forked from lijiext/lammps
128 lines
3.9 KiB
C++
128 lines
3.9 KiB
C++
/* ----------------------------------------------------------------------
|
|
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 "fix_nvt_sllod.h"
|
|
#include <cstring>
|
|
#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;
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
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;
|
|
tcomputeflag = 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 (strncmp(modify->fix[i]->style,"deform",6) == 0) {
|
|
if (((FixDeform *) modify->fix[i])->remapflag != Domain::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]);
|
|
}
|
|
}
|
|
}
|