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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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81
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++) {
@ -208,7 +204,7 @@ void ComputeRHEOSurface::compute_peratom()
wp = compute_kernel->calc_dw_quintic(i, j, dx[0], dx[1], dx[2], sqrt(rsq), dWij, dWji);
for (a = 0; a < dim; a++){
for (a = 0; a < dim; a++) {
divr[i] -= dWij[a] * dx[a] * Volj;
gradC[i][a] += dWij[a] * Volj;
}
@ -245,35 +241,32 @@ void ComputeRHEOSurface::compute_peratom()
}
}
// Find the free-surface
if (threshold_style == DIVR) {
for (i = 0; i < nall; i++) {
if (mask[i] & groupbit) {
// 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) {
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 {
status[i] |= STATUS_BULK;
rsurface[i] = cut;
if (divr[i] < threshold_divr) {
status[i] |= STATUS_SURFACE;
rsurface[i] = 0.0;
if (coordination[i] < threshold_splash)
status[i] |= STATUS_SPLASH;
}
}
}
} 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);
}
}
}