use tokenizer to read neb initial replica files

examples/SPIN/gneb/iron/final.iron_spin

@@ -32,37 +32,3 @@
 31 2.2000000000000002e+00 7.1662499999999998e+00 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
 32 2.2000000000000002e+00 1.0032750000000000e+01 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
 
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-

examples/SPIN/gneb/iron/initial.iron_spin

@@ -5,7 +5,7 @@ LAMMPS data file via write_data, version 4 Jan 2019, timestep = 0
 
 0.0000000000000000e+00 1.1465999999999999e+01 xlo xhi
 0.0000000000000000e+00 1.1465999999999999e+01 ylo yhi
-0.0000000000000000e+00 2.8664999999999998e+00 zlo zhi
+-1.0000000000000000e+00 10.0664999999999998e+00 zlo zhi
 
 Masses
 

src/REPLICA/fix_neb.cpp

@@ -135,24 +135,24 @@ FixNEB::FixNEB(LAMMPS *lmp, int narg, char **arg) :
   else procnext = -1;
 
   uworld = universe->uworld;
+  if (NEBLongRange) {
     int *iroots = new int[nreplica];
     MPI_Group uworldgroup,rootgroup;
-  if (NEBLongRange) {
+
-    for (int i=0; i<nreplica; i++)
+    for (int i=0; i<nreplica; i++) iroots[i] = universe->root_proc[i];
-      iroots[i] = universe->root_proc[i];
     MPI_Comm_group(uworld, &uworldgroup);
     MPI_Group_incl(uworldgroup, nreplica, iroots, &rootgroup);
     MPI_Comm_create(uworld, rootgroup, &rootworld);
-  }
+    if (rootgroup != MPI_GROUP_NULL) MPI_Group_free(&rootgroup);
+    if (uworldgroup != MPI_GROUP_NULL) MPI_Group_free(&uworldgroup);
     delete [] iroots;
+  }
 
   // create a new compute pe style
   // id = fix-ID + pe, compute group = all
 
-  std::string cmd = id + std::string("_pe");
+  id_pe = utils::strdup(std::string(id)+"_pe");
-  id_pe = new char[cmd.size()+1];
+  modify->add_compute(std::string(id_pe)+" all pe");
-  strcpy(id_pe,cmd.c_str());
-  modify->add_compute(cmd + " all pe");
 
   // initialize local storage
 

src/REPLICA/neb.cpp

@@ -27,6 +27,7 @@
 #include "output.h"
 #include "thermo.h"
 #include "timer.h"
+#include "tokenizer.h"
 #include "universe.h"
 #include "update.h"
 
@@ -173,12 +174,11 @@ void NEB::run()
   else color = 1;
   MPI_Comm_split(uworld,color,0,&roots);
 
-  int ineb;
+  auto fixes = modify->get_fix_by_style("^neb$");
-  for (ineb = 0; ineb < modify->nfix; ineb++)
+  if (fixes.size() != 1)
-    if (strcmp(modify->fix[ineb]->style,"neb") == 0) break;
+    error->all(FLERR,"NEB requires use of exactly one fix neb instance");
-  if (ineb == modify->nfix) error->all(FLERR,"NEB requires use of fix neb");
 
-  fneb = (FixNEB *) modify->fix[ineb];
+  fneb = (FixNEB *) fixes[0];
   if (verbose) numall =7;
   else  numall = 4;
   memory->create(all,nreplica,numall,"neb:all");
@@ -376,11 +376,11 @@ void NEB::run()
 
 void NEB::readfile(char *file, int flag)
 {
-  int i,j,m,nchunk,eofflag,nlines;
+  int i,nchunk,eofflag,nlines;
   tagint tag;
   char *eof,*start,*next,*buf;
   char line[MAXLINE];
-  double xx,yy,zz,delx,dely,delz;
+  double delx,dely,delz;
 
   if (me_universe == 0 && universe->uscreen)
     fprintf(universe->uscreen,"Reading NEB coordinate file(s) ...\n");
@@ -424,10 +424,7 @@ void NEB::readfile(char *file, int flag)
   }
 
   char *buffer = new char[CHUNK*MAXLINE];
-  char **values = new char*[ATTRIBUTE_PERLINE];
-
   double fraction = ireplica/(nreplica-1.0);
-
   double **x = atom->x;
   int nlocal = atom->nlocal;
 
@@ -435,9 +432,7 @@ void NEB::readfile(char *file, int flag)
   // two versions of read_lines_from_file() for world vs universe bcast
   // count # of atom coords changed so can check for invalid atom IDs in file
 
-  int ncount = 0;
+  int ncount = 0, nread = 0;
-
-  int nread = 0;
   while (nread < nlines) {
     nchunk = MIN(nlines-nread,CHUNK);
     if (flag == 0)
@@ -461,10 +456,10 @@ void NEB::readfile(char *file, int flag)
 
     for (i = 0; i < nchunk; i++) {
       next = strchr(buf,'\n');
+      *next = '\0';
 
-      values[0] = strtok(buf," \t\n\r\f");
+      try {
-      for (j = 1; j < nwords; j++)
+        ValueTokenizer values(buf," \t\n\r\f");
-        values[j] = strtok(nullptr," \t\n\r\f");
 
         // adjust atom coord based on replica fraction
         // for flag = 0, interpolate for intermediate and final replicas
@@ -476,17 +471,14 @@ void NEB::readfile(char *file, int flag)
         //   will be remapped back into box when simulation starts
         //   its image flags will then be adjusted
 
-      tag = ATOTAGINT(values[0]);
+        tag = values.next_tagint();
-      m = atom->map(tag);
+        int m = atom->map(tag);
         if (m >= 0 && m < nlocal) {
           ncount++;
-        xx = atof(values[1]);
-        yy = atof(values[2]);
-        zz = atof(values[3]);
 
-        delx = xx - x[m][0];
+          delx = values.next_double() - x[m][0];
-        dely = yy - x[m][1];
+          dely = values.next_double() - x[m][1];
-        delz = zz - x[m][2];
+          delz = values.next_double() - x[m][2];
 
           domain->minimum_image(delx,dely,delz);
 
@@ -500,10 +492,11 @@ void NEB::readfile(char *file, int flag)
             x[m][2] += delz;
           }
         }
-
+      } catch (std::exception &e) {
+        error->universe_one(FLERR,"Incorrectly formatted NEB file: " + std::string(e.what()));
+      }
       buf = next + 1;
     }
-
     nread += nchunk;
   }
 
@@ -522,9 +515,7 @@ void NEB::readfile(char *file, int flag)
   }
 
   // clean up
-
+  delete[] buffer;
-  delete [] buffer;
-  delete [] values;
 
   if (flag == 0) {
     if (me_universe == 0) {

src/SPIN/fix_neb_spin.cpp

@@ -56,7 +56,7 @@ FixNEBSpin::FixNEBSpin(LAMMPS *lmp, int narg, char **arg) :
   counts(nullptr), displacements(nullptr)
 {
 
-  if (narg < 4) error->all(FLERR,"Illegal fix neb_spin command");
+  if (narg < 4) error->all(FLERR,"Illegal fix neb/spin command");
 
   kspring = utils::numeric(FLERR,arg[3],false,lmp);
   if (kspring <= 0.0) error->all(FLERR,"Illegal fix neb command");
@@ -77,16 +77,16 @@ FixNEBSpin::FixNEBSpin(LAMMPS *lmp, int narg, char **arg) :
   int iarg = 4;
   while (iarg < narg) {
     if (strcmp(arg[iarg],"parallel") == 0) {
-      error->all(FLERR,"Illegal fix neb command");
+      error->all(FLERR,"Illegal fix neb/spin command");
       iarg += 2;
     } else if (strcmp(arg[iarg],"perp") == 0) {
-      error->all(FLERR,"Illegal fix neb command");
+      error->all(FLERR,"Illegal fix neb/spin command");
       iarg += 2;
     } else if (strcmp (arg[iarg],"end") == 0) {
       iarg += 3;
     } else if (strcmp (arg[iarg],"lattice") == 0) {
       iarg += 2;
-    } else error->all(FLERR,"Illegal fix neb command");
+    } else error->all(FLERR,"Illegal fix neb/spin command");
   }
 
   // nreplica = number of partitions
@@ -107,16 +107,18 @@ FixNEBSpin::FixNEBSpin(LAMMPS *lmp, int narg, char **arg) :
   else procnext = -1;
 
   uworld = universe->uworld;
+  if (NEBLongRange) {
     int *iroots = new int[nreplica];
     MPI_Group uworldgroup,rootgroup;
-  if (NEBLongRange) {
+
-    for (int i=0; i<nreplica; i++)
+    for (int i=0; i<nreplica; i++) iroots[i] = universe->root_proc[i];
-      iroots[i] = universe->root_proc[i];
     MPI_Comm_group(uworld, &uworldgroup);
     MPI_Group_incl(uworldgroup, nreplica, iroots, &rootgroup);
     MPI_Comm_create(uworld, rootgroup, &rootworld);
-  }
+    if (rootgroup != MPI_GROUP_NULL) MPI_Group_free(&rootgroup);
+    if (uworldgroup != MPI_GROUP_NULL) MPI_Group_free(&uworldgroup);
     delete [] iroots;
+  }
 
   // create a new compute pe style
   // id = fix-ID + pe, compute group = all

src/SPIN/neb_spin.cpp

@@ -38,6 +38,7 @@
 #include "output.h"
 #include "thermo.h"
 #include "timer.h"
+#include "tokenizer.h"
 #include "universe.h"
 #include "update.h"
 
@@ -147,6 +148,7 @@ void NEBSpin::command(int narg, char **arg)
 
   verbose=false;
   if (strcmp(arg[narg-1],"verbose") == 0) verbose=true;
+  // run the NEB calculation
 
   run();
 }
@@ -166,12 +168,11 @@ void NEBSpin::run()
 
   // search for neb_spin fix, allocate it
 
-  int ineb;
+  auto fixes = modify->get_fix_by_style("^neb/spin");
-  for (ineb = 0; ineb < modify->nfix; ineb++)
+  if (fixes.size() != 1)
-    if (strcmp(modify->fix[ineb]->style,"neb/spin") == 0) break;
+    error->all(FLERR,"NEBSpin requires use of exactly one fix neb/spin instance");
-  if (ineb == modify->nfix) error->all(FLERR,"NEBSpin requires use of fix neb/spin");
 
-  fneb = (FixNEBSpin *) modify->fix[ineb];
+  fneb = (FixNEBSpin *) fixes[0];
   if (verbose) numall =7;
   else  numall = 4;
   memory->create(all,nreplica,numall,"neb:all");
@@ -370,12 +371,11 @@ void NEBSpin::run()
 
 void NEBSpin::readfile(char *file, int flag)
 {
-  int i,j,m,nchunk,eofflag,nlines;
+  int i,nchunk,eofflag,nlines;
   tagint tag;
   char *eof,*start,*next,*buf;
   char line[MAXLINE];
-  double xx,yy,zz;
+  double musp,xx,yy,zz,spx,spy,spz;
-  double musp,spx,spy,spz;
 
   if (me_universe == 0 && universe->uscreen)
     fprintf(universe->uscreen,"Reading NEBSpin coordinate file(s) ...\n");
@@ -393,10 +393,12 @@ void NEBSpin::readfile(char *file, int flag)
         start = &line[strspn(line," \t\n\v\f\r")];
         if (*start != '\0' && *start != '#') break;
       }
-      sscanf(line,"%d",&nlines);
+      int rv = sscanf(line,"%d",&nlines);
+      if (rv != 1) nlines = -1;
     }
     MPI_Bcast(&nlines,1,MPI_INT,0,uworld);
-
+    if (nlines < 0)
+      error->universe_all(FLERR,"Incorrectly formatted NEB file");
   } else {
     if (me == 0) {
       if (ireplica) {
@@ -407,17 +409,17 @@ void NEBSpin::readfile(char *file, int flag)
           start = &line[strspn(line," \t\n\v\f\r")];
           if (*start != '\0' && *start != '#') break;
         }
-        sscanf(line,"%d",&nlines);
+        int rv = sscanf(line,"%d",&nlines);
+        if (rv != 1) nlines = -1;
       } else nlines = 0;
     }
     MPI_Bcast(&nlines,1,MPI_INT,0,world);
+    if (nlines < 0)
+      error->all(FLERR,"Incorrectly formatted NEB file");
   }
 
   char *buffer = new char[CHUNK*MAXLINE];
-  char **values = new char*[ATTRIBUTE_PERLINE];
-
   double fraction = ireplica/(nreplica-1.0);
-
   double **x = atom->x;
   double **sp = atom->sp;
   double spinit[3],spfinal[3];
@@ -427,11 +429,7 @@ void NEBSpin::readfile(char *file, int flag)
   // two versions of read_lines_from_file() for world vs universe bcast
   // count # of atom coords changed so can check for invalid atom IDs in file
 
-  int ncount = 0;
+  int ncount=0, nread=0, temp_flag=0, rot_flag=0;
-
-  int temp_flag,rot_flag;
-  temp_flag = rot_flag = 0;
-  int nread = 0;
   while (nread < nlines) {
     nchunk = MIN(nlines-nread,CHUNK);
     if (flag == 0)
@@ -444,7 +442,7 @@ void NEBSpin::readfile(char *file, int flag)
     buf = buffer;
     next = strchr(buf,'\n');
     *next = '\0';
-    int nwords = utils::trim_and_count_words(buf);
+    int nwords = utils::count_words(utils::trim_comment(buf));
     *next = '\n';
 
     if (nwords != ATTRIBUTE_PERLINE)
@@ -455,10 +453,10 @@ void NEBSpin::readfile(char *file, int flag)
 
     for (i = 0; i < nchunk; i++) {
       next = strchr(buf,'\n');
+      *next = '\0';
 
-      values[0] = strtok(buf," \t\n\r\f");
+      try {
-      for (j = 1; j < nwords; j++)
+        ValueTokenizer values(buf," \t\n\r\f");
-        values[j] = strtok(nullptr," \t\n\r\f");
 
         // adjust spin coord based on replica fraction
         // for flag = 0, interpolate for intermediate and final replicas
@@ -471,17 +469,18 @@ void NEBSpin::readfile(char *file, int flag)
         //     will be remapped back into box when simulation starts
         //     its image flags will then be adjusted
 
-      tag = ATOTAGINT(values[0]);
+        tag = values.next_tagint();
-      m = atom->map(tag);
+        int m = atom->map(tag);
         if (m >= 0 && m < nlocal) {
           ncount++;
-        musp = atof(values[1]);
+
-        xx = atof(values[2]);
+          musp = values.next_double();
-        yy = atof(values[3]);
+          xx = values.next_double();
-        zz = atof(values[4]);
+          yy = values.next_double();
-        spx = atof(values[5]);
+          zz = values.next_double();
-        spy = atof(values[6]);
+          spx = values.next_double();
-        spz = atof(values[7]);
+          spy = values.next_double();
+          spz = values.next_double();
 
           if (flag == 0) {
 
@@ -520,10 +519,11 @@ void NEBSpin::readfile(char *file, int flag)
             sp[m][2] = spz;
           }
         }
-
+      } catch (std::exception &e) {
+        error->universe_one(FLERR,"Incorrectly formatted NEB file: " + std::string(e.what()));
+      }
       buf = next + 1;
     }
-
     nread += nchunk;
   }
 
@@ -549,9 +549,7 @@ void NEBSpin::readfile(char *file, int flag)
   }
 
   // clean up
-
   delete[] buffer;
-  delete[] values;
 
   if (flag == 0) {
     if (me_universe == 0) {