Renamed to multi2, initial stencil edits
This commit is contained in:
Joel Clemmer
250
src/nstencil.cpp
250
src/nstencil.cpp
@ -51,6 +51,15 @@ using namespace LAMMPS_NS;
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stencil follows same rules for half/full, newton on/off, triclinic
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cutoff is not cutneighmaxsq, but max cutoff for that atom type
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no versions that allow ghost on (any need for it?)
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for multi/tiered:
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create one stencil for each itype-jtype pairing
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stencils do not generally follow the same rules for half/full or newton on/off
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whole stencils including all surrounding bins are always used except
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for same-type stencils with newton on which uses a split stencil
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for orthogonal boxes, a split stencil includes bins to the "upper right" of central bin
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for triclinic, a split stencil includes bins in the z (3D) or y (2D) plane of self and above
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cutoff is not cutneighmaxsq, but max cutoff for that atom type
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no versions that allow ghost on (any need for it?)
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------------------------------------------------------------------------- */
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NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp)
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@ -64,6 +73,11 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp)
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nstencil_multi = nullptr;
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stencil_multi = nullptr;
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distsq_multi = nullptr;
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stencil_split = nullptr;
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stencil_skip = nullptr;
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stencil_bin_type = nullptr;
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stencil_cut = nullptr;
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dimension = domain->dimension;
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}
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@ -75,16 +89,44 @@ NStencil::~NStencil()
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memory->destroy(stencil);
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memory->destroy(stencilxyz);
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if (!stencil_multi) return;
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if (stencil_multi) {
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int n = atom->ntypes;
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for (int i = 1; i <= n; i++) {
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memory->destroy(stencil_multi[i]);
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memory->destroy(distsq_multi[i]);
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int n = atom->ntypes;
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for (int i = 1; i <= n; i++) {
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memory->destroy(stencil_multi[i]);
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memory->destroy(distsq_multi[i]);
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}
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delete [] nstencil_multi;
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delete [] stencil_multi;
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delete [] distsq_multi;
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}
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if (stencil_multi_tiered) {
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int n = atom->ntypes;
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memory->destroy(nstencil_multi_tiered);
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for (int i = 1; i <= n; i++) {
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for (int j = 0; j <= n; j++) {
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if (! stencil_skip[i][j])
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memory->destroy(stencil_multi_tiered[i][j]);
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}
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delete [] stencil_multi_tiered[i];
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}
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delete [] stencil_multi_tiered;
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memory->destroy(maxstencil_multi_tiered);
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memory->destroy(stencil_split);
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memory->destroy(stencil_skip);
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memory->destroy(stencil_bin_type);
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memory->destroy(stencil_cut);
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memory->destroy(sx_multi_tiered);
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memory->destroy(sy_multi_tiered);
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memory->destroy(sz_multi_tiered);
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memory->destroy(binsizex_multi_tiered);
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memory->destroy(binsizey_multi_tiered);
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memory->destroy(binsizez_multi_tiered);
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}
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delete [] nstencil_multi;
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delete [] stencil_multi;
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delete [] distsq_multi;
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}
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/* ---------------------------------------------------------------------- */
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@ -105,6 +147,7 @@ void NStencil::copy_neighbor_info()
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cutneighmax = neighbor->cutneighmax;
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cutneighmaxsq = neighbor->cutneighmaxsq;
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cuttypesq = neighbor->cuttypesq;
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cutneighsq = neighbor->cutneighsq;
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// overwrite Neighbor cutoff with custom value set by requestor
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// only works for style = BIN (checked by Neighbor class)
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@ -132,6 +175,23 @@ void NStencil::copy_bin_info()
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bininvz = nb->bininvz;
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}
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/* ----------------------------------------------------------------------
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copy needed info for a given type from NBin class to this stencil class
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------------------------------------------------------------------------- */
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void NStencil::copy_bin_info_multi_tiered(int type)
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{
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mbinx = nb->mbinx_tiered[type];
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mbiny = nb->mbiny_tiered[type];
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mbinz = nb->mbinz_tiered[type];
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binsizex = nb->binsizex_tiered[type];
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binsizey = nb->binsizey_tiered[type];
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binsizez = nb->binsizez_tiered[type];
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bininvx = nb->bininvx_tiered[type];
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bininvy = nb->bininvy_tiered[type];
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bininvz = nb->bininvz_tiered[type];
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}
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/* ----------------------------------------------------------------------
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insure NBin data is current
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insure stencils are allocated large enough
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@ -139,59 +199,131 @@ void NStencil::copy_bin_info()
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void NStencil::create_setup()
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{
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if (nb) copy_bin_info();
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last_stencil = update->ntimestep;
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// sx,sy,sz = max range of stencil in each dim
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// smax = max possible size of entire 3d stencil
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// stencil will be empty if cutneighmax = 0.0
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sx = static_cast<int> (cutneighmax*bininvx);
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if (sx*binsizex < cutneighmax) sx++;
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sy = static_cast<int> (cutneighmax*bininvy);
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if (sy*binsizey < cutneighmax) sy++;
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sz = static_cast<int> (cutneighmax*bininvz);
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if (sz*binsizez < cutneighmax) sz++;
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if (dimension == 2) sz = 0;
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int smax = (2*sx+1) * (2*sy+1) * (2*sz+1);
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// reallocate stencil structs if necessary
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// for BIN and MULTI styles
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if (neighstyle == Neighbor::BIN) {
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if (smax > maxstencil) {
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maxstencil = smax;
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memory->destroy(stencil);
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memory->create(stencil,maxstencil,"neighstencil:stencil");
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if (xyzflag) {
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memory->destroy(stencilxyz);
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memory->create(stencilxyz,maxstencil,3,"neighstencil:stencilxyz");
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if (neighstyle != Neighbor::MULTI_TIERED){
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if (nb) copy_bin_info();
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last_stencil = update->ntimestep;
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// sx,sy,sz = max range of stencil in each dim
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// smax = max possible size of entire 3d stencil
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// stencil will be empty if cutneighmax = 0.0
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sx = static_cast<int> (cutneighmax*bininvx);
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if (sx*binsizex < cutneighmax) sx++;
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sy = static_cast<int> (cutneighmax*bininvy);
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if (sy*binsizey < cutneighmax) sy++;
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sz = static_cast<int> (cutneighmax*bininvz);
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if (sz*binsizez < cutneighmax) sz++;
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if (dimension == 2) sz = 0;
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int smax = (2*sx+1) * (2*sy+1) * (2*sz+1);
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// reallocate stencil structs if necessary
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// for BIN and MULTI styles
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if (neighstyle == Neighbor::BIN) {
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if (smax > maxstencil) {
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maxstencil = smax;
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memory->destroy(stencil);
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memory->create(stencil,maxstencil,"neighstencil:stencil");
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if (xyzflag) {
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memory->destroy(stencilxyz);
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memory->create(stencilxyz,maxstencil,3,"neighstencil:stencilxyz");
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}
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}
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} else {
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int i;
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int n = atom->ntypes;
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if (maxstencil_multi == 0) {
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nstencil_multi = new int[n+1];
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stencil_multi = new int*[n+1];
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distsq_multi = new double*[n+1];
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for (i = 1; i <= n; i++) {
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nstencil_multi[i] = 0;
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stencil_multi[i] = nullptr;
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distsq_multi[i] = nullptr;
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}
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}
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if (smax > maxstencil_multi) {
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maxstencil_multi = smax;
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for (i = 1; i <= n; i++) {
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memory->destroy(stencil_multi[i]);
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memory->destroy(distsq_multi[i]);
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memory->create(stencil_multi[i],maxstencil_multi,
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"neighstencil:stencil_multi");
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memory->create(distsq_multi[i],maxstencil_multi,
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"neighstencil:distsq_multi");
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}
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}
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}
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} else {
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int i;
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int i, j, bin_type, smax;
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double stencil_range;
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int n = atom->ntypes;
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if (maxstencil_multi == 0) {
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nstencil_multi = new int[n+1];
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stencil_multi = new int*[n+1];
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distsq_multi = new double*[n+1];
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for (i = 1; i <= n; i++) {
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nstencil_multi[i] = 0;
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stencil_multi[i] = nullptr;
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distsq_multi[i] = nullptr;
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}
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}
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if (smax > maxstencil_multi) {
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maxstencil_multi = smax;
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for (i = 1; i <= n; i++) {
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memory->destroy(stencil_multi[i]);
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memory->destroy(distsq_multi[i]);
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memory->create(stencil_multi[i],maxstencil_multi,
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"neighstencil:stencil_multi");
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memory->create(distsq_multi[i],maxstencil_multi,
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"neighstencil:distsq_multi");
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// Allocate arrays to store stencil information
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memory->create(stencil_split, n, n,
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"neighstencil:stencil_split");"
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memory->create(stencil_skip, n, n,
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"neighstencil:stencil_skip");"
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memory->create(stencil_bin_type, n, n,
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"neighstencil:stencil_bin_type");"
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memory->create(stencil_cut, n, n,
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"neighstencil:stencil_cut");"
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memory->create(sx_multi_tiered, n, n,
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"neighstencil:sx_multi_tiered");"
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memory->create(sy_multi_tiered, n, n,
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"neighstencil:sy_multi_tiered");"
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memory->create(sz_multi_tiered, n, n,
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"neighstencil:sz_multi_tiered");"
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memory->create(binsizex_multi_tiered, n, n,
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"neighstencil:binsizex_multi_tiered");"
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memory->create(binsizey_multi_tiered, n, n,
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"neighstencil:binsizey_multi_tiered");"
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memory->create(binsizez_multi_tiered, n, n,
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"neighstencil:binsizez_multi_tiered");"
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// Determine which stencils need to be built
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set_stencil_properties();
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for (i = 1; i <= n; ++i) {
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for (j = 1; j <= n; ++j) {
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// Skip creation of unused stencils
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if (stencil_skip[i][j]) continue;
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// Copy bin info for this particular pair of types
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bin_type = stencil_bin_type[i][j];
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copy_bin_info_bytype(bin_type);
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binsizex_multi_tiered[i][j] = binsizex;
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binsizey_multi_tiered[i][j] = binsizey;
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binsizez_multi_tiered[i][j] = binsizez;
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stencil_range = stencil_cut[i][j];
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sx = static_cast<int> (stencil_range*bininvx);
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if (sx*binsizex < stencil_range) sx++;
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sy = static_cast<int> (stencil_range*bininvy);
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if (sy*binsizey < stencil_range) sy++;
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sz = static_cast<int> (stencil_range*bininvz);
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if (sz*binsizez < stencil_range) sz++;
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sx_multi_tiered[i][j] = sx;
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sy_multi_tiered[i][j] = sy;
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sz_multi_tiered[i][j] = sz;
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smax = ((2*sx+1) * (2*sy+1) * (2*sz+1));
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if (smax > maxstencil_multi_tiered[i][j]) {
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maxstencil_multi_tiered[i][j] = smax;
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memory->destroy(stencil_multi_tiered[i][j]);
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memory->create(stencil_multi_tiered[i][j], smax,
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"neighstencil::stencil_multi_tiered");
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}
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}
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}
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}
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@ -231,6 +363,10 @@ double NStencil::memory_usage()
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} else if (neighstyle == Neighbor::MULTI) {
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bytes += atom->ntypes*maxstencil_multi * sizeof(int);
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bytes += atom->ntypes*maxstencil_multi * sizeof(double);
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} else if (neighstyle == Neighbor::MULTI_TIERED) {
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bytes += atom->ntypes*maxstencil_multi * sizeof(int);
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bytes += atom->ntypes*maxstencil_multi * sizeof(int);
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bytes += atom->ntypes*maxstencil_multi * sizeof(double);
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}
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return bytes;
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}
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