162 lines
6.4 KiB
C
162 lines
6.4 KiB
C
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/*
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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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* Permission is hereby granted, free of charge, to any person obtaining a copy
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* of this software and associated documentation files (the "Software"), to deal
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* in the Software without restriction, including without limitation the rights
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* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the Software is
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* furnished to do so, subject to the following conditions:
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*
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* The above copyright notice and this permission notice shall be included in all
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* copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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* SOFTWARE.
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*
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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 *BorderMap;
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static int *PBCx, *PBCy, *PBCz;
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static void growPbc();
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void growPbc()
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{
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int nold = NmaxGhost;
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NmaxGhost += DELTA;
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BorderMap = (int*) reallocate(BorderMap, 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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void initPbc()
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{
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NmaxGhost = 0;
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BorderMap = NULL;
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PBCx = NULL; PBCy = NULL; PBCz = NULL;
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}
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void updatePbc(Atom *atom, Parameter *param)
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{
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int nlocal = atom->Nlocal;
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double* x = atom->x;
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double* y = atom->y;
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double* z = atom->z;
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double xprd = param->xprd;
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double yprd = param->yprd;
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double zprd = param->zprd;
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for(int i = 0; i < atom->Nghost; i++) {
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x[nlocal + i] = x[BorderMap[i]] + PBCx[i] * xprd;
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y[nlocal + i] = y[BorderMap[i]] + PBCy[i] * yprd;
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z[nlocal + i] = z[BorderMap[i]] + PBCz[i] * zprd;
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}
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}
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void updateAtomsPbc(Atom *atom, Parameter *param)
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{
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double* x = atom->x;
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double* y = atom->y;
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double* z = atom->z;
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double xprd = param->xprd;
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double yprd = param->yprd;
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double zprd = param->zprd;
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for(int i = 0; i < atom->Nlocal; i++) {
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if(x[i] < 0.0) {
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x[i] += xprd;
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} else if(x[i] >= xprd) {
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x[i] -= xprd;
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}
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if(y[i] < 0.0) {
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y[i] += yprd;
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} else if(y[i] >= yprd) {
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y[i] -= yprd;
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}
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if(z[i] < 0.0) {
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z[i] += zprd;
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} else if(z[i] >= zprd) {
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z[i] -= zprd;
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}
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}
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}
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#define ADDGHOST(dx,dy,dz) Nghost++; BorderMap[Nghost] = i; PBCx[Nghost] = dx; PBCy[Nghost] = dy; PBCz[Nghost] = dz;
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void setupPbc(Atom *atom, Parameter *param)
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{
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double* x = atom->x; double* y = atom->y; double* z = atom->z;
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double xprd = param->xprd;
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double yprd = param->yprd;
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double zprd = param->zprd;
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double 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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x = atom->x; y = atom->y; z = atom->z;
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}
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if (Nghost + 7 >= NmaxGhost) {
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growPbc();
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}
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/* Setup ghost atoms */
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/* 6 planes */
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if (x[i] < Cutneigh) { ADDGHOST(+1,0,0); }
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if (x[i] >= (xprd-Cutneigh)) { ADDGHOST(-1,0,0); }
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if (y[i] < Cutneigh) { ADDGHOST(0,+1,0); }
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if (y[i] >= (yprd-Cutneigh)) { ADDGHOST(0,-1,0); }
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if (z[i] < Cutneigh) { ADDGHOST(0,0,+1); }
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if (z[i] >= (zprd-Cutneigh)) { ADDGHOST(0,0,-1); }
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/* 8 corners */
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if (x[i] < Cutneigh && y[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(+1,+1,+1); }
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if (x[i] < Cutneigh && y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(+1,-1,+1); }
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if (x[i] < Cutneigh && y[i] >= Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(+1,+1,-1); }
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if (x[i] < Cutneigh && y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(+1,-1,-1); }
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if (x[i] >= (xprd-Cutneigh) && y[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(-1,+1,+1); }
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if (x[i] >= (xprd-Cutneigh) && y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(-1,-1,+1); }
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if (x[i] >= (xprd-Cutneigh) && y[i] < Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(-1,+1,-1); }
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if (x[i] >= (xprd-Cutneigh) && y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(-1,-1,-1); }
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/* 12 edges */
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if (x[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(+1,0,+1); }
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if (x[i] < Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(+1,0,-1); }
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if (x[i] >= (xprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(-1,0,+1); }
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if (x[i] >= (xprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(-1,0,-1); }
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if (y[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(0,+1,+1); }
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if (y[i] < Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(0,+1,-1); }
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if (y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(0,-1,+1); }
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if (y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(0,-1,-1); }
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if (y[i] < Cutneigh && x[i] < Cutneigh) { ADDGHOST(+1,+1,0); }
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if (y[i] < Cutneigh && x[i] >= (xprd-Cutneigh)) { ADDGHOST(-1,+1,0); }
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if (y[i] >= (yprd-Cutneigh) && x[i] < Cutneigh) { ADDGHOST(+1,-1,0); }
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if (y[i] >= (yprd-Cutneigh) && x[i] >= (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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