Add PotentialFileReader and use it in PairSW

src/MANYBODY/pair_sw.cpp

@@ -29,6 +29,8 @@
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "utils.h"
+#include "tokenizer.h"
+#include "potential_file_reader.h"
 
 using namespace LAMMPS_NS;
 
@@ -347,128 +349,84 @@ double PairSW::init_one(int i, int j)
 
 void PairSW::read_file(char *file)
 {
-  int params_per_line = 14;
-  char **words = new char*[params_per_line+1];
-
   memory->sfree(params);
   params = NULL;
   nparams = maxparam = 0;
 
   // open file on proc 0
 
-  FILE *fp;
   if (comm->me == 0) {
-    fp = force->open_potential(file);
+    PotentialFileReader reader(lmp, file, "Stillinger-Weber");
-    if (fp == NULL) {
+    char * line;
-      char str[128];
-      snprintf(str,128,"Cannot open Stillinger-Weber potential file %s",file);
-      error->one(FLERR,str);
-    }
-  }
 
-  // read each set of params from potential file
+    while(line = reader.next_line(Param::NPARAMS_PER_LINE)) {
-  // one set of params can span multiple lines
+      try {
-  // store params if all 3 element tags are in element list
+        ValueTokenizer values(line, " \t\n\r\f");
 
-  int n,nwords,ielement,jelement,kelement;
+        std::string iword = values.next_string();
-  char line[MAXLINE],*ptr;
+        std::string jword = values.next_string();
-  int eof = 0;
+        std::string kword = values.next_string();
 
-  while (1) {
+        // ielement,jelement,kelement = 1st args
-    if (comm->me == 0) {
+        // if all 3 args are in element list, then parse this line
-      ptr = fgets(line,MAXLINE,fp);
+        // else skip to next entry in file
-      if (ptr == NULL) {
+        int ielement, jelement, kelement;
-        eof = 1;
-        fclose(fp);
-      } else n = strlen(line) + 1;
-    }
-    MPI_Bcast(&eof,1,MPI_INT,0,world);
-    if (eof) break;
-    MPI_Bcast(&n,1,MPI_INT,0,world);
-    MPI_Bcast(line,n,MPI_CHAR,0,world);
 
-    // strip comment, skip line if blank
+        for (ielement = 0; ielement < nelements; ielement++)
+          if (iword == elements[ielement]) break;
+        if (ielement == nelements) continue;
+        for (jelement = 0; jelement < nelements; jelement++)
+          if (jword == elements[jelement]) break;
+        if (jelement == nelements) continue;
+        for (kelement = 0; kelement < nelements; kelement++)
+          if (kword == elements[kelement]) break;
+        if (kelement == nelements) continue;
 
-    if ((ptr = strchr(line,'#'))) *ptr = '\0';
+        // load up parameter settings and error check their values
-    nwords = utils::count_words(line);
-    if (nwords == 0) continue;
 
-    // concatenate additional lines until have params_per_line words
+        if (nparams == maxparam) {
+          maxparam += DELTA;
+          params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
+                                              "pair:params");
+        }
 
-    while (nwords < params_per_line) {
+        params[nparams].ielement = ielement;
-      n = strlen(line);
+        params[nparams].jelement = jelement;
-      if (comm->me == 0) {
+        params[nparams].kelement = kelement;
-        ptr = fgets(&line[n],MAXLINE-n,fp);
+        params[nparams].epsilon  = values.next_double();
-        if (ptr == NULL) {
+        params[nparams].sigma    = values.next_double();
-          eof = 1;
+        params[nparams].littlea  = values.next_double();
-          fclose(fp);
+        params[nparams].lambda   = values.next_double();
-        } else n = strlen(line) + 1;
+        params[nparams].gamma    = values.next_double();
+        params[nparams].costheta = values.next_double();
+        params[nparams].biga     = values.next_double();
+        params[nparams].bigb     = values.next_double();
+        params[nparams].powerp   = values.next_double();
+        params[nparams].powerq   = values.next_double();
+        params[nparams].tol      = values.next_double();
+      } catch (TokenizerException & e) {
+        error->one(FLERR, e.what());
       }
-      MPI_Bcast(&eof,1,MPI_INT,0,world);
+
-      if (eof) break;
+      if (params[nparams].epsilon < 0.0 || params[nparams].sigma < 0.0 ||
-      MPI_Bcast(&n,1,MPI_INT,0,world);
+          params[nparams].littlea < 0.0 || params[nparams].lambda < 0.0 ||
-      MPI_Bcast(line,n,MPI_CHAR,0,world);
+          params[nparams].gamma < 0.0 || params[nparams].biga < 0.0 ||
-      if ((ptr = strchr(line,'#'))) *ptr = '\0';
+          params[nparams].bigb < 0.0 || params[nparams].powerp < 0.0 ||
-      nwords = utils::count_words(line);
+          params[nparams].powerq < 0.0 || params[nparams].tol < 0.0)
+        error->one(FLERR,"Illegal Stillinger-Weber parameter");
+
+      nparams++;
     }
-
-    if (nwords != params_per_line)
-      error->all(FLERR,"Incorrect format in Stillinger-Weber potential file");
-
-    // words = ptrs to all words in line
-
-    nwords = 0;
-    words[nwords++] = strtok(line," \t\n\r\f");
-    while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
-
-    // ielement,jelement,kelement = 1st args
-    // if all 3 args are in element list, then parse this line
-    // else skip to next entry in file
-
-    for (ielement = 0; ielement < nelements; ielement++)
-      if (strcmp(words[0],elements[ielement]) == 0) break;
-    if (ielement == nelements) continue;
-    for (jelement = 0; jelement < nelements; jelement++)
-      if (strcmp(words[1],elements[jelement]) == 0) break;
-    if (jelement == nelements) continue;
-    for (kelement = 0; kelement < nelements; kelement++)
-      if (strcmp(words[2],elements[kelement]) == 0) break;
-    if (kelement == nelements) continue;
-
-    // load up parameter settings and error check their values
-
-    if (nparams == maxparam) {
-      maxparam += DELTA;
-      params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
-                                          "pair:params");
-    }
-
-    params[nparams].ielement = ielement;
-    params[nparams].jelement = jelement;
-    params[nparams].kelement = kelement;
-    params[nparams].epsilon = atof(words[3]);
-    params[nparams].sigma = atof(words[4]);
-    params[nparams].littlea = atof(words[5]);
-    params[nparams].lambda = atof(words[6]);
-    params[nparams].gamma = atof(words[7]);
-    params[nparams].costheta = atof(words[8]);
-    params[nparams].biga = atof(words[9]);
-    params[nparams].bigb = atof(words[10]);
-    params[nparams].powerp = atof(words[11]);
-    params[nparams].powerq = atof(words[12]);
-    params[nparams].tol = atof(words[13]);
-
-    if (params[nparams].epsilon < 0.0 || params[nparams].sigma < 0.0 ||
-        params[nparams].littlea < 0.0 || params[nparams].lambda < 0.0 ||
-        params[nparams].gamma < 0.0 || params[nparams].biga < 0.0 ||
-        params[nparams].bigb < 0.0 || params[nparams].powerp < 0.0 ||
-        params[nparams].powerq < 0.0 || params[nparams].tol < 0.0)
-      error->all(FLERR,"Illegal Stillinger-Weber parameter");
-
-    nparams++;
   }
 
-  delete [] words;
+  MPI_Bcast(&nparams, 1, MPI_INT, 0, world);
+  MPI_Bcast(&maxparam, 1, MPI_INT, 0, world);
+
+  if(comm->me != 0) {
+    params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), "pair:params");
+  }
+
+  MPI_Bcast(params, maxparam*sizeof(Param), MPI_BYTE, 0, world);
 }
 
 /* ---------------------------------------------------------------------- */

src/MANYBODY/pair_sw.h

@@ -44,6 +44,7 @@ class PairSW : public Pair {
     double sigma_gamma,lambda_epsilon,lambda_epsilon2;
     double c1,c2,c3,c4,c5,c6;
     int ielement,jelement,kelement;
+    static const int NPARAMS_PER_LINE = 14;
   };
 
  protected:

src/potential_file_reader.cpp

@@ -0,0 +1,82 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing authors: Richard Berger (Temple U)
+------------------------------------------------------------------------- */
+
+#include "lammps.h"
+#include "force.h"
+#include "error.h"
+#include "comm.h"
+#include "potential_file_reader.h"
+#include "utils.h"
+
+#include <cstring>
+
+using namespace LAMMPS_NS;
+
+PotentialFileReader::PotentialFileReader(LAMMPS *lmp,
+                                         const std::string &filename,
+                                         const std::string &potential_name) : Pointers(lmp) {
+  if (comm->me != 0) {
+    error->one(FLERR, "PotentialFileReader should only be called by proc 0!");
+  }
+
+  fp = force->open_potential(filename.c_str());
+
+  if (fp == NULL) {
+    char str[128];
+    snprintf(str, 128, "cannot open %s potential file %s", potential_name.c_str(), filename.c_str());
+    error->one(FLERR, str);
+  }
+}
+
+PotentialFileReader::~PotentialFileReader() {
+  fclose(fp);
+}
+
+char *PotentialFileReader::next_line(int nparams) {
+  // concatenate lines until have nparams words
+  int n = 0;
+  int nwords = 0;
+
+  do {
+    char *ptr = fgets(&line[n], MAXLINE - n, fp);
+
+    if (ptr == nullptr) {
+      // EOF
+      if (nwords > 0 && nwords < nparams)
+      {
+        char str[128];
+        snprintf(str, 128, "Incorrect format in %s potential file", potential_name.c_str());
+        error->all(FLERR, str);
+      }
+
+      return nullptr;
+    }
+
+    // strip comment
+    if ((ptr = strchr(line, '#'))) *ptr = '\0';
+
+    nwords = utils::count_words(line);
+
+    // skip line if blank
+    if (nwords == 0)
+      continue;
+
+    n = strlen(line) + 1;
+  } while (nwords < nparams);
+
+  return line;
+}

src/potential_file_reader.h

@@ -0,0 +1,42 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing authors: Richard Berger (Temple U)
+------------------------------------------------------------------------- */
+
+#ifndef LMP_POTENTIAL_FILE_READER_H
+#define LMP_POTENTIAL_FILE_READER_H
+
+#include <string>
+
+#include "pointers.h"
+
+namespace LAMMPS_NS
+{
+  class PotentialFileReader : protected Pointers {
+    std::string potential_name;
+    static const int MAXLINE = 1024;
+    char line[MAXLINE];
+    FILE *fp;
+
+  public:
+    PotentialFileReader(class LAMMPS *lmp, const std::string &filename, const std::string &potential_name);
+    ~PotentialFileReader();
+
+    char *next_line(int nparams);
+  };
+
+} // namespace LAMMPS_NS
+
+#endif