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improve parsing of data file header 

the header lines are now checked using regular expressions
instead of strstr() which allows for stricter checking, but
also is more forgiving in terms of extra or different whitespace

return value of sscanf() calls is checked and on failure LAMMPS errors out
This commit is contained in:
Axel Kohlmeyer 2019-07-19 11:16:41 -04:00
parent 8526e7a4cd
commit 1de00aaab0
No known key found for this signature in database
GPG Key ID: D9B44E93BF0C375A
1 changed files with 94 additions and 38 deletions
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132
src/read_data.cpp
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@ -45,6 +45,7 @@
#include "irregular.h"
#include "error.h"
#include "memory.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -999,74 +1000,115 @@ void ReadData::header(int firstpass)
// customize for new header lines
// check for triangles before angles so "triangles" not matched as "angles"
int extra_flag_value = 0;
int rv;
if (strstr(line,"atoms")) {
sscanf(line,BIGINT_FORMAT,&natoms);
if (utils::strmatch(line,"^\\s*\\d+\\s+atoms\\s")) {
rv = sscanf(line,BIGINT_FORMAT,&natoms);
if (rv != 1)
error->all(FLERR,"Could not parse 'atoms' line in data file header");
if (addflag == NONE) atom->natoms = natoms;
else if (firstpass) atom->natoms += natoms;
} else if (strstr(line,"ellipsoids")) {
} else if (utils::strmatch(line,"^\\s*\\d+\\s+ellipsoids\\s")) {
if (!avec_ellipsoid)
error->all(FLERR,"No ellipsoids allowed with this atom style");
sscanf(line,BIGINT_FORMAT,&nellipsoids);
rv = sscanf(line,BIGINT_FORMAT,&nellipsoids);
if (rv != 1)
error->all(FLERR,"Could not parse 'ellipsoids' line in data file header");
if (addflag == NONE) atom->nellipsoids = nellipsoids;
else if (firstpass) atom->nellipsoids += nellipsoids;
} else if (strstr(line,"lines")) {
} else if (utils::strmatch(line,"^\\s*\\d+\\s+lines\\s")) {
if (!avec_line)
error->all(FLERR,"No lines allowed with this atom style");
sscanf(line,BIGINT_FORMAT,&nlines);
rv = sscanf(line,BIGINT_FORMAT,&nlines);
if (rv != 1)
error->all(FLERR,"Could not parse 'lines' line in data file header");
if (addflag == NONE) atom->nlines = nlines;
else if (firstpass) atom->nlines += nlines;
} else if (strstr(line,"triangles")) {
} else if (utils::strmatch(line,"^\\s*\\d+\\s+triangles\\s")) {
if (!avec_tri)
error->all(FLERR,"No triangles allowed with this atom style");
sscanf(line,BIGINT_FORMAT,&ntris);
rv = sscanf(line,BIGINT_FORMAT,&ntris);
if (rv != 1)
error->all(FLERR,"Could not parse 'triangles' line in data file header");
if (addflag == NONE) atom->ntris = ntris;
else if (firstpass) atom->ntris += ntris;
} else if (strstr(line,"bodies")) {
} else if (utils::strmatch(line,"^\\s*\\d+\\s+bodies\\s")) {
if (!avec_body)
error->all(FLERR,"No bodies allowed with this atom style");
sscanf(line,BIGINT_FORMAT,&nbodies);
rv = sscanf(line,BIGINT_FORMAT,&nbodies);
if (rv != 1)
error->all(FLERR,"Could not parse 'bodies' line in data file header");
if (addflag == NONE) atom->nbodies = nbodies;
else if (firstpass) atom->nbodies += nbodies;
} else if (strstr(line,"bonds")) {
sscanf(line,BIGINT_FORMAT,&nbonds);
} else if (utils::strmatch(line,"^\\s*\\d+\\s+bonds\\s")) {
rv = sscanf(line,BIGINT_FORMAT,&nbonds);
if (rv != 1)
error->all(FLERR,"Could not parse 'bonds' line in data file header");
if (addflag == NONE) atom->nbonds = nbonds;
else if (firstpass) atom->nbonds += nbonds;
} else if (strstr(line,"angles")) {
sscanf(line,BIGINT_FORMAT,&nangles);
} else if (utils::strmatch(line,"^\\s*\\d+\\s+angles\\s")) {
rv = sscanf(line,BIGINT_FORMAT,&nangles);
if (rv != 1)
error->all(FLERR,"Could not parse 'angles' line in data file header");
if (addflag == NONE) atom->nangles = nangles;
else if (firstpass) atom->nangles += nangles;
} else if (strstr(line,"dihedrals")) {
sscanf(line,BIGINT_FORMAT,&ndihedrals);
} else if (utils::strmatch(line,"^\\s*\\d+\\s+dihedrals\\s")) {
rv = sscanf(line,BIGINT_FORMAT,&ndihedrals);
if (rv != 1)
error->all(FLERR,"Could not parse 'dihedrals' line in data file header");
if (addflag == NONE) atom->ndihedrals = ndihedrals;
else if (firstpass) atom->ndihedrals += ndihedrals;
} else if (strstr(line,"impropers")) {
sscanf(line,BIGINT_FORMAT,&nimpropers);
} else if (utils::strmatch(line,"^\\s*\\d+\\s+impropers\\s")) {
rv = sscanf(line,BIGINT_FORMAT,&nimpropers);
if (rv != 1)
error->all(FLERR,"Could not parse 'impropers' line in data file header");
if (addflag == NONE) atom->nimpropers = nimpropers;
else if (firstpass) atom->nimpropers += nimpropers;
// Atom class type settings are only set by first data file
} else if (strstr(line,"atom types")) {
sscanf(line,"%d",&ntypes);
} 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");
if (addflag == NONE) atom->ntypes = ntypes + extra_atom_types;
} else if (strstr(line,"bond types")) {
sscanf(line,"%d",&nbondtypes);
} 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");
if (addflag == NONE) atom->nbondtypes = nbondtypes + extra_bond_types;
} else if (strstr(line,"angle types")) {
sscanf(line,"%d",&nangletypes);
} 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");
if (addflag == NONE) atom->nangletypes = nangletypes + extra_angle_types;
} else if (strstr(line,"dihedral types")) {
sscanf(line,"%d",&ndihedraltypes);
} 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");
if (addflag == NONE)
atom->ndihedraltypes = ndihedraltypes + extra_dihedral_types;
} else if (strstr(line,"improper types")) {
sscanf(line,"%d",&nimpropertypes);
} 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");
if (addflag == NONE)
atom->nimpropertypes = nimpropertypes + extra_improper_types;
@ -1095,15 +1137,27 @@ void ReadData::header(int firstpass)
// local copy of box info
// so can treat differently for first vs subsequent data files
} else if (strstr(line,"xlo xhi")) {
sscanf(line,"%lg %lg",&boxlo[0],&boxhi[0]);
} else if (strstr(line,"ylo yhi")) {
sscanf(line,"%lg %lg",&boxlo[1],&boxhi[1]);
} else if (strstr(line,"zlo zhi")) {
sscanf(line,"%lg %lg",&boxlo[2],&boxhi[2]);
} else if (strstr(line,"xy xz yz")) {
} else if (utils::strmatch(line,"^\\s*\\f+\\s+\\f+\\s+xlo\\s+xhi\\s")) {
rv = sscanf(line,"%lg %lg",&boxlo[0],&boxhi[0]);
if (rv != 2)
error->all(FLERR,"Could not parse 'xlo xhi' line in data file header");
} else if (utils::strmatch(line,"^\\s*\\f+\\s+\\f+\\s+ylo\\s+yhi\\s")) {
rv = sscanf(line,"%lg %lg",&boxlo[1],&boxhi[1]);
if (rv != 2)
error->all(FLERR,"Could not parse 'ylo yhi' line in data file header");
} else if (utils::strmatch(line,"^\\s*\\f+\\s+\\f+\\s+zlo\\s+zhi\\s")) {
rv = sscanf(line,"%lg %lg",&boxlo[2],&boxhi[2]);
if (rv != 2)
error->all(FLERR,"Could not parse 'zlo zhi' line in data file header");
} else if (utils::strmatch(line,"^\\s*\\f+\\s+\\f+\\s+\\f+"
"\\s+xy\\s+xz\\s+yz\\s")) {
triclinic = 1;
sscanf(line,"%lg %lg %lg",&xy,&xz,&yz);
rv = sscanf(line,"%lg %lg %lg",&xy,&xz,&yz);
if (rv != 3)
error->all(FLERR,"Could not parse 'xy xz yz' line in data file header");
} else break;
}
@ -1638,7 +1692,7 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
void ReadData::bodies(int firstpass)
{
int m,nchunk,nline,nmax,ninteger,ndouble,nword,ncount,onebody,tmp;
int m,nchunk,nline,nmax,ninteger,ndouble,nword,ncount,onebody,tmp,rv;
char *eof;
int mapflag = 0;
@ -1666,7 +1720,9 @@ void ReadData::bodies(int firstpass)
while (nchunk < nmax && nline <= CHUNK-MAXBODY) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
sscanf(&buffer[m],"%d %d %d",&tmp,&ninteger,&ndouble);
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]);
// read lines one at a time into buffer and count words