Homec4science
Diffusion lammps (master) Browse

lammps/src/USER-OMP/fix_nvt_sllod_omp.cpp
b209a4e246b5master

Last Change
Raw File

fix_nvt_sllod_omp.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: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include <math.h>
#include <string.h>
#include "fix_nvt_sllod_omp.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
typedef struct { double x,y,z; } dbl3_t;
/* ---------------------------------------------------------------------- */
FixNVTSllodOMP::FixNVTSllodOMP(LAMMPS *lmp, int narg, char **arg) :
FixNHOMP(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 FixNVTSllodOMP::init()
{
FixNHOMP::init();
if (!temperature->tempbias)
error->all(FLERR,"Temperature for fix nvt/sllod/omp 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/omp with inconsistent fix "
"deform remap option");
break;
}
if (i == modify->nfix)
error->all(FLERR,"Using fix nvt/sllod/omp with no fix deform defined");
}
/* ----------------------------------------------------------------------
perform half-step scaling of velocities
-----------------------------------------------------------------------*/
void FixNVTSllodOMP::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
dbl3_t * _noalias const v = (dbl3_t *) atom->v[0];
const int * _noalias const mask = atom->mask;
const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
int i;
if (nondeformbias) temperature->compute_scalar();
double h_two[6];
MathExtra::multiply_shape_shape(domain->h_rate,domain->h_inv,h_two);
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(i) shared(h_two) schedule(static)
#endif
for (i = 0; i < nlocal; i++) {
double vdelu0,vdelu1,vdelu2,buf[3];
if (mask[i] & groupbit) {
vdelu0 = h_two[0]*v[i].x + h_two[5]*v[i].y + h_two[4]*v[i].z;
vdelu1 = h_two[1]*v[i].y + h_two[3]*v[i].z;
vdelu2 = h_two[2]*v[i].z;
temperature->remove_bias_thr(i,&v[i].x,buf);
v[i].x = v[i].x*factor_eta - dthalf*vdelu0;
v[i].y = v[i].y*factor_eta - dthalf*vdelu1;
v[i].z = v[i].z*factor_eta - dthalf*vdelu2;
temperature->restore_bias_thr(i,&v[i].x,buf);
}
}
}
c4science · Help