Update pair nb3b harmonic

src/MANYBODY/pair_nb3b_harmonic.cpp

@@ -30,10 +30,11 @@
 #include "memory.h"
 #include "error.h"
 #include "utils.h"
+#include "tokenizer.h"
+#include "potential_file_reader.h"
 
 using namespace LAMMPS_NS;
 
-#define MAXLINE 1024
 #define DELTA 4
 #define SMALL 0.001
 #define PI 3.141592653589793238462643383279
@@ -283,92 +284,37 @@ double PairNb3bHarmonic::init_one(int i, int j)
 
 void PairNb3bHarmonic::read_file(char *file)
 {
-  int params_per_line = 6;
-  char **words = new char*[params_per_line+1];
-
   memory->sfree(params);
-  params = NULL;
+  params = nullptr;
   nparams = maxparam = 0;
 
   // open file on proc 0
 
-  FILE *fp = NULL;
   if (comm->me == 0) {
-    fp = force->open_potential(file);
+    PotentialFileReader reader(lmp, file, "nb3b/harmonic");
-    if (fp == NULL) {
+    char * line;
-      char str[128];
-      snprintf(str,128,"Cannot open nb3b/harmonic potential file %s",file);
-      error->one(FLERR,str);
-    }
-  }
 
-  // read each set of params from potential file
+    while(line = reader.next_line(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 iname = values.next_string();
-  char line[MAXLINE],*ptr;
+        std::string jname = values.next_string();
-  int eof = 0;
+        std::string kname = values.next_string();
-
-  while (1) {
-    if (comm->me == 0) {
-      ptr = fgets(line,MAXLINE,fp);
-      if (ptr == NULL) {
-        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
-
-    if ((ptr = strchr(line,'#'))) *ptr = '\0';
-    nwords = utils::count_words(line);
-    if (nwords == 0) continue;
-
-    // concatenate additional lines until have params_per_line words
-
-    while (nwords < params_per_line) {
-      n = strlen(line);
-      if (comm->me == 0) {
-        ptr = fgets(&line[n],MAXLINE-n,fp);
-        if (ptr == NULL) {
-          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);
-      if ((ptr = strchr(line,'#'))) *ptr = '\0';
-      nwords = utils::count_words(line);
-    }
-
-    if (nwords != params_per_line)
-      error->all(FLERR,"Incorrect format in nb3b/harmonic 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
+        int ielement, jelement, kelement;
 
         for (ielement = 0; ielement < nelements; ielement++)
-      if (strcmp(words[0],elements[ielement]) == 0) break;
+          if (iname == elements[ielement]) break;
         if (ielement == nelements) continue;
         for (jelement = 0; jelement < nelements; jelement++)
-      if (strcmp(words[1],elements[jelement]) == 0) break;
+          if (jname == elements[jelement]) break;
         if (jelement == nelements) continue;
         for (kelement = 0; kelement < nelements; kelement++)
-      if (strcmp(words[2],elements[kelement]) == 0) break;
+          if (kname == elements[kelement]) break;
         if (kelement == nelements) continue;
 
         // load up parameter settings and error check their values
@@ -382,18 +328,29 @@ void PairNb3bHarmonic::read_file(char *file)
         params[nparams].ielement = ielement;
         params[nparams].jelement = jelement;
         params[nparams].kelement = kelement;
-    params[nparams].k_theta = atof(words[3]);
+        params[nparams].k_theta  = values.next_double();
-    params[nparams].theta0 = atof(words[4]);
+        params[nparams].theta0   = values.next_double();
-    params[nparams].cutoff = atof(words[5]);
+        params[nparams].cutoff   = values.next_double();
+      } catch (TokenizerException & e) {
+        error->one(FLERR, e.what());
+      }
 
       if (params[nparams].k_theta < 0.0 || params[nparams].theta0 < 0.0 ||
           params[nparams].cutoff < 0.0)
-      error->all(FLERR,"Illegal nb3b/harmonic parameter");
+        error->one(FLERR,"Illegal nb3b/harmonic 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_nb3b_harmonic.h

@@ -34,6 +34,8 @@ class PairNb3bHarmonic : public Pair {
   double init_one(int, int);
   void init_style();
 
+  static const int NPARAMS_PER_LINE = 6;
+
  protected:
   struct Param {
     double k_theta, theta0, cutoff;

unittest/formats/test_potential_file_reader.cpp

@@ -12,6 +12,7 @@
 #include "MANYBODY/pair_tersoff_zbl.h"
 #include "MANYBODY/pair_gw.h"
 #include "MANYBODY/pair_gw_zbl.h"
+#include "MANYBODY/pair_nb3b_harmonic.h"
 
 #include <mpi.h>
 
@@ -26,6 +27,7 @@ const int LAMMPS_NS::PairTersoffMODC::NPARAMS_PER_LINE;
 const int LAMMPS_NS::PairTersoffZBL::NPARAMS_PER_LINE;
 const int LAMMPS_NS::PairGW::NPARAMS_PER_LINE;
 const int LAMMPS_NS::PairGWZBL::NPARAMS_PER_LINE;
+const int LAMMPS_NS::PairNb3bHarmonic::NPARAMS_PER_LINE;
 
 class PotenialFileReaderTest : public ::testing::Test {
 protected:
@@ -85,7 +87,7 @@ TEST_F(PotenialFileReaderTest, Tersoff) {
 
 TEST_F(PotenialFileReaderTest, TersoffMod) {
     ::testing::internal::CaptureStdout();
-    PotentialFileReader reader(lmp, "Si.tersoff.mod", "Tersoff");
+    PotentialFileReader reader(lmp, "Si.tersoff.mod", "Tersoff/Mod");
     ::testing::internal::GetCapturedStdout();
 
     auto line = reader.next_line(PairTersoffMOD::NPARAMS_PER_LINE);
@@ -94,7 +96,7 @@ TEST_F(PotenialFileReaderTest, TersoffMod) {
 
 TEST_F(PotenialFileReaderTest, TersoffModC) {
     ::testing::internal::CaptureStdout();
-    PotentialFileReader reader(lmp, "Si.tersoff.modc", "Tersoff");
+    PotentialFileReader reader(lmp, "Si.tersoff.modc", "Tersoff/ModC");
     ::testing::internal::GetCapturedStdout();
 
     auto line = reader.next_line(PairTersoffMODC::NPARAMS_PER_LINE);
@@ -103,7 +105,7 @@ TEST_F(PotenialFileReaderTest, TersoffModC) {
 
 TEST_F(PotenialFileReaderTest, TersoffZBL) {
     ::testing::internal::CaptureStdout();
-    PotentialFileReader reader(lmp, "SiC.tersoff.zbl", "Tersoff");
+    PotentialFileReader reader(lmp, "SiC.tersoff.zbl", "Tersoff/ZBL");
     ::testing::internal::GetCapturedStdout();
 
     auto line = reader.next_line(PairTersoffZBL::NPARAMS_PER_LINE);
@@ -121,13 +123,22 @@ TEST_F(PotenialFileReaderTest, GW) {
 
 TEST_F(PotenialFileReaderTest, GWZBL) {
     ::testing::internal::CaptureStdout();
-    PotentialFileReader reader(lmp, "SiC.gw.zbl", "GWZBL");
+    PotentialFileReader reader(lmp, "SiC.gw.zbl", "GW/ZBL");
     ::testing::internal::GetCapturedStdout();
 
     auto line = reader.next_line(PairGWZBL::NPARAMS_PER_LINE);
     ASSERT_EQ(utils::count_words(line), PairGWZBL::NPARAMS_PER_LINE);
 }
 
+TEST_F(PotenialFileReaderTest, Nb3bHarmonic) {
+    ::testing::internal::CaptureStdout();
+    PotentialFileReader reader(lmp, "MOH.nb3b.harmonic", "NB3B Harmonic");
+    ::testing::internal::GetCapturedStdout();
+
+    auto line = reader.next_line(PairNb3bHarmonic::NPARAMS_PER_LINE);
+    ASSERT_EQ(utils::count_words(line), PairNb3bHarmonic::NPARAMS_PER_LINE);
+}
+
 int main(int argc, char **argv)
 {
     MPI_Init(&argc, &argv);