git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10366 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -1,406 +0,0 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
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 "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)
|
||||
{
|
||||
if (narg != 6) error->all(FLERR,"Illegal fix efield command");
|
||||
|
||||
vector_flag = 1;
|
||||
scalar_flag = 1;
|
||||
size_vector = 3;
|
||||
global_freq = 1;
|
||||
extvector = 1;
|
||||
extscalar = 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
|
||||
|
||||
estr = NULL;
|
||||
|
||||
int iarg = 6;
|
||||
while (iarg < narg) {
|
||||
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 = 0;
|
||||
efield = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixEfield::~FixEfield()
|
||||
{
|
||||
delete [] xstr;
|
||||
delete [] ystr;
|
||||
delete [] zstr;
|
||||
delete [] estr;
|
||||
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;
|
||||
|
||||
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"))
|
||||
nlevels_respa = ((Respa *) update->integrate)->nlevels;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixEfield::setup(int vflag)
|
||||
{
|
||||
if (strstr(update->integrate_style,"verlet"))
|
||||
post_force(vflag);
|
||||
else {
|
||||
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
|
||||
post_force_respa(vflag,nlevels_respa-1,0);
|
||||
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
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;
|
||||
tagint *image = atom->image;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
// reallocate efield array if necessary
|
||||
|
||||
if (varflag == ATOM && nlocal > maxatom) {
|
||||
maxatom = atom->nmax;
|
||||
memory->destroy(efield);
|
||||
memory->create(efield,maxatom,4,"efield:efield");
|
||||
}
|
||||
|
||||
// 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;
|
||||
|
||||
// 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) {
|
||||
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;
|
||||
}
|
||||
}
|
||||
|
||||
// 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) {
|
||||
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 && efield)
|
||||
input->variable->compute_atom(xvar,igroup,&efield[0][0],3,0);
|
||||
if (ystyle == EQUAL) ey = qe2f * input->variable->compute_equal(yvar);
|
||||
else if (ystyle == ATOM && efield)
|
||||
input->variable->compute_atom(yvar,igroup,&efield[0][1],3,0);
|
||||
if (zstyle == EQUAL) ez = qe2f * input->variable->compute_equal(zvar);
|
||||
else if (zstyle == ATOM && efield)
|
||||
input->variable->compute_atom(zvar,igroup,&efield[0][2],3,0);
|
||||
if (estyle == ATOM && efield)
|
||||
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 (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) {
|
||||
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 == nlevels_respa-1) 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];
|
||||
}
|
||||
Reference in New Issue
Block a user