Adding collection array, new user arguments, and multi communication
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 = 0; n < maxgroups; n++) {
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for (int n = 0; n < maxcollections; 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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@ -75,81 +75,80 @@ void NBinMulti::bin_atoms_setup(int nall)
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for triclinic boxes:
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tilted simulation box cannot contain integer # of bins
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stencil & neigh list built differently to account for this
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mbinlo_multi = lowest global bin any of my ghost atoms could fall into for each grouping
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mbinhi_multi = highest global bin any of my ghost atoms could fall into for each grouping
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mbin_multi = number of bins I need in a dimension for each grouping
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mbinlo_multi = lowest global bin any of my ghost atoms could fall into for each collection
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mbinhi_multi = highest global bin any of my ghost atoms could fall into for each collection
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mbin_multi = number of bins I need in a dimension for each collection
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------------------------------------------------------------------------- */
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void NBinMulti::setup_bins(int style)
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void NBinMulti::setup_bins(int /*style*/)
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{
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int n;
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// Initialize arrays
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if (n_multi_groups > maxgroups) {
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if (ncollections > maxcollections) {
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// Clear any/all memory for existing groupings
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for (n = 0; n < maxgroups; n++)
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for (n = 0; n < maxcollections; n++)
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memory->destroy(binhead_multi[n]);
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delete [] binhead_multi;
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// Realloacte at updated maxgroups
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maxgroups = n_multi_groups;
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maxcollections = ncollections;
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binhead_multi = new int*[maxgroups]();
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binhead_multi = new int*[maxcollections]();
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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, 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->create(nbinx_multi, maxcollections, "neigh:nbinx_multi");
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memory->create(nbiny_multi, maxcollections, "neigh:nbiny_multi");
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memory->create(nbinz_multi, maxcollections, "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, 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->create(mbins_multi, maxcollections, "neigh:mbins_multi");
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memory->create(mbinx_multi, maxcollections, "neigh:mbinx_multi");
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memory->create(mbiny_multi, maxcollections, "neigh:mbiny_multi");
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memory->create(mbinz_multi, maxcollections, "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, 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->create(mbinxlo_multi, maxcollections, "neigh:mbinxlo_multi");
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memory->create(mbinylo_multi, maxcollections, "neigh:mbinylo_multi");
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memory->create(mbinzlo_multi, maxcollections, "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, 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->create(binsizex_multi, maxcollections, "neigh:binsizex_multi");
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memory->create(binsizey_multi, maxcollections, "neigh:binsizey_multi");
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memory->create(binsizez_multi, maxcollections, "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, 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->create(bininvx_multi, maxcollections, "neigh:bininvx_multi");
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memory->create(bininvy_multi, maxcollections, "neigh:bininvy_multi");
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memory->create(bininvz_multi, maxcollections, "neigh:bininvz_multi");
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memory->destroy(maxbins_multi);
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memory->create(maxbins_multi, maxgroups, "neigh:maxbins_multi");
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memory->create(maxbins_multi, maxcollections, "neigh:maxbins_multi");
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// ensure reallocation occurs in bin_atoms_setup()
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for (n = 0; n < maxgroups; n++) {
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for (n = 0; n < maxcollections; 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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// Identify smallest group
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int igroupmin = 0;
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for (n = 0; n < maxgroups; n++)
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if (cutmultisq[n][n] < cutmultisq[igroupmin][igroupmin])
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igroupmin = n;
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// Identify smallest collection
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int icollectionmin = 0;
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for (n = 0; n < maxcollections; n++)
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if (cutcollectionsq[n][n] < cutcollectionsq[icollectionmin][icollectionmin])
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icollectionmin = n;
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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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@ -189,13 +188,13 @@ void NBinMulti::setup_bins(int style)
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double binsize_optimal, binsizeinv, coord;
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int mbinxhi,mbinyhi,mbinzhi;
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for (n = 0; n < maxgroups; n++) {
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// binsize_user only relates to smallest group
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// optimal bin size is roughly 1/2 the group-group cutoff
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for (n = 0; n < maxcollections; n++) {
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// binsize_user only relates to smallest collection
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// optimal bin size is roughly 1/2 the collection-collection cutoff
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// special case of all cutoffs = 0.0, binsize = box size
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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 (n == icollectionmin && binsizeflag) binsize_optimal = binsize_user;
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else binsize_optimal = 0.5*sqrt(cutcollectionsq[n][n]);
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if (binsize_optimal == 0.0) binsize_optimal = bbox[0];
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binsizeinv = 1.0/binsize_optimal;
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@ -296,16 +295,15 @@ 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 = 0; n < maxgroups; n++) {
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for (n = 0; n < maxcollections; 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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// bin in reverse order so linked list will be in forward order
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// also puts ghost atoms at end of list, which is necessary
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int *collection = neighbor->collection;
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double **x = atom->x;
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int *mask = atom->mask;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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int nall = nlocal + atom->nghost;
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@ -313,7 +311,7 @@ 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 = map_type_multi[type[i]];
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n = collection[i];
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ibin = coord2bin_multi(x[i], n);
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atom2bin[i] = ibin;
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bins[i] = binhead_multi[n][ibin];
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@ -321,15 +319,15 @@ 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 = map_type_multi[type[i]];
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n = collection[i];
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ibin = coord2bin_multi(x[i], n);
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atom2bin[i] = ibin;
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bins[i] = binhead_multi[n][ibin];
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binhead_multi[n][ibin] = i;
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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 = map_type_multi[type[i]];
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for (i = nall-1; i >= 0; i--) {
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n = collection[i];
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ibin = coord2bin_multi(x[i], n);
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atom2bin[i] = ibin;
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bins[i] = binhead_multi[n][ibin];
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@ -343,7 +341,7 @@ void NBinMulti::bin_atoms()
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double NBinMulti::memory_usage()
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{
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double bytes = 0;
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for (int m = 0; m < maxgroups; m++)
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for (int m = 0; m < maxcollections; m++)
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bytes += maxbins_multi[m]*sizeof(int);
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bytes += 2*maxatom*sizeof(int);
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return bytes;
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