235 lines
7.2 KiB
C
235 lines
7.2 KiB
C
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/*
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* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
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* All rights reserved. This file is part of MD-Bench.
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* Use of this source code is governed by a LGPL-3.0
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* license that can be found in the LICENSE file.
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*/
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#include <stdbool.h>
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#include <stdio.h>
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#include <stdlib.h>
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//---
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#include <allocate.h>
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#include <atom.h>
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#include <pbc.h>
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#define DELTA 20000
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int nmaxGhost;
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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;
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PBCy = NULL;
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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_cpu(Atom* atom, Parameter* param, bool doReneighbor)
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{
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int* borderMap = 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(borderMap[i]) + PBCx[i] * xprd;
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atom_y(nlocal + i) = atom_y(borderMap[i]) + PBCy[i] * yprd;
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atom_z(nlocal + i) = atom_z(borderMap[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_cpu(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 (param->pbc_x != 0) {
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if (x < cutneigh) {
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ADDGHOST(+1, 0, 0);
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}
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if (x >= (xprd - cutneigh)) {
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ADDGHOST(-1, 0, 0);
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}
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}
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if (param->pbc_y != 0) {
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if (y < cutneigh) {
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ADDGHOST(0, +1, 0);
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}
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if (y >= (yprd - cutneigh)) {
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ADDGHOST(0, -1, 0);
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}
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}
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if (param->pbc_z != 0) {
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if (z < cutneigh) {
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ADDGHOST(0, 0, +1);
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}
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if (z >= (zprd - cutneigh)) {
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ADDGHOST(0, 0, -1);
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}
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}
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/* 8 corners */
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if (param->pbc_x != 0 && param->pbc_y != 0 && param->pbc_z != 0) {
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if (x < cutneigh && y < cutneigh && z < cutneigh) {
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ADDGHOST(+1, +1, +1);
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}
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if (x < cutneigh && y >= (yprd - cutneigh) && z < cutneigh) {
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ADDGHOST(+1, -1, +1);
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}
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if (x < cutneigh && y < cutneigh && z >= (zprd - cutneigh)) {
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ADDGHOST(+1, +1, -1);
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}
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if (x < cutneigh && y >= (yprd - cutneigh) && z >= (zprd - cutneigh)) {
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ADDGHOST(+1, -1, -1);
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}
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if (x >= (xprd - cutneigh) && y < cutneigh && z < cutneigh) {
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ADDGHOST(-1, +1, +1);
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}
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if (x >= (xprd - cutneigh) && y >= (yprd - cutneigh) && z < cutneigh) {
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ADDGHOST(-1, -1, +1);
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}
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if (x >= (xprd - cutneigh) && y < cutneigh && z >= (zprd - cutneigh)) {
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ADDGHOST(-1, +1, -1);
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}
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if (x >= (xprd - cutneigh) && y >= (yprd - cutneigh) &&
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z >= (zprd - cutneigh)) {
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ADDGHOST(-1, -1, -1);
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}
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}
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/* 12 edges */
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if (param->pbc_x != 0 && param->pbc_z != 0) {
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if (x < cutneigh && z < cutneigh) {
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ADDGHOST(+1, 0, +1);
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}
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if (x < cutneigh && z >= (zprd - cutneigh)) {
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ADDGHOST(+1, 0, -1);
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}
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if (x >= (xprd - cutneigh) && z < cutneigh) {
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ADDGHOST(-1, 0, +1);
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}
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if (x >= (xprd - cutneigh) && z >= (zprd - cutneigh)) {
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ADDGHOST(-1, 0, -1);
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}
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}
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if (param->pbc_y != 0 && param->pbc_z != 0) {
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if (y < cutneigh && z < cutneigh) {
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ADDGHOST(0, +1, +1);
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}
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if (y < cutneigh && z >= (zprd - cutneigh)) {
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ADDGHOST(0, +1, -1);
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}
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if (y >= (yprd - cutneigh) && z < cutneigh) {
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ADDGHOST(0, -1, +1);
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}
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if (y >= (yprd - cutneigh) && z >= (zprd - cutneigh)) {
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ADDGHOST(0, -1, -1);
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}
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}
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if (param->pbc_x != 0 && param->pbc_y != 0) {
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if (y < cutneigh && x < cutneigh) {
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ADDGHOST(+1, +1, 0);
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}
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if (y < cutneigh && x >= (xprd - cutneigh)) {
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ADDGHOST(-1, +1, 0);
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}
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if (y >= (yprd - cutneigh) && x < cutneigh) {
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ADDGHOST(+1, -1, 0);
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}
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if (y >= (yprd - cutneigh) && x >= (xprd - cutneigh)) {
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ADDGHOST(-1, -1, 0);
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}
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}
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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,
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ALIGNMENT,
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nmaxGhost * sizeof(int),
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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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