Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F86881517
fix_temp_berendsen.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Wed, Oct 9, 04:35
Size
6 KB
Mime Type
text/x-c
Expires
Fri, Oct 11, 04:35 (1 d, 22 h)
Engine
blob
Format
Raw Data
Handle
21454391
Attached To
rLAMMPS lammps
fix_temp_berendsen.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.
------------------------------------------------------------------------- */
#include <string.h>
#include <stdlib.h>
#include <math.h>
#include "fix_temp_berendsen.h"
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "input.h"
#include "variable.h"
#include "group.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{NOBIAS,BIAS};
enum{CONSTANT,EQUAL};
/* ---------------------------------------------------------------------- */
FixTempBerendsen::FixTempBerendsen(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 6) error->all(FLERR,"Illegal fix temp/berendsen command");
// Berendsen thermostat should be applied every step
dynamic_group_allow = 1;
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]);
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]);
// error checks
if (t_period <= 0.0)
error->all(FLERR,"Fix temp/berendsen period must be > 0.0");
// 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;
}
/* ---------------------------------------------------------------------- */
FixTempBerendsen::~FixTempBerendsen()
{
delete [] tstr;
// delete temperature if fix created it
if (tflag) modify->delete_compute(id_temp);
delete [] id_temp;
}
/* ---------------------------------------------------------------------- */
int FixTempBerendsen::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
mask |= THERMO_ENERGY;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixTempBerendsen::init()
{
// check variable
if (tstr) {
tvar = input->variable->find(tstr);
if (tvar < 0)
error->all(FLERR,"Variable name for fix temp/berendsen does not exist");
if (input->variable->equalstyle(tvar)) tstyle = EQUAL;
else error->all(FLERR,"Variable for fix temp/berendsen is invalid style");
}
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Temperature ID for fix temp/berendsen does not exist");
temperature = modify->compute[icompute];
if (temperature->tempbias) which = BIAS;
else which = NOBIAS;
}
/* ---------------------------------------------------------------------- */
void FixTempBerendsen::end_of_step()
{
double t_current = temperature->compute_scalar();
double tdof = temperature->dof;
// there is nothing to do, if there are no degrees of freedom
if (tdof < 1) return;
if (t_current == 0.0)
error->all(FLERR,
"Computed temperature for fix temp/berendsen cannot be 0.0");
double delta = update->ntimestep - update->beginstep;
if (delta != 0.0) delta /= update->endstep - update->beginstep;
// set current t_target
// if variable temp, evaluate variable, wrap with clear/add
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/berendsen variable returned negative temperature");
modify->addstep_compute(update->ntimestep + nevery);
}
// rescale velocities by lamda
// for BIAS:
// temperature is current, so do not need to re-compute
// OK to not test returned v = 0, since lamda is multiplied by v
double lamda = sqrt(1.0 + update->dt/t_period*(t_target/t_current - 1.0));
double efactor = 0.5 * force->boltz * tdof;
energy += t_current * (1.0-lamda*lamda) * efactor;
double **v = atom->v;
int *mask = atom->mask;
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]);
}
}
}
}
/* ---------------------------------------------------------------------- */
int FixTempBerendsen::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 FixTempBerendsen::reset_target(double t_new)
{
t_target = t_start = t_stop = t_new;
}
/* ---------------------------------------------------------------------- */
double FixTempBerendsen::compute_scalar()
{
return energy;
}
/* ----------------------------------------------------------------------
extract thermostat properties
------------------------------------------------------------------------- */
void *FixTempBerendsen::extract(const char *str, int &dim)
{
dim=0;
if (strcmp(str,"t_target") == 0) {
return &t_target;
}
return NULL;
}
Event Timeline
Log In to Comment