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lammps/src/RHEO/compute_rheo_interface.cpp
jtclemm 09cd209c62 typo
2024-11-26 15:56:03 -07:00

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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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
Joel Clemmer (SNL), Thomas O'Connor (CMU), Eric Palermo (CMU)
----------------------------------------------------------------------- */
#include "compute_rheo_interface.h"
#include "atom.h"
#include "comm.h"
#include "compute_rheo_kernel.h"
#include "domain.h"
#include "error.h"
#include "fix_rheo.h"
#include "fix_rheo_pressure.h"
#include "force.h"
#include "math_extra.h"
#include "memory.h"
#include "modify.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor.h"
#include <cmath>
using namespace LAMMPS_NS;
using namespace RHEO_NS;
using namespace MathExtra;
static constexpr double EPSILON = 1e-1;
/* ---------------------------------------------------------------------- */
ComputeRHEOInterface::ComputeRHEOInterface(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg), chi(nullptr), fp_store(nullptr), fix_rheo(nullptr), rho0(nullptr),
norm(nullptr), normwf(nullptr), id_fix_pa(nullptr), list(nullptr), compute_kernel(nullptr),
fix_pressure(nullptr)
{
if (narg != 3) error->all(FLERR, "Illegal compute rheo/interface command");
comm_forward = 3;
comm_reverse = 4;
nmax_store = atom->nmax;
memory->create(chi, nmax_store, "rheo:chi");
memory->create(norm, nmax_store, "rheo/interface:norm");
memory->create(normwf, nmax_store, "rheo/interface:normwf");
// For fp_store, create an instance of fix property atom
// Need restarts + exchanging with neighbors since it needs to persist
// between timesteps (fix property atom will handle callbacks)
int tmp1, tmp2;
int index = atom->find_custom("fp_store", tmp1, tmp2);
if (index == -1) {
id_fix_pa = utils::strdup(id + std::string("_fix_property_atom"));
modify->add_fix(fmt::format("{} all property/atom d2_fp_store 3", id_fix_pa));
index = atom->find_custom("fp_store", tmp1, tmp2);
}
fp_store = atom->darray[index];
}
/* ---------------------------------------------------------------------- */
ComputeRHEOInterface::~ComputeRHEOInterface()
{
if (id_fix_pa && modify->nfix) modify->delete_fix(id_fix_pa);
delete[] id_fix_pa;
memory->destroy(chi);
memory->destroy(norm);
memory->destroy(normwf);
}
/* ---------------------------------------------------------------------- */
void ComputeRHEOInterface::init()
{
compute_kernel = fix_rheo->compute_kernel;
rho0 = fix_rheo->rho0;
cut = fix_rheo->cut;
cutsq = cut * cut;
wall_max = sqrt(3.0) / 12.0 * cut;
auto fixes = modify->get_fix_by_style("rheo/pressure");
fix_pressure = dynamic_cast<FixRHEOPressure *>(fixes[0]);
if (!fix_pressure->invertible_pressure)
error->all(FLERR, "RHEO interface reconstruction incompatible with pressure equation of state");
neighbor->add_request(this, NeighConst::REQ_DEFAULT);
}
/* ---------------------------------------------------------------------- */
void ComputeRHEOInterface::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void ComputeRHEOInterface::compute_peratom()
{
int a, i, j, ii, jj, jnum, itype, jtype, fluidi, fluidj, status_match;
double xtmp, ytmp, ztmp, rsq, w, dot, dx[3];
int inum, *ilist, *jlist, *numneigh, **firstneigh;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double **x = atom->x;
int *type = atom->type;
int newton = force->newton;
int *status = atom->rheo_status;
double *rho = atom->rho;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
if (atom->nmax > nmax_store) {
nmax_store = atom->nmax;
memory->grow(norm, nmax_store, "rheo/interface:norm");
memory->grow(normwf, nmax_store, "rheo/interface:normwf");
memory->grow(chi, nmax_store, "rheo:chi");
}
for (i = 0; i < nall; i++) {
if (status[i] & PHASECHECK) rho[i] = 0.0;
normwf[i] = 0.0;
norm[i] = 0.0;
chi[i] = 0.0;
}
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
fluidi = !(status[i] & PHASECHECK);
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
dx[0] = xtmp - x[j][0];
dx[1] = ytmp - x[j][1];
dx[2] = ztmp - x[j][2];
rsq = lensq3(dx);
if (rsq < cutsq) {
jtype = type[j];
fluidj = !(status[j] & PHASECHECK);
w = compute_kernel->calc_w_quintic(sqrt(rsq));
norm[i] += w;
status_match = 0;
if ((fluidi && fluidj) || ((!fluidi) && (!fluidj))) status_match = 1;
if (status_match) {
chi[i] += w;
} else {
if (!fluidi) {
dot = 0;
for (a = 0; a < 3; a++) dot += (-fp_store[j][a] + fp_store[i][a]) * dx[a];
rho[i] += w * (fix_pressure->calc_pressure(rho[j], j) - rho[j] * dot);
normwf[i] += w;
}
}
if (newton || j < nlocal) {
norm[j] += w;
if (status_match) {
chi[j] += w;
} else {
if (!fluidj) {
dot = 0;
for (a = 0; a < 3; a++) dot += (-fp_store[i][a] + fp_store[j][a]) * dx[a];
rho[j] += w * (fix_pressure->calc_pressure(rho[i], i) + rho[i] * dot);
normwf[j] += w;
}
}
}
}
}
}
if (newton) comm->reverse_comm(this);
for (i = 0; i < nlocal; i++) {
if (norm[i] != 0.0) chi[i] /= norm[i];
// Recalculate rho for non-fluid particles
if (status[i] & PHASECHECK) {
if (normwf[i] != 0.0) {
// Stores rho for solid particles 1+Pw in Adami Adams 2012
rho[i] = MAX(EPSILON, fix_pressure->calc_rho(rho[i] / normwf[i], i));
} else {
rho[i] = rho0[itype];
}
}
}
comm_stage = 1;
comm->forward_comm(this, 2);
}
/* ---------------------------------------------------------------------- */
int ComputeRHEOInterface::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/,
int * /*pbc*/)
{
int m = 0;
double *rho = atom->rho;
for (int i = 0; i < n; i++) {
int j = list[i];
if (comm_stage == 0) {
buf[m++] = fp_store[j][0];
buf[m++] = fp_store[j][1];
buf[m++] = fp_store[j][2];
} else {
buf[m++] = chi[j];
buf[m++] = rho[j];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void ComputeRHEOInterface::unpack_forward_comm(int n, int first, double *buf)
{
double *rho = atom->rho;
int m = 0;
int last = first + n;
for (int i = first; i < last; i++) {
if (comm_stage == 0) {
fp_store[i][0] = buf[m++];
fp_store[i][1] = buf[m++];
fp_store[i][2] = buf[m++];
} else {
chi[i] = buf[m++];
rho[i] = buf[m++];
}
}
}
/* ---------------------------------------------------------------------- */
int ComputeRHEOInterface::pack_reverse_comm(int n, int first, double *buf)
{
double *rho = atom->rho;
int m = 0;
int last = first + n;
for (int i = first; i < last; i++) {
buf[m++] = norm[i];
buf[m++] = chi[i];
buf[m++] = normwf[i];
buf[m++] = rho[i];
}
return m;
}
/* ---------------------------------------------------------------------- */
void ComputeRHEOInterface::unpack_reverse_comm(int n, int *list, double *buf)
{
double *rho = atom->rho;
int *status = atom->rheo_status;
int m = 0;
for (int i = 0; i < n; i++) {
int j = list[i];
norm[j] += buf[m++];
chi[j] += buf[m++];
if (status[j] & PHASECHECK) {
normwf[j] += buf[m++];
rho[j] += buf[m++];
} else {
m++;
m++;
}
}
}
/* ---------------------------------------------------------------------- */
void ComputeRHEOInterface::correct_v(double *v_solid, double *v_fluid, int i_solid, int i_fluid)
{
double wall_prefactor, wall_denom, wall_numer;
wall_numer = MAX(2.0 * cut * (chi[i_solid] - 0.5), 0.0);
wall_denom = MAX(2.0 * cut * (chi[i_fluid] - 0.5), wall_max);
wall_prefactor = wall_numer / wall_denom;
v_solid[0] = (v_solid[0] - v_fluid[0]) * wall_prefactor;
v_solid[1] = (v_solid[1] - v_fluid[1]) * wall_prefactor;
v_solid[2] = (v_solid[2] - v_fluid[2]) * wall_prefactor;
}
/* ---------------------------------------------------------------------- */
double ComputeRHEOInterface::correct_rho(int i_solid)
{
int itype = atom->type[i_solid];
return MAX(rho0[itype], atom->rho[i_solid]);
}
/* ---------------------------------------------------------------------- */
void ComputeRHEOInterface::store_forces()
{
double minv;
int *type = atom->type;
int *mask = atom->mask;
double *mass = atom->mass;
double *rmass = atom->rmass;
double **f = atom->f;
// When this is called, fp_store stores the pressure force
// After this method, fp_store instead stores non-pressure forces
// and is also normalized by the particles mass
// If forces are overwritten by a fix, there are no pressure forces
// so just normalize
auto fixlist = modify->get_fix_by_style("setforce");
if (fixlist.size() != 0) {
for (const auto &fix : fixlist) {
for (int i = 0; i < atom->nlocal; i++) {
if (rmass)
minv = 1.0 / rmass[i];
else
minv = 1.0 / mass[type[i]];
if (mask[i] & fix->groupbit)
for (int a = 0; a < 3; a++) fp_store[i][a] = f[i][a] * minv;
else
for (int a = 0; a < 3; a++) fp_store[i][a] = (f[i][a] - fp_store[i][a]) * minv;
}
}
} else {
if (rmass) {
for (int i = 0; i < atom->nlocal; i++) {
minv = 1.0 / rmass[i];
for (int a = 0; a < 3; a++) fp_store[i][a] = (f[i][a] - fp_store[i][a]) * minv;
}
} else {
for (int i = 0; i < atom->nlocal; i++) {
minv = 1.0 / mass[type[i]];
for (int a = 0; a < 3; a++) fp_store[i][a] = (f[i][a] - fp_store[i][a]) * minv;
}
}
}
// Forward comm forces
comm_stage = 0;
comm->forward_comm(this, 3);
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeRHEOInterface::memory_usage()
{
double bytes = 3 * nmax_store * sizeof(double);
return bytes;
}
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