git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -5,7 +5,7 @@
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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@ -86,7 +86,7 @@ void ReadData::command(int narg, char **arg)
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{
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if (narg < 1) error->all(FLERR,"Illegal read_data command");
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if (domain->box_exist)
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if (domain->box_exist)
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error->all(FLERR,"Cannot read_data after simulation box is defined");
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if (domain->dimension == 2 && domain->zperiodic == 0)
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error->all(FLERR,"Cannot run 2d simulation with nonperiodic Z dimension");
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@ -102,17 +102,17 @@ void ReadData::command(int narg, char **arg)
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while (iarg < narg) {
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if (strcmp(arg[iarg],"fix") == 0) {
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if (iarg+4 > narg)
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error->all(FLERR,"Illegal read_data command");
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error->all(FLERR,"Illegal read_data command");
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memory->grow(fix_index,nfix+1,"read_data:fix_index");
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fix_header = (char **)
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memory->srealloc(fix_header,(nfix+1)*sizeof(char *),
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"read_data:fix_header");
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fix_section = (char **)
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memory->srealloc(fix_section,(nfix+1)*sizeof(char *),
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"read_data:fix_section");
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fix_header = (char **)
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memory->srealloc(fix_header,(nfix+1)*sizeof(char *),
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"read_data:fix_header");
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fix_section = (char **)
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memory->srealloc(fix_section,(nfix+1)*sizeof(char *),
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"read_data:fix_section");
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fix_index[nfix] = modify->find_fix(arg[iarg+1]);
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if (fix_index[nfix] < 0)
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error->all(FLERR,"Fix ID for Read_data does not exist");
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if (fix_index[nfix] < 0)
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error->all(FLERR,"Fix ID for Read_data does not exist");
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int n = strlen(arg[iarg+2]) + 1;
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fix_header[nfix] = new char[n];
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strcpy(fix_header[nfix],arg[iarg+2]);
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@ -124,7 +124,7 @@ void ReadData::command(int narg, char **arg)
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} else error->all(FLERR,"Illegal read_data command");
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}
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// scan data file to determine max topology needed per atom
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// scan data file to determine max topology needed per atom
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// allocate initial topology arrays
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if (atom->molecular) {
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@ -133,7 +133,7 @@ void ReadData::command(int narg, char **arg)
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open(arg[0]);
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header(0);
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scan(atom->bond_per_atom,atom->angle_per_atom,
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atom->dihedral_per_atom,atom->improper_per_atom);
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atom->dihedral_per_atom,atom->improper_per_atom);
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if (compressed) pclose(fp);
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else fclose(fp);
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atom->bond_per_atom += atom->extra_bond_per_atom;
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@ -187,13 +187,13 @@ void ReadData::command(int narg, char **arg)
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if (nfix) {
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for (n = 0; n < nfix; n++)
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if (strstr(line,fix_section[n])) {
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bigint nlines =
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modify->fix[fix_index[n]]->read_data_skip_lines(keyword);
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fix(n,keyword,nlines);
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parse_keyword(0,1);
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break;
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}
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if (strstr(line,fix_section[n])) {
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bigint nlines =
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modify->fix[fix_index[n]]->read_data_skip_lines(keyword);
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fix(n,keyword,nlines);
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parse_keyword(0,1);
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break;
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}
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if (n < nfix) continue;
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}
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@ -205,128 +205,128 @@ void ReadData::command(int narg, char **arg)
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velocities();
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} else if (strcmp(keyword,"Ellipsoids") == 0) {
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if (!avec_ellipsoid)
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error->all(FLERR,"Invalid data file section: Ellipsoids");
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if (!avec_ellipsoid)
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error->all(FLERR,"Invalid data file section: Ellipsoids");
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if (atomflag == 0) error->all(FLERR,"Must read Atoms before Ellipsoids");
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bonus(nellipsoids,(AtomVec *) avec_ellipsoid,"ellipsoids");
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} else if (strcmp(keyword,"Lines") == 0) {
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if (!avec_line)
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error->all(FLERR,"Invalid data file section: Lines");
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if (!avec_line)
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error->all(FLERR,"Invalid data file section: Lines");
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if (atomflag == 0) error->all(FLERR,"Must read Atoms before Lines");
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bonus(nlines,(AtomVec *) avec_line,"lines");
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} else if (strcmp(keyword,"Triangles") == 0) {
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if (!avec_tri)
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error->all(FLERR,"Invalid data file section: Triangles");
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if (!avec_tri)
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error->all(FLERR,"Invalid data file section: Triangles");
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if (atomflag == 0) error->all(FLERR,"Must read Atoms before Triangles");
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bonus(ntris,(AtomVec *) avec_tri,"triangles");
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} else if (strcmp(keyword,"Bonds") == 0) {
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if (atom->avec->bonds_allow == 0)
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error->all(FLERR,"Invalid data file section: Bonds");
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if (atom->avec->bonds_allow == 0)
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error->all(FLERR,"Invalid data file section: Bonds");
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if (atomflag == 0) error->all(FLERR,"Must read Atoms before Bonds");
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bonds();
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} else if (strcmp(keyword,"Angles") == 0) {
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if (atom->avec->angles_allow == 0)
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error->all(FLERR,"Invalid data file section: Angles");
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error->all(FLERR,"Invalid data file section: Angles");
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if (atomflag == 0) error->all(FLERR,"Must read Atoms before Angles");
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angles();
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} else if (strcmp(keyword,"Dihedrals") == 0) {
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if (atom->avec->dihedrals_allow == 0)
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error->all(FLERR,"Invalid data file section: Dihedrals");
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error->all(FLERR,"Invalid data file section: Dihedrals");
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if (atomflag == 0) error->all(FLERR,"Must read Atoms before Dihedrals");
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dihedrals();
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} else if (strcmp(keyword,"Impropers") == 0) {
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if (atom->avec->impropers_allow == 0)
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error->all(FLERR,"Invalid data file section: Impropers");
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if (atom->avec->impropers_allow == 0)
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error->all(FLERR,"Invalid data file section: Impropers");
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if (atomflag == 0) error->all(FLERR,"Must read Atoms before Impropers");
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impropers();
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} else if (strcmp(keyword,"Masses") == 0) {
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mass();
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} else if (strcmp(keyword,"Pair Coeffs") == 0) {
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if (force->pair == NULL)
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error->all(FLERR,"Must define pair_style before Pair Coeffs");
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if (force->pair == NULL)
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error->all(FLERR,"Must define pair_style before Pair Coeffs");
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paircoeffs();
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} else if (strcmp(keyword,"Bond Coeffs") == 0) {
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if (atom->avec->bonds_allow == 0)
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error->all(FLERR,"Invalid data file section: Bond Coeffs");
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if (force->bond == NULL)
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error->all(FLERR,"Must define bond_style before Bond Coeffs");
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if (atom->avec->bonds_allow == 0)
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error->all(FLERR,"Invalid data file section: Bond Coeffs");
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if (force->bond == NULL)
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error->all(FLERR,"Must define bond_style before Bond Coeffs");
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bondcoeffs();
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} else if (strcmp(keyword,"Angle Coeffs") == 0) {
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if (atom->avec->angles_allow == 0)
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error->all(FLERR,"Invalid data file section: Angle Coeffs");
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if (force->angle == NULL)
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error->all(FLERR,"Must define angle_style before Angle Coeffs");
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if (atom->avec->angles_allow == 0)
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error->all(FLERR,"Invalid data file section: Angle Coeffs");
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if (force->angle == NULL)
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error->all(FLERR,"Must define angle_style before Angle Coeffs");
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anglecoeffs(0);
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} else if (strcmp(keyword,"Dihedral Coeffs") == 0) {
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if (atom->avec->dihedrals_allow == 0)
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error->all(FLERR,"Invalid data file section: Dihedral Coeffs");
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if (force->dihedral == NULL)
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error->all(FLERR,"Must define dihedral_style before Dihedral Coeffs");
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if (atom->avec->dihedrals_allow == 0)
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error->all(FLERR,"Invalid data file section: Dihedral Coeffs");
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if (force->dihedral == NULL)
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error->all(FLERR,"Must define dihedral_style before Dihedral Coeffs");
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dihedralcoeffs(0);
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} else if (strcmp(keyword,"Improper Coeffs") == 0) {
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if (atom->avec->impropers_allow == 0)
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error->all(FLERR,"Invalid data file section: Improper Coeffs");
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if (force->improper == NULL)
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error->all(FLERR,"Must define improper_style before Improper Coeffs");
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if (atom->avec->impropers_allow == 0)
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error->all(FLERR,"Invalid data file section: Improper Coeffs");
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if (force->improper == NULL)
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error->all(FLERR,"Must define improper_style before Improper Coeffs");
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impropercoeffs(0);
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} else if (strcmp(keyword,"BondBond Coeffs") == 0) {
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if (atom->avec->angles_allow == 0)
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error->all(FLERR,"Invalid data file section: BondBond Coeffs");
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if (force->angle == NULL)
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error->all(FLERR,"Must define angle_style before BondBond Coeffs");
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if (atom->avec->angles_allow == 0)
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error->all(FLERR,"Invalid data file section: BondBond Coeffs");
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if (force->angle == NULL)
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error->all(FLERR,"Must define angle_style before BondBond Coeffs");
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anglecoeffs(1);
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} else if (strcmp(keyword,"BondAngle Coeffs") == 0) {
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if (atom->avec->angles_allow == 0)
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error->all(FLERR,"Invalid data file section: BondAngle Coeffs");
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if (force->angle == NULL)
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error->all(FLERR,"Must define angle_style before BondAngle Coeffs");
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if (atom->avec->angles_allow == 0)
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error->all(FLERR,"Invalid data file section: BondAngle Coeffs");
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if (force->angle == NULL)
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error->all(FLERR,"Must define angle_style before BondAngle Coeffs");
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anglecoeffs(2);
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} else if (strcmp(keyword,"MiddleBondTorsion Coeffs") == 0) {
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if (atom->avec->dihedrals_allow == 0)
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error->all(FLERR,"Invalid data file section: MiddleBondTorsion Coeffs");
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if (force->dihedral == NULL)
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error->all(FLERR,
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"Must define dihedral_style before "
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"MiddleBondTorsion Coeffs");
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if (atom->avec->dihedrals_allow == 0)
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error->all(FLERR,"Invalid data file section: MiddleBondTorsion Coeffs");
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if (force->dihedral == NULL)
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error->all(FLERR,
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"Must define dihedral_style before "
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"MiddleBondTorsion Coeffs");
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dihedralcoeffs(1);
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} else if (strcmp(keyword,"EndBondTorsion Coeffs") == 0) {
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if (atom->avec->dihedrals_allow == 0)
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error->all(FLERR,"Invalid data file section: EndBondTorsion Coeffs");
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if (force->dihedral == NULL)
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error->all(FLERR,
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"Must define dihedral_style before EndBondTorsion Coeffs");
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if (atom->avec->dihedrals_allow == 0)
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error->all(FLERR,"Invalid data file section: EndBondTorsion Coeffs");
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if (force->dihedral == NULL)
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error->all(FLERR,
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"Must define dihedral_style before EndBondTorsion Coeffs");
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dihedralcoeffs(2);
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} else if (strcmp(keyword,"AngleTorsion Coeffs") == 0) {
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if (atom->avec->dihedrals_allow == 0)
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error->all(FLERR,"Invalid data file section: AngleTorsion Coeffs");
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if (force->dihedral == NULL)
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error->all(FLERR,
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"Must define dihedral_style before AngleTorsion Coeffs");
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if (atom->avec->dihedrals_allow == 0)
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error->all(FLERR,"Invalid data file section: AngleTorsion Coeffs");
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if (force->dihedral == NULL)
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error->all(FLERR,
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"Must define dihedral_style before AngleTorsion Coeffs");
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dihedralcoeffs(3);
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} else if (strcmp(keyword,"AngleAngleTorsion Coeffs") == 0) {
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if (atom->avec->dihedrals_allow == 0)
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error->all(FLERR,"Invalid data file section: AngleAngleTorsion Coeffs");
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if (force->dihedral == NULL)
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error->all(FLERR,
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"Must define dihedral_style before "
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"AngleAngleTorsion Coeffs");
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if (atom->avec->dihedrals_allow == 0)
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error->all(FLERR,"Invalid data file section: AngleAngleTorsion Coeffs");
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if (force->dihedral == NULL)
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error->all(FLERR,
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"Must define dihedral_style before "
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"AngleAngleTorsion Coeffs");
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dihedralcoeffs(4);
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} else if (strcmp(keyword,"BondBond13 Coeffs") == 0) {
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if (atom->avec->dihedrals_allow == 0)
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error->all(FLERR,"Invalid data file section: BondBond13 Coeffs");
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if (force->dihedral == NULL)
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error->all(FLERR,"Must define dihedral_style before BondBond13 Coeffs");
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if (atom->avec->dihedrals_allow == 0)
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error->all(FLERR,"Invalid data file section: BondBond13 Coeffs");
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if (force->dihedral == NULL)
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error->all(FLERR,"Must define dihedral_style before BondBond13 Coeffs");
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dihedralcoeffs(5);
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} else if (strcmp(keyword,"AngleAngle Coeffs") == 0) {
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if (atom->avec->impropers_allow == 0)
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error->all(FLERR,"Invalid data file section: AngleAngle Coeffs");
|
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if (force->improper == NULL)
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error->all(FLERR,"Must define improper_style before AngleAngle Coeffs");
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if (atom->avec->impropers_allow == 0)
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error->all(FLERR,"Invalid data file section: AngleAngle Coeffs");
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if (force->improper == NULL)
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error->all(FLERR,"Must define improper_style before AngleAngle Coeffs");
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impropercoeffs(1);
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} else {
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||||
@ -344,10 +344,10 @@ void ReadData::command(int narg, char **arg)
|
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if (compressed) pclose(fp);
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else fclose(fp);
|
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}
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||||
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||||
// error if natoms > 0 yet no atoms were read
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|
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if (atom->natoms > 0 && atomflag == 0)
|
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if (atom->natoms > 0 && atomflag == 0)
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error->all(FLERR,"No atoms in data file");
|
||||
|
||||
// create bond topology now that system is defined
|
||||
@ -376,7 +376,7 @@ void ReadData::header(int flag)
|
||||
|
||||
// customize for new sections
|
||||
|
||||
const char *section_keywords[NSECTIONS] =
|
||||
const char *section_keywords[NSECTIONS] =
|
||||
{"Atoms","Velocities","Ellipsoids","Lines","Triangles",
|
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"Bonds","Angles","Dihedrals","Impropers",
|
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"Masses","Pair Coeffs","Bond Coeffs","Angle Coeffs",
|
||||
@ -426,10 +426,10 @@ void ReadData::header(int flag)
|
||||
|
||||
if (nfix) {
|
||||
for (n = 0; n < nfix; n++)
|
||||
if (strstr(line,fix_header[n])) {
|
||||
modify->fix[fix_index[n]]->read_data_header(line);
|
||||
break;
|
||||
}
|
||||
if (strstr(line,fix_header[n])) {
|
||||
modify->fix[fix_index[n]]->read_data_header(line);
|
||||
break;
|
||||
}
|
||||
if (n < nfix) continue;
|
||||
}
|
||||
|
||||
@ -442,41 +442,41 @@ void ReadData::header(int flag)
|
||||
|
||||
else if (strstr(line,"ellipsoids")) {
|
||||
if (!avec_ellipsoid && me == 0)
|
||||
error->one(FLERR,"No ellipsoids allowed with this atom style");
|
||||
error->one(FLERR,"No ellipsoids allowed with this atom style");
|
||||
sscanf(line,BIGINT_FORMAT,&nellipsoids);
|
||||
} else if (strstr(line,"lines")) {
|
||||
if (!avec_line && me == 0)
|
||||
error->one(FLERR,"No lines allowed with this atom style");
|
||||
error->one(FLERR,"No lines allowed with this atom style");
|
||||
sscanf(line,BIGINT_FORMAT,&nlines);
|
||||
} else if (strstr(line,"triangles")) {
|
||||
if (!avec_tri && me == 0)
|
||||
error->one(FLERR,"No triangles allowed with this atom style");
|
||||
error->one(FLERR,"No triangles allowed with this atom style");
|
||||
sscanf(line,BIGINT_FORMAT,&ntris);
|
||||
}
|
||||
|
||||
else if (strstr(line,"bonds")) sscanf(line,BIGINT_FORMAT,&atom->nbonds);
|
||||
else if (strstr(line,"angles")) sscanf(line,BIGINT_FORMAT,&atom->nangles);
|
||||
else if (strstr(line,"dihedrals")) sscanf(line,BIGINT_FORMAT,
|
||||
&atom->ndihedrals);
|
||||
&atom->ndihedrals);
|
||||
else if (strstr(line,"impropers")) sscanf(line,BIGINT_FORMAT,
|
||||
&atom->nimpropers);
|
||||
&atom->nimpropers);
|
||||
|
||||
else if (strstr(line,"atom types")) sscanf(line,"%d",&atom->ntypes);
|
||||
else if (strstr(line,"bond types")) sscanf(line,"%d",&atom->nbondtypes);
|
||||
else if (strstr(line,"angle types")) sscanf(line,"%d",&atom->nangletypes);
|
||||
else if (strstr(line,"dihedral types"))
|
||||
else if (strstr(line,"dihedral types"))
|
||||
sscanf(line,"%d",&atom->ndihedraltypes);
|
||||
else if (strstr(line,"improper types"))
|
||||
else if (strstr(line,"improper types"))
|
||||
sscanf(line,"%d",&atom->nimpropertypes);
|
||||
|
||||
else if (strstr(line,"extra bond per atom"))
|
||||
sscanf(line,"%d",&atom->extra_bond_per_atom);
|
||||
|
||||
else if (strstr(line,"xlo xhi"))
|
||||
else if (strstr(line,"xlo xhi"))
|
||||
sscanf(line,"%lg %lg",&domain->boxlo[0],&domain->boxhi[0]);
|
||||
else if (strstr(line,"ylo yhi"))
|
||||
else if (strstr(line,"ylo yhi"))
|
||||
sscanf(line,"%lg %lg",&domain->boxlo[1],&domain->boxhi[1]);
|
||||
else if (strstr(line,"zlo zhi"))
|
||||
else if (strstr(line,"zlo zhi"))
|
||||
sscanf(line,"%lg %lg",&domain->boxlo[2],&domain->boxhi[2]);
|
||||
else if (strstr(line,"xy xz yz")) {
|
||||
domain->triclinic = 1;
|
||||
@ -507,16 +507,16 @@ void ReadData::header(int flag)
|
||||
|
||||
// error check on consistency of header values
|
||||
|
||||
if ((atom->nbonds || atom->nbondtypes) &&
|
||||
if ((atom->nbonds || atom->nbondtypes) &&
|
||||
atom->avec->bonds_allow == 0 && me == 0)
|
||||
error->one(FLERR,"No bonds allowed with this atom style");
|
||||
if ((atom->nangles || atom->nangletypes) &&
|
||||
if ((atom->nangles || atom->nangletypes) &&
|
||||
atom->avec->angles_allow == 0 && me == 0)
|
||||
error->one(FLERR,"No angles allowed with this atom style");
|
||||
if ((atom->ndihedrals || atom->ndihedraltypes) &&
|
||||
if ((atom->ndihedrals || atom->ndihedraltypes) &&
|
||||
atom->avec->dihedrals_allow == 0 && me == 0)
|
||||
error->one(FLERR,"No dihedrals allowed with this atom style");
|
||||
if ((atom->nimpropers || atom->nimpropertypes) &&
|
||||
if ((atom->nimpropers || atom->nimpropertypes) &&
|
||||
atom->avec->impropers_allow == 0 && me == 0)
|
||||
error->one(FLERR,"No impropers allowed with this atom style");
|
||||
|
||||
@ -537,7 +537,7 @@ void ReadData::header(int flag)
|
||||
void ReadData::atoms()
|
||||
{
|
||||
int i,m,nchunk;
|
||||
|
||||
|
||||
bigint nread = 0;
|
||||
bigint natoms = atom->natoms;
|
||||
|
||||
@ -548,9 +548,9 @@ void ReadData::atoms()
|
||||
char *eof;
|
||||
m = 0;
|
||||
for (i = 0; i < nchunk; i++) {
|
||||
eof = fgets(&buffer[m],MAXLINE,fp);
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
|
||||
m += strlen(&buffer[m]);
|
||||
eof = fgets(&buffer[m],MAXLINE,fp);
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
|
||||
m += strlen(&buffer[m]);
|
||||
}
|
||||
m++;
|
||||
}
|
||||
@ -571,14 +571,14 @@ void ReadData::atoms()
|
||||
if (logfile) fprintf(logfile," " BIGINT_FORMAT " atoms\n",natoms);
|
||||
}
|
||||
|
||||
if (natoms != atom->natoms)
|
||||
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
|
||||
// if any atom ID > 0, error if any atom ID == 0
|
||||
// not checking if atom IDs > natoms or are unique
|
||||
|
||||
|
||||
int nlocal = atom->nlocal;
|
||||
int *tag = atom->tag;
|
||||
|
||||
@ -615,7 +615,7 @@ void ReadData::atoms()
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
read all velocities
|
||||
to find atoms, must build atom map if not a molecular system
|
||||
to find atoms, must build atom map if not a molecular system
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ReadData::velocities()
|
||||
@ -640,9 +640,9 @@ void ReadData::velocities()
|
||||
char *eof;
|
||||
m = 0;
|
||||
for (i = 0; i < nchunk; i++) {
|
||||
eof = fgets(&buffer[m],MAXLINE,fp);
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
|
||||
m += strlen(&buffer[m]);
|
||||
eof = fgets(&buffer[m],MAXLINE,fp);
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
|
||||
m += strlen(&buffer[m]);
|
||||
}
|
||||
m++;
|
||||
}
|
||||
@ -666,7 +666,7 @@ void ReadData::velocities()
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
read all bonus data
|
||||
to find atoms, must build atom map if not a molecular system
|
||||
to find atoms, must build atom map if not a molecular system
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
|
||||
@ -691,9 +691,9 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
|
||||
char *eof;
|
||||
m = 0;
|
||||
for (i = 0; i < nchunk; i++) {
|
||||
eof = fgets(&buffer[m],MAXLINE,fp);
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
|
||||
m += strlen(&buffer[m]);
|
||||
eof = fgets(&buffer[m],MAXLINE,fp);
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
|
||||
m += strlen(&buffer[m]);
|
||||
}
|
||||
m++;
|
||||
}
|
||||
@ -730,9 +730,9 @@ void ReadData::bonds()
|
||||
char *eof;
|
||||
m = 0;
|
||||
for (i = 0; i < nchunk; i++) {
|
||||
eof = fgets(&buffer[m],MAXLINE,fp);
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
|
||||
m += strlen(&buffer[m]);
|
||||
eof = fgets(&buffer[m],MAXLINE,fp);
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
|
||||
m += strlen(&buffer[m]);
|
||||
}
|
||||
m++;
|
||||
}
|
||||
@ -757,7 +757,7 @@ 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)
|
||||
if (sum != factor*atom->nbonds)
|
||||
error->all(FLERR,"Bonds assigned incorrectly");
|
||||
}
|
||||
|
||||
@ -776,9 +776,9 @@ void ReadData::angles()
|
||||
char *eof;
|
||||
m = 0;
|
||||
for (i = 0; i < nchunk; i++) {
|
||||
eof = fgets(&buffer[m],MAXLINE,fp);
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
|
||||
m += strlen(&buffer[m]);
|
||||
eof = fgets(&buffer[m],MAXLINE,fp);
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
|
||||
m += strlen(&buffer[m]);
|
||||
}
|
||||
m++;
|
||||
}
|
||||
@ -803,7 +803,7 @@ 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)
|
||||
if (sum != factor*atom->nangles)
|
||||
error->all(FLERR,"Angles assigned incorrectly");
|
||||
}
|
||||
|
||||
@ -822,9 +822,9 @@ void ReadData::dihedrals()
|
||||
char *eof;
|
||||
m = 0;
|
||||
for (i = 0; i < nchunk; i++) {
|
||||
eof = fgets(&buffer[m],MAXLINE,fp);
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
|
||||
m += strlen(&buffer[m]);
|
||||
eof = fgets(&buffer[m],MAXLINE,fp);
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
|
||||
m += strlen(&buffer[m]);
|
||||
}
|
||||
m++;
|
||||
}
|
||||
@ -849,7 +849,7 @@ void ReadData::dihedrals()
|
||||
if (screen) fprintf(screen," " BIGINT_FORMAT " dihedrals\n",sum/factor);
|
||||
if (logfile) fprintf(logfile," " BIGINT_FORMAT " dihedrals\n",sum/factor);
|
||||
}
|
||||
if (sum != factor*atom->ndihedrals)
|
||||
if (sum != factor*atom->ndihedrals)
|
||||
error->all(FLERR,"Dihedrals assigned incorrectly");
|
||||
}
|
||||
|
||||
@ -868,9 +868,9 @@ void ReadData::impropers()
|
||||
char *eof;
|
||||
m = 0;
|
||||
for (i = 0; i < nchunk; i++) {
|
||||
eof = fgets(&buffer[m],MAXLINE,fp);
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
|
||||
m += strlen(&buffer[m]);
|
||||
eof = fgets(&buffer[m],MAXLINE,fp);
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
|
||||
m += strlen(&buffer[m]);
|
||||
}
|
||||
m++;
|
||||
}
|
||||
@ -895,7 +895,7 @@ void ReadData::impropers()
|
||||
if (screen) fprintf(screen," " BIGINT_FORMAT " impropers\n",sum/factor);
|
||||
if (logfile) fprintf(logfile," " BIGINT_FORMAT " impropers\n",sum/factor);
|
||||
}
|
||||
if (sum != factor*atom->nimpropers)
|
||||
if (sum != factor*atom->nimpropers)
|
||||
error->all(FLERR,"Impropers assigned incorrectly");
|
||||
}
|
||||
|
||||
@ -1109,9 +1109,9 @@ void ReadData::fix(int ifix, char *line, bigint nlines)
|
||||
char *eof;
|
||||
m = 0;
|
||||
for (i = 0; i < nchunk; i++) {
|
||||
eof = fgets(&buffer[m],MAXLINE,fp);
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
|
||||
m += strlen(&buffer[m]);
|
||||
eof = fgets(&buffer[m],MAXLINE,fp);
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
|
||||
m += strlen(&buffer[m]);
|
||||
}
|
||||
m++;
|
||||
}
|
||||
@ -1124,11 +1124,11 @@ void ReadData::fix(int ifix, char *line, bigint nlines)
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 scans the data file for topology maximums
|
||||
proc 0 scans the data file for topology maximums
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
|
||||
int &dihedral_per_atom, int &improper_per_atom)
|
||||
int &dihedral_per_atom, int &improper_per_atom)
|
||||
{
|
||||
int i,tmp1,tmp2,atom1,atom2,atom3,atom4;
|
||||
char *eof;
|
||||
@ -1160,14 +1160,14 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
|
||||
|
||||
if (nfix) {
|
||||
for (i = 0; i < nfix; i++) {
|
||||
printf("LINE SECTION %s %s\n",line,fix_section[i]);
|
||||
if (strstr(line,fix_section[i])) {
|
||||
int n = modify->fix[fix_index[i]]->read_data_skip_lines(keyword);
|
||||
printf("NLINES SKIP %d\n",n);
|
||||
skip_lines(n);
|
||||
parse_keyword(0,0);
|
||||
break;
|
||||
}
|
||||
printf("LINE SECTION %s %s\n",line,fix_section[i]);
|
||||
if (strstr(line,fix_section[i])) {
|
||||
int n = modify->fix[fix_index[i]]->read_data_skip_lines(keyword);
|
||||
printf("NLINES SKIP %d\n",n);
|
||||
skip_lines(n);
|
||||
parse_keyword(0,0);
|
||||
break;
|
||||
}
|
||||
}
|
||||
if (i < nfix) continue;
|
||||
}
|
||||
@ -1177,8 +1177,8 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
|
||||
else if (strcmp(keyword,"Velocities") == 0) skip_lines(natoms);
|
||||
|
||||
else if (strcmp(keyword,"Ellipsoids") == 0) {
|
||||
if (!avec_ellipsoid)
|
||||
error->one(FLERR,"Invalid data file section: Ellipsoids");
|
||||
if (!avec_ellipsoid)
|
||||
error->one(FLERR,"Invalid data file section: Ellipsoids");
|
||||
ellipsoid_flag = 1;
|
||||
skip_lines(nellipsoids);
|
||||
} else if (strcmp(keyword,"Lines") == 0) {
|
||||
@ -1191,109 +1191,109 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
|
||||
skip_lines(ntris);
|
||||
|
||||
} else if (strcmp(keyword,"Pair Coeffs") == 0) {
|
||||
if (force->pair == NULL)
|
||||
error->one(FLERR,"Must define pair_style before Pair Coeffs");
|
||||
if (force->pair == NULL)
|
||||
error->one(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->one(FLERR,"Invalid data file section: Bond Coeffs");
|
||||
if (force->bond == NULL)
|
||||
error->one(FLERR,"Must define bond_style before Bond Coeffs");
|
||||
if (atom->avec->bonds_allow == 0)
|
||||
error->one(FLERR,"Invalid data file section: Bond Coeffs");
|
||||
if (force->bond == NULL)
|
||||
error->one(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->one(FLERR,"Invalid data file section: Angle Coeffs");
|
||||
if (force->angle == NULL)
|
||||
error->one(FLERR,"Must define angle_style before Angle Coeffs");
|
||||
if (atom->avec->angles_allow == 0)
|
||||
error->one(FLERR,"Invalid data file section: Angle Coeffs");
|
||||
if (force->angle == NULL)
|
||||
error->one(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->one(FLERR,"Invalid data file section: Dihedral Coeffs");
|
||||
if (force->dihedral == NULL)
|
||||
error->one(FLERR,"Must define dihedral_style before Dihedral Coeffs");
|
||||
if (atom->avec->dihedrals_allow == 0)
|
||||
error->one(FLERR,"Invalid data file section: Dihedral Coeffs");
|
||||
if (force->dihedral == NULL)
|
||||
error->one(FLERR,"Must define dihedral_style before Dihedral Coeffs");
|
||||
} else if (strcmp(keyword,"Improper Coeffs") == 0) {
|
||||
if (atom->avec->impropers_allow == 0)
|
||||
error->one(FLERR,"Invalid data file section: Improper Coeffs");
|
||||
if (force->improper == NULL)
|
||||
error->one(FLERR,"Must define improper_style before Improper Coeffs");
|
||||
if (atom->avec->impropers_allow == 0)
|
||||
error->one(FLERR,"Invalid data file section: Improper Coeffs");
|
||||
if (force->improper == NULL)
|
||||
error->one(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->one(FLERR,"Invalid data file section: BondBond Coeffs");
|
||||
if (force->angle == NULL)
|
||||
error->one(FLERR,"Must define angle_style before BondBond Coeffs");
|
||||
if (atom->avec->angles_allow == 0)
|
||||
error->one(FLERR,"Invalid data file section: BondBond Coeffs");
|
||||
if (force->angle == NULL)
|
||||
error->one(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->one(FLERR,"Invalid data file section: BondAngle Coeffs");
|
||||
if (force->angle == NULL)
|
||||
error->one(FLERR,"Must define angle_style before BondAngle Coeffs");
|
||||
if (atom->avec->angles_allow == 0)
|
||||
error->one(FLERR,"Invalid data file section: BondAngle Coeffs");
|
||||
if (force->angle == NULL)
|
||||
error->one(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->one(FLERR,"Invalid data file section: MiddleBondTorsion Coeffs");
|
||||
if (force->dihedral == NULL)
|
||||
error->one(FLERR,
|
||||
"Must define dihedral_style before "
|
||||
"MiddleBondTorsion Coeffs");
|
||||
if (atom->avec->dihedrals_allow == 0)
|
||||
error->one(FLERR,"Invalid data file section: MiddleBondTorsion Coeffs");
|
||||
if (force->dihedral == NULL)
|
||||
error->one(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->one(FLERR,"Invalid data file section: EndBondTorsion Coeffs");
|
||||
if (force->dihedral == NULL)
|
||||
error->one(FLERR,
|
||||
"Must define dihedral_style before EndBondTorsion Coeffs");
|
||||
if (atom->avec->dihedrals_allow == 0)
|
||||
error->one(FLERR,"Invalid data file section: EndBondTorsion Coeffs");
|
||||
if (force->dihedral == NULL)
|
||||
error->one(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->one(FLERR,"Invalid data file section: AngleTorsion Coeffs");
|
||||
if (force->dihedral == NULL)
|
||||
error->one(FLERR,
|
||||
"Must define dihedral_style before AngleTorsion Coeffs");
|
||||
if (atom->avec->dihedrals_allow == 0)
|
||||
error->one(FLERR,"Invalid data file section: AngleTorsion Coeffs");
|
||||
if (force->dihedral == NULL)
|
||||
error->one(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->one(FLERR,"Invalid data file section: AngleAngleTorsion Coeffs");
|
||||
if (force->dihedral == NULL)
|
||||
error->one(FLERR,
|
||||
"Must define dihedral_style before "
|
||||
"AngleAngleTorsion Coeffs");
|
||||
if (atom->avec->dihedrals_allow == 0)
|
||||
error->one(FLERR,"Invalid data file section: AngleAngleTorsion Coeffs");
|
||||
if (force->dihedral == NULL)
|
||||
error->one(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->one(FLERR,"Invalid data file section: BondBond13 Coeffs");
|
||||
if (force->dihedral == NULL)
|
||||
error->one(FLERR,"Must define dihedral_style before BondBond13 Coeffs");
|
||||
if (atom->avec->dihedrals_allow == 0)
|
||||
error->one(FLERR,"Invalid data file section: BondBond13 Coeffs");
|
||||
if (force->dihedral == NULL)
|
||||
error->one(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->one(FLERR,"Invalid data file section: AngleAngle Coeffs");
|
||||
if (force->improper == NULL)
|
||||
error->one(FLERR,"Must define improper_style before AngleAngle Coeffs");
|
||||
if (atom->avec->impropers_allow == 0)
|
||||
error->one(FLERR,"Invalid data file section: AngleAngle Coeffs");
|
||||
if (force->improper == NULL)
|
||||
error->one(FLERR,"Must define improper_style before AngleAngle Coeffs");
|
||||
skip_lines(atom->nimpropertypes);
|
||||
|
||||
} else if (strcmp(keyword,"Bonds") == 0) {
|
||||
for (i = 1; i < cmax; i++) count[i] = 0;
|
||||
if (force->newton_bond)
|
||||
for (i = 0; i < atom->nbonds; i++) {
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
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]++;
|
||||
}
|
||||
for (i = 0; i < atom->nbonds; i++) {
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
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]++;
|
||||
}
|
||||
else
|
||||
for (i = 0; i < atom->nbonds; i++) {
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
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);
|
||||
count[atom1]++;
|
||||
count[atom2]++;
|
||||
}
|
||||
for (i = 0; i < atom->nbonds; i++) {
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
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);
|
||||
count[atom1]++;
|
||||
count[atom2]++;
|
||||
}
|
||||
for (i = 1; i < cmax; i++) bond_per_atom = MAX(bond_per_atom,count[i]);
|
||||
if (screen) fprintf(screen," %d = max bonds/atom\n",bond_per_atom);
|
||||
if (logfile) fprintf(logfile," %d = max bonds/atom\n",bond_per_atom);
|
||||
@ -1301,25 +1301,25 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
|
||||
} else if (strcmp(keyword,"Angles") == 0) {
|
||||
for (i = 1; i < cmax; i++) count[i] = 0;
|
||||
if (force->newton_bond)
|
||||
for (i = 0; i < atom->nangles; i++) {
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
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]++;
|
||||
}
|
||||
for (i = 0; i < atom->nangles; i++) {
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
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]++;
|
||||
}
|
||||
else
|
||||
for (i = 0; i < atom->nangles; i++) {
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
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);
|
||||
if (amax >= cmax) cmax = reallocate(&count,cmax,amax);
|
||||
count[atom1]++;
|
||||
count[atom2]++;
|
||||
count[atom3]++;
|
||||
}
|
||||
for (i = 0; i < atom->nangles; i++) {
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
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);
|
||||
if (amax >= cmax) cmax = reallocate(&count,cmax,amax);
|
||||
count[atom1]++;
|
||||
count[atom2]++;
|
||||
count[atom3]++;
|
||||
}
|
||||
for (i = 1; i < cmax; i++) angle_per_atom = MAX(angle_per_atom,count[i]);
|
||||
if (screen) fprintf(screen," %d = max angles/atom\n",angle_per_atom);
|
||||
if (logfile) fprintf(logfile," %d = max angles/atom\n",angle_per_atom);
|
||||
@ -1327,68 +1327,68 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
|
||||
} else if (strcmp(keyword,"Dihedrals") == 0) {
|
||||
for (i = 1; i < cmax; i++) count[i] = 0;
|
||||
if (force->newton_bond)
|
||||
for (i = 0; i < atom->ndihedrals; i++) {
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
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);
|
||||
count[atom2]++;
|
||||
}
|
||||
for (i = 0; i < atom->ndihedrals; i++) {
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
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);
|
||||
count[atom2]++;
|
||||
}
|
||||
else
|
||||
for (i = 0; i < atom->ndihedrals; i++) {
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
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);
|
||||
amax = MAX(amax,atom3);
|
||||
amax = MAX(amax,atom4);
|
||||
if (amax >= cmax) cmax = reallocate(&count,cmax,amax);
|
||||
count[atom1]++;
|
||||
count[atom2]++;
|
||||
count[atom3]++;
|
||||
count[atom4]++;
|
||||
}
|
||||
for (i = 1; i < cmax; i++)
|
||||
dihedral_per_atom = MAX(dihedral_per_atom,count[i]);
|
||||
if (screen)
|
||||
fprintf(screen," %d = max dihedrals/atom\n",dihedral_per_atom);
|
||||
if (logfile)
|
||||
fprintf(logfile," %d = max dihedrals/atom\n",dihedral_per_atom);
|
||||
for (i = 0; i < atom->ndihedrals; i++) {
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
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);
|
||||
amax = MAX(amax,atom3);
|
||||
amax = MAX(amax,atom4);
|
||||
if (amax >= cmax) cmax = reallocate(&count,cmax,amax);
|
||||
count[atom1]++;
|
||||
count[atom2]++;
|
||||
count[atom3]++;
|
||||
count[atom4]++;
|
||||
}
|
||||
for (i = 1; i < cmax; i++)
|
||||
dihedral_per_atom = MAX(dihedral_per_atom,count[i]);
|
||||
if (screen)
|
||||
fprintf(screen," %d = max dihedrals/atom\n",dihedral_per_atom);
|
||||
if (logfile)
|
||||
fprintf(logfile," %d = max dihedrals/atom\n",dihedral_per_atom);
|
||||
|
||||
} else if (strcmp(keyword,"Impropers") == 0) {
|
||||
for (i = 1; i < cmax; i++) count[i] = 0;
|
||||
if (force->newton_bond)
|
||||
for (i = 0; i < atom->nimpropers; i++) {
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
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);
|
||||
count[atom2]++;
|
||||
}
|
||||
for (i = 0; i < atom->nimpropers; i++) {
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
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);
|
||||
count[atom2]++;
|
||||
}
|
||||
else
|
||||
for (i = 0; i < atom->nimpropers; i++) {
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
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);
|
||||
amax = MAX(amax,atom3);
|
||||
amax = MAX(amax,atom4);
|
||||
if (amax >= cmax) cmax = reallocate(&count,cmax,amax);
|
||||
count[atom1]++;
|
||||
count[atom2]++;
|
||||
count[atom3]++;
|
||||
count[atom4]++;
|
||||
}
|
||||
for (i = 0; i < atom->nimpropers; i++) {
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
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);
|
||||
amax = MAX(amax,atom3);
|
||||
amax = MAX(amax,atom4);
|
||||
if (amax >= cmax) cmax = reallocate(&count,cmax,amax);
|
||||
count[atom1]++;
|
||||
count[atom2]++;
|
||||
count[atom3]++;
|
||||
count[atom4]++;
|
||||
}
|
||||
for (i = 1; i < cmax; i++)
|
||||
improper_per_atom = MAX(improper_per_atom,count[i]);
|
||||
if (screen)
|
||||
fprintf(screen," %d = max impropers/atom\n",improper_per_atom);
|
||||
if (logfile)
|
||||
fprintf(logfile," %d = max impropers/atom\n",improper_per_atom);
|
||||
improper_per_atom = MAX(improper_per_atom,count[i]);
|
||||
if (screen)
|
||||
fprintf(screen," %d = max impropers/atom\n",improper_per_atom);
|
||||
if (logfile)
|
||||
fprintf(logfile," %d = max impropers/atom\n",improper_per_atom);
|
||||
|
||||
} else {
|
||||
char str[128];
|
||||
@ -1408,7 +1408,7 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
|
||||
if ((atom->nbonds && !bond_per_atom) ||
|
||||
(atom->nangles && !angle_per_atom) ||
|
||||
(atom->ndihedrals && !dihedral_per_atom) ||
|
||||
(atom->nimpropers && !improper_per_atom))
|
||||
(atom->nimpropers && !improper_per_atom))
|
||||
error->one(FLERR,"Needed topology not in data file");
|
||||
|
||||
// customize for new sections
|
||||
@ -1513,8 +1513,8 @@ void ReadData::parse_keyword(int first, int flag)
|
||||
|
||||
int start = strspn(line," \t\n\r");
|
||||
int stop = strlen(line) - 1;
|
||||
while (line[stop] == ' ' || line[stop] == '\t'
|
||||
|| line[stop] == '\n' || line[stop] == '\r') stop--;
|
||||
while (line[stop] == ' ' || line[stop] == '\t'
|
||||
|| line[stop] == '\n' || line[stop] == '\r') stop--;
|
||||
line[stop+1] = '\0';
|
||||
strcpy(keyword,&line[start]);
|
||||
}
|
||||
@ -1550,8 +1550,8 @@ void ReadData::parse_coeffs(char *line, const char *addstr, int dupflag)
|
||||
while (word) {
|
||||
if (narg == maxarg) {
|
||||
maxarg += DELTA;
|
||||
arg = (char **)
|
||||
memory->srealloc(arg,maxarg*sizeof(char *),"read_data:arg");
|
||||
arg = (char **)
|
||||
memory->srealloc(arg,maxarg*sizeof(char *),"read_data:arg");
|
||||
}
|
||||
if (addstr && narg == 1 && !islower(word[0])) arg[narg++] = (char *) addstr;
|
||||
arg[narg++] = word;
|
||||
|
||||
Reference in New Issue
Block a user