git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13019 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/comm.cpp

@@ -559,6 +559,11 @@ int Comm::coord2proc(double *x, int &igx, int &igy, int &igz)
   double *prd = domain->prd;
   double *boxlo = domain->boxlo;
 
+  // initialize triclinic b/c coord2proc can be called before Comm::init()
+  // via Irregular::migrate_atoms()
+
+  triclinic = domain->triclinic;
+
   if (layout == LAYOUT_UNIFORM) {
     if (triclinic == 0) {
       igx = static_cast<int> (procgrid[0] * (x[0]-boxlo[0]) / prd[0]);

src/read_data.cpp

@@ -589,6 +589,27 @@ void ReadData::command(int narg, char **arg)
   //   in case data file re-defined them
 
   if (atom->molecular == 2) atom->avec->onemols[0]->check_attributes(1);
+
+  // shrink-wrap the box if necessary and move atoms to new procs
+  // if atoms are lost is b/c data file box was far from shrink-wrapped
+  // do not use irregular() comm, which would not lose atoms,
+  //   b/c then user could specify data file box as far too big and empty
+
+  if (domain->nonperiodic == 2) {
+    if (domain->triclinic) domain->x2lamda(atom->nlocal);
+    domain->reset_box();
+    comm->init();
+    comm->setup();
+    comm->exchange();
+    if (domain->triclinic) domain->lamda2x(atom->nlocal);
+
+    bigint natoms;
+    bigint nblocal = atom->nlocal;
+    MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
+    if (natoms != atom->natoms)
+      error->all(FLERR,
+                 "Read_data shrink wrap did not assign all atoms correctly");
+  }
 }
 
 /* ----------------------------------------------------------------------