git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11300 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/GRANULAR/fix_pour.cpp

@@ -832,7 +832,10 @@ void FixPour::options(int narg, char **arg)
       if (iarg+2 > narg) error->all(FLERR,"Illegal fix pour command");
       int imol = atom->find_molecule(arg[iarg+1]);
       if (imol == -1)
-        error->all(FLERR,"Molecule ID for fix pour does not exist");
+        error->all(FLERR,"Molecule template ID for fix pour does not exist");
+      if (atom->molecules[imol]->nset > 1 && comm->me == 0)
+        error->warning(FLERR,"Molecule template for "
+                       "fix pour has multiple molecules");
       mode = MOLECULE;
       onemol = atom->molecules[imol];
       iarg += 2;

src/MISC/fix_deposit.cpp

@@ -577,7 +577,10 @@ void FixDeposit::options(int narg, char **arg)
       if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
       int imol = atom->find_molecule(arg[iarg+1]);
       if (imol == -1)
-        error->all(FLERR,"Molecule ID for fix deposit does not exist");
+        error->all(FLERR,"Molecule template ID for fix deposit does not exist");
+      if (atom->molecules[imol]->nset > 1 && comm->me == 0)
+        error->warning(FLERR,"Molecule template for "
+                       "fix deposit has multiple molecules");
       mode = MOLECULE;
       onemol = atom->molecules[imol];
       iarg += 2;

src/RIGID/fix_rigid_small.cpp

@@ -152,7 +152,11 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
       if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
       int imol = atom->find_molecule(arg[iarg+1]);
       if (imol == -1)
-        error->all(FLERR,"Molecule ID for fix rigid/small does not exist");
+        error->all(FLERR,"Molecule template ID for "
+                   "fix rigid/small does not exist");
+      if (atom->molecules[imol]->nset > 1 && comm->me == 0)
+        error->warning(FLERR,"Molecule template for "
+                       "fix rigid/small has multiple molecules");
       onemol = atom->molecules[imol];
       iarg += 2;
     } else error->all(FLERR,"Illegal fix rigid/small command");

src/RIGID/fix_shake.cpp

@@ -155,7 +155,10 @@ FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
       if (iarg+2 > narg) error->all(FLERR,"Illegal fix shake command");
       int imol = atom->find_molecule(arg[iarg+1]);
       if (imol == -1)
-        error->all(FLERR,"Molecule ID for fix shake does not exist");
+        error->all(FLERR,"Molecule template ID for fix shake does not exist");
+      if (atom->molecules[imol]->nset > 1 && comm->me == 0)
+        error->warning(FLERR,"Molecule template for "
+                       "fix shake has multiple molecules");
       onemol = atom->molecules[imol];
       iarg += 2;
     } else error->all(FLERR,"Illegal fix shake command");
@@ -164,7 +167,7 @@ FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
   // error check for Molecule template
 
   if (onemol && onemol->shakeflag == 0)
-    error->all(FLERR,"Fix shake molecule must have shake info");
+    error->all(FLERR,"Fix shake molecule template must have shake info");
 
   // allocate bond and angle distance arrays, indexed from 1 to n
 

src/atom.cpp

@@ -42,7 +42,6 @@ using namespace LAMMPS_NS;
 using namespace MathConst;
 
 #define DELTA 1
-#define DELTA_MOLECULE 1
 #define DELTA_MEMSTR 1024
 #define EPSILON 1.0e-6
 #define CUDA_CHUNK 3000
@@ -117,7 +116,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
 
   // user-defined molecules
 
-  nmolecule = maxmol = 0;
+  nmolecule = 0;
   molecules = NULL;
 
   // custom atom arrays
@@ -1293,27 +1292,30 @@ int Atom::shape_consistency(int itype,
 }
 
 /* ----------------------------------------------------------------------
-   add a new molecule template
+   add a new molecule template = set of molecules
 ------------------------------------------------------------------------- */
 
 void Atom::add_molecule(int narg, char **arg)
 {
-  if (narg < 1) error->all(FLERR,"Illegal molecule command");
+  if (narg < 2) error->all(FLERR,"Illegal molecule command");
-  if (find_molecule(arg[0]) >= 0) error->all(FLERR,"Reuse of molecule ID");
+  if (find_molecule(arg[0]) >= 0) 
+    error->all(FLERR,"Reuse of molecule template ID");
 
-  // extend molecule list if necessary
+  int nprevious = nmolecule;
-
+  nmolecule += narg-1;
-  if (nmolecule == maxmol) {
-    maxmol += DELTA_MOLECULE;
   molecules = (Molecule **)
-      memory->srealloc(molecules,maxmol*sizeof(Molecule *),"atom::molecules");
+    memory->srealloc(molecules,nmolecule*sizeof(Molecule *),"atom::molecules");
-  }
 
-  molecules[nmolecule++] = new Molecule(lmp,narg,arg);
+  for (int i = 1; i < narg; i++) {
+    molecules[nprevious] = new Molecule(lmp,arg[0],arg[i]);
+    if (i == 1) molecules[nprevious]->nset = narg-1;
+    else molecules[nprevious]->nset = 0;
+    nprevious++;
+  }
 }
 
 /* ----------------------------------------------------------------------
-   find which molecule has molecule ID
+   find first molecule in set with template ID
    return -1 if does not exist
 ------------------------------------------------------------------------- */
 
@@ -1328,6 +1330,7 @@ int Atom::find_molecule(char *id)
 /* ----------------------------------------------------------------------
    add info to current atom ilocal from molecule template onemol and its iatom
    offset = atom ID preceeding IDs of atoms in this molecule
+   called by fixes and commands that add molecules
 ------------------------------------------------------------------------- */
 
 void Atom::add_molecule_atom(Molecule *onemol, int iatom,

src/atom.h

@@ -113,9 +113,12 @@ class Atom : protected Pointers {
   int cs_flag,csforce_flag,vforce_flag,ervelforce_flag,etag_flag;
   int rho_flag,e_flag,cv_flag,vest_flag;
 
-  // molecules
+  // molecule templates
+  // each template can be a set of consecutive molecules
+  // each with same ID (stored in molecules)
+  // 1st molecule in template stores nset = # in set
 
-  int nmolecule,maxmol;
+  int nmolecule;
   class Molecule **molecules;
 
   // extra peratom info in restart file destined for fix & diag

src/create_atoms.cpp

@@ -124,8 +124,11 @@ void CreateAtoms::command(int narg, char **arg)
     } else if (strcmp(arg[iarg],"mol") == 0) {
       if (iarg+3 > narg) error->all(FLERR,"Illegal create_atoms command");
       int imol = atom->find_molecule(arg[iarg+1]);
-      if (imol == -1)
+      if (imol == -1) error->all(FLERR,"Molecule template ID for "
-        error->all(FLERR,"Molecule ID for create_atoms does not exist");
+                                 "create_atoms does not exist");
+      if (atom->molecules[imol]->nset > 1 && comm->me == 0)
+        error->warning(FLERR,"Molecule template for "
+                       "create_atoms has multiple molecules");
       mode = MOLECULE;
       onemol = atom->molecules[imol];
       molseed = force->inumeric(FLERR,arg[iarg+2]);

src/molecule.cpp

@@ -33,22 +33,18 @@ using namespace MathConst;
 
 /* ---------------------------------------------------------------------- */
 
-Molecule::Molecule(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
+Molecule::Molecule(LAMMPS *lmp, char *idarg, char *file) : Pointers(lmp)
 {
   me = comm->me;
 
-  if (narg != 2) error->all(FLERR,"Illegal molecule command");
+  int n = strlen(idarg) + 1;
-
-  int n = strlen(arg[0]) + 1;
   id = new char[n];
-  strcpy(id,arg[0]);
+  strcpy(id,idarg);
 
   for (int i = 0; i < n-1; i++)
     if (!isalnum(id[i]) && id[i] != '_')
-      error->all(FLERR,
+      error->all(FLERR,"Molecule template ID must be "
-                 "Molecule ID must be alphanumeric or underscore characters");
+                 "alphanumeric or underscore characters");
-
-  char *file = arg[1];
 
   // initialize all fields to empty
 

src/molecule.h

@@ -20,7 +20,9 @@ namespace LAMMPS_NS {
 
 class Molecule : protected Pointers {
  public:
-  char *id;
+  char *id;   // template id of this molecule, same for all molecules in set
+  int nset;   // if first in set, # of molecules in this set
+              // else 0 if not first in set
 
   // number of atoms,bonds,etc in molecule
 
@@ -97,7 +99,7 @@ class Molecule : protected Pointers {
   double **dxbody;     // displacement of each atom relative to COM
                        // in body frame (diagonalized interia tensor)
 
-  Molecule(class LAMMPS *, int, char **);
+  Molecule(class LAMMPS *, char *, char *);
   ~Molecule();
   void compute_center();
   void compute_mass();