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Merge branch 'master' into improve-include-consistency

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# Conflicts:
#	src/utils.cpp
This commit is contained in:
Axel Kohlmeyer
2019-07-19 17:57:58 -04:00
parent ceb2ce5814 981b9a1f7a
commit a50d57bceb
23 changed files with 346 additions and 185 deletions
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132
src/read_data.cpp
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@ -41,6 +41,7 @@
#include "irregular.h"
#include "error.h"
#include "memory.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -995,74 +996,115 @@ 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;
@ -1091,15 +1133,27 @@ 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;
}
@ -1634,7 +1688,7 @@ 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;
@ -1662,7 +1716,9 @@ 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