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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10080 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2013-06-17 15:50:52 +00:00
parent fbdc189121
commit 1234c724cd
2 changed files with 138 additions and 37 deletions
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166
src/fix_efield.cpp
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@ -13,6 +13,7 @@
/* ----------------------------------------------------------------------
Contributing author: Christina Payne (Vanderbilt U)
Stan Moore (Sandia) for dipole terms
------------------------------------------------------------------------- */
#include "math.h"
@ -21,6 +22,7 @@
#include "fix_efield.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "modify.h"
#include "force.h"
#include "respa.h"
@ -32,7 +34,7 @@
using namespace LAMMPS_NS;
using namespace FixConst;
enum{CONSTANT,EQUAL,ATOM};
enum{NONE,CONSTANT,EQUAL,ATOM};
/* ---------------------------------------------------------------------- */
@ -78,6 +80,23 @@ FixEfield::FixEfield(LAMMPS *lmp, int narg, char **arg) :
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 addforce 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 addforce command");
iarg += 2;
} else error->all(FLERR,"Illegal fix addforce command");
}
force_flag = 0;
fsum[0] = fsum[1] = fsum[2] = fsum[3] = 0.0;
@ -92,6 +111,7 @@ FixEfield::~FixEfield()
delete [] xstr;
delete [] ystr;
delete [] zstr;
delete [] estr;
memory->destroy(efield);
}
@ -111,7 +131,11 @@ int FixEfield::setmask()
void FixEfield::init()
{
if (!atom->q_flag) error->all(FLERR,"Fix efield requires atom attribute q");
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
@ -139,6 +163,13 @@ void FixEfield::init()
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;
@ -146,6 +177,16 @@ void FixEfield::init()
varflag = EQUAL;
else varflag = CONSTANT;
if (muflag && varflag == ATOM)
error->all(FLERR,"Fix efield with dipoles cannot use atom-style variables");
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;
}
@ -179,6 +220,7 @@ 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
@ -186,7 +228,7 @@ void FixEfield::post_force(int vflag)
if (varflag == ATOM && nlocal > maxatom) {
maxatom = atom->nmax;
memory->destroy(efield);
memory->create(efield,maxatom,3,"efield:efield");
memory->create(efield,maxatom,4,"efield:efield");
}
// fsum[0] = "potential energy" for added force
@ -198,23 +240,53 @@ void FixEfield::post_force(int vflag)
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;
// constant efield
fsum[0] -= fx*x[i][0]+fy*x[i][1]+fz*x[i][2];
fsum[1] += fx;
fsum[2] += fy;
fsum[3] += fz;
}
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 {
@ -229,25 +301,50 @@ void FixEfield::post_force(int vflag)
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);
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];
}
// 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;
}
}
}
}
@ -272,7 +369,7 @@ void FixEfield::min_post_force(int vflag)
double FixEfield::memory_usage()
{
double bytes = 0.0;
if (varflag == ATOM) bytes = atom->nmax*3 * sizeof(double);
if (varflag == ATOM) bytes = atom->nmax*4 * sizeof(double);
return bytes;
}
@ -301,4 +398,3 @@ double FixEfield::compute_vector(int n)
}
return fsum_all[n+1];
}