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Merge remote-tracking branch 'origin/master' into more-unit-tests

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This commit is contained in:
Richard Berger
2021-04-26 14:48:14 -04:00
parent 462f27d661 39f3c1684f
commit 18215ff3e7
151 changed files with 882 additions and 1233 deletions
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30
src/read_data.cpp
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@ -1232,7 +1232,7 @@ 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;
@ -1288,7 +1288,7 @@ 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;
@ -1330,7 +1330,7 @@ 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;
@ -1404,7 +1404,7 @@ 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;
@ -1478,7 +1478,7 @@ 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;
@ -1552,7 +1552,7 @@ 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;
@ -1619,7 +1619,7 @@ 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;
@ -1745,7 +1745,7 @@ 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;
@ -1765,7 +1765,7 @@ 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;
@ -1791,7 +1791,7 @@ 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;
@ -1817,7 +1817,7 @@ 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;
@ -1842,7 +1842,7 @@ 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;
@ -1868,7 +1868,7 @@ 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;
@ -1898,7 +1898,7 @@ 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;
@ -1928,7 +1928,7 @@ 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;