Merge remote-tracking branch 'lammps-ro/master' into lammps-icms

doc/html/Manual.html

@@ -135,7 +135,7 @@
   <H1></H1><div class="section" id="lammps-icms-documentation">
 <h1>LAMMPS-ICMS Documentation</h1>
 <div class="section" id="aug-2016-version">
-<h2>13 Aug 2016 version</h2>
+<h2>20 Aug 2016 version</h2>
 </div>
 <div class="section" id="version-info">
 <h2>Version info:</h2>

doc/html/_sources/Manual.txt

@@ -5,7 +5,7 @@
 LAMMPS Documentation
 ====================
 
-13 Aug 2016 version
+20 Aug 2016 version
 -------------------
 
 Version info:

doc/html/_sources/dump.txt

@@ -169,6 +169,9 @@ or multiple smaller files).
    Because periodic boundary conditions are enforced only on
    timesteps when neighbor lists are rebuilt, the coordinates of an atom
    written to a dump file may be slightly outside the simulation box.
+   Re-neighbor timesteps will not typically coincide with the timesteps
+   dump snapshots are written.  See the :doc:`dump_modify pbc <dump_modify>` command if you with to force coordinates to be
+   strictly inside the simulation box.
 
 .. note::
 

doc/html/_sources/dump_modify.txt

@@ -36,6 +36,7 @@ Syntax
      *nfile* arg = Nf
        Nf = write this many files, one from each of Nf processors
      *pad* arg = Nchar = # of characters to convert timestep to
+     *pbc* arg = *yes* or *no* = remap atoms via periodic boundary conditions
      *precision* arg = power-of-10 value from 10 to 1000000
      *region* arg = region-ID or "none"
      *scale* arg = *yes* or *no*
@@ -428,6 +429,21 @@ timestep order.
 ----------
 
 
+The *pbc* keyword applies to all the dump styles.  As explained on the
+:doc:`dump <dump>` doc page, atom coordinates in a dump file may be
+slightly outside the simulation box.  This is because periodic
+boundary conditions are enforced only on timesteps when neighbor lists
+are rebuilt, which will not typically coincide with the timesteps dump
+snapshots are written.  If the setting of this keyword is set to
+*yes*\ , then all atoms will be remapped to the periodic box before the
+snapshot is written, then restored to their original position.  If it
+is set to *no* they will not be.  The *no* setting is the default
+because it requires no extra computation.
+
+
+----------
+
+
 The *precision* keyword only applies to the dump *xtc* style.  A
 specified value of N means that coordinates are stored to 1/N
 nanometer accuracy, e.g. for N = 1000, the coordinates are written to
@@ -846,6 +862,7 @@ The option defaults are
 * label = ENTRIES
 * nfile = 1
 * pad = 0
+* pbc = no
 * precision = 1000
 * region = none
 * scale = yes

doc/html/_sources/fix_ave_histo.txt

@@ -145,8 +145,9 @@ length.  The first value (a scalar or vector) is what is histogrammed
 into bins, in the same manner the fix ave/histo command operates.  The
 second value (a scalar or vector) is used as a "weight".  This means
 that instead of each value tallying a "1" to its bin, the
-corresponding weight is tallied.  E.g. the Nth entry in the first
-vector tallies the Nth entry (weight) in the second vector.
+corresponding weight is tallied.  E.g. The Nth entry (weight) in the
+second vector is tallied to the bin corresponding to the Nth entry in
+the first vector.
 
 
 ----------

doc/html/dump.html

@@ -274,7 +274,10 @@ or multiple smaller files).</p>
 <p class="first admonition-title">Note</p>
 <p class="last">Because periodic boundary conditions are enforced only on
 timesteps when neighbor lists are rebuilt, the coordinates of an atom
-written to a dump file may be slightly outside the simulation box.</p>
+written to a dump file may be slightly outside the simulation box.
+Re-neighbor timesteps will not typically coincide with the timesteps
+dump snapshots are written.  See the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify pbc</span></a> command if you with to force coordinates to be
+strictly inside the simulation box.</p>
 </div>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>

doc/html/dump_modify.html

@@ -158,6 +158,7 @@
 <em>nfile</em> arg = Nf
   Nf = write this many files, one from each of Nf processors
 <em>pad</em> arg = Nchar = # of characters to convert timestep to
+<em>pbc</em> arg = <em>yes</em> or <em>no</em> = remap atoms via periodic boundary conditions
 <em>precision</em> arg = power-of-10 value from 10 to 1000000
 <em>region</em> arg = region-ID or &quot;none&quot;
 <em>scale</em> arg = <em>yes</em> or <em>no</em>
@@ -468,6 +469,17 @@ yield 0000100, 0012000, 2000000.  This can be useful so that
 post-processing programs can easily read the files in ascending
 timestep order.</p>
 <hr class="docutils" />
+<p>The <em>pbc</em> keyword applies to all the dump styles.  As explained on the
+<a class="reference internal" href="dump.html"><span class="doc">dump</span></a> doc page, atom coordinates in a dump file may be
+slightly outside the simulation box.  This is because periodic
+boundary conditions are enforced only on timesteps when neighbor lists
+are rebuilt, which will not typically coincide with the timesteps dump
+snapshots are written.  If the setting of this keyword is set to
+<em>yes</em>, then all atoms will be remapped to the periodic box before the
+snapshot is written, then restored to their original position.  If it
+is set to <em>no</em> they will not be.  The <em>no</em> setting is the default
+because it requires no extra computation.</p>
+<hr class="docutils" />
 <p>The <em>precision</em> keyword only applies to the dump <em>xtc</em> style.  A
 specified value of N means that coordinates are stored to 1/N
 nanometer accuracy, e.g. for N = 1000, the coordinates are written to
@@ -790,6 +802,7 @@ images less frequently.</p>
 <li>label = ENTRIES</li>
 <li>nfile = 1</li>
 <li>pad = 0</li>
+<li>pbc = no</li>
 <li>precision = 1000</li>
 <li>region = none</li>
 <li>scale = yes</li>

doc/html/fix_ave_histo.html

@@ -254,8 +254,9 @@ length.  The first value (a scalar or vector) is what is histogrammed
 into bins, in the same manner the fix ave/histo command operates.  The
 second value (a scalar or vector) is used as a “weight”.  This means
 that instead of each value tallying a “1” to its bin, the
-corresponding weight is tallied.  E.g. the Nth entry in the first
-vector tallies the Nth entry (weight) in the second vector.</p>
+corresponding weight is tallied.  E.g. The Nth entry (weight) in the
+second vector is tallied to the bin corresponding to the Nth entry in
+the first vector.</p>
 <hr class="docutils" />
 <p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what
 timesteps the input values will be used in order to contribute to the

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS-ICMS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="13 Aug 2016 version">
+<META NAME="docnumber" CONTENT="20 Aug 2016 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@@ -21,7 +21,7 @@
 <H1></H1>
 
 LAMMPS-ICMS Documentation :c,h3
-13 Aug 2016 version :c,h4
+20 Aug 2016 version :c,h4
 
 Version info: :h4
 

doc/src/dump.txt

@@ -130,6 +130,10 @@ or multiple smaller files).
 NOTE: Because periodic boundary conditions are enforced only on
 timesteps when neighbor lists are rebuilt, the coordinates of an atom
 written to a dump file may be slightly outside the simulation box.
+Re-neighbor timesteps will not typically coincide with the timesteps
+dump snapshots are written.  See the "dump_modify
+pbc"_dump_modify.html command if you with to force coordinates to be
+strictly inside the simulation box.
 
 NOTE: Unless the "dump_modify sort"_dump_modify.html option is
 invoked, the lines of atom information written to dump files

doc/src/dump_modify.txt

@@ -36,6 +36,7 @@ keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} o
   {nfile} arg = Nf
     Nf = write this many files, one from each of Nf processors
   {pad} arg = Nchar = # of characters to convert timestep to
+  {pbc} arg = {yes} or {no} = remap atoms via periodic boundary conditions
   {precision} arg = power-of-10 value from 10 to 1000000
   {region} arg = region-ID or "none"
   {scale} arg = {yes} or {no}
@@ -377,6 +378,19 @@ timestep order.
 
 :line
 
+The {pbc} keyword applies to all the dump styles.  As explained on the
+"dump"_dump.html doc page, atom coordinates in a dump file may be
+slightly outside the simulation box.  This is because periodic
+boundary conditions are enforced only on timesteps when neighbor lists
+are rebuilt, which will not typically coincide with the timesteps dump
+snapshots are written.  If the setting of this keyword is set to
+{yes}, then all atoms will be remapped to the periodic box before the
+snapshot is written, then restored to their original position.  If it
+is set to {no} they will not be.  The {no} setting is the default
+because it requires no extra computation.
+
+:line
+
 The {precision} keyword only applies to the dump {xtc} style.  A
 specified value of N means that coordinates are stored to 1/N
 nanometer accuracy, e.g. for N = 1000, the coordinates are written to
@@ -755,6 +769,7 @@ image = no
 label = ENTRIES
 nfile = 1
 pad = 0
+pbc = no
 precision = 1000
 region = none
 scale = yes

doc/src/fix_ave_histo.txt

@@ -136,8 +136,9 @@ length.  The first value (a scalar or vector) is what is histogrammed
 into bins, in the same manner the fix ave/histo command operates.  The
 second value (a scalar or vector) is used as a "weight".  This means
 that instead of each value tallying a "1" to its bin, the
-corresponding weight is tallied.  E.g. the Nth entry in the first
-vector tallies the Nth entry (weight) in the second vector.
+corresponding weight is tallied.  E.g. The Nth entry (weight) in the
+second vector is tallied to the bin corresponding to the Nth entry in
+the first vector.
 
 :line
 

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();
 }
 
 /* ---------------------------------------------------------------------- */
@@ -283,6 +298,9 @@ int Dump::count()
 
 void Dump::write()
 {
+  imageint *imagehold;
+  double **xhold,**vhold;
+
   // if file per timestep, open new file
 
   if (multifile) openfile();
@@ -352,6 +370,25 @@ 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));
+    }
+    xhold = atom->x;
+    vhold = atom->v;
+    imagehold = atom->image;
+    atom->x = xpbc;
+    atom->v = vpbc;
+    atom->image = imagepbc;
+    domain->pbc();
+  }
+  
   // pack my data into buf
   // if sorting on IDs also request ID list from pack()
   // sort buf as needed
@@ -430,6 +467,14 @@ void Dump::write()
     }
   }
 
+  // restore original x,v,image unaltered by PBC
+
+  if (pbcflag) {
+    atom->x = xhold;
+    atom->v = vhold;
+    atom->image = imagehold;
+  }
+
   // if file per timestep, close file if I am filewriter
 
   if (multifile) {
@@ -887,6 +932,13 @@ 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 +971,21 @@ 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 +998,9 @@ 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;
 }

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 *);

src/version.h

@@ -1 +1 @@
-#define LAMMPS_VERSION "13 Aug 2016"
+#define LAMMPS_VERSION "20 Aug 2016"