Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/fix_efield.cpp
ddd79fe59961efficient_neuronet

Last Change
Raw File

fix_efield.cpp
View Options

/* ----------------------------------------------------------------------
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)
------------------------------------------------------------------------- */
#include "math.h"
#include "string.h"
#include "stdlib.h"
#include "fix_efield.h"
#include "atom.h"
#include "update.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{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 * atof(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 * atof(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 * atof(arg[5]);
zstyle = CONSTANT;
}
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;
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()
{
if (!atom->q_flag) error->all(FLERR,"Fix efield requires atom attribute q");
// 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 (xstyle == ATOM || ystyle == ATOM || zstyle == ATOM)
varflag = ATOM;
else if (xstyle == EQUAL || ystyle == EQUAL || zstyle == EQUAL)
varflag = EQUAL;
else varflag = CONSTANT;
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;
int nlocal = atom->nlocal;
// reallocate efield array if necessary
if (varflag == ATOM && nlocal > maxatom) {
maxatom = atom->nmax;
memory->destroy(efield);
memory->create(efield,maxatom,3,"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;
if (varflag == CONSTANT) {
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;
fsum[0] -= fx*x[i][0]+fy*x[i][1]+fz*x[i][2];
fsum[1] += fx;
fsum[2] += fy;
fsum[3] += fz;
}
// variable efield, wrap with clear/add
} 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);
modify->addstep_compute(update->ntimestep + 1);
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;
fsum[0] -= fx*x[i][0]+fy*x[i][1]+fz*x[i][2];
}
}
}
/* ---------------------------------------------------------------------- */
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*3 * 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];
}
c4science · Help