change 'groups' to 'fragments'

doc/src/Errors_messages.rst

@@ -4801,7 +4801,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    Atom IDs must be positive integers and within range of defined
    atoms.
 
-*Invalid atom ID in Groups section of molecule file*
+*Invalid atom ID in Fragments section of molecule file*
    Self-explanatory.
 
 *Invalid atom ID in Impropers section of data file*

doc/src/molecule.rst

@@ -64,6 +64,7 @@ templates include:
 * :doc:`fix rigid/small <fix_rigid>`
 * :doc:`fix shake <fix_shake>`
 * :doc:`fix gcmc <fix_gcmc>`
+* :doc:`fix bond/react <fix_bond_react>`
 * :doc:`create_atoms <create_atoms>`
 * :doc:`atom_style template <atom_style>`
 
@@ -148,7 +149,7 @@ appear if the value(s) are different than the default.
 * Na *angles* = # of angles Na in molecule, default = 0
 * Nd *dihedrals* = # of dihedrals Nd in molecule, default = 0
 * Ni *impropers* = # of impropers Ni in molecule, default = 0
-* Ng *groups* = # of groups in molecule, default = 0
+* Nf *fragments* = # of fragments in molecule, default = 0
 * Mtotal *mass* = total mass of molecule
 * Xc Yc Zc *com* = coordinates of center-of-mass of molecule
 * Ixx Iyy Izz Ixy Ixz Iyz *inertia* = 6 components of inertia tensor of molecule
@@ -171,7 +172,7 @@ internally.
 
 These are the allowed section keywords for the body of the file.
 
-* *Coords, Types, Molecules, Groups, Charges, Diameters, Masses* = atom-property sections
+* *Coords, Types, Molecules, Fragments, Charges, Diameters, Masses* = atom-property sections
 * *Bonds, Angles, Dihedrals, Impropers* = molecular topology sections
 * *Special Bond Counts, Special Bonds* = special neighbor info
 * *Shake Flags, Shake Atoms, Shake Bond Types* = SHAKE info
@@ -244,13 +245,13 @@ listed in order from 1 to Nlines, but LAMMPS does not check for this.
 ----------
 
 
-*Groups* section:
+*Fragments* section:
 
-* one line per group
+* one line per fragment
 * line syntax: ID a b c d ...
-* a,b,c,d,... = IDs of atoms in group
+* a,b,c,d,... = IDs of atoms in fragment
 
-The ID of a group can only contain alphanumeric characters and
+The ID of a fragment can only contain alphanumeric characters and
 underscores.  The atom IDs should be values from 1 to Natoms, where
 Natoms = # of atoms in the molecule.
 

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), groupmask(NULL)
+  fp(NULL), count(NULL), fragmentmask(NULL)
 {
   me = comm->me;
 
@@ -447,8 +447,8 @@ void Molecule::read(int flag)
     } else if (strstr(line,"impropers")) {
       nmatch = sscanf(line,"%d",&nimpropers);
       nwant = 1;
-    } else if (strstr(line,"groups")) {
+    } else if (strstr(line,"fragments")) {
-      nmatch = sscanf(line,"%d",&ngroups);
+      nmatch = sscanf(line,"%d",&nfragments);
       nwant = 1;
     } else if (strstr(line,"mass")) {
       massflag = 1;
@@ -526,10 +526,10 @@ void Molecule::read(int flag)
       moleculeflag = 1;
       if (flag) molecules(line);
       else skip_lines(natoms,line);
-    } else if (strcmp(keyword,"Groups") == 0) {
+    } else if (strcmp(keyword,"Fragments") == 0) {
-      groupflag = 1;
+      fragmentflag = 1;
-      if (flag) groups(line);
+      if (flag) fragments(line);
-      else skip_lines(ngroups,line);
+      else skip_lines(nfragments,line);
     } else if (strcmp(keyword,"Charges") == 0) {
       qflag = 1;
       if (flag) charges(line);
@@ -729,28 +729,28 @@ void Molecule::molecules(char *line)
 }
 
 /* ----------------------------------------------------------------------
-   read groups from file
+   read fragments from file
 ------------------------------------------------------------------------- */
 
-void Molecule::groups(char *line)
+void Molecule::fragments(char *line)
 {
   int n,m,atomID,nwords;
   char **words = new char*[natoms+1];
 
-  for (int i = 0; i < ngroups; i++) {
+  for (int i = 0; i < nfragments; 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");
+      error->all(FLERR,"Invalid atom ID in Fragments section of molecule file");
     n = strlen(words[0]) + 1;
-    groupnames[i] = new char[n];
+    fragmentnames[i] = new char[n];
-    strcpy(groupnames[i],words[0]);
+    strcpy(fragmentnames[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");
+        error->all(FLERR,"Invalid atom ID in Fragments section of molecule file");
-      groupmask[i][atomID-1] = 1;
+      fragmentmask[i][atomID-1] = 1;
     }
   }
 
@@ -1423,13 +1423,13 @@ void Molecule::body(int flag, int pflag, char *line)
 }
 
 /* ----------------------------------------------------------------------
-   return group index if name matches existing group, -1 if no such group
+   return fragment index if name matches existing fragment, -1 if no such fragment
 ------------------------------------------------------------------------- */
 
-int Molecule::findgroup(const char *name)
+int Molecule::findfragment(const char *name)
 {
-  for (int igroup = 0; igroup < ngroups; igroup++)
+  for (int i = 0; i < nfragments; i++)
-    if (groupnames[igroup] && strcmp(name,groupnames[igroup]) == 0) return igroup;
+    if (fragmentnames[i] && strcmp(name,fragmentnames[i]) == 0) return i;
   return -1;
 }
 
@@ -1513,7 +1513,7 @@ void Molecule::initialize()
   bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
   maxspecial = 0;
 
-  xflag = typeflag = moleculeflag = groupflag = qflag = radiusflag = rmassflag = 0;
+  xflag = typeflag = moleculeflag = fragmentflag = qflag = radiusflag = rmassflag = 0;
   bondflag = angleflag = dihedralflag = improperflag = 0;
   nspecialflag = specialflag = 0;
   shakeflag = shakeflagflag = shakeatomflag = shaketypeflag = 0;
@@ -1569,10 +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 (fragmentflag) fragmentnames = new char*[nfragments];
-  if (groupflag) memory->create(groupmask,ngroups,natoms,"molecule:groupmask");
+  if (fragmentflag) memory->create(fragmentmask,nfragments,natoms,"molecule:fragmentmask");
-  for (int i = 0; i < ngroups; i++)
+  for (int i = 0; i < nfragments; i++)
-    for (int j = 0; j < natoms; j++) groupmask[i][j] = 0;
+    for (int j = 0; j < natoms; j++) fragmentmask[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");
@@ -1665,10 +1665,10 @@ void Molecule::deallocate()
   memory->destroy(radius);
   memory->destroy(rmass);
 
-  memory->destroy(groupmask);
+  memory->destroy(fragmentmask);
-  if (groupflag) {
+  if (fragmentflag) {
-    for (int i = 0; i < ngroups; i++) delete [] groupnames[i];
+    for (int i = 0; i < nfragments; i++) delete [] fragmentnames[i];
-    delete [] groupnames;
+    delete [] fragmentnames;
   }
 
   memory->destroy(num_bond);

src/molecule.h

@@ -30,13 +30,13 @@ class Molecule : protected Pointers {
 
   int natoms;
   int nbonds,nangles,ndihedrals,nimpropers;
-  int ntypes,nmolecules,ngroups;
+  int ntypes,nmolecules,nfragments;
   int nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
   int nibody,ndbody;
 
-  // group info
+  // fragment info
-  char **groupnames;
+  char **fragmentnames;
-  int **groupmask; // ngroups by natoms
+  int **fragmentmask; // nfragments by natoms
 
   // max bond,angle,etc per atom
 
@@ -45,7 +45,7 @@ class Molecule : protected Pointers {
 
   // 1 if attribute defined in file, 0 if not
 
-  int xflag,typeflag,moleculeflag,groupflag,qflag,radiusflag,rmassflag;
+  int xflag,typeflag,moleculeflag,fragmentflag,qflag,radiusflag,rmassflag;
   int bondflag,angleflag,dihedralflag,improperflag;
   int nspecialflag,specialflag;
   int shakeflag,shakeflagflag,shakeatomflag,shaketypeflag;
@@ -123,7 +123,7 @@ class Molecule : protected Pointers {
   void compute_mass();
   void compute_com();
   void compute_inertia();
-  int findgroup(const char *);
+  int findfragment(const char *);
   void check_attributes(int);
 
  private:
@@ -138,7 +138,7 @@ class Molecule : protected Pointers {
   void coords(char *);
   void types(char *);
   void molecules(char *);
-  void groups(char *);
+  void fragments(char *);
   void charges(char *);
   void diameters(char *);
   void masses(char *);
@@ -379,7 +379,7 @@ E: Invalid Molecules section in molecule file
 
 Self-explanatory.
 
-E: Invalid atom ID in Groups section of molecule file
+E: Invalid atom ID in Fragments section of molecule file
 
 Self-explanatory.