523 lines
16 KiB
C
523 lines
16 KiB
C
/*
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* =======================================================================================
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*
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* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
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* Copyright (c) 2021 RRZE, University Erlangen-Nuremberg
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*
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* This file is part of MD-Bench.
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*
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* MD-Bench is free software: you can redistribute it and/or modify it
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* under the terms of the GNU Lesser General Public License as published
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* by the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* MD-Bench is distributed in the hope that it will be useful, but WITHOUT ANY
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* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
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* PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
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* details.
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*
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* You should have received a copy of the GNU Lesser General Public License along
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* with MD-Bench. If not, see <https://www.gnu.org/licenses/>.
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* =======================================================================================
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*/
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#include <stdlib.h>
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#include <stdio.h>
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#include <math.h>
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#include <neighbor.h>
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#include <parameter.h>
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#include <atom.h>
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#include <util.h>
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#define SMALL 1.0e-6
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#define FACTOR 0.999
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static MD_FLOAT xprd, yprd;
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static MD_FLOAT bininvx, bininvy;
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static int mbinxlo, mbinylo;
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static int nbinx, nbiny;
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static int mbinx, mbiny; // n bins in x, y
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static int *bincount;
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static int *bins;
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static int *cluster_bincount;
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static int *cluster_bins;
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static int mbins; //total number of bins
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static int atoms_per_bin; // max atoms per bin
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static int clusters_per_bin; // max clusters per bin
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static MD_FLOAT cutneigh;
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static MD_FLOAT cutneighsq; // neighbor cutoff squared
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static int nmax;
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static int nstencil; // # of bins in stencil
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static int* stencil; // stencil list of bin offsets
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static MD_FLOAT binsizex, binsizey;
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static int coord2bin(MD_FLOAT, MD_FLOAT);
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static MD_FLOAT bindist(int, int);
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/* exported subroutines */
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void initNeighbor(Neighbor *neighbor, Parameter *param)
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{
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MD_FLOAT neighscale = 5.0 / 6.0;
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xprd = param->nx * param->lattice;
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yprd = param->ny * param->lattice;
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cutneigh = param->cutneigh;
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nbinx = neighscale * param->nx;
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nbiny = neighscale * param->ny;
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nmax = 0;
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atoms_per_bin = 8;
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clusters_per_bin = (atoms_per_bin / CLUSTER_DIM_N) + 4;
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stencil = NULL;
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bins = NULL;
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bincount = NULL;
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cluster_bins = NULL;
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cluster_bincount = NULL;
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neighbor->maxneighs = 100;
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neighbor->numneigh = NULL;
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neighbor->neighbors = NULL;
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}
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void setupNeighbor(Parameter* param) {
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MD_FLOAT coord;
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int mbinxhi, mbinyhi;
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int nextx, nexty, nextz;
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if(param->input_file != NULL) {
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xprd = param->xprd;
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yprd = param->yprd;
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}
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// TODO: update lo and hi for standard case and use them here instead
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MD_FLOAT xlo = 0.0; MD_FLOAT xhi = xprd;
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MD_FLOAT ylo = 0.0; MD_FLOAT yhi = yprd;
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cutneighsq = cutneigh * cutneigh;
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if(param->input_file != NULL) {
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binsizex = cutneigh * 0.5;
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binsizey = cutneigh * 0.5;
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nbinx = (int)((param->xhi - param->xlo) / binsizex);
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nbiny = (int)((param->yhi - param->ylo) / binsizey);
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if(nbinx == 0) { nbinx = 1; }
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if(nbiny == 0) { nbiny = 1; }
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bininvx = nbinx / (param->xhi - param->xlo);
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bininvy = nbiny / (param->yhi - param->ylo);
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} else {
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binsizex = xprd / nbinx;
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binsizey = yprd / nbiny;
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bininvx = 1.0 / binsizex;
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bininvy = 1.0 / binsizey;
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}
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coord = xlo - cutneigh - SMALL * xprd;
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mbinxlo = (int) (coord * bininvx);
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if (coord < 0.0) {
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mbinxlo = mbinxlo - 1;
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}
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coord = xhi + cutneigh + SMALL * xprd;
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mbinxhi = (int) (coord * bininvx);
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coord = ylo - cutneigh - SMALL * yprd;
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mbinylo = (int) (coord * bininvy);
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if (coord < 0.0) {
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mbinylo = mbinylo - 1;
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}
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coord = yhi + cutneigh + SMALL * yprd;
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mbinyhi = (int) (coord * bininvy);
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mbinxlo = mbinxlo - 1;
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mbinxhi = mbinxhi + 1;
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mbinx = mbinxhi - mbinxlo + 1;
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mbinylo = mbinylo - 1;
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mbinyhi = mbinyhi + 1;
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mbiny = mbinyhi - mbinylo + 1;
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nextx = (int) (cutneigh * bininvx);
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if(nextx * binsizex < FACTOR * cutneigh) nextx++;
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nexty = (int) (cutneigh * bininvy);
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if(nexty * binsizey < FACTOR * cutneigh) nexty++;
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if (stencil) {
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free(stencil);
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}
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stencil = (int *) malloc((2 * nexty + 1) * (2 * nextx + 1) * sizeof(int));
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nstencil = 0;
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for(int j = -nexty; j <= nexty; j++) {
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for(int i = -nextx; i <= nextx; i++) {
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if(bindist(i, j) < cutneighsq) {
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stencil[nstencil++] = j * mbinx + i;
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}
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}
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}
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mbins = mbinx * mbiny;
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if (bincount) { free(bincount); }
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bincount = (int*) malloc(mbins * sizeof(int));
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if (bins) { free(bins); }
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bins = (int*) malloc(mbins * atoms_per_bin * sizeof(int));
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if (cluster_bincount) { free(cluster_bincount); }
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cluster_bincount = (int*) malloc(mbins * sizeof(int));
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if (cluster_bins) { free(cluster_bins); }
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cluster_bins = (int*) malloc(mbins * clusters_per_bin * sizeof(int));
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}
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MD_FLOAT getBoundingBoxDistanceSq(Atom *atom, int ci, int cj) {
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MD_FLOAT dl = atom->clusters[ci].bbminx - atom->clusters[cj].bbmaxx;
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MD_FLOAT dh = atom->clusters[cj].bbminx - atom->clusters[ci].bbmaxx;
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MD_FLOAT dm = MAX(dl, dh);
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MD_FLOAT dm0 = MAX(dm, 0.0);
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MD_FLOAT d2 = dm0 * dm0;
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dl = atom->clusters[ci].bbminy - atom->clusters[cj].bbmaxy;
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dh = atom->clusters[cj].bbminy - atom->clusters[ci].bbmaxy;
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dm = MAX(dl, dh);
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dm0 = MAX(dm, 0.0);
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d2 += dm0 * dm0;
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dl = atom->clusters[ci].bbminz - atom->clusters[cj].bbmaxz;
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dh = atom->clusters[cj].bbminz - atom->clusters[ci].bbmaxz;
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dm = MAX(dl, dh);
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dm0 = MAX(dm, 0.0);
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d2 += dm0 * dm0;
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return d2;
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}
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int atomDistanceInRange(Atom *atom, int ci, int cj, MD_FLOAT rsq) {
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MD_FLOAT *ciptr = cluster_ptr(ci);
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MD_FLOAT *cjptr = cluster_ptr(cj);
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for(int cii = 0; cii < atom->clusters[ci].natoms; cii++) {
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for(int cjj = 0; cjj < atom->clusters[cj].natoms; cjj++) {
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MD_FLOAT delx = cluster_x(ciptr, cii) - cluster_x(cjptr, cjj);
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MD_FLOAT dely = cluster_y(ciptr, cii) - cluster_y(cjptr, cjj);
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MD_FLOAT delz = cluster_z(ciptr, cii) - cluster_z(cjptr, cjj);
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if(delx * delx + dely * dely + delz * delz < rsq) {
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return 1;
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}
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}
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}
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return 0;
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}
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void buildNeighbor(Parameter *param, Atom *atom, Neighbor *neighbor) {
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int nall = atom->Nlocal + atom->Nghost;
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/* extend atom arrays if necessary */
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if(nall > nmax) {
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nmax = nall;
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if(neighbor->numneigh) free(neighbor->numneigh);
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if(neighbor->neighbors) free(neighbor->neighbors);
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neighbor->numneigh = (int*) malloc(nmax * sizeof(int));
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neighbor->neighbors = (int*) malloc(nmax * neighbor->maxneighs * sizeof(int*));
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}
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/* bin local & ghost atoms */
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binatoms(atom);
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buildClusters(param, atom);
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const MD_FLOAT rBB = cutneighsq / 2.0; // TODO: change this
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int resize = 1;
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/* loop over each atom, storing neighbors */
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while(resize) {
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int new_maxneighs = neighbor->maxneighs;
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resize = 0;
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for(int ci = 0; ci < atom->Nclusters_local; ci++) {
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int* neighptr = &(neighbor->neighbors[ci * neighbor->maxneighs]);
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int n = 0;
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int ibin = atom->clusters[ci].bin;
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MD_FLOAT ibb_zmin = atom->clusters[ci].bbminz;
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MD_FLOAT ibb_zmax = atom->clusters[ci].bbmaxz;
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for(int k = 0; k < nstencil; k++) {
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int jbin = ibin + stencil[k];
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int *loc_bin = &cluster_bins[jbin * clusters_per_bin];
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int cj, m = -1;
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MD_FLOAT jbb_zmin, jbb_zmax;
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do {
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m++;
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cj = loc_bin[m];
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jbb_zmin = atom->clusters[cj].bbminz;
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jbb_zmax = atom->clusters[cj].bbmaxz;
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} while((ibb_zmin - jbb_zmax) * (ibb_zmin - jbb_zmax) > cutneighsq);
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while(m < cluster_bincount[jbin] && jbb_zmax - ibb_zmax < cutneighsq) {
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if((jbb_zmin - ibb_zmax) * (jbb_zmin - ibb_zmax) > cutneighsq) {
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break;
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}
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double d_bb_sq = getBoundingBoxDistanceSq(atom, ci, cj);
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if(d_bb_sq < cutneighsq) {
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if(d_bb_sq < rBB || atomDistanceInRange(atom, ci, cj, cutneighsq)) {
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if(cj == ci) {
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// Add to neighbor list with diagonal interaction mask
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}
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neighptr[n++] = cj;
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}
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}
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m++;
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cj = loc_bin[m];
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jbb_zmin = atom->clusters[cj].bbminz;
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jbb_zmax = atom->clusters[cj].bbmaxz;
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}
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}
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neighbor->numneigh[ci] = n;
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if(n >= neighbor->maxneighs) {
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resize = 1;
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if(n >= new_maxneighs) {
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new_maxneighs = n;
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}
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}
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}
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if(resize) {
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printf("RESIZE %d\n", neighbor->maxneighs);
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neighbor->maxneighs = new_maxneighs * 1.2;
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free(neighbor->neighbors);
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neighbor->neighbors = (int*) malloc(atom->Nmax * neighbor->maxneighs * sizeof(int));
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}
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}
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}
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/* internal subroutines */
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MD_FLOAT bindist(int i, int j) {
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MD_FLOAT delx, dely, delz;
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if(i > 0) {
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delx = (i - 1) * binsizex;
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} else if(i == 0) {
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delx = 0.0;
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} else {
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delx = (i + 1) * binsizex;
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}
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if(j > 0) {
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dely = (j - 1) * binsizey;
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} else if(j == 0) {
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dely = 0.0;
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} else {
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dely = (j + 1) * binsizey;
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}
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return (delx * delx + dely * dely);
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}
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int coord2bin(MD_FLOAT xin, MD_FLOAT yin) {
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int ix, iy;
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if(xin >= xprd) {
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ix = (int)((xin - xprd) * bininvx) + nbinx - mbinxlo;
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} else if(xin >= 0.0) {
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ix = (int)(xin * bininvx) - mbinxlo;
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} else {
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ix = (int)(xin * bininvx) - mbinxlo - 1;
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}
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if(yin >= yprd) {
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iy = (int)((yin - yprd) * bininvy) + nbiny - mbinylo;
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} else if(yin >= 0.0) {
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iy = (int)(yin * bininvy) - mbinylo;
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} else {
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iy = (int)(yin * bininvy) - mbinylo - 1;
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}
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return (iy * mbinx + ix + 1);
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}
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void coord2bin2D(MD_FLOAT xin, MD_FLOAT yin, int *ix, int *iy) {
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if(xin >= xprd) {
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*ix = (int)((xin - xprd) * bininvx) + nbinx - mbinxlo;
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} else if(xin >= 0.0) {
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*ix = (int)(xin * bininvx) - mbinxlo;
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} else {
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*ix = (int)(xin * bininvx) - mbinxlo - 1;
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}
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if(yin >= yprd) {
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*iy = (int)((yin - yprd) * bininvy) + nbiny - mbinylo;
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} else if(yin >= 0.0) {
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*iy = (int)(yin * bininvy) - mbinylo;
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} else {
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*iy = (int)(yin * bininvy) - mbinylo - 1;
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}
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}
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void binatoms(Atom *atom) {
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int nall = atom->Nlocal + atom->Nghost;
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int resize = 1;
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while(resize > 0) {
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resize = 0;
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for(int i = 0; i < mbins; i++) {
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bincount[i] = 0;
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}
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for(int i = 0; i < nall; i++) {
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int ibin = coord2bin(atom_x(i), atom_y(i));
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if(bincount[ibin] < atoms_per_bin) {
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int ac = bincount[ibin]++;
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bins[ibin * atoms_per_bin + ac] = i;
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} else {
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resize = 1;
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}
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}
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if(resize) {
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free(bins);
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atoms_per_bin *= 2;
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bins = (int*) malloc(mbins * atoms_per_bin * sizeof(int));
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}
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}
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}
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// TODO: Use pigeonhole sorting
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void sortBinAtomsByZCoord(Parameter *param, Atom *atom, int bin) {
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int c = bincount[bin];
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int *bin_ptr = &bins[bin * atoms_per_bin];
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for(int ac_i = 0; ac_i < c; ac_i++) {
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int i = bin_ptr[ac_i];
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int min_ac = ac_i;
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int min_idx = i;
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MD_FLOAT min_z = atom_z(i);
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for(int ac_j = ac_i + 1; ac_j < c; ac_j++) {
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int j = bin_ptr[ac_j];
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MD_FLOAT zj = atom_z(j);
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if(zj < min_z) {
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min_ac = zj;
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min_idx = j;
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min_z = zj;
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}
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}
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bin_ptr[ac_i] = min_idx;
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bin_ptr[min_ac] = i;
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}
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}
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void buildClusters(Parameter *param, Atom *atom) {
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for(int bin = 0; bin < mbins; bin++) {
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sortBinAtomsByZCoord(param, atom, bin);
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}
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int resize = 1;
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while(resize > 0) {
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resize = 0;
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for(int bin = 0; bin < mbins; bin++) {
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int c = bincount[bin];
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int ac = 0;
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const int nclusters = ((c + CLUSTER_DIM_N - 1) / CLUSTER_DIM_N);
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if(nclusters < clusters_per_bin) {
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for(int cl = 0; cl < nclusters; cl++) {
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const int ci = atom->Nclusters_local;
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MD_FLOAT *cptr = cluster_ptr(ci);
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MD_FLOAT bbminx = INFINITY, bbmaxx = -INFINITY;
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MD_FLOAT bbminy = INFINITY, bbmaxy = -INFINITY;
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MD_FLOAT bbminz = INFINITY, bbmaxz = -INFINITY;
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atom->clusters[ci].natoms = 0;
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for(int cii = 0; cii < CLUSTER_DIM_N; cii++) {
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if(ac < c) {
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int i = bins[bin * atoms_per_bin + ac];
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MD_FLOAT xtmp = atom_x(i);
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MD_FLOAT ytmp = atom_y(i);
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MD_FLOAT ztmp = atom_z(i);
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cluster_x(cptr, cii) = xtmp;
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cluster_y(cptr, cii) = ytmp;
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cluster_z(cptr, cii) = ztmp;
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// TODO: To create the bounding boxes faster, we can use SIMD operations
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if(bbminx > xtmp) { bbminx = xtmp; }
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if(bbmaxx < xtmp) { bbmaxx = xtmp; }
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if(bbminy > ytmp) { bbminy = ytmp; }
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if(bbmaxy < ytmp) { bbmaxy = ytmp; }
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if(bbminz > ytmp) { bbminz = ytmp; }
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if(bbmaxz < ytmp) { bbmaxz = ytmp; }
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atom->clusters[ci].type[cii] = atom->type[i];
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atom->clusters[ci].natoms++;
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} else {
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cluster_x(cptr, cii) = INFINITY;
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cluster_y(cptr, cii) = INFINITY;
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cluster_z(cptr, cii) = INFINITY;
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}
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ac++;
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}
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cluster_bins[bin * clusters_per_bin + cl] = ci;
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atom->clusters[ci].bin = bin;
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atom->clusters[ci].bbminx = bbminx;
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atom->clusters[ci].bbmaxx = bbmaxx;
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atom->clusters[ci].bbminy = bbminy;
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atom->clusters[ci].bbmaxy = bbmaxy;
|
|
atom->clusters[ci].bbminz = bbminz;
|
|
atom->clusters[ci].bbmaxz = bbmaxz;
|
|
atom->Nclusters_local++;
|
|
}
|
|
|
|
cluster_bincount[bin] = nclusters;
|
|
} else {
|
|
resize = 1;
|
|
}
|
|
}
|
|
|
|
if(resize) {
|
|
free(cluster_bins);
|
|
clusters_per_bin *= 2;
|
|
cluster_bins = (int*) malloc(mbins * clusters_per_bin * sizeof(int));
|
|
}
|
|
}
|
|
}
|
|
|
|
void binGhostClusters(Parameter *param, Atom *atom) {
|
|
int nlocal = atom->Nclusters_local;
|
|
|
|
for(int ci = 0; ci < atom->Nclusters_ghost; ci++) {
|
|
MD_FLOAT *cptr = cluster_ptr(nlocal + ci);
|
|
MD_FLOAT xtmp, ytmp;
|
|
int ix = -1, iy = -1;
|
|
|
|
xtmp = cluster_x(cptr, 0);
|
|
ytmp = cluster_y(cptr, 0);
|
|
coord2bin2D(xtmp, ytmp, &ix, &iy);
|
|
|
|
for(int cii = 1; cii < atom->clusters[ci].natoms; cii++) {
|
|
int nix, niy;
|
|
xtmp = cluster_x(cptr, cii);
|
|
ytmp = cluster_y(cptr, cii);
|
|
coord2bin2D(xtmp, ytmp, &nix, &niy);
|
|
// Always put the cluster on the bin of its innermost atom so
|
|
// the cluster should be closer to local clusters
|
|
if(atom->PBCx[ci] > 0 && ix > nix) { ix = nix; }
|
|
if(atom->PBCx[ci] < 0 && ix < nix) { ix = nix; }
|
|
if(atom->PBCy[ci] > 0 && iy > niy) { iy = niy; }
|
|
if(atom->PBCy[ci] < 0 && iy < niy) { iy = niy; }
|
|
}
|
|
|
|
int bin = iy * mbinx + ix + 1;
|
|
int c = cluster_bincount[bin];
|
|
cluster_bins[bin * clusters_per_bin + c] = nlocal + ci;
|
|
cluster_bincount[bin]++;
|
|
}
|
|
}
|