296 lines
8.7 KiB
C++
296 lines
8.7 KiB
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.
|
|
------------------------------------------------------------------------- */
|
|
|
|
/* ----------------------------------------------------------------------
|
|
Contributing authors:
|
|
Joel Clemmer (SNL)
|
|
----------------------------------------------------------------------- */
|
|
|
|
#include "fix_rheo_oxidation.h"
|
|
|
|
#include "atom.h"
|
|
#include "atom_vec.h"
|
|
#include "citeme.h"
|
|
#include "comm.h"
|
|
#include "compute_rheo_surface.h"
|
|
#include "error.h"
|
|
#include "fix_rheo.h"
|
|
#include "force.h"
|
|
#include "modify.h"
|
|
#include "neighbor.h"
|
|
#include "neigh_list.h"
|
|
#include "neigh_request.h"
|
|
#include "update.h"
|
|
|
|
using namespace LAMMPS_NS;
|
|
using namespace RHEO_NS;
|
|
using namespace FixConst;
|
|
enum {NONE, CONSTANT};
|
|
|
|
static const char cite_rheo_oxide[] =
|
|
"@article{ApplMathModel.130.310,\n"
|
|
" title = {A hybrid smoothed-particle hydrodynamics model of oxide skins on molten aluminum},\n"
|
|
" journal = {Applied Mathematical Modelling},\n"
|
|
" volume = {130},\n"
|
|
" pages = {310-326},\n"
|
|
" year = {2024},\n"
|
|
" issn = {0307-904X},\n"
|
|
" doi = {https://doi.org/10.1016/j.apm.2024.02.027},\n"
|
|
" author = {Joel T. Clemmer and Flint Pierce and Thomas C. O'Connor and Thomas D. Nevins and Elizabeth M.C. Jones and Jeremy B. Lechman and John Tencer},\n"
|
|
"}\n\n";
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
FixRHEOOxidation::FixRHEOOxidation(LAMMPS *lmp, int narg, char **arg) :
|
|
Fix(lmp, narg, arg), compute_surface(nullptr), fix_rheo(nullptr)
|
|
{
|
|
if (narg != 6) error->all(FLERR,"Illegal fix command");
|
|
|
|
force_reneighbor = 1;
|
|
next_reneighbor = -1;
|
|
comm_forward = 3;
|
|
|
|
cut = utils::numeric(FLERR, arg[3], false, lmp);
|
|
if (cut <= 0.0) error->all(FLERR, "Illegal bond cutoff {} in fix rheo/oxidation", cut);
|
|
|
|
btype = utils::inumeric(FLERR, arg[4], false, lmp);
|
|
if (btype < 1 || btype > atom->nbondtypes) error->all(FLERR, "Illegal value {} for bond type in fix rheo/oxidation", btype);
|
|
|
|
rsurf = utils::numeric(FLERR, arg[5], false, lmp);
|
|
if (rsurf <= 0.0) error->all(FLERR, "Illegal surface distance {} in fix rheo/oxidation", cut);
|
|
|
|
cutsq = cut * cut;
|
|
|
|
if (lmp->citeme) lmp->citeme->add(cite_rheo_oxide);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
FixRHEOOxidation::~FixRHEOOxidation()
|
|
{
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
int FixRHEOOxidation::setmask()
|
|
{
|
|
int mask = 0;
|
|
mask |= POST_INTEGRATE;
|
|
mask |= PRE_FORCE;
|
|
mask |= POST_FORCE;
|
|
return mask;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void FixRHEOOxidation::init()
|
|
{
|
|
auto fixes = modify->get_fix_by_style("^rheo$");
|
|
if (fixes.size() == 0) error->all(FLERR, "Need to define fix rheo to use fix rheo/oxidation");
|
|
fix_rheo = dynamic_cast<FixRHEO *>(fixes[0]);
|
|
|
|
if (cut > fix_rheo->cut)
|
|
error->all(FLERR, "Bonding length exceeds kernel cutoff");
|
|
|
|
if (rsurf >= fix_rheo->cut)
|
|
error->all(FLERR, "Surface distance must be less than kernel cutoff");
|
|
|
|
if (!force->bond) error->all(FLERR, "Must define a bond style with fix rheo/oxidation");
|
|
if (!atom->avec->bonds_allow) error->all(FLERR, "Fix rheo/oxidation requires atom bonds");
|
|
|
|
int tmp1, tmp2;
|
|
index_nb = atom->find_custom("shell_nbond", tmp1, tmp2);
|
|
if (index_nb == -1)
|
|
error->all(FLERR, "Must use bond style rheo/shell to use fix rheo/oxidation");
|
|
nbond = atom->ivector[index_nb];
|
|
|
|
// need a half neighbor list
|
|
auto req = neighbor->add_request(this, NeighConst::REQ_FULL);
|
|
req->set_cutoff(cut);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void FixRHEOOxidation::init_list(int /*id*/, NeighList *ptr)
|
|
{
|
|
list = ptr;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void FixRHEOOxidation::setup_pre_force(int /*vflag*/)
|
|
{
|
|
// Not strictly required that this fix be after FixRHEO,
|
|
// but enforce to be consistent with other RHEO fixes
|
|
fix_rheo->oxidation_fix_defined = 1;
|
|
|
|
if (!fix_rheo->surface_flag) error->all(FLERR,
|
|
"fix rheo/oxidation requires surface calculation in fix rheo");
|
|
compute_surface = fix_rheo->compute_surface;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void FixRHEOOxidation::pre_force(int /*vflag*/)
|
|
{
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void FixRHEOOxidation::post_integrate()
|
|
{
|
|
int i, j, n, ii, jj, inum, jnum, bflag, fluidi, fluidj;
|
|
int *ilist, *jlist, *numneigh, **firstneigh;
|
|
double delx, dely, delz, rsq;
|
|
tagint tagi, tagj;
|
|
|
|
int nlocal = atom->nlocal;
|
|
int newton_bond = force->newton_bond;
|
|
|
|
tagint *tag = atom->tag;
|
|
tagint **bond_atom = atom->bond_atom;
|
|
int **bond_type = atom->bond_type;
|
|
int *num_bond = atom->num_bond;
|
|
int *mask = atom->mask;
|
|
int *status = atom->status;
|
|
double *rsurface = compute_surface->rsurface;
|
|
double **x = atom->x;
|
|
|
|
inum = list->inum;
|
|
ilist = list->ilist;
|
|
numneigh = list->numneigh;
|
|
firstneigh = list->firstneigh;
|
|
|
|
// Forward positions (after inititial integrate, before comm)
|
|
// Note: surface designation lags one timestep, acceptable error
|
|
comm->forward_comm(this);
|
|
|
|
int added_bonds = 0;
|
|
// loop over neighbors of my atoms
|
|
for (ii = 0; ii < inum; ii++) {
|
|
i = ilist[ii];
|
|
if (!(mask[i] & groupbit)) continue;
|
|
|
|
// Exclude particles that aren't solid or surface
|
|
fluidi = !(status[i] & PHASECHECK);
|
|
if (fluidi && (rsurface[i] > rsurf)) continue;
|
|
|
|
tagi = tag[i];
|
|
|
|
jlist = firstneigh[i];
|
|
jnum = numneigh[i];
|
|
|
|
for (jj = 0; jj < jnum; jj++) {
|
|
j = jlist[jj];
|
|
j &= NEIGHMASK;
|
|
if (!(mask[j] & groupbit)) continue;
|
|
|
|
fluidj = !(status[j] & PHASECHECK);
|
|
if (fluidj && (rsurface[j] > rsurf)) continue;
|
|
|
|
// Skip solid-solid, leaves surface-surface or surface-solid
|
|
if ((!fluidi) && (!fluidj)) continue;
|
|
|
|
tagj = tag[j];
|
|
|
|
// Ensure pair is always ordered to ensure numerical operations
|
|
// are identical to minimize the possibility that a bond straddling
|
|
// an mpi grid (newton off) isn't created on one proc but not the other
|
|
if (tagi < tagj) {
|
|
delx = x[i][0] - x[j][0];
|
|
dely = x[i][1] - x[j][1];
|
|
delz = x[i][2] - x[j][2];
|
|
} else {
|
|
delx = x[j][0] - x[i][0];
|
|
dely = x[j][1] - x[i][1];
|
|
delz = x[j][2] - x[i][2];
|
|
}
|
|
rsq = delx * delx + dely * dely + delz * delz;
|
|
if (rsq > cutsq) continue;
|
|
|
|
// Check if already have an oxide bond
|
|
bflag = 0;
|
|
for (n = 0; n < num_bond[i]; n++) {
|
|
if (bond_type[i][n] == btype && bond_atom[i][n] == tagj) {
|
|
bflag = 1;
|
|
break;
|
|
}
|
|
}
|
|
if (bflag) continue;
|
|
|
|
added_bonds += 1;
|
|
|
|
// Add bonds to owned atoms
|
|
// If newton bond off, add to both, otherwise add to whichever has a smaller tag
|
|
|
|
if (!newton_bond || (tagi < tagj)) {
|
|
if (num_bond[i] == atom->bond_per_atom)
|
|
error->one(FLERR,"New bond exceeded bonds per atom in fix rheo/oxidation for atom {}", tagi);
|
|
bond_type[i][num_bond[i]] = btype;
|
|
bond_atom[i][num_bond[i]] = tagj;
|
|
num_bond[i]++;
|
|
}
|
|
}
|
|
}
|
|
|
|
int added_bonds_all;
|
|
MPI_Allreduce(&added_bonds, &added_bonds_all, 1, MPI_INT, MPI_SUM, world);
|
|
|
|
if (added_bonds_all > 0)
|
|
next_reneighbor = update->ntimestep;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void FixRHEOOxidation::post_force(int /*vflag*/)
|
|
{
|
|
int *status = atom->status;
|
|
int *num_bond = atom->num_bond;
|
|
for (int i = 0; i < atom->nlocal; i++)
|
|
if (num_bond[i] != 0)
|
|
status[i] |= STATUS_NO_SHIFT;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
int FixRHEOOxidation::pack_forward_comm(int n, int *list, double *buf,
|
|
int /*pbc_flag*/, int * /*pbc*/)
|
|
{
|
|
int i, j, k, m;
|
|
double **x = atom->x;
|
|
m = 0;
|
|
|
|
for (i = 0; i < n; i++) {
|
|
j = list[i];
|
|
buf[m++] = x[j][0];
|
|
buf[m++] = x[j][1];
|
|
buf[m++] = x[j][2];
|
|
}
|
|
return m;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void FixRHEOOxidation::unpack_forward_comm(int n, int first, double *buf)
|
|
{
|
|
int i, k, m, last;
|
|
double **x = atom->x;
|
|
m = 0;
|
|
last = first + n;
|
|
for (i = first; i < last; i++) {
|
|
x[i][0] = buf[m++];
|
|
x[i][1] = buf[m++];
|
|
x[i][2] = buf[m++];
|
|
}
|
|
}
|