Merge pull request #824 from jrgissing/write_data-noextra

Write_data nofix option

doc/src/write_data.txt

@@ -16,6 +16,7 @@ file = name of data file to write out :ulb,l
 zero or more keyword/value pairs may be appended :l
 keyword = {pair} or {nocoeff} :l
   {nocoeff} = do not write out force field info
+  {nofix} = do not write out extra sections read by fixes
   {pair} value = {ii} or {ij}
     {ii} = write one line of pair coefficient info per atom type
     {ij} = write one line of pair coefficient info per IJ atom type pair :pre
@@ -83,6 +84,12 @@ be written to the data file. This can be very helpful, if one wants
 to make significant changes to the force field or if the parameters
 are read in separately anyway, e.g. from an include file.
 
+The {nofix} keyword requests that no extra sections read by fixes
+should be written to the data file (see the {fix} option of the
+"read_data"_read_data.html command for details). For example, this
+option excludes sections for user-created per-atom properties 
+from "fix property/atom"_fix_property_atom.html.
+
 The {pair} keyword lets you specify in what format the pair
 coefficient information is written into the data file.  If the value
 is specified as {ii}, then one line per atom type is written, to
@@ -120,4 +127,3 @@ setup, atom masses initialized, etc).
 [Default:]
 
 The option defaults are pair = ii.
-

src/write_data.cpp

@@ -74,6 +74,7 @@ void WriteData::command(int narg, char **arg)
 
   pairflag = II;
   coeffflag = 1;
+  fixflag = 1;
   int noinit = 0;
 
   int iarg = 1;
@@ -90,6 +91,9 @@ void WriteData::command(int narg, char **arg)
     } else if (strcmp(arg[iarg],"nocoeff") == 0) {
       coeffflag = 0;
       iarg++;
+    } else if (strcmp(arg[iarg],"nofix") == 0) {
+      fixflag = 0;
+      iarg++;
     } else error->all(FLERR,"Illegal write_data command");
   }
 
@@ -206,10 +210,10 @@ void WriteData::write(char *file)
   }
 
   // extra sections managed by fixes
-
-  for (int i = 0; i < modify->nfix; i++)
-    if (modify->fix[i]->wd_section)
-      for (int m = 0; m < modify->fix[i]->wd_section; m++) fix(i,m);
+  if (fixflag)
+    for (int i = 0; i < modify->nfix; i++)
+      if (modify->fix[i]->wd_section)
+        for (int m = 0; m < modify->fix[i]->wd_section; m++) fix(i,m);
 
   // close data file
 
@@ -252,10 +256,11 @@ void WriteData::header()
     }
   }
 
-  for (int i = 0; i < modify->nfix; i++)
-    if (modify->fix[i]->wd_header)
-      for (int m = 0; m < modify->fix[i]->wd_header; m++)
-        modify->fix[i]->write_data_header(fp,m);
+  if (fixflag) 
+    for (int i = 0; i < modify->nfix; i++)
+      if (modify->fix[i]->wd_header)
+        for (int m = 0; m < modify->fix[i]->wd_header; m++)
+          modify->fix[i]->write_data_header(fp,m);
 
   fprintf(fp,"\n");
 

src/write_data.h

@@ -35,6 +35,7 @@ class WriteData : protected Pointers {
   int me,nprocs;
   int pairflag;
   int coeffflag;
+  int fixflag;
   FILE *fp;
   bigint nbonds_local,nbonds;
   bigint nangles_local,nangles;