218 lines
6.8 KiB
C++
218 lines
6.8 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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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: Efrem Braun (UC Berkeley)
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------------------------------------------------------------------------- */
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#include "fix_nvk.h"
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#include <mpi.h>
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#include <cmath>
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#include <cstring>
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#include "atom.h"
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#include "force.h"
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#include "update.h"
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#include "respa.h"
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#include "error.h"
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#include "math_extra.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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FixNVK::FixNVK(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg < 3)
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error->all(FLERR,"Illegal fix nvk command");
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if (igroup) error->all(FLERR,"Fix nvk only supports group all");
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dynamic_group_allow = 1;
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time_integrate = 1;
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}
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/* ---------------------------------------------------------------------- */
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int FixNVK::setmask()
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{
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int mask = 0;
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mask |= INITIAL_INTEGRATE;
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mask |= FINAL_INTEGRATE;
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mask |= INITIAL_INTEGRATE_RESPA;
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mask |= FINAL_INTEGRATE_RESPA;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixNVK::init()
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{
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dtv = update->dt;
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dtf = 0.5 * update->dt;
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if (strstr(update->integrate_style,"respa")) {
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error->all(FLERR,"Fix nvk not yet enabled for RESPA");
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step_respa = ((Respa *) update->integrate)->step;
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}
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// compute initial kinetic energy
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// make better by calling compute_ke instead of copy/pasting code from compute_ke.cpp
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double pfactor = 0.5 * force->mvv2e;
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double **v = atom->v;
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double *rmass = atom->rmass;
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double *mass = atom->mass;
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int *mask = atom->mask;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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double ke = 0.0;
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if (rmass) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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ke += rmass[i] * (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
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} else {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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ke += mass[type[i]] *
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(v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
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}
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MPI_Allreduce(&ke,&K_target,1,MPI_DOUBLE,MPI_SUM,world);
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K_target *= pfactor;
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}
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/* ----------------------------------------------------------------------
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allow for both per-type and per-atom mass
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------------------------------------------------------------------------- */
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void FixNVK::initial_integrate(int /*vflag*/)
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{
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double sm;
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double a,b,sqtb,s,sdot;
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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 *rmass = atom->rmass;
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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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if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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// calculate s and sdot from Minary 2003, equations 4.12 and 4.13
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double a_local = 0.0;
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double b_local = 0.0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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a_local += MathExtra::dot3(f[i], v[i]);
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if (rmass) b_local += MathExtra::dot3(f[i], f[i]) / rmass[i];
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else b_local += MathExtra::dot3(f[i], f[i]) / mass[type[i]];
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}
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MPI_Allreduce(&a_local,&a,1,MPI_DOUBLE,MPI_SUM,world);
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MPI_Allreduce(&b_local,&b,1,MPI_DOUBLE,MPI_SUM,world);
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a /= (2.0*K_target); // units of inverse time
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b /= (2.0*K_target * force->mvv2e); // units of inverse time squared
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sqtb = sqrt(b);
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s = a/b * (cosh(dtf*sqtb) - 1.0) + sinh(dtf*sqtb) / sqtb;
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sdot = a/b * sqtb * sinh(dtf*sqtb) + cosh(dtf*sqtb);
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// update v and x of atoms in group per Minary 2003, equations 4.15-4.17
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// note that equation 4.15, 4.17 should read p = (p+F*s/m)/sdot
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// note that equation 4.16 should read r = r + delt*p/m
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (rmass) sm = s / rmass[i];
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else sm = s / mass[type[i]];
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v[i][0] = (v[i][0] + f[i][0] * sm * force->ftm2v) / sdot;
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v[i][1] = (v[i][1] + f[i][1] * sm * force->ftm2v) / sdot;
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v[i][2] = (v[i][2] + f[i][2] * sm * force->ftm2v) / sdot;
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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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void FixNVK::final_integrate()
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{
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double sm;
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double a,b,sqtb,s,sdot;
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double **v = atom->v;
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double **f = atom->f;
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double *rmass = atom->rmass;
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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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if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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// calculate s and sdot from Minary 2003, equations 4.12 and 4.13
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double a_local = 0.0;
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double b_local = 0.0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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a_local += MathExtra::dot3(f[i], v[i]);
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if (rmass) b_local += MathExtra::dot3(f[i], f[i]) / rmass[i];
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else b_local += MathExtra::dot3(f[i], f[i]) / mass[type[i]];
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}
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MPI_Allreduce(&a_local,&a,1,MPI_DOUBLE,MPI_SUM,world);
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MPI_Allreduce(&b_local,&b,1,MPI_DOUBLE,MPI_SUM,world);
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a /= (2.0*K_target); // units of inverse time
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b /= (2.0*K_target * force->mvv2e); // units of inverse time squared
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sqtb = sqrt(b);
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s = a/b * (cosh(dtf*sqtb) - 1.0) + sinh(dtf*sqtb) / sqtb;
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sdot = a/b * sqtb * sinh(dtf*sqtb) + cosh(dtf*sqtb);
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// update v and x of atoms in group per Minary 2003, equations 4.15-4.17
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// note that equation 4.15, 4.17 should read p = (p+F*s/m)/sdot
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// note that equation 4.16 should read r = r + delt*p/m
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (rmass) sm = s / rmass[i];
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else sm = s / mass[type[i]];
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v[i][0] = (v[i][0] + f[i][0] * sm * force->ftm2v) / sdot;
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v[i][1] = (v[i][1] + f[i][1] * sm * force->ftm2v) / sdot;
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v[i][2] = (v[i][2] + f[i][2] * sm * force->ftm2v) / sdot;
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixNVK::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
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{
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dtv = step_respa[ilevel];
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dtf = 0.5 * step_respa[ilevel];
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// innermost level - NVK update of v and x
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// all other levels - NVK update of v
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if (ilevel == 0) initial_integrate(vflag);
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else final_integrate();
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}
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/* ---------------------------------------------------------------------- */
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void FixNVK::final_integrate_respa(int ilevel, int /*iloop*/)
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{
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dtf = 0.5 * step_respa[ilevel];
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final_integrate();
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}
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/* ---------------------------------------------------------------------- */
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void FixNVK::reset_dt()
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{
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dtv = update->dt;
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dtf = 0.5 * update->dt;
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}
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