add support for loading plugins for fixes

doc/src/Developer_plugins.rst

@@ -57,17 +57,54 @@ function would look like this:
     plugin.name    = "morse2";
     plugin.info    = "Morse2 variant pair style v1.0";
     plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
-    plugin.creator = (lammpsplugin_factory *) &morse2creator;
+    plugin.creator1 = (lammpsplugin_factory1 *) &morse2creator;
+    plugin.creator2 = nullptr;
     plugin.handle  = handle;
     (*register_plugin)(&plugin,lmp);
   }
 
 The factory function in this example is called ``morse2creator()``.  It
-receives a pointer to the LAMMPS class as argument and returns a
+receives a pointer to the LAMMPS class as only argument and thus has to
+be assigned to the *creator1* member of the plugin struct and cast to the
+``lammpsplugin_factory1`` pointer type.  It returns a
 pointer to the allocated class instance derived from the ``Pair`` class.
 This function may be declared static to avoid clashes with other plugins.
 The name of the derived class, ``PairMorse2``, must be unique inside
 the entire LAMMPS executable.
+If the factory function would be for a fix or compute, which take three
+arguments (a pointer to the LAMMPS class, the number of arguments and the
+list of argument strings), then the pointer type is ``lammpsplugin_factory2``
+and it must be assigned to the *creator2* member of the plugin struct.
+Below is an example for that:
+
+.. code-block:: C++
+
+  #include "lammpsplugin.h"
+  #include "version.h"
+  #include "fix_nve2.h"
+
+  using namespace LAMMPS_NS;
+
+  static Fix *nve2creator(LAMMPS *lmp, int argc, char **argv)
+  {
+    return new FixNVE2(lmp,argc,argv);
+  }
+
+  extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
+  {
+    lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
+    lammpsplugin_t plugin;
+
+    plugin.version = LAMMPS_VERSION;
+    plugin.style   = "fix";
+    plugin.name    = "nve2";
+    plugin.info    = "NVE2 variant fix style v1.0";
+    plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
+    plugin.creator1 = nullptr;
+    plugin.creator2 = (lammpsplugin_factory2 *) &nve2creator;
+    plugin.handle  = handle;
+    (*register_plugin)(&plugin,lmp);
+  }
 
 The initialization function **must** be called ``lammpsplugin_init``, it
 **must** have C bindings and it takes three void pointers as arguments.

examples/plugins/Makefile

@@ -2,9 +2,14 @@ CXX=mpicxx
 CXXFLAGS=-I../../src -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP -fopenmp
 LD=$(CXX) -shared -rdynamic -fopenmp
 
+default: morse2plugin.so nve2plugin.so
+
 morse2plugin.so: morse2plugin.o pair_morse2.o pair_morse2_omp.o
 	$(LD) -o $@ $^
 
+nve2plugin.so: nve2plugin.o fix_nve2.o
+	$(LD) -o $@ $^
+
 .cpp.o:
 	$(CXX) -o $@ $(CXXFLAGS) -c $<
 
@@ -12,6 +17,9 @@ pair_morse2.o: pair_morse2.cpp pair_morse2.h
 pair_morse2_omp.o: pair_morse2_omp.cpp pair_morse2_omp.h pair_morse2.h
 morse2plugin.o: morse2plugin.cpp pair_morse2.h pair_morse2_omp.h
 
+fix_nve2.o: fix_nve2.cpp fix_nve2.h
+nve2plugin.o: nve2plugin.cpp fix_nve2.h
+
 clean:
 	rm -f *~ *.so *.o log.lammps
 

examples/plugins/fix_nve2.cpp

@@ -0,0 +1,171 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://lammps.sandia.gov/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "fix_nve2.h"
+#include <cstring>
+#include "atom.h"
+#include "force.h"
+#include "update.h"
+#include "respa.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+/* ---------------------------------------------------------------------- */
+
+FixNVE2::FixNVE2(LAMMPS *lmp, int narg, char **arg) :
+  Fix(lmp, narg, arg)
+{
+  if (strcmp(style,"nve/sphere") != 0 && narg < 3)
+    error->all(FLERR,"Illegal fix nve command");
+
+  dynamic_group_allow = 1;
+  time_integrate = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixNVE2::setmask()
+{
+  int mask = 0;
+  mask |= INITIAL_INTEGRATE;
+  mask |= FINAL_INTEGRATE;
+  mask |= INITIAL_INTEGRATE_RESPA;
+  mask |= FINAL_INTEGRATE_RESPA;
+  return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNVE2::init()
+{
+  dtv = update->dt;
+  dtf = 0.5 * update->dt * force->ftm2v;
+
+  if (strstr(update->integrate_style,"respa"))
+    step_respa = ((Respa *) update->integrate)->step;
+}
+
+/* ----------------------------------------------------------------------
+   allow for both per-type and per-atom mass
+------------------------------------------------------------------------- */
+
+void FixNVE2::initial_integrate(int /*vflag*/)
+{
+  double dtfm;
+
+  // update v and x of atoms in group
+
+  double **x = atom->x;
+  double **v = atom->v;
+  double **f = atom->f;
+  double *rmass = atom->rmass;
+  double *mass = atom->mass;
+  int *type = atom->type;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+  if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+  if (rmass) {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+        dtfm = dtf / rmass[i];
+        v[i][0] += dtfm * f[i][0];
+        v[i][1] += dtfm * f[i][1];
+        v[i][2] += dtfm * f[i][2];
+        x[i][0] += dtv * v[i][0];
+        x[i][1] += dtv * v[i][1];
+        x[i][2] += dtv * v[i][2];
+      }
+
+  } else {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+        dtfm = dtf / mass[type[i]];
+        v[i][0] += dtfm * f[i][0];
+        v[i][1] += dtfm * f[i][1];
+        v[i][2] += dtfm * f[i][2];
+        x[i][0] += dtv * v[i][0];
+        x[i][1] += dtv * v[i][1];
+        x[i][2] += dtv * v[i][2];
+      }
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNVE2::final_integrate()
+{
+  double dtfm;
+
+  // update v of atoms in group
+
+  double **v = atom->v;
+  double **f = atom->f;
+  double *rmass = atom->rmass;
+  double *mass = atom->mass;
+  int *type = atom->type;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+  if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+  if (rmass) {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+        dtfm = dtf / rmass[i];
+        v[i][0] += dtfm * f[i][0];
+        v[i][1] += dtfm * f[i][1];
+        v[i][2] += dtfm * f[i][2];
+      }
+
+  } else {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+        dtfm = dtf / mass[type[i]];
+        v[i][0] += dtfm * f[i][0];
+        v[i][1] += dtfm * f[i][1];
+        v[i][2] += dtfm * f[i][2];
+      }
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNVE2::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
+{
+  dtv = step_respa[ilevel];
+  dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
+
+  // innermost level - NVE update of v and x
+  // all other levels - NVE update of v
+
+  if (ilevel == 0) initial_integrate(vflag);
+  else final_integrate();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNVE2::final_integrate_respa(int ilevel, int /*iloop*/)
+{
+  dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
+  final_integrate();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNVE2::reset_dt()
+{
+  dtv = update->dt;
+  dtf = 0.5 * update->dt * force->ftm2v;
+}

examples/plugins/fix_nve2.h

@@ -0,0 +1,58 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(nve2,FixNVE2)
+
+#else
+
+#ifndef LMP_FIX_NVE2_H
+#define LMP_FIX_NVE2_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixNVE2 : public Fix {
+ public:
+  FixNVE2(class LAMMPS *, int, char **);
+  virtual ~FixNVE2() {}
+  int setmask();
+  virtual void init();
+  virtual void initial_integrate(int);
+  virtual void final_integrate();
+  virtual void initial_integrate_respa(int, int, int);
+  virtual void final_integrate_respa(int, int);
+  virtual void reset_dt();
+
+ protected:
+  double dtv,dtf;
+  double *step_respa;
+  int mass_require;
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+*/

examples/plugins/morse2plugin.cpp

@@ -31,13 +31,14 @@ extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
   plugin.name    = "morse2";
   plugin.info    = "Morse2 variant pair style v1.0";
   plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
-  plugin.creator = (lammpsplugin_factory *) &morse2creator;
+  plugin.creator1 = (lammpsplugin_factory1 *) &morse2creator;
+  plugin.creator2 = nullptr;
   plugin.handle  = handle;
   (*register_plugin)(&plugin,lmp);
 
   // also register morse2/omp pair style. only need to update changed fields
   plugin.name    = "morse2/omp";
   plugin.info    = "Morse2 variant pair style for OpenMP v1.0";
-  plugin.creator = (lammpsplugin_factory *) &morse2ompcreator;
+  plugin.creator1 = (lammpsplugin_factory1 *) &morse2ompcreator;
   (*register_plugin)(&plugin,lmp);
 }

examples/plugins/nve2plugin.cpp

@@ -0,0 +1,30 @@
+
+#include "lammpsplugin.h"
+
+#include "version.h"
+
+#include <cstring>
+
+#include "fix_nve2.h"
+
+using namespace LAMMPS_NS;
+
+static Fix *nve2creator(LAMMPS *lmp, int argc, char **argv)
+{
+    return new FixNVE2(lmp, argc, argv);
+}
+
+extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
+{
+  lammpsplugin_t plugin;
+  lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
+
+  plugin.version = LAMMPS_VERSION;
+  plugin.style   = "fix";
+  plugin.name    = "nve2";
+  plugin.info    = "NVE2 variant fix style v1.0";
+  plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
+  plugin.creator2 = (lammpsplugin_factory2 *) &nve2creator;
+  plugin.handle  = handle;
+  (*register_plugin)(&plugin,lmp);
+}

src/lammpsplugin.h

@@ -18,7 +18,8 @@
 
 extern "C" {
 
-  typedef void *(lammpsplugin_factory)(void *);
+  typedef void *(lammpsplugin_factory1)(void *);
+  typedef void *(lammpsplugin_factory2)(void *, int, char **);
 
   typedef struct {
     const char *version;
@@ -26,7 +27,8 @@ extern "C" {
     const char *name;
     const char *info;
     const char *author;
-    lammpsplugin_factory *creator;
+    lammpsplugin_factory1 *creator1;
+    lammpsplugin_factory2 *creator2;
     void *handle;
   } lammpsplugin_t;
 

src/plugin.cpp

@@ -114,7 +114,17 @@ namespace LAMMPS_NS
                                                 plugin->name));
       }
 
-      (*pair_map)[plugin->name] = (Force::PairCreator)plugin->creator;
+      (*pair_map)[plugin->name] = (Force::PairCreator)plugin->creator1;
+    } else if (pstyle == "fix") {
+      auto fix_map = lmp->modify->fix_map;
+      if (fix_map->find(plugin->name) != fix_map->end()) {
+        if (lmp->comm->me == 0)
+          lmp->error->warning(FLERR,fmt::format("Overriding built-in fix "
+                                                "style {} from plugin",
+                                                plugin->name));
+      }
+
+      (*fix_map)[plugin->name] = (Modify::FixCreator)plugin->creator2;
     } else {
       utils::logmesg(lmp,fmt::format("Loading plugin for {} styles not "
                                      "yet implemented\n",pstyle));