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set.cpp
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Tue, Jun 4, 00:46

set.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "set.h"
#include "atom.h"
#include "atom_vec.h"
#include "domain.h"
#include "group.h"
#include "comm.h"
#include "neighbor.h"
#include "force.h"
#include "pair.h"
#include "random_park.h"
#include "error.h"
using namespace LAMMPS_NS;
#define ONEATOM 0
#define ATOM 1
#define BOND 2
#define ANGLE 3
#define DIHEDRAL 4
#define IMPROPER 5
#define CHARGE 6
#define DIPOLE 7
#define WARMUP 100
/* ---------------------------------------------------------------------- */
Set::Set(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void Set::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all("Set command before simulation box is defined");
if (atom->natoms == 0)
error->all("Set command with no atoms existing");
if (narg != 3) error->all("Illegal set command");
// set style
int style;
if (strcmp(arg[1],"atom") == 0) style = ATOM;
else if (strcmp(arg[1],"bond") == 0) style = BOND;
else if (strcmp(arg[1],"angle") == 0) style = ANGLE;
else if (strcmp(arg[1],"dihedral") == 0) style = DIHEDRAL;
else if (strcmp(arg[1],"improper") == 0) style = IMPROPER;
else if (strcmp(arg[1],"charge") == 0) style = CHARGE;
else if (strcmp(arg[1],"dipole") == 0) style = DIPOLE;
else style = ONEATOM;
// set atom or group
int atomid,igroup,groupbit;
if (style == ONEATOM) atomid = atoi(arg[0]);
else {
igroup = group->find(arg[0]);
if (igroup == -1) error->all("Cannot find set command group ID");
groupbit = group->bitmask[igroup];
}
// consistency checks
if ((style == BOND && atom->avec->bonds_allow == 0) ||
(style == ANGLE && atom->avec->angles_allow == 0) ||
(style == DIHEDRAL && atom->avec->dihedrals_allow == 0) ||
(style == IMPROPER && atom->avec->impropers_allow == 0) ||
(style == CHARGE && atom->q == NULL) ||
(style == DIPOLE && atom->dipole == NULL))
error->all("Cannot set this attribute for this atom style");
if (style == ONEATOM && strcmp(arg[1],"q") == 0 && atom->q == NULL)
error->all("Cannot set this attribute for this atom style");
if (style == ONEATOM && strcmp(arg[1],"mol") == 0 && atom->molecular == 0)
error->all("Cannot set this attribute for this atom style");
// border swap to insure type and mask is current for off-proc atoms
// only needed for BOND, ANGLE, etc types
// enforce PBC before in case atoms are outside box
// init entire system since comm->exchange is done
// comm::init needs neighbor::init needs pair::init needs kspace::init, etc
if (style == BOND || style == ANGLE ||
style == DIHEDRAL || style == IMPROPER) {
if (comm->me == 0 && screen) fprintf(screen,"System init for set ...\n");
lmp->init();
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
comm->exchange();
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
}
if (comm->me == 0 && screen) fprintf(screen,"Setting atom values ...\n");
// set new values
int *mask = atom->mask;
int nlocal = atom->nlocal;
int m,atom1,atom2,atom3,atom4;
int count = 0;
// for style ATOM, atom must be in group
if (style == ATOM) {
int ivalue = atoi(arg[2]);
if (ivalue < 1 || ivalue > atom->ntypes)
error->all("Invalid type in set command");
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
atom->type[i] = ivalue;
count++;
}
}
// for style BOND, each of 2 atoms must be in group
if (style == BOND) {
int ivalue = atoi(arg[2]);
if (ivalue < 1 || ivalue > atom->nbondtypes)
error->all("Invalid type in set command");
for (int i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_bond[i]; m++) {
atom1 = atom->map(atom->bond_atom[i][m]);
if (atom1 == -1) error->one("Bond atom missing in set command");
if (mask[i] & groupbit && mask[atom1] & groupbit) {
atom->bond_type[i][m] = ivalue;
count++;
}
}
}
// for style ANGLE, each of 3 atoms must be in group
if (style == ANGLE) {
int ivalue = atoi(arg[2]);
if (ivalue < 1 || ivalue > atom->nangletypes)
error->all("Invalid type in set command");
for (int i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_angle[i]; m++) {
atom1 = atom->map(atom->angle_atom1[i][m]);
atom2 = atom->map(atom->angle_atom2[i][m]);
atom3 = atom->map(atom->angle_atom3[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1)
error->one("Angle atom missing in set command");
if (mask[atom1] & groupbit && mask[atom2] & groupbit &&
mask[atom3] & groupbit) {
atom->angle_type[i][m] = ivalue;
count++;
}
}
}
// for style DIHEDRAL, each of 4 atoms must be in group
if (style == DIHEDRAL) {
int ivalue = atoi(arg[2]);
if (ivalue < 1 || ivalue > atom->ndihedraltypes)
error->all("Invalid type in set command");
for (int i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_dihedral[i]; m++) {
atom1 = atom->map(atom->dihedral_atom1[i][m]);
atom2 = atom->map(atom->dihedral_atom2[i][m]);
atom3 = atom->map(atom->dihedral_atom3[i][m]);
atom4 = atom->map(atom->dihedral_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1)
error->one("Dihedral atom missing in set command");
if (mask[atom1] & groupbit && mask[atom2] & groupbit &&
mask[atom3] & groupbit && mask[atom4] & groupbit) {
atom->dihedral_type[i][m] = ivalue;
count++;
}
}
}
// for style IMPROPER, each of 4 atoms must be in group
if (style == IMPROPER) {
int ivalue = atoi(arg[2]);
if (ivalue < 1 || ivalue > atom->nimpropertypes)
error->all("Invalid type in set command");
for (int i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_improper[i]; m++) {
atom1 = atom->map(atom->improper_atom1[i][m]);
atom2 = atom->map(atom->improper_atom2[i][m]);
atom3 = atom->map(atom->improper_atom3[i][m]);
atom4 = atom->map(atom->improper_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1)
error->one("Improper atom missing in set command");
if (mask[atom1] & groupbit && mask[atom2] & groupbit &&
mask[atom3] & groupbit && mask[atom4] & groupbit) {
atom->improper_type[i][m] = ivalue;
count++;
}
}
}
// for style CHARGE, set charge of all atoms in group
if (style == CHARGE) {
double value = atof(arg[2]);
double *q = atom->q;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
q[i] = value;
count++;
}
}
// for style DIPOLE, create unique random number stream for each proc
// set dipole moment of each atom in group to random orientation
// dipole length is determined by dipole type array
if (style == DIPOLE) {
int ivalue = atoi(arg[2]);
if (ivalue <= 0) error->all("Invalid random number seed in set command");
double msq,scale;
RanPark *random = new RanPark(lmp,ivalue + comm->me);
for (int i = 0; i < WARMUP; i++) random->uniform();
int *type = atom->type;
double *dipole = atom->dipole;
double **mu = atom->mu;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
mu[i][0] = random->uniform() - 0.5;
mu[i][1] = random->uniform() - 0.5;
mu[i][2] = random->uniform() - 0.5;
msq = mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2];
scale = dipole[type[i]]/sqrt(msq);
mu[i][0] *= scale;
mu[i][1] *= scale;
mu[i][2] *= scale;
count++;
}
delete random;
}
// for style ONEATOM, set attribute of single atom ID
if (style == ONEATOM) {
int *tag = atom->tag;
for (int i = 0; i < nlocal; i++)
if (atomid == tag[i]) {
if (strcmp(arg[1],"type") == 0) {
atom->type[i] = atoi(arg[2]);
if (atom->type[i] < 1 || atom->type[i] > atom->ntypes)
error->one("Invalid type in set command");
} else if (strcmp(arg[1],"mol") == 0) atom->molecule[i] = atoi(arg[2]);
else if (strcmp(arg[1],"x") == 0) atom->x[i][0] = atof(arg[2]);
else if (strcmp(arg[1],"y") == 0) atom->x[i][1] = atof(arg[2]);
else if (strcmp(arg[1],"z") == 0) atom->x[i][2] = atof(arg[2]);
else if (strcmp(arg[1],"vx") == 0) atom->v[i][0] = atof(arg[2]);
else if (strcmp(arg[1],"vy") == 0) atom->v[i][1] = atof(arg[2]);
else if (strcmp(arg[1],"vz") == 0) atom->v[i][2] = atof(arg[2]);
else if (strcmp(arg[1],"q") == 0) atom->q[i] = atof(arg[2]);
else error->one("Illegal set command");
count++;
}
}
// statistics
int allcount;
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
if (comm->me == 0) {
if (screen) fprintf(screen," %d settings made\n",allcount);
if (logfile) fprintf(logfile," %d settings made\n",allcount);
}
}

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