Homec4science
Diffusion lammps (lammps-icms) Browse

lammps/src/fix_temp_csld.cpp
268d59866f0alammps-icms

Last Change
Raw File

fix_temp_csld.cpp
View Options

/* ----------------------------------------------------------------------
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)
------------------------------------------------------------------------- */
#include <string.h>
#include <stdlib.h>
#include <math.h>
#include "fix_temp_csld.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};
/* ---------------------------------------------------------------------- */
FixTempCSLD::FixTempCSLD(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 7) error->all(FLERR,"Illegal fix temp/csld command");
// CSLD 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/csld command");
if (seed <= 0) error->all(FLERR,"Illegal fix temp/csld 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;
vhold = NULL;
nmax = -1;
energy = 0.0;
}
/* ---------------------------------------------------------------------- */
FixTempCSLD::~FixTempCSLD()
{
delete [] tstr;
// delete temperature if fix created it
if (tflag) modify->delete_compute(id_temp);
delete [] id_temp;
delete random;
memory->destroy(vhold);
vhold = NULL;
nmax = -1;
}
/* ---------------------------------------------------------------------- */
int FixTempCSLD::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
mask |= THERMO_ENERGY;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixTempCSLD::init()
{
// we cannot handle constraints via rattle or shake correctly.
int has_shake = 0;
for (int i = 0; i < modify->nfix; i++)
if ((strcmp(modify->fix[i]->style,"shake") == 0)
|| (strcmp(modify->fix[i]->style,"rattle") == 0)) ++has_shake;
if (has_shake > 0)
error->all(FLERR,"Fix temp/csld is not compatible with fix rattle or fix shake");
// check variable
if (tstr) {
tvar = input->variable->find(tstr);
if (tvar < 0)
error->all(FLERR,"Variable name for fix temp/csld does not exist");
if (input->variable->equalstyle(tvar)) tstyle = EQUAL;
else error->all(FLERR,"Variable for fix temp/csld is invalid style");
}
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Temperature ID for fix temp/csld does not exist");
temperature = modify->compute[icompute];
if (temperature->tempbias) which = BIAS;
else which = NOBIAS;
}
/* ---------------------------------------------------------------------- */
void FixTempCSLD::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/csld variable returned negative temperature");
modify->addstep_compute(update->ntimestep + nevery);
}
double t_current = temperature->compute_scalar();
double ekin_old = t_current * 0.5 * temperature->dof * force->boltz;
// there is nothing to do, if there are no degrees of freedom
if (temperature->dof < 1) return;
double * const * const v = atom->v;
const int * const mask = atom->mask;
const int * const type = atom->type;
const int nlocal = atom->nlocal;
// adjust holding space, if needed and copy existing velocities
if (nmax < atom->nlocal) {
nmax = atom->nlocal + 1;
memory->destroy(vhold);
memory->create(vhold,nmax,3,"csld:vhold");
}
// The CSLD thermostat is a linear combination of old and new velocities,
// where the new ones are randomly chosen from a gaussian distribution.
// see Bussi and Parrinello, Phys. Rev. E (2007).
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
double m;
if (atom->rmass_flag) m = atom->rmass[i];
else m = atom->mass[type[i]];
const double factor = 1.0/sqrt(m);
const double vx = random->gaussian() * factor;
vhold[i][0] = v[i][0];
v[i][0] = vx;
const double vy = random->gaussian() * factor;
vhold[i][1] = v[i][1];
v[i][1] = vy;
const double vz = random->gaussian() * factor;
vhold[i][2] = v[i][2];
v[i][2] = vz;
}
}
// mixing factors
const double c1 = exp(-update->dt/t_period);
const double c2 = sqrt((1.0-c1*c1)*t_target/temperature->compute_scalar());
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
v[i][0] = vhold[i][0]*c1 + v[i][0]*c2;
v[i][1] = vhold[i][1]*c1 + v[i][1]*c2;
v[i][2] = vhold[i][2]*c1 + v[i][2]*c2;
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,vhold[i]);
v[i][0] = vhold[i][0]*c1 + v[i][0]*c2;
v[i][1] = vhold[i][1]*c1 + v[i][1]*c2;
v[i][2] = vhold[i][2]*c1 + v[i][2]*c2;
temperature->restore_bias(i,v[i]);
}
}
}
// tally the kinetic energy transferred between heat bath and system
t_current = temperature->compute_scalar();
energy += ekin_old - t_current * 0.5 * temperature->dof * force->boltz;
}
/* ---------------------------------------------------------------------- */
int FixTempCSLD::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 FixTempCSLD::reset_target(double t_new)
{
t_target = t_start = t_stop = t_new;
}
/* ---------------------------------------------------------------------- */
double FixTempCSLD::compute_scalar()
{
return energy;
}
/* ----------------------------------------------------------------------
extract thermostat properties
------------------------------------------------------------------------- */
void *FixTempCSLD::extract(const char *str, int &dim)
{
dim=0;
if (strcmp(str,"t_target") == 0) {
return &t_target;
}
return NULL;
}
c4science · Help