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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3951 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2010-04-02 16:53:40 +00:00
parent 02ac8178c5
commit 75c51a178d
30 changed files with 3477 additions and 3896 deletions
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214
src/fix_nvt_sllod.cpp
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@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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
@ -16,16 +16,11 @@
------------------------------------------------------------------------- */
#include "math.h"
#include "string.h"
#include "stdlib.h"
#include "fix_nvt_sllod.h"
#include "math_extra.h"
#include "fix_nvt_sllod.h"
#include "atom.h"
#include "force.h"
#include "domain.h"
#include "group.h"
#include "update.h"
#include "respa.h"
#include "modify.h"
#include "fix.h"
#include "fix_deform.h"
@ -35,17 +30,41 @@
using namespace LAMMPS_NS;
enum{NO_REMAP,X_REMAP,V_REMAP}; // same as fix_deform.cpp
enum{NOBIAS,BIAS};
/* ---------------------------------------------------------------------- */
FixNVTSlodd::FixNVTSlodd(LAMMPS *lmp, int narg, char **arg) :
FixNVT(lmp, narg, arg) {}
/* ---------------------------------------------------------------------- */
void FixNVTSlodd::init()
FixNVTSllod::FixNVTSllod(LAMMPS *lmp, int narg, char **arg) :
FixNH(lmp, narg, arg)
{
FixNVT::init();
if (!tstat_flag)
error->all("Temperature control must be used with fix nvt/sllod");
if (pstat_flag)
error->all("Pressure control can not be used with fix nvt/sllod");
// 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("Temperature for fix nvt/sllod does not have a bias");
@ -67,25 +86,12 @@ void FixNVTSlodd::init()
error->all("Using fix nvt/sllod with no fix deform defined");
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
perform half-step scaling of velocities
-----------------------------------------------------------------------*/
void FixNVTSlodd::initial_integrate(int vflag)
void FixNVTSllod::nh_v_temp()
{
double dtfm;
double delta = update->ntimestep - update->firststep;
delta /= update->nsteps;
t_target = t_start + delta * (t_stop-t_start);
// update eta_dot
f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
eta_dot += f_eta*dthalf;
eta_dot *= drag_factor;
eta += dtv*eta_dot;
factor = exp(-dthalf*eta_dot);
// update v and x of atoms in group
// remove and restore bias = streaming velocity = Hrate*lamda + Hratelo
// thermostat thermal velocity only
// vdelu = SLLOD correction = Hrate*Hinv*vthermal
@ -95,11 +101,7 @@ void FixNVTSlodd::initial_integrate(int vflag)
if (nondeformbias) double tmp = temperature->compute_scalar();
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
@ -113,144 +115,10 @@ void FixNVTSlodd::initial_integrate(int vflag)
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];
dtfm = dtf / mass[type[i]];
v[i][0] = v[i][0]*factor + dtfm*f[i][0] - dthalf*vdelu[0];
v[i][1] = v[i][1]*factor + dtfm*f[i][1] - dthalf*vdelu[1];
v[i][2] = v[i][2]*factor + dtfm*f[i][2] - dthalf*vdelu[2];
temperature->restore_bias(i,v[i]);
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
}
}
}
/* ---------------------------------------------------------------------- */
void FixNVTSlodd::final_integrate()
{
double dtfm;
// update v of atoms in group
// 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
// OK to not test returned v = 0, since factor is multiplied by v
if (nondeformbias) double tmp = temperature->compute_scalar();
double **v = atom->v;
double **f = atom->f;
double *mass = atom->mass;
int *type = atom->type;
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) {
temperature->remove_bias(i,v[i]);
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];
//dtfm = dtf / mass[type[i]] * factor;
dtfm = dtf / mass[type[i]];
v[i][0] = v[i][0]*factor + dtfm*f[i][0] - dthalf*vdelu[0];
v[i][1] = v[i][1]*factor + dtfm*f[i][1] - dthalf*vdelu[1];
v[i][2] = v[i][2]*factor + dtfm*f[i][2] - dthalf*vdelu[2];
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]);
}
}
// compute current T
t_current = temperature->compute_scalar();
// update eta_dot
f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
eta_dot += f_eta*dthalf;
eta_dot *= drag_factor;
}
/* ---------------------------------------------------------------------- */
void FixNVTSlodd::initial_integrate_respa(int vflag, int ilevel, int flag)
{
if (flag) return; // only used by NPT,NPH
// set timesteps by level
double dtfm;
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
dthalf = 0.5 * step_respa[ilevel];
// atom quantities
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
// outermost level - update eta_dot and apply to v
// all other levels - NVE update of v
if (ilevel == nlevels_respa-1) {
double delta = update->ntimestep - update->firststep;
delta /= update->nsteps;
t_target = t_start + delta * (t_stop-t_start);
// update eta_dot
f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
eta_dot += f_eta*dthalf;
eta_dot *= drag_factor;
eta += dtv*eta_dot;
factor = exp(-dthalf*eta_dot);
} else factor = 1.0;
// update v of atoms in group
if (nondeformbias) double tmp = temperature->compute_scalar();
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) {
temperature->remove_bias(i,v[i]);
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];
dtfm = dtf / mass[type[i]];
v[i][0] = v[i][0]*factor + dtfm*f[i][0] - dthalf*vdelu[0];
v[i][1] = v[i][1]*factor + dtfm*f[i][1] - dthalf*vdelu[1];
v[i][2] = v[i][2]*factor + dtfm*f[i][2] - dthalf*vdelu[2];
temperature->restore_bias(i,v[i]);
}
}
// innermost level - also update x of only atoms in group
if (ilevel == 0) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
}
}
}
}