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Fixing errors in oxide model

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This commit is contained in:
jtclemm
2023-11-07 14:47:46 -07:00
parent 44ae758bf5
commit b8b2141993
4 changed files with 56 additions and 55 deletions
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2
src/RHEO/compute_rheo_property_atom.cpp
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@ -103,7 +103,7 @@ ComputeRHEOPropertyAtom::ComputeRHEOPropertyAtom(LAMMPS *lmp, int narg, char **a
if (avec_index[i] < 0)
error->all(FLERR,
"Invalid keyword {} for atom style {} in compute rheo/property/atom command ",
atom->get_style(), arg[iarg]);
arg[iarg], atom->get_style());
pack_choice[i] = &ComputeRHEOPropertyAtom::pack_atom_style;
if (strcmp(arg[iarg],"temperature") == 0) thermal_flag = 1;

69
src/RHEO/compute_rheo_surface.cpp
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@ -152,16 +152,12 @@ void ComputeRHEOSurface::compute_peratom()
grow_arrays(atom->nmax);
size_t nbytes = nmax_store * sizeof(double);
memset(&divr, 0, nbytes);
memset(&rsurface, 0, nbytes);
memset(&nsurface, 0, 3 * nbytes);
memset(&gradC, 0, 3 * 3 * nbytes);
memset(&B, 0, 3 * 3 * nbytes);
memset(&divr[0], 0, nbytes);
memset(&rsurface[0], 0, nbytes);
memset(&nsurface[0][0], 0, dim * nbytes);
memset(&gradC[0][0], 0, dim * dim * nbytes);
memset(&B[0][0], 0, dim * dim * nbytes);
// Remove surface settings
int nall = nlocal + atom->nghost;
for (i = 0; i < nall; i++)
status[i] &= SURFACEMASK;
// loop over neighbors to calculate the average orientation of neighbors
for (ii = 0; ii < inum; ii++) {
@ -245,35 +241,32 @@ void ComputeRHEOSurface::compute_peratom()
}
}
// Find the free-surface
if (threshold_style == DIVR) {
// Remove surface settings and assign new values
int nall = nlocal + atom->nghost;
int test;
for (i = 0; i < nall; i++) {
status[i] &= SURFACEMASK;
if (mask[i] & groupbit) {
status[i] |= STATUS_BULK;
rsurface[i] = cut;
if (divr[i] < threshold_divr) {
status[i] |= STATUS_SURFACE;
rsurface[i] = 0.0;
if (threshold_style == DIVR)
test = divr[i] < threshold_divr;
else
test = coordination[i] < threshold_z;
if (test) {
if (coordination[i] < threshold_splash)
status[i] |= STATUS_SPLASH;
}
}
}
else
status[i] |= STATUS_SURFACE;
rsurface[i] = 0.0;
} else {
for (i = 0; i < nall; i++) {
if (mask[i] & groupbit) {
status[i] |= STATUS_BULK;
rsurface[i] = cut;
if (coordination[i] < threshold_z) {
status[i] |= STATUS_SURFACE;
rsurface[i] = 0.0;
if (coordination[i] < threshold_splash)
status[i] |= STATUS_SPLASH;
}
}
}
}
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
@ -297,7 +290,8 @@ void ComputeRHEOSurface::compute_peratom()
status[i] |= STATUS_LAYER;
}
if (status[j] & STATUS_SURFACE) rsurface[i] = MIN(rsurface[i], sqrt(rsq));
if (status[j] & STATUS_SURFACE)
rsurface[i] = MIN(rsurface[i], sqrt(rsq));
if (j < nlocal || newton) {
@ -306,7 +300,8 @@ void ComputeRHEOSurface::compute_peratom()
status[j] |= STATUS_LAYER;
}
if (status[i] & STATUS_SURFACE) rsurface[j] = MIN(rsurface[j], sqrt(rsq));
if (status[i] & STATUS_SURFACE)
rsurface[j] = MIN(rsurface[j], sqrt(rsq));
}
}
}
@ -351,7 +346,8 @@ void ComputeRHEOSurface::unpack_reverse_comm(int n, int *list, double *buf)
int i,a,b,k,j,m;
int dim = domain->dimension;
int *status = atom->status;
int temp;
int tmp1;
double tmp2;
m = 0;
for (i = 0; i < n; i++) {
@ -362,12 +358,13 @@ void ComputeRHEOSurface::unpack_reverse_comm(int n, int *list, double *buf)
for (b = 0; b < dim; b ++)
gradC[j][a * dim + b] += buf[m++];
} else if (comm_stage == 1) {
temp = (int) buf[m++];
if ((status[j] & STATUS_BULK) && (temp & STATUS_LAYER))
status[j] = temp;
rsurface[j] = MIN(rsurface[j], buf[m++]);
tmp1 = (int) buf[m++];
if ((status[j] & STATUS_BULK) && (tmp1 & STATUS_LAYER)) {
status[j] &= SURFACEMASK;
status[j] |= STATUS_LAYER;
}
tmp2 = buf[m++];
rsurface[j] = MIN(rsurface[j], tmp2);
}
}
}

7
src/RHEO/fix_rheo.cpp
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@ -133,7 +133,7 @@ FixRHEO::~FixRHEO()
if (compute_kernel) modify->delete_compute("rheo_kernel");
if (compute_grad) modify->delete_compute("rheo_grad");
if (compute_interface) modify->delete_compute("rheo_interface");
if (compute_surface) modify->delete_compute("compute_surface");
if (compute_surface) modify->delete_compute("rheo_surface");
if (compute_rhosum) modify->delete_compute("rheo_rhosum");
if (compute_vshift) modify->delete_compute("rheo_vshift");
}
@ -211,7 +211,10 @@ void FixRHEO::setup_pre_force(int /*vflag*/)
error->all(FLERR, "Fix RHEO must be defined before all other RHEO fixes");
// Calculate surfaces
if (surface_flag) compute_surface->compute_peratom();
if (surface_flag) {
compute_kernel->compute_coordination();
compute_surface->compute_peratom();
}
pre_force(0);
}

17
src/RHEO/pair_rheo_react.cpp
View File

@ -61,13 +61,13 @@ PairRHEOReact::PairRHEOReact(LAMMPS *lmp) : Pair(lmp),
// between timesteps (fix property atom will handle callbacks)
int tmp1, tmp2;
int index = atom->find_custom("react_nbond", tmp1, tmp2);
if (index == -1) {
index_nb = atom->find_custom("react_nbond", tmp1, tmp2);
if (index_nb == -1) {
id_fix = utils::strdup("pair_rheo_react_fix_property_atom");
modify->add_fix(fmt::format("{} all property/atom i_react_nbond", id_fix));
index = atom->find_custom("nbond", tmp1, tmp2);
index_nb = atom->find_custom("react_nbond", tmp1, tmp2);
}
nbond = atom->ivector[index];
nbond = atom->ivector[index_nb];
//Store non-persistent per atom quantities, intermediate
@ -79,9 +79,10 @@ PairRHEOReact::PairRHEOReact(LAMMPS *lmp) : Pair(lmp),
PairRHEOReact::~PairRHEOReact()
{
if (modify->nfix && fix_history) modify->delete_fix("NEIGH_HISTORY_RHEO_REACT");
if (modify->nfix && fix_dummy) modify->delete_fix("NEIGH_HISTORY_RHEO_REACT_DUMMY");
if (modify->nfix) modify->delete_fix("PROPERTY_ATOM_RHEO_REACT");
if (modify->nfix && fix_history) modify->delete_fix("NEIGH_HISTORY_RHEO_REACT" + std::to_string(instance_me));
if (modify->nfix && fix_dummy) modify->delete_fix("NEIGH_HISTORY_RHEO_REACT_DUMMY" + std::to_string(instance_me));
if (modify->nfix) modify->delete_fix(id_fix);
delete[] id_fix;
if (allocated) {
memory->destroy(setflag);
@ -146,7 +147,7 @@ void PairRHEOReact::compute(int eflag, int vflag)
}
size_t nbytes = nmax_store * sizeof(int);
memset(&dbond, 0, nbytes);
memset(&dbond[0], 0, nbytes);
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {