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fix_ehex.cpp
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Fri, Jul 5, 23:25

fix_ehex.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: Peter Wirnsberger (University of Cambridge)
This source file implements the asymmetric version of the enhanced heat
exchange (eHEX/a) algorithm. The paper is available for download on
arXiv: http://arxiv.org/pdf/1507.07081.pdf.
This file is based on fix_heat.cpp written by Paul Crozier (SNL)
which implements the heat exchange (HEX) algorithm.
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "fix_ehex.h"
#include "atom.h"
#include "domain.h"
#include "region.h"
#include "group.h"
#include "force.h"
#include "update.h"
#include "modify.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
#include "fix_shake.h"
#include "neighbor.h"
#include "comm.h"
#include "timer.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{CONSTANT,EQUAL,ATOM};
/* ---------------------------------------------------------------------- */
FixEHEX::FixEHEX(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
{
MPI_Comm_rank(world, &me);
// check
if (narg < 4) error->all(FLERR,"Illegal fix ehex command: wrong number of parameters ");
scalar_flag = 1;
global_freq = 1;
extscalar = 0;
// apply fix every nevery timesteps
nevery = force->inumeric(FLERR,arg[3]);
if (nevery <= 0) error->all(FLERR,"Illegal fix ehex command");
// heat flux into the reservoir
heat_input = force->numeric(FLERR,arg[4]);
// optional args
iregion = -1;
idregion = NULL;
// NOTE: constraints are deactivated by default
constraints = 0;
// NOTE: cluster rescaling is deactivated by default
cluster = 0;
// NOTE: hex = 1 means that no coordinate correction is applied in which case eHEX reduces to HEX
hex = 0;
int iarg = 5;
while (iarg < narg) {
if (strcmp(arg[iarg],"region") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ehex command: wrong number of parameters ");
iregion = domain->find_region(arg[iarg+1]);
if (iregion == -1)
error->all(FLERR,"Region ID for fix ehex does not exist");
int n = strlen(arg[iarg+1]) + 1;
idregion = new char[n];
strcpy(idregion,arg[iarg+1]);
iarg += 2;
}
// apply constraints (shake/rattle) at the end of the timestep
else if (strcmp(arg[iarg], "constrain") == 0) {
constraints = 1;
iarg += 1;
}
// rescale only if the entire molecule is contained within the region
else if (strcmp(arg[iarg], "com") == 0) {
cluster = 1;
iarg += 1;
}
// don't apply a coordinate correction if this keyword is specified
else if (strcmp(arg[iarg], "hex") == 0) {
hex = 1;
iarg+= 1;
}
else
error->all(FLERR, "Illegal fix ehex keyword ");
}
// check options
if (cluster && !constraints)
error->all(FLERR, "You can only use the keyword 'com' together with the keyword 'constrain' ");
scale = 1.0;
scalingmask = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
}
/* ---------------------------------------------------------------------- */
void FixEHEX::grow_arrays(int nmax) {
memory->grow(scalingmask, nmax,"ehex:scalingmask");
}
/* ---------------------------------------------------------------------- */
FixEHEX::~FixEHEX()
{
atom->delete_callback(id,0);
delete [] idregion;
memory->destroy(scalingmask);
}
/* ---------------------------------------------------------------------- */
int FixEHEX::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixEHEX::init()
{
// set index and check validity of region
if (iregion >= 0) {
iregion = domain->find_region(idregion);
if (iregion == -1)
error->all(FLERR,"Region ID for fix ehex does not exist");
}
// cannot have 0 atoms in group
if (group->count(igroup) == 0)
error->all(FLERR,"Fix ehex group has no atoms");
fshake = NULL;
if (constraints) {
// check if constraining algorithm is used (FixRattle inherits from FixShake)
int cnt_shake = 0;
int id_shake;
for (int i = 0; i < modify->nfix; i++) {
if (strcmp("rattle", modify->fix[i]->style) == 0 ||
strcmp("shake", modify->fix[i]->style) == 0) {
cnt_shake++;
id_shake = i;
}
}
if (cnt_shake > 1)
error->all(FLERR,"Multiple instances of fix shake/rattle detected (not supported yet)");
else if (cnt_shake == 1) {
fshake = ((FixShake*) modify->fix[id_shake]);
}
else if (cnt_shake == 0)
error->all(FLERR, "Fix ehex was configured with keyword constrain, but shake/rattle was not defined");
}
}
/* ---------------------------------------------------------------------- */
void FixEHEX::end_of_step() {
// store local pointers
x = atom->x;
f = atom->f;
v = atom->v;
mass = atom->mass;
rmass = atom->rmass;
type = atom->type;
nlocal = atom->nlocal;
// determine which sites are to be rescaled
update_scalingmask();
// rescale velocities
rescale();
// if required use shake/rattle to correct coordinates and velocities
if (constraints && fshake)
fshake->shake_end_of_step(0);
}
/* ----------------------------------------------------------------------
Iterate over all atoms, rescale the velocities and apply coordinate
corrections.
------------------------------------------------------------------------- */
void FixEHEX::rescale() {
double Kr, Ke, escale;
double vsub[3],vcm[3], sfr[3];
double mi;
double dt;
double F, mr, epsr_ik, sfvr, eta_ik;
dt = update->dt;
// calculate centre of mass properties
com_properties(vcm, sfr, &sfvr, &Ke, &Kr, &masstotal);
// heat flux into the reservoir
F = heat_input * force->ftm2v * nevery;
// total mass
mr = masstotal;
// energy scaling factor
escale = 1. + (F*dt)/Kr;
// safety check for kinetic energy
if (escale < 0.0) error->all(FLERR,"Fix ehex kinetic energy went negative");
scale = sqrt(escale);
vsub[0] = (scale-1.0) * vcm[0];
vsub[1] = (scale-1.0) * vcm[1];
vsub[2] = (scale-1.0) * vcm[2];
for (int i = 0; i < nlocal; i++){
if (scalingmask[i]) {
mi = (rmass) ? rmass[i] : mass[type[i]];
for (int k=0; k<3; k++) {
// apply coordinate correction unless running in hex mode
if (!hex) {
// epsr_ik implements Eq. (20) in the paper
eta_ik = mi * F/(2.*Kr) * (v[i][k] - vcm[k]);
epsr_ik = eta_ik / (mi*Kr) * (F/48. + sfvr/6.*force->ftm2v) - F/(12.*Kr) * (f[i][k]/mi - sfr[k]/mr)*force->ftm2v;
x[i][k] -= dt*dt*dt * epsr_ik;
}
// rescale the velocity
v[i][k] = scale*v[i][k] - vsub[k];
}
}
}
}
/* ---------------------------------------------------------------------- */
double FixEHEX::compute_scalar()
{
return scale;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixEHEX::memory_usage()
{
double bytes = 0.0;
bytes += atom->nmax * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
Update the array scalingmask depending on which individual atoms
will be rescaled or not.
------------------------------------------------------------------------- */
void FixEHEX::update_scalingmask() {
int m;
int lid;
bool stat;
int nsites;
// prematch region
Region *region = NULL;
if (iregion >= 0) {
region = domain->regions[iregion];
region->prematch();
}
// only rescale molecules whose center of mass if fully contained in the region
if (cluster) {
// loop over all clusters
for (int i=0; i < fshake->nlist; i++) {
// cluster id
m = fshake->list[i];
// check if the centre of mass of the cluster is inside the region
// if region == NULL, just check the group information of all sites
if (fshake->shake_flag[m] == 1) nsites = 3;
else if (fshake->shake_flag[m] == 2) nsites = 2;
else if (fshake->shake_flag[m] == 3) nsites = 3;
else if (fshake->shake_flag[m] == 4) nsites = 4;
else nsites = 0;
if (nsites == 0) {
error->all(FLERR,"Internal error: shake_flag[m] has to be between 1 and 4 for m in nlist");
}
stat = check_cluster(fshake->shake_atom[m], nsites, region);
for (int l=0; l < nsites; l++) {
lid = atom->map(fshake->shake_atom[m][l]);
scalingmask[lid] = stat;
}
}
// check atoms that do not belong to any cluster
for (int i=0; i<atom->nlocal; i++) {
if (fshake->shake_flag[i] == 0)
scalingmask[i] = rescale_atom(i,region);
}
}
// no clusters, just individual sites (e.g. monatomic system or flexible molecules)
else {
for (int i=0; i<atom->nlocal; i++)
scalingmask[i] = rescale_atom(i,region);
}
}
/* ----------------------------------------------------------------------
Check if the centre of mass of the cluster to be constrained is
inside the region.
------------------------------------------------------------------------- */
bool FixEHEX::check_cluster(tagint *shake_atom, int n, Region * region) {
// IMPORTANT NOTE: If any site of the cluster belongs to a group
// which should not be rescaled than all of the sites
// will be ignored!
double **x = atom->x;
double * rmass = atom->rmass;
double * mass = atom->mass;
int * type = atom->type;
int * mask = atom->mask;
double xcom[3], xtemp[3];
double mcluster, mi;
bool stat;
int lid[4];
// accumulate mass and centre of mass position
stat = true;
xcom[0] = 0.;
xcom[1] = 0.;
xcom[2] = 0.;
mcluster = 0;
for (int i = 0; i < n; i++) {
// get local id
lid[i] = atom->map(shake_atom[i]);
// check if all sites of the cluster belong to the correct group
stat = stat && (mask[lid[i]] & groupbit);
if (region && stat) {
// check if reduced mass is used
mi = (rmass) ? rmass[lid[i]] : mass[type[lid[i]]];
mcluster += mi;
// accumulate centre of mass
// NOTE: you can either use unwrapped coordinates or take site x[lid[0]] as reference,
// i.e. reconstruct the molecule around this site and calculate the com.
for (int k=0; k<3; k++)
xtemp[k] = x[lid[i]][k] - x[lid[0]][k];
// take into account pbc
domain->minimum_image(xtemp);
for (int k=0; k<3; k++)
xcom[k] += mi * (x[lid[0]][k] + xtemp[k]) ;
}
}
// check if centre of mass is inside the region (if specified)
if (region && stat) {
// check mass
if (mcluster < 1.e-14) {
error->all(FLERR, "Fix ehex shake cluster has almost zero mass.");
}
// divide by total mass
for (int k=0; k<3; k++)
xcom[k] = xcom[k]/mcluster;
// apply periodic boundary conditions (centre of mass could be outside the box)
// and check if molecule is inside the region
domain->remap(xcom);
stat = stat && region->match(xcom[0], xcom[1], xcom[2]);
}
return stat;
}
/* ----------------------------------------------------------------------
Check if atom i has the correct group and is inside the region.
------------------------------------------------------------------------- */
bool FixEHEX::rescale_atom(int i, Region*region) {
bool stat;
double x_r[3];
// check mask and group
stat = (atom->mask[i] & groupbit);
if (region) {
x_r[0] = atom->x[i][0];
x_r[1] = atom->x[i][1];
x_r[2] = atom->x[i][2];
// apply periodic boundary conditions
domain->remap(x_r);
// check if the atom is in the group/region
stat = stat && region->match(x_r[0],x_r[1],x_r[2]);
}
return stat;
}
/* ----------------------------------------------------------------------
Calculate global properties of the atoms inside the reservoir.
(e.g. com velocity, kinetic energy, total mass,...)
------------------------------------------------------------------------- */
void FixEHEX::com_properties(double * vr, double * sfr, double *sfvr, double *K, double *Kr, double *mr) {
double ** f = atom->f;
double ** v = atom->v;
int nlocal = atom->nlocal;
double *rmass= atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
double l_vr[3];
double l_mr;
double l_sfr[3];
double l_sfvr;
double l_K;
double mi;
double l_buf[9];
double buf[9];
// calculate partial sums
l_vr[0] = l_vr[1] = l_vr[2] = 0;
l_sfr[0] = l_sfr[1] = l_sfr[2] = 0;
l_sfvr = 0;
l_mr = 0;
l_K = 0;
for (int i = 0; i < nlocal; i++) {
if (scalingmask[i]) {
// check if reduced mass is used
mi = (rmass) ? rmass[i] : mass[type[i]];
// accumulate total mass
l_mr += mi;
// accumulate kinetic energy
l_K += mi/2. * (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
// sum_j f_j * v_j
l_sfvr += f[i][0]*v[i][0] + f[i][1]*v[i][1] + f[i][2]*v[i][2];
// accumulate com velocity and sum of forces
for (int k=0; k<3; k++) {
l_vr[k] += mi * v[i][k];
l_sfr[k]+= f[i][k];
}
}
}
// reduce sums
l_buf[0] = l_vr[0];
l_buf[1] = l_vr[1];
l_buf[2] = l_vr[2];
l_buf[3] = l_K;
l_buf[4] = l_mr;
l_buf[5] = l_sfr[0];
l_buf[6] = l_sfr[1];
l_buf[7] = l_sfr[2];
l_buf[8] = l_sfvr;
MPI_Allreduce(l_buf, buf, 9, MPI_DOUBLE, MPI_SUM, world);
// total mass of region
*mr = buf[4];
if (*mr < 1.e-14) {
error->all(FLERR, "Fix ehex error mass of region is close to zero");
}
// total kinetic energy of region
*K = buf[3];
// centre of mass velocity of region
vr[0] = buf[0]/(*mr);
vr[1] = buf[1]/(*mr);
vr[2] = buf[2]/(*mr);
// sum of forces
sfr[0] = buf[5];
sfr[1] = buf[6];
sfr[2] = buf[7];
// calculate non-translational kinetic energy
*Kr = *K - 0.5* (*mr) * (vr[0]*vr[0]+vr[1]*vr[1]+vr[2]*vr[2]);
// calculate sum_j f_j * (v_j - v_r) = sum_j f_j * v_j - v_r * sum_j f_j
*sfvr = buf[8] - (vr[0]*sfr[0] + vr[1]*sfr[1] + vr[2]*sfr[2]);
}

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