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Merge pull request #1575 from akohlmey/better-error-checking-on-parsing 

Better error checking on parsing files
This commit is contained in:
Axel Kohlmeyer 2019-07-19 17:25:16 -04:00 committed by GitHub
parent 67b74aea63 276e3b2df1
commit 895d4fa927
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
13 changed files with 232 additions and 99 deletions
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5
doc/src/Errors_messages.txt
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@ -5890,6 +5890,11 @@ The element names in the ADP file do not match those requested. :dd
The element names in the EAM file do not match those requested. :dd The element names in the EAM file do not match those requested. :dd
{Incorrect format of ... section in data file} :dt
Number or type of values per line in the given section of the data file
is not consistent with the requirements for this section. :dd
{Incorrect format in COMB potential file} :dt {Incorrect format in COMB potential file} :dt
Incorrect number of words per line in the potential file. :dd Incorrect number of words per line in the potential file. :dd

23
src/REPLICA/neb.cpp
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@ -397,28 +397,33 @@ void NEB::readfile(char *file, int flag)
open(file); open(file);
while (1) { while (1) {
eof = fgets(line,MAXLINE,fp); eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of neb file"); if (eof == NULL) error->one(FLERR,"Unexpected end of NEB file");
start = &line[strspn(line," \t\n\v\f\r")]; start = &line[strspn(line," \t\n\v\f\r")];
if (*start != '\0' && *start != '#') break; if (*start != '\0' && *start != '#') break;
} }
sscanf(line,"%d",&nlines); int rv = sscanf(line,"%d",&nlines);
if (rv != 1) nlines = -1;
} }
MPI_Bcast(&nlines,1,MPI_INT,0,uworld); MPI_Bcast(&nlines,1,MPI_INT,0,uworld);
if (nlines < 0)
error->universe_all(FLERR,"Incorrectly formatted NEB file");
} else { } else {
if (me == 0) { if (me == 0) {
if (ireplica) { if (ireplica) {
open(file); open(file);
while (1) { while (1) {
eof = fgets(line,MAXLINE,fp); eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of neb file"); if (eof == NULL) error->one(FLERR,"Unexpected end of NEB file");
start = &line[strspn(line," \t\n\v\f\r")]; start = &line[strspn(line," \t\n\v\f\r")];
if (*start != '\0' && *start != '#') break; if (*start != '\0' && *start != '#') break;
} }
sscanf(line,"%d",&nlines); int rv = sscanf(line,"%d",&nlines);
if (rv != 1) nlines = -1;
} else nlines = 0; } else nlines = 0;
} }
MPI_Bcast(&nlines,1,MPI_INT,0,world); MPI_Bcast(&nlines,1,MPI_INT,0,world);
if (nlines < 0)
error->all(FLERR,"Incorrectly formatted NEB file");
} }
char *buffer = new char[CHUNK*MAXLINE]; char *buffer = new char[CHUNK*MAXLINE];
@ -442,7 +447,7 @@ void NEB::readfile(char *file, int flag)
eofflag = comm->read_lines_from_file_universe(fp,nchunk,MAXLINE,buffer); eofflag = comm->read_lines_from_file_universe(fp,nchunk,MAXLINE,buffer);
else else
eofflag = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); eofflag = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eofflag) error->all(FLERR,"Unexpected end of neb file"); if (eofflag) error->all(FLERR,"Unexpected end of NEB file");
buf = buffer; buf = buffer;
next = strchr(buf,'\n'); next = strchr(buf,'\n');
@ -451,7 +456,7 @@ void NEB::readfile(char *file, int flag)
*next = '\n'; *next = '\n';
if (nwords != ATTRIBUTE_PERLINE) if (nwords != ATTRIBUTE_PERLINE)
error->all(FLERR,"Incorrect atom format in neb file"); error->all(FLERR,"Incorrect atom format in NEB file");
// loop over lines of atom coords // loop over lines of atom coords
// tokenize the line into values // tokenize the line into values
@ -509,12 +514,12 @@ void NEB::readfile(char *file, int flag)
int ntotal; int ntotal;
MPI_Allreduce(&ncount,&ntotal,1,MPI_INT,MPI_SUM,uworld); MPI_Allreduce(&ncount,&ntotal,1,MPI_INT,MPI_SUM,uworld);
if (ntotal != nreplica*nlines) if (ntotal != nreplica*nlines)
error->universe_all(FLERR,"Invalid atom IDs in neb file"); error->universe_all(FLERR,"Invalid atom IDs in NEB file");
} else { } else {
int ntotal; int ntotal;
MPI_Allreduce(&ncount,&ntotal,1,MPI_INT,MPI_SUM,world); MPI_Allreduce(&ncount,&ntotal,1,MPI_INT,MPI_SUM,world);
if (ntotal != nlines) if (ntotal != nlines)
error->all(FLERR,"Invalid atom IDs in neb file"); error->all(FLERR,"Invalid atom IDs in NEB file");
} }
// clean up // clean up

8
src/USER-REAXC/fix_qeq_reax.cpp
View File

@ -200,7 +200,7 @@ void FixQEqReax::pertype_parameters(char *arg)
return; return;
} }
int i,itype,ntypes; int i,itype,ntypes,rv;
double v1,v2,v3; double v1,v2,v3;
FILE *pf; FILE *pf;
@ -216,9 +216,11 @@ void FixQEqReax::pertype_parameters(char *arg)
error->one(FLERR,"Fix qeq/reax parameter file could not be found"); error->one(FLERR,"Fix qeq/reax parameter file could not be found");
for (i = 1; i <= ntypes && !feof(pf); i++) { for (i = 1; i <= ntypes && !feof(pf); i++) {
fscanf(pf,"%d %lg %lg %lg",&itype,&v1,&v2,&v3); rv = fscanf(pf,"%d %lg %lg %lg",&itype,&v1,&v2,&v3);
if (rv != 4)
error->one(FLERR,"Fix qeq/reax: Incorrect format of param file");
if (itype < 1 || itype > ntypes) if (itype < 1 || itype > ntypes)
error->one(FLERR,"Fix qeq/reax invalid atom type in param file"); error->one(FLERR,"Fix qeq/reax: invalid atom type in param file");
chi[itype] = v1; chi[itype] = v1;
eta[itype] = v2; eta[itype] = v2;
gamma[itype] = v3; gamma[itype] = v3;

36
src/atom.cpp
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@ -1071,7 +1071,7 @@ void Atom::data_vels(int n, char *buf, tagint id_offset)
void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset, void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
int type_offset) int type_offset)
{ {
int m,tmp,itype; int m,tmp,itype,rv;
tagint atom1,atom2; tagint atom1,atom2;
char *next; char *next;
int newton_bond = force->newton_bond; int newton_bond = force->newton_bond;
@ -1079,8 +1079,10 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
next = strchr(buf,'\n'); next = strchr(buf,'\n');
*next = '\0'; *next = '\0';
sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT, rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2); &tmp,&itype,&atom1,&atom2);
if (rv != 4)
error->one(FLERR,"Incorrect format of Bonds section in data file");
if (id_offset) { if (id_offset) {
atom1 += id_offset; atom1 += id_offset;
atom2 += id_offset; atom2 += id_offset;
@ -1124,7 +1126,7 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
void Atom::data_angles(int n, char *buf, int *count, tagint id_offset, void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
int type_offset) int type_offset)
{ {
int m,tmp,itype; int m,tmp,itype,rv;
tagint atom1,atom2,atom3; tagint atom1,atom2,atom3;
char *next; char *next;
int newton_bond = force->newton_bond; int newton_bond = force->newton_bond;
@ -1132,8 +1134,10 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
next = strchr(buf,'\n'); next = strchr(buf,'\n');
*next = '\0'; *next = '\0';
sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT, rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3); &tmp,&itype,&atom1,&atom2,&atom3);
if (rv != 5)
error->one(FLERR,"Incorrect format of Angles section in data file");
if (id_offset) { if (id_offset) {
atom1 += id_offset; atom1 += id_offset;
atom2 += id_offset; atom2 += id_offset;
@ -1194,7 +1198,7 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset, void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
int type_offset) int type_offset)
{ {
int m,tmp,itype; int m,tmp,itype,rv;
tagint atom1,atom2,atom3,atom4; tagint atom1,atom2,atom3,atom4;
char *next; char *next;
int newton_bond = force->newton_bond; int newton_bond = force->newton_bond;
@ -1202,9 +1206,11 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
next = strchr(buf,'\n'); next = strchr(buf,'\n');
*next = '\0'; *next = '\0';
sscanf(buf,"%d %d " rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT, " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3,&atom4); &tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (rv != 6)
error->one(FLERR,"Incorrect format of Dihedrals section in data file");
if (id_offset) { if (id_offset) {
atom1 += id_offset; atom1 += id_offset;
atom2 += id_offset; atom2 += id_offset;
@ -1283,7 +1289,7 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset, void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
int type_offset) int type_offset)
{ {
int m,tmp,itype; int m,tmp,itype,rv;
tagint atom1,atom2,atom3,atom4; tagint atom1,atom2,atom3,atom4;
char *next; char *next;
int newton_bond = force->newton_bond; int newton_bond = force->newton_bond;
@ -1291,9 +1297,11 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
next = strchr(buf,'\n'); next = strchr(buf,'\n');
*next = '\0'; *next = '\0';
sscanf(buf,"%d %d " rv = sscanf(buf,"%d %d "
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT, TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3,&atom4); &tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (rv != 6)
error->one(FLERR,"Incorrect format of Impropers section in data file");
if (id_offset) { if (id_offset) {
atom1 += id_offset; atom1 += id_offset;
atom2 += id_offset; atom2 += id_offset;

5
src/atom.h
View File

@ -426,6 +426,11 @@ E: Incorrect atom format in data file
Number of values per atom line in the data file is not consistent with Number of values per atom line in the data file is not consistent with
the atom style. the atom style.
E: Incorrect format of ... section in data file
Number or type of values per line in the given section of the data file
is not consistent with the requirements for this section.
E: Invalid atom type in Atoms section of data file E: Invalid atom type in Atoms section of data file
Atom types must range from 1 to specified # of types. Atom types must range from 1 to specified # of types.

32
src/fix_tmd.cpp
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@ -30,6 +30,7 @@
#include "force.h" #include "force.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"
#include "utils.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace FixConst; using namespace FixConst;
@ -164,7 +165,7 @@ void FixTMD::init()
dtv = update->dt; dtv = update->dt;
dtf = update->dt * force->ftm2v; dtf = update->dt * force->ftm2v;
if (strstr(update->integrate_style,"respa")) if (utils::strmatch(update->integrate_style,"^respa"))
step_respa = ((Respa *) update->integrate)->step; step_respa = ((Respa *) update->integrate)->step;
} }
@ -423,21 +424,27 @@ void FixTMD::readfile(char *file)
*next = '\0'; *next = '\0';
if (firstline) { if (firstline) {
if (strstr(bufptr,"xlo xhi")) { if (utils::strmatch(bufptr,"^\\s*\\f+\\s+\\f+\\s+xlo\\s+xhi")) {
double lo,hi; double lo,hi;
sscanf(bufptr,"%lg %lg",&lo,&hi); n = sscanf(bufptr,"%lg %lg",&lo,&hi);
if (n != 2)
error->all(FLERR,"Incorrect format in TMD target file");
xprd = hi - lo; xprd = hi - lo;
bufptr = next + 1; bufptr = next + 1;
continue; continue;
} else if (strstr(bufptr,"ylo yhi")) { } else if (utils::strmatch(bufptr,"^\\s*\\f+\\s+\\f+\\s+ylo\\s+yhi")) {
double lo,hi; double lo,hi;
sscanf(bufptr,"%lg %lg",&lo,&hi); n = sscanf(bufptr,"%lg %lg",&lo,&hi);
if (n != 2)
error->all(FLERR,"Incorrect format in TMD target file");
yprd = hi - lo; yprd = hi - lo;
bufptr = next + 1; bufptr = next + 1;
continue; continue;
} else if (strstr(bufptr,"zlo zhi")) { } else if (utils::strmatch(bufptr,"^\\s*\\f+\\s+\\f+\\s+zlo\\s+zhi")) {
double lo,hi; double lo,hi;
sscanf(bufptr,"%lg %lg",&lo,&hi); n = sscanf(bufptr,"%lg %lg",&lo,&hi);
if (n != 2)
error->all(FLERR,"Incorrect format in TMD target file");
zprd = hi - lo; zprd = hi - lo;
bufptr = next + 1; bufptr = next + 1;
continue; continue;
@ -455,14 +462,13 @@ void FixTMD::readfile(char *file)
} }
if (imageflag) if (imageflag)
n = sscanf(bufptr,TAGINT_FORMAT " %lg %lg %lg %d %d %d", n = 7 - sscanf(bufptr,TAGINT_FORMAT " %lg %lg %lg %d %d %d",
&itag,&x,&y,&z,&ix,&iy,&iz); &itag,&x,&y,&z,&ix,&iy,&iz);
else else
n = sscanf(bufptr,TAGINT_FORMAT " %lg %lg %lg",&itag,&x,&y,&z); n = 4 - sscanf(bufptr,TAGINT_FORMAT " %lg %lg %lg",&itag,&x,&y,&z);
if (n < 0) { if (n != 0) {
if (me == 0) error->warning(FLERR,"Ignoring empty or incorrectly" error->all(FLERR,"Incorrectly formatted line in TMD target file");
" formatted line in target file");
bufptr = next + 1; bufptr = next + 1;
continue; continue;
} }

9
src/procmap.cpp
View File

@ -301,7 +301,8 @@ void ProcMap::custom_grid(char *cfile, int nprocs,
MPI_Bcast(&n,1,MPI_INT,0,world); MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world); MPI_Bcast(line,n,MPI_CHAR,0,world);
sscanf(line,"%d %d %d",&procgrid[0],&procgrid[1],&procgrid[2]); int rv = sscanf(line,"%d %d %d",&procgrid[0],&procgrid[1],&procgrid[2]);
if (rv != 3) error->all(FLERR,"Processors custom grid file is inconsistent");
int flag = 0; int flag = 0;
if (procgrid[0]*procgrid[1]*procgrid[2] != nprocs) flag = 1; if (procgrid[0]*procgrid[1]*procgrid[2] != nprocs) flag = 1;
@ -320,8 +321,10 @@ void ProcMap::custom_grid(char *cfile, int nprocs,
for (int i = 0; i < nprocs; i++) { for (int i = 0; i < nprocs; i++) {
if (!fgets(line,MAXLINE,fp)) if (!fgets(line,MAXLINE,fp))
error->one(FLERR,"Unexpected end of custom file"); error->one(FLERR,"Unexpected end of custom file");
sscanf(line,"%d %d %d %d", rv = sscanf(line,"%d %d %d %d",
&cmap[i][0],&cmap[i][1],&cmap[i][2],&cmap[i][3]); &cmap[i][0],&cmap[i][1],&cmap[i][2],&cmap[i][3]);
if (rv != 4)
error->one(FLERR,"Processors custom grid file is inconsistent");
} }
fclose(fp); fclose(fp);
} }

132
src/read_data.cpp
View File

@ -45,6 +45,7 @@
#include "irregular.h" #include "irregular.h"
#include "error.h" #include "error.h"
#include "memory.h" #include "memory.h"
#include "utils.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -999,74 +1000,115 @@ void ReadData::header(int firstpass)
// customize for new header lines // customize for new header lines
// check for triangles before angles so "triangles" not matched as "angles" // check for triangles before angles so "triangles" not matched as "angles"
int extra_flag_value = 0; int extra_flag_value = 0;
int rv;
if (strstr(line,"atoms")) { if (utils::strmatch(line,"^\\s*\\d+\\s+atoms\\s")) {
sscanf(line,BIGINT_FORMAT,&natoms); 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; if (addflag == NONE) atom->natoms = natoms;
else if (firstpass) 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) if (!avec_ellipsoid)
error->all(FLERR,"No ellipsoids allowed with this atom style"); 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; if (addflag == NONE) atom->nellipsoids = nellipsoids;
else if (firstpass) 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) if (!avec_line)
error->all(FLERR,"No lines allowed with this atom style"); 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; if (addflag == NONE) atom->nlines = nlines;
else if (firstpass) 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) if (!avec_tri)
error->all(FLERR,"No triangles allowed with this atom style"); 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; if (addflag == NONE) atom->ntris = ntris;
else if (firstpass) 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) if (!avec_body)
error->all(FLERR,"No bodies allowed with this atom style"); 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; if (addflag == NONE) atom->nbodies = nbodies;
else if (firstpass) atom->nbodies += nbodies; else if (firstpass) atom->nbodies += nbodies;
} else if (strstr(line,"bonds")) { } else if (utils::strmatch(line,"^\\s*\\d+\\s+bonds\\s")) {
sscanf(line,BIGINT_FORMAT,&nbonds); 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; if (addflag == NONE) atom->nbonds = nbonds;
else if (firstpass) 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; if (addflag == NONE) atom->nangles = nangles;
else if (firstpass) 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; if (addflag == NONE) atom->ndihedrals = ndihedrals;
else if (firstpass) 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; if (addflag == NONE) atom->nimpropers = nimpropers;
else if (firstpass) atom->nimpropers += nimpropers; else if (firstpass) atom->nimpropers += nimpropers;
// Atom class type settings are only set by first data file // Atom class type settings are only set by first data file
} else if (strstr(line,"atom types")) { } else if (utils::strmatch(line,"^\\s*\\d+\\s+atom\\s+types\\s")) {
sscanf(line,"%d",&ntypes); 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; 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; 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; 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) if (addflag == NONE)
atom->ndihedraltypes = ndihedraltypes + extra_dihedral_types; 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) if (addflag == NONE)
atom->nimpropertypes = nimpropertypes + extra_improper_types; atom->nimpropertypes = nimpropertypes + extra_improper_types;
@ -1095,15 +1137,27 @@ void ReadData::header(int firstpass)
// local copy of box info // local copy of box info
// so can treat differently for first vs subsequent data files // so can treat differently for first vs subsequent data files
} else if (strstr(line,"xlo xhi")) { } else if (utils::strmatch(line,"^\\s*\\f+\\s+\\f+\\s+xlo\\s+xhi\\s")) {
sscanf(line,"%lg %lg",&boxlo[0],&boxhi[0]); rv = sscanf(line,"%lg %lg",&boxlo[0],&boxhi[0]);
} else if (strstr(line,"ylo yhi")) { if (rv != 2)
sscanf(line,"%lg %lg",&boxlo[1],&boxhi[1]); error->all(FLERR,"Could not parse 'xlo xhi' line in data file header");
} else if (strstr(line,"zlo zhi")) {
sscanf(line,"%lg %lg",&boxlo[2],&boxhi[2]); } else if (utils::strmatch(line,"^\\s*\\f+\\s+\\f+\\s+ylo\\s+yhi\\s")) {
} else if (strstr(line,"xy xz yz")) { 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; 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; } else break;
} }
@ -1638,7 +1692,7 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
void ReadData::bodies(int firstpass) 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; char *eof;
int mapflag = 0; int mapflag = 0;
@ -1666,7 +1720,9 @@ void ReadData::bodies(int firstpass)
while (nchunk < nmax && nline <= CHUNK-MAXBODY) { while (nchunk < nmax && nline <= CHUNK-MAXBODY) {
eof = fgets(&buffer[m],MAXLINE,fp); eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file"); 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]); m += strlen(&buffer[m]);
// read lines one at a time into buffer and count words // read lines one at a time into buffer and count words

32
src/reader_native.cpp
View File

@ -59,8 +59,9 @@ int ReaderNative::read_time(bigint &ntimestep)
if (strstr(line,"ITEM: TIMESTEP") != line) if (strstr(line,"ITEM: TIMESTEP") != line)
error->one(FLERR,"Dump file is incorrectly formatted"); error->one(FLERR,"Dump file is incorrectly formatted");
read_lines(1); read_lines(1);
sscanf(line,BIGINT_FORMAT,&ntimestep); int rv = sscanf(line,BIGINT_FORMAT,&ntimestep);
if (rv != 1)
error->one(FLERR,"Dump file is incorrectly formatted");
return 0; return 0;
} }
@ -73,7 +74,9 @@ void ReaderNative::skip()
{ {
read_lines(2); read_lines(2);
bigint natoms; bigint natoms;
sscanf(line,BIGINT_FORMAT,&natoms); int rv = sscanf(line,BIGINT_FORMAT,&natoms);
if (rv != 1)
error->one(FLERR,"Dump file is incorrectly formatted");
read_lines(5); read_lines(5);
@ -110,8 +113,12 @@ bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic,
int &xflag, int &yflag, int &zflag) int &xflag, int &yflag, int &zflag)
{ {
bigint natoms; bigint natoms;
int rv;
read_lines(2); read_lines(2);
sscanf(line,BIGINT_FORMAT,&natoms); rv = sscanf(line,BIGINT_FORMAT,&natoms);
if (rv != 1)
error->one(FLERR,"Dump file is incorrectly formatted");
boxinfo = 1; boxinfo = 1;
triclinic = 0; triclinic = 0;
@ -120,14 +127,19 @@ bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic,
if (line[strlen("ITEM: BOX BOUNDS ")] == 'x') triclinic = 1; if (line[strlen("ITEM: BOX BOUNDS ")] == 'x') triclinic = 1;
read_lines(1); read_lines(1);
if (!triclinic) sscanf(line,"%lg %lg",&box[0][0],&box[0][1]); if (!triclinic) rv = 2 - sscanf(line,"%lg %lg",&box[0][0],&box[0][1]);
else sscanf(line,"%lg %lg %lg",&box[0][0],&box[0][1],&box[0][2]); else rv = 3 - sscanf(line,"%lg %lg %lg",&box[0][0],&box[0][1],&box[0][2]);
if (rv != 0) error->one(FLERR,"Dump file is incorrectly formatted");
read_lines(1); read_lines(1);
if (!triclinic) sscanf(line,"%lg %lg",&box[1][0],&box[1][1]); if (!triclinic) rv = 2 - sscanf(line,"%lg %lg",&box[1][0],&box[1][1]);
else sscanf(line,"%lg %lg %lg",&box[1][0],&box[1][1],&box[1][2]); else rv = 3 - sscanf(line,"%lg %lg %lg",&box[1][0],&box[1][1],&box[1][2]);
if (rv != 0) error->one(FLERR,"Dump file is incorrectly formatted");
read_lines(1); read_lines(1);
if (!triclinic) sscanf(line,"%lg %lg",&box[2][0],&box[2][1]); if (!triclinic) rv = 2 - sscanf(line,"%lg %lg",&box[2][0],&box[2][1]);
else sscanf(line,"%lg %lg %lg",&box[2][0],&box[2][1],&box[2][2]); else rv = 3 - sscanf(line,"%lg %lg %lg",&box[2][0],&box[2][1],&box[2][2]);
if (rv != 0) error->one(FLERR,"Dump file is incorrectly formatted");
read_lines(1); read_lines(1);

6
src/reader_xyz.cpp
View File

@ -170,7 +170,7 @@ bigint ReaderXYZ::read_header(double /*box*/[3][3], int &boxinfo, int &/*triclin
void ReaderXYZ::read_atoms(int n, int nfield, double **fields) void ReaderXYZ::read_atoms(int n, int nfield, double **fields)
{ {
int i,m; int i,m,rv;
char *eof; char *eof;
int mytype; int mytype;
double myx, myy, myz; double myx, myy, myz;
@ -180,7 +180,9 @@ void ReaderXYZ::read_atoms(int n, int nfield, double **fields)
if (eof == NULL) error->one(FLERR,"Unexpected end of dump file"); if (eof == NULL) error->one(FLERR,"Unexpected end of dump file");
++nid; ++nid;
sscanf(line,"%*s%lg%lg%lg", &myx, &myy, &myz); rv = sscanf(line,"%*s%lg%lg%lg", &myx, &myy, &myz);
if (rv != 3)
error->one(FLERR,"Dump file is incorrectly formatted");
// XXX: we could insert an element2type translation here // XXX: we could insert an element2type translation here
// XXX: for now we flag unrecognized types as type 0, // XXX: for now we flag unrecognized types as type 0,

10
src/universe.cpp
View File

@ -114,19 +114,19 @@ void Universe::reorder(char *style, char *arg)
// read nprocs lines // read nprocs lines
// uni2orig = inverse mapping // uni2orig = inverse mapping
int me_orig,me_new; int me_orig,me_new,rv;
sscanf(line,"%d %d",&me_orig,&me_new); rv = sscanf(line,"%d %d",&me_orig,&me_new);
if (me_orig < 0 || me_orig >= nprocs || if (me_orig < 0 || me_orig >= nprocs ||
me_new < 0 || me_new >= nprocs) me_new < 0 || me_new >= nprocs || rv != 2)
error->one(FLERR,"Invalid entry in -reorder file"); error->one(FLERR,"Invalid entry in -reorder file");
uni2orig[me_new] = me_orig; uni2orig[me_new] = me_orig;
for (int i = 1; i < nprocs; i++) { for (int i = 1; i < nprocs; i++) {
if (!fgets(line,MAXLINE,fp)) if (!fgets(line,MAXLINE,fp))
error->one(FLERR,"Unexpected end of -reorder file"); error->one(FLERR,"Unexpected end of -reorder file");
sscanf(line,"%d %d",&me_orig,&me_new); rv = sscanf(line,"%d %d",&me_orig,&me_new);
if (me_orig < 0 || me_orig >= nprocs || if (me_orig < 0 || me_orig >= nprocs ||
me_new < 0 || me_new >= nprocs) me_new < 0 || me_new >= nprocs || rv != 2)
error->one(FLERR,"Invalid entry in -reorder file"); error->one(FLERR,"Invalid entry in -reorder file");
uni2orig[me_new] = me_orig; uni2orig[me_new] = me_orig;
} }

29
src/utils.cpp
View File

@ -39,6 +39,10 @@
* '\W' Non-alphanumeric * '\W' Non-alphanumeric
* '\d' Digits, [0-9] * '\d' Digits, [0-9]
* '\D' Non-digits * '\D' Non-digits
* '\i' Integer chars, [0-9], '+' and '-'
* '\I' Non-integers
* '\f' Floating point number chars, [0-9], '.', 'e', 'E', '+' and '-'
* '\F' Non-floats
* *
* *NOT* supported: * *NOT* supported:
* '[^abc]' Inverted class * '[^abc]' Inverted class
@ -307,6 +311,7 @@ extern "C" {
enum { UNUSED, DOT, BEGIN, END, QUESTIONMARK, STAR, PLUS, enum { UNUSED, DOT, BEGIN, END, QUESTIONMARK, STAR, PLUS,
CHAR, CHAR_CLASS, INV_CHAR_CLASS, DIGIT, NOT_DIGIT, CHAR, CHAR_CLASS, INV_CHAR_CLASS, DIGIT, NOT_DIGIT,
INTEGER, NOT_INTEGER, FLOAT, NOT_FLOAT,
ALPHA, NOT_ALPHA, WHITESPACE, NOT_WHITESPACE /*, BRANCH */ }; ALPHA, NOT_ALPHA, WHITESPACE, NOT_WHITESPACE /*, BRANCH */ };
typedef struct regex_t { typedef struct regex_t {
@ -324,6 +329,8 @@ extern "C" {
static int matchplus(regex_t p, regex_t *pattern, const char *text); static int matchplus(regex_t p, regex_t *pattern, const char *text);
static int matchone(regex_t p, char c); static int matchone(regex_t p, char c);
static int matchdigit(char c); static int matchdigit(char c);
static int matchint(char c);
static int matchfloat(char c);
static int matchalpha(char c); static int matchalpha(char c);
static int matchwhitespace(char c); static int matchwhitespace(char c);
static int matchmetachar(char c, const char *str); static int matchmetachar(char c, const char *str);
@ -395,6 +402,10 @@ extern "C" {
/* Meta-character: */ /* Meta-character: */
case 'd': { re_compiled[j].type = DIGIT; } break; case 'd': { re_compiled[j].type = DIGIT; } break;
case 'D': { re_compiled[j].type = NOT_DIGIT; } break; case 'D': { re_compiled[j].type = NOT_DIGIT; } break;
case 'i': { re_compiled[j].type = INTEGER; } break;
case 'I': { re_compiled[j].type = NOT_INTEGER; } break;
case 'f': { re_compiled[j].type = FLOAT; } break;
case 'F': { re_compiled[j].type = NOT_FLOAT; } break;
case 'w': { re_compiled[j].type = ALPHA; } break; case 'w': { re_compiled[j].type = ALPHA; } break;
case 'W': { re_compiled[j].type = NOT_ALPHA; } break; case 'W': { re_compiled[j].type = NOT_ALPHA; } break;
case 's': { re_compiled[j].type = WHITESPACE; } break; case 's': { re_compiled[j].type = WHITESPACE; } break;
@ -467,6 +478,16 @@ extern "C" {
return ((c >= '0') && (c <= '9')); return ((c >= '0') && (c <= '9'));
} }
static int matchint(char c)
{
return (matchdigit(c) || (c == '-') || (c == '+'));
}
static int matchfloat(char c)
{
return (matchint(c) || (c == '.') || (c == 'e') || (c == 'E'));
}
static int matchalpha(char c) static int matchalpha(char c)
{ {
return ((c >= 'a') && (c <= 'z')) || ((c >= 'A') && (c <= 'Z')); return ((c >= 'a') && (c <= 'z')) || ((c >= 'A') && (c <= 'Z'));
@ -502,6 +523,10 @@ extern "C" {
switch (str[0]) { switch (str[0]) {
case 'd': return matchdigit(c); case 'd': return matchdigit(c);
case 'D': return !matchdigit(c); case 'D': return !matchdigit(c);
case 'i': return matchint(c);
case 'I': return !matchint(c);
case 'f': return matchfloat(c);
case 'F': return !matchfloat(c);
case 'w': return matchalphanum(c); case 'w': return matchalphanum(c);
case 'W': return !matchalphanum(c); case 'W': return !matchalphanum(c);
case 's': return matchwhitespace(c); case 's': return matchwhitespace(c);
@ -544,6 +569,10 @@ extern "C" {
case INV_CHAR_CLASS: return !matchcharclass(c, (const char *)p.ccl); case INV_CHAR_CLASS: return !matchcharclass(c, (const char *)p.ccl);
case DIGIT: return matchdigit(c); case DIGIT: return matchdigit(c);
case NOT_DIGIT: return !matchdigit(c); case NOT_DIGIT: return !matchdigit(c);
case INTEGER: return matchint(c);
case NOT_INTEGER: return !matchint(c);
case FLOAT: return matchfloat(c);
case NOT_FLOAT: return !matchfloat(c);
case ALPHA: return matchalphanum(c); case ALPHA: return matchalphanum(c);
case NOT_ALPHA: return !matchalphanum(c); case NOT_ALPHA: return !matchalphanum(c);
case WHITESPACE: return matchwhitespace(c); case WHITESPACE: return matchwhitespace(c);

4
src/variable.cpp
View File

@ -5162,8 +5162,8 @@ int VarReader::read_peratom()
for (i = 0; i < nchunk; i++) { for (i = 0; i < nchunk; i++) {
next = strchr(buf,'\n'); next = strchr(buf,'\n');
*next = '\0'; *next = '\0';
sscanf(buf,TAGINT_FORMAT " %lg",&tag,&value); int rv = sscanf(buf,TAGINT_FORMAT " %lg",&tag,&value);
if (tag <= 0 || tag > map_tag_max) if (tag <= 0 || tag > map_tag_max || rv != 2)
error->one(FLERR,"Invalid atom ID in variable file"); error->one(FLERR,"Invalid atom ID in variable file");
if ((m = atom->map(tag)) >= 0) vstore[m] = value; if ((m = atom->map(tag)) >= 0) vstore[m] = value;
buf = next + 1; buf = next + 1;