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fix_efield.cpp
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Fri, May 24, 10:41

fix_efield.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Christina Payne (Vanderbilt U)
Stan Moore (Sandia) for dipole terms
------------------------------------------------------------------------- */
#include <math.h>
#include <string.h>
#include <stdlib.h>
#include "fix_efield.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "comm.h"
#include "modify.h"
#include "force.h"
#include "respa.h"
#include "input.h"
#include "variable.h"
#include "region.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{NONE,CONSTANT,EQUAL,ATOM};
/* ---------------------------------------------------------------------- */
FixEfield::FixEfield(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), xstr(NULL), ystr(NULL), zstr(NULL),
estr(NULL), idregion(NULL), efield(NULL)
{
if (narg < 6) error->all(FLERR,"Illegal fix efield command");
dynamic_group_allow = 1;
vector_flag = 1;
scalar_flag = 1;
size_vector = 3;
global_freq = 1;
extvector = 1;
extscalar = 1;
respa_level_support = 1;
ilevel_respa = 0;
virial_flag = 1;
qe2f = force->qe2f;
xstr = ystr = zstr = NULL;
if (strstr(arg[3],"v_") == arg[3]) {
int n = strlen(&arg[3][2]) + 1;
xstr = new char[n];
strcpy(xstr,&arg[3][2]);
} else {
ex = qe2f * force->numeric(FLERR,arg[3]);
xstyle = CONSTANT;
}
if (strstr(arg[4],"v_") == arg[4]) {
int n = strlen(&arg[4][2]) + 1;
ystr = new char[n];
strcpy(ystr,&arg[4][2]);
} else {
ey = qe2f * force->numeric(FLERR,arg[4]);
ystyle = CONSTANT;
}
if (strstr(arg[5],"v_") == arg[5]) {
int n = strlen(&arg[5][2]) + 1;
zstr = new char[n];
strcpy(zstr,&arg[5][2]);
} else {
ez = qe2f * force->numeric(FLERR,arg[5]);
zstyle = CONSTANT;
}
// optional args
iregion = -1;
idregion = NULL;
estr = NULL;
int iarg = 6;
while (iarg < narg) {
if (strcmp(arg[iarg],"region") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix efield command");
iregion = domain->find_region(arg[iarg+1]);
if (iregion == -1)
error->all(FLERR,"Region ID for fix efield does not exist");
int n = strlen(arg[iarg+1]) + 1;
idregion = new char[n];
strcpy(idregion,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"energy") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix efield command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
int n = strlen(&arg[iarg+1][2]) + 1;
estr = new char[n];
strcpy(estr,&arg[iarg+1][2]);
} else error->all(FLERR,"Illegal fix efield command");
iarg += 2;
} else error->all(FLERR,"Illegal fix efield command");
}
force_flag = 0;
fsum[0] = fsum[1] = fsum[2] = fsum[3] = 0.0;
maxatom = atom->nmax;
memory->create(efield,maxatom,4,"efield:efield");
}
/* ---------------------------------------------------------------------- */
FixEfield::~FixEfield()
{
delete [] xstr;
delete [] ystr;
delete [] zstr;
delete [] estr;
delete [] idregion;
memory->destroy(efield);
}
/* ---------------------------------------------------------------------- */
int FixEfield::setmask()
{
int mask = 0;
mask |= THERMO_ENERGY;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
mask |= MIN_POST_FORCE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixEfield::init()
{
qflag = muflag = 0;
if (atom->q_flag) qflag = 1;
if (atom->mu_flag && atom->torque_flag) muflag = 1;
if (!qflag && !muflag)
error->all(FLERR,"Fix efield requires atom attribute q or mu");
// check variables
if (xstr) {
xvar = input->variable->find(xstr);
if (xvar < 0)
error->all(FLERR,"Variable name for fix efield does not exist");
if (input->variable->equalstyle(xvar)) xstyle = EQUAL;
else if (input->variable->atomstyle(xvar)) xstyle = ATOM;
else error->all(FLERR,"Variable for fix efield is invalid style");
}
if (ystr) {
yvar = input->variable->find(ystr);
if (yvar < 0)
error->all(FLERR,"Variable name for fix efield does not exist");
if (input->variable->equalstyle(yvar)) ystyle = EQUAL;
else if (input->variable->atomstyle(yvar)) ystyle = ATOM;
else error->all(FLERR,"Variable for fix efield is invalid style");
}
if (zstr) {
zvar = input->variable->find(zstr);
if (zvar < 0)
error->all(FLERR,"Variable name for fix efield does not exist");
if (input->variable->equalstyle(zvar)) zstyle = EQUAL;
else if (input->variable->atomstyle(zvar)) zstyle = ATOM;
else error->all(FLERR,"Variable for fix efield is invalid style");
}
if (estr) {
evar = input->variable->find(estr);
if (evar < 0)
error->all(FLERR,"Variable name for fix efield does not exist");
if (input->variable->atomstyle(evar)) estyle = ATOM;
else error->all(FLERR,"Variable for fix efield is invalid style");
} else estyle = NONE;
// set index and check validity of region
if (iregion >= 0) {
iregion = domain->find_region(idregion);
if (iregion == -1)
error->all(FLERR,"Region ID for fix aveforce does not exist");
}
if (xstyle == ATOM || ystyle == ATOM || zstyle == ATOM)
varflag = ATOM;
else if (xstyle == EQUAL || ystyle == EQUAL || zstyle == EQUAL)
varflag = EQUAL;
else varflag = CONSTANT;
if (muflag && varflag == ATOM)
error->all(FLERR,"Fix efield with dipoles cannot use atom-style variables");
if (muflag && update->whichflag == 2 && comm->me == 0)
error->warning(FLERR,
"The minimizer does not re-orient dipoles "
"when using fix efield");
if (varflag == CONSTANT && estyle != NONE)
error->all(FLERR,"Cannot use variable energy with "
"constant efield in fix efield");
if ((varflag == EQUAL || varflag == ATOM) &&
update->whichflag == 2 && estyle == NONE)
error->all(FLERR,"Must use variable energy with fix efield");
if (strstr(update->integrate_style,"respa")) {
ilevel_respa = ((Respa *) update->integrate)->nlevels-1;
if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa);
}
}
/* ---------------------------------------------------------------------- */
void FixEfield::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(ilevel_respa);
post_force_respa(vflag,ilevel_respa,0);
((Respa *) update->integrate)->copy_f_flevel(ilevel_respa);
}
}
/* ---------------------------------------------------------------------- */
void FixEfield::min_setup(int vflag)
{
post_force(vflag);
}
/* ----------------------------------------------------------------------
apply F = qE
------------------------------------------------------------------------- */
void FixEfield::post_force(int vflag)
{
double **f = atom->f;
double *q = atom->q;
int *mask = atom->mask;
imageint *image = atom->image;
int nlocal = atom->nlocal;
// energy and virial setup
if (vflag) v_setup(vflag);
else evflag = 0;
// reallocate efield array if necessary
if (varflag == ATOM && atom->nmax > maxatom) {
maxatom = atom->nmax;
memory->destroy(efield);
memory->create(efield,maxatom,4,"efield:efield");
}
// update region if necessary
Region *region = NULL;
if (iregion >= 0) {
region = domain->regions[iregion];
region->prematch();
}
// fsum[0] = "potential energy" for added force
// fsum[123] = extra force added to atoms
fsum[0] = fsum[1] = fsum[2] = fsum[3] = 0.0;
force_flag = 0;
double **x = atom->x;
double fx,fy,fz;
double v[6];
// constant efield
if (varflag == CONSTANT) {
double unwrap[3];
// charge interactions
// force = qE, potential energy = F dot x in unwrapped coords
if (qflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;
fx = q[i]*ex;
fy = q[i]*ey;
fz = q[i]*ez;
f[i][0] += fx;
f[i][1] += fy;
f[i][2] += fz;
domain->unmap(x[i],image[i],unwrap);
fsum[0] -= fx*unwrap[0]+fy*unwrap[1]+fz*unwrap[2];
fsum[1] += fx;
fsum[2] += fy;
fsum[3] += fz;
if (evflag) {
v[0] = fx*unwrap[0];
v[1] = fy*unwrap[1];
v[2] = fz*unwrap[2];
v[3] = fx*unwrap[1];
v[4] = fx*unwrap[2];
v[5] = fy*unwrap[2];
v_tally(i, v);
}
}
}
// dipole interactions
// no force, torque = mu cross E, potential energy = -mu dot E
if (muflag) {
double **mu = atom->mu;
double **t = atom->torque;
double tx,ty,tz;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;
tx = ez*mu[i][1] - ey*mu[i][2];
ty = ex*mu[i][2] - ez*mu[i][0];
tz = ey*mu[i][0] - ex*mu[i][1];
t[i][0] += tx;
t[i][1] += ty;
t[i][2] += tz;
fsum[0] -= mu[i][0]*ex + mu[i][1]*ey + mu[i][2]*ez;
}
}
// variable efield, wrap with clear/add
// potential energy = evar if defined, else 0.0
} else {
modify->clearstep_compute();
if (xstyle == EQUAL) ex = qe2f * input->variable->compute_equal(xvar);
else if (xstyle == ATOM)
input->variable->compute_atom(xvar,igroup,&efield[0][0],4,0);
if (ystyle == EQUAL) ey = qe2f * input->variable->compute_equal(yvar);
else if (ystyle == ATOM)
input->variable->compute_atom(yvar,igroup,&efield[0][1],4,0);
if (zstyle == EQUAL) ez = qe2f * input->variable->compute_equal(zvar);
else if (zstyle == ATOM)
input->variable->compute_atom(zvar,igroup,&efield[0][2],4,0);
if (estyle == ATOM)
input->variable->compute_atom(evar,igroup,&efield[0][3],4,0);
modify->addstep_compute(update->ntimestep + 1);
// charge interactions
// force = qE
if (qflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;
if (xstyle == ATOM) fx = qe2f * q[i]*efield[i][0];
else fx = q[i]*ex;
f[i][0] += fx;
fsum[1] += fx;
if (ystyle == ATOM) fy = qe2f * q[i]*efield[i][1];
else fy = q[i]*ey;
f[i][1] += fy;
fsum[2] += fy;
if (zstyle == ATOM) fz = qe2f * q[i]*efield[i][2];
else fz = q[i]*ez;
f[i][2] += fz;
fsum[3] += fz;
if (estyle == ATOM) fsum[0] += efield[0][3];
}
}
// dipole interactions
// no force, torque = mu cross E
if (muflag) {
double **mu = atom->mu;
double **t = atom->torque;
double tx,ty,tz;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;
tx = ez*mu[i][1] - ey*mu[i][2];
ty = ex*mu[i][2] - ez*mu[i][0];
tz = ey*mu[i][0] - ex*mu[i][1];
t[i][0] += tx;
t[i][1] += ty;
t[i][2] += tz;
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixEfield::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixEfield::min_post_force(int vflag)
{
post_force(vflag);
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double FixEfield::memory_usage()
{
double bytes = 0.0;
if (varflag == ATOM) bytes = atom->nmax*4 * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
return energy added by fix
------------------------------------------------------------------------- */
double FixEfield::compute_scalar(void)
{
if (force_flag == 0) {
MPI_Allreduce(fsum,fsum_all,4,MPI_DOUBLE,MPI_SUM,world);
force_flag = 1;
}
return fsum_all[0];
}
/* ----------------------------------------------------------------------
return total extra force due to fix
------------------------------------------------------------------------- */
double FixEfield::compute_vector(int n)
{
if (force_flag == 0) {
MPI_Allreduce(fsum,fsum_all,4,MPI_DOUBLE,MPI_SUM,world);
force_flag = 1;
}
return fsum_all[n+1];
}

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