git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11124 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/atom.h

@@ -35,7 +35,8 @@ class Atom : protected Pointers {
   bigint nbonds,nangles,ndihedrals,nimpropers;
   int ntypes,nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
   int bond_per_atom,angle_per_atom,dihedral_per_atom,improper_per_atom;
-  int extra_bond_per_atom;
+  int extra_bond_per_atom,extra_angle_per_atom;
+  int extra_dihedral_per_atom,extra_improper_per_atom;
 
   int firstgroup;               // store atoms in this group first, -1 if unset
   int nfirst;                   // # of atoms in first group on this proc

src/create_box.cpp

@@ -15,10 +15,12 @@
 #include "string.h"
 #include "create_box.h"
 #include "atom.h"
+#include "atom_vec.h"
 #include "force.h"
 #include "domain.h"
 #include "region.h"
 #include "region_prism.h"
+#include "force.h"
 #include "comm.h"
 #include "update.h"
 #include "error.h"
@@ -33,7 +35,7 @@ CreateBox::CreateBox(LAMMPS *lmp) : Pointers(lmp) {}
 
 void CreateBox::command(int narg, char **arg)
 {
-  if (narg != 2) error->all(FLERR,"Illegal create_box command");
+  if (narg < 2) error->all(FLERR,"Illegal create_box command");
 
   if (domain->box_exist)
     error->all(FLERR,"Cannot create_box after simulation box is defined");
@@ -102,6 +104,61 @@ void CreateBox::command(int narg, char **arg)
   atom->ndihedraltypes = 0;
   atom->nimpropertypes = 0;
 
+  // process optional args that can overwrite default settings
+
+  int iarg = 2;
+  while (iarg < narg) {
+    if (strcmp(arg[iarg],"bond types") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
+      if (!atom->avec->bonds_allow) 
+        error->all(FLERR,"No bonds allowed with this atom style");
+      atom->nbondtypes = force->inumeric(FLERR,arg[iarg+1]);
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"angle types") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
+      if (!atom->avec->angles_allow) 
+        error->all(FLERR,"No angles allowed with this atom style");
+      atom->nangletypes = force->inumeric(FLERR,arg[iarg+1]);
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"dihedral types") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
+      if (!atom->avec->dihedrals_allow) 
+        error->all(FLERR,"No dihedrals allowed with this atom style");
+      atom->ndihedraltypes = force->inumeric(FLERR,arg[iarg+1]);
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"improper types") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
+      if (!atom->avec->impropers_allow) 
+        error->all(FLERR,"No impropers allowed with this atom style");
+      atom->nimpropertypes = force->inumeric(FLERR,arg[iarg+1]);
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"extra bond per atom") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
+      if (!atom->avec->bonds_allow) 
+        error->all(FLERR,"No bonds allowed with this atom style");
+      atom->bond_per_atom = force->inumeric(FLERR,arg[iarg+1]);
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"extra angle per atom") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
+      if (!atom->avec->angles_allow) 
+        error->all(FLERR,"No angles allowed with this atom style");
+      atom->angle_per_atom = force->inumeric(FLERR,arg[iarg+1]);
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"extra dihedral per atom") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
+      if (!atom->avec->dihedrals_allow) 
+        error->all(FLERR,"No dihedrals allowed with this atom style");
+      atom->dihedral_per_atom = force->inumeric(FLERR,arg[iarg+1]);
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"extra improper per atom") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
+      if (!atom->avec->impropers_allow) 
+        error->all(FLERR,"No impropers allowed with this atom style");
+      atom->improper_per_atom = force->inumeric(FLERR,arg[iarg+1]);
+      iarg += 2;
+    } else error->all(FLERR,"Illegal create_box command");
+  }
+
   // problem setup using info from header
   // no call to atom->grow since create_atoms or fixes will do it
 

src/dump_movie.cpp

@@ -52,7 +52,7 @@ void DumpMovie::openfile()
     sprintf(moviecmd,"ffmpeg -v error -y -r %.2f -f image2pipe -c:v ppm -i - "
             "-r 24.0 -b:v %dk %s ", framerate, bitrate, filename);
 #else
-    error->one(FLERR,"Cannot generate movie file");
+    error->one(FLERR,"Support for writing movies not included");
 #endif
 
 #if defined(_WIN32)

src/molecule.cpp

@@ -331,6 +331,10 @@ void Molecule::types(char *line)
     readline(line);
     sscanf(line,"%d %d",&tmp,&type[i]);
   }
+
+  for (int i = 0; i < natoms; i++)
+    if (type[i] <= 0 || type[i] > atom->ntypes)
+      error->all(FLERR,"Invalid atom type in molecule file");
 }
 
 /* ----------------------------------------------------------------------

src/read_data.cpp

@@ -151,6 +151,9 @@ void ReadData::command(int narg, char **arg)
       if (compressed) pclose(fp);
       else fclose(fp);
       atom->bond_per_atom += atom->extra_bond_per_atom;
+      atom->angle_per_atom += atom->extra_angle_per_atom;
+      atom->dihedral_per_atom += atom->extra_dihedral_per_atom;
+      atom->improper_per_atom += atom->extra_improper_per_atom;
     }
 
     MPI_Bcast(&atom->bond_per_atom,1,MPI_INT,0,world);
@@ -499,6 +502,12 @@ void ReadData::header(int flag)
 
     else if (strstr(line,"extra bond per atom"))
       sscanf(line,"%d",&atom->extra_bond_per_atom);
+    else if (strstr(line,"extra angle per atom"))
+      sscanf(line,"%d",&atom->extra_angle_per_atom);
+    else if (strstr(line,"extra dihedral per atom"))
+      sscanf(line,"%d",&atom->extra_dihedral_per_atom);
+    else if (strstr(line,"extra improper per atom"))
+      sscanf(line,"%d",&atom->extra_improper_per_atom);
 
     else if (strstr(line,"xlo xhi"))
       sscanf(line,"%lg %lg",&domain->boxlo[0],&domain->boxhi[0]);