add groups to molecule templates

src/molecule.cpp

@@ -46,7 +46,7 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
   improper_atom3(NULL), improper_atom4(NULL), nspecial(NULL), special(NULL),
   shake_flag(NULL), shake_atom(NULL), shake_type(NULL), avec_body(NULL), ibodyparams(NULL),
   dbodyparams(NULL), dx(NULL), dxcom(NULL), dxbody(NULL), quat_external(NULL),
-  fp(NULL), count(NULL)
+  fp(NULL), count(NULL), groupmask(NULL)
 {
   me = comm->me;
 
@@ -447,6 +447,9 @@ void Molecule::read(int flag)
     } else if (strstr(line,"impropers")) {
       nmatch = sscanf(line,"%d",&nimpropers);
       nwant = 1;
+    } else if (strstr(line,"groups")) {
+      nmatch = sscanf(line,"%d",&ngroups);
+      nwant = 1;
     } else if (strstr(line,"mass")) {
       massflag = 1;
       nmatch = sscanf(line,"%lg",&masstotal);
@@ -523,6 +526,10 @@ void Molecule::read(int flag)
       moleculeflag = 1;
       if (flag) molecules(line);
       else skip_lines(natoms,line);
+    } else if (strcmp(keyword,"Groups") == 0) {
+      groupflag = 1;
+      if (flag) groups(line);
+      else skip_lines(ngroups,line);
     } else if (strcmp(keyword,"Charges") == 0) {
       qflag = 1;
       if (flag) charges(line);
@@ -721,6 +728,35 @@ void Molecule::molecules(char *line)
     nmolecules = MAX(nmolecules,molecule[i]);
 }
 
+/* ----------------------------------------------------------------------
+   read groups from file
+------------------------------------------------------------------------- */
+
+void Molecule::groups(char *line)
+{
+  int n,m,atomID,nwords;
+  char **words = new char*[natoms+1];
+
+  for (int i = 0; i < ngroups; i++) {
+    readline(line);
+    nwords = parse(line,words,natoms+1);
+    if (nwords > natoms+1)
+      error->all(FLERR,"Invalid atom ID in Groups section of molecule file");
+    n = strlen(words[0]) + 1;
+    groupnames[i] = new char[n];
+    strcpy(groupnames[i],words[0]);
+
+    for (m = 1; m < nwords; m++) {
+      atomID = atoi(words[m]);
+      if (atomID <= 0 || atomID > natoms)
+        error->all(FLERR,"Invalid atom ID in Groups section of molecule file");
+      groupmask[i][atomID-1] = 1;
+    }
+  }
+
+  delete [] words;
+}
+
 /* ----------------------------------------------------------------------
    read charges from file
 ------------------------------------------------------------------------- */
@@ -1386,6 +1422,17 @@ void Molecule::body(int flag, int pflag, char *line)
   }
 }
 
+/* ----------------------------------------------------------------------
+   return group index if name matches existing group, -1 if no such group
+------------------------------------------------------------------------- */
+
+int Molecule::findgroup(const char *name)
+{
+  for (int igroup = 0; igroup < ngroups; igroup++)
+    if (groupnames[igroup] && strcmp(name,groupnames[igroup]) == 0) return igroup;
+  return -1;
+}
+
 /* ----------------------------------------------------------------------
    error check molecule attributes and topology against system settings
    flag = 0, just check this molecule
@@ -1466,7 +1513,7 @@ void Molecule::initialize()
   bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
   maxspecial = 0;
 
-  xflag = typeflag = moleculeflag = qflag = radiusflag = rmassflag = 0;
+  xflag = typeflag = moleculeflag = groupflag = qflag = radiusflag = rmassflag = 0;
   bondflag = angleflag = dihedralflag = improperflag = 0;
   nspecialflag = specialflag = 0;
   shakeflag = shakeflagflag = shakeatomflag = shaketypeflag = 0;
@@ -1522,6 +1569,10 @@ void Molecule::allocate()
   if (xflag) memory->create(x,natoms,3,"molecule:x");
   if (typeflag) memory->create(type,natoms,"molecule:type");
   if (moleculeflag) memory->create(molecule,natoms,"molecule:molecule");
+  if (groupflag) groupnames = new char*[ngroups];
+  if (groupflag) memory->create(groupmask,ngroups,natoms,"molecule:groupmask");
+  for (int i = 0; i < ngroups; i++)
+    for (int j = 0; j < natoms; j++) groupmask[i][j] = 0;
   if (qflag) memory->create(q,natoms,"molecule:q");
   if (radiusflag) memory->create(radius,natoms,"molecule:radius");
   if (rmassflag) memory->create(rmass,natoms,"molecule:rmass");
@@ -1614,6 +1665,12 @@ void Molecule::deallocate()
   memory->destroy(radius);
   memory->destroy(rmass);
 
+  memory->destroy(groupmask);
+  if (groupflag) {
+    for (int i = 0; i < ngroups; i++) delete [] groupnames[i];
+    delete [] groupnames;
+  }
+
   memory->destroy(num_bond);
   memory->destroy(bond_type);
   memory->destroy(bond_atom);

src/molecule.h

@@ -30,10 +30,14 @@ class Molecule : protected Pointers {
 
   int natoms;
   int nbonds,nangles,ndihedrals,nimpropers;
-  int ntypes,nmolecules;
+  int ntypes,nmolecules,ngroups;
   int nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
   int nibody,ndbody;
 
+  // group info
+  char **groupnames;
+  int **groupmask; // ngroups by natoms
+
   // max bond,angle,etc per atom
 
   int bond_per_atom,angle_per_atom,dihedral_per_atom,improper_per_atom;
@@ -41,7 +45,7 @@ class Molecule : protected Pointers {
 
   // 1 if attribute defined in file, 0 if not
 
-  int xflag,typeflag,moleculeflag,qflag,radiusflag,rmassflag;
+  int xflag,typeflag,moleculeflag,groupflag,qflag,radiusflag,rmassflag;
   int bondflag,angleflag,dihedralflag,improperflag;
   int nspecialflag,specialflag;
   int shakeflag,shakeflagflag,shakeatomflag,shaketypeflag;
@@ -119,6 +123,7 @@ class Molecule : protected Pointers {
   void compute_mass();
   void compute_com();
   void compute_inertia();
+  int findgroup(const char *);
   void check_attributes(int);
 
  private:
@@ -133,6 +138,7 @@ class Molecule : protected Pointers {
   void coords(char *);
   void types(char *);
   void molecules(char *);
+  void groups(char *);
   void charges(char *);
   void diameters(char *);
   void masses(char *);