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Merge branch 'develop' into type-labels

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This commit is contained in:
Jacob Gissinger
2022-03-23 01:08:35 -04:00
committed by GitHub
parent 44522221ad 3e7de83e6e
commit e13a70ad2f
3143 changed files with 258487 additions and 425132 deletions
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68
src/read_data.cpp
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@ -36,11 +36,11 @@
#include "molecule.h"
#include "pair.h"
#include "special.h"
#include "tokenizer.h"
#include "update.h"
#include <cctype>
#include <cstring>
#include <string>
#include <unordered_set>
using namespace LAMMPS_NS;
@ -968,23 +968,28 @@ void ReadData::command(int narg, char **arg)
// restore old styles, when reading with nocoeff flag given
if (coeffflag == 0) {
if (force->pair) delete force->pair;
delete force->pair;
delete[] force->pair_style;
force->pair = saved_pair;
force->pair_style = saved_pair_style;
if (force->bond) delete force->bond;
delete force->bond;
delete[] force->bond_style;
force->bond = saved_bond;
force->bond_style = saved_bond_style;
if (force->angle) delete force->angle;
delete force->angle;
delete[] force->angle_style;
force->angle = saved_angle;
force->angle_style = saved_angle_style;
if (force->dihedral) delete force->dihedral;
delete force->dihedral;
delete[] force->dihedral_style;
force->dihedral = saved_dihedral;
force->dihedral_style = saved_dihedral_style;
if (force->improper) delete force->improper;
delete force->improper;
delete[] force->improper_style;
force->improper = saved_improper;
force->improper_style = saved_improper_style;
@ -1154,37 +1159,32 @@ void ReadData::header(int firstpass)
} else if (utils::strmatch(line,"^\\s*\\d+\\s+atom\\s+types\\s")) {
rv = sscanf(line,"%d",&ntypes);
if (rv != 1)
error->all(FLERR,"Could not parse 'atom types' line "
"in data file header");
error->all(FLERR,"Could not parse 'atom types' line in data file header");
if (addflag == NONE) atom->ntypes = ntypes + extra_atom_types;
} else if (utils::strmatch(line,"\\s*\\d+\\s+bond\\s+types\\s")) {
rv = sscanf(line,"%d",&nbondtypes);
if (rv != 1)
error->all(FLERR,"Could not parse 'bond types' line "
"in data file header");
error->all(FLERR,"Could not parse 'bond types' line in data file header");
if (addflag == NONE) atom->nbondtypes = nbondtypes + extra_bond_types;
} else if (utils::strmatch(line,"^\\s*\\d+\\s+angle\\s+types\\s")) {
rv = sscanf(line,"%d",&nangletypes);
if (rv != 1)
error->all(FLERR,"Could not parse 'angle types' line "
"in data file header");
error->all(FLERR,"Could not parse 'angle types' line in data file header");
if (addflag == NONE) atom->nangletypes = nangletypes + extra_angle_types;
} else if (utils::strmatch(line,"^\\s*\\d+\\s+dihedral\\s+types\\s")) {
rv = sscanf(line,"%d",&ndihedraltypes);
if (rv != 1)
error->all(FLERR,"Could not parse 'dihedral types' line "
"in data file header");
error->all(FLERR,"Could not parse 'dihedral types' line in data file header");
if (addflag == NONE)
atom->ndihedraltypes = ndihedraltypes + extra_dihedral_types;
} else if (utils::strmatch(line,"^\\s*\\d+\\s+improper\\s+types\\s")) {
rv = sscanf(line,"%d",&nimpropertypes);
if (rv != 1)
error->all(FLERR,"Could not parse 'improper types' line "
"in data file header");
error->all(FLERR,"Could not parse 'improper types' line in data file header");
if (addflag == NONE)
atom->nimpropertypes = nimpropertypes + extra_improper_types;
@ -1744,12 +1744,12 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
read all body data
variable amount of info per body, described by ninteger and ndouble
to find atoms, must build atom map if not a molecular system
if not firstpass, just read past data, but no processing of data
if not firstpass, just read past body data and only process body header
------------------------------------------------------------------------- */
void ReadData::bodies(int firstpass, AtomVec *ptr)
{
int m,nchunk,nline,nmax,ninteger,ndouble,nword,ncount,onebody,tmp,rv;
int m,nchunk,nline,nmax,ninteger,ndouble,nword,ncount,onebody;
char *eof;
int mapflag = 0;
@ -1763,11 +1763,11 @@ void ReadData::bodies(int firstpass, AtomVec *ptr)
// nchunk = actual # read
bigint nread = 0;
bigint natoms = nbodies;
bigint nblocks = nbodies;
while (nread < natoms) {
if (natoms-nread > CHUNK) nmax = CHUNK;
else nmax = natoms-nread;
while (nread < nblocks) {
if (nblocks-nread > CHUNK) nmax = CHUNK;
else nmax = nblocks-nread;
if (me == 0) {
nchunk = 0;
@ -1776,11 +1776,25 @@ void ReadData::bodies(int firstpass, AtomVec *ptr)
while (nchunk < nmax && nline <= CHUNK-MAXBODY) {
eof = utils::fgets_trunc(&buffer[m],MAXLINE,fp);
const char *buf = &buffer[m];
if (eof == nullptr) error->one(FLERR,"Unexpected end of data file");
rv = sscanf(&buffer[m],"%d %d %d",&tmp,&ninteger,&ndouble);
if (rv != 3)
error->one(FLERR,"Incorrect format in Bodies section of data file");
m += strlen(&buffer[m]);
try {
auto values = ValueTokenizer(utils::trim_comment(buf));
tagint tagdata = values.next_tagint() + id_offset;
ninteger = values.next_int();
ndouble = values.next_double();
if (tagdata <= 0 || tagdata > atom->map_tag_max)
throw TokenizerException("Invalid atom ID in body header", utils::trim(buf));
if (ninteger < 0)
throw TokenizerException("Invalid number of integers", utils::trim(buf));
if (ndouble < 0)
throw TokenizerException("Invalid number of doubles", utils::trim(buf));
if (values.has_next())
throw TokenizerException("Too many tokens in body header", utils::trim(buf));
} catch (TokenizerException &e) {
error->one(FLERR,std::string(e.what()) + " while reading Bodies section of data file");
}
m += strlen(buf);
// read lines one at a time into buffer and count words
// count to ninteger and ndouble until have enough lines
@ -1840,7 +1854,7 @@ void ReadData::bodies(int firstpass, AtomVec *ptr)
}
if (me == 0 && firstpass)
utils::logmesg(lmp," {} bodies\n",natoms);
utils::logmesg(lmp," {} bodies\n",nblocks);
}
/* ---------------------------------------------------------------------- */