git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@624 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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src/fix_nvt_sllod.cpp
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278
src/fix_nvt_sllod.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Pieter in 't Veld (SNL)
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "string.h"
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#include "stdlib.h"
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#include "fix_nvt_sllod.h"
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#include "math_extra.h"
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#include "atom.h"
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#include "force.h"
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#include "domain.h"
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#include "comm.h"
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#include "group.h"
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#include "update.h"
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#include "respa.h"
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#include "modify.h"
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#include "fix.h"
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#include "fix_deform.h"
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#include "compute.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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enum{NO_REMAP,X_REMAP,V_REMAP}; // same as fix_deform.cpp
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/* ---------------------------------------------------------------------- */
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FixNVTSlodd::FixNVTSlodd(LAMMPS *lmp, int narg, char **arg) :
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FixNVT(lmp, narg, arg) {}
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/* ---------------------------------------------------------------------- */
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void FixNVTSlodd::init()
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{
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FixNVT::init();
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// check fix deform remap settings
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int i;
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for (i = 0; i < modify->nfix; i++)
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if (strcmp(modify->fix[i]->style,"deform") == 0) {
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if (((FixDeform *) modify->fix[i])->remapflag == X_REMAP &&
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comm->me == 0)
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error->warning("Using compute temp/deform with fix deform remapping coords");
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break;
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}
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if (i == modify->nfix && comm->me == 0)
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error->warning("Using compute temp/deform with no fix deform defined");
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}
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/* ---------------------------------------------------------------------- */
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void FixNVTSlodd::initial_integrate()
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{
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double dtfm;
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double delta = update->ntimestep - update->firststep;
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delta /= update->nsteps;
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t_target = t_start + delta * (t_stop-t_start);
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// update eta_dot
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f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
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eta_dot += f_eta*dthalf;
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eta_dot *= drag_factor;
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eta += dtv*eta_dot;
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factor = exp(-dthalf*eta_dot);
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// update vthermal and x of only atoms in NVT group
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// lamda = 0-1 triclinic lamda coords
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// vstream = streaming velocity = Hrate*lamda + Hratelo
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// vthermal = thermal velocity = v - vstream
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// vdelu = Hrate*Hinv*vthermal
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double **x = atom->x;
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double **v = atom->v;
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double **f = atom->f;
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double *mass = atom->mass;
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int *type = atom->type;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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double *h_rate = domain->h_rate;
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double *h_ratelo = domain->h_ratelo;
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double h_two[6],lamda[3],vstream[3],vthermal[3],vdelu[3];
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MathExtra::multiply_shape_shape(h_rate,domain->h_inv,h_two);
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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dtfm = dtf / mass[type[i]];
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domain->x2lamda(x[i],lamda);
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vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
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h_rate[4]*lamda[2] + h_ratelo[0];
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vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
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vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
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vthermal[0] = v[i][0] - vstream[0];
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vthermal[1] = v[i][1] - vstream[1];
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vthermal[2] = v[i][2] - vstream[2];
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vdelu[0] = h_two[0]*vthermal[0] + h_two[5]*vthermal[1] +
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h_two[4]*vthermal[2];
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vdelu[1] = h_two[1]*vthermal[1] + h_two[3]*vthermal[2];
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vdelu[2] = h_two[2]*vthermal[2];
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v[i][0] = vstream[0] +
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vthermal[0]*factor + dtfm*f[i][0] - dthalf*vdelu[0];
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v[i][1] = vstream[1] +
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vthermal[1]*factor + dtfm*f[i][1] - dthalf*vdelu[1];
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v[i][2] = vstream[2] +
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vthermal[2]*factor + dtfm*f[i][2] - dthalf*vdelu[2];
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x[i][0] += dtv * v[i][0];
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x[i][1] += dtv * v[i][1];
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x[i][2] += dtv * v[i][2];
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixNVTSlodd::final_integrate()
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{
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double dtfm;
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// update vthermal of only atoms in NVT group
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// lamda = 0-1 triclinic lamda coords
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// vstream = streaming velocity = Hrate*lamda + Hratelo
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// vthermal = thermal velocity = v - vstream
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// vdelu = Hrate*Hinv*vthermal
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double **x = atom->x;
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double **v = atom->v;
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double **f = atom->f;
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double *mass = atom->mass;
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int *type = atom->type;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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double *h_rate = domain->h_rate;
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double *h_ratelo = domain->h_ratelo;
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double h_two[6],lamda[3],vstream[3],vthermal[3],vdelu[3];
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MathExtra::multiply_shape_shape(h_rate,domain->h_inv,h_two);
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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dtfm = dtf / mass[type[i]];
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domain->x2lamda(x[i],lamda);
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vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
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h_rate[4]*lamda[2] + h_ratelo[0];
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vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
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vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
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vthermal[0] = v[i][0] - vstream[0];
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vthermal[1] = v[i][1] - vstream[1];
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vthermal[2] = v[i][2] - vstream[2];
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vdelu[0] = h_two[0]*vthermal[0] + h_two[5]*vthermal[1] +
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h_two[4]*vthermal[2];
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vdelu[1] = h_two[1]*vthermal[1] + h_two[3]*vthermal[2];
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vdelu[2] = h_two[2]*vthermal[2];
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v[i][0] = vstream[0] +
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vthermal[0]*factor + dtfm*f[i][0] - dthalf*vdelu[0];
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v[i][1] = vstream[1] +
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vthermal[1]*factor + dtfm*f[i][1] - dthalf*vdelu[1];
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v[i][2] = vstream[2] +
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vthermal[2]*factor + dtfm*f[i][2] - dthalf*vdelu[2];
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}
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}
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// compute current T
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t_current = temperature->compute_scalar();
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// update eta_dot
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f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
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eta_dot += f_eta*dthalf;
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eta_dot *= drag_factor;
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}
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/* ---------------------------------------------------------------------- */
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void FixNVTSlodd::initial_integrate_respa(int ilevel, int flag)
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{
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if (flag) return; // only used by NPT,NPH
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// set timesteps by level
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double dtfm;
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dtv = step_respa[ilevel];
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dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
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dthalf = 0.5 * step_respa[ilevel];
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// atom quantities
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double **x = atom->x;
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double **v = atom->v;
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double **f = atom->f;
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double *mass = atom->mass;
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int *type = atom->type;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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// outermost level - update eta_dot and apply to v
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// all other levels - NVE update of v
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if (ilevel == nlevels_respa-1) {
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double delta = update->ntimestep - update->firststep;
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delta /= update->nsteps;
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t_target = t_start + delta * (t_stop-t_start);
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// update eta_dot
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f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
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eta_dot += f_eta*dthalf;
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eta_dot *= drag_factor;
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eta += dtv*eta_dot;
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factor = exp(-dthalf*eta_dot);
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} else factor = 1.0;
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// update v of only atoms in NVT group
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double *h_rate = domain->h_rate;
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double *h_ratelo = domain->h_ratelo;
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double h_two[6],lamda[3],vstream[3],vthermal[3],vdelu[3];
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MathExtra::multiply_shape_shape(h_rate,domain->h_inv,h_two);
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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dtfm = dtf / mass[type[i]];
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domain->x2lamda(x[i],lamda);
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vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
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h_rate[4]*lamda[2] + h_ratelo[0];
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vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
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vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
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vthermal[0] = v[i][0] - vstream[0];
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vthermal[1] = v[i][1] - vstream[1];
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vthermal[2] = v[i][2] - vstream[2];
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vdelu[0] = h_two[0]*vthermal[0] + h_two[5]*vthermal[1] +
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h_two[4]*vthermal[2];
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vdelu[1] = h_two[1]*vthermal[1] + h_two[3]*vthermal[2];
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vdelu[2] = h_two[2]*vthermal[2];
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v[i][0] = vstream[0] +
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vthermal[0]*factor + dtfm*f[i][0] - dthalf*vdelu[0];
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v[i][1] = vstream[1] +
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vthermal[1]*factor + dtfm*f[i][1] - dthalf*vdelu[1];
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v[i][2] = vstream[2] +
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vthermal[2]*factor + dtfm*f[i][2] - dthalf*vdelu[2];
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}
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}
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// innermost level - also update x of only atoms in NVT group
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if (ilevel == 0) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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x[i][0] += dtv * v[i][0];
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x[i][1] += dtv * v[i][1];
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x[i][2] += dtv * v[i][2];
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}
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}
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}
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}
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