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multi-data-file support for bond, angles, diheddral, impropers

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This commit is contained in:
Jacob Gissinger
2021-01-11 16:00:37 -05:00
parent 03b697a6e0
commit d7fb74f0be
5 changed files with 34 additions and 15 deletions
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18
src/read_data.cpp
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@ -124,7 +124,7 @@ void ReadData::command(int narg, char **arg)
addflag = NONE;
coeffflag = 1;
id_offset = mol_offset = 0;
offsetflag = shiftflag = labelflag = 0;
offsetflag = shiftflag = settypeflag = labelflag = 0;
toffset = boffset = aoffset = doffset = ioffset = 0;
shift[0] = shift[1] = shift[2] = 0.0;
extra_atom_types = extra_bond_types = extra_angle_types =
@ -1379,7 +1379,8 @@ void ReadData::bonds(int firstpass)
nchunk = MIN(nbonds-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_bonds(nchunk,buffer,count,id_offset,boffset);
atom->data_bonds(nchunk,buffer,count,id_offset,boffset,
labelflag,lmap->lmap2lmap.bond);
nread += nchunk;
}
@ -1453,7 +1454,8 @@ void ReadData::angles(int firstpass)
nchunk = MIN(nangles-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_angles(nchunk,buffer,count,id_offset,aoffset);
atom->data_angles(nchunk,buffer,count,id_offset,aoffset,
labelflag,lmap->lmap2lmap.angle);
nread += nchunk;
}
@ -1527,7 +1529,8 @@ void ReadData::dihedrals(int firstpass)
nchunk = MIN(ndihedrals-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_dihedrals(nchunk,buffer,count,id_offset,doffset);
atom->data_dihedrals(nchunk,buffer,count,id_offset,doffset,
labelflag,lmap->lmap2lmap.dihedral);
nread += nchunk;
}
@ -1601,7 +1604,8 @@ void ReadData::impropers(int firstpass)
nchunk = MIN(nimpropers-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_impropers(nchunk,buffer,count,id_offset,ioffset);
atom->data_impropers(nchunk,buffer,count,id_offset,ioffset,
labelflag,lmap->lmap2lmap.improper);
nread += nchunk;
}
@ -1789,6 +1793,7 @@ void ReadData::bodies(int firstpass, AtomVec *ptr)
void ReadData::mass()
{
settypeflag = 1;
char *next;
char *buf = new char[ntypes*MAXLINE];
@ -1965,11 +1970,13 @@ void ReadData::impropercoeffs(int which)
void ReadData::typelabels(std::vector<std::string> &mytypelabel, int myntypes, int mode)
{
if (settypeflag) error->all(FLERR,"Must read Type Labels before any section involving types");
int n;
char *next;
char *buf = new char[myntypes*MAXLINE];
labelflag = 1;
atom->labelmapflag = 1;
int eof = comm->read_lines_from_file(fp,myntypes,MAXLINE,buf);
if (eof) error->all(FLERR,"Unexpected end of data file");
@ -2158,6 +2165,7 @@ void ReadData::skip_lines(bigint n)
void ReadData::parse_coeffs(char *line, const char *addstr, int dupflag,
int noffset, int offset, int *ilabel)
{
settypeflag = 1;
char *ptr;
if ((ptr = strchr(line,'#'))) *ptr = '\0';