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fix_nvk.cpp
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Fri, Nov 15, 20:48

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

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