git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14424 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/CORESHELL/compute_temp_cs.cpp

@@ -74,13 +74,14 @@ ComputeTempCS::ComputeTempCS(LAMMPS *lmp, int narg, char **arg) :
   strcpy(id_fix,id);
   strcat(id_fix,"_COMPUTE_STORE");
 
-  char **newarg = new char*[5];
+  char **newarg = new char*[6];
   newarg[0] = id_fix;
   newarg[1] = group->names[igroup];
   newarg[2] = (char *) "STORE";
-  newarg[3] = (char *) "0";
+  newarg[3] = (char *) "peratom";
-  newarg[4] = (char *) "1";
+  newarg[4] = (char *) "0";
-  modify->add_fix(5,newarg);
+  newarg[5] = (char *) "1";
+  modify->add_fix(6,newarg);
   fix = (FixStore *) modify->fix[modify->nfix-1];
   delete [] newarg;
 

src/REPLICA/tad.cpp

@@ -154,13 +154,14 @@ void TAD::command(int narg, char **arg)
 
   // create FixStore object to store revert state
 
-  narg2 = 5;
+  narg2 = 6;
   args = new char*[narg2];
   args[0] = (char *) "tad_revert";
   args[1] = (char *) "all";
   args[2] = (char *) "STORE";
-  args[3] = (char *) "0";
+  args[3] = (char *) "peratom";
-  args[4] = (char *) "7";
+  args[4] = (char *) "0";
+  args[5] = (char *) "7";
   modify->add_fix(narg2,args);
   fix_revert = (FixStore *) modify->fix[modify->nfix-1];
   delete [] args;

src/compute_chunk_atom.cpp

@@ -579,13 +579,14 @@ void ComputeChunkAtom::init()
     strcpy(id_fix,id);
     strcat(id_fix,"_COMPUTE_STORE");
 
-    char **newarg = new char*[5];
+    char **newarg = new char*[6];
     newarg[0] = id_fix;
     newarg[1] = group->names[igroup];
     newarg[2] = (char *) "STORE";
-    newarg[3] = (char *) "1";
+    newarg[3] = (char *) "peratom";
     newarg[4] = (char *) "1";
-    modify->add_fix(5,newarg);
+    newarg[5] = (char *) "1";
+    modify->add_fix(6,newarg);
     fixstore = (FixStore *) modify->fix[modify->nfix-1];
     delete [] newarg;
   }

src/compute_displace_atom.cpp

@@ -45,13 +45,14 @@ ComputeDisplaceAtom::ComputeDisplaceAtom(LAMMPS *lmp, int narg, char **arg) :
   strcpy(id_fix,id);
   strcat(id_fix,"_COMPUTE_STORE");
 
-  char **newarg = new char*[5];
+  char **newarg = new char*[6];
   newarg[0] = id_fix;
   newarg[1] = group->names[igroup];
   newarg[2] = (char *) "STORE";
-  newarg[3] = (char *) "1";
+  newarg[3] = (char *) "peratom";
-  newarg[4] = (char *) "3";
+  newarg[4] = (char *) "1";
-  modify->add_fix(5,newarg);
+  newarg[5] = (char *) "3";
+  modify->add_fix(6,newarg);
   fix = (FixStore *) modify->fix[modify->nfix-1];
   delete [] newarg;
 

src/compute_msd.cpp

@@ -65,13 +65,14 @@ ComputeMSD::ComputeMSD(LAMMPS *lmp, int narg, char **arg) :
   strcpy(id_fix,id);
   strcat(id_fix,"_COMPUTE_STORE");
 
-  char **newarg = new char*[5];
+  char **newarg = new char*[6];
   newarg[0] = id_fix;
   newarg[1] = group->names[igroup];
   newarg[2] = (char *) "STORE";
-  newarg[3] = (char *) "1";
+  newarg[3] = (char *) "peratom";
-  newarg[4] = (char *) "3";
+  newarg[4] = (char *) "1";
-  modify->add_fix(5,newarg);
+  newarg[5] = (char *) "3";
+  modify->add_fix(6,newarg);
   fix = (FixStore *) modify->fix[modify->nfix-1];
   delete [] newarg;
 

src/compute_vacf.cpp

@@ -42,13 +42,14 @@ ComputeVACF::ComputeVACF(LAMMPS *lmp, int narg, char **arg) :
   strcpy(id_fix,id);
   strcat(id_fix,"_COMPUTE_STORE");
 
-  char **newarg = new char*[5];
+  char **newarg = new char*[6];
   newarg[0] = id_fix;
   newarg[1] = group->names[igroup];
   newarg[2] = (char *) "STORE";
-  newarg[3] = (char *) "1";
+  newarg[3] = (char *) "peratom";
-  newarg[4] = (char *) "3";
+  newarg[4] = (char *) "1";
-  modify->add_fix(5,newarg);
+  newarg[5] = (char *) "3";
+  modify->add_fix(6,newarg);
   fix = (FixStore *) modify->fix[modify->nfix-1];
   delete [] newarg;
 

src/fix_adapt.cpp

@@ -210,11 +210,12 @@ void FixAdapt::post_constructor()
   id_fix_diam = NULL;
   id_fix_chg = NULL;
 
-  char **newarg = new char*[5];
+  char **newarg = new char*[6];
   newarg[1] = group->names[igroup];
   newarg[2] = (char *) "STORE";
-  newarg[3] = (char *) "1";
+  newarg[3] = (char *) "peratom";
   newarg[4] = (char *) "1";
+  newarg[5] = (char *) "1";
 
   if (diamflag) {
     int n = strlen(id) + strlen("_FIX_STORE_DIAM") + 1;
@@ -222,7 +223,7 @@ void FixAdapt::post_constructor()
     strcpy(id_fix_diam,id);
     strcat(id_fix_diam,"_FIX_STORE_DIAM");
     newarg[0] = id_fix_diam;
-    modify->add_fix(5,newarg);
+    modify->add_fix(6,newarg);
     fix_diam = (FixStore *) modify->fix[modify->nfix-1];
 
     if (fix_diam->restart_reset) fix_diam->restart_reset = 0;
@@ -245,7 +246,7 @@ void FixAdapt::post_constructor()
     strcpy(id_fix_chg,id);
     strcat(id_fix_chg,"_FIX_STORE_CHG");
     newarg[0] = id_fix_chg;
-    modify->add_fix(5,newarg);
+    modify->add_fix(6,newarg);
     fix_chg = (FixStore *) modify->fix[modify->nfix-1];
 
     if (fix_chg->restart_reset) fix_chg->restart_reset = 0;

src/fix_store.cpp

@@ -22,41 +22,82 @@
 using namespace LAMMPS_NS;
 using namespace FixConst;
 
+enum{GLOBAL,PERATOM};
+
 /* ---------------------------------------------------------------------- */
 
 FixStore::FixStore(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
 {
-  if (narg != 5) error->all(FLERR,"Illegal fix store command");
+  if (narg != 6) error->all(FLERR,"Illegal fix store command");
 
-  // syntax: id group style 0/1 nvalue
+  // 4th arg determines GLOBAL vs PERATOM values
-  // 0/1 flag = not-store or store values in restart file
+  // syntax: id group style peratom 0/1 nvalue
+  //   0/1 flag = not-store or store peratom values in restart file
+  //   nvalue = # of peratom values, N=1 is vector, N>1 is array
+  // syntax: id group style global nrow ncol
+  //   Nrow by Ncol array of global values
+  //   Ncol=1 is vector, Nrow>1 is array
 
-  restart_peratom = force->inumeric(FLERR,arg[3]);
+  if (strcmp(arg[3],"peratom") == 0) flavor = PERATOM;
-  nvalues = force->inumeric(FLERR,arg[4]);
+  else if (strcmp(arg[3],"global") == 0) flavor = GLOBAL;
+  else error->all(FLERR,"Invalid fix store command");
 
-  vecflag = 0;
+  // GLOBAL values are always written to restart file
-  if (nvalues == 1) vecflag = 1;
+  // PERATOM restart_peratom is set by caller
 
-  // perform initial allocation of atom-based array
+  if (flavor == GLOBAL) {
-  // register with Atom class
+    restart_global = 1;
+    nrow = force->inumeric(FLERR,arg[4]);
+    ncol = force->inumeric(FLERR,arg[5]);
+    if (nrow <= 0 || ncol <= 0)
+      error->all(FLERR,"Invalid fix store command");
+    vecflag = 0;
+    if (ncol == 1) vecflag = 1;
+  } else {
+    restart_peratom = force->inumeric(FLERR,arg[4]);
+    nvalues = force->inumeric(FLERR,arg[5]);
+    if (restart_peratom < 0 or restart_peratom > 1 || nvalues <= 0)
+      error->all(FLERR,"Invalid fix store command");
+    vecflag = 0;
+    if (nvalues == 1) vecflag = 1;
+  }
 
   vstore = NULL;
   astore = NULL;
-  grow_arrays(atom->nmax);
+
-  atom->add_callback(0);
+  // allocate vector or array
-  if (restart_peratom) atom->add_callback(1);
+  // for PERATOM, register with Atom class
+
+  if (flavor == GLOBAL) {
+    if (vecflag) memory->create(vstore,nrow,"fix/store:vstore");
+    else memory->create(astore,nrow,ncol,"fix/store:astore");
+  }
+  if (flavor == PERATOM) {
+    grow_arrays(atom->nmax);
+    atom->add_callback(0);
+    if (restart_peratom) atom->add_callback(1);
+  }
 
   // zero the storage
-  // since may be exchanged before filled by caller
+  // PERATOM may be exchanged before filled by caller
 
-  int nlocal = atom->nlocal;
+  if (flavor == GLOBAL) {
-  if (vecflag)
+    if (vecflag)
-    for (int i = 0; i < nlocal; i++)
+      for (int i = 0; i < nrow; i++) vstore[i] = 0.0;
-      vstore[i] = 0.0;
+    else
-  else
+      for (int i = 0; i < nrow; i++)
-    for (int i = 0; i < nlocal; i++)
+        for (int j = 0; j < ncol; j++)
-      for (int j = 0; j < nvalues; j++)
+          astore[i][j] = 0.0;
-	astore[i][j] = 0.0;
+  }
+  if (flavor == PERATOM) {
+    int nlocal = atom->nlocal;
+    if (vecflag)
+      for (int i = 0; i < nlocal; i++) vstore[i] = 0.0;
+    else
+      for (int i = 0; i < nlocal; i++)
+        for (int j = 0; j < nvalues; j++)
+          astore[i][j] = 0.0;
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -65,8 +106,10 @@ FixStore::~FixStore()
 {
   // unregister callbacks to this fix from Atom class
 
-  atom->delete_callback(id,0);
+  if (flavor == PERATOM) {
-  if (restart_peratom) atom->delete_callback(id,1);
+    atom->delete_callback(id,0);
+    if (restart_peratom) atom->delete_callback(id,1);
+  }
 
   memory->destroy(vstore);
   memory->destroy(astore);
@@ -186,7 +229,8 @@ int FixStore::size_restart(int nlocal)
 
 double FixStore::memory_usage()
 {
-  double bytes = atom->nmax*nvalues * sizeof(double);
+  double bytes;
+  if (flavor == GLOBAL) bytes += nrow*ncol * sizeof(double);
+  if (flavor == PERATOM) bytes += atom->nmax*nvalues * sizeof(double);
   return bytes;
 }
-

src/fix_store.h

@@ -26,8 +26,10 @@ namespace LAMMPS_NS {
 
 class FixStore : public Fix {
  public:
-  double *vstore;        // vector storage if nvalues = 1
+  int nrow,ncol;         // size of global data array
-  double **astore;       // array storage if nvalues > 1
+  int nvalues;           // number of per-atom values
+  double *vstore;        // vector storage for GLOBAL or PERATOM
+  double **astore;       // array storage for GLOBAL or PERATOM
 
   FixStore(class LAMMPS *, int, char **);
   ~FixStore();
@@ -45,8 +47,8 @@ class FixStore : public Fix {
   double memory_usage();
 
  private:
-  int nvalues;                  // total # of values per atom
+  int flavor;                   // GLOBAL or PERATOM
-  int vecflag;                  // 1 if nvalues = 1
+  int vecflag;                  // 1 if ncol=1 or nvalues=1
 };
 
 }

src/variable.cpp

@@ -4480,13 +4480,14 @@ VarReader::VarReader(LAMMPS *lmp, char *name, char *file, int flag) :
     strcpy(id_fix,name);
     strcat(id_fix,"_VARIABLE_STORE");
 
-    char **newarg = new char*[5];
+    char **newarg = new char*[6];
     newarg[0] = id_fix;
     newarg[1] = (char *) "all";
     newarg[2] = (char *) "STORE";
-    newarg[3] = (char *) "0";
+    newarg[3] = (char *) "peratom";
-    newarg[4] = (char *) "1";
+    newarg[4] = (char *) "0";
-    modify->add_fix(5,newarg);
+    newarg[5] = (char *) "1";
+    modify->add_fix(6,newarg);
     fixstore = (FixStore *) modify->fix[modify->nfix-1];
     delete [] newarg;