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fix_temp_stochastic.cpp
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Tue, Jan 28, 10:02

fix_temp_stochastic.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.
------------------------------------------------------------------------- */
#include "string.h"
#include "stdlib.h"
#include "math.h"
#include "fix_temp_stochastic.h"
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "group.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "error.h"
#include "random_mars.h"
#include "velocity.h"
#include "input.h"
#include "variable.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{NOBIAS,BIAS};
enum{CONSTANT,EQUAL,ATOM};
/* ---------------------------------------------------------------------- */
FixTempStochastic::FixTempStochastic(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 7) error->all(FLERR,"Illegal fix temp/stochastic command");
// Stochastic thermostat should be applied every step
nevery = 1;
scalar_flag = 1;
global_freq = nevery;
extscalar = 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 = force->numeric(FLERR,arg[3]);
t_target = t_start;
tstyle = CONSTANT;
}
t_stop = force->numeric(FLERR,arg[4]);
t_period = force->numeric(FLERR,arg[5]);
int seed = force->inumeric(FLERR,arg[6]);
// error checks
if (t_period <= 0.0) error->all(FLERR,"Fix temp/stochastic period must be > 0.0");
if (seed <= 0) error->all(FLERR,"Illegal fix temp/stochastic command");
// initialize Marsaglia RNG with processor-unique seed
random = new RanMars(lmp,seed + comm->me);
// create a new compute temp style
// id = fix-ID + temp, compute group = fix group
int n = strlen(id) + 6;
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = group->names[igroup];
newarg[2] = (char *) "temp";
modify->add_compute(3,newarg);
delete [] newarg;
tflag = 1;
energy = 0;
}
/* ---------------------------------------------------------------------- */
FixTempStochastic::~FixTempStochastic()
{
// delete temperature if fix created it
if (tflag) modify->delete_compute(id_temp);
delete random;
delete [] tstr;
delete [] id_temp;
}
/* ---------------------------------------------------------------------- */
int FixTempStochastic::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
mask |= THERMO_ENERGY;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixTempStochastic::init()
{
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Temperature ID for fix temp/stochastic does not exist");
temperature = modify->compute[icompute];
if (temperature->tempbias) which = BIAS;
else which = NOBIAS;
if (tstr) {
tvar = input->variable->find(tstr);
if (tvar < 0)
error->all(FLERR,"Variable name for fix temp/stochastic 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 temp/stochastic is invalid style");
}
}
/* ---------------------------------------------------------------------- */
void FixTempStochastic::end_of_step()
{
t_current = temperature->compute_scalar();
if (t_current == 0.0)
error->all(FLERR,"Computed temperature for fix temp/stochastic cannot be 0.0");
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double tfactor = force->mvv2e / (3 * nlocal * force->boltz);
double efactor = 0.5 * force->boltz * 3 * nlocal;
double t = 0.0;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
mass[type[i]];
}
t *= tfactor;
if (t == 0.0)
error->all(FLERR,"Computed temperature for fix temp/stochastic cannot be 0.0");
double delta = update->ntimestep - update->beginstep;
delta /= update->endstep - update->beginstep;
t_target = t_start + delta * (t_stop-t_start);
double ekin0 = efactor * t;
double kbt = 0.5 * force->boltz * t_target;
double lambda = resamplekin(kbt, ekin0, 3*nlocal, t_period/update->dt);
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
v[i][0] *= lambda;
v[i][1] *= lambda;
v[i][2] *= lambda;
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
v[i][0] *= lambda;
v[i][1] *= lambda;
v[i][2] *= lambda;
temperature->restore_bias(i,v[i]);
}
}
}
if (group->count(igroup) == 0)
error->all(FLERR,"Cannot zero momentum of 0 atoms");
// compute velocity of center-of-mass of group
double masstotal = group->mass(igroup);
double vcm[3];
group->vcm(igroup,masstotal,vcm);
// adjust velocities by vcm to zero linear momentum
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] -= vcm[0];
v[i][1] -= vcm[1];
v[i][2] -= vcm[2];
}
double t_current = temperature->compute_scalar();
energy += t_current * efactor;
}
/* ---------------------------------------------------------------------- */
int FixTempStochastic::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"temp") == 0) {
if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
if (tflag) {
modify->delete_compute(id_temp);
tflag = 0;
}
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;
}
/* ---------------------------------------------------------------------- */
void FixTempStochastic::reset_target(double t_new)
{
t_start = t_stop = t_new;
}
/* ---------------------------------------------------------------------- */
double FixTempStochastic::compute_scalar()
{
return energy;
}
//////////////////////////////////////////////////////////////////////////
double FixTempStochastic::resamplekin(double kbt, double ekin0, int ndeg, double taut){
/*
ndeg: number of degrees of freedom of the atoms to be thermalized
taut: relaxation time of the thermostat, in units of 'how often this routine is called'
*/
double c1, c2, r1, r2, fscale2;
if(taut>0.1){
c1=exp(-1.0/taut);
} else{
c1=0.0;
}
c2 = (1.0-c1)*kbt/ekin0;
r1 = random->gaussian();
r2 = resamplekin_sumnoises(ndeg-1);
fscale2 = c1 + c2*(r1*r1+r2) + 2.0*r1*sqrt(c1*c2);
return sqrt(fscale2);
}
double FixTempStochastic::resamplekin_sumnoises(int nn){
/*
returns the sum of n independent gaussian noises squared
(i.e. equivalent to summing the square of the return values of nn calls to random->gaussian)
*/
double rr;
if(nn==0) {
return 0.0;
} else if(nn==1) {
rr=random->gaussian();
return rr*rr;
} else if(nn%2==0) {
return 2.0*gamdev(nn/2);
} else {
rr=random->gaussian();
return 2.0*gamdev((nn-1)/2) + rr*rr;
}
}
double FixTempStochastic::gamdev(const int ia)
{
int j;
double am,e,s,v1,v2,x,y;
int iff;
if (ia < 1) {}; // FATAL ERROR
if (ia < 6) {
x=1.0;
for (j=1;j<=ia;j++) x *= random->uniform();
x = -log(x);
} else {
restart:
do {
do {
do {
v1=random->uniform();
v2=2.0*random->uniform()-1.0;
} while (v1*v1+v2*v2 > 1.0);
y=v2/v1;
am=ia-1;
s=sqrt(2.0*am+1.0);
x=s*y+am;
} while (x <= 0.0);
if (am*log(x/am)-s*y < -700 || v1<0.00001) {
goto restart;
}
e=(1.0+y*y)*exp(am*log(x/am)-s*y);
} while (random->uniform() > e);
}
return x;
}

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