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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7003 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2011-09-23 18:06:55 +00:00
parent 2d99de131d
commit 19e8c92a90
468 changed files with 4628 additions and 5204 deletions
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233
src/read_data.cpp
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@ -44,9 +44,6 @@ using namespace LAMMPS_NS;
// customize for new sections
#define NSECTIONS 21 // change when add to header::section_keywords
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
ReadData::ReadData(LAMMPS *lmp) : Pointers(lmp)
@ -79,12 +76,12 @@ ReadData::~ReadData()
void ReadData::command(int narg, char **arg)
{
if (narg != 1) error->all("Illegal read_data command");
if (narg != 1) error->all(FLERR,"Illegal read_data command");
if (domain->box_exist)
error->all("Cannot read_data after simulation box is defined");
error->all(FLERR,"Cannot read_data after simulation box is defined");
if (domain->dimension == 2 && domain->zperiodic == 0)
error->all("Cannot run 2d simulation with nonperiodic Z dimension");
error->all(FLERR,"Cannot run 2d simulation with nonperiodic Z dimension");
// scan data file to determine max topology needed per atom
// allocate initial topology arrays
@ -147,122 +144,122 @@ void ReadData::command(int narg, char **arg)
atoms();
atomflag = 1;
} else if (strcmp(keyword,"Velocities") == 0) {
if (atomflag == 0) error->all("Must read Atoms before Velocities");
if (atomflag == 0) error->all(FLERR,"Must read Atoms before Velocities");
velocities();
} else if (strcmp(keyword,"Ellipsoids") == 0) {
if (!avec_ellipsoid)
error->all("Invalid data file section: Ellipsoids");
if (atomflag == 0) error->all("Must read Atoms before Ellipsoids");
error->all(FLERR,"Invalid data file section: Ellipsoids");
if (atomflag == 0) error->all(FLERR,"Must read Atoms before Ellipsoids");
ellipsoids();
} else if (strcmp(keyword,"Bonds") == 0) {
if (atom->avec->bonds_allow == 0)
error->all("Invalid data file section: Bonds");
if (atomflag == 0) error->all("Must read Atoms before Bonds");
error->all(FLERR,"Invalid data file section: Bonds");
if (atomflag == 0) error->all(FLERR,"Must read Atoms before Bonds");
bonds();
} else if (strcmp(keyword,"Angles") == 0) {
if (atom->avec->angles_allow == 0)
error->all("Invalid data file section: Angles");
if (atomflag == 0) error->all("Must read Atoms before Angles");
error->all(FLERR,"Invalid data file section: Angles");
if (atomflag == 0) error->all(FLERR,"Must read Atoms before Angles");
angles();
} else if (strcmp(keyword,"Dihedrals") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: Dihedrals");
if (atomflag == 0) error->all("Must read Atoms before Dihedrals");
error->all(FLERR,"Invalid data file section: Dihedrals");
if (atomflag == 0) error->all(FLERR,"Must read Atoms before Dihedrals");
dihedrals();
} else if (strcmp(keyword,"Impropers") == 0) {
if (atom->avec->impropers_allow == 0)
error->all("Invalid data file section: Impropers");
if (atomflag == 0) error->all("Must read Atoms before Impropers");
error->all(FLERR,"Invalid data file section: Impropers");
if (atomflag == 0) error->all(FLERR,"Must read Atoms before Impropers");
impropers();
} else if (strcmp(keyword,"Masses") == 0) {
mass();
} else if (strcmp(keyword,"Pair Coeffs") == 0) {
if (force->pair == NULL)
error->all("Must define pair_style before Pair Coeffs");
error->all(FLERR,"Must define pair_style before Pair Coeffs");
paircoeffs();
} else if (strcmp(keyword,"Bond Coeffs") == 0) {
if (atom->avec->bonds_allow == 0)
error->all("Invalid data file section: Bond Coeffs");
error->all(FLERR,"Invalid data file section: Bond Coeffs");
if (force->bond == NULL)
error->all("Must define bond_style before Bond Coeffs");
error->all(FLERR,"Must define bond_style before Bond Coeffs");
bondcoeffs();
} else if (strcmp(keyword,"Angle Coeffs") == 0) {
if (atom->avec->angles_allow == 0)
error->all("Invalid data file section: Angle Coeffs");
error->all(FLERR,"Invalid data file section: Angle Coeffs");
if (force->angle == NULL)
error->all("Must define angle_style before Angle Coeffs");
error->all(FLERR,"Must define angle_style before Angle Coeffs");
anglecoeffs(0);
} else if (strcmp(keyword,"Dihedral Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: Dihedral Coeffs");
error->all(FLERR,"Invalid data file section: Dihedral Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before Dihedral Coeffs");
error->all(FLERR,"Must define dihedral_style before Dihedral Coeffs");
dihedralcoeffs(0);
} else if (strcmp(keyword,"Improper Coeffs") == 0) {
if (atom->avec->impropers_allow == 0)
error->all("Invalid data file section: Improper Coeffs");
error->all(FLERR,"Invalid data file section: Improper Coeffs");
if (force->improper == NULL)
error->all("Must define improper_style before Improper Coeffs");
error->all(FLERR,"Must define improper_style before Improper Coeffs");
impropercoeffs(0);
} else if (strcmp(keyword,"BondBond Coeffs") == 0) {
if (atom->avec->angles_allow == 0)
error->all("Invalid data file section: BondBond Coeffs");
error->all(FLERR,"Invalid data file section: BondBond Coeffs");
if (force->angle == NULL)
error->all("Must define angle_style before BondBond Coeffs");
error->all(FLERR,"Must define angle_style before BondBond Coeffs");
anglecoeffs(1);
} else if (strcmp(keyword,"BondAngle Coeffs") == 0) {
if (atom->avec->angles_allow == 0)
error->all("Invalid data file section: BondAngle Coeffs");
error->all(FLERR,"Invalid data file section: BondAngle Coeffs");
if (force->angle == NULL)
error->all("Must define angle_style before BondAngle Coeffs");
error->all(FLERR,"Must define angle_style before BondAngle Coeffs");
anglecoeffs(2);
} else if (strcmp(keyword,"MiddleBondTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: MiddleBondTorsion Coeffs");
error->all(FLERR,"Invalid data file section: MiddleBondTorsion Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before MiddleBondTorsion Coeffs");
error->all(FLERR,"Must define dihedral_style before MiddleBondTorsion Coeffs");
dihedralcoeffs(1);
} else if (strcmp(keyword,"EndBondTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: EndBondTorsion Coeffs");
error->all(FLERR,"Invalid data file section: EndBondTorsion Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before EndBondTorsion Coeffs");
error->all(FLERR,"Must define dihedral_style before EndBondTorsion Coeffs");
dihedralcoeffs(2);
} else if (strcmp(keyword,"AngleTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: AngleTorsion Coeffs");
error->all(FLERR,"Invalid data file section: AngleTorsion Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before AngleTorsion Coeffs");
error->all(FLERR,"Must define dihedral_style before AngleTorsion Coeffs");
dihedralcoeffs(3);
} else if (strcmp(keyword,"AngleAngleTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: AngleAngleTorsion Coeffs");
error->all(FLERR,"Invalid data file section: AngleAngleTorsion Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before AngleAngleTorsion Coeffs");
error->all(FLERR,"Must define dihedral_style before AngleAngleTorsion Coeffs");
dihedralcoeffs(4);
} else if (strcmp(keyword,"BondBond13 Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: BondBond13 Coeffs");
error->all(FLERR,"Invalid data file section: BondBond13 Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before BondBond13 Coeffs");
error->all(FLERR,"Must define dihedral_style before BondBond13 Coeffs");
dihedralcoeffs(5);
} else if (strcmp(keyword,"AngleAngle Coeffs") == 0) {
if (atom->avec->impropers_allow == 0)
error->all("Invalid data file section: AngleAngle Coeffs");
error->all(FLERR,"Invalid data file section: AngleAngle Coeffs");
if (force->improper == NULL)
error->all("Must define improper_style before AngleAngle Coeffs");
error->all(FLERR,"Must define improper_style before AngleAngle Coeffs");
impropercoeffs(1);
} else {
char str[128];
sprintf(str,"Unknown identifier in data file: %s",keyword);
error->all(str);
error->all(FLERR,str);
}
parse_keyword(0,1);
@ -277,7 +274,7 @@ void ReadData::command(int narg, char **arg)
// error if natoms > 0 yet no atoms were read
if (atom->natoms > 0 && atomflag == 0) error->all("No atoms in data file");
if (atom->natoms > 0 && atomflag == 0) error->all(FLERR,"No atoms in data file");
// create bond topology now that system is defined
@ -318,7 +315,7 @@ void ReadData::header(int flag)
if (me == 0) {
char *eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
}
// customize for new header lines
@ -374,7 +371,7 @@ void ReadData::header(int flag)
else if (strstr(line,"ellipsoids")) {
if (!avec_ellipsoid)
error->all("No ellipsoids allowed with this atom style");
error->all(FLERR,"No ellipsoids allowed with this atom style");
sscanf(line,BIGINT_FORMAT,&nellipsoids);
}
@ -397,8 +394,8 @@ void ReadData::header(int flag)
atom->nangles < 0 || atom->nangles > MAXBIGINT ||
atom->ndihedrals < 0 || atom->ndihedrals > MAXBIGINT ||
atom->nimpropers < 0 || atom->nimpropers > MAXBIGINT) {
if (flag == 0) error->one("System in data file is too big");
else error->all("System in data file is too big");
if (flag == 0) error->one(FLERR,"System in data file is too big");
else error->all(FLERR,"System in data file is too big");
}
// check that exiting string is a valid section keyword
@ -409,32 +406,32 @@ void ReadData::header(int flag)
if (n == NSECTIONS) {
char str[128];
sprintf(str,"Unknown identifier in data file: %s",keyword);
error->all(str);
error->all(FLERR,str);
}
// error check on consistency of header values
if ((atom->nbonds || atom->nbondtypes) &&
atom->avec->bonds_allow == 0)
error->one("No bonds allowed with this atom style");
error->one(FLERR,"No bonds allowed with this atom style");
if ((atom->nangles || atom->nangletypes) &&
atom->avec->angles_allow == 0)
error->one("No angles allowed with this atom style");
error->one(FLERR,"No angles allowed with this atom style");
if ((atom->ndihedrals || atom->ndihedraltypes) &&
atom->avec->dihedrals_allow == 0)
error->one("No dihedrals allowed with this atom style");
error->one(FLERR,"No dihedrals allowed with this atom style");
if ((atom->nimpropers || atom->nimpropertypes) &&
atom->avec->impropers_allow == 0)
error->one("No impropers allowed with this atom style");
error->one(FLERR,"No impropers allowed with this atom style");
if (atom->nbonds > 0 && atom->nbondtypes <= 0)
error->one("Bonds defined but no bond types");
error->one(FLERR,"Bonds defined but no bond types");
if (atom->nangles > 0 && atom->nangletypes <= 0)
error->one("Angles defined but no angle types");
error->one(FLERR,"Angles defined but no angle types");
if (atom->ndihedrals > 0 && atom->ndihedraltypes <= 0)
error->one("Dihedrals defined but no dihedral types");
error->one(FLERR,"Dihedrals defined but no dihedral types");
if (atom->nimpropers > 0 && atom->nimpropertypes <= 0)
error->one("Impropers defined but no improper types");
error->one(FLERR,"Impropers defined but no improper types");
}
/* ----------------------------------------------------------------------
@ -456,7 +453,7 @@ void ReadData::atoms()
m = 0;
for (i = 0; i < nchunk; i++) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buffer[m]);
}
m++;
@ -478,7 +475,7 @@ void ReadData::atoms()
if (logfile) fprintf(logfile," " BIGINT_FORMAT " atoms\n",natoms);
}
if (natoms != atom->natoms) error->all("Did not assign all atoms correctly");
if (natoms != atom->natoms) error->all(FLERR,"Did not assign all atoms correctly");
// if any atom ID < 0, error
// if all atom IDs = 0, tag_enable = 0
@ -494,7 +491,7 @@ void ReadData::atoms()
int flag_all;
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all)
error->all("Invalid atom ID in Atoms section of data file");
error->all(FLERR,"Invalid atom ID in Atoms section of data file");
flag = 0;
for (int i = 0; i < nlocal; i++)
@ -508,7 +505,7 @@ void ReadData::atoms()
if (tag[i] == 0) flag = 1;
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all)
error->all("Invalid atom ID in Atoms section of data file");
error->all(FLERR,"Invalid atom ID in Atoms section of data file");
}
// create global mapping
@ -547,7 +544,7 @@ void ReadData::velocities()
m = 0;
for (i = 0; i < nchunk; i++) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buffer[m]);
}
m++;
@ -598,7 +595,7 @@ void ReadData::ellipsoids()
m = 0;
for (i = 0; i < nchunk; i++) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buffer[m]);
}
m++;
@ -637,7 +634,7 @@ void ReadData::bonds()
m = 0;
for (i = 0; i < nchunk; i++) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buffer[m]);
}
m++;
@ -663,7 +660,7 @@ void ReadData::bonds()
if (screen) fprintf(screen," " BIGINT_FORMAT " bonds\n",sum/factor);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " bonds\n",sum/factor);
}
if (sum != factor*atom->nbonds) error->all("Bonds assigned incorrectly");
if (sum != factor*atom->nbonds) error->all(FLERR,"Bonds assigned incorrectly");
}
/* ---------------------------------------------------------------------- */
@ -682,7 +679,7 @@ void ReadData::angles()
m = 0;
for (i = 0; i < nchunk; i++) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buffer[m]);
}
m++;
@ -708,7 +705,7 @@ void ReadData::angles()
if (screen) fprintf(screen," " BIGINT_FORMAT " angles\n",sum/factor);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " angles\n",sum/factor);
}
if (sum != factor*atom->nangles) error->all("Angles assigned incorrectly");
if (sum != factor*atom->nangles) error->all(FLERR,"Angles assigned incorrectly");
}
/* ---------------------------------------------------------------------- */
@ -727,7 +724,7 @@ void ReadData::dihedrals()
m = 0;
for (i = 0; i < nchunk; i++) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buffer[m]);
}
m++;
@ -754,7 +751,7 @@ void ReadData::dihedrals()
if (logfile) fprintf(logfile," " BIGINT_FORMAT " dihedrals\n",sum/factor);
}
if (sum != factor*atom->ndihedrals)
error->all("Dihedrals assigned incorrectly");
error->all(FLERR,"Dihedrals assigned incorrectly");
}
/* ---------------------------------------------------------------------- */
@ -773,7 +770,7 @@ void ReadData::impropers()
m = 0;
for (i = 0; i < nchunk; i++) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buffer[m]);
}
m++;
@ -800,7 +797,7 @@ void ReadData::impropers()
if (logfile) fprintf(logfile," " BIGINT_FORMAT " impropers\n",sum/factor);
}
if (sum != factor*atom->nimpropers)
error->all("Impropers assigned incorrectly");
error->all(FLERR,"Impropers assigned incorrectly");
}
/* ---------------------------------------------------------------------- */
@ -816,7 +813,7 @@ void ReadData::mass()
m = 0;
for (i = 0; i < atom->ntypes; i++) {
eof = fgets(&buf[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buf[m]);
buf[m-1] = '\0';
}
@ -845,7 +842,7 @@ void ReadData::paircoeffs()
m = 0;
for (i = 0; i < atom->ntypes; i++) {
eof = fgets(&buf[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buf[m]);
buf[m-1] = '\0';
}
@ -876,7 +873,7 @@ void ReadData::bondcoeffs()
m = 0;
for (i = 0; i < atom->nbondtypes; i++) {
eof = fgets(&buf[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buf[m]);
buf[m-1] = '\0';
}
@ -907,7 +904,7 @@ void ReadData::anglecoeffs(int which)
m = 0;
for (i = 0; i < atom->nangletypes; i++) {
eof = fgets(&buf[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buf[m]);
buf[m-1] = '\0';
}
@ -940,7 +937,7 @@ void ReadData::dihedralcoeffs(int which)
m = 0;
for (i = 0; i < atom->ndihedraltypes; i++) {
eof = fgets(&buf[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buf[m]);
buf[m-1] = '\0';
}
@ -976,7 +973,7 @@ void ReadData::impropercoeffs(int which)
m = 0;
for (i = 0; i < atom->nimpropertypes; i++) {
eof = fgets(&buf[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buf[m]);
buf[m-1] = '\0';
}
@ -1006,7 +1003,7 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
char *eof;
if (atom->natoms > MAXSMALLINT)
error->all("Molecular data file has too many atoms");
error->all(FLERR,"Molecular data file has too many atoms");
// customize for new sections
@ -1031,86 +1028,86 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
else if (strcmp(keyword,"Ellipsoids") == 0) {
if (!avec_ellipsoid)
error->all("Invalid data file section: Ellipsoids");
error->all(FLERR,"Invalid data file section: Ellipsoids");
ellipsoid_flag = 1;
skip_lines(nellipsoids);
} else if (strcmp(keyword,"Pair Coeffs") == 0) {
if (force->pair == NULL)
error->all("Must define pair_style before Pair Coeffs");
error->all(FLERR,"Must define pair_style before Pair Coeffs");
skip_lines(atom->ntypes);
} else if (strcmp(keyword,"Bond Coeffs") == 0) {
if (atom->avec->bonds_allow == 0)
error->all("Invalid data file section: Bond Coeffs");
error->all(FLERR,"Invalid data file section: Bond Coeffs");
if (force->bond == NULL)
error->all("Must define bond_style before Bond Coeffs");
error->all(FLERR,"Must define bond_style before Bond Coeffs");
skip_lines(atom->nbondtypes);
} else if (strcmp(keyword,"Angle Coeffs") == 0) {
if (atom->avec->angles_allow == 0)
error->all("Invalid data file section: Angle Coeffs");
error->all(FLERR,"Invalid data file section: Angle Coeffs");
if (force->angle == NULL)
error->all("Must define angle_style before Angle Coeffs");
error->all(FLERR,"Must define angle_style before Angle Coeffs");
skip_lines(atom->nangletypes);
} else if (strcmp(keyword,"Dihedral Coeffs") == 0) {
skip_lines(atom->ndihedraltypes);
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: Dihedral Coeffs");
error->all(FLERR,"Invalid data file section: Dihedral Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before Dihedral Coeffs");
error->all(FLERR,"Must define dihedral_style before Dihedral Coeffs");
} else if (strcmp(keyword,"Improper Coeffs") == 0) {
if (atom->avec->impropers_allow == 0)
error->all("Invalid data file section: Improper Coeffs");
error->all(FLERR,"Invalid data file section: Improper Coeffs");
if (force->improper == NULL)
error->all("Must define improper_style before Improper Coeffs");
error->all(FLERR,"Must define improper_style before Improper Coeffs");
skip_lines(atom->nimpropertypes);
} else if (strcmp(keyword,"BondBond Coeffs") == 0) {
if (atom->avec->angles_allow == 0)
error->all("Invalid data file section: BondBond Coeffs");
error->all(FLERR,"Invalid data file section: BondBond Coeffs");
if (force->angle == NULL)
error->all("Must define angle_style before BondBond Coeffs");
error->all(FLERR,"Must define angle_style before BondBond Coeffs");
skip_lines(atom->nangletypes);
} else if (strcmp(keyword,"BondAngle Coeffs") == 0) {
if (atom->avec->angles_allow == 0)
error->all("Invalid data file section: BondAngle Coeffs");
error->all(FLERR,"Invalid data file section: BondAngle Coeffs");
if (force->angle == NULL)
error->all("Must define angle_style before BondAngle Coeffs");
error->all(FLERR,"Must define angle_style before BondAngle Coeffs");
skip_lines(atom->nangletypes);
} else if (strcmp(keyword,"MiddleBondTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: MiddleBondTorsion Coeffs");
error->all(FLERR,"Invalid data file section: MiddleBondTorsion Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before MiddleBondTorsion Coeffs");
error->all(FLERR,"Must define dihedral_style before MiddleBondTorsion Coeffs");
skip_lines(atom->ndihedraltypes);
} else if (strcmp(keyword,"EndBondTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: EndBondTorsion Coeffs");
error->all(FLERR,"Invalid data file section: EndBondTorsion Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before EndBondTorsion Coeffs");
error->all(FLERR,"Must define dihedral_style before EndBondTorsion Coeffs");
skip_lines(atom->ndihedraltypes);
} else if (strcmp(keyword,"AngleTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: AngleTorsion Coeffs");
error->all(FLERR,"Invalid data file section: AngleTorsion Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before AngleTorsion Coeffs");
error->all(FLERR,"Must define dihedral_style before AngleTorsion Coeffs");
skip_lines(atom->ndihedraltypes);
} else if (strcmp(keyword,"AngleAngleTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: AngleAngleTorsion Coeffs");
error->all(FLERR,"Invalid data file section: AngleAngleTorsion Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before AngleAngleTorsion Coeffs");
error->all(FLERR,"Must define dihedral_style before AngleAngleTorsion Coeffs");
skip_lines(atom->ndihedraltypes);
} else if (strcmp(keyword,"BondBond13 Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: BondBond13 Coeffs");
error->all(FLERR,"Invalid data file section: BondBond13 Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before BondBond13 Coeffs");
error->all(FLERR,"Must define dihedral_style before BondBond13 Coeffs");
skip_lines(atom->ndihedraltypes);
} else if (strcmp(keyword,"AngleAngle Coeffs") == 0) {
if (atom->avec->impropers_allow == 0)
error->all("Invalid data file section: AngleAngle Coeffs");
error->all(FLERR,"Invalid data file section: AngleAngle Coeffs");
if (force->improper == NULL)
error->all("Must define improper_style before AngleAngle Coeffs");
error->all(FLERR,"Must define improper_style before AngleAngle Coeffs");
skip_lines(atom->nimpropertypes);
} else if (strcmp(keyword,"Bonds") == 0) {
@ -1118,7 +1115,7 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
if (force->newton_bond)
for (i = 0; i < atom->nbonds; i++) {
eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
sscanf(line,"%d %d %d %d",&tmp1,&tmp2,&atom1,&atom2);
if (atom1 >= cmax) cmax = reallocate(&count,cmax,atom1);
count[atom1]++;
@ -1126,7 +1123,7 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
else
for (i = 0; i < atom->nbonds; i++) {
eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
sscanf(line,"%d %d %d %d",&tmp1,&tmp2,&atom1,&atom2);
int amax = MAX(atom1,atom2);
if (amax >= cmax) cmax = reallocate(&count,cmax,amax);
@ -1142,7 +1139,7 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
if (force->newton_bond)
for (i = 0; i < atom->nangles; i++) {
eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
sscanf(line,"%d %d %d %d %d",&tmp1,&tmp2,&atom1,&atom2,&atom3);
if (atom2 >= cmax) cmax = reallocate(&count,cmax,atom2);
count[atom2]++;
@ -1150,7 +1147,7 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
else
for (i = 0; i < atom->nangles; i++) {
eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
sscanf(line,"%d %d %d %d %d",&tmp1,&tmp2,&atom1,&atom2,&atom3);
int amax = MAX(atom1,atom2);
amax = MAX(amax,atom3);
@ -1168,7 +1165,7 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
if (force->newton_bond)
for (i = 0; i < atom->ndihedrals; i++) {
eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
sscanf(line,"%d %d %d %d %d %d",
&tmp1,&tmp2,&atom1,&atom2,&atom3,&atom4);
if (atom2 >= cmax) cmax = reallocate(&count,cmax,atom2);
@ -1177,7 +1174,7 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
else
for (i = 0; i < atom->ndihedrals; i++) {
eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
sscanf(line,"%d %d %d %d %d %d",
&tmp1,&tmp2,&atom1,&atom2,&atom3,&atom4);
int amax = MAX(atom1,atom2);
@ -1201,7 +1198,7 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
if (force->newton_bond)
for (i = 0; i < atom->nimpropers; i++) {
eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
sscanf(line,"%d %d %d %d %d %d",
&tmp1,&tmp2,&atom1,&atom2,&atom3,&atom4);
if (atom2 >= cmax) cmax = reallocate(&count,cmax,atom2);
@ -1210,7 +1207,7 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
else
for (i = 0; i < atom->nimpropers; i++) {
eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
sscanf(line,"%d %d %d %d %d %d",
&tmp1,&tmp2,&atom1,&atom2,&atom3,&atom4);
int amax = MAX(atom1,atom2);
@ -1232,7 +1229,7 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
} else {
char str[128];
sprintf(str,"Unknown identifier in data file: %s",keyword);
error->one(str);
error->one(FLERR,str);
}
parse_keyword(0,0);
@ -1248,13 +1245,13 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
(atom->nangles && !angle_per_atom) ||
(atom->ndihedrals && !dihedral_per_atom) ||
(atom->nimpropers && !improper_per_atom))
error->one("Needed topology not in data file");
error->one(FLERR,"Needed topology not in data file");
// customize for new sections
// error check that Bonus sections were speficied in file
if (nellipsoids && !ellipsoid_flag)
error->one("Needed bonus data not in data file");
error->one(FLERR,"Needed bonus data not in data file");
}
/* ----------------------------------------------------------------------
@ -1288,14 +1285,14 @@ void ReadData::open(char *file)
sprintf(gunzip,"gunzip -c %s",file);
fp = popen(gunzip,"r");
#else
error->one("Cannot open gzipped file");
error->one(FLERR,"Cannot open gzipped file");
#endif
}
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open file %s",file);
error->one(str);
error->one(FLERR,str);
}
}
@ -1362,7 +1359,7 @@ void ReadData::skip_lines(int n)
{
char *eof;
for (int i = 0; i < n; i++) eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
}
/* ----------------------------------------------------------------------