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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11250 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-01-17 18:43:09 +00:00
parent 961be6ee48
commit bad19033d0
172 changed files with 2523 additions and 2184 deletions
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129
src/create_atoms.cpp
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@ -22,6 +22,7 @@
#include "irregular.h"
#include "modify.h"
#include "force.h"
#include "special.h"
#include "fix.h"
#include "domain.h"
#include "lattice.h"
@ -121,7 +122,7 @@ void CreateAtoms::command(int narg, char **arg)
else error->all(FLERR,"Illegal create_atoms command");
iarg += 2;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix create_atoms command");
if (iarg+3 > narg) error->all(FLERR,"Illegal create_atoms command");
int imol = atom->find_molecule(arg[iarg+1]);
if (imol == -1)
error->all(FLERR,"Molecule ID for create_atoms does not exist");
@ -152,20 +153,21 @@ void CreateAtoms::command(int narg, char **arg)
ranmol = NULL;
if (mode == MOLECULE) {
if (atom->molecule_flag == 0)
error->all(FLERR,"Create_atoms mol requires atom attribute molecule");
if (onemol->xflag == 0)
error->all(FLERR,"Create_atoms molecule must have coordinates");
if (onemol->typeflag == 0)
error->all(FLERR,"Create_atoms molecule must have atom types");
if (ntype+onemol->maxtype <= 0 || ntype+onemol->maxtype > atom->ntypes)
error->all(FLERR,"Invalid atom type in create_atoms mol command");
if (onemol->tag_require && !atom->tag_enable)
error->all(FLERR,
"Create_atoms molecule has atom IDs, but system does not");
// create_atoms uses geoemetric center of molecule for insertion
onemol->compute_center();
// molecule random number generator, same for all procs
// molecule random number generator, different for each proc
ranmol = new RanMars(lmp,molseed+comm->me);
}
@ -251,99 +253,88 @@ void CreateAtoms::command(int narg, char **arg)
fix->set_arrays(i);
}
// new total # of atoms and error check
// for MOLECULE mode, require atom IDs
// set new total # of atoms and error check
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
if (atom->natoms < 0 || atom->natoms >= MAXBIGINT)
error->all(FLERR,"Too many total atoms");
if (atom->natoms > MAXSMALLINT) {
if (mode == ATOM) {
if (comm->me == 0)
error->warning(FLERR,"Total atom count exceeds ID limit, "
"atoms will not have individual IDs");
atom->tag_enable = 0;
} else error->all(FLERR,"Total atom count exceeds ID limit");
}
// for ATOM mode:
// add IDs for newly created atoms if IDs are still enabled
// if global map exists, reset it
// add IDs for newly created atoms
// check that atom IDs are valid
if (mode == ATOM) {
if (atom->natoms <= MAXSMALLINT) atom->tag_extend();
if (atom->map_style) {
atom->nghost = 0;
atom->map_init();
atom->map_set();
}
}
if (atom->tag_enable) atom->tag_extend();
atom->tag_check();
// for MOLECULE mode:
// set atom and molecule IDs for created atoms
// send atoms to new owning procs via irregular comm
// since not all created atoms will be within my sub-domain
// if molecular system or user-requested, create global mapping of atoms
// zero nghost in case are adding new atoms to existing atoms
if (mode == MOLECULE) {
// add atom IDs for newly created atoms and reset global map
// global map must exist since atom->molecular is required to be set
atom->tag_extend();
if (atom->molecular || atom->map_user) {
atom->nghost = 0;
atom->map_init();
atom->map_set();
// maxmol = max molecule ID across all procs, for previous atoms
}
int *molecule = atom->molecule;
// for MOLECULE mode:
// set molecule IDs for created atoms if used
// reset new molecule bond,angle,etc and special values
// send atoms to new owning procs via irregular comm
// since not all atoms I created will be within my sub-domain
// perform special list build if needed
if (mode == MOLECULE) {
int max = 0;
for (int i = 0; i < nlocal_previous; i++) max = MAX(max,molecule[i]);
int maxmol;
MPI_Allreduce(&max,&maxmol,1,MPI_INT,MPI_MAX,world);
// molcreate = # of molecules I created
int molcreate = (atom->nlocal - nlocal_previous) / onemol->natoms;
// maxmol = max molecule ID across all procs, for previous atoms
// moloffset = max molecule ID for all molecules owned by previous procs
// including molecules existing before this creation
int molcreate = (atom->nlocal - nlocal_previous) / onemol->natoms;
int moloffset;
MPI_Scan(&molcreate,&moloffset,1,MPI_INT,MPI_SUM,world);
moloffset = moloffset - molcreate + maxmol;
int *molecule = atom->molecule;
if (molecule) {
int max = 0;
for (int i = 0; i < nlocal_previous; i++) max = MAX(max,molecule[i]);
int maxmol;
MPI_Allreduce(&max,&maxmol,1,MPI_INT,MPI_MAX,world);
MPI_Scan(&molcreate,&moloffset,1,MPI_INT,MPI_SUM,world);
moloffset = moloffset - molcreate + maxmol;
}
// loop over molecules I created
// set their molecule ID
// reset their bond,angle,etc and special values
int natoms = onemol->natoms;
tagint offset = 0;
int *tag = atom->tag;
tagint *tag = atom->tag;
int *num_bond = atom->num_bond;
int *num_angle = atom->num_angle;
int *num_dihedral = atom->num_dihedral;
int *num_improper = atom->num_improper;
int **bond_atom = atom->bond_atom;
int **angle_atom1 = atom->angle_atom1;
int **angle_atom2 = atom->angle_atom2;
int **angle_atom3 = atom->angle_atom3;
int **dihedral_atom1 = atom->dihedral_atom1;
int **dihedral_atom2 = atom->dihedral_atom2;
int **dihedral_atom3 = atom->dihedral_atom3;
int **dihedral_atom4 = atom->dihedral_atom4;
int **improper_atom1 = atom->improper_atom1;
int **improper_atom2 = atom->improper_atom2;
int **improper_atom3 = atom->improper_atom3;
int **improper_atom4 = atom->improper_atom4;
tagint **bond_atom = atom->bond_atom;
tagint **angle_atom1 = atom->angle_atom1;
tagint **angle_atom2 = atom->angle_atom2;
tagint **angle_atom3 = atom->angle_atom3;
tagint **dihedral_atom1 = atom->dihedral_atom1;
tagint **dihedral_atom2 = atom->dihedral_atom2;
tagint **dihedral_atom3 = atom->dihedral_atom3;
tagint **dihedral_atom4 = atom->dihedral_atom4;
tagint **improper_atom1 = atom->improper_atom1;
tagint **improper_atom2 = atom->improper_atom2;
tagint **improper_atom3 = atom->improper_atom3;
tagint **improper_atom4 = atom->improper_atom4;
int **nspecial = atom->nspecial;
int **special = atom->special;
tagint **special = atom->special;
int ilocal = nlocal_previous;
for (int i = 0; i < molcreate; i++) {
int offset = tag[ilocal]-1;
if (tag) offset = tag[ilocal]-1;
for (int m = 0; m < natoms; m++) {
molecule[ilocal] = moloffset + i+1;
if (molecule) molecule[ilocal] = moloffset + i+1;
if (onemol->bondflag)
for (int j = 0; j < num_bond[ilocal]; j++)
bond_atom[ilocal][j] += offset;
@ -404,6 +395,17 @@ void CreateAtoms::command(int narg, char **arg)
fprintf(logfile,"Created " BIGINT_FORMAT " atoms\n",
atom->natoms-natoms_previous);
}
// for MOLECULE mode:
// create special bond lists for molecular systems
// only if onemol added bonds but not special info
if (mode == MOLECULE) {
if (atom->molecular && onemol->bondflag && !onemol->specialflag) {
Special special(lmp);
special.build();
}
}
}
/* ----------------------------------------------------------------------
@ -439,7 +441,6 @@ void CreateAtoms::add_single()
}
}
/* ----------------------------------------------------------------------
add Nrandom atoms at random locations
------------------------------------------------------------------------- */