 
@@ -158,6 +204,7 @@ namespace LAMMPS_NS
                                      "yet implemented\n",pstyle));
       pluginlist.pop_back();
     }
+#endif
   }
 
   /* --------------------------------------------------------------------
@@ -168,6 +215,7 @@ namespace LAMMPS_NS
 
   void plugin_unload(const char *style, const char *name, LAMMPS *lmp)
   {
+#if defined(LMP_PLUGIN)
     int me = lmp->comm->me;
 
     // ignore unload request from unsupported style categories
@@ -246,6 +294,7 @@ namespace LAMMPS_NS
       dlclose(handle);
 #endif
     }
+#endif
   }
 
   /* --------------------------------------------------------------------

src/plugin.h → src/PLUGIN/plugin.h

@@ -11,14 +11,26 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#ifdef COMMAND_CLASS
+
+CommandStyle(plugin,Plugin)
+
+#else
+
 #ifndef LMP_PLUGIN_H
 #define LMP_PLUGIN_H
 
 #include "lammpsplugin.h"
+#include "pointers.h"
 
 namespace LAMMPS_NS
 {
-  class LAMMPS;
+
+  class Plugin : protected Pointers {
+  public:
+    Plugin(class LAMMPS *);
+    void command(int, char **);
+  };
 
   void plugin_load(const char *, LAMMPS *);
   void plugin_register(lammpsplugin_t *, void *);
@@ -33,3 +45,4 @@ namespace LAMMPS_NS
 }
 
 #endif
+#endif