Drafting tension model
This commit is contained in:
jtclemm
2
src/.gitignore
vendored
2
src/.gitignore
vendored
@ -223,6 +223,8 @@
|
||||
/fix_rheo_viscosity.h
|
||||
/pair_rheo.cpp
|
||||
/pair_rheo.h
|
||||
/pair_rheo_tension.cpp
|
||||
/pair_rheo_tension.h
|
||||
|
||||
/compute_grid.cpp
|
||||
/compute_grid.h
|
||||
|
||||
369
src/RHEO/pair_rheo_tension.cpp
Normal file
369
src/RHEO/pair_rheo_tension.cpp
Normal file
@ -0,0 +1,369 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
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)
|
||||
----------------------------------------------------------------------- */
|
||||
|
||||
#include "pair_rheo_tension.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "compute_rheo_kernel.h"
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "fix_rheo.h"
|
||||
#include "force.h"
|
||||
#include "math_extra.h"
|
||||
#include "memory.h"
|
||||
#include "modify.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "update.h"
|
||||
#include "utils.h"
|
||||
|
||||
#include <cmath>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace RHEO_NS;
|
||||
using namespace MathExtra;
|
||||
|
||||
static constexpr double EPSILON = 1e-2;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairRHEOTension::PairRHEOTension(LAMMPS *lmp) :
|
||||
Pair(lmp), compute_kernel(nullptr), fix_rheo(nullptr)
|
||||
{
|
||||
restartinfo = 0;
|
||||
single_enable = 0;
|
||||
|
||||
comm_forward = 3;
|
||||
comm_reverse = 3;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairRHEOTension::~PairRHEOTension()
|
||||
{
|
||||
// Remove custom property if it exists
|
||||
int tmp1, tmp2, index;
|
||||
|
||||
index = atom->find_custom("rheo_c_tension", tmp1, tmp2);
|
||||
if (index != -1) atom->remove_custom(index, 1, 0);
|
||||
|
||||
index = atom->find_custom("rheo_n_tension", tmp1, tmp2);
|
||||
if (index != -1) atom->remove_custom(index, 1, 3);
|
||||
|
||||
if (allocated) {
|
||||
memory->destroy(alpha);
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairRHEOTension::compute(int eflag, int vflag)
|
||||
{
|
||||
int i, j, a, b, ii, jj, inum, jnum, itype, jtype;
|
||||
int fluidi, fluidj;
|
||||
double xtmp, ytmp, ztmp, w, wp;
|
||||
double rhoi, rhoj, voli, volj;
|
||||
double *dWij, *dWji;
|
||||
double dx[3], ft[3];
|
||||
|
||||
int *ilist, *jlist, *numneigh, **firstneigh;
|
||||
double imass, jmass, rsq, r, rinv;
|
||||
|
||||
int nlocal = atom->nlocal;
|
||||
int newton_pair = force->newton_pair;
|
||||
int dim = domain->dimension;
|
||||
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
double *rho = atom->rho;
|
||||
double *mass = atom->mass;
|
||||
double *special_lj = force->special_lj;
|
||||
int *type = atom->type;
|
||||
int *status = atom->status;
|
||||
tagint *tag = atom->tag;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
int nmax = atom->nmax;
|
||||
if (nmax_store <= nmax) {
|
||||
memory->grow(c_tension, nmax, "atom:rheo_c_tension");
|
||||
memory->grow(n_tension, nmax, 3, "atom:rheo_n_tension");
|
||||
nmax_store = atom->nmax;
|
||||
}
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
imass = mass[itype];
|
||||
rhoi = rho[i];
|
||||
voli = imass / rhoi;
|
||||
fluidi = !(status[i] & PHASECHECK);
|
||||
|
||||
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);
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq > hsq) continue;
|
||||
|
||||
r = sqrt(rsq);
|
||||
rinv = 1 / r;
|
||||
|
||||
jmass = mass[jtype];
|
||||
rhoj = rho[j];
|
||||
volj = jmass / rhoj;
|
||||
fluidj = !(status[j] & PHASECHECK);
|
||||
|
||||
wp = compute_kernel->calc_dw(i, j, dx[0], dx[1], dx[2],r);
|
||||
dWij = compute_kernel->dWij;
|
||||
dWji = compute_kernel->dWji;
|
||||
|
||||
|
||||
|
||||
f[i][0] += ft[0];
|
||||
f[i][1] += ft[1];
|
||||
f[i][2] += ft[2];
|
||||
|
||||
if (evflag) // Does not account for unbalanced forces
|
||||
ev_tally_xyz(i, j, nlocal, newton_pair, 0.0, 0.0, ft[0], ft[1], ft[2], dx[0], dx[1], dx[2]);
|
||||
|
||||
if (newton_pair || j < nlocal) {
|
||||
|
||||
f[j][0] -= ft[0];
|
||||
f[j][1] -= ft[1];
|
||||
f[j][2] -= ft[2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
|
||||
if (compute_interface) {
|
||||
comm->reverse_comm(this);
|
||||
comm->forward_comm(this);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairRHEOTension::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag, n + 1, n + 1, "pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
memory->create(alpha, n + 1, n + 1, "pair:alpha");
|
||||
memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairRHEOTension::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 3)
|
||||
error->all(FLERR,"Incorrect number of args for pair_style rheo coefficients");
|
||||
if (!allocated)
|
||||
allocate();
|
||||
|
||||
int ilo, ihi, jlo, jhi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi,error);
|
||||
utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi,error);
|
||||
|
||||
alpha_one = utils::numeric(FLERR, arg[2], false, lmp);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = 0; j <= atom->ntypes; j++) {
|
||||
alpha[i][j] = alpha_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0)
|
||||
error->all(FLERR,"Incorrect args for pair rheo/tension coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
setup specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairRHEOTension::setup()
|
||||
{
|
||||
auto fixes = modify->get_fix_by_style("rheo");
|
||||
if (fixes.size() == 0) error->all(FLERR, "Need to define fix rheo to use pair rheo");
|
||||
fix_rheo = dynamic_cast<FixRHEO *>(fixes[0]);
|
||||
|
||||
compute_kernel = fix_rheo->compute_kernel;
|
||||
compute_grad = fix_rheo->compute_grad;
|
||||
compute_interface = fix_rheo->compute_interface;
|
||||
h = fix_rheo->h;
|
||||
csq = fix_rheo->csq;
|
||||
rho0 = fix_rheo->rho0;
|
||||
|
||||
hsq = h * h;
|
||||
hinv = 1.0 / h;
|
||||
hinv3 = hinv * 3.0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairRHEOTension::init_style()
|
||||
{
|
||||
neighbor->add_request(this);
|
||||
|
||||
|
||||
// Create c_tension arrays n_tension arrays if they don't already exist
|
||||
// Create a custom atom property so it works with compute property/atom
|
||||
// Do not create grow callback as there's no reason to copy/exchange data
|
||||
// Manually grow if nmax_store exceeded
|
||||
// For B and gradC, create a local array since they are unlikely to be printed
|
||||
|
||||
int tmp1, tmp2;
|
||||
int index = atom->find_custom("rheo_c_tension", tmp1, tmp2);
|
||||
if (index == -1) index = atom->add_custom("rheo_c_tension", 1, 0);
|
||||
ct = atom->dvector[index];
|
||||
|
||||
index = atom->find_custom("rheo_n_tension", tmp1, tmp2);
|
||||
if (index == -1) index = atom->add_custom("rheo_n_tension", 1, 3);
|
||||
nt = atom->darray[index];
|
||||
|
||||
nmax_store = atom->nmax;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairRHEOTension::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0)
|
||||
error->all(FLERR,"All pair rheo/tension coeffs are not set");
|
||||
|
||||
alpha[j][i] = alpha[i][j];
|
||||
|
||||
return h;
|
||||
}
|
||||
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int PairRHEOTension::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
|
||||
{
|
||||
int i,j,k,m;
|
||||
m = 0;
|
||||
double *rho = atom->rho;
|
||||
|
||||
for (i = 0; i < n; i++) {
|
||||
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 PairRHEOTension::unpack_forward_comm(int n, int first, double *buf)
|
||||
{
|
||||
int i, k, m, last;
|
||||
double *rho = atom->rho;
|
||||
m = 0;
|
||||
last = first + n;
|
||||
for (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 PairRHEOTension::pack_reverse_comm(int n, int first, double *buf)
|
||||
{
|
||||
int i, k, m, last;
|
||||
double **fp_store = compute_interface->fp_store;
|
||||
|
||||
m = 0;
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++) {
|
||||
buf[m++] = fp_store[i][0];
|
||||
buf[m++] = fp_store[i][1];
|
||||
buf[m++] = fp_store[i][2];
|
||||
}
|
||||
|
||||
return m;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairRHEOTension::unpack_reverse_comm(int n, int *list, double *buf)
|
||||
{
|
||||
int i, j, k, m;
|
||||
double **fp_store = compute_interface->fp_store;
|
||||
|
||||
m = 0;
|
||||
for (i = 0; i < n; i++) {
|
||||
j = list[i];
|
||||
fp_store[j][0] += buf[m++];
|
||||
fp_store[j][1] += buf[m++];
|
||||
fp_store[j][2] += buf[m++];
|
||||
}
|
||||
}
|
||||
56
src/RHEO/pair_rheo_tension.h
Normal file
56
src/RHEO/pair_rheo_tension.h
Normal file
@ -0,0 +1,56 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
// clang-format off
|
||||
PairStyle(rheo/tension,PairRHEOTension)
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_RHEO_TENSION_H
|
||||
#define LMP_PAIR_RHEO_TENSION_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairRHEOTension : public Pair {
|
||||
public:
|
||||
PairRHEOTension(class LAMMPS *);
|
||||
~PairRHEOTension() override;
|
||||
void compute(int, int) override;
|
||||
void coeff(int, char **) override;
|
||||
void setup() override;
|
||||
void init_style() override;
|
||||
double init_one(int, int) override;
|
||||
void unpack_forward_comm(int, int, double *) override;
|
||||
int pack_reverse_comm(int, int, double *) override;
|
||||
int pack_reverse_comm(int, int, double *) override;
|
||||
void unpack_reverse_comm(int, int *, double *) override;
|
||||
|
||||
protected:
|
||||
int nmax_store;
|
||||
double **nt, *ct;
|
||||
double *alpha;
|
||||
double hsq, hinv, hinv3;
|
||||
|
||||
void allocate();
|
||||
|
||||
class ComputeRHEOKernel *compute_kernel;
|
||||
class FixRHEO *fix_rheo;
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
Reference in New Issue
Block a user