Adding custom grouping option
This commit is contained in:
Joel Clemmer
@ -38,7 +38,7 @@ void NBinMulti::bin_atoms_setup(int nall)
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{
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// binhead_multi[n] = per-bin vector mbins in length mbins_multi[n]
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for (int n = 1; n <= maxtypes; n++) {
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for (int n = 0; n < maxgroups; n++) {
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if (mbins_multi[n] > maxbins_multi[n]) {
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maxbins_multi[n] = mbins_multi[n];
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memory->destroy(binhead_multi[n]);
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@ -48,10 +48,12 @@ void NBinMulti::bin_atoms_setup(int nall)
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// bins_multi[n] and atom2bin_multi[n] = per-atom vectors
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// for both local and ghost atoms
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// TODO: maxatom should be maxatom per group
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if (nall > maxatom) {
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maxatom = nall;
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for (int n = 1; n <= maxtypes; n++) {
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for (int n = 0; n < maxgroups; n++) {
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memory->destroy(bins_multi[n]);
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memory->destroy(atom2bin_multi[n]);
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memory->create(bins_multi[n], maxatom, "neigh:bin_multi");
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@ -61,23 +63,16 @@ void NBinMulti::bin_atoms_setup(int nall)
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}
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/* ---------------------------------------------------------------------
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Identify index of type with smallest cutoff
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Identify index of group with smallest cutoff
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------------------------------------------------------------------------ */
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int NBinMulti::itype_min() {
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int NBinMulti::igroup_min()
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{
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int imin = 0;
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for (int n = 0; n < maxgroups; n++)
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if (cutmultisq[n][n] < cutmultisq[imin][imin]) imin = n;
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int itypemin = 1;
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double ** cutneighsq;
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cutneighsq = neighbor->cutneighsq;
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for (int n = 1; n <= atom->ntypes; n++) {
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if (cutneighsq[n][n] < cutneighsq[itypemin][itypemin]) {
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itypemin = n;
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}
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}
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return itypemin;
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return imin;
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}
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/* ----------------------------------------------------------------------
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@ -87,15 +82,15 @@ int NBinMulti::itype_min() {
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void NBinMulti::setup_bins(int style)
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{
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int n;
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int itypemin;
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int igroupmin;
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// Initialize arrays
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if (atom->ntypes > maxtypes) {
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if (n_multi_groups > maxgroups) {
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// Clear any/all memory for existing types
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for (n = 1; n <= maxtypes; n++) {
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for (n = 0; n < maxgroups; n++) {
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memory->destroy(atom2bin_multi[n]);
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memory->destroy(binhead_multi[n]);
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memory->destroy(bins_multi[n]);
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@ -106,59 +101,60 @@ void NBinMulti::setup_bins(int style)
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// Realloacte at updated maxtypes
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maxtypes = atom->ntypes;
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maxgroups = n_multi_groups;
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atom2bin_multi = new int*[maxtypes+1]();
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binhead_multi = new int*[maxtypes+1]();
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bins_multi = new int*[maxtypes+1]();
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atom2bin_multi = new int*[maxgroups]();
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binhead_multi = new int*[maxgroups]();
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bins_multi = new int*[maxgroups]();
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memory->destroy(nbinx_multi);
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memory->destroy(nbiny_multi);
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memory->destroy(nbinz_multi);
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memory->create(nbinx_multi, maxtypes+1, "neigh:nbinx_multi");
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memory->create(nbiny_multi, maxtypes+1, "neigh:nbiny_multi");
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memory->create(nbinz_multi, maxtypes+1, "neigh:nbinz_multi");
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memory->create(nbinx_multi, maxgroups, "neigh:nbinx_multi");
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memory->create(nbiny_multi, maxgroups, "neigh:nbiny_multi");
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memory->create(nbinz_multi, maxgroups, "neigh:nbinz_multi");
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memory->destroy(mbins_multi);
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memory->destroy(mbinx_multi);
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memory->destroy(mbiny_multi);
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memory->destroy(mbinz_multi);
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memory->create(mbins_multi, maxtypes+1, "neigh:mbins_multi");
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memory->create(mbinx_multi, maxtypes+1, "neigh:mbinx_multi");
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memory->create(mbiny_multi, maxtypes+1, "neigh:mbiny_multi");
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memory->create(mbinz_multi, maxtypes+1, "neigh:mbinz_multi");
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memory->create(mbins_multi, maxgroups, "neigh:mbins_multi");
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memory->create(mbinx_multi, maxgroups, "neigh:mbinx_multi");
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memory->create(mbiny_multi, maxgroups, "neigh:mbiny_multi");
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memory->create(mbinz_multi, maxgroups, "neigh:mbinz_multi");
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memory->destroy(mbinxlo_multi);
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memory->destroy(mbinylo_multi);
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memory->destroy(mbinzlo_multi);
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memory->create(mbinxlo_multi, maxtypes+1, "neigh:mbinxlo_multi");
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memory->create(mbinylo_multi, maxtypes+1, "neigh:mbinylo_multi");
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memory->create(mbinzlo_multi, maxtypes+1, "neigh:mbinzlo_multi");
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memory->create(mbinxlo_multi, maxgroups, "neigh:mbinxlo_multi");
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memory->create(mbinylo_multi, maxgroups, "neigh:mbinylo_multi");
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memory->create(mbinzlo_multi, maxgroups, "neigh:mbinzlo_multi");
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memory->destroy(binsizex_multi);
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memory->destroy(binsizey_multi);
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memory->destroy(binsizez_multi);
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memory->create(binsizex_multi, maxtypes+1, "neigh:binsizex_multi");
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memory->create(binsizey_multi, maxtypes+1, "neigh:binsizey_multi");
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memory->create(binsizez_multi, maxtypes+1, "neigh:binsizez_multi");
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memory->create(binsizex_multi, maxgroups, "neigh:binsizex_multi");
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memory->create(binsizey_multi, maxgroups, "neigh:binsizey_multi");
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memory->create(binsizez_multi, maxgroups, "neigh:binsizez_multi");
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memory->destroy(bininvx_multi);
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memory->destroy(bininvy_multi);
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memory->destroy(bininvz_multi);
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memory->create(bininvx_multi, maxtypes+1, "neigh:bininvx_multi");
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memory->create(bininvy_multi, maxtypes+1, "neigh:bininvy_multi");
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memory->create(bininvz_multi, maxtypes+1, "neigh:bininvz_multi");
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memory->create(bininvx_multi, maxgroups, "neigh:bininvx_multi");
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memory->create(bininvy_multi, maxgroups, "neigh:bininvy_multi");
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memory->create(bininvz_multi, maxgroups, "neigh:bininvz_multi");
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memory->destroy(maxbins_multi);
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memory->create(maxbins_multi, maxtypes+1, "neigh:maxbins_multi");
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memory->create(maxbins_multi, maxgroups, "neigh:maxbins_multi");
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// make sure reallocation occurs in bin_atoms_setup()
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for (n = 1; n <= maxtypes; n++) {
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for (n = 0; n < maxgroups; n++) {
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maxbins_multi[n] = 0;
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}
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maxatom = 0;
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}
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itypemin = itype_min();
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igroupmin = igroup_min();
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// bbox = size of bbox of entire domain
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// bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost
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@ -193,16 +189,16 @@ void NBinMulti::setup_bins(int style)
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bbox[1] = bboxhi[1] - bboxlo[1];
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bbox[2] = bboxhi[2] - bboxlo[2];
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// For each type...
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// For each grouping...
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for (n = 1; n <= atom->ntypes; n++) {
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for (n = 0; n < maxgroups; n++) {
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// binsize_user only relates to smallest type
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// optimal bin size is roughly 1/2 the type-type cutoff
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// special case of all cutoffs = 0.0, binsize = box size
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double binsize_optimal;
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if (n == itypemin && binsizeflag) binsize_optimal = binsize_user;
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else binsize_optimal = 0.5*sqrt(neighbor->cutneighsq[n][n]);
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if (n == igroupmin && binsizeflag) binsize_optimal = binsize_user;
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else binsize_optimal = 0.5*sqrt(cutmultisq[n][n]);
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if (binsize_optimal == 0.0) binsize_optimal = bbox[0];
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double binsizeinv = 1.0/binsize_optimal;
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@ -306,7 +302,7 @@ void NBinMulti::bin_atoms()
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int i,ibin,n;
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last_bin = update->ntimestep;
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for (n = 1; n <= maxtypes; n++) {
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for (n = 0; n < maxgroups; n++) {
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for (i = 0; i < mbins_multi[n]; i++) binhead_multi[n][i] = -1;
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}
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@ -323,7 +319,7 @@ void NBinMulti::bin_atoms()
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int bitmask = group->bitmask[includegroup];
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for (i = nall-1; i >= nlocal; i--) {
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if (mask[i] & bitmask) {
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n = type[i];
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n = map_type_multi[type[i]];
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ibin = coord2bin_multi(x[i], n);
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atom2bin_multi[n][i] = ibin;
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bins_multi[n][i] = binhead_multi[n][ibin];
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@ -331,7 +327,7 @@ void NBinMulti::bin_atoms()
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}
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}
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for (i = atom->nfirst-1; i >= 0; i--) {
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n = type[i];
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n = map_type_multi[type[i]];
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ibin = coord2bin_multi(x[i], n);
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atom2bin_multi[n][i] = ibin;
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bins_multi[n][i] = binhead_multi[n][ibin];
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@ -339,7 +335,7 @@ void NBinMulti::bin_atoms()
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}
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} else {
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for (i = nall-1; i >= 0; i--) {
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n = type[i];
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n = map_type_multi[type[i]];
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ibin = coord2bin_multi(x[i], n);
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atom2bin_multi[n][i] = ibin;
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bins_multi[n][i] = binhead_multi[n][ibin];
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@ -354,7 +350,7 @@ double NBinMulti::memory_usage()
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{
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double bytes = 0;
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for (int m = 1; m < maxtypes; m++) {
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for (int m = 0; m < maxgroups; m++) {
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bytes += maxbins_multi[m]*sizeof(int);
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bytes += 2*maxatom*sizeof(int);
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}
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