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11871ceb2ebf9d1e00354fea9774973e8ec36ec5
lammps/src/REPLICA/fix_pimd.cpp
Axel Kohlmeyer ba0d24d028 must initialize "np" in constructor
2023-01-26 18:33:48 -05:00

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Package FixPIMD
Purpose Quantum Path Integral Algorithm for Quantum Chemistry
Copyright Voth Group @ University of Chicago
Authors Chris Knight & Yuxing Peng (yuxing at uchicago.edu)
Updated Oct-01-2011
Version 1.0
------------------------------------------------------------------------- */
#include "fix_pimd.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "universe.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
enum { PIMD, NMPIMD, CMD };
/* ---------------------------------------------------------------------- */
FixPIMD::FixPIMD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
{
max_nsend = 0;
tag_send = nullptr;
buf_send = nullptr;
max_nlocal = 0;
buf_recv = nullptr;
buf_beads = nullptr;
size_plan = 0;
plan_send = plan_recv = nullptr;
M_x2xp = M_xp2x = M_f2fp = M_fp2f = nullptr;
lam = nullptr;
mode_index = nullptr;
mass = nullptr;
array_atom = nullptr;
nhc_eta = nullptr;
nhc_eta_dot = nullptr;
nhc_eta_dotdot = nullptr;
nhc_eta_mass = nullptr;
method = PIMD;
fmass = 1.0;
nhc_temp = 298.15;
nhc_nchain = 2;
sp = 1.0;
np = universe->nworlds;
for (int i = 3; i < narg - 1; i += 2) {
if (strcmp(arg[i], "method") == 0) {
if (strcmp(arg[i + 1], "pimd") == 0)
method = PIMD;
else if (strcmp(arg[i + 1], "nmpimd") == 0)
method = NMPIMD;
else if (strcmp(arg[i + 1], "cmd") == 0)
method = CMD;
else
error->universe_all(FLERR, fmt::format("Unknown method parameter {} for fix pimd",
arg[i + 1]));
} else if (strcmp(arg[i], "fmass") == 0) {
fmass = utils::numeric(FLERR, arg[i + 1], false, lmp);
if ((fmass < 0.0) || (fmass > np))
error->universe_all(FLERR, fmt::format("Invalid fmass value {} for fix pimd", fmass));
} else if (strcmp(arg[i], "sp") == 0) {
sp = utils::numeric(FLERR, arg[i + 1], false, lmp);
if (sp < 0.0) error->universe_all(FLERR, "Invalid sp value for fix pimd");
} else if (strcmp(arg[i], "temp") == 0) {
nhc_temp = utils::numeric(FLERR, arg[i + 1], false, lmp);
if (nhc_temp < 0.0) error->universe_all(FLERR, "Invalid temp value for fix pimd");
} else if (strcmp(arg[i], "nhc") == 0) {
nhc_nchain = utils::inumeric(FLERR, arg[i + 1], false, lmp);
if (nhc_nchain < 2) error->universe_all(FLERR, "Invalid nhc value for fix pimd");
} else
error->universe_all(FLERR, fmt::format("Unknown keyword {} for fix pimd", arg[i]));
}
if (strcmp(update->unit_style, "lj") == 0)
error->all(FLERR, "Fix pimd does not support lj units");
/* Initiation */
size_peratom_cols = 12 * nhc_nchain + 3;
nhc_offset_one_1 = 3 * nhc_nchain;
nhc_offset_one_2 = 3 * nhc_nchain + 3;
nhc_size_one_1 = sizeof(double) * nhc_offset_one_1;
nhc_size_one_2 = sizeof(double) * nhc_offset_one_2;
restart_peratom = 1;
peratom_flag = 1;
peratom_freq = 1;
global_freq = 1;
vector_flag = 1;
size_vector = 3;
extvector = 1;
comm_forward = 3;
atom->add_callback(Atom::GROW); // Call LAMMPS to allocate memory for per-atom array
atom->add_callback(Atom::RESTART); // Call LAMMPS to re-assign restart-data for per-atom array
grow_arrays(atom->nmax);
// some initilizations
nhc_ready = false;
}
/* ---------------------------------------------------------------------- */
FixPIMD::~FixPIMD()
{
delete[] mass;
atom->delete_callback(id, Atom::GROW);
atom->delete_callback(id, Atom::RESTART);
memory->destroy(M_x2xp);
memory->destroy(M_xp2x);
memory->destroy(M_f2fp);
memory->destroy(M_fp2f);
memory->sfree(lam);
if (buf_beads)
for (int i = 0; i < np; i++) memory->sfree(buf_beads[i]);
delete[] buf_beads;
delete[] plan_send;
delete[] plan_recv;
delete[] mode_index;
memory->sfree(tag_send);
memory->sfree(buf_send);
memory->sfree(buf_recv);
memory->destroy(array_atom);
memory->destroy(nhc_eta);
memory->destroy(nhc_eta_dot);
memory->destroy(nhc_eta_dotdot);
memory->destroy(nhc_eta_mass);
}
/* ---------------------------------------------------------------------- */
int FixPIMD::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixPIMD::init()
{
if (atom->map_style == Atom::MAP_NONE)
error->all(FLERR, "Fix pimd requires an atom map, see atom_modify");
if (universe->me == 0 && universe->uscreen)
fprintf(universe->uscreen, "Fix pimd initializing Path-Integral ...\n");
// prepare the constants
inverse_np = 1.0 / np;
/* The first solution for the force constant, using SI units
const double Boltzmann = 1.3806488E-23; // SI unit: J/K
const double Plank = 6.6260755E-34; // SI unit: m^2 kg / s
double hbar = Plank / ( 2.0 * MY_PI ) * sp;
double beta = 1.0 / ( Boltzmann * input.nh_temp);
// - P / ( beta^2 * hbar^2) SI unit: s^-2
double _fbond = -1.0 / (beta*beta*hbar*hbar) * input.nbeads;
// convert the units: s^-2 -> (kcal/mol) / (g/mol) / (A^2)
fbond = _fbond * 4.184E+26;
*/
/* The current solution, using LAMMPS internal real units */
const double Boltzmann = force->boltz;
const double Plank = force->hplanck;
double hbar = Plank / (2.0 * MY_PI);
double beta = 1.0 / (Boltzmann * nhc_temp);
double _fbond = 1.0 * np / (beta * beta * hbar * hbar);
omega_np = sqrt((double) np) / (hbar * beta) * sqrt(force->mvv2e);
fbond = -_fbond * force->mvv2e;
if (universe->me == 0)
printf("Fix pimd -P/(beta^2 * hbar^2) = %20.7lE (kcal/mol/A^2)\n\n", fbond);
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
comm_init();
mass = new double[atom->ntypes + 1];
if (method == CMD || method == NMPIMD)
nmpimd_init();
else
for (int i = 1; i <= atom->ntypes; i++) mass[i] = atom->mass[i] / np * fmass;
if (!nhc_ready) nhc_init();
}
/* ---------------------------------------------------------------------- */
void FixPIMD::setup(int vflag)
{
if (universe->me == 0 && universe->uscreen)
fprintf(universe->uscreen, "Setting up Path-Integral ...\n");
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixPIMD::initial_integrate(int /*vflag*/)
{
nhc_update_v();
nhc_update_x();
}
/* ---------------------------------------------------------------------- */
void FixPIMD::final_integrate()
{
nhc_update_v();
}
/* ---------------------------------------------------------------------- */
void FixPIMD::post_force(int /*flag*/)
{
for (int i = 0; i < atom->nlocal; i++)
for (int j = 0; j < 3; j++) atom->f[i][j] /= np;
comm_exec(atom->x);
spring_force();
if (method == CMD || method == NMPIMD) {
/* forward comm for the force on ghost atoms */
nmpimd_fill(atom->f);
/* inter-partition comm */
comm_exec(atom->f);
/* normal-mode transform */
nmpimd_transform(buf_beads, atom->f, M_f2fp[universe->iworld]);
}
}
/* ----------------------------------------------------------------------
Nose-Hoover Chains
------------------------------------------------------------------------- */
void FixPIMD::nhc_init()
{
double tau = 1.0 / omega_np;
double KT = force->boltz * nhc_temp;
double mass0 = KT * tau * tau;
int max = 3 * atom->nlocal;
for (int i = 0; i < max; i++) {
for (int ichain = 0; ichain < nhc_nchain; ichain++) {
nhc_eta[i][ichain] = 0.0;
nhc_eta_dot[i][ichain] = 0.0;
nhc_eta_dot[i][ichain] = 0.0;
nhc_eta_dotdot[i][ichain] = 0.0;
nhc_eta_mass[i][ichain] = mass0;
if ((method == CMD || method == NMPIMD) && universe->iworld == 0)
; // do nothing
else
nhc_eta_mass[i][ichain] *= fmass;
}
nhc_eta_dot[i][nhc_nchain] = 0.0;
for (int ichain = 1; ichain < nhc_nchain; ichain++)
nhc_eta_dotdot[i][ichain] = (nhc_eta_mass[i][ichain - 1] * nhc_eta_dot[i][ichain - 1] *
nhc_eta_dot[i][ichain - 1] * force->mvv2e -
KT) /
nhc_eta_mass[i][ichain];
}
// Zero NH acceleration for CMD
if (method == CMD && universe->iworld == 0)
for (int i = 0; i < max; i++)
for (int ichain = 0; ichain < nhc_nchain; ichain++) nhc_eta_dotdot[i][ichain] = 0.0;
nhc_ready = true;
}
/* ---------------------------------------------------------------------- */
void FixPIMD::nhc_update_x()
{
int n = atom->nlocal;
double **x = atom->x;
double **v = atom->v;
if (method == CMD || method == NMPIMD) {
nmpimd_fill(atom->v);
comm_exec(atom->v);
/* borrow the space of atom->f to store v in cartisian */
v = atom->f;
nmpimd_transform(buf_beads, v, M_xp2x[universe->iworld]);
}
for (int i = 0; i < n; i++) {
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
}
}
/* ---------------------------------------------------------------------- */
void FixPIMD::nhc_update_v()
{
int n = atom->nlocal;
int *type = atom->type;
double **v = atom->v;
double **f = atom->f;
for (int i = 0; i < n; i++) {
double dtfm = dtf / mass[type[i]];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
}
t_sys = 0.0;
if (method == CMD && universe->iworld == 0) return;
double expfac;
int nmax = 3 * atom->nlocal;
double KT = force->boltz * nhc_temp;
double kecurrent, t_current;
double dthalf = 0.5 * update->dt;
double dt4 = 0.25 * update->dt;
double dt8 = 0.125 * update->dt;
for (int i = 0; i < nmax; i++) {
int iatm = i / 3;
int idim = i % 3;
double *vv = v[iatm];
kecurrent = mass[type[iatm]] * vv[idim] * vv[idim] * force->mvv2e;
t_current = kecurrent / force->boltz;
double *eta = nhc_eta[i];
double *eta_dot = nhc_eta_dot[i];
double *eta_dotdot = nhc_eta_dotdot[i];
eta_dotdot[0] = (kecurrent - KT) / nhc_eta_mass[i][0];
for (int ichain = nhc_nchain - 1; ichain > 0; ichain--) {
expfac = exp(-dt8 * eta_dot[ichain + 1]);
eta_dot[ichain] *= expfac;
eta_dot[ichain] += eta_dotdot[ichain] * dt4;
eta_dot[ichain] *= expfac;
}
expfac = exp(-dt8 * eta_dot[1]);
eta_dot[0] *= expfac;
eta_dot[0] += eta_dotdot[0] * dt4;
eta_dot[0] *= expfac;
// Update particle velocities half-step
double factor_eta = exp(-dthalf * eta_dot[0]);
vv[idim] *= factor_eta;
t_current *= (factor_eta * factor_eta);
kecurrent = force->boltz * t_current;
eta_dotdot[0] = (kecurrent - KT) / nhc_eta_mass[i][0];
for (int ichain = 0; ichain < nhc_nchain; ichain++) eta[ichain] += dthalf * eta_dot[ichain];
eta_dot[0] *= expfac;
eta_dot[0] += eta_dotdot[0] * dt4;
eta_dot[0] *= expfac;
for (int ichain = 1; ichain < nhc_nchain; ichain++) {
expfac = exp(-dt8 * eta_dot[ichain + 1]);
eta_dot[ichain] *= expfac;
eta_dotdot[ichain] =
(nhc_eta_mass[i][ichain - 1] * eta_dot[ichain - 1] * eta_dot[ichain - 1] - KT) /
nhc_eta_mass[i][ichain];
eta_dot[ichain] += eta_dotdot[ichain] * dt4;
eta_dot[ichain] *= expfac;
}
t_sys += t_current;
}
t_sys /= nmax;
}
/* ----------------------------------------------------------------------
Normal Mode PIMD
------------------------------------------------------------------------- */
void FixPIMD::nmpimd_init()
{
memory->create(M_x2xp, np, np, "fix_feynman:M_x2xp");
memory->create(M_xp2x, np, np, "fix_feynman:M_xp2x");
memory->create(M_f2fp, np, np, "fix_feynman:M_f2fp");
memory->create(M_fp2f, np, np, "fix_feynman:M_fp2f");
lam = (double *) memory->smalloc(sizeof(double) * np, "FixPIMD::lam");
// Set up eigenvalues
lam[0] = 0.0;
if (np % 2 == 0) lam[np - 1] = 4.0 * np;
for (int i = 2; i <= np / 2; i++) {
lam[2 * i - 3] = lam[2 * i - 2] = 2.0 * np * (1.0 - 1.0 * cos(2.0 * MY_PI * (i - 1) / np));
}
// Set up eigenvectors for non-degenerated modes
for (int i = 0; i < np; i++) {
M_x2xp[0][i] = 1.0 / np;
if (np % 2 == 0) M_x2xp[np - 1][i] = 1.0 / np * pow(-1.0, i);
}
// Set up eigenvectors for degenerated modes
for (int i = 0; i < (np - 1) / 2; i++)
for (int j = 0; j < np; j++) {
M_x2xp[2 * i + 1][j] = sqrt(2.0) * cos(2.0 * MY_PI * (i + 1) * j / np) / np;
M_x2xp[2 * i + 2][j] = -sqrt(2.0) * sin(2.0 * MY_PI * (i + 1) * j / np) / np;
}
// Set up Ut
for (int i = 0; i < np; i++)
for (int j = 0; j < np; j++) {
M_xp2x[i][j] = M_x2xp[j][i] * np;
M_f2fp[i][j] = M_x2xp[i][j] * np;
M_fp2f[i][j] = M_xp2x[i][j];
}
// Set up masses
int iworld = universe->iworld;
for (int i = 1; i <= atom->ntypes; i++) {
mass[i] = atom->mass[i];
if (iworld) {
mass[i] *= lam[iworld];
mass[i] *= fmass;
}
}
}
/* ---------------------------------------------------------------------- */
void FixPIMD::nmpimd_fill(double **ptr)
{
comm_ptr = ptr;
comm->forward_comm(this);
}
/* ---------------------------------------------------------------------- */
void FixPIMD::nmpimd_transform(double **src, double **des, double *vector)
{
int n = atom->nlocal;
int m = 0;
for (int i = 0; i < n; i++)
for (int d = 0; d < 3; d++) {
des[i][d] = 0.0;
for (int j = 0; j < np; j++) { des[i][d] += (src[j][m] * vector[j]); }
m++;
}
}
/* ---------------------------------------------------------------------- */
void FixPIMD::spring_force()
{
spring_energy = 0.0;
double **x = atom->x;
double **f = atom->f;
double *_mass = atom->mass;
int *type = atom->type;
int nlocal = atom->nlocal;
double *xlast = buf_beads[x_last];
double *xnext = buf_beads[x_next];
virial = 0.0;
for (int i = 0; i < nlocal; i++) {
double delx1 = xlast[0] - x[i][0];
double dely1 = xlast[1] - x[i][1];
double delz1 = xlast[2] - x[i][2];
xlast += 3;
domain->minimum_image(delx1, dely1, delz1);
double delx2 = xnext[0] - x[i][0];
double dely2 = xnext[1] - x[i][1];
double delz2 = xnext[2] - x[i][2];
xnext += 3;
domain->minimum_image(delx2, dely2, delz2);
double ff = fbond * _mass[type[i]];
double dx = delx1 + delx2;
double dy = dely1 + dely2;
double dz = delz1 + delz2;
virial += -0.5 * (x[i][0] * f[i][0] + x[i][1] * f[i][1] + x[i][2] * f[i][2]);
f[i][0] -= (dx) *ff;
f[i][1] -= (dy) *ff;
f[i][2] -= (dz) *ff;
spring_energy += -0.5 * ff * (delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
}
}
/* ----------------------------------------------------------------------
Comm operations
------------------------------------------------------------------------- */
void FixPIMD::comm_init()
{
if (size_plan) {
delete[] plan_send;
delete[] plan_recv;
}
if (method == PIMD) {
size_plan = 2;
plan_send = new int[2];
plan_recv = new int[2];
mode_index = new int[2];
int rank_last = universe->me - comm->nprocs;
int rank_next = universe->me + comm->nprocs;
if (rank_last < 0) rank_last += universe->nprocs;
if (rank_next >= universe->nprocs) rank_next -= universe->nprocs;
plan_send[0] = rank_next;
plan_send[1] = rank_last;
plan_recv[0] = rank_last;
plan_recv[1] = rank_next;
mode_index[0] = 0;
mode_index[1] = 1;
x_last = 1;
x_next = 0;
} else {
size_plan = np - 1;
plan_send = new int[size_plan];
plan_recv = new int[size_plan];
mode_index = new int[size_plan];
for (int i = 0; i < size_plan; i++) {
plan_send[i] = universe->me + comm->nprocs * (i + 1);
if (plan_send[i] >= universe->nprocs) plan_send[i] -= universe->nprocs;
plan_recv[i] = universe->me - comm->nprocs * (i + 1);
if (plan_recv[i] < 0) plan_recv[i] += universe->nprocs;
mode_index[i] = (universe->iworld + i + 1) % (universe->nworlds);
}
x_next = (universe->iworld + 1 + universe->nworlds) % (universe->nworlds);
x_last = (universe->iworld - 1 + universe->nworlds) % (universe->nworlds);
}
if (buf_beads) {
for (int i = 0; i < np; i++) delete[] buf_beads[i];
delete[] buf_beads;
}
buf_beads = new double *[np];
for (int i = 0; i < np; i++) buf_beads[i] = nullptr;
}
/* ---------------------------------------------------------------------- */
void FixPIMD::comm_exec(double **ptr)
{
int nlocal = atom->nlocal;
if (nlocal > max_nlocal) {
max_nlocal = nlocal + 200;
int size = sizeof(double) * max_nlocal * 3;
buf_recv = (double *) memory->srealloc(buf_recv, size, "FixPIMD:x_recv");
for (int i = 0; i < np; i++)
buf_beads[i] = (double *) memory->srealloc(buf_beads[i], size, "FixPIMD:x_beads[i]");
}
// copy local positions
memcpy(buf_beads[universe->iworld], &(ptr[0][0]), sizeof(double) * nlocal * 3);
// go over comm plans
for (int iplan = 0; iplan < size_plan; iplan++) {
// sendrecv nlocal
int nsend;
MPI_Sendrecv(&(nlocal), 1, MPI_INT, plan_send[iplan], 0, &(nsend), 1, MPI_INT, plan_recv[iplan],
0, universe->uworld, MPI_STATUS_IGNORE);
// allocate arrays
if (nsend > max_nsend) {
max_nsend = nsend + 200;
tag_send =
(tagint *) memory->srealloc(tag_send, sizeof(tagint) * max_nsend, "FixPIMD:tag_send");
buf_send =
(double *) memory->srealloc(buf_send, sizeof(double) * max_nsend * 3, "FixPIMD:x_send");
}
// send tags
MPI_Sendrecv(atom->tag, nlocal, MPI_LMP_TAGINT, plan_send[iplan], 0, tag_send, nsend,
MPI_LMP_TAGINT, plan_recv[iplan], 0, universe->uworld, MPI_STATUS_IGNORE);
// wrap positions
double *wrap_ptr = buf_send;
int ncpy = sizeof(double) * 3;
for (int i = 0; i < nsend; i++) {
int index = atom->map(tag_send[i]);
if (index < 0) {
auto mesg = fmt::format("Atom {} is missing at world [{}] rank [{}] "
"required by rank [{}] ({}, {}, {}).\n",
tag_send[i], universe->iworld, comm->me, plan_recv[iplan],
atom->tag[0], atom->tag[1], atom->tag[2]);
error->universe_one(FLERR, mesg);
}
memcpy(wrap_ptr, ptr[index], ncpy);
wrap_ptr += 3;
}
// sendrecv x
MPI_Sendrecv(buf_send, nsend * 3, MPI_DOUBLE, plan_recv[iplan], 0, buf_recv, nlocal * 3,
MPI_DOUBLE, plan_send[iplan], 0, universe->uworld, MPI_STATUS_IGNORE);
// copy x
memcpy(buf_beads[mode_index[iplan]], buf_recv, sizeof(double) * nlocal * 3);
}
}
/* ---------------------------------------------------------------------- */
int FixPIMD::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
{
int i, j, m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = comm_ptr[j][0];
buf[m++] = comm_ptr[j][1];
buf[m++] = comm_ptr[j][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
void FixPIMD::unpack_forward_comm(int n, int first, double *buf)
{
int i, m, last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
comm_ptr[i][0] = buf[m++];
comm_ptr[i][1] = buf[m++];
comm_ptr[i][2] = buf[m++];
}
}
/* ----------------------------------------------------------------------
Memory operations
------------------------------------------------------------------------- */
double FixPIMD::memory_usage()
{
return (double) atom->nmax * size_peratom_cols * sizeof(double);
}
/* ---------------------------------------------------------------------- */
void FixPIMD::grow_arrays(int nmax)
{
if (nmax == 0) return;
int count = nmax * 3;
memory->grow(array_atom, nmax, size_peratom_cols, "FixPIMD::array_atom");
memory->grow(nhc_eta, count, nhc_nchain, "FixPIMD::nh_eta");
memory->grow(nhc_eta_dot, count, nhc_nchain + 1, "FixPIMD::nh_eta_dot");
memory->grow(nhc_eta_dotdot, count, nhc_nchain, "FixPIMD::nh_eta_dotdot");
memory->grow(nhc_eta_mass, count, nhc_nchain, "FixPIMD::nh_eta_mass");
}
/* ---------------------------------------------------------------------- */
void FixPIMD::copy_arrays(int i, int j, int /*delflag*/)
{
int i_pos = i * 3;
int j_pos = j * 3;
memcpy(nhc_eta[j_pos], nhc_eta[i_pos], nhc_size_one_1);
memcpy(nhc_eta_dot[j_pos], nhc_eta_dot[i_pos], nhc_size_one_2);
memcpy(nhc_eta_dotdot[j_pos], nhc_eta_dotdot[i_pos], nhc_size_one_1);
memcpy(nhc_eta_mass[j_pos], nhc_eta_mass[i_pos], nhc_size_one_1);
}
/* ---------------------------------------------------------------------- */
int FixPIMD::pack_exchange(int i, double *buf)
{
int offset = 0;
int pos = i * 3;
memcpy(buf + offset, nhc_eta[pos], nhc_size_one_1);
offset += nhc_offset_one_1;
memcpy(buf + offset, nhc_eta_dot[pos], nhc_size_one_2);
offset += nhc_offset_one_2;
memcpy(buf + offset, nhc_eta_dotdot[pos], nhc_size_one_1);
offset += nhc_offset_one_1;
memcpy(buf + offset, nhc_eta_mass[pos], nhc_size_one_1);
offset += nhc_offset_one_1;
return size_peratom_cols;
}
/* ---------------------------------------------------------------------- */
int FixPIMD::unpack_exchange(int nlocal, double *buf)
{
int offset = 0;
int pos = nlocal * 3;
memcpy(nhc_eta[pos], buf + offset, nhc_size_one_1);
offset += nhc_offset_one_1;
memcpy(nhc_eta_dot[pos], buf + offset, nhc_size_one_2);
offset += nhc_offset_one_2;
memcpy(nhc_eta_dotdot[pos], buf + offset, nhc_size_one_1);
offset += nhc_offset_one_1;
memcpy(nhc_eta_mass[pos], buf + offset, nhc_size_one_1);
offset += nhc_offset_one_1;
return size_peratom_cols;
}
/* ---------------------------------------------------------------------- */
int FixPIMD::pack_restart(int i, double *buf)
{
int offset = 0;
int pos = i * 3;
// pack buf[0] this way because other fixes unpack it
buf[offset++] = size_peratom_cols + 1;
memcpy(buf + offset, nhc_eta[pos], nhc_size_one_1);
offset += nhc_offset_one_1;
memcpy(buf + offset, nhc_eta_dot[pos], nhc_size_one_2);
offset += nhc_offset_one_2;
memcpy(buf + offset, nhc_eta_dotdot[pos], nhc_size_one_1);
offset += nhc_offset_one_1;
memcpy(buf + offset, nhc_eta_mass[pos], nhc_size_one_1);
offset += nhc_offset_one_1;
return size_peratom_cols + 1;
}
/* ---------------------------------------------------------------------- */
void FixPIMD::unpack_restart(int nlocal, int nth)
{
double **extra = atom->extra;
// skip to Nth set of extra values
// unpack the Nth first values this way because other fixes pack them
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int>(extra[nlocal][m]);
m++;
int pos = nlocal * 3;
memcpy(nhc_eta[pos], extra[nlocal] + m, nhc_size_one_1);
m += nhc_offset_one_1;
memcpy(nhc_eta_dot[pos], extra[nlocal] + m, nhc_size_one_2);
m += nhc_offset_one_2;
memcpy(nhc_eta_dotdot[pos], extra[nlocal] + m, nhc_size_one_1);
m += nhc_offset_one_1;
memcpy(nhc_eta_mass[pos], extra[nlocal] + m, nhc_size_one_1);
m += nhc_offset_one_1;
nhc_ready = true;
}
/* ---------------------------------------------------------------------- */
int FixPIMD::maxsize_restart()
{
return size_peratom_cols + 1;
}
/* ---------------------------------------------------------------------- */
int FixPIMD::size_restart(int /*nlocal*/)
{
return size_peratom_cols + 1;
}
/* ---------------------------------------------------------------------- */
double FixPIMD::compute_vector(int n)
{
if (n == 0) { return spring_energy; }
if (n == 1) { return t_sys; }
if (n == 2) { return virial; }
return 0.0;
}
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