add flag "reinit" with args "yes" / "no" to fixes rigid & rigid/small

src/RIGID/fix_rigid.cpp

@@ -267,6 +267,8 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
 
   int seed;
   langflag = 0;
+  reinitflag = 1;
+
   tstat_flag = 0;
   pstat_flag = 0;
   allremap = 1;
@@ -501,6 +503,14 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
       infile = new char[n];
       strcpy(infile,arg[iarg+1]);
       restart_file = 1;
+      reinitflag = 0;
+      iarg += 2;
+
+    } else if (strcmp(arg[iarg],"reinit") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
+      if (strcmp("yes",arg[iarg+1]) == 0) reinitflag = 1;
+      else if  (strcmp("no",arg[iarg+1]) == 0) reinitflag = 0;
+      else error->all(FLERR,"Illegal fix rigid command");
       iarg += 2;
 
     } else error->all(FLERR,"Illegal fix rigid command");
@@ -679,15 +689,15 @@ void FixRigid::init()
   if (strstr(update->integrate_style,"respa"))
     step_respa = ((Respa *) update->integrate)->step;
 
-  // setup rigid bodies, using current atom info
+  // setup rigid bodies, using current atom info. if reinitflag is not set,
-  // only do initialization once, b/c properties may not be re-computable
+  // do the initialization only once, b/c properties may not be re-computable
-  //   especially if overlapping particles
+  // especially if overlapping particles.
-  // do not do dynamic init if read body properties from infile
+  //   do not do dynamic init if read body properties from infile.
-  //   this is b/c the infile defines the static and dynamic properties
+  // this is b/c the infile defines the static and dynamic properties and may
-  //   and may not be computable if contain overlapping particles
+  // not be computable if contain overlapping particles.
   //   setup_bodies_static() reads infile itself
 
-  if (!setupflag) {
+  if (reinitflag || !setupflag) {
     setup_bodies_static();
     if (!infile) setup_bodies_dynamic();
     setupflag = 1;

src/RIGID/fix_rigid.h

@@ -104,6 +104,7 @@ class FixRigid : public Fix {
   int extended;             // 1 if any particles have extended attributes
   int orientflag;           // 1 if particles store spatial orientation
   int dorientflag;          // 1 if particles store dipole orientation
+  int reinitflag;           // 1 if re-initialize rigid bodies between runs
 
   imageint *xcmimage;       // internal image flags for atoms in rigid bodies
                             // set relative to in-box xcm of each body

src/RIGID/fix_rigid_small.cpp

@@ -138,6 +138,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
   langflag = 0;
   infile = NULL;
   onemols = NULL;
+  reinitflag = 1;
 
   tstat_flag = 0;
   pstat_flag = 0;
@@ -173,6 +174,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
         error->all(FLERR,"Fix rigid/small langevin period must be > 0.0");
       if (seed <= 0) error->all(FLERR,"Illegal fix rigid/small command");
       iarg += 5;
+
     } else if (strcmp(arg[iarg],"infile") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
       delete [] infile;
@@ -180,7 +182,16 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
       infile = new char[n];
       strcpy(infile,arg[iarg+1]);
       restart_file = 1;
+      reinitflag = 0;
       iarg += 2;
+
+    } else if (strcmp(arg[iarg],"reinit") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
+      if (strcmp("yes",arg[iarg+1]) == 0) reinitflag = 1;
+      else if  (strcmp("no",arg[iarg+1]) == 0) reinitflag = 0;
+      else error->all(FLERR,"Illegal fix rigid/small command");
+      iarg += 2;
+
     } else if (strcmp(arg[iarg],"mol") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
       int imol = atom->find_molecule(arg[iarg+1]);
@@ -520,14 +531,15 @@ void FixRigidSmall::init()
 }
 
 /* ----------------------------------------------------------------------
-   setup static/dynamic properties of rigid bodies, using current atom info
+   setup static/dynamic properties of rigid bodies, using current atom info.
-   only do initialization once, b/c properties may not be re-computable
+   if reinitflag is not set, do the initialization only once, b/c properties
-     especially if overlapping particles or bodies inserted from mol template
+   may not be re-computable especially if overlapping particles or bodies
-   do not do dynamic init if read body properties from infile
+   are inserted from mol template.
-     this is b/c the infile defines the static and dynamic properties
+     do not do dynamic init if read body properties from infile. this
-     and may not be computable if contain overlapping particles
+   is b/c the infile defines the static and dynamic properties and may not
-     setup_bodies_static() reads infile itself
+   be computable if contain overlapping particles setup_bodies_static()
-   cannot do this until now, b/c requires comm->setup() to have setup stencil
+   reads infile itself.
+     cannot do this until now, b/c requires comm->setup() to have setup stencil
    invoke pre_neighbor() to insure body xcmimage flags are reset
      needed if Verlet::setup::pbc() has remapped/migrated atoms for 2nd run
      setup_bodies_static() invokes pre_neighbor itself
@@ -535,9 +547,13 @@ void FixRigidSmall::init()
 
 void FixRigidSmall::setup_pre_neighbor()
 {
-  if (!setupflag) setup_bodies_static();
+  if (reinitflag || !setupflag)
+    setup_bodies_static();
   else pre_neighbor();
-  if (!setupflag && !infile) setup_bodies_dynamic();
+
+  if ((reinitflag || !setupflag) && !infile)
+    setup_bodies_dynamic();
+
   setupflag = 1;
 }
 

src/RIGID/fix_rigid_small.h

@@ -131,6 +131,7 @@ class FixRigidSmall : public Fix {
   int extended;         // 1 if any particles have extended attributes
   int orientflag;       // 1 if particles store spatial orientation
   int dorientflag;      // 1 if particles store dipole orientation
+  int reinitflag;       // 1 if re-initialize rigid bodies between runs
 
   int POINT,SPHERE,ELLIPSOID,LINE,TRIANGLE,DIPOLE;   // bitmasks for eflags
   int OMEGA,ANGMOM,TORQUE;