git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2143 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/fix.cpp

@@ -53,6 +53,7 @@ Fix::Fix(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
   virial_flag = 0;
   no_change_box = 0;
   time_integrate = 0;
+  restart_pbc = 0;
 
   scalar_flag = vector_flag = peratom_flag = 0;
 

src/fix.h

@@ -34,6 +34,8 @@ class Fix : protected Pointers {
   int virial_flag;               // 1 if Fix contributes to virial, 0 if not
   int no_change_box;             // 1 if cannot swap ortho <-> triclinic
   int time_integrate;            // 1 if fix performs time integration, 0 if no
+  int restart_pbc;               // 1 if fix moves atoms (except integrate)
+                                 //   so that write_restart must remap to PBC
 
   int scalar_flag;               // 0/1 if compute_scalar() function exists
   int vector_flag;               // 0/1 if compute_vector() function exists

src/modify.cpp

@@ -166,6 +166,12 @@ void Modify::init()
   for (i = 0; i < ncompute; i++) compute[i]->init();
   modify->addstep_compute_all(update->ntimestep);
 
+  // set global flag if any fix has its restart_pbc flag set
+
+  restart_pbc_any = 0;
+  for (i = 0; i < nfix; i++)
+    if (fix[i]->restart_pbc) restart_pbc_any = 1;
+  
   // warn if any particle is time integrated more than once
 
   int nlocal = atom->nlocal;

src/modify.h

@@ -28,6 +28,8 @@ class Modify : protected Pointers {
   int n_min_post_force,n_min_energy;
   int nfix_restart_peratom;
 
+  int restart_pbc_any;       // 1 if any fix sets restart_pbc
+
   class Fix **fix;           // list of fixes
   int *fmask;                // bit mask for when each fix is applied
 

src/write_restart.cpp

@@ -36,6 +36,9 @@
 
 using namespace LAMMPS_NS;
 
+#define MIN(A,B) ((A) < (B)) ? (A) : (B)
+#define MAX(A,B) ((A) > (B)) ? (A) : (B)
+
 // same as read_restart.cpp and tools/restart2data.cpp
 
 enum{VERSION,UNITS,NTIMESTEP,DIMENSION,NPROCS,PROCGRID_0,PROCGRID_1,PROCGRID_2,
@@ -106,7 +109,7 @@ void WriteRestart::command(int narg, char **arg)
 }
 
 /* ----------------------------------------------------------------------
-   called from output within run/minimize loop
+   called from command() and directly from output within run/minimize loop
    file = final file name to write, except may contain a "%"
 ------------------------------------------------------------------------- */
 
@@ -179,6 +182,55 @@ void WriteRestart::write(char *file)
   int n = 0;
   for (int i = 0; i < atom->nlocal; i++) n += avec->pack_restart(i,&buf[n]);
 
+  // if any fix requires it, remap each atom's coords via PBC
+  // is because fix changes atom coords (excepting an integrate fix)
+  // just remap in buffer, not actual atoms
+
+  if (modify->restart_pbc_any) {
+    int triclinic = domain->triclinic;
+    double *lo,*hi,*period;
+
+    if (triclinic == 0) {
+      lo = domain->boxlo;
+      hi = domain->boxhi;
+      period = domain->prd;
+    } else {
+      lo = domain->boxlo_lamda;
+      hi = domain->boxhi_lamda;
+      period = domain->prd_lamda;
+    }
+
+    int xperiodic = domain->xperiodic;
+    int yperiodic = domain->yperiodic;
+    int zperiodic = domain->zperiodic;
+
+    double *x;
+    int m = 0;
+    for (int i = 0; i < atom->nlocal; i++) {
+      x = &buf[m+1];
+      if (triclinic) domain->x2lamda(x,x);
+
+      if (xperiodic) {
+	if (x[0] < lo[0]) x[0] += period[0];
+	if (x[0] >= hi[0]) x[0] -= period[0];
+	x[0] = MAX(x[0],lo[0]);
+      }
+      if (yperiodic) {
+	if (x[1] < lo[1]) x[1] += period[1];
+	if (x[1] >= hi[1]) x[1] -= period[1];
+	x[1] = MAX(x[1],lo[1]);
+      }
+      if (zperiodic) {
+	if (x[2] < lo[2]) x[2] += period[2];
+	if (x[2] >= hi[2]) x[2] -= period[2];
+	x[2] = MAX(x[2],lo[2]);
+      }
+
+      if (triclinic) domain->x2lamda(x,x);
+      m += static_cast<int> (buf[m]);
+    }
+  }
+
   // if single file:
   //   write one chunk of atoms per proc to file
   //   proc 0 pings each proc, receives its chunk, writes to file