git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11476 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/fix_langevin.cpp

@@ -201,7 +201,6 @@ int FixLangevin::setmask()
   int mask = 0;
   mask |= POST_FORCE;
   mask |= POST_FORCE_RESPA;
-  mask |= POST_INTEGRATE;
   mask |= END_OF_STEP;
   mask |= THERMO_ENERGY;
   return mask;

src/fix_vector.cpp

@@ -11,10 +11,6 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-/* ----------------------------------------------------------------------
-   Contributing author: Pieter in 't Veld (SNL)
-------------------------------------------------------------------------- */
-
 #include "string.h"
 #include "fix_vector.h"
 #include "update.h"

src/fix_vector.h

@@ -20,7 +20,6 @@ FixStyle(vector,FixVector)
 #ifndef LMP_FIX_VECTOR_H
 #define LMP_FIX_VECTOR_H
 
-#include "stdio.h"
 #include "fix.h"
 
 namespace LAMMPS_NS {
@@ -53,99 +52,4 @@ class FixVector : public Fix {
 
 /* ERROR/WARNING messages:
 
-E: Illegal ... command
-
-Self-explanatory.  Check the input script syntax and compare to the
-documentation for the command.  You can use -echo screen as a
-command-line option when running LAMMPS to see the offending line.
-
-E: Compute ID for fix ave/time does not exist
-
-Self-explanatory.
-
-E: Fix ID for fix ave/time does not exist
-
-Self-explanatory.
-
-E: Invalid fix ave/time off column
-
-Self-explantory.
-
-E: Fix ave/time compute does not calculate a scalar
-
-Self-explantory.
-
-E: Fix ave/time compute does not calculate a vector
-
-Self-explantory.
-
-E: Fix ave/time compute vector is accessed out-of-range
-
-The index for the vector is out of bounds.
-
-E: Fix ave/time compute does not calculate an array
-
-Self-explanatory.
-
-E: Fix ave/time compute array is accessed out-of-range
-
-An index for the array is out of bounds.
-
-E: Fix ave/time fix does not calculate a scalar
-
-Self-explanatory.
-
-E: Fix ave/time fix does not calculate a vector
-
-Self-explanatory.
-
-E: Fix ave/time fix vector is accessed out-of-range
-
-The index for the vector is out of bounds.
-
-E: Fix for fix ave/time not computed at compatible time
-
-Fixes generate their values on specific timesteps.  Fix ave/time
-is requesting a value on a non-allowed timestep.
-
-E: Fix ave/time fix does not calculate an array
-
-Self-explanatory.
-
-E: Fix ave/time fix array is accessed out-of-range
-
-An index for the array is out of bounds.
-
-E: Variable name for fix ave/time does not exist
-
-Self-explanatory.
-
-E: Fix ave/time variable is not equal-style variable
-
-Self-explanatory.
-
-E: Fix ave/time cannot use variable with vector mode
-
-Variables produce scalar values.
-
-E: Fix ave/time columns are inconsistent lengths
-
-Self-explanatory.
-
-E: Fix ave/time cannot set output array intensive/extensive from these inputs
-
-One of more of the vector inputs has individual elements which are
-flagged as intensive or extensive.  Such an input cannot be flagged as
-all intensive/extensive when turned into an array by fix ave/time.
-
-E: Cannot open fix ave/time file %s
-
-The specified file cannot be opened.  Check that the path and name are
-correct.
-
-E: Fix ave/time missed timestep
-
-You cannot reset the timestep to a value beyond where the fix
-expects to next perform averaging.
-
 */

src/group.cpp

@@ -51,10 +51,12 @@ Group::Group(LAMMPS *lmp) : Pointers(lmp)
   names = new char*[MAX_GROUP];
   bitmask = new int[MAX_GROUP];
   inversemask = new int[MAX_GROUP];
+  dynamic = new int[MAX_GROUP];
 
   for (int i = 0; i < MAX_GROUP; i++) names[i] = NULL;
   for (int i = 0; i < MAX_GROUP; i++) bitmask[i] = 1 << i;
   for (int i = 0; i < MAX_GROUP; i++) inversemask[i] = bitmask[i] ^ ~0;
+  for (int i = 0; i < MAX_GROUP; i++) dynamic[i] = 0;
 
   // create "all" group
 
@@ -75,6 +77,7 @@ Group::~Group()
   delete [] names;
   delete [] bitmask;
   delete [] inversemask;
+  delete [] dynamic;
 }
 
 /* ----------------------------------------------------------------------
@@ -114,8 +117,17 @@ void Group::assign(int narg, char **arg)
     int bits = inversemask[igroup];
     for (i = 0; i < nlocal; i++) mask[i] &= bits;
 
+    if (dynamic[igroup]) {
+      int n = strlen("GROUP_") + strlen(names[igroup]) + 1;
+      char *fixID = new char[n];
+      sprintf(fixID,"GROUP_%s",names[igroup]);
+      modify->delete_fix(fixID);
+      delete [] fixID;
+    }
+
     delete [] names[igroup];
     names[igroup] = NULL;
+    dynamic[igroup] = 0;
     ngroup--;
 
     return;
@@ -156,6 +168,7 @@ void Group::assign(int narg, char **arg)
         mask[i] |= bit;
 
   // style = type, molecule, id
+  // add to group if atom matches type/molecule/id or condition
 
   } else if (strcmp(arg[1],"type") == 0 || strcmp(arg[1],"molecule") == 0 ||
              strcmp(arg[1],"id") == 0) {
@@ -296,6 +309,7 @@ void Group::assign(int narg, char **arg)
     }
 
   // style = variable
+  // add to group if atom-atyle variable is non-zero
 
   } else if (strcmp(arg[1],"variable") == 0) {
 
@@ -331,6 +345,8 @@ void Group::assign(int narg, char **arg)
     for (int iarg = 2; iarg < narg; iarg++) {
       jgroup = find(arg[iarg]);
       if (jgroup == -1) error->all(FLERR,"Group ID does not exist");
+      if (dynamic[jgroup]) 
+        error->all(FLERR,"Cannot subtract groups using a dynamic group");
       list[iarg-2] = jgroup;
     }
 
@@ -367,6 +383,8 @@ void Group::assign(int narg, char **arg)
     for (int iarg = 2; iarg < narg; iarg++) {
       jgroup = find(arg[iarg]);
       if (jgroup == -1) error->all(FLERR,"Group ID does not exist");
+      if (dynamic[jgroup]) 
+        error->all(FLERR,"Cannot union groups using a dynamic group");
       list[iarg-2] = jgroup;
     }
 
@@ -395,6 +413,8 @@ void Group::assign(int narg, char **arg)
     for (int iarg = 2; iarg < narg; iarg++) {
       jgroup = find(arg[iarg]);
       if (jgroup == -1) error->all(FLERR,"Group ID does not exist");
+      if (dynamic[jgroup]) 
+        error->all(FLERR,"Cannot intersect groups using a dynamic group");
       list[iarg-2] = jgroup;
     }
 
@@ -413,6 +433,55 @@ void Group::assign(int narg, char **arg)
 
     delete [] list;
 
+  // style = dynamic
+  // create a new FixGroup to dynamically determine atoms in group
+
+  } else if (strcmp(arg[1],"dynamic") == 0) {
+
+    if (narg < 4) error->all(FLERR,"Illegal group command");
+
+    // if group is already dynamic, delete current FixGroup
+
+    if (dynamic[igroup]) {
+      int n = strlen("GROUP_") + strlen(names[igroup]) + 1;
+      char *fixID = new char[n];
+      sprintf(fixID,"GROUP_%s",names[igroup]);
+      modify->delete_fix(fixID);
+      delete [] fixID;
+    }
+
+    dynamic[igroup] = 1;
+
+    int n = strlen("GROUP_") + strlen(names[igroup]) + 1;
+    char *fixID = new char[n];
+    sprintf(fixID,"GROUP_%s",names[igroup]);
+
+    char **newarg = new char*[narg];
+    newarg[0] = fixID;
+    newarg[1] = arg[2];
+    newarg[2] = (char *) "GROUP";
+    for (int i = 3; i < narg; i++) newarg[i] = arg[i];
+    modify->add_fix(narg,newarg);
+    delete [] newarg;
+    delete [] fixID;
+
+  // style = static
+  // remove dynamic FixGroup if necessary
+
+  } else if (strcmp(arg[1],"static") == 0) {
+
+    if (narg != 2) error->all(FLERR,"Illegal group command");
+
+    if (dynamic[igroup]) {
+      int n = strlen("GROUP_") + strlen(names[igroup]) + 1;
+      char *fixID = new char[n];
+      sprintf(fixID,"GROUP_%s",names[igroup]);
+      modify->delete_fix(fixID);
+      delete [] fixID;
+    }
+
+    dynamic[igroup] = 0;
+
   // not a valid group style
 
   } else error->all(FLERR,"Illegal group command");

src/group.h

@@ -25,6 +25,7 @@ class Group : protected Pointers {
   char **names;                // name of each group
   int *bitmask;                // one-bit mask for each group
   int *inversemask;            // inverse mask for each group
+  int *dynamic;                // 1 if dynamic, 0 if not
 
   Group(class LAMMPS *);
   ~Group();