Homec4science
Diffusion lammps (lammps-icms) Browse

lammps/src/fix_nvt_sllod.cpp
b0861454f53blammps-icms

Last Change
Raw File

fix_nvt_sllod.cpp
View Options

/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "string.h"
#include "fix_nvt_sllod.h"
#include "math_extra.h"
#include "atom.h"
#include "domain.h"
#include "group.h"
#include "modify.h"
#include "fix.h"
#include "fix_deform.h"
#include "compute.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{NO_REMAP,X_REMAP,V_REMAP}; // same as fix_deform.cpp
/* ---------------------------------------------------------------------- */
FixNVTSllod::FixNVTSllod(LAMMPS *lmp, int narg, char **arg) :
FixNH(lmp, narg, arg)
{
if (!tstat_flag)
error->all(FLERR,"Temperature control must be used with fix nvt/sllod");
if (pstat_flag)
error->all(FLERR,"Pressure control can not be used with fix nvt/sllod");
// default values
if (mtchain_default_flag) mtchain = 1;
// create a new compute temp style
// id = fix-ID + temp
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/deform";
modify->add_compute(3,newarg);
delete [] newarg;
tflag = 1;
}
/* ---------------------------------------------------------------------- */
void FixNVTSllod::init()
{
FixNH::init();
if (!temperature->tempbias)
error->all(FLERR,"Temperature for fix nvt/sllod does not have a bias");
nondeformbias = 0;
if (strcmp(temperature->style,"temp/deform") != 0) nondeformbias = 1;
// check fix deform remap settings
int i;
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
error->all(FLERR,"Using fix nvt/sllod with inconsistent fix deform "
"remap option");
break;
}
if (i == modify->nfix)
error->all(FLERR,"Using fix nvt/sllod with no fix deform defined");
}
/* ----------------------------------------------------------------------
perform half-step scaling of velocities
-----------------------------------------------------------------------*/
void FixNVTSllod::nh_v_temp()
{
// remove and restore bias = streaming velocity = Hrate*lamda + Hratelo
// thermostat thermal velocity only
// vdelu = SLLOD correction = Hrate*Hinv*vthermal
// for non temp/deform BIAS:
// calculate temperature since some computes require temp
// computed on current nlocal atoms to remove bias
if (nondeformbias) temperature->compute_scalar();
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double h_two[6],vdelu[3];
MathExtra::multiply_shape_shape(domain->h_rate,domain->h_inv,h_two);
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
vdelu[0] = h_two[0]*v[i][0] + h_two[5]*v[i][1] + h_two[4]*v[i][2];
vdelu[1] = h_two[1]*v[i][1] + h_two[3]*v[i][2];
vdelu[2] = h_two[2]*v[i][2];
temperature->remove_bias(i,v[i]);
v[i][0] = v[i][0]*factor_eta - dthalf*vdelu[0];
v[i][1] = v[i][1]*factor_eta - dthalf*vdelu[1];
v[i][2] = v[i][2]*factor_eta - dthalf*vdelu[2];
temperature->restore_bias(i,v[i]);
}
}
}
c4science · Help