git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13643 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -29,6 +29,7 @@
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#include "atom_vec_tri.h"
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#include "force.h"
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#include "molecule.h"
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#include "group.h"
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#include "comm.h"
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#include "update.h"
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#include "modify.h"
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@ -41,6 +42,7 @@
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#include "dihedral.h"
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#include "improper.h"
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#include "special.h"
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#include "irregular.h"
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#include "error.h"
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#include "memory.h"
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@ -55,6 +57,8 @@ using namespace LAMMPS_NS;
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// customize for new sections
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#define NSECTIONS 25 // change when add to header::section_keywords
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enum{NONE,APPEND,VALUE,MERGE};
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// pair style suffixes to ignore
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// when matching Pair Coeffs comment to currently-defined pair style
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@ -115,8 +119,16 @@ void ReadData::command(int narg, char **arg)
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// optional args
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addflag = mergeflag = 0;
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offset[0] = offset[1] = offset[2] = 0.0;
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addflag = NONE;
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id_offset = 0;
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offsetflag = shiftflag = 0;
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toffset = boffset = aoffset = doffset = ioffset = 0;
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shift[0] = shift[1] = shift[2] = 0.0;
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extra_atom_types = extra_bond_types = extra_angle_types =
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extra_dihedral_types = extra_improper_types = 0;
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groupbit = 0;
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nfix = 0;
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fix_index = NULL;
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fix_header = NULL;
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@ -125,18 +137,81 @@ void ReadData::command(int narg, char **arg)
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int iarg = 1;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"add") == 0) {
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addflag = 1;
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iarg++;
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} else if (strcmp(arg[iarg],"merge") == 0) {
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mergeflag = 1;
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iarg++;
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if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
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if (strcmp(arg[iarg+1],"append") == 0) addflag = APPEND;
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else if (strcmp(arg[iarg+1],"merge") == 0) addflag = MERGE;
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else {
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addflag = VALUE;
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bigint offset = force->bnumeric(FLERR,arg[iarg+1]);
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if (offset > MAXTAGINT)
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error->all(FLERR,"Read data add offset is too big");
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id_offset = offset;
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}
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iarg += 2;
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} else if (strcmp(arg[iarg],"offset") == 0) {
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if (iarg+4 > narg)
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if (iarg+6 > narg) error->all(FLERR,"Illegal read_data command");
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offsetflag = 1;
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toffset = force->inumeric(FLERR,arg[iarg+1]);
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boffset = force->inumeric(FLERR,arg[iarg+2]);
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aoffset = force->inumeric(FLERR,arg[iarg+3]);
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doffset = force->inumeric(FLERR,arg[iarg+4]);
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ioffset = force->inumeric(FLERR,arg[iarg+5]);
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if (toffset < 0 || boffset < 0 || aoffset < 0 ||
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doffset < 0 || ioffset < 0)
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error->all(FLERR,"Illegal read_data command");
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offset[0] = force->numeric(FLERR,arg[iarg+1]);
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offset[1] = force->numeric(FLERR,arg[iarg+2]);
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offset[2] = force->numeric(FLERR,arg[iarg+3]);
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iarg += 6;
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} else if (strcmp(arg[iarg],"shift") == 0) {
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if (iarg+4 > narg) error->all(FLERR,"Illegal read_data command");
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shiftflag = 1;
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shift[0] = force->numeric(FLERR,arg[iarg+1]);
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shift[1] = force->numeric(FLERR,arg[iarg+2]);
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shift[2] = force->numeric(FLERR,arg[iarg+3]);
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if (domain->dimension == 2 && shift[2] != 0.0)
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error->all(FLERR,"Non-zero read_data shift z value for 2d simulation");
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iarg += 4;
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} else if (strcmp(arg[iarg],"extra/atom/types") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
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extra_atom_types = force->inumeric(FLERR,arg[iarg+1]);
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if (extra_atom_types < 0) error->all(FLERR,"Illegal read_data command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"extra/bond/types") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
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if (!atom->avec->bonds_allow)
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error->all(FLERR,"No bonds allowed with this atom style");
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extra_bond_types = force->inumeric(FLERR,arg[iarg+1]);
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if (extra_bond_types < 0) error->all(FLERR,"Illegal read_data command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"extra/angle/types") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
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if (!atom->avec->angles_allow)
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error->all(FLERR,"No angles allowed with this atom style");
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extra_angle_types = force->inumeric(FLERR,arg[iarg+1]);
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if (extra_angle_types < 0) error->all(FLERR,"Illegal read_data command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"extra/dihedral/types") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
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if (!atom->avec->dihedrals_allow)
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error->all(FLERR,"No dihedrals allowed with this atom style");
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extra_dihedral_types = force->inumeric(FLERR,arg[iarg+1]);
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if (extra_dihedral_types < 0)
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error->all(FLERR,"Illegal read_data command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"extra/improper/types") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
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if (!atom->avec->impropers_allow)
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error->all(FLERR,"No impropers allowed with this atom style");
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extra_improper_types = force->inumeric(FLERR,arg[iarg+1]);
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if (extra_improper_types < 0)
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error->all(FLERR,"Illegal read_data command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"group") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
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int igroup = group->find_or_create(arg[iarg+1]);
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groupbit = group->bitmask[igroup];
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iarg += 2;
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} else 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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@ -161,25 +236,54 @@ void ReadData::command(int narg, char **arg)
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strcpy(fix_section[nfix],arg[iarg+3]);
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nfix++;
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iarg += 4;
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} else error->all(FLERR,"Illegal read_data command");
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}
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// error checks
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if (domain->box_exist && !addflag && !mergeflag)
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error->all(FLERR,"Cannot read_data after simulation box is defined");
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if (addflag && mergeflag) error->all(FLERR,"Cannot read_data add and merge");
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if (domain->dimension == 2 && offset[2] != 0.0)
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error->all(FLERR,"Cannot use non-zero z offset in read_data "
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"for 2d simulation");
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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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if (domain->box_exist && !addflag)
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error->all(FLERR,"Cannot read_data without add keyword "
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"after simulation box is defined");
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if (!domain->box_exist && addflag)
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error->all(FLERR,"Cannot use read_data add before "
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"simulation box is defined");
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if (offsetflag && addflag == NONE)
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error->all(FLERR,"Cannot use read_data offset without add flag");
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if (shiftflag && addflag == NONE)
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error->all(FLERR,"Cannot use read_data shift without add flag");
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if (addflag != NONE &&
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(extra_atom_types || extra_bond_types || extra_angle_types ||
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extra_dihedral_types || extra_improper_types))
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error->all(FLERR,"Cannot use read_data extra with add flag");
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// first time system initialization
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if (addflag == NONE) {
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domain->box_exist = 1;
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update->ntimestep = 0;
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}
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// compute atomID offset for addflag = MERGE
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if (addflag == APPEND) {
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tagint *tag = atom->tag;
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int nlocal = atom->nlocal;
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tagint max = 0;
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for (int i = 0; i < nlocal; i++) max = MAX(max,tag[i]);
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MPI_Allreduce(&max,&id_offset,1,MPI_LMP_TAGINT,MPI_MAX,world);
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}
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// -----------------------------------------------------------------
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// perform 1-pass read if no molecular topoogy in file
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// perform 2-pass read if molecular topology,
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// first pass calculates max topology/atom
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// flags for this data file
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int atomflag,topoflag;
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int bondflag,angleflag,dihedralflag,improperflag;
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int ellipsoidflag,lineflag,triflag,bodyflag;
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@ -188,6 +292,14 @@ void ReadData::command(int narg, char **arg)
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bondflag = angleflag = dihedralflag = improperflag = 0;
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ellipsoidflag = lineflag = triflag = bodyflag = 0;
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// values in this data file
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natoms = ntypes = 0;
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nbonds = nangles = ndihedrals = nimpropers = 0;
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nbondtypes = nangletypes = ndihedraltypes = nimpropertypes = 0;
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triclinic = 0;
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int nlocal_previous = atom->nlocal;
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int firstpass = 1;
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while (1) {
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@ -204,16 +316,12 @@ void ReadData::command(int narg, char **arg)
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header();
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// problem setup using info from header
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// 1st pass only
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if (firstpass) {
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domain->box_exist = 1;
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update->ntimestep = 0;
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// apply extra settings before grow(), even if no topology in file
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// deallocate() insures new settings are used for topology arrays
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// if per-atom topology is in file, another grow() is done below
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// only done once, if firstpass and first data file
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// apply extra settings before grow(), even if no topology in file
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// deallocate() insures new settings are used for topology arrays
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// if per-atom topology is in file, another grow() is done below
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if (firstpass && addflag == NONE) {
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atom->bond_per_atom = atom->extra_bond_per_atom;
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atom->angle_per_atom = atom->extra_angle_per_atom;
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atom->dihedral_per_atom = atom->extra_dihedral_per_atom;
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@ -227,6 +335,37 @@ void ReadData::command(int narg, char **arg)
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atom->deallocate_topology();
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atom->avec->grow(n);
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domain->boxlo[0] = boxlo[0]; domain->boxhi[0] = boxhi[0];
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domain->boxlo[1] = boxlo[1]; domain->boxhi[1] = boxhi[1];
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domain->boxlo[2] = boxlo[2]; domain->boxhi[2] = boxhi[2];
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if (triclinic) {
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domain->xy = xy; domain->xz = xz; domain->yz = yz;
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}
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domain->print_box(" ");
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domain->set_initial_box();
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domain->set_global_box();
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comm->set_proc_grid();
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domain->set_local_box();
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}
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// change simulation box to be union of existing box and new box + shift
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// only done if firstpass and not first data file
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if (firstpass && addflag != NONE) {
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domain->boxlo[0] = MIN(domain->boxlo[0],boxlo[0]+shift[0]);
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domain->boxhi[0] = MAX(domain->boxhi[0],boxhi[0]+shift[0]);
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domain->boxlo[1] = MIN(domain->boxlo[1],boxlo[1]+shift[1]);
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domain->boxhi[1] = MAX(domain->boxhi[1],boxhi[1]+shift[1]);
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domain->boxlo[2] = MIN(domain->boxlo[2],boxlo[2]+shift[2]);
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domain->boxhi[2] = MAX(domain->boxhi[2],boxhi[2]+shift[2]);
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// NOTE: not sure what to do about this:
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//if (triclinic) {
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// domain->xy = xy; domain->xz = xz; domain->yz = yz;
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// }
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domain->print_box(" ");
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domain->set_initial_box();
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domain->set_global_box();
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@ -261,34 +400,34 @@ void ReadData::command(int narg, char **arg)
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error->warning(FLERR,"Atom style in data file differs "
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"from currently defined atom style");
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atoms();
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} else skip_lines(atom->natoms);
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} else skip_lines(natoms);
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} else if (strcmp(keyword,"Velocities") == 0) {
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if (atomflag == 0)
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error->all(FLERR,"Must read Atoms before Velocities");
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if (firstpass) velocities();
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else skip_lines(atom->natoms);
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else skip_lines(natoms);
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} else if (strcmp(keyword,"Bonds") == 0) {
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topoflag = bondflag = 1;
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if (atom->nbonds == 0)
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if (nbonds == 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(firstpass);
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} else if (strcmp(keyword,"Angles") == 0) {
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topoflag = angleflag = 1;
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if (atom->nangles == 0)
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if (nangles == 0)
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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(firstpass);
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} else if (strcmp(keyword,"Dihedrals") == 0) {
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topoflag = dihedralflag = 1;
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if (atom->ndihedrals == 0)
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if (ndihedrals == 0)
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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(firstpass);
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} else if (strcmp(keyword,"Impropers") == 0) {
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topoflag = improperflag = 1;
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if (atom->nimpropers == 0)
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if (nimpropers == 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(firstpass);
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@ -325,7 +464,7 @@ void ReadData::command(int narg, char **arg)
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} else if (strcmp(keyword,"Masses") == 0) {
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if (firstpass) mass();
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else skip_lines(atom->ntypes);
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else skip_lines(ntypes);
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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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@ -334,7 +473,7 @@ void ReadData::command(int narg, char **arg)
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error->warning(FLERR,"Pair style in data file differs "
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"from currently defined pair style");
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paircoeffs();
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} else skip_lines(atom->ntypes);
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} else skip_lines(ntypes);
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} else if (strcmp(keyword,"PairIJ Coeffs") == 0) {
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if (force->pair == NULL)
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error->all(FLERR,"Must define pair_style before PairIJ Coeffs");
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@ -343,7 +482,7 @@ void ReadData::command(int narg, char **arg)
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error->warning(FLERR,"Pair style in data file differs "
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"from currently defined pair style");
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pairIJcoeffs();
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} else skip_lines(atom->ntypes*(atom->ntypes+1)/2);
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} else skip_lines(ntypes*(ntypes+1)/2);
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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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@ -354,7 +493,7 @@ void ReadData::command(int narg, char **arg)
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error->warning(FLERR,"Bond style in data file differs "
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"from currently defined bond style");
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bondcoeffs();
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} else skip_lines(atom->nbondtypes);
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} else skip_lines(nbondtypes);
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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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@ -365,7 +504,7 @@ void ReadData::command(int narg, char **arg)
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error->warning(FLERR,"Angle style in data file differs "
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"from currently defined angle style");
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anglecoeffs(0);
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} else skip_lines(atom->nangletypes);
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} else skip_lines(nangletypes);
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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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@ -376,7 +515,7 @@ void ReadData::command(int narg, char **arg)
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error->warning(FLERR,"Dihedral style in data file differs "
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"from currently defined dihedral style");
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dihedralcoeffs(0);
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} else skip_lines(atom->ndihedraltypes);
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} else skip_lines(ndihedraltypes);
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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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@ -387,7 +526,7 @@ void ReadData::command(int narg, char **arg)
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error->warning(FLERR,"Improper style in data file differs "
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"from currently defined improper style");
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impropercoeffs(0);
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} else skip_lines(atom->nimpropertypes);
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} else skip_lines(nimpropertypes);
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||||
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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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@ -395,14 +534,14 @@ void ReadData::command(int narg, char **arg)
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if (force->angle == NULL)
|
||||
error->all(FLERR,"Must define angle_style before BondBond Coeffs");
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||||
if (firstpass) anglecoeffs(1);
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else skip_lines(atom->nangletypes);
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else skip_lines(nangletypes);
|
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} else if (strcmp(keyword,"BondAngle Coeffs") == 0) {
|
||||
if (atom->avec->angles_allow == 0)
|
||||
error->all(FLERR,"Invalid data file section: BondAngle Coeffs");
|
||||
if (force->angle == NULL)
|
||||
error->all(FLERR,"Must define angle_style before BondAngle Coeffs");
|
||||
if (firstpass) anglecoeffs(2);
|
||||
else skip_lines(atom->nangletypes);
|
||||
else skip_lines(nangletypes);
|
||||
|
||||
} else if (strcmp(keyword,"MiddleBondTorsion Coeffs") == 0) {
|
||||
if (atom->avec->dihedrals_allow == 0)
|
||||
@ -413,7 +552,7 @@ void ReadData::command(int narg, char **arg)
|
||||
"Must define dihedral_style before "
|
||||
"MiddleBondTorsion Coeffs");
|
||||
if (firstpass) dihedralcoeffs(1);
|
||||
else skip_lines(atom->ndihedraltypes);
|
||||
else skip_lines(ndihedraltypes);
|
||||
} else if (strcmp(keyword,"EndBondTorsion Coeffs") == 0) {
|
||||
if (atom->avec->dihedrals_allow == 0)
|
||||
error->all(FLERR,"Invalid data file section: EndBondTorsion Coeffs");
|
||||
@ -421,7 +560,7 @@ void ReadData::command(int narg, char **arg)
|
||||
error->all(FLERR,
|
||||
"Must define dihedral_style before EndBondTorsion Coeffs");
|
||||
if (firstpass) dihedralcoeffs(2);
|
||||
else skip_lines(atom->ndihedraltypes);
|
||||
else skip_lines(ndihedraltypes);
|
||||
} else if (strcmp(keyword,"AngleTorsion Coeffs") == 0) {
|
||||
if (atom->avec->dihedrals_allow == 0)
|
||||
error->all(FLERR,"Invalid data file section: AngleTorsion Coeffs");
|
||||
@ -429,7 +568,7 @@ void ReadData::command(int narg, char **arg)
|
||||
error->all(FLERR,
|
||||
"Must define dihedral_style before AngleTorsion Coeffs");
|
||||
if (firstpass) dihedralcoeffs(3);
|
||||
else skip_lines(atom->ndihedraltypes);
|
||||
else skip_lines(ndihedraltypes);
|
||||
} else if (strcmp(keyword,"AngleAngleTorsion Coeffs") == 0) {
|
||||
if (atom->avec->dihedrals_allow == 0)
|
||||
error->all(FLERR,
|
||||
@ -439,7 +578,7 @@ void ReadData::command(int narg, char **arg)
|
||||
"Must define dihedral_style before "
|
||||
"AngleAngleTorsion Coeffs");
|
||||
if (firstpass) dihedralcoeffs(4);
|
||||
else skip_lines(atom->ndihedraltypes);
|
||||
else skip_lines(ndihedraltypes);
|
||||
} else if (strcmp(keyword,"BondBond13 Coeffs") == 0) {
|
||||
if (atom->avec->dihedrals_allow == 0)
|
||||
error->all(FLERR,"Invalid data file section: BondBond13 Coeffs");
|
||||
@ -447,7 +586,7 @@ void ReadData::command(int narg, char **arg)
|
||||
error->all(FLERR,
|
||||
"Must define dihedral_style before BondBond13 Coeffs");
|
||||
if (firstpass) dihedralcoeffs(5);
|
||||
else skip_lines(atom->ndihedraltypes);
|
||||
else skip_lines(ndihedraltypes);
|
||||
|
||||
} else if (strcmp(keyword,"AngleAngle Coeffs") == 0) {
|
||||
if (atom->avec->impropers_allow == 0)
|
||||
@ -456,7 +595,7 @@ void ReadData::command(int narg, char **arg)
|
||||
error->all(FLERR,
|
||||
"Must define improper_style before AngleAngle Coeffs");
|
||||
if (firstpass) impropercoeffs(1);
|
||||
else skip_lines(atom->nimpropertypes);
|
||||
else skip_lines(nimpropertypes);
|
||||
|
||||
} else {
|
||||
char str[128];
|
||||
@ -469,7 +608,7 @@ void ReadData::command(int narg, char **arg)
|
||||
|
||||
// error if natoms > 0 yet no atoms were read
|
||||
|
||||
if (atom->natoms > 0 && atomflag == 0)
|
||||
if (natoms > 0 && atomflag == 0)
|
||||
error->all(FLERR,"No atoms in data file");
|
||||
|
||||
// close file
|
||||
@ -486,9 +625,8 @@ void ReadData::command(int narg, char **arg)
|
||||
// at end of 1st pass, error check for required sections
|
||||
// customize for new sections
|
||||
|
||||
if ((atom->nbonds && !bondflag) || (atom->nangles && !angleflag) ||
|
||||
(atom->ndihedrals && !dihedralflag) ||
|
||||
(atom->nimpropers && !improperflag))
|
||||
if ((nbonds && !bondflag) || (nangles && !angleflag) ||
|
||||
(ndihedrals && !dihedralflag) || (nimpropers && !improperflag))
|
||||
error->one(FLERR,"Needed molecular topology not in data file");
|
||||
|
||||
if ((nellipsoids && !ellipsoidflag) || (nlines && !lineflag) ||
|
||||
@ -510,6 +648,15 @@ void ReadData::command(int narg, char **arg)
|
||||
atom->avec->grow(atom->nmax);
|
||||
}
|
||||
|
||||
// assign atoms added by this data file to specified group
|
||||
|
||||
if (groupbit) {
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
for (int i = nlocal_previous; i < nlocal; i++)
|
||||
mask[i] |= groupbit;
|
||||
}
|
||||
|
||||
// create special bond lists for molecular systems
|
||||
|
||||
if (atom->molecular == 1) {
|
||||
@ -590,6 +737,19 @@ void ReadData::command(int narg, char **arg)
|
||||
|
||||
if (atom->molecular == 2) atom->avec->onemols[0]->check_attributes(1);
|
||||
|
||||
// if adding atoms, migrate atoms to new processors
|
||||
// use irregular() b/c box size could have changed dramaticaly
|
||||
// resulting in procs now owning very different subboxes
|
||||
// with their previously owned atoms now far outside the subbox
|
||||
|
||||
if (addflag != NONE) {
|
||||
if (domain->triclinic) domain->x2lamda(atom->nlocal);
|
||||
Irregular *irregular = new Irregular(lmp);
|
||||
irregular->migrate_atoms(1);
|
||||
delete irregular;
|
||||
if (domain->triclinic) domain->lamda2x(atom->nlocal);
|
||||
}
|
||||
|
||||
// shrink-wrap the box if necessary and move atoms to new procs
|
||||
// if atoms are lost is b/c data file box was far from shrink-wrapped
|
||||
// do not use irregular() comm, which would not lose atoms,
|
||||
@ -621,6 +781,7 @@ void ReadData::command(int narg, char **arg)
|
||||
header ends with EOF or non-blank line containing no header keyword
|
||||
if EOF, line is set to blank line
|
||||
else line has first keyword line for rest of file
|
||||
some logic differs if adding atoms
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ReadData::header()
|
||||
@ -648,7 +809,7 @@ void ReadData::header()
|
||||
|
||||
while (1) {
|
||||
|
||||
// read a line and bcast length if flag is set
|
||||
// read a line and bcast length
|
||||
|
||||
if (me == 0) {
|
||||
if (fgets(line,MAXLINE,fp) == NULL) n = 0;
|
||||
@ -689,7 +850,9 @@ void ReadData::header()
|
||||
// customize for new header lines
|
||||
|
||||
if (strstr(line,"atoms")) {
|
||||
sscanf(line,BIGINT_FORMAT,&atom->natoms);
|
||||
sscanf(line,BIGINT_FORMAT,&natoms);
|
||||
if (addflag == NONE) atom->natoms = natoms;
|
||||
else atom->natoms += natoms;
|
||||
|
||||
// check for these first
|
||||
// otherwise "triangles" will be matched as "angles"
|
||||
@ -710,43 +873,70 @@ void ReadData::header()
|
||||
if (!avec_body)
|
||||
error->all(FLERR,"No bodies allowed with this atom style");
|
||||
sscanf(line,BIGINT_FORMAT,&nbodies);
|
||||
}
|
||||
|
||||
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);
|
||||
else if (strstr(line,"impropers")) sscanf(line,BIGINT_FORMAT,
|
||||
&atom->nimpropers);
|
||||
} else if (strstr(line,"bonds")) {
|
||||
sscanf(line,BIGINT_FORMAT,&nbonds);
|
||||
if (addflag == NONE) atom->nbonds = nbonds;
|
||||
else atom->nbonds += nbonds;
|
||||
} else if (strstr(line,"angles")) {
|
||||
sscanf(line,BIGINT_FORMAT,&nangles);
|
||||
if (addflag == NONE) atom->nangles = nangles;
|
||||
else atom->nangles += nangles;
|
||||
} else if (strstr(line,"dihedrals")) {
|
||||
sscanf(line,BIGINT_FORMAT,&ndihedrals);
|
||||
if (addflag == NONE) atom->ndihedrals = ndihedrals;
|
||||
else atom->ndihedrals += natoms;
|
||||
} else if (strstr(line,"impropers")) {
|
||||
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")) 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"))
|
||||
sscanf(line,"%d",&atom->ndihedraltypes);
|
||||
else if (strstr(line,"improper types"))
|
||||
sscanf(line,"%d",&atom->nimpropertypes);
|
||||
} else if (strstr(line,"atom types")) {
|
||||
sscanf(line,"%d",&ntypes);
|
||||
if (addflag == NONE) atom->ntypes = ntypes + extra_atom_types;
|
||||
} else if (strstr(line,"bond types")) {
|
||||
sscanf(line,"%d",&nbondtypes);
|
||||
if (addflag == NONE) atom->nbondtypes = nbondtypes + extra_bond_types;
|
||||
} else if (strstr(line,"angle types")) {
|
||||
sscanf(line,"%d",&nangletypes);
|
||||
if (addflag == NONE) atom->nangletypes = nangletypes + extra_angle_types;
|
||||
} else if (strstr(line,"dihedral types")) {
|
||||
sscanf(line,"%d",&ndihedraltypes);
|
||||
if (addflag == NONE)
|
||||
atom->ndihedraltypes = ndihedraltypes + extra_dihedral_types;
|
||||
} else if (strstr(line,"improper types")) {
|
||||
sscanf(line,"%d",&nimpropertypes);
|
||||
if (addflag == NONE)
|
||||
atom->nimpropertypes = nimpropertypes + extra_improper_types;
|
||||
|
||||
else if (strstr(line,"extra bond per atom"))
|
||||
sscanf(line,"%d",&atom->extra_bond_per_atom);
|
||||
else if (strstr(line,"extra angle per atom"))
|
||||
sscanf(line,"%d",&atom->extra_angle_per_atom);
|
||||
else if (strstr(line,"extra dihedral per atom"))
|
||||
sscanf(line,"%d",&atom->extra_dihedral_per_atom);
|
||||
else if (strstr(line,"extra improper per atom"))
|
||||
sscanf(line,"%d",&atom->extra_improper_per_atom);
|
||||
else if (strstr(line,"extra special per atom"))
|
||||
sscanf(line,"%d",&force->special_extra);
|
||||
// these settings only used by first data file
|
||||
|
||||
} else if (strstr(line,"extra bond per atom")) {
|
||||
if (addflag == NONE) sscanf(line,"%d",&atom->extra_bond_per_atom);
|
||||
} else if (strstr(line,"extra angle per atom")) {
|
||||
if (addflag == NONE) sscanf(line,"%d",&atom->extra_angle_per_atom);
|
||||
} else if (strstr(line,"extra dihedral per atom")) {
|
||||
if (addflag == NONE) sscanf(line,"%d",&atom->extra_dihedral_per_atom);
|
||||
} else if (strstr(line,"extra improper per atom")) {
|
||||
if (addflag == NONE) sscanf(line,"%d",&atom->extra_improper_per_atom);
|
||||
} else if (strstr(line,"extra special per atom")) {
|
||||
if (addflag == NONE) sscanf(line,"%d",&force->special_extra);
|
||||
|
||||
// local copy of box info
|
||||
// so can treat differently for first vs subsequent data files
|
||||
|
||||
} else if (strstr(line,"xlo xhi")) {
|
||||
sscanf(line,"%lg %lg",&boxlo[0],&boxhi[0]);
|
||||
} else if (strstr(line,"ylo yhi")) {
|
||||
sscanf(line,"%lg %lg",&boxlo[1],&boxhi[1]);
|
||||
} else if (strstr(line,"zlo zhi")) {
|
||||
sscanf(line,"%lg %lg",&boxlo[2],&boxhi[2]);
|
||||
} else if (strstr(line,"xy xz yz")) {
|
||||
triclinic = 1;
|
||||
sscanf(line,"%lg %lg %lg",&xy,&xz,&yz);
|
||||
|
||||
else if (strstr(line,"xlo xhi"))
|
||||
sscanf(line,"%lg %lg",&domain->boxlo[0],&domain->boxhi[0]);
|
||||
else if (strstr(line,"ylo yhi"))
|
||||
sscanf(line,"%lg %lg",&domain->boxlo[1],&domain->boxhi[1]);
|
||||
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;
|
||||
sscanf(line,"%lg %lg %lg",&domain->xy,&domain->xz,&domain->yz);
|
||||
} else break;
|
||||
}
|
||||
|
||||
@ -815,27 +1005,28 @@ void ReadData::atoms()
|
||||
}
|
||||
|
||||
bigint nread = 0;
|
||||
bigint natoms = atom->natoms;
|
||||
|
||||
while (nread < natoms) {
|
||||
nchunk = MIN(natoms-nread,CHUNK);
|
||||
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
|
||||
if (eof) error->all(FLERR,"Unexpected end of data file");
|
||||
atom->data_atoms(nchunk,buffer);
|
||||
atom->data_atoms(nchunk,buffer,id_offset,toffset,shiftflag,shift);
|
||||
nread += nchunk;
|
||||
}
|
||||
|
||||
// check that all atoms were assigned correctly
|
||||
|
||||
bigint tmp = atom->nlocal;
|
||||
MPI_Allreduce(&tmp,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
|
||||
bigint n = atom->nlocal;
|
||||
bigint sum;
|
||||
MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world);
|
||||
bigint nassign = sum - (atom->natoms - natoms);
|
||||
|
||||
if (me == 0) {
|
||||
if (screen) fprintf(screen," " BIGINT_FORMAT " atoms\n",natoms);
|
||||
if (logfile) fprintf(logfile," " BIGINT_FORMAT " atoms\n",natoms);
|
||||
if (screen) fprintf(screen," " BIGINT_FORMAT " atoms\n",nassign);
|
||||
if (logfile) fprintf(logfile," " BIGINT_FORMAT " atoms\n",nassign);
|
||||
}
|
||||
|
||||
if (natoms != atom->natoms)
|
||||
if (sum != atom->natoms)
|
||||
error->all(FLERR,"Did not assign all atoms correctly");
|
||||
|
||||
// check that atom IDs are valid
|
||||
@ -872,13 +1063,12 @@ void ReadData::velocities()
|
||||
}
|
||||
|
||||
bigint nread = 0;
|
||||
bigint natoms = atom->natoms;
|
||||
|
||||
while (nread < natoms) {
|
||||
nchunk = MIN(natoms-nread,CHUNK);
|
||||
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
|
||||
if (eof) error->all(FLERR,"Unexpected end of data file");
|
||||
atom->data_vels(nchunk,buffer);
|
||||
atom->data_vels(nchunk,buffer,id_offset);
|
||||
nread += nchunk;
|
||||
}
|
||||
|
||||
@ -928,7 +1118,7 @@ void ReadData::bonds(int firstpass)
|
||||
nchunk = MIN(nbonds-nread,CHUNK);
|
||||
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
|
||||
if (eof) error->all(FLERR,"Unexpected end of data file");
|
||||
atom->data_bonds(nchunk,buffer,count);
|
||||
atom->data_bonds(nchunk,buffer,count,id_offset);
|
||||
nread += nchunk;
|
||||
}
|
||||
|
||||
@ -1003,7 +1193,7 @@ void ReadData::angles(int firstpass)
|
||||
nchunk = MIN(nangles-nread,CHUNK);
|
||||
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
|
||||
if (eof) error->all(FLERR,"Unexpected end of data file");
|
||||
atom->data_angles(nchunk,buffer,count);
|
||||
atom->data_angles(nchunk,buffer,count,id_offset);
|
||||
nread += nchunk;
|
||||
}
|
||||
|
||||
@ -1078,7 +1268,7 @@ void ReadData::dihedrals(int firstpass)
|
||||
nchunk = MIN(ndihedrals-nread,CHUNK);
|
||||
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
|
||||
if (eof) error->all(FLERR,"Unexpected end of data file");
|
||||
atom->data_dihedrals(nchunk,buffer,count);
|
||||
atom->data_dihedrals(nchunk,buffer,count,id_offset);
|
||||
nread += nchunk;
|
||||
}
|
||||
|
||||
@ -1153,7 +1343,7 @@ void ReadData::impropers(int firstpass)
|
||||
nchunk = MIN(nimpropers-nread,CHUNK);
|
||||
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
|
||||
if (eof) error->all(FLERR,"Unexpected end of data file");
|
||||
atom->data_impropers(nchunk,buffer,count);
|
||||
atom->data_impropers(nchunk,buffer,count,id_offset);
|
||||
nread += nchunk;
|
||||
}
|
||||
|
||||
@ -1216,7 +1406,7 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
|
||||
nchunk = MIN(natoms-nread,CHUNK);
|
||||
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
|
||||
if (eof) error->all(FLERR,"Unexpected end of data file");
|
||||
atom->data_bonus(nchunk,buffer,ptr);
|
||||
atom->data_bonus(nchunk,buffer,ptr,id_offset);
|
||||
nread += nchunk;
|
||||
}
|
||||
|
||||
@ -1296,7 +1486,7 @@ void ReadData::bodies(int firstpass)
|
||||
MPI_Bcast(&m,1,MPI_INT,0,world);
|
||||
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
|
||||
|
||||
if (firstpass) atom->data_bodies(nchunk,buffer,avec_body);
|
||||
if (firstpass) atom->data_bodies(nchunk,buffer,avec_body,id_offset);
|
||||
nread += nchunk;
|
||||
}
|
||||
|
||||
@ -1316,16 +1506,16 @@ void ReadData::bodies(int firstpass)
|
||||
void ReadData::mass()
|
||||
{
|
||||
char *next;
|
||||
char *buf = new char[atom->ntypes*MAXLINE];
|
||||
char *buf = new char[ntypes*MAXLINE];
|
||||
|
||||
int eof = comm->read_lines_from_file(fp,atom->ntypes,MAXLINE,buf);
|
||||
int eof = comm->read_lines_from_file(fp,ntypes,MAXLINE,buf);
|
||||
if (eof) error->all(FLERR,"Unexpected end of data file");
|
||||
|
||||
char *original = buf;
|
||||
for (int i = 0; i < atom->ntypes; i++) {
|
||||
for (int i = 0; i < ntypes; i++) {
|
||||
next = strchr(buf,'\n');
|
||||
*next = '\0';
|
||||
atom->set_mass(buf);
|
||||
atom->set_mass(buf,toffset);
|
||||
buf = next + 1;
|
||||
}
|
||||
delete [] original;
|
||||
@ -1336,16 +1526,16 @@ void ReadData::mass()
|
||||
void ReadData::paircoeffs()
|
||||
{
|
||||
char *next;
|
||||
char *buf = new char[atom->ntypes*MAXLINE];
|
||||
char *buf = new char[ntypes*MAXLINE];
|
||||
|
||||
int eof = comm->read_lines_from_file(fp,atom->ntypes,MAXLINE,buf);
|
||||
int eof = comm->read_lines_from_file(fp,ntypes,MAXLINE,buf);
|
||||
if (eof) error->all(FLERR,"Unexpected end of data file");
|
||||
|
||||
char *original = buf;
|
||||
for (int i = 0; i < atom->ntypes; i++) {
|
||||
for (int i = 0; i < ntypes; i++) {
|
||||
next = strchr(buf,'\n');
|
||||
*next = '\0';
|
||||
parse_coeffs(buf,NULL,1);
|
||||
parse_coeffs(buf,NULL,1,2,toffset);
|
||||
if (narg == 0) error->all(FLERR,"Unexpected end of PairCoeffs section");
|
||||
force->pair->coeff(narg,arg);
|
||||
buf = next + 1;
|
||||
@ -1360,18 +1550,18 @@ void ReadData::pairIJcoeffs()
|
||||
int i,j;
|
||||
char *next;
|
||||
|
||||
int nsq = atom->ntypes* (atom->ntypes+1) / 2;
|
||||
int nsq = ntypes * (ntypes+1) / 2;
|
||||
char *buf = new char[nsq * MAXLINE];
|
||||
|
||||
int eof = comm->read_lines_from_file(fp,nsq,MAXLINE,buf);
|
||||
if (eof) error->all(FLERR,"Unexpected end of data file");
|
||||
|
||||
char *original = buf;
|
||||
for (i = 0; i < atom->ntypes; i++)
|
||||
for (j = i; j < atom->ntypes; j++) {
|
||||
for (i = 0; i < ntypes; i++)
|
||||
for (j = i; j < ntypes; j++) {
|
||||
next = strchr(buf,'\n');
|
||||
*next = '\0';
|
||||
parse_coeffs(buf,NULL,0);
|
||||
parse_coeffs(buf,NULL,0,2,toffset);
|
||||
if (narg == 0) error->all(FLERR,"Unexpected end of PairCoeffs section");
|
||||
force->pair->coeff(narg,arg);
|
||||
buf = next + 1;
|
||||
@ -1384,16 +1574,16 @@ void ReadData::pairIJcoeffs()
|
||||
void ReadData::bondcoeffs()
|
||||
{
|
||||
char *next;
|
||||
char *buf = new char[atom->nbondtypes*MAXLINE];
|
||||
char *buf = new char[nbondtypes*MAXLINE];
|
||||
|
||||
int eof = comm->read_lines_from_file(fp,atom->nbondtypes,MAXLINE,buf);
|
||||
int eof = comm->read_lines_from_file(fp,nbondtypes,MAXLINE,buf);
|
||||
if (eof) error->all(FLERR,"Unexpected end of data file");
|
||||
|
||||
char *original = buf;
|
||||
for (int i = 0; i < atom->nbondtypes; i++) {
|
||||
for (int i = 0; i < nbondtypes; i++) {
|
||||
next = strchr(buf,'\n');
|
||||
*next = '\0';
|
||||
parse_coeffs(buf,NULL,0);
|
||||
parse_coeffs(buf,NULL,0,1,boffset);
|
||||
if (narg == 0) error->all(FLERR,"Unexpected end of BondCoeffs section");
|
||||
force->bond->coeff(narg,arg);
|
||||
buf = next + 1;
|
||||
@ -1406,18 +1596,18 @@ void ReadData::bondcoeffs()
|
||||
void ReadData::anglecoeffs(int which)
|
||||
{
|
||||
char *next;
|
||||
char *buf = new char[atom->nangletypes*MAXLINE];
|
||||
char *buf = new char[nangletypes*MAXLINE];
|
||||
|
||||
int eof = comm->read_lines_from_file(fp,atom->nangletypes,MAXLINE,buf);
|
||||
int eof = comm->read_lines_from_file(fp,nangletypes,MAXLINE,buf);
|
||||
if (eof) error->all(FLERR,"Unexpected end of data file");
|
||||
|
||||
char *original = buf;
|
||||
for (int i = 0; i < atom->nangletypes; i++) {
|
||||
for (int i = 0; i < nangletypes; i++) {
|
||||
next = strchr(buf,'\n');
|
||||
*next = '\0';
|
||||
if (which == 0) parse_coeffs(buf,NULL,0);
|
||||
else if (which == 1) parse_coeffs(buf,"bb",0);
|
||||
else if (which == 2) parse_coeffs(buf,"ba",0);
|
||||
if (which == 0) parse_coeffs(buf,NULL,0,1,aoffset);
|
||||
else if (which == 1) parse_coeffs(buf,"bb",0,1,aoffset);
|
||||
else if (which == 2) parse_coeffs(buf,"ba",0,1,aoffset);
|
||||
if (narg == 0) error->all(FLERR,"Unexpected end of AngleCoeffs section");
|
||||
force->angle->coeff(narg,arg);
|
||||
buf = next + 1;
|
||||
@ -1430,21 +1620,21 @@ void ReadData::anglecoeffs(int which)
|
||||
void ReadData::dihedralcoeffs(int which)
|
||||
{
|
||||
char *next;
|
||||
char *buf = new char[atom->ndihedraltypes*MAXLINE];
|
||||
char *buf = new char[ndihedraltypes*MAXLINE];
|
||||
|
||||
int eof = comm->read_lines_from_file(fp,atom->ndihedraltypes,MAXLINE,buf);
|
||||
int eof = comm->read_lines_from_file(fp,ndihedraltypes,MAXLINE,buf);
|
||||
if (eof) error->all(FLERR,"Unexpected end of data file");
|
||||
|
||||
char *original = buf;
|
||||
for (int i = 0; i < atom->ndihedraltypes; i++) {
|
||||
for (int i = 0; i < ndihedraltypes; i++) {
|
||||
next = strchr(buf,'\n');
|
||||
*next = '\0';
|
||||
if (which == 0) parse_coeffs(buf,NULL,0);
|
||||
else if (which == 1) parse_coeffs(buf,"mbt",0);
|
||||
else if (which == 2) parse_coeffs(buf,"ebt",0);
|
||||
else if (which == 3) parse_coeffs(buf,"at",0);
|
||||
else if (which == 4) parse_coeffs(buf,"aat",0);
|
||||
else if (which == 5) parse_coeffs(buf,"bb13",0);
|
||||
if (which == 0) parse_coeffs(buf,NULL,0,1,doffset);
|
||||
else if (which == 1) parse_coeffs(buf,"mbt",0,1,doffset);
|
||||
else if (which == 2) parse_coeffs(buf,"ebt",0,1,doffset);
|
||||
else if (which == 3) parse_coeffs(buf,"at",0,1,doffset);
|
||||
else if (which == 4) parse_coeffs(buf,"aat",0,1,doffset);
|
||||
else if (which == 5) parse_coeffs(buf,"bb13",0,1,doffset);
|
||||
if (narg == 0) error->all(FLERR,"Unexpected end of DihedralCoeffs section");
|
||||
force->dihedral->coeff(narg,arg);
|
||||
buf = next + 1;
|
||||
@ -1457,17 +1647,17 @@ void ReadData::dihedralcoeffs(int which)
|
||||
void ReadData::impropercoeffs(int which)
|
||||
{
|
||||
char *next;
|
||||
char *buf = new char[atom->nimpropertypes*MAXLINE];
|
||||
char *buf = new char[nimpropertypes*MAXLINE];
|
||||
|
||||
int eof = comm->read_lines_from_file(fp,atom->nimpropertypes,MAXLINE,buf);
|
||||
int eof = comm->read_lines_from_file(fp,nimpropertypes,MAXLINE,buf);
|
||||
if (eof) error->all(FLERR,"Unexpected end of data file");
|
||||
|
||||
char *original = buf;
|
||||
for (int i = 0; i < atom->nimpropertypes; i++) {
|
||||
for (int i = 0; i < nimpropertypes; i++) {
|
||||
next = strchr(buf,'\n');
|
||||
*next = '\0';
|
||||
if (which == 0) parse_coeffs(buf,NULL,0);
|
||||
else if (which == 1) parse_coeffs(buf,"aa",0);
|
||||
if (which == 0) parse_coeffs(buf,NULL,0,1,ioffset);
|
||||
else if (which == 1) parse_coeffs(buf,"aa",0,1,ioffset);
|
||||
if (narg == 0) error->all(FLERR,"Unexpected end of ImproperCoeffs section");
|
||||
force->improper->coeff(narg,arg);
|
||||
buf = next + 1;
|
||||
@ -1634,9 +1824,11 @@ void ReadData::skip_lines(bigint n)
|
||||
if 2nd word starts with letter, then is hybrid style, add addstr after it
|
||||
else add addstr before 2nd word
|
||||
if dupflag, duplicate 1st word, so pair_coeff "2" becomes "2 2"
|
||||
if noffset, add offset to first noffset args, which are atom/bond/etc types
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ReadData::parse_coeffs(char *line, const char *addstr, int dupflag)
|
||||
void ReadData::parse_coeffs(char *line, const char *addstr,
|
||||
int dupflag, int noffset, int offset)
|
||||
{
|
||||
char *ptr;
|
||||
if ((ptr = strchr(line,'#'))) *ptr = '\0';
|
||||
@ -1655,6 +1847,17 @@ void ReadData::parse_coeffs(char *line, const char *addstr, int dupflag)
|
||||
if (dupflag && narg == 1) arg[narg++] = word;
|
||||
word = strtok(NULL," \t\n\r\f");
|
||||
}
|
||||
|
||||
if (noffset) {
|
||||
int value = force->inumeric(FLERR,arg[0]);
|
||||
sprintf(argoffset1,"%d",value+offset);
|
||||
arg[0] = argoffset1;
|
||||
if (noffset == 2) {
|
||||
value = force->inumeric(FLERR,arg[1]);
|
||||
sprintf(argoffset2,"%d",value+offset);
|
||||
arg[1] = argoffset2;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
||||
Reference in New Issue
Block a user