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fix_temp_csvr.cpp
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Mon, May 27, 02:13

fix_temp_csvr.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 author: Axel Kohlmeyer (Temple U)
Based on code by Paolo Raiteri (Curtin U) and Giovanni Bussi (SISSA)
------------------------------------------------------------------------- */
#include <string.h>
#include <stdlib.h>
#include <math.h>
#include "fix_temp_csvr.h"
#include "atom.h"
#include "force.h"
#include "memory.h"
#include "comm.h"
#include "input.h"
#include "variable.h"
#include "group.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "random_mars.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{NOBIAS,BIAS};
enum{CONSTANT,EQUAL};
double FixTempCSVR::gamdev(const int ia)
{
int j;
double am,e,s,v1,v2,x,y;
if (ia < 1) return 0.0;
if (ia < 6) {
x=1.0;
for (j=1; j<=ia; j++)
x *= random->uniform();
// make certain, that -log() doesn't overflow.
if (x < 2.2250759805e-308)
x = 708.4;
else
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;
}
/* -------------------------------------------------------------------
returns the sum of n independent gaussian noises squared
(i.e. equivalent to summing the square of the return values of nn
calls to gasdev)
---------------------------------------------------------------------- */
double FixTempCSVR::sumnoises(int nn) {
if (nn == 0) {
return 0.0;
} else if (nn == 1) {
const double rr = random->gaussian();
return rr*rr;
} else if (nn % 2 == 0) {
return 2.0 * gamdev(nn / 2);
} else {
const double rr = random->gaussian();
return 2.0 * gamdev((nn-1) / 2) + rr*rr;
}
}
/* -------------------------------------------------------------------
returns the scaling factor for velocities to thermalize
the system so it samples the canonical ensemble
---------------------------------------------------------------------- */
double FixTempCSVR::resamplekin(double ekin_old, double ekin_new){
const double tdof = temperature->dof;
const double c1 = exp(-update->dt/t_period);
const double c2 = (1.0-c1)*ekin_new/ekin_old/tdof;
const double r1 = random->gaussian();
const double r2 = sumnoises(tdof - 1);
const double scale = c1 + c2*(r1*r1+r2) + 2.0*r1*sqrt(c1*c2);
return sqrt(scale);
}
/* ---------------------------------------------------------------------- */
FixTempCSVR::FixTempCSVR(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
tstr(NULL), id_temp(NULL), random(NULL)
{
if (narg != 7) error->all(FLERR,"Illegal fix temp/csvr command");
// CSVR thermostat should be applied every step
nevery = 1;
scalar_flag = 1;
global_freq = nevery;
dynamic_group_allow = 1;
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]);
tstyle = EQUAL;
} 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,"Illegal fix temp/csvr command");
if (seed <= 0) error->all(FLERR,"Illegal fix temp/csvr command");
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;
nmax = -1;
energy = 0.0;
}
/* ---------------------------------------------------------------------- */
FixTempCSVR::~FixTempCSVR()
{
delete [] tstr;
// delete temperature if fix created it
if (tflag) modify->delete_compute(id_temp);
delete [] id_temp;
delete random;
nmax = -1;
}
/* ---------------------------------------------------------------------- */
int FixTempCSVR::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
mask |= THERMO_ENERGY;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixTempCSVR::init()
{
// check variable
if (tstr) {
tvar = input->variable->find(tstr);
if (tvar < 0)
error->all(FLERR,"Variable name for fix temp/csvr does not exist");
if (input->variable->equalstyle(tvar)) tstyle = EQUAL;
else error->all(FLERR,"Variable for fix temp/csvr is invalid style");
}
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Temperature ID for fix temp/csvr does not exist");
temperature = modify->compute[icompute];
if (temperature->tempbias) which = BIAS;
else which = NOBIAS;
}
/* ---------------------------------------------------------------------- */
void FixTempCSVR::end_of_step()
{
// set current t_target
// if variable temp, evaluate variable, wrap with clear/add
double delta = update->ntimestep - update->beginstep;
if (delta != 0.0) delta /= update->endstep - update->beginstep;
if (tstyle == CONSTANT)
t_target = t_start + delta * (t_stop-t_start);
else {
modify->clearstep_compute();
t_target = input->variable->compute_equal(tvar);
if (t_target < 0.0)
error->one(FLERR,
"Fix temp/csvr variable returned negative temperature");
modify->addstep_compute(update->ntimestep + nevery);
}
const double t_current = temperature->compute_scalar();
const double efactor = 0.5 * temperature->dof * force->boltz;
const double ekin_old = t_current * efactor;
const double ekin_new = t_target * efactor;
// there is nothing to do, if there are no degrees of freedom
if (temperature->dof < 1) return;
// compute velocity scaling factor on root node and broadcast
double lamda;
if (comm->me == 0) {
lamda = resamplekin(ekin_old, ekin_new);
}
MPI_Bcast(&lamda,1,MPI_DOUBLE,0,world);
double * const * const v = atom->v;
const int * const mask = atom->mask;
const int nlocal = atom->nlocal;
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
v[i][0] *= lamda;
v[i][1] *= lamda;
v[i][2] *= lamda;
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
v[i][0] *= lamda;
v[i][1] *= lamda;
v[i][2] *= lamda;
temperature->restore_bias(i,v[i]);
}
}
}
// tally the kinetic energy transferred between heat bath and system
energy += ekin_old * (1.0 - lamda*lamda);
}
/* ---------------------------------------------------------------------- */
int FixTempCSVR::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 FixTempCSVR::reset_target(double t_new)
{
t_target = t_start = t_stop = t_new;
}
/* ---------------------------------------------------------------------- */
double FixTempCSVR::compute_scalar()
{
return energy;
}
/* ----------------------------------------------------------------------
extract thermostat properties
------------------------------------------------------------------------- */
void *FixTempCSVR::extract(const char *str, int &dim)
{
dim=0;
if (strcmp(str,"t_target") == 0) {
return &t_target;
}
return NULL;
}

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