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lammps/src/USER-DPD/fix_shardlow.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:
James Larentzos (U.S. Army Research Laboratory)
and Timothy I. Mattox (Engility Corporation)
Martin Lisal (Institute of Chemical Process Fundamentals
of the Czech Academy of Sciences and J. E. Purkinje University)
John Brennan, Joshua Moore and William Mattson (Army Research Lab)
Please cite the related publications:
J. P. Larentzos, J. K. Brennan, J. D. Moore, M. Lisal, W. D. Mattson,
"Parallel implementation of isothermal and isoenergetic Dissipative
Particle Dynamics using Shardlow-like splitting algorithms",
Computer Physics Communications, 2014, 185, pp 1987--1998.
M. Lisal, J. K. Brennan, J. Bonet Avalos, "Dissipative particle dynamics
at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using
Shardlow-like splitting algorithms", Journal of Chemical Physics, 2011,
135, 204105.
------------------------------------------------------------------------- */
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "fix_shardlow.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "respa.h"
#include "error.h"
#include <math.h>
#include "atom_vec.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "random_mars.h"
#include "memory.h"
#include "domain.h"
#include "modify.h"
#include "pair_dpd_fdt.h"
#include "pair_dpd_fdt_energy.h"
#include "pair.h"
#include "npair_half_bin_newton_ssa.h"
#include "citeme.h"
using namespace LAMMPS_NS;
using namespace FixConst;
#define EPSILON 1.0e-10
#define EPSILON_SQUARED ((EPSILON) * (EPSILON))
static const char cite_fix_shardlow[] =
"fix shardlow command:\n\n"
"@Article{Larentzos14,\n"
" author = {J. P. Larentzos, J. K. Brennan, J. D. Moore, M. Lisal, W. D. Mattson},\n"
" title = {Parallel implementation of isothermal and isoenergetic Dissipative Particle Dynamics using Shardlow-like splitting algorithms},\n"
" journal = {Computer Physics Communications},\n"
" year = 2014,\n"
" volume = 185\n"
" pages = {1987--1998}\n"
"}\n\n"
"@Article{Lisal11,\n"
" author = {M. Lisal, J. K. Brennan, J. Bonet Avalos},\n"
" title = {Dissipative particle dynamics at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms},\n"
" journal = {Journal of Chemical Physics},\n"
" year = 2011,\n"
" volume = 135\n"
" pages = {204105}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
FixShardlow::FixShardlow(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), pairDPD(NULL), pairDPDE(NULL), v_t0(NULL)
{
if (lmp->citeme) lmp->citeme->add(cite_fix_shardlow);
if (narg != 3) error->all(FLERR,"Illegal fix shardlow command");
pairDPD = NULL;
pairDPDE = NULL;
pairDPD = (PairDPDfdt *) force->pair_match("dpd/fdt",1);
pairDPDE = (PairDPDfdtEnergy *) force->pair_match("dpd/fdt/energy",1);
if (pairDPDE == NULL)
pairDPDE = (PairDPDfdtEnergy *) force->pair_match("dpd/fdt/energy/kk",1);
if(pairDPDE){
comm_forward = 3;
comm_reverse = 5;
} else {
comm_forward = 3;
comm_reverse = 3;
}
if(pairDPD == NULL && pairDPDE == NULL)
error->all(FLERR,"Must use pair_style dpd/fdt or dpd/fdt/energy with fix shardlow");
}
/* ---------------------------------------------------------------------- */
FixShardlow::~FixShardlow()
{
}
/* ---------------------------------------------------------------------- */
int FixShardlow::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixShardlow::init()
{
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->ghost = 1;
neighbor->requests[irequest]->ssa = 1;
neighbor->requests[irequest]->newton = 1; // SSA requires newton on
}
/* ---------------------------------------------------------------------- */
void FixShardlow::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void FixShardlow::setup(int vflag)
{
bool fixShardlow = false;
for (int i = 0; i < modify->nfix; i++)
if (strncmp(modify->fix[i]->style,"nvt",3) == 0 || strncmp(modify->fix[i]->style,"npt",3) == 0)
error->all(FLERR,"Cannot use constant temperature integration routines with DPD.");
for (int i = 0; i < modify->nfix; i++){
if (strncmp(modify->fix[i]->style,"shardlow",3) == 0) fixShardlow = true;
if (strncmp(modify->fix[i]->style,"nve",3) == 0 || (strncmp(modify->fix[i]->style,"nph",3) == 0)){
if(fixShardlow) break;
else error->all(FLERR,"The deterministic integrator must follow fix shardlow in the input file.");
}
if (i == modify->nfix-1) error->all(FLERR,"A deterministic integrator (e.g. fix nve or fix nph) is required when using fix shardlow.");
}
}
/* ----------------------------------------------------------------------
Perform the stochastic integration and Shardlow update for constant temperature
Allow for both per-type and per-atom mass
NOTE: only implemented for orthogonal boxes, not triclinic
------------------------------------------------------------------------- */
void FixShardlow::ssa_update_dpd(
int i,
int *jlist,
int jlen
)
{
class RanMars *pRNG;
double **x = atom->x;
double **v = atom->v;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
double *cut_i, *cut2_i, *sigma_i;
double theta_ij_inv;
const double boltz_inv = 1.0/force->boltz;
const double ftm2v = force->ftm2v;
const double dt = update->dt;
const double xtmp = x[i][0];
const double ytmp = x[i][1];
const double ztmp = x[i][2];
// load velocity for i from memory
double vxi = v[i][0];
double vyi = v[i][1];
double vzi = v[i][2];
int itype = type[i];
pRNG = pairDPD->random;
cut2_i = pairDPD->cutsq[itype];
cut_i = pairDPD->cut[itype];
sigma_i = pairDPD->sigma[itype];
theta_ij_inv = 1.0/pairDPD->temperature; // independent of i,j
const double mass_i = (rmass) ? rmass[i] : mass[itype];
const double massinv_i = 1.0 / mass_i;
#ifdef DEBUG_PAIR_CT
const int nlocal = atom->nlocal;
#endif
// Loop over Directional Neighbors only
for (int jj = 0; jj < jlen; jj++) {
int j = jlist[jj] & NEIGHMASK;
int jtype = type[j];
double delx = xtmp - x[j][0];
double dely = ytmp - x[j][1];
double delz = ztmp - x[j][2];
double rsq = delx*delx + dely*dely + delz*delz;
#ifdef DEBUG_PAIR_CT
if ((i < nlocal) && (j < nlocal)) ++(counters[0][0]);
else ++(counters[0][1]);
++(counters[0][2]);
int rsqi = rsq / 8;
if (rsqi < 0) rsqi = 0;
else if (rsqi > 31) rsqi = 31;
++(hist[rsqi]);
#endif
// NOTE: r can be 0.0 in DPD systems, so do EPSILON_SQUARED test
if ((rsq < cut2_i[jtype]) && (rsq >= EPSILON_SQUARED)) {
#ifdef DEBUG_PAIR_CT
if ((i < nlocal) && (j < nlocal)) ++(counters[1][0]);
else ++(counters[1][1]);
++(counters[1][2]);
#endif
double r = sqrt(rsq);
double rinv = 1.0/r;
double delx_rinv = delx*rinv;
double dely_rinv = dely*rinv;
double delz_rinv = delz*rinv;
double wr = 1.0 - r/cut_i[jtype];
double wdt = wr*wr*dt;
double halfsigma_ij = 0.5*sigma_i[jtype];
double halfgamma_ij = halfsigma_ij*halfsigma_ij*boltz_inv*theta_ij_inv;
double sigmaRand = halfsigma_ij*wr*dtsqrt*ftm2v * pRNG->gaussian();
double mass_j = (rmass) ? rmass[j] : mass[jtype];
double massinv_j = 1.0 / mass_j;
double gammaFactor = halfgamma_ij*wdt*ftm2v;
double inv_1p_mu_gammaFactor = 1.0/(1.0 + (massinv_i + massinv_j)*gammaFactor);
double vxj = v[j][0];
double vyj = v[j][1];
double vzj = v[j][2];
// Compute the initial velocity difference between atom i and atom j
double delvx = vxi - vxj;
double delvy = vyi - vyj;
double delvz = vzi - vzj;
double dot_rinv = (delx_rinv*delvx + dely_rinv*delvy + delz_rinv*delvz);
// Compute momentum change between t and t+dt
double factorA = sigmaRand - gammaFactor*dot_rinv;
// Update the velocity on i
vxi += delx_rinv*factorA*massinv_i;
vyi += dely_rinv*factorA*massinv_i;
vzi += delz_rinv*factorA*massinv_i;
// Update the velocity on j
vxj -= delx_rinv*factorA*massinv_j;
vyj -= dely_rinv*factorA*massinv_j;
vzj -= delz_rinv*factorA*massinv_j;
//ii. Compute the new velocity diff
delvx = vxi - vxj;
delvy = vyi - vyj;
delvz = vzi - vzj;
dot_rinv = delx_rinv*delvx + dely_rinv*delvy + delz_rinv*delvz;
// Compute the new momentum change between t and t+dt
double factorB = (sigmaRand - gammaFactor*dot_rinv)*inv_1p_mu_gammaFactor;
// Update the velocity on i
vxi += delx_rinv*factorB*massinv_i;
vyi += dely_rinv*factorB*massinv_i;
vzi += delz_rinv*factorB*massinv_i;
// Update the velocity on j
vxj -= delx_rinv*factorB*massinv_j;
vyj -= dely_rinv*factorB*massinv_j;
vzj -= delz_rinv*factorB*massinv_j;
// Store updated velocity for j
v[j][0] = vxj;
v[j][1] = vyj;
v[j][2] = vzj;
}
}
// store updated velocity for i
v[i][0] = vxi;
v[i][1] = vyi;
v[i][2] = vzi;
}
/* ----------------------------------------------------------------------
Perform the stochastic integration and Shardlow update for constant energy
Allow for both per-type and per-atom mass
NOTE: only implemented for orthogonal boxes, not triclinic
------------------------------------------------------------------------- */
void FixShardlow::ssa_update_dpde(
int i,
int *jlist,
int jlen
)
{
class RanMars *pRNG;
double **x = atom->x;
double **v = atom->v;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
double *uCond = atom->uCond;
double *uMech = atom->uMech;
double *dpdTheta = atom->dpdTheta;
double *cut_i, *cut2_i, *sigma_i, *kappa_i;
double theta_ij_inv, theta_i_inv;
const double boltz2 = 2.0*force->boltz;
const double boltz_inv = 1.0/force->boltz;
const double ftm2v = force->ftm2v;
const double dt = update->dt;
const double xtmp = x[i][0];
const double ytmp = x[i][1];
const double ztmp = x[i][2];
// load velocity for i from memory
double vxi = v[i][0];
double vyi = v[i][1];
double vzi = v[i][2];
double uMech_i = uMech[i];
double uCond_i = uCond[i];
int itype = type[i];
pRNG = pairDPDE->random;
cut2_i = pairDPDE->cutsq[itype];
cut_i = pairDPDE->cut[itype];
sigma_i = pairDPDE->sigma[itype];
kappa_i = pairDPDE->kappa[itype];
theta_i_inv = 1.0/dpdTheta[i];
const double mass_i = (rmass) ? rmass[i] : mass[itype];
const double massinv_i = 1.0 / mass_i;
const double mass_i_div_neg4_ftm2v = mass_i*(-0.25)/ftm2v;
#ifdef DEBUG_PAIR_CT
const int nlocal = atom->nlocal;
#endif
// Loop over Directional Neighbors only
for (int jj = 0; jj < jlen; jj++) {
int j = jlist[jj] & NEIGHMASK;
int jtype = type[j];
double delx = xtmp - x[j][0];
double dely = ytmp - x[j][1];
double delz = ztmp - x[j][2];
double rsq = delx*delx + dely*dely + delz*delz;
#ifdef DEBUG_PAIR_CT
if ((i < nlocal) && (j < nlocal)) ++(counters[0][0]);
else ++(counters[0][1]);
++(counters[0][2]);
int rsqi = rsq / 8;
if (rsqi < 0) rsqi = 0;
else if (rsqi > 31) rsqi = 31;
++(hist[rsqi]);
#endif
// NOTE: r can be 0.0 in DPD systems, so do EPSILON_SQUARED test
if ((rsq < cut2_i[jtype]) && (rsq >= EPSILON_SQUARED)) {
#ifdef DEBUG_PAIR_CT
if ((i < nlocal) && (j < nlocal)) ++(counters[1][0]);
else ++(counters[1][1]);
++(counters[1][2]);
#endif
double r = sqrt(rsq);
double rinv = 1.0/r;
double delx_rinv = delx*rinv;
double dely_rinv = dely*rinv;
double delz_rinv = delz*rinv;
double wr = 1.0 - r/cut_i[jtype];
double wdt = wr*wr*dt;
// Compute the current temperature
double theta_j_inv = 1.0/dpdTheta[j];
theta_ij_inv = 0.5*(theta_i_inv + theta_j_inv);
double halfsigma_ij = 0.5*sigma_i[jtype];
double halfgamma_ij = halfsigma_ij*halfsigma_ij*boltz_inv*theta_ij_inv;
double sigmaRand = halfsigma_ij*wr*dtsqrt*ftm2v * pRNG->gaussian();
double mass_j = (rmass) ? rmass[j] : mass[jtype];
double mass_ij_div_neg4_ftm2v = mass_j*mass_i_div_neg4_ftm2v;
double massinv_j = 1.0 / mass_j;
// Compute uCond
double kappa_ij = kappa_i[jtype];
double alpha_ij = sqrt(boltz2*kappa_ij);
double del_uCond = alpha_ij*wr*dtsqrt * pRNG->gaussian();
del_uCond += kappa_ij*(theta_i_inv - theta_j_inv)*wdt;
uCond[j] -= del_uCond;
uCond_i += del_uCond;
double gammaFactor = halfgamma_ij*wdt*ftm2v;
double inv_1p_mu_gammaFactor = 1.0/(1.0 + (massinv_i + massinv_j)*gammaFactor);
double vxj = v[j][0];
double vyj = v[j][1];
double vzj = v[j][2];
double dot4 = vxj*vxj + vyj*vyj + vzj*vzj;
double dot3 = vxi*vxi + vyi*vyi + vzi*vzi;
// Compute the initial velocity difference between atom i and atom j
double delvx = vxi - vxj;
double delvy = vyi - vyj;
double delvz = vzi - vzj;
double dot_rinv = (delx_rinv*delvx + dely_rinv*delvy + delz_rinv*delvz);
// Compute momentum change between t and t+dt
double factorA = sigmaRand - gammaFactor*dot_rinv;
// Update the velocity on i
vxi += delx_rinv*factorA*massinv_i;
vyi += dely_rinv*factorA*massinv_i;
vzi += delz_rinv*factorA*massinv_i;
// Update the velocity on j
vxj -= delx_rinv*factorA*massinv_j;
vyj -= dely_rinv*factorA*massinv_j;
vzj -= delz_rinv*factorA*massinv_j;
//ii. Compute the new velocity diff
delvx = vxi - vxj;
delvy = vyi - vyj;
delvz = vzi - vzj;
dot_rinv = delx_rinv*delvx + dely_rinv*delvy + delz_rinv*delvz;
// Compute the new momentum change between t and t+dt
double factorB = (sigmaRand - gammaFactor*dot_rinv)*inv_1p_mu_gammaFactor;
// Update the velocity on i
vxi += delx_rinv*factorB*massinv_i;
vyi += dely_rinv*factorB*massinv_i;
vzi += delz_rinv*factorB*massinv_i;
double partial_uMech = (vxi*vxi + vyi*vyi + vzi*vzi - dot3)*massinv_j;
// Update the velocity on j
vxj -= delx_rinv*factorB*massinv_j;
vyj -= dely_rinv*factorB*massinv_j;
vzj -= delz_rinv*factorB*massinv_j;
partial_uMech += (vxj*vxj + vyj*vyj + vzj*vzj - dot4)*massinv_i;
// Store updated velocity for j
v[j][0] = vxj;
v[j][1] = vyj;
v[j][2] = vzj;
// Compute uMech
double del_uMech = partial_uMech*mass_ij_div_neg4_ftm2v;
uMech_i += del_uMech;
uMech[j] += del_uMech;
}
}
// store updated velocity for i
v[i][0] = vxi;
v[i][1] = vyi;
v[i][2] = vzi;
// store updated uMech and uCond for i
uMech[i] = uMech_i;
uCond[i] = uCond_i;
}
void FixShardlow::initial_integrate(int vflag)
{
int i,ii,inum;
int *ilist;
int nlocal = atom->nlocal;
int nghost = atom->nghost;
int airnum;
const bool useDPDE = (pairDPDE != NULL);
// NOTE: this logic is specific to orthogonal boxes, not triclinic
// Enforce the constraint that ghosts must be contained in the nearest sub-domains
double bbx = domain->subhi[0] - domain->sublo[0];
double bby = domain->subhi[1] - domain->sublo[1];
double bbz = domain->subhi[2] - domain->sublo[2];
double rcut = 2.0*neighbor->cutneighmax;
if (domain->triclinic)
error->all(FLERR,"Fix shardlow does not yet support triclinic geometries");
if(rcut >= bbx || rcut >= bby || rcut>= bbz )
{
char fmt[] = {"Shardlow algorithm requires sub-domain length > 2*(rcut+skin). Either reduce the number of processors requested, or change the cutoff/skin: rcut= %e bbx= %e bby= %e bbz= %e\n"};
char *msg = (char *) malloc(sizeof(fmt) + 4*15);
sprintf(msg, fmt, rcut, bbx, bby, bbz);
error->one(FLERR, msg);
}
#ifdef DEBUG_PAIR_CT
for (int i = 0; i < 2; ++i)
for (int j = 0; j < 3; ++j)
counters[i][j] = 0;
for (int i = 0; i < 32; ++i) hist[i] = 0;
#endif
// Allocate memory for v_t0 to hold the initial velocities for the ghosts
v_t0 = (double (*)[3]) memory->smalloc(sizeof(double)*3*nghost, "FixShardlow:v_t0");
inum = list->inum;
ilist = list->ilist;
dtsqrt = sqrt(update->dt);
NPairHalfBinNewtonSSA *np_ssa = dynamic_cast<NPairHalfBinNewtonSSA*>(list->np);
if (!np_ssa) error->one(FLERR, "NPair wasn't a NPairHalfBinNewtonSSA object");
int ssa_phaseCt = np_ssa->ssa_phaseCt;
int *ssa_phaseLen = np_ssa->ssa_phaseLen;
int **ssa_itemLoc = np_ssa->ssa_itemLoc;
int **ssa_itemLen = np_ssa->ssa_itemLen;
// process neighbors in the local AIR
for (int workPhase = 0; workPhase < ssa_phaseCt; ++workPhase) {
int workItemCt = ssa_phaseLen[workPhase];
for (int workItem = 0; workItem < workItemCt; ++workItem) {
int ct = ssa_itemLen[workPhase][workItem];
ii = ssa_itemLoc[workPhase][workItem];
while (ct-- > 0) {
int len = list->numneigh[ii];
if (len > 0) {
if (useDPDE) ssa_update_dpde(ilist[ii], list->firstneigh[ii], len);
else ssa_update_dpd(ilist[ii], list->firstneigh[ii], len);
}
ii++;
}
}
}
ii = inum;
//Loop over all 13 outward directions (7 stages)
for (airnum = 1; airnum <=7; airnum++){
int ct = list->AIRct_ssa[airnum];
// Communicate the updated velocities to all nodes
comm->forward_comm_fix(this);
if(useDPDE){
// Zero out the ghosts' uCond & uMech to be used as delta accumulators
memset(&(atom->uCond[nlocal]), 0, sizeof(double)*nghost);
memset(&(atom->uMech[nlocal]), 0, sizeof(double)*nghost);
}
// process neighbors in this AIR
while (ct-- > 0) {
int len = list->numneigh[ii];
if (useDPDE) ssa_update_dpde(ilist[ii], list->firstneigh[ii], len);
else ssa_update_dpd(ilist[ii], list->firstneigh[ii], len);
ii++;
}
// Communicate the ghost deltas to the atom owners
comm->reverse_comm_fix(this);
} //End Loop over all directions For airnum = Top, Top-Right, Right, Bottom-Right, Back
#ifdef DEBUG_PAIR_CT
for (int i = 0; i < 32; ++i) fprintf(stdout, "%8d", hist[i]);
fprintf(stdout, "\n%6d %6d,%6d %6d: "
,counters[0][2]
,counters[1][2]
,counters[0][1]
,counters[1][1]
);
#endif
memory->sfree(v_t0);
v_t0 = NULL;
}
/* ---------------------------------------------------------------------- */
int FixShardlow::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
int ii,jj,m;
double **v = atom->v;
m = 0;
for (ii = 0; ii < n; ii++) {
jj = list[ii];
buf[m++] = v[jj][0];
buf[m++] = v[jj][1];
buf[m++] = v[jj][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
void FixShardlow::unpack_forward_comm(int n, int first, double *buf)
{
int ii,m,last;
int nlocal = atom->nlocal;
double **v = atom->v;
m = 0;
last = first + n ;
for (ii = first; ii < last; ii++) {
v_t0[ii - nlocal][0] = v[ii][0] = buf[m++];
v_t0[ii - nlocal][1] = v[ii][1] = buf[m++];
v_t0[ii - nlocal][2] = v[ii][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int FixShardlow::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
int nlocal = atom->nlocal;
double **v = atom->v;
double *uCond = atom->uCond;
double *uMech = atom->uMech;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = v[i][0] - v_t0[i - nlocal][0];
buf[m++] = v[i][1] - v_t0[i - nlocal][1];
buf[m++] = v[i][2] - v_t0[i - nlocal][2];
if(pairDPDE){
buf[m++] = uCond[i]; // for ghosts, this is an accumulated delta
buf[m++] = uMech[i]; // for ghosts, this is an accumulated delta
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void FixShardlow::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
double **v = atom->v;
double *uCond = atom->uCond;
double *uMech = atom->uMech;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
v[j][0] += buf[m++];
v[j][1] += buf[m++];
v[j][2] += buf[m++];
if(pairDPDE){
uCond[j] += buf[m++]; // add in the accumulated delta
uMech[j] += buf[m++]; // add in the accumulated delta
}
}
}
/* ---------------------------------------------------------------------- */
double FixShardlow::memory_usage()
{
double bytes = 0.0;
bytes += sizeof(double)*3*atom->nghost; // v_t0[]
return bytes;
}
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