215 lines
9.1 KiB
C
215 lines
9.1 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) 2020 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 <pbc.h>
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#include <atom.h>
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#include <allocate.h>
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#include <neighbor.h>
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#define DELTA 20000
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static int NmaxGhost;
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static void growPbc(Atom*);
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/* exported subroutines */
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void initPbc(Atom* atom) {
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NmaxGhost = 0;
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atom->border_map = NULL;
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atom->PBCx = NULL; atom->PBCy = NULL; atom->PBCz = NULL;
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}
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/* update coordinates of ghost atoms */
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/* uses mapping created in setupPbc */
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void updatePbc(Atom *atom, Parameter *param, int updateBoundingBoxes) {
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int *border_map = atom->border_map;
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int nlocal = atom->Nclusters_local;
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MD_FLOAT xprd = param->xprd;
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MD_FLOAT yprd = param->yprd;
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MD_FLOAT zprd = param->zprd;
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for(int cg = 0; cg < atom->Nclusters_ghost; cg++) {
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const int ci = nlocal + cg;
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MD_FLOAT *cptr = cluster_pos_ptr(ci);
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MD_FLOAT *bmap_cptr = cluster_pos_ptr(border_map[cg]);
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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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for(int cii = 0; cii < atom->clusters[ci].natoms; cii++) {
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MD_FLOAT xtmp = cluster_x(bmap_cptr, cii) + atom->PBCx[cg] * xprd;
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MD_FLOAT ytmp = cluster_y(bmap_cptr, cii) + atom->PBCy[cg] * yprd;
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MD_FLOAT ztmp = cluster_z(bmap_cptr, cii) + atom->PBCz[cg] * zprd;
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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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if(updateBoundingBoxes) {
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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 > ztmp) { bbminz = ztmp; }
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if(bbmaxz < ztmp) { bbmaxz = ztmp; }
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}
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}
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if(updateBoundingBoxes) {
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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;
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atom->clusters[ci].bbminz = bbminz;
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atom->clusters[ci].bbmaxz = bbmaxz;
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}
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}
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}
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/* relocate atoms that have left domain according
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* to periodic boundary conditions */
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void updateAtomsPbc(Atom *atom, Parameter *param) {
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MD_FLOAT xprd = param->xprd;
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MD_FLOAT yprd = param->yprd;
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MD_FLOAT zprd = param->zprd;
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for(int i = 0; i < atom->Nlocal; i++) {
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if(atom_x(i) < 0.0) {
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atom_x(i) += xprd;
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} else if(atom_x(i) >= xprd) {
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atom_x(i) -= xprd;
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}
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if(atom_y(i) < 0.0) {
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atom_y(i) += yprd;
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} else if(atom_y(i) >= yprd) {
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atom_y(i) -= yprd;
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}
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if(atom_z(i) < 0.0) {
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atom_z(i) += zprd;
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} else if(atom_z(i) >= zprd) {
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atom_z(i) -= zprd;
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}
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}
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}
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/* setup periodic boundary conditions by
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* defining ghost atoms around domain
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* only creates mapping and coordinate corrections
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* that are then enforced in updatePbc */
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#define ADDGHOST(dx,dy,dz); \
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Nghost++; \
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const int g_atom_idx = atom->Nclusters_local + Nghost; \
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border_map[Nghost] = ci; \
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atom->PBCx[Nghost] = dx; \
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atom->PBCy[Nghost] = dy; \
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atom->PBCz[Nghost] = dz; \
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atom->clusters[g_atom_idx].natoms = atom->clusters[ci].natoms; \
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Nghost_atoms += atom->clusters[g_atom_idx].natoms; \
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for(int cii = 0; cii < atom->clusters[ci].natoms; cii++) { \
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atom->clusters[g_atom_idx].type[cii] = atom->clusters[ci].type[cii]; \
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}
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/* internal subroutines */
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void growPbc(Atom* atom) {
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int nold = NmaxGhost;
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NmaxGhost += DELTA;
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atom->border_map = (int*) reallocate(atom->border_map, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
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atom->PBCx = (int*) reallocate(atom->PBCx, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
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atom->PBCy = (int*) reallocate(atom->PBCy, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
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atom->PBCz = (int*) reallocate(atom->PBCz, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
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}
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void setupPbc(Atom *atom, Parameter *param) {
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int *border_map = atom->border_map;
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MD_FLOAT xprd = param->xprd;
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MD_FLOAT yprd = param->yprd;
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MD_FLOAT zprd = param->zprd;
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MD_FLOAT Cutneigh = param->cutneigh;
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int Nghost = -1;
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int Nghost_atoms = 0;
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for(int ci = 0; ci < atom->Nclusters_local; ci++) {
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if (atom->Nclusters_local + Nghost + 7 >= atom->Nclusters_max) {
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growClusters(atom);
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}
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if (Nghost + 7 >= NmaxGhost) {
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growPbc(atom);
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border_map = atom->border_map;
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}
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MD_FLOAT bbminx = atom->clusters[ci].bbminx;
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MD_FLOAT bbmaxx = atom->clusters[ci].bbmaxx;
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MD_FLOAT bbminy = atom->clusters[ci].bbminy;
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MD_FLOAT bbmaxy = atom->clusters[ci].bbmaxy;
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MD_FLOAT bbminz = atom->clusters[ci].bbminz;
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MD_FLOAT bbmaxz = atom->clusters[ci].bbmaxz;
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/* Setup ghost atoms */
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/* 6 planes */
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if (bbminx < Cutneigh) { ADDGHOST(+1,0,0); }
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if (bbmaxx >= (xprd-Cutneigh)) { ADDGHOST(-1,0,0); }
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if (bbminy < Cutneigh) { ADDGHOST(0,+1,0); }
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if (bbmaxy >= (yprd-Cutneigh)) { ADDGHOST(0,-1,0); }
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if (bbminz < Cutneigh) { ADDGHOST(0,0,+1); }
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if (bbmaxz >= (zprd-Cutneigh)) { ADDGHOST(0,0,-1); }
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/* 8 corners */
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if (bbminx < Cutneigh && bbminy < Cutneigh && bbminz < Cutneigh) { ADDGHOST(+1,+1,+1); }
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if (bbminx < Cutneigh && bbmaxy >= (yprd-Cutneigh) && bbminz < Cutneigh) { ADDGHOST(+1,-1,+1); }
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if (bbminx < Cutneigh && bbminy < Cutneigh && bbmaxz >= (zprd-Cutneigh)) { ADDGHOST(+1,+1,-1); }
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if (bbminx < Cutneigh && bbmaxy >= (yprd-Cutneigh) && bbmaxz >= (zprd-Cutneigh)) { ADDGHOST(+1,-1,-1); }
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if (bbmaxx >= (xprd-Cutneigh) && bbminy < Cutneigh && bbminz < Cutneigh) { ADDGHOST(-1,+1,+1); }
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if (bbmaxx >= (xprd-Cutneigh) && bbmaxy >= (yprd-Cutneigh) && bbminz < Cutneigh) { ADDGHOST(-1,-1,+1); }
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if (bbmaxx >= (xprd-Cutneigh) && bbminy < Cutneigh && bbmaxz >= (zprd-Cutneigh)) { ADDGHOST(-1,+1,-1); }
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if (bbmaxx >= (xprd-Cutneigh) && bbmaxy >= (yprd-Cutneigh) && bbmaxz >= (zprd-Cutneigh)) { ADDGHOST(-1,-1,-1); }
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/* 12 edges */
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if (bbminx < Cutneigh && bbminz < Cutneigh) { ADDGHOST(+1,0,+1); }
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if (bbminx < Cutneigh && bbmaxz >= (zprd-Cutneigh)) { ADDGHOST(+1,0,-1); }
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if (bbmaxx >= (xprd-Cutneigh) && bbminz < Cutneigh) { ADDGHOST(-1,0,+1); }
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if (bbmaxx >= (xprd-Cutneigh) && bbmaxz >= (zprd-Cutneigh)) { ADDGHOST(-1,0,-1); }
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if (bbminy < Cutneigh && bbminz < Cutneigh) { ADDGHOST(0,+1,+1); }
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if (bbminy < Cutneigh && bbmaxz >= (zprd-Cutneigh)) { ADDGHOST(0,+1,-1); }
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if (bbmaxy >= (yprd-Cutneigh) && bbminz < Cutneigh) { ADDGHOST(0,-1,+1); }
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if (bbmaxy >= (yprd-Cutneigh) && bbmaxz >= (zprd-Cutneigh)) { ADDGHOST(0,-1,-1); }
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if (bbminy < Cutneigh && bbminx < Cutneigh) { ADDGHOST(+1,+1,0); }
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if (bbminy < Cutneigh && bbmaxx >= (xprd-Cutneigh)) { ADDGHOST(-1,+1,0); }
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if (bbmaxy >= (yprd-Cutneigh) && bbminx < Cutneigh) { ADDGHOST(+1,-1,0); }
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if (bbmaxy >= (yprd-Cutneigh) && bbmaxx >= (xprd-Cutneigh)) { ADDGHOST(-1,-1,0); }
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}
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// increase by one to make it the ghost atom count
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atom->Nghost = Nghost_atoms;
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atom->Nclusters_ghost = Nghost + 1;
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atom->Nclusters = atom->Nclusters_local + Nghost + 1;
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// Update created ghost clusters positions
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updatePbc(atom, param, 1);
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}
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