git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15304 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/molecule.cpp

@@ -103,9 +103,6 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
       sizescale = force->numeric(FLERR,arg[iarg+1]);
       if (sizescale <= 0.0) error->all(FLERR,"Illegal molecule command");
       iarg += 2;
-
-    // NOTE: add other geometric ops for points/lines/tris
-
     } else break;
   }
 
@@ -120,14 +117,11 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
 
   initialize();
 
-  // scan file for sizes of all fields
+  // scan file for sizes of all fields and allocate them
 
   if (me == 0) open(arg[ifile]);
   read(0);
   if (me == 0) fclose(fp);
-
-  // allocate memory for all fields defined in file
-
   allocate();
 
   // read file again to populate all fields
@@ -139,34 +133,22 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
   // stats
 
   if (me == 0) {
-    if (screen) {
+    if (screen)
-      fprintf(screen,"Read molecule %s:\n",id);
+      fprintf(screen,"Read molecule %s:\n"
-      if (natoms) 
+              "  %d atoms with %d types\n  %d bonds with %d types\n"
-        fprintf(screen,"  %d atoms with %d types\n  %d bonds with %d types\n"
               "  %d angles with %d types\n  %d dihedrals with %d types\n"
               "  %d impropers with %d types\n",
-                natoms,ntypes,
+              id,natoms,ntypes,
               nbonds,nbondtypes,nangles,nangletypes,
               ndihedrals,ndihedraltypes,nimpropers,nimpropertypes);
-      if (npoints && nlines) 
+    if (logfile)
-        fprintf(screen,"  %d lines with %d points\n",nlines,npoints);
+      fprintf(logfile,"Read molecule %s:\n"
-      if (npoints && ntris) 
+              "  %d atoms with %d types\n  %d bonds with %d types\n"
-        fprintf(screen,"  %d triangles with %d points\n",ntris,npoints);
-    }
-    if (logfile) {
-      fprintf(logfile,"Read molecule %s:\n",id);
-      if (natoms) 
-        fprintf(logfile,"  %d atoms with %d types\n  %d bonds with %d types\n"
               "  %d angles with %d types\n  %d dihedrals with %d types\n"
               "  %d impropers with %d types\n",
-                natoms,ntypes,
+              id,natoms,ntypes,
               nbonds,nbondtypes,nangles,nangletypes,
               ndihedrals,ndihedraltypes,nimpropers,nimpropertypes);
-      if (npoints && nlines) 
-        fprintf(logfile,"  %d lines with %d points\n",nlines,npoints);
-      if (npoints && ntris) 
-        fprintf(logfile,"  %d triangles with %d points\n",ntris,npoints);
-    }
   }
 }
 
@@ -435,14 +417,8 @@ void Molecule::read(int flag)
     if (strspn(line," \t\n\r") == strlen(line)) continue;
 
     // search line for header keywords and set corresponding variable
-    // check for triangles before angles so "triangles" not matched as "angles"
 
     if (strstr(line,"atoms")) sscanf(line,"%d",&natoms);
-
-    else if (strstr(line,"points")) sscanf(line,"%d",&npoints);
-    else if (strstr(line,"lines")) sscanf(line,"%d",&nlines);
-    else if (strstr(line,"triangles")) sscanf(line,"%d",&ntris);
-
     else if (strstr(line,"bonds")) sscanf(line,"%d",&nbonds);
     else if (strstr(line,"angles")) sscanf(line,"%d",&nangles);
     else if (strstr(line,"dihedrals")) sscanf(line,"%d",&ndihedrals);
@@ -487,11 +463,8 @@ void Molecule::read(int flag)
 
   // error checks
 
-  if (natoms < 0) error->all(FLERR,"Invalid atom count in molecule file");
+  if (natoms < 1) 
-  if (npoints < 0) error->all(FLERR,"Invalid point count in molecule file");
+    error->all(FLERR,"No count or invalid atom count in molecule file");
-  if (nlines < 0) error->all(FLERR,"Invalid line count in molecule file");
-  if (ntris < 0) error->all(FLERR,"Invalid triangle count in molecule file");
-
   if (nbonds < 0) error->all(FLERR,"Invalid bond count in molecule file");
   if (nangles < 0) error->all(FLERR,"Invalid angle count in molecule file");
   if (ndihedrals < 0)
@@ -499,21 +472,6 @@ void Molecule::read(int flag)
   if (nimpropers < 0)
     error->all(FLERR,"Invalid improper count in molecule file");
 
-  if (natoms == 0 && npoints == 0) 
-    error->all(FLERR,"Molecule file must define either atoms or points");
-  if (natoms && npoints) 
-    error->all(FLERR,"Molecule file cannot define both atoms and points");
-
-  if (npoints && domain->dimension == 2 && nlines == 0)
-    error->all(FLERR,"Molecule file must define lines with points");
-  if (npoints && domain->dimension == 2 && ntris)
-    error->all(FLERR,"Molecule file cannot define triangles for 2d model");
-
-  if (npoints && domain->dimension == 3 && ntris == 0)
-    error->all(FLERR,"Molecule file must define triangles with points");
-  if (npoints && domain->dimension == 3 && nlines)
-    error->all(FLERR,"Molecule file cannot define lines for 3d model");
-
   // count = vector for tallying bonds,angles,etc per atom
 
   if (flag == 0) memory->create(count,natoms,"molecule:count");
@@ -548,19 +506,6 @@ void Molecule::read(int flag)
       if (flag) masses(line);
       else skip_lines(natoms,line);
 
-    } else if (strcmp(keyword,"Points") == 0) {
-      pointflag = 1;
-      if (flag) pts(line);
-      else skip_lines(npoints,line);
-    } else if (strcmp(keyword,"Lines") == 0) {
-      lineflag = 1;
-      if (flag) line_segments(line);
-      else skip_lines(nlines,line);
-    } else if (strcmp(keyword,"Triangles") == 0) {
-      triflag = 1;
-      if (flag) triangles(line);
-      else skip_lines(ntris,line);
-
     } else if (strcmp(keyword,"Bonds") == 0) {
       if (nbonds == 0)
 	error->all(FLERR,"Molecule file has bonds but no nbonds setting");
@@ -634,15 +579,6 @@ void Molecule::read(int flag)
   // error check
 
   if (flag == 0) {
-    if (natoms && !xflag)
-      error->all(FLERR,"Molecule file has no Coords section");
-    if (npoints && !pointflag)
-      error->all(FLERR,"Molecule file has no Points section");
-    if (nlines && !lineflag)
-      error->all(FLERR,"Molecule file has no Lines section");
-    if (ntris && !triflag)
-      error->all(FLERR,"Molecule file has no Triangles section");
-
     if ((nspecialflag && !specialflag) || (!nspecialflag && specialflag))
       error->all(FLERR,"Molecule file needs both Special Bond sections");
     if (specialflag && !bondflag)
@@ -803,100 +739,6 @@ void Molecule::masses(char *line)
     if (rmass[i] <= 0.0) error->all(FLERR,"Invalid atom mass in molecule file");
 }
 
-/* ----------------------------------------------------------------------
-   read line/tri points from file
-------------------------------------------------------------------------- */
-
-void Molecule::pts(char *line)
-{
-  int tmp;
-  for (int i = 0; i < npoints; i++) {
-    readline(line);
-    if (i == 0) {
-      int nwords = atom->count_words(line);
-      if (nwords != 4)
-        error->all(FLERR,"Invalid Points section in molecule file");
-    }
-    sscanf(line,"%d %lg %lg %lg",&tmp,
-           &points[i][0],&points[i][1],&points[i][2]);
-
-    // apply geometric operations to each point
-
-    points[i][0] *= sizescale;
-    points[i][1] *= sizescale;
-    points[i][2] *= sizescale;
-  }
-
-  if (domain->dimension == 2) {
-    for (int i = 0; i < natoms; i++)
-      if (points[i][2] != 0.0)
-        error->all(FLERR,"Molecule file z point must be 0.0 for 2d");
-  }
-}
-
-/* ----------------------------------------------------------------------
-   read line segments from file
-   do not subtract one from point indices
-------------------------------------------------------------------------- */
-
-void Molecule::line_segments(char *line)
-{
-  int tmp;
-  for (int i = 0; i < nlines; i++) {
-    readline(line);
-    if (i == 0) {
-      int nwords = atom->count_words(line);
-      if (nwords != 5)
-        error->all(FLERR,"Invalid Lines section in molecule file");
-    }
-    sscanf(line,"%d %d %d %d %d",&tmp,&molline[i],&typeline[i],
-           &lines[i][0],&lines[i][1]);
-    typeline[i] += toffset;
-  }
-
-  // check all types and point indices
-
-  for (int i = 0; i < nlines; i++) {
-    if (typeline[i] <= 0)
-      error->all(FLERR,"Invalid line type in molecule file");
-    if (lines[i][0] <= 0 || lines[i][0] > npoints ||
-        lines[i][1] <= 0 || lines[i][1] > npoints)
-      error->all(FLERR,"Invalid point index for line in molecule file");
-  }
-}
-
-/* ----------------------------------------------------------------------
-   read triangles from file
-   do not subtract one from point indices
-------------------------------------------------------------------------- */
-
-void Molecule::triangles(char *line)
-{
-  int tmp;
-  for (int i = 0; i < ntris; i++) {
-    readline(line);
-    if (i == 0) {
-      int nwords = atom->count_words(line);
-      if (nwords != 6)
-        error->all(FLERR,"Invalid Triangles section in molecule file");
-    }
-    sscanf(line,"%d %d %d %d %d %d",&tmp,&moltri[i],&typetri[i],
-           &tris[i][0],&tris[i][1],&tris[i][2]);
-    typetri[i] += toffset;
-  }
-
-  // check all types and point indices
-
-  for (int i = 0; i < ntris; i++) {
-    if (typetri[i] <= 0)
-      error->all(FLERR,"Invalid triangle type in molecule file");
-    if (tris[i][0] <= 0 || tris[i][0] > npoints ||
-        tris[i][1] <= 0 || tris[i][1] > npoints ||
-        tris[i][2] <= 0 || tris[i][2] > npoints)
-      error->all(FLERR,"Invalid point index for triangle in molecule file");
-  }
-}
-
 /* ----------------------------------------------------------------------
    read bonds from file
    set nbondtypes = max type of any bond
@@ -1563,15 +1405,10 @@ void Molecule::initialize()
   nbondtypes = nangletypes = ndihedraltypes = nimpropertypes = 0;
   nibody = ndbody = 0;
 
-  npoints = 0;
-  nlines = 0;
-  ntris = 0;
-
   bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
   maxspecial = 0;
 
   xflag = typeflag = qflag = radiusflag = rmassflag = 0;
-  pointflag = lineflag = triflag = 0;
   bondflag = angleflag = dihedralflag = improperflag = 0;
   nspecialflag = specialflag = 0;
   shakeflag = shakeflagflag = shakeatomflag = shaketypeflag = 0;
@@ -1586,14 +1423,6 @@ void Molecule::initialize()
   radius = NULL;
   rmass = NULL;
 
-  points = NULL;
-  lines = NULL;
-  molline = NULL;
-  typeline = NULL;
-  tris = NULL;
-  moltri = NULL;
-  typetri = NULL;
-
   num_bond = NULL;
   bond_type = NULL;
   bond_atom = NULL;
@@ -1638,20 +1467,6 @@ void Molecule::allocate()
   if (radiusflag) memory->create(radius,natoms,"molecule:radius");
   if (rmassflag) memory->create(rmass,natoms,"molecule:rmass");
 
-  // lines or triangles with corner points
-
-  if (pointflag) memory->create(points,npoints,3,"molecule:points");
-  if (lineflag) {
-    memory->create(lines,nlines,2,"molecule:lines");
-    memory->create(molline,nlines,"molecule:molline");
-    memory->create(typeline,nlines,"molecule:typeline");
-  }
-  if (triflag) {
-    memory->create(tris,ntris,3,"molecule:tris");
-    memory->create(moltri,ntris,"molecule:moltri");
-    memory->create(typetri,ntris,"molecule:typetri");
-  }
-
   // always allocate num_bond,num_angle,etc and special+nspecial
   // even if not in molecule file, initialize to 0
   // this is so methods that use these arrays don't have to check they exist
@@ -1739,14 +1554,6 @@ void Molecule::deallocate()
   memory->destroy(radius);
   memory->destroy(rmass);
 
-  memory->destroy(points);
-  memory->destroy(lines);
-  memory->destroy(molline);
-  memory->destroy(typeline);
-  memory->destroy(tris);
-  memory->destroy(moltri);
-  memory->destroy(typetri);
-
   memory->destroy(num_bond);
   memory->destroy(bond_type);
   memory->destroy(bond_atom);

src/molecule.h

@@ -34,10 +34,6 @@ class Molecule : protected Pointers {
   int nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
   int nibody,ndbody;
 
-  // for surface lines or tris with corner points
-
-  int npoints,nlines,ntris;
-
   // max bond,angle,etc per atom
 
   int bond_per_atom,angle_per_atom,dihedral_per_atom,improper_per_atom;
@@ -50,7 +46,6 @@ class Molecule : protected Pointers {
   int nspecialflag,specialflag;
   int shakeflag,shakeflagflag,shakeatomflag,shaketypeflag;
   int bodyflag,ibodyflag,dbodyflag;
-  int pointflag,lineflag,triflag;
 
   // 1 if attribute defined or computed, 0 if not
 
@@ -68,14 +63,6 @@ class Molecule : protected Pointers {
   double *radius;      // radius of each atom
   double *rmass;       // mass of each atom
 
-  double **points;     // end/corner pts of lines or tris
-  int **lines;         // list of line indices into points
-  int **tris;          // list of tri indices into points
-  int *molline;
-  int *typeline;
-  int *moltri;
-  int *typetri;
-
   int *num_bond;       // bonds, angles, dihedrals, impropers for each atom
   int **bond_type;
   tagint **bond_atom;
@@ -147,10 +134,6 @@ class Molecule : protected Pointers {
   void charges(char *);
   void diameters(char *);
   void masses(char *);
-  void pts(char *);
-  void line_segments(char *);
-  void triangles(char *);
-
   void bonds(int, char *);
   void angles(int, char *);
   void dihedrals(int, char *);