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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6033 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2011-04-29 15:52:26 +00:00
parent 995a92b9f3
commit 199c005d93
10 changed files with 601 additions and 153 deletions
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176
src/fix_langevin.cpp
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@ -20,7 +20,9 @@
#include "string.h"
#include "stdlib.h"
#include "fix_langevin.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "force.h"
#include "update.h"
#include "modify.h"
@ -38,6 +40,9 @@ using namespace LAMMPS_NS;
enum{NOBIAS,BIAS};
#define SINERTIA 0.4 // moment of inertia for sphere
#define EINERTIA 0.2 // moment of inertia for ellipsoid
/* ---------------------------------------------------------------------- */
FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
@ -71,6 +76,7 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
// optional args
for (int i = 1; i <= atom->ntypes; i++) ratio[i] = 1.0;
oflag = aflag = 0;
tally = 0;
zeroflag = 0;
@ -96,9 +102,29 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
else if (strcmp(arg[iarg+1],"yes") == 0) zeroflag = 1;
else error->all("Illegal fix langevin command");
iarg += 2;
} else if (strcmp(arg[iarg],"omega") == 0) {
if (iarg+2 > narg) error->all("Illegal fix langevin command");
if (strcmp(arg[iarg+1],"no") == 0) oflag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) oflag = 1;
else error->all("Illegal fix langevin command");
iarg += 2;
} else if (strcmp(arg[iarg],"angmom") == 0) {
if (iarg+2 > narg) error->all("Illegal fix langevin command");
if (strcmp(arg[iarg+1],"no") == 0) aflag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) aflag = 1;
else error->all("Illegal fix langevin command");
iarg += 2;
} else error->all("Illegal fix langevin command");
}
// error check
if (aflag) {
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec)
error->all("Fix langevin angmom requires atom style ellipsoid");
}
// set temperature = NULL, user can override via fix_modify if wants bias
id_temp = NULL;
@ -140,6 +166,35 @@ int FixLangevin::setmask()
void FixLangevin::init()
{
if (oflag && !atom->sphere_flag)
error->all("Fix langevin omega require atom style sphere");
if (aflag && !atom->ellipsoid_flag)
error->all("Fix langevin angmom require atom style ellipsoid");
// if oflag or aflag set, check that all group particles are finite-size
if (oflag) {
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (radius[i] == 0.0)
error->one("Fix langevin omega requires extended particles");
}
if (aflag) {
int *ellipsoid = atom->ellipsoid;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (ellipsoid[i] < 0)
error->one("Fix langevin angmom requires extended particles");
}
// set force prefactors
if (!atom->rmass) {
@ -219,6 +274,11 @@ void FixLangevin::post_force_no_tally()
double fran[3],fsum[3],fsumall[3];
fsum[0] = fsum[1] = fsum[2] = 0.0;
bigint count;
double boltz = force->boltz;
double dt = update->dt;
double mvv2e = force->mvv2e;
double ftm2v = force->ftm2v;
if (zeroflag) {
count = group->count(igroup);
@ -227,11 +287,6 @@ void FixLangevin::post_force_no_tally()
}
if (rmass) {
double boltz = force->boltz;
double dt = update->dt;
double mvv2e = force->mvv2e;
double ftm2v = force->ftm2v;
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
@ -280,7 +335,6 @@ void FixLangevin::post_force_no_tally()
} else {
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
gamma1 = gfactor1[type[i]];
@ -295,7 +349,6 @@ void FixLangevin::post_force_no_tally()
fsum[1] += fran[1];
fsum[2] += fran[2];
}
}
} else if (which == BIAS) {
@ -338,6 +391,11 @@ void FixLangevin::post_force_no_tally()
}
}
}
// thermostat omega and angmom
if (oflag) omega_thermostat(tsqrt);
if (aflag) angmom_thermostat(tsqrt);
}
/* ---------------------------------------------------------------------- */
@ -373,12 +431,12 @@ void FixLangevin::post_force_tally()
// test v = 0 since some computes mask non-participating atoms via v = 0
// and added force has extra term not multiplied by v = 0
if (rmass) {
double boltz = force->boltz;
double dt = update->dt;
double mvv2e = force->mvv2e;
double ftm2v = force->ftm2v;
double boltz = force->boltz;
double dt = update->dt;
double mvv2e = force->mvv2e;
double ftm2v = force->ftm2v;
if (rmass) {
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
@ -454,6 +512,100 @@ void FixLangevin::post_force_tally()
}
}
}
// thermostat omega and angmom
if (oflag) omega_thermostat(tsqrt);
if (aflag) angmom_thermostat(tsqrt);
}
/* ----------------------------------------------------------------------
thermostat rotational dof via omega
------------------------------------------------------------------------- */
void FixLangevin::omega_thermostat(double tsqrt)
{
double gamma1,gamma2;
double boltz = force->boltz;
double dt = update->dt;
double mvv2e = force->mvv2e;
double ftm2v = force->ftm2v;
double **torque = atom->torque;
double **omega = atom->omega;
double *radius = atom->radius;
double *rmass = atom->rmass;
int *mask = atom->mask;
int *type = atom->type;
int nlocal = atom->nlocal;
double tran[3];
double inertiaone;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
inertiaone = SINERTIA*radius[i]*radius[i]*rmass[i];
gamma1 = -inertiaone / t_period / ftm2v;
gamma2 = sqrt(inertiaone) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
gamma1 *= 1.0/ratio[type[i]];
gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
tran[0] = gamma2*(random->uniform()-0.5);
tran[1] = gamma2*(random->uniform()-0.5);
tran[2] = gamma2*(random->uniform()-0.5);
torque[i][0] += gamma1*omega[i][0] + tran[0];
torque[i][1] += gamma1*omega[i][1] + tran[1];
torque[i][2] += gamma1*omega[i][2] + tran[2];
}
}
}
/* ----------------------------------------------------------------------
thermostat rotational dof via angmom
------------------------------------------------------------------------- */
void FixLangevin::angmom_thermostat(double tsqrt)
{
double gamma1,gamma2;
double boltz = force->boltz;
double dt = update->dt;
double mvv2e = force->mvv2e;
double ftm2v = force->ftm2v;
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
double **torque = atom->torque;
double **angmom = atom->angmom;
double *rmass = atom->rmass;
int *ellipsoid = atom->ellipsoid;
int *mask = atom->mask;
int *type = atom->type;
int nlocal = atom->nlocal;
double inertia[3],wbody[3],omega[3],tran[3],rot[3][3];
double *shape,*quat;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
shape = bonus[ellipsoid[i]].shape;
inertia[0] = EINERTIA*rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]);
inertia[1] = EINERTIA*rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]);
inertia[2] = EINERTIA*rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]);
quat = bonus[ellipsoid[i]].quat;
MathExtra::mq_to_omega(angmom[i],quat,inertia,omega);
gamma1 = -1.0 / t_period / ftm2v;
gamma2 = sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
gamma1 *= 1.0/ratio[type[i]];
gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
tran[0] = sqrt(inertia[0])*gamma2*(random->uniform()-0.5);
tran[1] = sqrt(inertia[1])*gamma2*(random->uniform()-0.5);
tran[2] = sqrt(inertia[2])*gamma2*(random->uniform()-0.5);
torque[i][0] += inertia[0]*gamma1*omega[0] + tran[0];
torque[i][1] += inertia[1]*gamma1*omega[1] + tran[1];
torque[i][2] += inertia[2]*gamma1*omega[2] + tran[2];
}
}
}
/* ----------------------------------------------------------------------