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fix_ti_spring.cpp
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Thu, May 30, 09:39

fix_ti_spring.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 authors:
Rodrigo Freitas (UC Berkeley) - rodrigof@berkeley.edu
Mark Asta (UC Berkeley) - mdasta@berkeley.edu
Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
------------------------------------------------------------------------- */
#include <stdlib.h>
#include <string.h>
#include "fix_ti_spring.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "respa.h"
#include "memory.h"
#include "error.h"
#include "citeme.h"
#include "force.h"
using namespace LAMMPS_NS;
using namespace FixConst;
static const char cite_fix_ti_spring[] =
"ti/spring command:\n\n"
"@article{freitas2016,\n"
" author={Freitas, Rodrigo and Asta, Mark and de Koning, Maurice},\n"
" title={Nonequilibrium free-energy calculation of solids using LAMMPS},\n"
" journal={Computational Materials Science},\n"
" volume={112},\n"
" pages={333--341},\n"
" year={2016},\n"
" publisher={Elsevier}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (lmp->citeme) lmp->citeme->add(cite_fix_ti_spring);
if (narg < 6 || narg > 8)
error->all(FLERR,"Illegal fix ti/spring command");
// Flags.
restart_peratom = 1;
scalar_flag = 1;
global_freq = 1;
vector_flag = 1;
size_vector = 2;
global_freq = 1;
extscalar = 1;
extvector = 1;
// disallow resetting the time step, while this fix is defined
time_depend = 1;
// Spring constant.
k = force->numeric(FLERR,arg[3]);
if (k <= 0.0) error->all(FLERR,"Illegal fix ti/spring command");
// Perform initial allocation of atom-based array
// Register with Atom class
xoriginal = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
atom->add_callback(1);
// xoriginal = initial unwrapped positions of atoms
double **x = atom->x;
int *mask = atom->mask;
imageint *image = atom->image;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) domain->unmap(x[i],image[i],xoriginal[i]);
else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
}
// Time variables.
t0 = update->ntimestep; // timestep of original/starting coordinates
t_switch = force->bnumeric(FLERR,arg[4]); // Number of steps for switching
t_equil = force->bnumeric(FLERR,arg[5]); // Number of steps for equilibration
if ((t_switch <= 0) || (t_equil < 0))
error->all(FLERR,"Illegal fix ti/spring command");
// Coupling parameter initialization
sf = 1;
if (narg > 6) {
if (strcmp(arg[6], "function") == 0) sf = force->inumeric(FLERR,arg[7]);
else error->all(FLERR,"Illegal fix ti/spring switching function");
if ((sf!=1) && (sf!=2))
error->all(FLERR,"Illegal fix ti/spring switching function");
}
lambda = switch_func(0);
dlambda = dswitch_func(0);
espring = 0.0;
}
/* ---------------------------------------------------------------------- */
FixTISpring::~FixTISpring()
{
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
atom->delete_callback(id,1);
// delete locally stored array
memory->destroy(xoriginal);
}
/* ---------------------------------------------------------------------- */
int FixTISpring::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
mask |= MIN_POST_FORCE;
mask |= THERMO_ENERGY;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixTISpring::init()
{
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixTISpring::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
}
}
/* ---------------------------------------------------------------------- */
void FixTISpring::min_setup(int vflag)
{
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixTISpring::post_force(int vflag)
{
// do not calculate forces during equilibration
if ((update->ntimestep - t0) < t_equil) return;
double **x = atom->x;
double **f = atom->f;
int *mask = atom->mask;
imageint *image = atom->image;
int nlocal = atom->nlocal;
double dx, dy, dz;
double unwrap[3];
espring = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - xoriginal[i][0];
dy = unwrap[1] - xoriginal[i][1];
dz = unwrap[2] - xoriginal[i][2];
f[i][0] = (1-lambda) * f[i][0] + lambda * (-k*dx);
f[i][1] = (1-lambda) * f[i][1] + lambda * (-k*dy);
f[i][2] = (1-lambda) * f[i][2] + lambda * (-k*dz);
espring += k * (dx*dx + dy*dy + dz*dz);
}
espring *= 0.5;
}
/* ---------------------------------------------------------------------- */
void FixTISpring::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixTISpring::min_post_force(int vflag)
{
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixTISpring::initial_integrate(int vflag)
{
// Update the coupling parameter value if needed
if ((update->ntimestep - t0) < t_equil) return;
const bigint t = update->ntimestep - (t0+t_equil);
const double r_switch = 1.0/t_switch;
if ( (t >= 0) && (t <= t_switch) ) {
lambda = switch_func(t*r_switch);
dlambda = dswitch_func(t*r_switch);
}
if ( (t >= t_equil+t_switch) && (t <= (t_equil+2*t_switch)) ) {
lambda = switch_func(1.0 - (t - t_switch - t_equil)*r_switch);
dlambda = - dswitch_func(1.0 - (t - t_switch - t_equil)*r_switch);
}
}
/* ----------------------------------------------------------------------
energy of stretched springs
------------------------------------------------------------------------- */
double FixTISpring::compute_scalar()
{
double all;
MPI_Allreduce(&espring,&all,1,MPI_DOUBLE,MPI_SUM,world);
return all;
}
/* ----------------------------------------------------------------------
information about coupling parameter
------------------------------------------------------------------------- */
double FixTISpring::compute_vector(int n)
{
linfo[0] = lambda;
linfo[1] = dlambda;
return linfo[n];
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double FixTISpring::memory_usage()
{
double bytes = atom->nmax*3 * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
allocate atom-based array
------------------------------------------------------------------------- */
void FixTISpring::grow_arrays(int nmax)
{
memory->grow(xoriginal,nmax,3,"fix_ti/spring:xoriginal");
}
/* ----------------------------------------------------------------------
copy values within local atom-based array
------------------------------------------------------------------------- */
void FixTISpring::copy_arrays(int i, int j, int delflag)
{
xoriginal[j][0] = xoriginal[i][0];
xoriginal[j][1] = xoriginal[i][1];
xoriginal[j][2] = xoriginal[i][2];
}
/* ----------------------------------------------------------------------
pack values in local atom-based array for exchange with another proc
------------------------------------------------------------------------- */
int FixTISpring::pack_exchange(int i, double *buf)
{
buf[0] = xoriginal[i][0];
buf[1] = xoriginal[i][1];
buf[2] = xoriginal[i][2];
return 3;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based array from exchange with another proc
------------------------------------------------------------------------- */
int FixTISpring::unpack_exchange(int nlocal, double *buf)
{
xoriginal[nlocal][0] = buf[0];
xoriginal[nlocal][1] = buf[1];
xoriginal[nlocal][2] = buf[2];
return 3;
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for restart file
------------------------------------------------------------------------- */
int FixTISpring::pack_restart(int i, double *buf)
{
buf[0] = 4;
buf[1] = xoriginal[i][0];
buf[2] = xoriginal[i][1];
buf[3] = xoriginal[i][2];
return 4;
}
/* ----------------------------------------------------------------------
unpack values from atom->extra array to restart the fix
------------------------------------------------------------------------- */
void FixTISpring::unpack_restart(int nlocal, int nth)
{
double **extra = atom->extra;
// skip to Nth set of extra values
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
m++;
xoriginal[nlocal][0] = extra[nlocal][m++];
xoriginal[nlocal][1] = extra[nlocal][m++];
xoriginal[nlocal][2] = extra[nlocal][m++];
}
/* ----------------------------------------------------------------------
maxsize of any atom's restart data
------------------------------------------------------------------------- */
int FixTISpring::maxsize_restart()
{
return 4;
}
/* ----------------------------------------------------------------------
size of atom nlocal's restart data
------------------------------------------------------------------------- */
int FixTISpring::size_restart(int nlocal)
{
return 4;
}
/* ----------------------------------------------------------------------
Switching function
------------------------------------------------------------------------- */
double FixTISpring::switch_func(double t)
{
if (sf == 1) return t;
double t2 = t*t;
double t5 = t2*t2*t;
return ((70.0*t2*t2 - 315.0*t2*t + 540.0*t2 - 420.0*t + 126.0)*t5);
}
/* ----------------------------------------------------------------------
Switching function derivative
------------------------------------------------------------------------- */
double FixTISpring::dswitch_func(double t)
{
if(sf == 1) return 1.0/t_switch;
double t2 = t*t;
double t4 = t2*t2;
return ((630*t2*t2 - 2520*t2*t + 3780*t2 - 2520*t + 630)*t4) / t_switch;
}

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