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fix_langevin.cpp
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Wed, Jun 26, 18:13

fix_langevin.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 authors: Carolyn Phillips (U Mich), reservoir energy tally
Aidan Thompson (SNL) GJF formulation
------------------------------------------------------------------------- */
#include "mpi.h"
#include "math.h"
#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"
#include "compute.h"
#include "domain.h"
#include "region.h"
#include "respa.h"
#include "comm.h"
#include "input.h"
#include "variable.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h"
#include "group.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{NOBIAS,BIAS};
enum{CONSTANT,EQUAL,ATOM};
#define SINERTIA 0.4 // moment of inertia prefactor for sphere
#define EINERTIA 0.2 // moment of inertia prefactor for ellipsoid
/* ---------------------------------------------------------------------- */
FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 7) error->all(FLERR,"Illegal fix langevin command");
scalar_flag = 1;
global_freq = 1;
extscalar = 1;
nevery = 1;
tstr = NULL;
if (strstr(arg[3],"v_") == arg[3]) {
int n = strlen(&arg[3][2]) + 1;
tstr = new char[n];
strcpy(tstr,&arg[3][2]);
} else {
t_start = atof(arg[3]);
t_target = t_start;
tstyle = CONSTANT;
}
t_stop = atof(arg[4]);
t_period = atof(arg[5]);
int seed = atoi(arg[6]);
if (t_period <= 0.0) error->all(FLERR,"Fix langevin period must be > 0.0");
if (seed <= 0) error->all(FLERR,"Illegal fix langevin command");
// initialize Marsaglia RNG with processor-unique seed
random = new RanMars(lmp,seed + comm->me);
// allocate per-type arrays for force prefactors
gfactor1 = new double[atom->ntypes+1];
gfactor2 = new double[atom->ntypes+1];
ratio = new double[atom->ntypes+1];
// optional args
for (int i = 1; i <= atom->ntypes; i++) ratio[i] = 1.0;
ascale = 0.0;
gjfflag = 0;
oflag = 0;
tallyflag = 0;
zeroflag = 0;
int iarg = 7;
while (iarg < narg) {
if (strcmp(arg[iarg],"angmom") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix langevin command");
if (strcmp(arg[iarg+1],"no") == 0) ascale = 0.0;
else ascale = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"gjf") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix langevin command");
if (strcmp(arg[iarg+1],"no") == 0) gjfflag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) gjfflag = 1;
else error->all(FLERR,"Illegal fix langevin command");
iarg += 2;
} else if (strcmp(arg[iarg],"omega") == 0) {
if (iarg+2 > narg) error->all(FLERR,"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(FLERR,"Illegal fix langevin command");
iarg += 2;
} else if (strcmp(arg[iarg],"scale") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix langevin command");
int itype = atoi(arg[iarg+1]);
double scale = atof(arg[iarg+2]);
if (itype <= 0 || itype > atom->ntypes)
error->all(FLERR,"Illegal fix langevin command");
ratio[itype] = scale;
iarg += 3;
} else if (strcmp(arg[iarg],"tally") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix langevin command");
if (strcmp(arg[iarg+1],"no") == 0) tallyflag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) tallyflag = 1;
else error->all(FLERR,"Illegal fix langevin command");
iarg += 2;
} else if (strcmp(arg[iarg],"zero") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix langevin command");
if (strcmp(arg[iarg+1],"no") == 0) zeroflag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) zeroflag = 1;
else error->all(FLERR,"Illegal fix langevin command");
iarg += 2;
} else error->all(FLERR,"Illegal fix langevin command");
}
// set temperature = NULL, user can override via fix_modify if wants bias
id_temp = NULL;
temperature = NULL;
// flangevin is unallocated until first call to setup()
// compute_scalar checks for this and returns 0.0 if flangevin is NULL
energy = 0.0;
flangevin = NULL;
franprev = NULL;
tforce = NULL;
maxatom1 = maxatom2 = 0;
// Setup atom-based array for franprev
// register with Atom class
// No need to set peratom_flag
// as this data is for internal use only
if (gjfflag) {
nvalues = 3;
grow_arrays(atom->nmax);
atom->add_callback(0);
// initialize franprev to zero
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
franprev[i][0] = 0.0;
franprev[i][1] = 0.0;
franprev[i][2] = 0.0;
}
}
}
/* ---------------------------------------------------------------------- */
FixLangevin::~FixLangevin()
{
delete random;
delete [] tstr;
delete [] gfactor1;
delete [] gfactor2;
delete [] ratio;
delete [] id_temp;
memory->destroy(flangevin);
memory->destroy(tforce);
if (gjfflag) {
memory->destroy(franprev);
atom->delete_callback(id,0);
}
}
/* ---------------------------------------------------------------------- */
int FixLangevin::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
mask |= POST_INTEGRATE;
mask |= END_OF_STEP;
mask |= THERMO_ENERGY;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixLangevin::init()
{
if (oflag && !atom->sphere_flag)
error->all(FLERR,"Fix langevin omega requires atom style sphere");
if (ascale && !atom->ellipsoid_flag)
error->all(FLERR,"Fix langevin angmom requires atom style ellipsoid");
// check variable
if (tstr) {
tvar = input->variable->find(tstr);
if (tvar < 0)
error->all(FLERR,"Variable name for fix langevin does not exist");
if (input->variable->equalstyle(tvar)) tstyle = EQUAL;
else if (input->variable->atomstyle(tvar)) tstyle = ATOM;
else error->all(FLERR,"Variable for fix langevin is invalid style");
}
// if oflag or ascale 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(FLERR,"Fix langevin omega requires extended particles");
}
if (ascale) {
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec)
error->all(FLERR,"Fix langevin angmom requires atom style ellipsoid");
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(FLERR,"Fix langevin angmom requires extended particles");
}
// set force prefactors
if (!atom->rmass) {
for (int i = 1; i <= atom->ntypes; i++) {
gfactor1[i] = -atom->mass[i] / t_period / force->ftm2v;
gfactor2[i] = sqrt(atom->mass[i]) *
sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) /
force->ftm2v;
gfactor1[i] *= 1.0/ratio[i];
gfactor2[i] *= 1.0/sqrt(ratio[i]);
}
}
if (temperature && temperature->tempbias) tbiasflag = BIAS;
else tbiasflag = NOBIAS;
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
if (gjfflag) gjffac = 1.0/(1.0+update->dt/2.0/t_period);
}
/* ---------------------------------------------------------------------- */
void FixLangevin::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 FixLangevin::post_force(int vflag)
{
double *rmass = atom->rmass;
// enumerate all 2^6 possibilities for template parameters
// this avoids testing them inside inner loop:
// TSTYLEATOM, GJF, TALLY, BIAS, RMASS, ZERO
#ifdef TEMPLATED_FIX_LANGEVIN
if (tstyle == ATOM)
if (gjfflag)
if (tallyflag)
if (tbiasflag == BIAS)
if (rmass)
if (zeroflag) post_force_templated<1,1,1,1,1,1>();
else post_force_templated<1,1,1,1,1,0>();
else
if (zeroflag) post_force_templated<1,1,1,1,0,1>();
else post_force_templated<1,1,1,1,0,0>();
else
if (rmass)
if (zeroflag) post_force_templated<1,1,1,0,1,1>();
else post_force_templated<1,1,1,0,1,0>();
else
if (zeroflag) post_force_templated<1,1,1,0,0,1>();
else post_force_templated<1,1,1,0,0,0>();
else
if (tbiasflag == BIAS)
if (rmass)
if (zeroflag) post_force_templated<1,1,0,1,1,1>();
else post_force_templated<1,1,0,1,1,0>();
else
if (zeroflag) post_force_templated<1,1,0,1,0,1>();
else post_force_templated<1,1,0,1,0,0>();
else
if (rmass)
if (zeroflag) post_force_templated<1,1,0,0,1,1>();
else post_force_templated<1,1,0,0,1,0>();
else
if (zeroflag) post_force_templated<1,1,0,0,0,1>();
else post_force_templated<1,1,0,0,0,0>();
else
if (tallyflag)
if (tbiasflag == BIAS)
if (rmass)
if (zeroflag) post_force_templated<1,0,1,1,1,1>();
else post_force_templated<1,0,1,1,1,0>();
else
if (zeroflag) post_force_templated<1,0,1,1,0,1>();
else post_force_templated<1,0,1,1,0,0>();
else
if (rmass)
if (zeroflag) post_force_templated<1,0,1,0,1,1>();
else post_force_templated<1,0,1,0,1,0>();
else
if (zeroflag) post_force_templated<1,0,1,0,0,1>();
else post_force_templated<1,0,1,0,0,0>();
else
if (tbiasflag == BIAS)
if (rmass)
if (zeroflag) post_force_templated<1,0,0,1,1,1>();
else post_force_templated<1,0,0,1,1,0>();
else
if (zeroflag) post_force_templated<1,0,0,1,0,1>();
else post_force_templated<1,0,0,1,0,0>();
else
if (rmass)
if (zeroflag) post_force_templated<1,0,0,0,1,1>();
else post_force_templated<1,0,0,0,1,0>();
else
if (zeroflag) post_force_templated<1,0,0,0,0,1>();
else post_force_templated<1,0,0,0,0,0>();
else
if (gjfflag)
if (tallyflag)
if (tbiasflag == BIAS)
if (rmass)
if (zeroflag) post_force_templated<0,1,1,1,1,1>();
else post_force_templated<0,1,1,1,1,0>();
else
if (zeroflag) post_force_templated<0,1,1,1,0,1>();
else post_force_templated<0,1,1,1,0,0>();
else
if (rmass)
if (zeroflag) post_force_templated<0,1,1,0,1,1>();
else post_force_templated<0,1,1,0,1,0>();
else
if (zeroflag) post_force_templated<0,1,1,0,0,1>();
else post_force_templated<0,1,1,0,0,0>();
else
if (tbiasflag == BIAS)
if (rmass)
if (zeroflag) post_force_templated<0,1,0,1,1,1>();
else post_force_templated<0,1,0,1,1,0>();
else
if (zeroflag) post_force_templated<0,1,0,1,0,1>();
else post_force_templated<0,1,0,1,0,0>();
else
if (rmass)
if (zeroflag) post_force_templated<0,1,0,0,1,1>();
else post_force_templated<0,1,0,0,1,0>();
else
if (zeroflag) post_force_templated<0,1,0,0,0,1>();
else post_force_templated<0,1,0,0,0,0>();
else
if (tallyflag)
if (tbiasflag == BIAS)
if (rmass)
if (zeroflag) post_force_templated<0,0,1,1,1,1>();
else post_force_templated<0,0,1,1,1,0>();
else
if (zeroflag) post_force_templated<0,0,1,1,0,1>();
else post_force_templated<0,0,1,1,0,0>();
else
if (rmass)
if (zeroflag) post_force_templated<0,0,1,0,1,1>();
else post_force_templated<0,0,1,0,1,0>();
else
if (zeroflag) post_force_templated<0,0,1,0,0,1>();
else post_force_templated<0,0,1,0,0,0>();
else
if (tbiasflag == BIAS)
if (rmass)
if (zeroflag) post_force_templated<0,0,0,1,1,1>();
else post_force_templated<0,0,0,1,1,0>();
else
if (zeroflag) post_force_templated<0,0,0,1,0,1>();
else post_force_templated<0,0,0,1,0,0>();
else
if (rmass)
if (zeroflag) post_force_templated<0,0,0,0,1,1>();
else post_force_templated<0,0,0,0,1,0>();
else
if (zeroflag) post_force_templated<0,0,0,0,0,1>();
else post_force_templated<0,0,0,0,0,0>();
#else
post_force_untemplated(int(tstyle==ATOM), gjfflag, tallyflag,
int(tbiasflag==BIAS), int(rmass!=NULL), zeroflag);
#endif
}
/* ---------------------------------------------------------------------- */
void FixLangevin::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ----------------------------------------------------------------------
modify forces using one of the many Langevin styles
------------------------------------------------------------------------- */
#ifdef TEMPLATED_FIX_LANGEVIN
template < int Tp_TSTYLEATOM, int Tp_GJF, int Tp_TALLY,
int Tp_BIAS, int Tp_RMASS, int Tp_ZERO >
void FixLangevin::post_force_templated()
#else
void FixLangevin::post_force_untemplated
(int Tp_TSTYLEATOM, int Tp_GJF, int Tp_TALLY,
int Tp_BIAS, int Tp_RMASS, int Tp_ZERO)
#endif
{
double gamma1,gamma2;
double **v = atom->v;
double **f = atom->f;
double *rmass = atom->rmass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// apply damping and thermostat to atoms in group
// for Tp_TSTYLEATOM:
// use per-atom per-coord target temperature
// for Tp_GJF:
// use Gronbech-Jensen/Farago algorithm
// else use regular algorithm
// for Tp_TALLY:
// store drag plus random forces in flangevin[nlocal][3]
// for Tp_BIAS:
// calculate temperature since some computes require temp
// computed on current nlocal atoms to remove bias
// test v = 0 since some computes mask non-participating atoms via v = 0
// and added force has extra term not multiplied by v = 0
// for Tp_RMASS:
// use per-atom masses
// else use per-type masses
// for Tp_ZERO:
// sum random force over all atoms in group
// subtract sum/count from each atom in group
double fdrag[3],fran[3],fsum[3],fsumall[3];
bigint count;
double fswap;
double boltz = force->boltz;
double dt = update->dt;
double mvv2e = force->mvv2e;
double ftm2v = force->ftm2v;
compute_target();
if (Tp_ZERO) {
fsum[0] = fsum[1] = fsum[2] = 0.0;
count = group->count(igroup);
if (count == 0)
error->all(FLERR,"Cannot zero Langevin force of 0 atoms");
}
// reallocate flangevin if necessary
if (Tp_TALLY) {
if (atom->nlocal > maxatom1) {
memory->destroy(flangevin);
maxatom1 = atom->nmax;
memory->create(flangevin,maxatom1,3,"langevin:flangevin");
}
}
if (Tp_BIAS) temperature->compute_scalar();
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (Tp_TSTYLEATOM) tsqrt = sqrt(tforce[i]);
if (Tp_RMASS) {
gamma1 = -rmass[i] / t_period / ftm2v;
gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
gamma1 *= 1.0/ratio[type[i]];
gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
} else {
gamma1 = gfactor1[type[i]];
gamma2 = gfactor2[type[i]] * tsqrt;
}
fran[0] = gamma2*(random->uniform()-0.5);
fran[1] = gamma2*(random->uniform()-0.5);
fran[2] = gamma2*(random->uniform()-0.5);
if (Tp_BIAS) {
temperature->remove_bias(i,v[i]);
fdrag[1] = gamma1*v[i][1];
fdrag[2] = gamma1*v[i][2];
fdrag[0] = gamma1*v[i][0];
if (v[i][0] != 0.0) f[i][0] += fdrag[0] + fran[0];
else fran[0] = 0.0;
if (v[i][1] != 0.0) f[i][1] += fdrag[1] + fran[1];
else fran[1] = 0.0;
if (v[i][2] != 0.0) f[i][2] += fdrag[2] + fran[2];
else fran[2] = 0.0;
temperature->restore_bias(i,v[i]);
} else {
fdrag[0] = gamma1*v[i][0];
fdrag[1] = gamma1*v[i][1];
fdrag[2] = gamma1*v[i][2];
}
if (Tp_GJF) {
fswap = 0.5*(fran[0]+franprev[i][0]);
franprev[i][0] = fran[0];
fran[0] = fswap;
fswap = 0.5*(fran[1]+franprev[i][1]);
franprev[i][1] = fran[1];
fran[1] = fswap;
fswap = 0.5*(fran[2]+franprev[i][2]);
franprev[i][2] = fran[2];
fran[2] = fswap;
fdrag[0] *= gjffac;
fdrag[1] *= gjffac;
fdrag[2] *= gjffac;
fran[0] *= gjffac;
fran[1] *= gjffac;
fran[2] *= gjffac;
f[i][0] *= gjffac;
f[i][1] *= gjffac;
f[i][2] *= gjffac;
}
f[i][0] += fdrag[0] + fran[0];
f[i][1] += fdrag[1] + fran[1];
f[i][2] += fdrag[2] + fran[2];
if (Tp_TALLY) {
flangevin[i][0] = fdrag[0] + fran[0];
flangevin[i][1] = fdrag[1] + fran[1];
flangevin[i][2] = fdrag[2] + fran[2];
}
if (Tp_ZERO) {
fsum[0] += fran[0];
fsum[1] += fran[1];
fsum[2] += fran[2];
}
}
}
// set total force to zero
if (Tp_ZERO) {
MPI_Allreduce(fsum,fsumall,3,MPI_DOUBLE,MPI_SUM,world);
fsumall[0] /= count;
fsumall[1] /= count;
fsumall[2] /= count;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
f[i][0] -= fsumall[0];
f[i][1] -= fsumall[1];
f[i][2] -= fsumall[2];
}
}
}
// thermostat omega and angmom
if (oflag) omega_thermostat();
if (ascale) angmom_thermostat();
}
/* ----------------------------------------------------------------------
set current t_target and t_sqrt
------------------------------------------------------------------------- */
void FixLangevin::compute_target()
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
double delta = update->ntimestep - update->beginstep;
if (delta != 0.0) delta /= update->endstep - update->beginstep;
// if variable temp, evaluate variable, wrap with clear/add
// reallocate tforce array if necessary
if (tstyle == CONSTANT) {
t_target = t_start + delta * (t_stop-t_start);
tsqrt = sqrt(t_target);
} else {
modify->clearstep_compute();
if (tstyle == EQUAL) {
t_target = input->variable->compute_equal(tvar);
if (t_target < 0.0)
error->one(FLERR,"Fix langevin variable returned negative temperature");
tsqrt = sqrt(t_target);
} else {
if (nlocal > maxatom2) {
maxatom2 = atom->nmax;
memory->destroy(tforce);
memory->create(tforce,maxatom2,"langevin:tforce");
}
input->variable->compute_atom(tvar,igroup,tforce,1,0);
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (tforce[i] < 0.0)
error->one(FLERR,
"Fix langevin variable returned negative temperature");
}
modify->addstep_compute(update->ntimestep + 1);
}
}
/* ----------------------------------------------------------------------
thermostat rotational dof via omega
------------------------------------------------------------------------- */
void FixLangevin::omega_thermostat()
{
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;
// rescale gamma1/gamma2 by 10/3 & sqrt(10/3) for spherical particles
// does not affect rotational thermosatting
// gives correct rotational diffusivity behavior
double tendivthree = 10.0/3.0;
double tran[3];
double inertiaone;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
inertiaone = SINERTIA*radius[i]*radius[i]*rmass[i];
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
gamma1 = -tendivthree*inertiaone / t_period / ftm2v;
gamma2 = sqrt(inertiaone) * sqrt(80.0*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 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;
// rescale gamma1/gamma2 by ascale for aspherical particles
// does not affect rotational thermosatting
// gives correct rotational diffusivity behavior if (nearly) spherical
// any value will be incorrect for rotational diffusivity if aspherical
double inertia[3],omega[3],tran[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);
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
gamma1 = -ascale / t_period / ftm2v;
gamma2 = sqrt(ascale*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];
}
}
}
/* ----------------------------------------------------------------------
tally energy transfer to thermal reservoir
------------------------------------------------------------------------- */
void FixLangevin::end_of_step()
{
if (!tallyflag) return;
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
energy_onestep = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
flangevin[i][2]*v[i][2];
energy += energy_onestep*update->dt;
}
/* ---------------------------------------------------------------------- */
void FixLangevin::reset_target(double t_new)
{
t_target = t_start = t_stop = t_new;
}
/* ---------------------------------------------------------------------- */
void FixLangevin::reset_dt()
{
if (atom->mass) {
for (int i = 1; i <= atom->ntypes; i++) {
gfactor2[i] = sqrt(atom->mass[i]) *
sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) /
force->ftm2v;
gfactor2[i] *= 1.0/sqrt(ratio[i]);
}
}
}
/* ---------------------------------------------------------------------- */
int FixLangevin::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"temp") == 0) {
if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
delete [] id_temp;
int n = strlen(arg[1]) + 1;
id_temp = new char[n];
strcpy(id_temp,arg[1]);
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Could not find fix_modify temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all(FLERR,
"Fix_modify temperature ID does not compute temperature");
if (temperature->igroup != igroup && comm->me == 0)
error->warning(FLERR,"Group for fix_modify temp != fix group");
return 2;
}
return 0;
}
/* ---------------------------------------------------------------------- */
double FixLangevin::compute_scalar()
{
if (!tallyflag || flangevin == NULL) return 0.0;
// capture the very first energy transfer to thermal reservoir
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (update->ntimestep == update->beginstep) {
energy_onestep = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
flangevin[i][2]*v[i][2];
energy = 0.5*energy_onestep*update->dt;
}
// convert midstep energy back to previous fullstep energy
double energy_me = energy - 0.5*energy_onestep*update->dt;
double energy_all;
MPI_Allreduce(&energy_me,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
return -energy_all;
}
/* ----------------------------------------------------------------------
extract thermostat properties
------------------------------------------------------------------------- */
void *FixLangevin::extract(const char *str, int &dim)
{
dim = 0;
if (strcmp(str,"t_target") == 0) {
return &t_target;
}
return NULL;
}
/* ----------------------------------------------------------------------
memory usage of tally array
------------------------------------------------------------------------- */
double FixLangevin::memory_usage()
{
double bytes = 0.0;
if (gjfflag) bytes += atom->nmax*3 * sizeof(double);
if (tallyflag) bytes += atom->nmax*3 * sizeof(double);
if (tforce) bytes += atom->nmax * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
allocate atom-based array for franprev
------------------------------------------------------------------------- */
void FixLangevin::grow_arrays(int nmax)
{
memory->grow(franprev,nmax,3,"fix_langevin:franprev");
}
/* ----------------------------------------------------------------------
copy values within local atom-based array
------------------------------------------------------------------------- */
void FixLangevin::copy_arrays(int i, int j, int delflag)
{
for (int m = 0; m < nvalues; m++)
franprev[j][m] = franprev[i][m];
}
/* ----------------------------------------------------------------------
pack values in local atom-based array for exchange with another proc
------------------------------------------------------------------------- */
int FixLangevin::pack_exchange(int i, double *buf)
{
for (int m = 0; m < nvalues; m++) buf[m] = franprev[i][m];
return nvalues;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based array from exchange with another proc
------------------------------------------------------------------------- */
int FixLangevin::unpack_exchange(int nlocal, double *buf)
{
for (int m = 0; m < nvalues; m++) franprev[nlocal][m] = buf[m];
return nvalues;
}

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