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

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2015-10-30 20:04:06 +00:00
parent 0aa77408f8
commit 354e20f431
1219 changed files with 10111 additions and 10111 deletions
Download Patch File Download Diff File Expand all files Collapse all files

80
src/read_data.cpp
View File

@ -15,12 +15,12 @@
// due to OpenMPI bug which sets INT64_MAX via its mpi.h
// before lmptype.h can set flags to insure it is done correctly
#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "string.h"
#include "stdlib.h"
#include "ctype.h"
#include "lmptype.h"
#include <mpi.h>
#include <math.h>
#include <string.h>
#include <stdlib.h>
#include <ctype.h>
#include "read_data.h"
#include "atom.h"
#include "atom_vec.h"
@ -125,7 +125,7 @@ void ReadData::command(int narg, char **arg)
offsetflag = shiftflag = 0;
toffset = boffset = aoffset = doffset = ioffset = 0;
shift[0] = shift[1] = shift[2] = 0.0;
extra_atom_types = extra_bond_types = extra_angle_types =
extra_atom_types = extra_bond_types = extra_angle_types =
extra_dihedral_types = extra_improper_types = 0;
groupbit = 0;
@ -144,7 +144,7 @@ void ReadData::command(int narg, char **arg)
else {
addflag = VALUE;
bigint offset = force->bnumeric(FLERR,arg[iarg+1]);
if (offset > MAXTAGINT)
if (offset > MAXTAGINT)
error->all(FLERR,"Read data add offset is too big");
id_offset = offset;
}
@ -157,8 +157,8 @@ void ReadData::command(int narg, char **arg)
aoffset = force->inumeric(FLERR,arg[iarg+3]);
doffset = force->inumeric(FLERR,arg[iarg+4]);
ioffset = force->inumeric(FLERR,arg[iarg+5]);
if (toffset < 0 || boffset < 0 || aoffset < 0 ||
doffset < 0 || ioffset < 0)
if (toffset < 0 || boffset < 0 || aoffset < 0 ||
doffset < 0 || ioffset < 0)
error->all(FLERR,"Illegal read_data command");
iarg += 6;
} else if (strcmp(arg[iarg],"shift") == 0) {
@ -178,32 +178,32 @@ void ReadData::command(int narg, char **arg)
iarg += 2;
} else if (strcmp(arg[iarg],"extra/bond/types") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
if (!atom->avec->bonds_allow)
if (!atom->avec->bonds_allow)
error->all(FLERR,"No bonds allowed with this atom style");
extra_bond_types = force->inumeric(FLERR,arg[iarg+1]);
if (extra_bond_types < 0) error->all(FLERR,"Illegal read_data command");
iarg += 2;
} else if (strcmp(arg[iarg],"extra/angle/types") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
if (!atom->avec->angles_allow)
if (!atom->avec->angles_allow)
error->all(FLERR,"No angles allowed with this atom style");
extra_angle_types = force->inumeric(FLERR,arg[iarg+1]);
if (extra_angle_types < 0) error->all(FLERR,"Illegal read_data command");
iarg += 2;
} else if (strcmp(arg[iarg],"extra/dihedral/types") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
if (!atom->avec->dihedrals_allow)
if (!atom->avec->dihedrals_allow)
error->all(FLERR,"No dihedrals allowed with this atom style");
extra_dihedral_types = force->inumeric(FLERR,arg[iarg+1]);
if (extra_dihedral_types < 0)
if (extra_dihedral_types < 0)
error->all(FLERR,"Illegal read_data command");
iarg += 2;
} else if (strcmp(arg[iarg],"extra/improper/types") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
if (!atom->avec->impropers_allow)
if (!atom->avec->impropers_allow)
error->all(FLERR,"No impropers allowed with this atom style");
extra_improper_types = force->inumeric(FLERR,arg[iarg+1]);
if (extra_improper_types < 0)
if (extra_improper_types < 0)
error->all(FLERR,"Illegal read_data command");
iarg += 2;
@ -255,8 +255,8 @@ void ReadData::command(int narg, char **arg)
error->all(FLERR,"Cannot use read_data offset without add flag");
if (shiftflag && addflag == NONE)
error->all(FLERR,"Cannot use read_data shift without add flag");
if (addflag != NONE &&
(extra_atom_types || extra_bond_types || extra_angle_types ||
if (addflag != NONE &&
(extra_atom_types || extra_bond_types || extra_angle_types ||
extra_dihedral_types || extra_improper_types))
error->all(FLERR,"Cannot use read_data extra with add flag");
@ -312,9 +312,9 @@ void ReadData::command(int narg, char **arg)
if (firstpass && screen) fprintf(screen,"Reading data file ...\n");
open(arg[0]);
} else fp = NULL;
// read header info
header(firstpass);
// problem setup using info from header
@ -405,7 +405,7 @@ void ReadData::command(int narg, char **arg)
atoms();
} else skip_lines(natoms);
} else if (strcmp(keyword,"Velocities") == 0) {
if (atomflag == 0)
if (atomflag == 0)
error->all(FLERR,"Must read Atoms before Velocities");
if (firstpass) velocities();
else skip_lines(natoms);
@ -434,14 +434,14 @@ void ReadData::command(int narg, char **arg)
error->all(FLERR,"Invalid data file section: Impropers");
if (atomflag == 0) error->all(FLERR,"Must read Atoms before Impropers");
impropers(firstpass);
} else if (strcmp(keyword,"Ellipsoids") == 0) {
ellipsoidflag = 1;
if (!avec_ellipsoid)
error->all(FLERR,"Invalid data file section: Ellipsoids");
if (atomflag == 0)
if (atomflag == 0)
error->all(FLERR,"Must read Atoms before Ellipsoids");
if (firstpass)
if (firstpass)
bonus(nellipsoids,(AtomVec *) avec_ellipsoid,"ellipsoids");
else skip_lines(nellipsoids);
} else if (strcmp(keyword,"Lines") == 0) {
@ -590,7 +590,7 @@ void ReadData::command(int narg, char **arg)
"Must define dihedral_style before BondBond13 Coeffs");
if (firstpass) dihedralcoeffs(5);
else skip_lines(ndihedraltypes);
} else if (strcmp(keyword,"AngleAngle Coeffs") == 0) {
if (atom->avec->impropers_allow == 0)
error->all(FLERR,"Invalid data file section: AngleAngle Coeffs");
@ -605,7 +605,7 @@ void ReadData::command(int narg, char **arg)
sprintf(str,"Unknown identifier in data file: %s",keyword);
error->all(FLERR,str);
}
parse_keyword(0);
}
@ -613,9 +613,9 @@ void ReadData::command(int narg, char **arg)
if (natoms > 0 && atomflag == 0)
error->all(FLERR,"No atoms in data file");
// close file
if (me == 0) {
if (compressed) pclose(fp);
else fclose(fp);
@ -639,7 +639,7 @@ void ReadData::command(int narg, char **arg)
// break out of loop if no molecular topology in file
// else make 2nd pass
if (!topoflag) break;
firstpass = 0;
@ -668,7 +668,7 @@ void ReadData::command(int narg, char **arg)
special.build();
}
// for atom style template systems, count total bonds,angles,etc
// for atom style template systems, count total bonds,angles,etc
if (atom->molecular == 2) {
Molecule **onemols = atom->avec->onemols;
@ -894,7 +894,7 @@ void ReadData::header(int firstpass)
sscanf(line,BIGINT_FORMAT,&nimpropers);
if (addflag == NONE) atom->nimpropers = nimpropers;
else atom->nimpropers += nimpropers;
// Atom class type settings are only set by first data file
} else if (strstr(line,"atom types")) {
@ -908,11 +908,11 @@ void ReadData::header(int firstpass)
if (addflag == NONE) atom->nangletypes = nangletypes + extra_angle_types;
} else if (strstr(line,"dihedral types")) {
sscanf(line,"%d",&ndihedraltypes);
if (addflag == NONE)
if (addflag == NONE)
atom->ndihedraltypes = ndihedraltypes + extra_dihedral_types;
} else if (strstr(line,"improper types")) {
sscanf(line,"%d",&nimpropertypes);
if (addflag == NONE)
if (addflag == NONE)
atom->nimpropertypes = nimpropertypes + extra_improper_types;
// these settings only used by first data file
@ -979,7 +979,7 @@ void ReadData::header(int firstpass)
if ((atom->nimpropers || atom->nimpropertypes) &&
atom->avec->impropers_allow == 0)
error->all(FLERR,"No impropers allowed with this atom style");
if (atom->nbonds > 0 && atom->nbondtypes <= 0)
error->all(FLERR,"Bonds defined but no bond types");
if (atom->nangles > 0 && atom->nangletypes <= 0)
@ -1032,7 +1032,7 @@ void ReadData::atoms()
if (sum != atom->natoms)
error->all(FLERR,"Did not assign all atoms correctly");
// check that atom IDs are valid
atom->tag_check();
@ -1143,7 +1143,7 @@ void ReadData::bonds(int firstpass)
}
if (addflag != NONE) {
if (maxall > atom->bond_per_atom)
if (maxall > atom->bond_per_atom)
error->all(FLERR,"Subsequent read data induced "
"too many bonds per atom");
} else atom->bond_per_atom = maxall;
@ -1226,7 +1226,7 @@ void ReadData::angles(int firstpass)
}
if (addflag != NONE) {
if (maxall > atom->angle_per_atom)
if (maxall > atom->angle_per_atom)
error->all(FLERR,"Subsequent read data induced "
"too many angles per atom");
} else atom->angle_per_atom = maxall;
@ -1309,7 +1309,7 @@ void ReadData::dihedrals(int firstpass)
}
if (addflag != NONE) {
if (maxall > atom->dihedral_per_atom)
if (maxall > atom->dihedral_per_atom)
error->all(FLERR,"Subsequent read data induced "
"too many dihedrals per atom");
} else atom->dihedral_per_atom = maxall;
@ -1393,7 +1393,7 @@ void ReadData::impropers(int firstpass)
}
if (addflag != NONE) {
if (maxall > atom->improper_per_atom)
if (maxall > atom->improper_per_atom)
error->all(FLERR,"Subsequent read data induced "
"too many impropers per atom");
} else atom->improper_per_atom = maxall;
@ -1586,7 +1586,7 @@ void ReadData::pairIJcoeffs()
{
int i,j;
char *next;
int nsq = ntypes * (ntypes+1) / 2;
char *buf = new char[nsq * MAXLINE];