173 lines
6.5 KiB
C
173 lines
6.5 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 <pbc.h>
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#include <atom.h>
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#include <allocate.h>
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#define DELTA 20000
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static int NmaxGhost;
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static int *PBCx, *PBCy, *PBCz;
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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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{
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NmaxGhost = 0;
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atom->border_map = NULL;
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PBCx = NULL; PBCy = NULL; 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)
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{
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int *border_map = atom->border_map;
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int nlocal = atom->Nlocal;
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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->Nghost; i++) {
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atom_x(nlocal + i) = atom_x(border_map[i]) + PBCx[i] * xprd;
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atom_y(nlocal + i) = atom_y(border_map[i]) + PBCy[i] * yprd;
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atom_z(nlocal + i) = atom_z(border_map[i]) + PBCz[i] * zprd;
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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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{
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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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border_map[Nghost] = i; \
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PBCx[Nghost] = dx; \
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PBCy[Nghost] = dy; \
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PBCz[Nghost] = dz; \
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atom->type[atom->Nlocal + Nghost] = atom->type[i]
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void setupPbc(Atom *atom, Parameter *param)
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{
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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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for(int i = 0; i < atom->Nlocal; i++) {
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if (atom->Nlocal + Nghost + 7 >= atom->Nmax) {
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growAtom(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 x = atom_x(i);
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MD_FLOAT y = atom_y(i);
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MD_FLOAT z = atom_z(i);
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/* Setup ghost atoms */
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/* 6 planes */
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if (x < Cutneigh) { ADDGHOST(+1,0,0); }
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if (x >= (xprd-Cutneigh)) { ADDGHOST(-1,0,0); }
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if (y < Cutneigh) { ADDGHOST(0,+1,0); }
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if (y >= (yprd-Cutneigh)) { ADDGHOST(0,-1,0); }
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if (z < Cutneigh) { ADDGHOST(0,0,+1); }
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if (z >= (zprd-Cutneigh)) { ADDGHOST(0,0,-1); }
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/* 8 corners */
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if (x < Cutneigh && y < Cutneigh && z < Cutneigh) { ADDGHOST(+1,+1,+1); }
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if (x < Cutneigh && y >= (yprd-Cutneigh) && z < Cutneigh) { ADDGHOST(+1,-1,+1); }
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if (x < Cutneigh && y >= Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(+1,+1,-1); }
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if (x < Cutneigh && y >= (yprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(+1,-1,-1); }
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if (x >= (xprd-Cutneigh) && y < Cutneigh && z < Cutneigh) { ADDGHOST(-1,+1,+1); }
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if (x >= (xprd-Cutneigh) && y >= (yprd-Cutneigh) && z < Cutneigh) { ADDGHOST(-1,-1,+1); }
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if (x >= (xprd-Cutneigh) && y < Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(-1,+1,-1); }
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if (x >= (xprd-Cutneigh) && y >= (yprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(-1,-1,-1); }
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/* 12 edges */
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if (x < Cutneigh && z < Cutneigh) { ADDGHOST(+1,0,+1); }
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if (x < Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(+1,0,-1); }
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if (x >= (xprd-Cutneigh) && z < Cutneigh) { ADDGHOST(-1,0,+1); }
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if (x >= (xprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(-1,0,-1); }
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if (y < Cutneigh && z < Cutneigh) { ADDGHOST(0,+1,+1); }
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if (y < Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(0,+1,-1); }
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if (y >= (yprd-Cutneigh) && z < Cutneigh) { ADDGHOST(0,-1,+1); }
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if (y >= (yprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(0,-1,-1); }
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if (y < Cutneigh && x < Cutneigh) { ADDGHOST(+1,+1,0); }
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if (y < Cutneigh && x >= (xprd-Cutneigh)) { ADDGHOST(-1,+1,0); }
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if (y >= (yprd-Cutneigh) && x < Cutneigh) { ADDGHOST(+1,-1,0); }
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if (y >= (yprd-Cutneigh) && x >= (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 + 1;
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}
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/* internal subroutines */
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void growPbc(Atom* atom)
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{
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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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PBCx = (int*) reallocate(PBCx, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
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PBCy = (int*) reallocate(PBCy, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
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PBCz = (int*) reallocate(PBCz, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
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}
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