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lammps/src/displace_atoms.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 <stdlib.h>
#include <string.h>
#include "displace_atoms.h"
#include "atom.h"
#include "modify.h"
#include "domain.h"
#include "lattice.h"
#include "comm.h"
#include "irregular.h"
#include "group.h"
#include "math_const.h"
#include "random_park.h"
#include "force.h"
#include "input.h"
#include "variable.h"
#include "atom_vec_ellipsoid.h"
#include "atom_vec_line.h"
#include "atom_vec_tri.h"
#include "atom_vec_body.h"
#include "math_extra.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
enum{MOVE,RAMP,RANDOM,ROTATE};
/* ---------------------------------------------------------------------- */
DisplaceAtoms::DisplaceAtoms(LAMMPS *lmp) : Pointers(lmp)
{
mvec = NULL;
}
/* ---------------------------------------------------------------------- */
DisplaceAtoms::~DisplaceAtoms()
{
memory->destroy(mvec);
}
/* ---------------------------------------------------------------------- */
void DisplaceAtoms::command(int narg, char **arg)
{
int i;
if (domain->box_exist == 0)
error->all(FLERR,"Displace_atoms command before simulation box is defined");
if (narg < 2) error->all(FLERR,"Illegal displace_atoms command");
if (modify->nfix_restart_peratom)
error->all(FLERR,"Cannot displace_atoms after "
"reading restart file with per-atom info");
if (comm->me == 0 && screen) fprintf(screen,"Displacing atoms ...\n");
// group and style
igroup = group->find(arg[0]);
if (igroup == -1) error->all(FLERR,"Could not find displace_atoms group ID");
groupbit = group->bitmask[igroup];
if (modify->check_rigid_group_overlap(groupbit))
error->warning(FLERR,"Attempting to displace atoms in rigid bodies");
int style = -1;
if (strcmp(arg[1],"move") == 0) style = MOVE;
else if (strcmp(arg[1],"ramp") == 0) style = RAMP;
else if (strcmp(arg[1],"random") == 0) style = RANDOM;
else if (strcmp(arg[1],"rotate") == 0) style = ROTATE;
else error->all(FLERR,"Illegal displace_atoms command");
// set option defaults
scaleflag = 1;
// read options from end of input line
if (style == MOVE) options(narg-5,&arg[5]);
else if (style == RAMP) options(narg-8,&arg[8]);
else if (style == RANDOM) options(narg-6,&arg[6]);
else if (style == ROTATE) options(narg-9,&arg[9]);
// setup scaling
double xscale,yscale,zscale;
if (scaleflag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
}
else xscale = yscale = zscale = 1.0;
// move atoms by 3-vector or specified variable(s)
if (style == MOVE) {
move(0,arg[2],xscale);
move(1,arg[3],yscale);
move(2,arg[4],zscale);
}
// move atoms in ramped fashion
if (style == RAMP) {
int d_dim;
if (strcmp(arg[2],"x") == 0) d_dim = 0;
else if (strcmp(arg[2],"y") == 0) d_dim = 1;
else if (strcmp(arg[2],"z") == 0) d_dim = 2;
else error->all(FLERR,"Illegal displace_atoms ramp command");
double d_lo,d_hi;
if (d_dim == 0) {
d_lo = xscale*force->numeric(FLERR,arg[3]);
d_hi = xscale*force->numeric(FLERR,arg[4]);
} else if (d_dim == 1) {
d_lo = yscale*force->numeric(FLERR,arg[3]);
d_hi = yscale*force->numeric(FLERR,arg[4]);
} else if (d_dim == 2) {
d_lo = zscale*force->numeric(FLERR,arg[3]);
d_hi = zscale*force->numeric(FLERR,arg[4]);
}
int coord_dim;
if (strcmp(arg[5],"x") == 0) coord_dim = 0;
else if (strcmp(arg[5],"y") == 0) coord_dim = 1;
else if (strcmp(arg[5],"z") == 0) coord_dim = 2;
else error->all(FLERR,"Illegal displace_atoms ramp command");
double coord_lo,coord_hi;
if (coord_dim == 0) {
coord_lo = xscale*force->numeric(FLERR,arg[6]);
coord_hi = xscale*force->numeric(FLERR,arg[7]);
} else if (coord_dim == 1) {
coord_lo = yscale*force->numeric(FLERR,arg[6]);
coord_hi = yscale*force->numeric(FLERR,arg[7]);
} else if (coord_dim == 2) {
coord_lo = zscale*force->numeric(FLERR,arg[6]);
coord_hi = zscale*force->numeric(FLERR,arg[7]);
}
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double fraction,dramp;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
fraction = (x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
fraction = MAX(fraction,0.0);
fraction = MIN(fraction,1.0);
dramp = d_lo + fraction*(d_hi - d_lo);
x[i][d_dim] += dramp;
}
}
}
// move atoms randomly
// makes atom result independent of what proc owns it via random->reset()
if (style == RANDOM) {
RanPark *random = new RanPark(lmp,1);
double dx = xscale*force->numeric(FLERR,arg[2]);
double dy = yscale*force->numeric(FLERR,arg[3]);
double dz = zscale*force->numeric(FLERR,arg[4]);
int seed = force->inumeric(FLERR,arg[5]);
if (seed <= 0) error->all(FLERR,"Illegal displace_atoms random command");
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
random->reset(seed,x[i]);
x[i][0] += dx * 2.0*(random->uniform()-0.5);
x[i][1] += dy * 2.0*(random->uniform()-0.5);
x[i][2] += dz * 2.0*(random->uniform()-0.5);
}
}
delete random;
}
// rotate atoms by right-hand rule by theta around R
// P = point = vector = point of rotation
// R = vector = axis of rotation
// R0 = runit = unit vector for R
// D = X - P = vector from P to X
// C = (D dot R0) R0 = projection of atom coord onto R line
// A = D - C = vector from R line to X
// B = R0 cross A = vector perp to A in plane of rotation
// A,B define plane of circular rotation around R line
// X = P + C + A cos(theta) + B sin(theta)
if (style == ROTATE) {
double theta_new;
double axis[3],point[3],qrotate[4],qnew[4];
double a[3],b[3],c[3],d[3],disp[3],runit[3];
double *quat;
int dim = domain->dimension;
point[0] = xscale*force->numeric(FLERR,arg[2]);
point[1] = yscale*force->numeric(FLERR,arg[3]);
point[2] = zscale*force->numeric(FLERR,arg[4]);
axis[0] = force->numeric(FLERR,arg[5]);
axis[1] = force->numeric(FLERR,arg[6]);
axis[2] = force->numeric(FLERR,arg[7]);
double theta = force->numeric(FLERR,arg[8]);
if (dim == 2 && (axis[0] != 0.0 || axis[1] != 0.0))
error->all(FLERR,"Invalid displace_atoms rotate axis for 2d");
double len = sqrt(axis[0]*axis[0] + axis[1]*axis[1] + axis[2]*axis[2]);
if (len == 0.0)
error->all(FLERR,"Zero length rotation vector with displace_atoms");
runit[0] = axis[0]/len;
runit[1] = axis[1]/len;
runit[2] = axis[2]/len;
double angle = MY_PI*theta/180.0;
double cosine = cos(angle);
double sine = sin(angle);
double qcosine = cos(0.5*angle);
double qsine = sin(0.5*angle);
qrotate[0] = qcosine;
qrotate[1] = runit[0]*qsine;
qrotate[2] = runit[1]*qsine;
qrotate[3] = runit[2]*qsine;
double ddotr;
// flags for additional orientation info stored by some atom styles
int ellipsoid_flag = atom->ellipsoid_flag;
int line_flag = atom->line_flag;
int tri_flag = atom->tri_flag;
int body_flag = atom->body_flag;
int theta_flag = 0;
int quat_flag = 0;
if (line_flag) theta_flag = 1;
if (ellipsoid_flag || tri_flag || body_flag) quat_flag = 1;
// AtomVec pointers to retrieve per-atom storage of extra quantities
AtomVecEllipsoid *avec_ellipsoid =
(AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecLine *avec_line = (AtomVecLine *) atom->style_match("line");
AtomVecTri *avec_tri = (AtomVecTri *) atom->style_match("tri");
AtomVecBody *avec_body = (AtomVecBody *) atom->style_match("body");
double **x = atom->x;
int *ellipsoid = atom->ellipsoid;
int *line = atom->line;
int *tri = atom->tri;
int *body = atom->body;
int *mask = atom->mask;
int nlocal = atom->nlocal;
imageint *image = atom->image;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
// unwrap coordinate and reset image flags accordingly
domain->unmap(x[i],image[i]);
image[i] = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
d[0] = x[i][0] - point[0];
d[1] = x[i][1] - point[1];
d[2] = x[i][2] - point[2];
ddotr = d[0]*runit[0] + d[1]*runit[1] + d[2]*runit[2];
c[0] = ddotr*runit[0];
c[1] = ddotr*runit[1];
c[2] = ddotr*runit[2];
a[0] = d[0] - c[0];
a[1] = d[1] - c[1];
a[2] = d[2] - c[2];
b[0] = runit[1]*a[2] - runit[2]*a[1];
b[1] = runit[2]*a[0] - runit[0]*a[2];
b[2] = runit[0]*a[1] - runit[1]*a[0];
disp[0] = a[0]*cosine + b[0]*sine;
disp[1] = a[1]*cosine + b[1]*sine;
disp[2] = a[2]*cosine + b[2]*sine;
x[i][0] = point[0] + c[0] + disp[0];
x[i][1] = point[1] + c[1] + disp[1];
if (dim == 3) x[i][2] = point[2] + c[2] + disp[2];
// theta for lines
if (theta_flag && line[i] >= 0.0) {
theta_new = fmod(avec_line->bonus[line[i]].theta+angle,MY_2PI);
avec_line->bonus[atom->line[i]].theta = theta_new;
}
// quats for ellipsoids, tris, and bodies
if (quat_flag) {
quat = NULL;
if (ellipsoid_flag && ellipsoid[i] >= 0)
quat = avec_ellipsoid->bonus[ellipsoid[i]].quat;
else if (tri_flag && tri[i] >= 0)
quat = avec_tri->bonus[tri[i]].quat;
else if (body_flag && body[i] >= 0)
quat = avec_body->bonus[body[i]].quat;
if (quat) {
MathExtra::quatquat(qrotate,quat,qnew);
quat[0] = qnew[0];
quat[1] = qnew[1];
quat[2] = qnew[2];
quat[3] = qnew[3];
}
}
}
}
}
// move atoms back inside simulation box and to new processors
// use remap() instead of pbc() in case atoms moved a long distance
// use irregular() in case atoms moved a long distance
double **x = atom->x;
imageint *image = atom->image;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) domain->remap(x[i],image[i]);
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->reset_box();
Irregular *irregular = new Irregular(lmp);
irregular->migrate_atoms(1);
delete irregular;
if (domain->triclinic) domain->lamda2x(atom->nlocal);
// check if any atoms were lost
bigint natoms;
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (natoms != atom->natoms && comm->me == 0) {
char str[128];
sprintf(str,"Lost atoms via displace_atoms: original " BIGINT_FORMAT
" current " BIGINT_FORMAT,atom->natoms,natoms);
error->warning(FLERR,str);
}
}
/* ----------------------------------------------------------------------
move atoms either by specified numeric displacement or variable evaluation
------------------------------------------------------------------------- */
void DisplaceAtoms::move(int idim, char *arg, double scale)
{
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (strstr(arg,"v_") != arg) {
double delta = scale*force->numeric(FLERR,arg);
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) x[i][idim] += delta;
} else {
int ivar = input->variable->find(arg+2);
if (ivar < 0)
error->all(FLERR,"Variable name for displace_atoms does not exist");
if (input->variable->equalstyle(ivar)) {
double delta = scale * input->variable->compute_equal(ivar);
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) x[i][idim] += delta;
} else if (input->variable->atomstyle(ivar)) {
if (mvec == NULL) memory->create(mvec,nlocal,"displace_atoms:mvec");
input->variable->compute_atom(ivar,igroup,mvec,1,0);
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) x[i][idim] += scale*mvec[i];
} else error->all(FLERR,"Variable for displace_atoms is invalid style");
}
}
/* ----------------------------------------------------------------------
parse optional parameters at end of displace_atoms input line
------------------------------------------------------------------------- */
void DisplaceAtoms::options(int narg, char **arg)
{
if (narg < 0) error->all(FLERR,"Illegal displace_atoms command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal displace_atoms command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
else error->all(FLERR,"Illegal displace_atoms command");
iarg += 2;
} else error->all(FLERR,"Illegal displace_atoms command");
}
}
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