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Adding custom grouping option

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This commit is contained in:
Joel Clemmer
2020-12-26 11:03:29 -07:00
parent b421c3d676
commit 2458eaf4f9
30 changed files with 599 additions and 551 deletions
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126
src/nstencil.cpp
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@ -52,14 +52,14 @@ using namespace LAMMPS_NS;
cutoff is not cutneighmaxsq, but max cutoff for that atom type
no versions that allow ghost on (any need for it?)
for multi:
create one stencil for each itype-jtype pairing
the full/half stencil label refers to the same-type stencil
a half list with newton on has a half same-type stencil
a full list or half list with newton of has a full same-type stencil
cross type stencils are always full to allow small-to-large lookups
create one stencil for each igroup-jgroup pairing
the full/half stencil label refers to the same-group stencil
a half list with newton on has a half same-group stencil
a full list or half list with newton of has a full same-group stencil
cross group stencils are always full to allow small-to-large lookups
for orthogonal boxes, a half stencil includes bins to the "upper right" of central bin
for triclinic, a half stencil includes bins in the z (3D) or y (2D) plane of self and above
cutoff is not cutneighmaxsq, but max cutoff for that atom type
cutoff is not cutneighmaxsq, but max cutoff for that atom group
no versions that allow ghost on (any need for it?)
------------------------------------------------------------------------- */
@ -81,7 +81,7 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp)
flag_half_multi = nullptr;
flag_skip_multi = nullptr;
bin_type_multi = nullptr;
bin_group_multi = nullptr;
dimension = domain->dimension;
}
@ -107,10 +107,10 @@ NStencil::~NStencil()
if (stencil_multi) {
int n = atom->ntypes;
int n = n_multi_groups;
memory->destroy(nstencil_multi);
for (int i = 1; i <= n; i++) {
for (int j = 0; j <= n; j++) {
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
if (! flag_skip_multi[i][j])
memory->destroy(stencil_multi[i][j]);
}
@ -120,7 +120,7 @@ NStencil::~NStencil()
memory->destroy(maxstencil_multi);
memory->destroy(flag_half_multi);
memory->destroy(flag_skip_multi);
memory->destroy(bin_type_multi);
memory->destroy(bin_group_multi);
memory->destroy(stencil_sx_multi);
memory->destroy(stencil_sy_multi);
@ -155,6 +155,10 @@ void NStencil::copy_neighbor_info()
cutneighmaxsq = neighbor->cutneighmaxsq;
cuttypesq = neighbor->cuttypesq;
cutneighsq = neighbor->cutneighsq;
n_multi_groups = neighbor->n_multi_groups;
map_type_multi = neighbor->map_type_multi;
cutmultisq = neighbor->cutmultisq;
// overwrite Neighbor cutoff with custom value set by requestor
// only works for style = BIN (checked by Neighbor class)
@ -265,44 +269,44 @@ void NStencil::create_setup()
}
}
} else {
int i, j, bin_type, smax;
int i, j, bin_group, smax;
double stencil_range;
int n = atom->ntypes;
int n = n_multi_groups;
if(nb) copy_bin_info_multi();
// Allocate arrays to store stencil information
memory->create(flag_half_multi, n+1, n+1,
memory->create(flag_half_multi, n, n,
"neighstencil:flag_half_multi");
memory->create(flag_skip_multi, n+1, n+1,
memory->create(flag_skip_multi, n, n,
"neighstencil:flag_skip_multi");
memory->create(bin_type_multi, n+1, n+1,
"neighstencil:bin_type_multi");
memory->create(bin_group_multi, n, n,
"neighstencil:bin_group_multi");
memory->create(stencil_sx_multi, n+1, n+1,
memory->create(stencil_sx_multi, n, n,
"neighstencil:stencil_sx_multi");
memory->create(stencil_sy_multi, n+1, n+1,
memory->create(stencil_sy_multi, n, n,
"neighstencil:stencil_sy_multi");
memory->create(stencil_sz_multi, n+1, n+1,
memory->create(stencil_sz_multi, n, n,
"neighstencil:stencil_sz_multi");
memory->create(stencil_binsizex_multi, n+1, n+1,
memory->create(stencil_binsizex_multi, n, n,
"neighstencil:stencil_binsizex_multi");
memory->create(stencil_binsizey_multi, n+1, n+1,
memory->create(stencil_binsizey_multi, n, n,
"neighstencil:stencil_binsizey_multi");
memory->create(stencil_binsizez_multi, n+1, n+1,
memory->create(stencil_binsizez_multi, n, n,
"neighstencil:stencil_binsizez_multi");
memory->create(stencil_mbinx_multi, n+1, n+1,
memory->create(stencil_mbinx_multi, n, n,
"neighstencil:stencil_mbinx_multi");
memory->create(stencil_mbiny_multi, n+1, n+1,
memory->create(stencil_mbiny_multi, n, n,
"neighstencil:stencil_mbiny_multi");
memory->create(stencil_mbinz_multi, n+1, n+1,
memory->create(stencil_mbinz_multi, n, n,
"neighstencil:stencil_mbinz_multi");
// Skip all stencils by default, initialize smax
for (i = 1; i <= n; i++) {
for (j = 1; j <= n; j++) {
for (i = 0; i < n; i++) {
for (j = 0; j < n; j++) {
flag_skip_multi[i][j] = 1;
}
}
@ -313,43 +317,43 @@ void NStencil::create_setup()
// Allocate arrays to store stencils
if (!maxstencil_multi) {
memory->create(maxstencil_multi, n+1, n+1, "neighstencil::stencil_multi");
memory->create(nstencil_multi, n+1, n+1, "neighstencil::nstencil_multi");
stencil_multi = new int**[n+1]();
for (i = 1; i <= n; ++i) {
stencil_multi[i] = new int*[n+1]();
for (j = 1; j <= n; ++j) {
memory->create(maxstencil_multi, n, n, "neighstencil::stencil_multi");
memory->create(nstencil_multi, n, n, "neighstencil::nstencil_multi");
stencil_multi = new int**[n]();
for (i = 0; i < n; ++i) {
stencil_multi[i] = new int*[n]();
for (j = 0; j < n; ++j) {
maxstencil_multi[i][j] = 0;
nstencil_multi[i][j] = 0;
}
}
}
for (i = 1; i <= n; i++) {
for (j = 1; j <= n; j++) {
for (i = 0; i < n; i++) {
for (j = 0; j < n; j++) {
// Skip creation of unused stencils
if (flag_skip_multi[i][j]) continue;
// Copy bin info for this pair of atom types
bin_type = bin_type_multi[i][j];
bin_group = bin_group_multi[i][j];
stencil_binsizex_multi[i][j] = binsizex_multi[bin_type];
stencil_binsizey_multi[i][j] = binsizey_multi[bin_type];
stencil_binsizez_multi[i][j] = binsizez_multi[bin_type];
stencil_binsizex_multi[i][j] = binsizex_multi[bin_group];
stencil_binsizey_multi[i][j] = binsizey_multi[bin_group];
stencil_binsizez_multi[i][j] = binsizez_multi[bin_group];
stencil_mbinx_multi[i][j] = mbinx_multi[bin_type];
stencil_mbiny_multi[i][j] = mbiny_multi[bin_type];
stencil_mbinz_multi[i][j] = mbinz_multi[bin_type];
stencil_mbinx_multi[i][j] = mbinx_multi[bin_group];
stencil_mbiny_multi[i][j] = mbiny_multi[bin_group];
stencil_mbinz_multi[i][j] = mbinz_multi[bin_group];
stencil_range = sqrt(cutneighsq[i][j]);
stencil_range = sqrt(cutmultisq[i][j]);
sx = static_cast<int> (stencil_range*bininvx_multi[bin_type]);
if (sx*binsizex_multi[bin_type] < stencil_range) sx++;
sy = static_cast<int> (stencil_range*bininvy_multi[bin_type]);
if (sy*binsizey_multi[bin_type] < stencil_range) sy++;
sz = static_cast<int> (stencil_range*bininvz_multi[bin_type]);
if (sz*binsizez_multi[bin_type] < stencil_range) sz++;
sx = static_cast<int> (stencil_range*bininvx_multi[bin_group]);
if (sx*binsizex_multi[bin_group] < stencil_range) sx++;
sy = static_cast<int> (stencil_range*bininvy_multi[bin_group]);
if (sy*binsizey_multi[bin_group] < stencil_range) sy++;
sz = static_cast<int> (stencil_range*bininvz_multi[bin_group]);
if (sz*binsizez_multi[bin_group] < stencil_range) sz++;
stencil_sx_multi[i][j] = sx;
stencil_sy_multi[i][j] = sy;
@ -393,24 +397,24 @@ double NStencil::bin_distance(int i, int j, int k)
/* ----------------------------------------------------------------------
compute closest distance for a given atom type
compute closest distance for a given atom grouping
------------------------------------------------------------------------- */
double NStencil::bin_distance_multi(int i, int j, int k, int type)
double NStencil::bin_distance_multi(int i, int j, int k, int group)
{
double delx,dely,delz;
if (i > 0) delx = (i-1)*binsizex_multi[type];
if (i > 0) delx = (i-1)*binsizex_multi[group];
else if (i == 0) delx = 0.0;
else delx = (i+1)*binsizex_multi[type];
else delx = (i+1)*binsizex_multi[group];
if (j > 0) dely = (j-1)*binsizey_multi[type];
if (j > 0) dely = (j-1)*binsizey_multi[group];
else if (j == 0) dely = 0.0;
else dely = (j+1)*binsizey_multi[type];
else dely = (j+1)*binsizey_multi[group];
if (k > 0) delz = (k-1)*binsizez_multi[type];
if (k > 0) delz = (k-1)*binsizez_multi[group];
else if (k == 0) delz = 0.0;
else delz = (k+1)*binsizez_multi[type];
else delz = (k+1)*binsizez_multi[group];
return (delx*delx + dely*dely + delz*delz);
}
@ -427,9 +431,9 @@ double NStencil::memory_usage()
bytes += atom->ntypes*maxstencil_multi_old * sizeof(int);
bytes += atom->ntypes*maxstencil_multi_old * sizeof(double);
} else if (neighstyle == Neighbor::MULTI) {
int n = atom->ntypes;
for (int i = 1; i <= n; i++) {
for (int j = 1; j <= n; j++) {
int n = n_multi_groups;
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
bytes += maxstencil_multi[i][j] * sizeof(int);
bytes += maxstencil_multi[i][j] * sizeof(int);
bytes += maxstencil_multi[i][j] * sizeof(double);