ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

preempt some read/write data file bugs

Browse Source 
currently, require all type labels (for all interactions) to be defined, if any are, when reading data files
This commit is contained in:
jrgissing
2021-01-31 20:44:19 -05:00
parent 4f219a94aa
commit ffa46ad951
5 changed files with 79 additions and 16 deletions
Download Patch File Download Diff File Expand all files Collapse all files

25
src/read_data.cpp
View File

@ -1279,6 +1279,9 @@ void ReadData::atoms()
nchunk = MIN(natoms-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
if (labelflag && !lmap->is_complete())
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a type label.");
atom->data_atoms(nchunk,buffer,id_offset,mol_offset,toffset,
shiftflag,shift,labelflag,lmap->lmap2lmap.atom);
nread += nchunk;
@ -1378,6 +1381,9 @@ 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");
if (labelflag && !lmap->is_complete())
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a type label.");
atom->data_bonds(nchunk,buffer,count,id_offset,boffset,
labelflag,lmap->lmap2lmap.bond);
nread += nchunk;
@ -1453,6 +1459,9 @@ 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");
if (labelflag && !lmap->is_complete())
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a type label.");
atom->data_angles(nchunk,buffer,count,id_offset,aoffset,
labelflag,lmap->lmap2lmap.angle);
nread += nchunk;
@ -1528,6 +1537,9 @@ 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");
if (labelflag && !lmap->is_complete())
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a type label.");
atom->data_dihedrals(nchunk,buffer,count,id_offset,doffset,
labelflag,lmap->lmap2lmap.dihedral);
nread += nchunk;
@ -1603,6 +1615,9 @@ 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");
if (labelflag && !lmap->is_complete())
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a type label.");
atom->data_impropers(nchunk,buffer,count,id_offset,ioffset,
labelflag,lmap->lmap2lmap.improper);
nread += nchunk;
@ -1798,6 +1813,9 @@ void ReadData::mass()
int eof = comm->read_lines_from_file(fp,ntypes,MAXLINE,buf);
if (eof) error->all(FLERR,"Unexpected end of data file");
if (labelflag && !lmap->is_complete())
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a type label.");
char *original = buf;
for (int i = 0; i < ntypes; i++) {
@ -1983,7 +2001,8 @@ void ReadData::typelabels(std::vector<std::string> &mytypelabel, int myntypes, i
for (int i = 0; i < myntypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
sscanf(buf,"%*d %s",typelabel);
int rv = sscanf(buf,"%*d %s",typelabel);
if (rv != 1) error->all(FLERR,"Invalid data file section: Type Labels");
if (isdigit(typelabel[0])) error->all(FLERR,"Type labels cannot start with a number");
mytypelabel[i] = typelabel;
buf = next + 1;
@ -2164,6 +2183,10 @@ void ReadData::skip_lines(bigint n)
void ReadData::parse_coeffs(char *line, const char *addstr, int dupflag,
int noffset, int offset, int *ilabel)
{
if (labelflag && !lmap->is_complete())
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a type label.");
settypeflag = 1;
char *ptr;
if ((ptr = strchr(line,'#'))) *ptr = '\0';