From bfba361f65f2acbede4892482a24c776f5745c09 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Sat, 20 Aug 2016 22:22:00 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15480
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/dump.cpp | 81 ++++++++++++++++++++++++++++++++++++++++++++++++++--
 src/dump.h   |  8 +++++-
 2 files changed, 86 insertions(+), 3 deletions(-)

diff --git a/src/dump.cpp b/src/dump.cpp
index ac69c43d10..8849282bb9 100644
--- a/src/dump.cpp
+++ b/src/dump.cpp
@@ -81,7 +81,8 @@ Dump::Dump(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
   buffer_allow = 0;
   buffer_flag = 0;
   padflag = 0;
-
+  pbcflag = 0;
+  
   maxbuf = maxids = maxsort = maxproc = 0;
   buf = bufsort = NULL;
   ids = idsort = NULL;
@@ -91,6 +92,10 @@ Dump::Dump(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
   maxsbuf = 0;
   sbuf = NULL;
 
+  maxpbc = 0;
+  xpbc = vpbc = NULL;
+  imagepbc = NULL;
+
   // parse filename for special syntax
   // if contains '%', write one file per proc and replace % with proc-ID
   // if contains '*', write one file per timestep and replace * with timestep
@@ -163,7 +168,13 @@ Dump::~Dump()
   delete irregular;
 
   memory->destroy(sbuf);
-
+  
+  if (pbcflag) {
+    memory->destroy(xpbc);
+    memory->destroy(vpbc);
+    memory->destroy(imagepbc);
+  }
+  
   if (multiproc) MPI_Comm_free(&clustercomm);
 
   // XTC style sets fp to NULL since it closes file in its destructor
@@ -262,6 +273,10 @@ void Dump::init()
       }
     }
   }
+
+  // preallocation for PBC copies if requested
+  
+  if (pbcflag && atom->nlocal > maxpbc) pbc_allocate();
 }
 
 /* ---------------------------------------------------------------------- */
@@ -352,6 +367,28 @@ void Dump::write()
     memory->create(ids,maxids,"dump:ids");
   }
 
+  // apply PBC on copy of x,v,image if requested
+
+  if (pbcflag) {
+    int nlocal = atom->nlocal;
+    if (nlocal > maxpbc) pbc_allocate();
+    if (nlocal) {
+      memcpy(&xpbc[0][0],&atom->x[0][0],3*nlocal*sizeof(double));
+      memcpy(&vpbc[0][0],&atom->v[0][0],3*nlocal*sizeof(double));
+      memcpy(imagepbc,atom->image,nlocal*sizeof(imageint));
+    }
+    double **dtmp = atom->x;
+    atom->x = xpbc;
+    xpbc = dtmp;
+    dtmp = atom->v;
+    atom->v = vpbc;
+    vpbc = dtmp;
+    imageint *itmp = atom->image;
+    atom->image = imagepbc;
+    imagepbc = itmp;
+    domain->pbc();
+  }
+  
   // pack my data into buf
   // if sorting on IDs also request ID list from pack()
   // sort buf as needed
@@ -430,6 +467,20 @@ void Dump::write()
     }
   }
 
+  // restore original x,v,image unaltered by PBC
+  
+  if (pbcflag) {
+    double **dtmp = atom->x;
+    atom->x = xpbc;
+    xpbc = dtmp;
+    dtmp = atom->v;
+    atom->v = vpbc;
+    vpbc = dtmp;
+    imageint *itmp = atom->image;
+    atom->image = imagepbc;
+    imagepbc = itmp;
+  }
+
   // if file per timestep, close file if I am filewriter
 
   if (multifile) {
@@ -887,6 +938,13 @@ void Dump::modify_params(int narg, char **arg)
       if (padflag < 0) error->all(FLERR,"Illegal dump_modify command");
       iarg += 2;
 
+    } else if (strcmp(arg[iarg],"pbc") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
+      if (strcmp(arg[iarg+1],"yes") == 0) pbcflag = 1;
+      else if (strcmp(arg[iarg+1],"no") == 0) pbcflag = 0;
+      else error->all(FLERR,"Illegal dump_modify command");
+      iarg += 2;
+
     } else if (strcmp(arg[iarg],"sort") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
       if (strcmp(arg[iarg+1],"off") == 0) sort_flag = 0;
@@ -919,6 +977,21 @@ void Dump::modify_params(int narg, char **arg)
    return # of bytes of allocated memory
 ------------------------------------------------------------------------- */
 
+void Dump::pbc_allocate()
+{
+  memory->destroy(xpbc);
+  memory->destroy(vpbc);
+  memory->destroy(imagepbc);
+  maxpbc = atom->nmax;
+  memory->create(xpbc,maxpbc,3,"dump:xbpc");
+  memory->create(vpbc,maxpbc,3,"dump:vbpc");
+  memory->create(imagepbc,maxpbc,"dump:imagebpc");
+}
+
+/* ----------------------------------------------------------------------
+   return # of bytes of allocated memory
+------------------------------------------------------------------------- */
+
 bigint Dump::memory_usage()
 {
   bigint bytes = memory->usage(buf,size_one*maxbuf);
@@ -931,5 +1004,9 @@ bigint Dump::memory_usage()
     bytes += memory->usage(proclist,maxproc);
     if (irregular) bytes += irregular->memory_usage();
   }
+  if (pbcflag) {
+    bytes += 6*maxpbc * sizeof(double);
+    bytes += maxpbc * sizeof(imageint);
+  }
   return bytes;
 }
diff --git a/src/dump.h b/src/dump.h
index dbcf8547fe..e92d048b9d 100644
--- a/src/dump.h
+++ b/src/dump.h
@@ -71,6 +71,7 @@ class Dump : protected Pointers {
   int buffer_allow;          // 1 if style allows for buffer_flag, 0 if not
   int buffer_flag;           // 1 if buffer output as one big string, 0 if not
   int padflag;               // timestep padding in filename
+  int pbcflag;               // 1 if remap dumped atoms via PBC, 0 if not
   int singlefile_opened;     // 1 = one big file, already opened, else 0
   int sortcol;               // 0 to sort on ID, 1-N on columns
   int sortcolm1;             // sortcol - 1
@@ -116,6 +117,10 @@ class Dump : protected Pointers {
   tagint *idsort;
   int *index,*proclist;
 
+  double **xpbc,**vpbc;
+  int *imagepbc;
+  int maxpbc;
+
   class Irregular *irregular;
 
   virtual void init_style() = 0;
@@ -126,7 +131,8 @@ class Dump : protected Pointers {
   virtual void pack(tagint *) = 0;
   virtual int convert_string(int, double *) {return 0;}
   virtual void write_data(int, double *) = 0;
-
+  void pbc_allocate();
+    
   void sort();
   static int idcompare(const void *, const void *);
   static int bufcompare(const void *, const void *);