git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7851 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/create_atoms.cpp

@@ -89,6 +89,7 @@ void CreateAtoms::command(int narg, char **arg)
   // process optional keywords
 
   int scaleflag = 1;
+  remapflag = 0;
 
   if (domain->lattice) {
     nbasis = domain->lattice->nbasis;
@@ -108,6 +109,12 @@ void CreateAtoms::command(int narg, char **arg)
 	error->all(FLERR,"Illegal create_atoms command");
       basistype[ibasis-1] = itype;
       iarg += 3;
+    } else if (strcmp(arg[iarg],"remap") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal create_atoms command");
+      if (strcmp(arg[iarg+1],"yes") == 0) remapflag = 1;
+      else if (strcmp(arg[iarg+1],"no") == 0) remapflag = 0;
+      else error->all(FLERR,"Illegal create_atoms command");
+      iarg += 2;
     } else if (strcmp(arg[iarg],"units") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal create_atoms command");
       if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
@@ -214,6 +221,13 @@ void CreateAtoms::add_single()
 {
   double *sublo,*subhi;
 
+  // remap atom if requested
+
+  if (remapflag) {
+    int imagetmp = (512 << 20) | (512 << 10) | 512;
+    domain->remap(xone,imagetmp);
+  }
+
   // sub-domain bounding box, in lamda units if triclinic
 
   if (domain->triclinic == 0) {

src/create_atoms.h

@@ -33,6 +33,7 @@ class CreateAtoms : protected Pointers {
   int itype,style,nregion,nbasis,nrandom,seed;
   int *basistype;
   double xone[3];
+  int remapflag;
 
   void add_single();
   void add_random();

src/delete_bonds.cpp

@@ -82,12 +82,14 @@ void DeleteBonds::command(int narg, char **arg)
 
   // grab optional keywords
 
+  int any_flag = 0;
   int undo_flag = 0;
   int remove_flag = 0;
   int special_flag = 0;
 
   while (iarg < narg) {
-    if (strcmp(arg[iarg],"undo") == 0) undo_flag = 1;
+    if (strcmp(arg[iarg],"any") == 0) any_flag = 1;
+    else if (strcmp(arg[iarg],"undo") == 0) undo_flag = 1;
     else if (strcmp(arg[iarg],"remove") == 0) remove_flag = 1;
     else if (strcmp(arg[iarg],"special") == 0) special_flag = 1;
     else error->all(FLERR,"Illegal delete_bonds command");
@@ -107,7 +109,7 @@ void DeleteBonds::command(int narg, char **arg)
 
   // set topology interactions either off or on
   // criteria for an interaction to potentially be changed (set flag = 1)
-  //   all atoms in interaction must be in group
+  //   all atoms or one atom in interaction must be in group, based on any_flag
   //   for style = MULTI, no other criteria
   //   for style = ATOM, at least one atom is specified type
   //   for style = BOND/ANGLE/DIHEDRAL/IMPROPER, interaction is specified type
@@ -120,7 +122,7 @@ void DeleteBonds::command(int narg, char **arg)
   int *type = atom->type;
   int nlocal = atom->nlocal;
 
-  int i,m,n,flag;
+  int i,m,n,consider,flag;
   int atom1,atom2,atom3,atom4;
 
   if (atom->avec->bonds_allow) {
@@ -131,7 +133,12 @@ void DeleteBonds::command(int narg, char **arg)
       for (m = 0; m < num_bond[i]; m++) {
 	atom1 = atom->map(atom->bond_atom[i][m]);
 	if (atom1 == -1) error->one(FLERR,"Bond atom missing in delete_bonds");
-	if (mask[i] & groupbit && mask[atom1] & groupbit) {
+	consider = 0;
+	if (!any_flag && mask[i] & groupbit && mask[atom1] & groupbit) 
+	  consider = 1;
+	if (any_flag && (mask[i] & groupbit || mask[atom1] & groupbit)) 
+	  consider = 1;
+	if (consider) {
 	  flag = 0;
 	  if (style == MULTI) flag = 1;
 	  if (style == ATOM && 
@@ -159,8 +166,12 @@ void DeleteBonds::command(int narg, char **arg)
 	atom3 = atom->map(atom->angle_atom3[i][m]);
 	if (atom1 == -1 || atom2 == -1 || atom3 == -1)
 	  error->one(FLERR,"Angle atom missing in delete_bonds");
-	if (mask[atom1] & groupbit && mask[atom2] & groupbit &&
+	consider = 0;
-	    mask[atom3] & groupbit) {
+	if (!any_flag && mask[atom1] & groupbit && mask[atom2] & groupbit &&
+	    mask[atom3] & groupbit) consider = 1;
+	if (any_flag && (mask[atom1] & groupbit || mask[atom2] & groupbit ||
+			  mask[atom3] & groupbit)) consider = 1;
+	if (consider) {
 	  flag = 0;
 	  if (style == MULTI) flag = 1;
 	  if (style == ATOM && 
@@ -190,8 +201,13 @@ void DeleteBonds::command(int narg, char **arg)
 	atom4 = atom->map(atom->dihedral_atom4[i][m]);
 	if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1)
 	  error->one(FLERR,"Dihedral atom missing in delete_bonds");
-	if (mask[atom1] & groupbit && mask[atom2] & groupbit &&
+	consider = 0;
-	    mask[atom3] & groupbit && mask[atom4] & groupbit) {
+	if (!any_flag && mask[atom1] & groupbit && mask[atom2] & groupbit &&
+	    mask[atom3] & groupbit && mask[atom4] & groupbit) consider = 1;
+	if (any_flag && (mask[atom1] & groupbit || mask[atom2] & groupbit ||
+			 mask[atom3] & groupbit || mask[atom4] & groupbit))
+	  consider = 1;
+	if (consider) {
 	  flag = 0;
 	  if (style == MULTI) flag = 1;
 	  if (style == ATOM && 
@@ -221,8 +237,13 @@ void DeleteBonds::command(int narg, char **arg)
 	atom4 = atom->map(atom->improper_atom4[i][m]);
 	if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1)
 	  error->one(FLERR,"Improper atom missing in delete_bonds");
-	if (mask[atom1] & groupbit && mask[atom2] & groupbit &&
+	consider = 0;
-	    mask[atom3] & groupbit && mask[atom4] & groupbit) {
+	if (!any_flag && mask[atom1] & groupbit && mask[atom2] & groupbit &&
+	    mask[atom3] & groupbit && mask[atom4] & groupbit) consider = 1;
+	if (any_flag && (mask[atom1] & groupbit || mask[atom2] & groupbit ||
+			 mask[atom3] & groupbit || mask[atom4] & groupbit))
+	  consider = 1;
+	if (consider) {
 	  flag = 0;
 	  if (style == MULTI) flag = 1;
 	  if (style == ATOM && 

src/input.cpp

@@ -284,7 +284,7 @@ void Input::parse()
 
   strcpy(copy,line);
 
-  // strip any # comment by resetting string terminator
+  // strip any # comment by replacing it with 0
   // do not strip # inside single/double quotes
 
   char quote = '\0';
@@ -306,40 +306,59 @@ void Input::parse()
 
   // command = 1st arg
 
-  command = strtok(copy," \t\n\r\f");
+  char *next;
+  command = nextword(copy,&next);
   if (command == NULL) return;
 
   // point arg[] at each subsequent arg
-  // treat text between single/double quotes as one arg
+  // nextword() inserts zeroes in copy to delimit args
-  // insert string terminators in copy to delimit args
+  // nextword() treats text between single/double quotes as one arg
-
-  quote = '\0';
-  int iarg,argstart;
 
   narg = 0;
-  while (1) {
+  ptr = next;
+  while (ptr) {
     if (narg == maxarg) {
       maxarg += DELTA;
       arg = (char **) memory->srealloc(arg,maxarg*sizeof(char *),"input:arg");
     }
-    arg[narg] = strtok(NULL," \t\n\r\f");
+    arg[narg] = nextword(ptr,&next);
     if (!arg[narg]) break;
-    if (!quote && (arg[narg][0] == '"' || arg[narg][0] == '\'')) {
-      quote = arg[narg][0];
-      argstart = narg;
-      arg[narg] = &arg[narg][1];
-    }
-    if (quote && arg[narg][strlen(arg[narg])-1] == quote) {
-      for (iarg = argstart; iarg < narg; iarg++)
-	arg[iarg][strlen(arg[iarg])] = ' ';
-      arg[narg][strlen(arg[narg])-1] = '\0';
-      narg = argstart;
-      quote = '\0';
-    }
     narg++;
+    ptr = next;
   }
+}
 
-  if (quote) error->all(FLERR,"Unbalanced quotes in input line");
+/* ----------------------------------------------------------------------
+   find next word in str
+   insert 0 at end of word
+   ignore leading whitespace
+   treat text between single/double quotes as one arg
+     matching quote must be followed by whitespace char if not end of string
+     strip quotes from returned word
+   return ptr to start of word
+   return next = ptr after word or NULL if word ended with 0
+   return NULL if no word in string
+------------------------------------------------------------------------- */
+
+char *Input::nextword(char *str, char **next)
+{
+  char *start,*stop;
+
+  start = &str[strspn(str," \t\n\v\f\r")];
+  if (*start == '\0') return NULL;
+
+  if (*start == '"' || *start == '\'') {
+    stop = strchr(&start[1],*start);
+    if (!stop) error->all(FLERR,"Unbalanced quotes in input line");
+    if (stop[1] && !isspace(stop[1]))
+      error->all(FLERR,"Input line quote not followed by whitespace");
+    start++;
+  } else stop = &start[strcspn(start," \t\n\v\f\r")];
+
+  if (*stop == '\0') *next = NULL;
+  else *next = stop+1;
+  *stop = '\0';
+  return start;
 }
 
 /* ----------------------------------------------------------------------

src/input.h

@@ -46,8 +46,9 @@ class Input : protected Pointers {
 
   FILE **infiles;              // list of open input files
 
-  void parse();                // parse an input text line
+  void parse();                      // parse an input text line
-  int execute_command();       // execute a single command
+  char *nextword(char *, char **);   // find next word in string, with quotes
+  int execute_command();             // execute a single command
 
   void clear();                // input script commands
   void echo();

src/output.cpp

@@ -502,6 +502,8 @@ void Output::create_restart(int narg, char **arg)
 
   restart = new WriteRestart(lmp);
 
+  if (narg != 2 && narg != 3) error->all(FLERR,"Illegal restart command");
+
   int n = strlen(arg[1]) + 3;
   restart1 = new char[n];
   strcpy(restart1,arg[1]);