remove the old versions of the utility function and use the new

lib/atc/LammpsInterface.cpp

@@ -26,6 +26,7 @@
 #include "bond.h" // bond potentials
 #include "comm.h" //
 #include "fix.h"
+#include "utils.h"
 
 // ATC includes
 #include "ATC_Error.h"
@@ -47,6 +48,7 @@ using std::pair;
 using std::string;
 using std::set;
 using LAMMPS_NS::bigint;
+using LAMMPS_NS::utils::read_lines_from_file;
 
 namespace ATC {
 
@@ -236,7 +238,7 @@ std::string LammpsInterface::read_file(std::string filename) const
   std::stringstream s;
   bool eof = false;
   while ( ! eof) {
-    eof = lammps_->comm->read_lines_from_file(fp,1,MAXLINE,buffer);
+    eof = read_lines_from_file(fp,1,MAXLINE,buffer,comm_rank(),lammps_->world);
     s << buffer;
   }
   fclose(fp);

src/REPLICA/neb.cpp

@@ -436,9 +436,10 @@ void NEB::readfile(char *file, int flag)
   while (nread < nlines) {
     nchunk = MIN(nlines-nread,CHUNK);
     if (flag == 0)
-      eofflag = comm->read_lines_from_file_universe(fp,nchunk,MAXLINE,buffer);
+      eofflag = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,
+                                            universe->me,universe->uworld);
     else
-      eofflag = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
+      eofflag = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
     if (eofflag) error->all(FLERR,"Unexpected end of NEB file");
 
     buf = buffer;

src/RIGID/fix_rigid.cpp

@@ -2302,7 +2302,7 @@ void FixRigid::readfile(int which, double *vec,
   int nread = 0;
   while (nread < nlines) {
     nchunk = MIN(nlines-nread,CHUNK);
-    eofflag = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
+    eofflag = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
     if (eofflag) error->all(FLERR,"Unexpected end of fix rigid file");
 
     buf = buffer;

src/RIGID/fix_rigid_small.cpp

@@ -2475,7 +2475,7 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
   int nread = 0;
   while (nread < nlines) {
     nchunk = MIN(nlines-nread,CHUNK);
-    eofflag = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
+    eofflag = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
     if (eofflag) error->all(FLERR,"Unexpected end of fix rigid/small file");
 
     buf = buffer;

src/SPIN/neb_spin.cpp

@@ -430,9 +430,10 @@ void NEBSpin::readfile(char *file, int flag)
   while (nread < nlines) {
     nchunk = MIN(nlines-nread,CHUNK);
     if (flag == 0)
-      eofflag = comm->read_lines_from_file_universe(fp,nchunk,MAXLINE,buffer);
+      eofflag = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,
+                                            universe->me,universe->uworld);
     else
-      eofflag = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
+      eofflag = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
     if (eofflag) error->all(FLERR,"Unexpected end of neb/spin file");
 
     buf = buffer;

src/comm.cpp

@@ -1240,71 +1240,3 @@ void Comm::rendezvous_stats(int n, int nout, int nrvous, int nrvous_out,
     utils::logmesg(lmp,mesg);
   }
 }
-
-/* ----------------------------------------------------------------------
-   proc 0 reads Nlines from file into buf and bcasts buf to all procs
-   caller allocates buf to max size needed
-   each line is terminated by newline, even if last line in file is not
-   return 0 if successful, 1 if get EOF error before read is complete
-------------------------------------------------------------------------- */
-
-int Comm::read_lines_from_file(FILE *fp, int nlines, int maxline, char *buf)
-{
-  int m;
-
-  if (me == 0) {
-    m = 0;
-    for (int i = 0; i < nlines; i++) {
-      if (!fgets(&buf[m],maxline,fp)) {
-        m = 0;
-        break;
-      }
-      m += strlen(&buf[m]);
-    }
-    if (m) {
-      if (buf[m-1] != '\n') strcpy(&buf[m++],"\n");
-      m++;
-    }
-  }
-
-  MPI_Bcast(&m,1,MPI_INT,0,world);
-  if (m == 0) return 1;
-  MPI_Bcast(buf,m,MPI_CHAR,0,world);
-  return 0;
-}
-
-/* ----------------------------------------------------------------------
-   proc 0 reads Nlines from file into buf and bcasts buf to all procs
-   caller allocates buf to max size needed
-   each line is terminated by newline, even if last line in file is not
-   return 0 if successful, 1 if get EOF error before read is complete
-------------------------------------------------------------------------- */
-
-int Comm::read_lines_from_file_universe(FILE *fp, int nlines, int maxline,
-                                        char *buf)
-{
-  int m;
-
-  int me_universe = universe->me;
-  MPI_Comm uworld = universe->uworld;
-
-  if (me_universe == 0) {
-    m = 0;
-    for (int i = 0; i < nlines; i++) {
-      if (!fgets(&buf[m],maxline,fp)) {
-        m = 0;
-        break;
-      }
-      m += strlen(&buf[m]);
-    }
-    if (m) {
-      if (buf[m-1] != '\n') strcpy(&buf[m++],"\n");
-      m++;
-    }
-  }
-
-  MPI_Bcast(&m,1,MPI_INT,0,uworld);
-  if (m == 0) return 1;
-  MPI_Bcast(buf,m,MPI_CHAR,0,uworld);
-  return 0;
-}

src/comm.h

@@ -114,9 +114,6 @@ class Comm : protected Pointers {
                  int (*)(int, char *, int &, int *&, char *&, void *),
                  int, char *&, int, void *, int statflag=0);
 
-  int read_lines_from_file(FILE *, int, int, char *);
-  int read_lines_from_file_universe(FILE *, int, int, char *);
-
   // extract data useful to other classes
   virtual void *extract(const char *, int &) {return nullptr;}
 

src/read_data.cpp

@@ -1226,7 +1226,7 @@ void ReadData::atoms()
 
   while (nread < natoms) {
     nchunk = MIN(natoms-nread,CHUNK);
-    eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
+    eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
     if (eof) error->all(FLERR,"Unexpected end of data file");
     atom->data_atoms(nchunk,buffer,id_offset,mol_offset,toffset,shiftflag,shift);
     nread += nchunk;
@@ -1282,7 +1282,7 @@ void ReadData::velocities()
 
   while (nread < natoms) {
     nchunk = MIN(natoms-nread,CHUNK);
-    eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
+    eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
     if (eof) error->all(FLERR,"Unexpected end of data file");
     atom->data_vels(nchunk,buffer,id_offset);
     nread += nchunk;
@@ -1324,7 +1324,7 @@ void ReadData::bonds(int firstpass)
 
   while (nread < nbonds) {
     nchunk = MIN(nbonds-nread,CHUNK);
-    eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
+    eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
     if (eof) error->all(FLERR,"Unexpected end of data file");
     atom->data_bonds(nchunk,buffer,count,id_offset,boffset);
     nread += nchunk;
@@ -1398,7 +1398,7 @@ void ReadData::angles(int firstpass)
 
   while (nread < nangles) {
     nchunk = MIN(nangles-nread,CHUNK);
-    eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
+    eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
     if (eof) error->all(FLERR,"Unexpected end of data file");
     atom->data_angles(nchunk,buffer,count,id_offset,aoffset);
     nread += nchunk;
@@ -1472,7 +1472,7 @@ void ReadData::dihedrals(int firstpass)
 
   while (nread < ndihedrals) {
     nchunk = MIN(ndihedrals-nread,CHUNK);
-    eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
+    eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
     if (eof) error->all(FLERR,"Unexpected end of data file");
     atom->data_dihedrals(nchunk,buffer,count,id_offset,doffset);
     nread += nchunk;
@@ -1546,7 +1546,7 @@ void ReadData::impropers(int firstpass)
 
   while (nread < nimpropers) {
     nchunk = MIN(nimpropers-nread,CHUNK);
-    eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
+    eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
     if (eof) error->all(FLERR,"Unexpected end of data file");
     atom->data_impropers(nchunk,buffer,count,id_offset,ioffset);
     nread += nchunk;
@@ -1613,7 +1613,7 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
 
   while (nread < natoms) {
     nchunk = MIN(natoms-nread,CHUNK);
-    eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
+    eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
     if (eof) error->all(FLERR,"Unexpected end of data file");
     atom->data_bonus(nchunk,buffer,ptr,id_offset);
     nread += nchunk;
@@ -1739,7 +1739,7 @@ void ReadData::mass()
   char *next;
   char *buf = new char[ntypes*MAXLINE];
 
-  int eof = comm->read_lines_from_file(fp,ntypes,MAXLINE,buf);
+  int eof = utils::read_lines_from_file(fp,ntypes,MAXLINE,buf,me,world);
   if (eof) error->all(FLERR,"Unexpected end of data file");
 
   char *original = buf;
@@ -1759,7 +1759,7 @@ void ReadData::paircoeffs()
   char *next;
   char *buf = new char[ntypes*MAXLINE];
 
-  int eof = comm->read_lines_from_file(fp,ntypes,MAXLINE,buf);
+  int eof = utils::read_lines_from_file(fp,ntypes,MAXLINE,buf,me,world);
   if (eof) error->all(FLERR,"Unexpected end of data file");
 
   char *original = buf;
@@ -1785,7 +1785,7 @@ void ReadData::pairIJcoeffs()
   int nsq = ntypes * (ntypes+1) / 2;
   char *buf = new char[nsq * MAXLINE];
 
-  int eof = comm->read_lines_from_file(fp,nsq,MAXLINE,buf);
+  int eof = utils::read_lines_from_file(fp,nsq,MAXLINE,buf,me,world);
   if (eof) error->all(FLERR,"Unexpected end of data file");
 
   char *original = buf;
@@ -1811,7 +1811,7 @@ void ReadData::bondcoeffs()
   char *next;
   char *buf = new char[nbondtypes*MAXLINE];
 
-  int eof = comm->read_lines_from_file(fp,nbondtypes,MAXLINE,buf);
+  int eof = utils::read_lines_from_file(fp,nbondtypes,MAXLINE,buf,me,world);
   if (eof) error->all(FLERR,"Unexpected end of data file");
 
   char *original = buf;
@@ -1836,7 +1836,7 @@ void ReadData::anglecoeffs(int which)
   char *next;
   char *buf = new char[nangletypes*MAXLINE];
 
-  int eof = comm->read_lines_from_file(fp,nangletypes,MAXLINE,buf);
+  int eof = utils::read_lines_from_file(fp,nangletypes,MAXLINE,buf,me,world);
   if (eof) error->all(FLERR,"Unexpected end of data file");
 
   char *original = buf;
@@ -1862,7 +1862,7 @@ void ReadData::dihedralcoeffs(int which)
   char *next;
   char *buf = new char[ndihedraltypes*MAXLINE];
 
-  int eof = comm->read_lines_from_file(fp,ndihedraltypes,MAXLINE,buf);
+  int eof = utils::read_lines_from_file(fp,ndihedraltypes,MAXLINE,buf,me,world);
   if (eof) error->all(FLERR,"Unexpected end of data file");
 
   char *original = buf;
@@ -1892,7 +1892,7 @@ void ReadData::impropercoeffs(int which)
   char *next;
   char *buf = new char[nimpropertypes*MAXLINE];
 
-  int eof = comm->read_lines_from_file(fp,nimpropertypes,MAXLINE,buf);
+  int eof = utils::read_lines_from_file(fp,nimpropertypes,MAXLINE,buf,me,world);
   if (eof) error->all(FLERR,"Unexpected end of data file");
 
   char *original = buf;
@@ -1922,7 +1922,7 @@ void ReadData::fix(int ifix, char *keyword)
   bigint nread = 0;
   while (nread < nline) {
     nchunk = MIN(nline-nread,CHUNK);
-    eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
+    eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
     if (eof) error->all(FLERR,"Unexpected end of data file");
     modify->fix[ifix]->read_data_section(keyword,nchunk,buffer,id_offset);
     nread += nchunk;

src/variable.cpp

@@ -5176,7 +5176,7 @@ int VarReader::read_peratom()
   bigint nread = 0;
   while (nread < nlines) {
     nchunk = MIN(nlines-nread,CHUNK);
-    eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
+    eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
     if (eof) return 1;
 
     char *buf = buffer;