MD-Bench/lammps/pbc.c

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/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.
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*/
#include <stdbool.h>
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#include <stdlib.h>
#include <stdio.h>
//---
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#include <pbc.h>
#include <atom.h>
#include <allocate.h>
#define DELTA 20000
int NmaxGhost;
int *PBCx, *PBCy, *PBCz;
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static void growPbc(Atom*);
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/* exported subroutines */
void initPbc(Atom* atom) {
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NmaxGhost = 0;
atom->border_map = NULL;
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PBCx = NULL; PBCy = NULL; PBCz = NULL;
}
/* update coordinates of ghost atoms */
/* uses mapping created in setupPbc */
void updatePbc_cpu(Atom *atom, Parameter *param, bool doReneighbor) {
int *border_map = atom->border_map;
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int nlocal = atom->Nlocal;
MD_FLOAT xprd = param->xprd;
MD_FLOAT yprd = param->yprd;
MD_FLOAT zprd = param->zprd;
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for(int i = 0; i < atom->Nghost; i++) {
atom_x(nlocal + i) = atom_x(border_map[i]) + PBCx[i] * xprd;
atom_y(nlocal + i) = atom_y(border_map[i]) + PBCy[i] * yprd;
atom_z(nlocal + i) = atom_z(border_map[i]) + PBCz[i] * zprd;
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}
}
/* relocate atoms that have left domain according
* to periodic boundary conditions */
void updateAtomsPbc_cpu(Atom *atom, Parameter *param) {
MD_FLOAT xprd = param->xprd;
MD_FLOAT yprd = param->yprd;
MD_FLOAT zprd = param->zprd;
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for(int i = 0; i < atom->Nlocal; i++) {
if(atom_x(i) < 0.0) {
atom_x(i) += xprd;
} else if(atom_x(i) >= xprd) {
atom_x(i) -= xprd;
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}
if(atom_y(i) < 0.0) {
atom_y(i) += yprd;
} else if(atom_y(i) >= yprd) {
atom_y(i) -= yprd;
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}
if(atom_z(i) < 0.0) {
atom_z(i) += zprd;
} else if(atom_z(i) >= zprd) {
atom_z(i) -= zprd;
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}
}
}
/* setup periodic boundary conditions by
* defining ghost atoms around domain
* only creates mapping and coordinate corrections
* that are then enforced in updatePbc */
#define ADDGHOST(dx,dy,dz) \
Nghost++; \
border_map[Nghost] = i; \
PBCx[Nghost] = dx; \
PBCy[Nghost] = dy; \
PBCz[Nghost] = dz; \
atom->type[atom->Nlocal + Nghost] = atom->type[i]
void setupPbc(Atom *atom, Parameter *param) {
int *border_map = atom->border_map;
MD_FLOAT xprd = param->xprd;
MD_FLOAT yprd = param->yprd;
MD_FLOAT zprd = param->zprd;
MD_FLOAT Cutneigh = param->cutneigh;
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int Nghost = -1;
for(int i = 0; i < atom->Nlocal; i++) {
if (atom->Nlocal + Nghost + 7 >= atom->Nmax) {
growAtom(atom);
}
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if (Nghost + 7 >= NmaxGhost) {
growPbc(atom);
border_map = atom->border_map;
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}
MD_FLOAT x = atom_x(i);
MD_FLOAT y = atom_y(i);
MD_FLOAT z = atom_z(i);
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/* Setup ghost atoms */
/* 6 planes */
if(param->pbc_x != 0) {
if (x < Cutneigh) { ADDGHOST(+1,0,0); }
if (x >= (xprd-Cutneigh)) { ADDGHOST(-1,0,0); }
}
if(param->pbc_y != 0) {
if (y < Cutneigh) { ADDGHOST(0,+1,0); }
if (y >= (yprd-Cutneigh)) { ADDGHOST(0,-1,0); }
}
if(param->pbc_z != 0) {
if (z < Cutneigh) { ADDGHOST(0,0,+1); }
if (z >= (zprd-Cutneigh)) { ADDGHOST(0,0,-1); }
}
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/* 8 corners */
if(param->pbc_x != 0 && param->pbc_y != 0 && param->pbc_z != 0) {
if (x < Cutneigh && y < Cutneigh && z < Cutneigh) { ADDGHOST(+1,+1,+1); }
if (x < Cutneigh && y >= (yprd-Cutneigh) && z < Cutneigh) { ADDGHOST(+1,-1,+1); }
if (x < Cutneigh && y >= Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(+1,+1,-1); }
if (x < Cutneigh && y >= (yprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(+1,-1,-1); }
if (x >= (xprd-Cutneigh) && y < Cutneigh && z < Cutneigh) { ADDGHOST(-1,+1,+1); }
if (x >= (xprd-Cutneigh) && y >= (yprd-Cutneigh) && z < Cutneigh) { ADDGHOST(-1,-1,+1); }
if (x >= (xprd-Cutneigh) && y < Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(-1,+1,-1); }
if (x >= (xprd-Cutneigh) && y >= (yprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(-1,-1,-1); }
}
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/* 12 edges */
if(param->pbc_x != 0 && param->pbc_z != 0) {
if (x < Cutneigh && z < Cutneigh) { ADDGHOST(+1,0,+1); }
if (x < Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(+1,0,-1); }
if (x >= (xprd-Cutneigh) && z < Cutneigh) { ADDGHOST(-1,0,+1); }
if (x >= (xprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(-1,0,-1); }
}
if(param->pbc_y != 0 && param->pbc_z != 0) {
if (y < Cutneigh && z < Cutneigh) { ADDGHOST(0,+1,+1); }
if (y < Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(0,+1,-1); }
if (y >= (yprd-Cutneigh) && z < Cutneigh) { ADDGHOST(0,-1,+1); }
if (y >= (yprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(0,-1,-1); }
}
if(param->pbc_x != 0 && param->pbc_y != 0) {
if (y < Cutneigh && x < Cutneigh) { ADDGHOST(+1,+1,0); }
if (y < Cutneigh && x >= (xprd-Cutneigh)) { ADDGHOST(-1,+1,0); }
if (y >= (yprd-Cutneigh) && x < Cutneigh) { ADDGHOST(+1,-1,0); }
if (y >= (yprd-Cutneigh) && x >= (xprd-Cutneigh)) { ADDGHOST(-1,-1,0); }
}
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}
// increase by one to make it the ghost atom count
atom->Nghost = Nghost + 1;
}
/* internal subroutines */
void growPbc(Atom* atom) {
int nold = NmaxGhost;
NmaxGhost += DELTA;
atom->border_map = (int*) reallocate(atom->border_map, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
PBCx = (int*) reallocate(PBCx, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
PBCy = (int*) reallocate(PBCy, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
PBCz = (int*) reallocate(PBCz, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
}