add restart support to fix temp/rescale, fix spring/chunk, and fix spring/rg

doc/src/fix_spring_chunk.rst

@@ -50,7 +50,16 @@ atom.
 
 **Restart, fix_modify, output, run start/stop, minimize info:**
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+This fix writes the locations of the initial per-chunk center of mass
+coordinates to :doc:`binary restart files <restart>`.  See the
+:doc:`read_restart <read_restart>` command for info on how to
+re-specify a fix in an input script that reads a restart file, so that
+the fix continues in an uninterrupted fashion.  Since this fix depends
+on an instance of :doc:`compute chunk/atom <compute_chunk_atom>`
+it will check when reading the restart if the chunk still exists and
+will define the same number of chunks. The restart data is only applied
+when the number of chunks matches. Otherwise the center of mass
+coordinates are recomputed.
 
 The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
 fix to add the energy stored in all the springs to the system's potential

doc/src/fix_spring_rg.rst

@@ -59,9 +59,20 @@ the time the fix is specified, and that value is used as the target.
 
 **Restart, fix_modify, output, run start/stop, minimize info:**
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
+This fix writes the currently used reference RG (:math:`R_{G0}`) to
-are relevant to this fix.  No global or per-atom quantities are stored
+:doc:`binary restart files <restart>`.  See the :doc:`read_restart
-by this fix for access by various :doc:`output commands <Howto_output>`.
+<read_restart>` command for info on how to re-specify a fix in an input
+script that reads a restart file, so that the fix continues in an
+uninterrupted fashion.
+
+None of the :doc:`fix_modify <fix_modify>` options
+are relevant to this fix.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the reference
+radius of gyration :math:`R_{G0}` used by the fix.  energy change due to
+this fix.  The scalar value calculated by this fix is "intensive".
+
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
 

doc/src/fix_temp_rescale.rst

@@ -126,7 +126,11 @@ thermal degrees of freedom, and the bias is added back in.
 
 **Restart, fix_modify, output, run start/stop, minimize info:**
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+This fix writes the cumulative global energy change to :doc:`binary
+restart files <restart>`.  See the :doc:`read_restart <read_restart>`
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the fix continues in an uninterrupted
+fashion.
 
 The :doc:`fix_modify <fix_modify>` *temp* option is supported by this
 fix.  You can use it to assign a temperature :doc:`compute <compute>`
@@ -136,7 +140,8 @@ this fix and by the compute should be the same.
 
 The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
 fix to add the energy change implied by a velocity rescaling to the
-system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+system's potential energy as part of :doc:`thermodynamic output
+<thermo_style>`.
 
 This fix computes a global scalar which can be accessed by various
 :doc:`output commands <Howto_output>`.  The scalar is the cumulative

src/fix_spring_chunk.cpp

@@ -15,6 +15,7 @@
 #include <cmath>
 #include <cstring>
 #include "atom.h"
+#include "comm.h"
 #include "update.h"
 #include "force.h"
 #include "respa.h"
@@ -37,6 +38,7 @@ FixSpringChunk::FixSpringChunk(LAMMPS *lmp, int narg, char **arg) :
 {
   if (narg != 6) error->all(FLERR,"Illegal fix spring/chunk command");
 
+  restart_global = 1;
   scalar_flag = 1;
   global_freq = 1;
   extscalar = 1;
@@ -241,6 +243,58 @@ void FixSpringChunk::min_post_force(int vflag)
   post_force(vflag);
 }
 
+/* ----------------------------------------------------------------------
+   writ number of chunks and position of original COM into restart
+------------------------------------------------------------------------- */
+
+void FixSpringChunk::write_restart(FILE *fp)
+{
+  double n = nchunk;
+
+  if (comm->me == 0) {
+    int size = (3*n+1) * sizeof(double);
+    fwrite(&size,sizeof(int),1,fp);
+    fwrite(&n,sizeof(double),1,fp);
+    fwrite(&com0[0][0],3*sizeof(double),nchunk,fp);
+  }
+}
+
+/* ----------------------------------------------------------------------
+   use state info from restart file to restart the Fix
+------------------------------------------------------------------------- */
+
+void FixSpringChunk::restart(char *buf)
+{
+  double *list = (double *) buf;
+  int n = list[0];
+
+  memory->destroy(com0);
+  memory->destroy(fcom);
+
+  int icompute = modify->find_compute(idchunk);
+  if (icompute < 0)
+    error->all(FLERR,"Chunk/atom compute does not exist for fix spring/chunk");
+  cchunk = (ComputeChunkAtom *) modify->compute[icompute];
+  if (strcmp(cchunk->style,"chunk/atom") != 0)
+    error->all(FLERR,"Fix spring/chunk does not use chunk/atom compute");
+  nchunk = cchunk->setup_chunks();
+  cchunk->compute_ichunk();
+  memory->create(com0,nchunk,3,"spring/chunk:com0");
+  memory->create(fcom,nchunk,3,"spring/chunk:fcom");
+  printf("restart chunks:%d  computed chunks: %d\n",n,nchunk);
+
+  if (n != nchunk) {
+    if (comm->me == 0)
+      error->warning(FLERR,"Number of chunks has changed. Cannot use restart");
+    memory->destroy(com0);
+    memory->destroy(fcom);
+    nchunk = 1;
+  } else {
+    cchunk->lock(this,update->ntimestep,-1);
+    memcpy(&com0[0][0],list+1,3*n*sizeof(double));
+  }
+}
+
 /* ----------------------------------------------------------------------
    energy of stretched spring
 ------------------------------------------------------------------------- */

src/fix_spring_chunk.h

@@ -35,6 +35,8 @@ class FixSpringChunk : public Fix {
   void post_force(int);
   void post_force_respa(int, int, int);
   void min_post_force(int);
+  void write_restart(FILE *);
+  void restart(char *);
   double compute_scalar();
 
  private:

src/fix_spring_rg.cpp

@@ -19,6 +19,7 @@
 #include "fix_spring_rg.h"
 #include <cstring>
 #include "atom.h"
+#include "comm.h"
 #include "update.h"
 #include "group.h"
 #include "respa.h"
@@ -41,6 +42,9 @@ FixSpringRG::FixSpringRG(LAMMPS *lmp, int narg, char **arg) :
   if (strcmp(arg[4],"NULL") == 0) rg0_flag = 1;
   else rg0 = force->numeric(FLERR,arg[4]);
 
+  restart_global = 1;
+  scalar_flag = 1;
+  restart_global = 1;
   dynamic_group_allow = 1;
   respa_level_support = 1;
   ilevel_respa = 0;
@@ -144,3 +148,43 @@ void FixSpringRG::post_force_respa(int vflag, int ilevel, int /*iloop*/)
 {
   if (ilevel == ilevel_respa) post_force(vflag);
 }
+
+/* ----------------------------------------------------------------------
+   pack entire state of Fix into one write
+------------------------------------------------------------------------- */
+
+void FixSpringRG::write_restart(FILE *fp)
+{
+  int n = 0;
+  double list[1];
+  list[n++] = rg0;
+
+  if (comm->me == 0) {
+    int size = n * sizeof(double);
+    fwrite(&size,sizeof(int),1,fp);
+    fwrite(list,sizeof(double),n,fp);
+  }
+}
+
+/* ----------------------------------------------------------------------
+   use state info from restart file to restart the Fix
+------------------------------------------------------------------------- */
+
+void FixSpringRG::restart(char *buf)
+{
+  int n = 0;
+  double *list = (double *) buf;
+
+  rg0 = list[n++];
+  rg0_flag = 0;
+}
+
+
+/* ----------------------------------------------------------------------
+   return reference radius of gyration
+------------------------------------------------------------------------- */
+
+double FixSpringRG::compute_scalar()
+{
+  return rg0;
+}

src/fix_spring_rg.h

@@ -32,6 +32,9 @@ class FixSpringRG : public Fix {
   void setup(int);
   void post_force(int);
   void post_force_respa(int, int, int);
+  void write_restart(FILE *);
+  void restart(char *);
+  double compute_scalar();
 
  private:
   int ilevel_respa,rg0_flag;

src/fix_temp_rescale.cpp

@@ -44,6 +44,7 @@ FixTempRescale::FixTempRescale(LAMMPS *lmp, int narg, char **arg) :
   nevery = force->inumeric(FLERR,arg[3]);
   if (nevery <= 0) error->all(FLERR,"Illegal fix temp/rescale command");
 
+  restart_global = 1;
   scalar_flag = 1;
   global_freq = nevery;
   extscalar = 1;
@@ -238,6 +239,35 @@ double FixTempRescale::compute_scalar()
   return energy;
 }
 
+/* ----------------------------------------------------------------------
+   pack entire state of Fix into one write
+------------------------------------------------------------------------- */
+
+void FixTempRescale::write_restart(FILE *fp)
+{
+  int n = 0;
+  double list[1];
+  list[n++] = energy;
+
+  if (comm->me == 0) {
+    int size = n * sizeof(double);
+    fwrite(&size,sizeof(int),1,fp);
+    fwrite(list,sizeof(double),n,fp);
+  }
+}
+
+/* ----------------------------------------------------------------------
+   use state info from restart file to restart the Fix
+------------------------------------------------------------------------- */
+
+void FixTempRescale::restart(char *buf)
+{
+  int n = 0;
+  double *list = (double *) buf;
+
+  energy = list[n++];
+}
+
 /* ----------------------------------------------------------------------
    extract thermostat properties
 ------------------------------------------------------------------------- */

src/fix_temp_rescale.h

@@ -34,6 +34,8 @@ class FixTempRescale : public Fix {
   int modify_param(int, char **);
   void reset_target(double);
   double compute_scalar();
+  void write_restart(FILE *);
+  void restart(char *buf);
   virtual void *extract(const char *, int &);
 
  protected: