modernize parsing of Velocities section of data files

src/KOKKOS/atom_vec_hybrid_kokkos.cpp

@@ -1019,21 +1019,21 @@ void AtomVecHybridKokkos::data_atom(double *coord, imageint imagetmp,
    unpack one line from Velocities section of data file
 ------------------------------------------------------------------------- */
 
-void AtomVecHybridKokkos::data_vel(int m, char **values)
+void AtomVecHybridKokkos::data_vel(int m, const std::vector<std::string> &values)
 {
   atomKK->sync(Host,V_MASK);
 
-  h_v(m,0) = utils::numeric(FLERR,values[0],true,lmp);
+  int ivalue = 1;
-  h_v(m,1) = utils::numeric(FLERR,values[1],true,lmp);
+  h_v(m,0) = utils::numeric(FLERR,values[ivalue++],true,lmp);
-  h_v(m,2) = utils::numeric(FLERR,values[2],true,lmp);
+  h_v(m,1) = utils::numeric(FLERR,values[ivalue++],true,lmp);
+  h_v(m,2) = utils::numeric(FLERR,values[ivalue++],true,lmp);
 
   atomKK->modified(Host,V_MASK);
 
   // each sub-style parses sub-style specific values
 
-  int n = 3;
   for (int k = 0; k < nstyles; k++)
-    n += styles[k]->data_vel_hybrid(m,&values[n]);
+    ivalue += styles[k]->data_vel_hybrid(m,values,ivalue);
 }
 
 /* ----------------------------------------------------------------------

src/KOKKOS/atom_vec_hybrid_kokkos.h

@@ -59,7 +59,7 @@ class AtomVecHybridKokkos : public AtomVecKokkos {
   void create_atom(int, double *);
   void data_atom(double *, imageint, const std::vector<std::string> &);
   int data_atom_hybrid(int, const std::vector<std::string> &, int) {return 0;}
-  void data_vel(int, char **);
+  void data_vel(int, const std::vector<std::string> &);
   void pack_data(double **);
   void write_data(FILE *, int, double **);
   void pack_vel(double **);

src/KOKKOS/atom_vec_kokkos.cpp

@@ -1016,12 +1016,13 @@ void AtomVecKokkos::unpack_reverse(int n, int *list, double *buf)
  *    unpack one line from Velocities section of data file
  *    ------------------------------------------------------------------------- */
 
-void AtomVecKokkos::data_vel(int m, char **values)
+void AtomVecKokkos::data_vel(int m, const std::vector<std::string> &values)
 {
   double **v = atom->v;
-  v[m][0] = utils::numeric(FLERR,values[0],true,lmp);
+  int ivalue = 1;
-  v[m][1] = utils::numeric(FLERR,values[1],true,lmp);
+  v[m][0] = utils::numeric(FLERR,values[ivalue++],true,lmp);
-  v[m][2] = utils::numeric(FLERR,values[2],true,lmp);
+  v[m][1] = utils::numeric(FLERR,values[ivalue++],true,lmp);
+  v[m][2] = utils::numeric(FLERR,values[ivalue++],true,lmp);
 
   atomKK->modified(Host,V_MASK);
 }

src/KOKKOS/atom_vec_kokkos.h

@@ -44,7 +44,7 @@ class AtomVecKokkos : public AtomVec {
   virtual void unpack_comm_vel(int, int, double *);
   virtual int pack_reverse(int, int, double *);
   virtual void unpack_reverse(int, int *, double *);
-  virtual void data_vel(int, char **);
+  virtual void data_vel(int, const std::vector<std::string> &);
   virtual void pack_vel(double **);
   virtual void write_vel(FILE *, int, double **);
 

src/KOKKOS/atom_vec_sphere_kokkos.cpp

@@ -2617,15 +2617,16 @@ int AtomVecSphereKokkos::data_atom_hybrid(int nlocal, const std::vector<std::str
    unpack one line from Velocities section of data file
 ------------------------------------------------------------------------- */
 
-void AtomVecSphereKokkos::data_vel(int m, char **values)
+void AtomVecSphereKokkos::data_vel(int m, const std::vector<std::string> &values)
 {
+  int ivalue = 1;
   atomKK->sync(Host,V_MASK|OMEGA_MASK);
-  h_v(m,0) = utils::numeric(FLERR,values[0],true,lmp);
+  h_v(m,0) = utils::numeric(FLERR,values[ivalue++],true,lmp);
-  h_v(m,1) = utils::numeric(FLERR,values[1],true,lmp);
+  h_v(m,1) = utils::numeric(FLERR,values[ivalue++],true,lmp);
-  h_v(m,2) = utils::numeric(FLERR,values[2],true,lmp);
+  h_v(m,2) = utils::numeric(FLERR,values[ivalue++],true,lmp);
-  h_omega(m,0) = utils::numeric(FLERR,values[3],true,lmp);
+  h_omega(m,0) = utils::numeric(FLERR,values[ivalue++],true,lmp);
-  h_omega(m,1) = utils::numeric(FLERR,values[4],true,lmp);
+  h_omega(m,1) = utils::numeric(FLERR,values[ivalue++],true,lmp);
-  h_omega(m,2) = utils::numeric(FLERR,values[5],true,lmp);
+  h_omega(m,2) = utils::numeric(FLERR,values[ivalue++],true,lmp);
   atomKK->modified(Host,V_MASK|OMEGA_MASK);
 }
 
@@ -2633,12 +2634,13 @@ void AtomVecSphereKokkos::data_vel(int m, char **values)
    unpack hybrid quantities from one line in Velocities section of data file
 ------------------------------------------------------------------------- */
 
-int AtomVecSphereKokkos::data_vel_hybrid(int m, char **values)
+int AtomVecSphereKokkos::data_vel_hybrid(int m, const std::vector<std::string> &values,
+                                         int offset)
 {
   atomKK->sync(Host,OMEGA_MASK);
-  omega[m][0] = utils::numeric(FLERR,values[0],true,lmp);
+  omega[m][0] = utils::numeric(FLERR,values[offset],true,lmp);
-  omega[m][1] = utils::numeric(FLERR,values[1],true,lmp);
+  omega[m][1] = utils::numeric(FLERR,values[offset+1],true,lmp);
-  omega[m][2] = utils::numeric(FLERR,values[2],true,lmp);
+  omega[m][2] = utils::numeric(FLERR,values[offset+2],true,lmp);
   atomKK->modified(Host,OMEGA_MASK);
   return 3;
 }

src/KOKKOS/atom_vec_sphere_kokkos.h

@@ -60,8 +60,8 @@ class AtomVecSphereKokkos : public AtomVecKokkos {
   void create_atom(int, double *);
   void data_atom(double *, imageint, const std::vector<std::string> &);
   int data_atom_hybrid(int, const std::vector<std::string> &, int);
-  void data_vel(int, char **);
+  void data_vel(int, const std::vector<std::string> &);
-  int data_vel_hybrid(int, char **);
+  int data_vel_hybrid(int, const std::vector<std::string> &, int);
   void pack_data(double **);
   int pack_data_hybrid(int, double *);
   void write_data(FILE *, int, double **);

src/atom.cpp

@@ -1209,31 +1209,24 @@ void Atom::data_vels(int n, char *buf, tagint id_offset)
   if (nwords != avec->size_data_vel)
     error->all(FLERR,"Incorrect velocity format in data file");
 
-  char **values = new char*[nwords];
-
   // loop over lines of atom velocities
   // tokenize the line into values
   // if I own atom tag, unpack its values
 
   for (int i = 0; i < n; i++) {
     next = strchr(buf,'\n');
+    *next = '\0';
+    auto values = Tokenizer(utils::trim_comment(buf)).as_vector();
+    if (values.size() != nwords)
+      error->all(FLERR, "Incorrect atom format in data file: {}", utils::trim(buf));
 
-    for (j = 0; j < nwords; j++) {
+    tagdata = utils::tnumeric(FLERR,values[0],false,lmp) + id_offset;
-      buf += strspn(buf," \t\n\r\f");
-      buf[strcspn(buf," \t\n\r\f")] = '\0';
-      values[j] = buf;
-      buf += strlen(buf)+1;
-    }
-
-    tagdata = ATOTAGINT(values[0]) + id_offset;
     if (tagdata <= 0 || tagdata > map_tag_max)
       error->one(FLERR,"Invalid atom ID in Velocities section of data file");
-    if ((m = map(tagdata)) >= 0) avec->data_vel(m,&values[1]);
+    if ((m = map(tagdata)) >= 0) avec->data_vel(m,values);
 
     buf = next + 1;
   }
-
-  delete [] values;
 }
 
 /* ----------------------------------------------------------------------

src/atom_vec.cpp

@@ -1890,18 +1890,18 @@ void AtomVec::write_data(FILE *fp, int n, double **buf)
    unpack one line from Velocities section of data file
 ------------------------------------------------------------------------- */
 
-void AtomVec::data_vel(int ilocal, char **values)
+void AtomVec::data_vel(int ilocal, const std::vector<std::string> &values)
 {
   int m,n,datatype,cols;
   void *pdata;
 
   double **v = atom->v;
-  v[ilocal][0] = utils::numeric(FLERR,values[0],true,lmp);
+  int ivalue = 1;
-  v[ilocal][1] = utils::numeric(FLERR,values[1],true,lmp);
+  v[ilocal][0] = utils::numeric(FLERR,values[ivalue++],true,lmp);
-  v[ilocal][2] = utils::numeric(FLERR,values[2],true,lmp);
+  v[ilocal][1] = utils::numeric(FLERR,values[ivalue++],true,lmp);
+  v[ilocal][2] = utils::numeric(FLERR,values[ivalue++],true,lmp);
 
   if (ndata_vel > 2) {
-    int ivalue = 3;
     for (n = 2; n < ndata_vel; n++) {
       pdata = mdata_vel.pdata[n];
       datatype = mdata_vel.datatype[n];

src/atom_vec.h

@@ -136,7 +136,7 @@ class AtomVec : protected Pointers {
   virtual void pack_data_pre(int) {}
   virtual void pack_data_post(int) {}
 
-  virtual void data_vel(int, char **);
+  virtual void data_vel(int, const std::vector<std::string> &);
   virtual void pack_vel(double **);
   virtual void write_vel(FILE *, int, double **);
 
@@ -167,7 +167,7 @@ class AtomVec : protected Pointers {
   virtual int pack_border_hybrid(int, int *, double *) { return 0; }
   virtual int unpack_border_hybrid(int, int, double *) { return 0; }
   virtual int data_atom_hybrid(int, const std::vector<std::string> &, int) { return 0; }
-  virtual int data_vel_hybrid(int, char **) { return 0; }
+  virtual int data_vel_hybrid(int, const std::vector<std::string> &, int) { return 0; }
   virtual int pack_data_hybrid(int, double *) { return 0; }
   virtual int write_data_hybrid(FILE *, double *) { return 0; }
   virtual int pack_vel_hybrid(int, double *) { return 0; }