git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12133 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/lammps.cpp

@@ -80,6 +80,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
   int cudaflag = 0;
   int kokkosflag = 0;
   int restartflag = 0;
+  int restartremapflag = 0;
   int citeflag = 1;
   int helpflag = 0;
 
@@ -188,6 +189,14 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
       restartflag = 1;
       rfile = arg[iarg+1];
       dfile = arg[iarg+2];
+      // check for restart remap flag
+      if (strcmp(dfile,"remap") == 0) {
+        if (iarg+4 > narg)
+          error->universe_all(FLERR,"Invalid command-line argument");
+        restartremapflag = 1;
+        dfile = arg[iarg+3];
+        iarg++;
+      }
       iarg += 3;
       // delimit any extra args for the write_data command
       wdfirst = iarg;
@@ -481,6 +490,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
   if (restartflag) {
     char cmd[128];
     sprintf(cmd,"read_restart %s\n",rfile);
+    if (restartremapflag) strcat(cmd," remap\n");
     input->one(cmd);
     sprintf(cmd,"write_data %s",dfile);
     for (iarg = wdfirst; iarg < wdlast; iarg++)

src/read_restart.cpp

@@ -73,7 +73,7 @@ ReadRestart::ReadRestart(LAMMPS *lmp) : Pointers(lmp) {}
 
 void ReadRestart::command(int narg, char **arg)
 {
-  if (narg != 1) error->all(FLERR,"Illegal read_restart command");
+  if (narg != 1 && narg != 2) error->all(FLERR,"Illegal read_restart command");
 
   if (domain->box_exist)
     error->all(FLERR,"Cannot read_restart after simulation box is defined");
@@ -81,6 +81,14 @@ void ReadRestart::command(int narg, char **arg)
   MPI_Comm_rank(world,&me);
   MPI_Comm_size(world,&nprocs);
 
+  // check for remap option
+
+  int remapflag = 0;
+  if (narg == 2) {
+    if (strcmp(arg[1],"remap") == 0) remapflag = 1;
+    else error->all(FLERR,"Illegal read_restart command");
+  }
+
   // if filename contains "*", search dir for latest restart file
 
   char *file = new char[strlen(arg[0]) + 16];
@@ -204,11 +212,13 @@ void ReadRestart::command(int narg, char **arg)
   // nprocs_file = # of chunks in file
   // proc 0 reads a chunk and bcasts it to other procs
   // each proc unpacks the atoms, saving ones in it's sub-domain
+  // if remapflag set, remap the atom to box before checking sub-domain
   // check for atom in sub-domain differs for orthogonal vs triclinic box
 
   else if (multiproc == 0) {
 
     int triclinic = domain->triclinic;
+    imageint *iptr;
     double *x,lamda[3];
     double *coord,*sublo,*subhi;
     if (triclinic == 0) {
@@ -234,6 +244,11 @@ void ReadRestart::command(int narg, char **arg)
       m = 0;
       while (m < n) {
         x = &buf[m+1];
+        if (remapflag) {
+          iptr = (imageint *) &buf[m+7];
+          domain->remap(x,*iptr);
+        }
+
         if (triclinic) {
           domain->x2lamda(x,lamda);
           coord = lamda;
@@ -411,6 +426,17 @@ void ReadRestart::command(int narg, char **arg)
 
   if (multiproc || mpiioflag) {
 
+    // if remapflag set, remap all atoms I read back to box before migrating
+
+    if (remapflag) {
+      double **x = atom->x;
+      imageint *image = atom->image;
+      int nlocal = atom->nlocal;
+
+      for (int i = 0; i < nlocal; i++)
+        domain->remap(x[i],image[i]);
+    }
+
     // create a temporary fix to hold and migrate extra atom info
     // necessary b/c irregular will migrate atoms