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lammps/src/set.cpp
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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 "region.h"
#include "group.h"
#include "comm.h"
#include "neighbor.h"
#include "force.h"
#include "pair.h"
#include "random_park.h"
#include "math_extra.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{ATOM,GROUP,REGION};
enum{TYPE,TYPE_FRACTION,MOLECULE,
X,Y,Z,CHARGE,
DIPOLE,DIPOLE_RANDOM,QUAT,QUAT_RANDOM,
DIAMETER,DENSITY,VOLUME,IMAGE,
BOND,ANGLE,DIHEDRAL,IMPROPER};
/* ---------------------------------------------------------------------- */
Set::Set(LAMMPS *lmp) : Pointers(lmp)
{
PI = 4.0*atan(1.0);
}
/* ---------------------------------------------------------------------- */
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");
// style and ID
if (strcmp(arg[0],"atom") == 0) style = ATOM;
else if (strcmp(arg[0],"group") == 0) style = GROUP;
else if (strcmp(arg[0],"region") == 0) style = REGION;
else error->all("Illegal set command");
int n = strlen(arg[1]) + 1;
id = new char[n];
strcpy(id,arg[1]);
select = NULL;
// loop over keyword/value pairs
// call appropriate routine to reset attributes
if (comm->me == 0 && screen) fprintf(screen,"Setting atom values ...\n");
int allcount,origarg;
int iarg = 2;
while (iarg < narg) {
count = 0;
origarg = iarg;
if (strcmp(arg[iarg],"type") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (ivalue <= 0 || ivalue > atom->ntypes)
error->all("Invalid value in set command");
set(TYPE);
iarg += 2;
} else if (strcmp(arg[iarg],"type/fraction") == 0) {
if (iarg+4 > narg) error->all("Illegal set command");
newtype = atoi(arg[iarg+1]);
fraction = atof(arg[iarg+2]);
ivalue = atoi(arg[iarg+3]);
if (fraction < 0.0 || fraction > 1.0)
error->all("Invalid value in set command");
if (ivalue <= 0) error->all("Invalid random number seed in set command");
setrandom(TYPE_FRACTION);
iarg += 4;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (!atom->molecule_flag)
error->all("Cannot set this attribute for this atom style");
set(MOLECULE);
iarg += 2;
} else if (strcmp(arg[iarg],"x") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
dvalue = atof(arg[iarg+1]);
set(X);
iarg += 2;
} else if (strcmp(arg[iarg],"y") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
dvalue = atof(arg[iarg+1]);
set(Y);
iarg += 2;
} else if (strcmp(arg[iarg],"z") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
dvalue = atof(arg[iarg+1]);
set(Z);
iarg += 2;
} else if (strcmp(arg[iarg],"charge") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->q_flag)
error->all("Cannot set this attribute for this atom style");
set(CHARGE);
iarg += 2;
} else if (strcmp(arg[iarg],"dipole") == 0) {
if (iarg+4 > narg) error->all("Illegal set command");
xvalue = atof(arg[iarg+1]);
yvalue = atof(arg[iarg+2]);
zvalue = atof(arg[iarg+3]);
if (!atom->mu_flag || atom->dipole == NULL)
error->all("Cannot set this attribute for this atom style");
set(DIPOLE);
iarg += 4;
} else if (strcmp(arg[iarg],"dipole/random") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (!atom->mu_flag || atom->shape == NULL)
error->all("Cannot set this attribute for this atom style");
if (ivalue <= 0) error->all("Invalid random number seed in set command");
setrandom(DIPOLE_RANDOM);
iarg += 2;
} else if (strcmp(arg[iarg],"quat") == 0) {
if (iarg+5 > narg) error->all("Illegal set command");
xvalue = atof(arg[iarg+1]);
yvalue = atof(arg[iarg+2]);
zvalue = atof(arg[iarg+3]);
wvalue = atof(arg[iarg+4]);
if (!atom->quat_flag)
error->all("Cannot set this attribute for this atom style");
set(QUAT);
iarg += 5;
} else if (strcmp(arg[iarg],"quat/random") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (!atom->quat_flag)
error->all("Cannot set this attribute for this atom style");
if (ivalue <= 0) error->all("Invalid random number seed in set command");
setrandom(QUAT_RANDOM);
iarg += 2;
} else if (strcmp(arg[iarg],"diameter") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->radius_flag)
error->all("Cannot set this attribute for this atom style");
set(DIAMETER);
iarg += 2;
} else if (strcmp(arg[iarg],"density") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->density_flag)
error->all("Cannot set this attribute for this atom style");
set(DENSITY);
iarg += 2;
} else if (strcmp(arg[iarg],"volume") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->vfrac_flag)
error->all("Cannot set this attribute for this atom style");
set(VOLUME);
iarg += 2;
} else if (strcmp(arg[iarg],"image") == 0) {
if (iarg+4 > narg) error->all("Illegal set command");
ximageflag = yimageflag = zimageflag = 0;
if (strcmp(arg[iarg+1],"NULL") != 0) {
ximageflag = 1;
ximage = atoi(arg[iarg+1]);
}
if (strcmp(arg[iarg+2],"NULL") != 0) {
yimageflag = 1;
yimage = atoi(arg[iarg+2]);
}
if (strcmp(arg[iarg+3],"NULL") != 0) {
zimageflag = 1;
zimage = atoi(arg[iarg+3]);
}
if (ximageflag && ximage && !domain->xperiodic)
error->all("Cannot set non-zero image flag for non-periodic dimension");
if (yimageflag && yimage && !domain->yperiodic)
error->all("Cannot set non-zero image flag for non-periodic dimension");
if (zimageflag && zimage && !domain->zperiodic)
error->all("Cannot set non-zero image flag for non-periodic dimension");
set(IMAGE);
iarg += 4;
} else if (strcmp(arg[iarg],"bond") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (atom->avec->bonds_allow == 0)
error->all("Cannot set this attribute for this atom style");
if (ivalue <= 0 || ivalue > atom->nbondtypes)
error->all("Invalid value in set command");
topology(BOND);
iarg += 2;
} else if (strcmp(arg[iarg],"angle") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (atom->avec->angles_allow == 0)
error->all("Cannot set this attribute for this atom style");
if (ivalue <= 0 || ivalue > atom->nangletypes)
error->all("Invalid value in set command");
topology(ANGLE);
iarg += 2;
} else if (strcmp(arg[iarg],"dihedral") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (atom->avec->dihedrals_allow == 0)
error->all("Cannot set this attribute for this atom style");
if (ivalue <= 0 || ivalue > atom->ndihedraltypes)
error->all("Invalid value in set command");
topology(DIHEDRAL);
iarg += 2;
} else if (strcmp(arg[iarg],"improper") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (atom->avec->impropers_allow == 0)
error->all("Cannot set this attribute for this atom style");
if (ivalue <= 0 || ivalue > atom->nimpropertypes)
error->all("Invalid value in set command");
topology(IMPROPER);
iarg += 2;
} else error->all("Illegal set command");
// statistics
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
if (comm->me == 0) {
if (screen) fprintf(screen," %d settings made for %s\n",
allcount,arg[origarg]);
if (logfile) fprintf(logfile," %d settings made for %s\n",
allcount,arg[origarg]);
}
}
// free local memory
delete [] id;
delete [] select;
}
/* ----------------------------------------------------------------------
select atoms according to ATOM, GROUP, REGION style
n = nlocal or nlocal+nghost depending on keyword
------------------------------------------------------------------------- */
void Set::selection(int n)
{
delete [] select;
select = new int[n];
if (style == ATOM) {
if (atom->tag_enable == 0)
error->all("Cannot use set atom with no atom IDs defined");
int idatom = atoi(id);
int *tag = atom->tag;
for (int i = 0; i < n; i++)
if (idatom == tag[i]) select[i] = 1;
else select[i] = 0;
} else if (style == GROUP) {
int igroup = group->find(id);
if (igroup == -1) error->all("Could not find set group ID");
int groupbit = group->bitmask[igroup];
int *mask = atom->mask;
for (int i = 0; i < n; i++)
if (mask[i] & groupbit) select[i] = 1;
else select[i] = 0;
} else {
int iregion = domain->find_region(id);
if (iregion == -1) error->all("Set region ID does not exist");
double **x = atom->x;
for (int i = 0; i < n; i++)
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
select[i] = 1;
else select[i] = 0;
}
}
/* ----------------------------------------------------------------------
set an owned atom property directly
------------------------------------------------------------------------- */
void Set::set(int keyword)
{
if (keyword == DIPOLE) atom->check_dipole();
selection(atom->nlocal);
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (select[i]) {
if (keyword == TYPE) atom->type[i] = ivalue;
else if (keyword == MOLECULE) atom->molecule[i] = ivalue;
else if (keyword == X) atom->x[i][0] = dvalue;
else if (keyword == Y) atom->x[i][1] = dvalue;
else if (keyword == Z) atom->x[i][2] = dvalue;
else if (keyword == CHARGE) atom->q[i] = dvalue;
// set radius from diameter
// set rmass if both rmass and density are defined
else if (keyword == DIAMETER) {
atom->radius[i] = 0.5 * dvalue;
if (atom->rmass_flag && atom->density_flag)
atom->rmass[i] = 4.0*PI/3.0 *
atom->radius[i]*atom->radius[i]*atom->radius[i] * atom->density[i];
// set density
// set rmass (granular) if both rmass and radius are defined
// set rmass (peri) if both rmass and vfrac are defined
} else if (keyword == DENSITY) {
atom->density[i] = dvalue;
if (atom->rmass_flag && atom->radius_flag)
atom->rmass[i] = 4.0*PI/3.0 *
atom->radius[i]*atom->radius[i]*atom->radius[i] *
atom->density[i];
else if (atom->rmass_flag && atom->vfrac_flag)
atom->rmass[i] = dvalue;
} else if (keyword == VOLUME) atom->vfrac[i] = dvalue;
// reset any or all of 3 image flags
else if (keyword == IMAGE) {
int xbox = (atom->image[i] & 1023) - 512;
int ybox = (atom->image[i] >> 10 & 1023) - 512;
int zbox = (atom->image[i] >> 20) - 512;
if (ximageflag) xbox = ximage;
if (yimageflag) ybox = yimage;
if (zimageflag) zbox = zimage;
atom->image[i] = ((zbox + 512 & 1023) << 20) |
((ybox + 512 & 1023) << 10) | (xbox + 512 & 1023);
} else if (keyword == DIPOLE) {
if (atom->dipole[atom->type[i]] > 0.0) {
double **mu = atom->mu;
mu[i][0] = xvalue;
mu[i][1] = yvalue;
mu[i][2] = zvalue;
double lensq =
mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2];
double scale = atom->dipole[atom->type[i]]/sqrt(lensq);
mu[i][0] *= scale;
mu[i][1] *= scale;
mu[i][2] *= scale;
}
} else if (keyword == QUAT) {
double PI = 4.0*atan(1.0);
double theta2 = 0.5 * PI * wvalue/180.0;
double sintheta2 = sin(theta2);
double **quat = atom->quat;
quat[i][0] = cos(theta2);
quat[i][1] = xvalue * sintheta2;
quat[i][2] = yvalue * sintheta2;
quat[i][3] = zvalue * sintheta2;
MathExtra::normalize4(quat[i]);
}
count++;
}
}
/* ----------------------------------------------------------------------
set an owned atom property randomly
set seed based on atom tag
make atom result independent of what proc owns it
------------------------------------------------------------------------- */
void Set::setrandom(int keyword)
{
int i;
if (keyword == DIPOLE_RANDOM) atom->check_dipole();
selection(atom->nlocal);
RanPark *random = new RanPark(lmp,1);
double **x = atom->x;
int seed = ivalue;
// set fraction of atom types to newtype
if (keyword == TYPE_FRACTION) {
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (select[i]) {
random->reset(seed,x[i]);
if (random->uniform() > fraction) continue;
atom->type[i] = newtype;
count++;
}
// set dipole moments to random orientations in 3d or 2d
// dipole length is determined by dipole type array
} else if (keyword == DIPOLE_RANDOM) {
int *type = atom->type;
double *dipole = atom->dipole;
double **mu = atom->mu;
int nlocal = atom->nlocal;
double msq,scale;
if (domain->dimension == 3) {
for (i = 0; i < nlocal; i++)
if (select[i]) {
if (dipole[type[i]] > 0.0) {
random->reset(seed,x[i]);
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++;
}
}
} else {
for (i = 0; i < nlocal; i++)
if (select[i]) {
if (dipole[type[i]] > 0.0) {
random->reset(seed,x[i]);
mu[i][0] = random->uniform() - 0.5;
mu[i][1] = random->uniform() - 0.5;
mu[i][2] = 0.0;
msq = mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1];
scale = dipole[type[i]]/sqrt(msq);
mu[i][0] *= scale;
mu[i][1] *= scale;
count++;
}
}
}
// set quaternions to random orientations in 3d or 2d
// no need to normalize quats since creations algorithms already do
} else if (keyword == QUAT_RANDOM) {
double **quat = atom->quat;
int nlocal = atom->nlocal;
if (domain->dimension == 3) {
double s,t1,t2,theta1,theta2;
double PI = 4.0*atan(1.0);
for (i = 0; i < nlocal; i++)
if (select[i]) {
random->reset(seed,x[i]);
s = random->uniform();
t1 = sqrt(1.0-s);
t2 = sqrt(s);
theta1 = 2.0*PI*random->uniform();
theta2 = 2.0*PI*random->uniform();
quat[i][0] = cos(theta2)*t2;
quat[i][1] = sin(theta1)*t1;
quat[i][2] = cos(theta1)*t1;
quat[i][3] = sin(theta2)*t2;
count++;
}
} else {
double theta2;
double PI = 4.0*atan(1.0);
for (i = 0; i < nlocal; i++)
if (select[i]) {
random->reset(seed,x[i]);
theta2 = PI*random->uniform();
quat[i][0] = cos(theta2);
quat[i][1] = 0.0;
quat[i][2] = 0.0;
quat[i][3] = sin(theta2);
count++;
}
}
}
delete random;
}
/* ---------------------------------------------------------------------- */
void Set::topology(int keyword)
{
int m,atom1,atom2,atom3,atom4;
// border swap to acquire ghost atom info
// 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 (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);
// select both owned and ghost atoms
selection(atom->nlocal + atom->nghost);
// for BOND, each of 2 atoms must be in group
if (keyword == BOND) {
int nlocal = atom->nlocal;
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 (select[i] && select[atom1]) {
atom->bond_type[i][m] = ivalue;
count++;
}
}
}
// for ANGLE, each of 3 atoms must be in group
if (keyword == ANGLE) {
int nlocal = atom->nlocal;
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 (select[atom1] && select[atom2] && select[atom3]) {
atom->angle_type[i][m] = ivalue;
count++;
}
}
}
// for DIHEDRAL, each of 4 atoms must be in group
if (keyword == DIHEDRAL) {
int nlocal = atom->nlocal;
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 (select[atom1] && select[atom2] && select[atom3] && select[atom4]) {
atom->dihedral_type[i][m] = ivalue;
count++;
}
}
}
// for IMPROPER, each of 4 atoms must be in group
if (keyword == IMPROPER) {
int nlocal = atom->nlocal;
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 (select[atom1] && select[atom2] && select[atom3] && select[atom4]) {
atom->improper_type[i][m] = ivalue;
count++;
}
}
}
}
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