Fix bug in logic of setupBoundary.
This commit is contained in:
Jan Eitzinger
parent
9e7cbf5687
commit
24a2e87e7e
241
src/main.c
241
src/main.c
@ -65,24 +65,6 @@ static int NmaxGhost;
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static int *BorderMap;
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static int *PBCx, *PBCy, *PBCz;
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typedef enum {
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LEFT = 0,
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RIGHT,
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FRONT,
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BACK,
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TOP,
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BOTTOM,
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TOPRIGHTBACK,
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TOPLEFTBACK,
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TOPRIGHTFRONT,
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TOPLEFTFRONT,
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BOTTOMRIGHTBACK,
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BOTTOMLEFTBACK,
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BOTTOMRIGHTFRONT,
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BOTTOMLEFTFRONT,
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DCOUNT
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} direction;
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typedef struct {
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int* numneigh;
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int* neighbors;
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@ -571,90 +553,6 @@ void growarray()
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}
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}
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int setupGhostAtom(int i, int lastidx)
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{
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/* Setup ghost atoms */
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if (x[i] < Cutneigh) { /* left plane */
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x[lastidx+1] = x[i] + xprd;
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y[lastidx+1] = y[i];
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z[lastidx+1] = z[i];
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lastidx++; Nghost++;
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/* treat corners */
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if (y[i] < Cutneigh && z[i] < Cutneigh) { /* bottom left front corner */
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x[lastidx+1] = x[i] + xprd;
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y[lastidx+1] = y[i] + yprd;
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z[lastidx+1] = z[i] + zprd;
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lastidx++; Nghost++;
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} else if (y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { /* bottom left back corner */
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x[lastidx+1] = x[i] + xprd;
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y[lastidx+1] = y[i] - yprd;
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z[lastidx+1] = z[i] + zprd;
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lastidx++; Nghost++;
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} else if (y[i] < Cutneigh && z[i] >= (zprd-Cutneigh)) { /* top left front corner */
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x[lastidx+1] = x[i] + xprd;
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y[lastidx+1] = y[i] + yprd;
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z[lastidx+1] = z[i] - zprd;
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lastidx++; Nghost++;
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} else if (y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { /* top left back corner */
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x[lastidx+1] = x[i] + xprd;
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y[lastidx+1] = y[i] - yprd;
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z[lastidx+1] = z[i] - zprd;
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lastidx++; Nghost++;
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}
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} else if (x[i] >= (xprd-Cutneigh)) { /* right plane */
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x[lastidx+1] = x[i] - xprd;
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y[lastidx+1] = y[i];
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z[lastidx+1] = z[i];
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lastidx++; Nghost++;
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/* treat corners */
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if (y[i] < Cutneigh && z[i] < Cutneigh) { /* bottom right front corner */
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x[lastidx+1] = x[i] - xprd;
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y[lastidx+1] = y[i] + yprd;
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z[lastidx+1] = z[i] + zprd;
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lastidx++; Nghost++;
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} else if (y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { /* bottom right back corner */
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x[lastidx+1] = x[i] - xprd;
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y[lastidx+1] = y[i] - yprd;
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z[lastidx+1] = z[i] + zprd;
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lastidx++; Nghost++;
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} else if (y[i] < Cutneigh && z[i] >= (zprd-Cutneigh)) { /* top right front corner */
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x[lastidx+1] = x[i] - xprd;
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y[lastidx+1] = y[i] + yprd;
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z[lastidx+1] = z[i] - zprd;
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lastidx++; Nghost++;
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} else if (y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { /* top right back corner */
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x[lastidx+1] = x[i] - xprd;
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y[lastidx+1] = y[i] - yprd;
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z[lastidx+1] = z[i] - zprd;
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lastidx++; Nghost++;
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}
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} else if (y[i] < Cutneigh) { /* front plane */
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x[lastidx+1] = x[i];
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y[lastidx+1] = y[i] + yprd;
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z[lastidx+1] = z[i];
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lastidx++; Nghost++;
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} else if (y[i] >= (yprd-Cutneigh)) { /* back plane */
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x[lastidx+1] = x[i];
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y[lastidx+1] = y[i] - yprd;
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z[lastidx+1] = z[i];
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lastidx++; Nghost++;
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} else if (z[i] < Cutneigh) { /* bottom plane */
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x[lastidx+1] = x[i];
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y[lastidx+1] = y[i];
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z[lastidx+1] = z[i] + zprd;
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lastidx++; Nghost++;
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} else if (z[i] >= (zprd-Cutneigh)) { /* top plane */
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x[lastidx+1] = x[i];
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y[lastidx+1] = y[i];
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z[lastidx+1] = z[i] - zprd;
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lastidx++; Nghost++;
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}
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return lastidx;
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}
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void updateBorders()
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{
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for(int i = 0; i < Nghost; i++) {
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@ -691,8 +589,9 @@ void updateAtomLocations()
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void setupBordersNew()
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{
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int nghostprev;
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Nghost = -1;
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int lastidx = 0;
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int nghostprev = 0;
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Nghost = 0;
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for (int i = 0; i < Nlocal; i++) {
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@ -700,23 +599,22 @@ void setupBordersNew()
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growarray();
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}
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if (Nghost + 1 >= NmaxGhost) {
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growBoundary();
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}
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if (x[i] < Cutneigh) {
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Nghost++;
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BorderMap[Nghost] = i;
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PBCx[Nghost] = +1; PBCy[Nghost] = 0; PBCz[Nghost] = 0;
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x[i+lastidx] = x[i] + xprd;
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y[i+lastidx] = y[i];
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z[i+lastidx] = z[i];
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lastidx++;
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} else if (x[i] >= xprd - Cutneigh) {
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Nghost++;
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BorderMap[Nghost] = i;
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PBCx[Nghost] = -1; PBCy[Nghost] = 0; PBCz[Nghost] = 0;
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x[i+lastidx] = x[i] - xprd;
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y[i+lastidx] = y[i];
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z[i+lastidx] = z[i];
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lastidx++;
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}
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}
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nghostprev = Nghost+1;
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printf("nghost 1 %d\n", nghostprev);
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for (int i = 0; i < Nlocal + nghostprev ; i++) {
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@ -724,35 +622,22 @@ void setupBordersNew()
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growarray();
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}
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if (Nghost + 1 >= NmaxGhost) {
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growBoundary();
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}
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if (y[i] < Cutneigh) {
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if (i >= Nlocal) {
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Nghost++;
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BorderMap[Nghost] = BorderMap[i - Nlocal];
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PBCx[Nghost] = 0; PBCy[Nghost] = +1; PBCz[Nghost] = 0;
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} else {
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Nghost++;
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BorderMap[Nghost] = i;
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PBCx[Nghost] = 0; PBCy[Nghost] = +1; PBCz[Nghost] = 0;
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}
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x[i+lastidx] = x[i];
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y[i+lastidx] = y[i] + yprd;
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z[i+lastidx] = z[i];
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lastidx++;
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} else if (y[i] >= yprd - Cutneigh) {
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if (i >= Nlocal) {
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Nghost++;
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BorderMap[Nghost] = BorderMap[i - Nlocal];
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PBCx[Nghost] = 0; PBCy[Nghost] = -1; PBCz[Nghost] = 0;
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} else {
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Nghost++;
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BorderMap[Nghost] = i;
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PBCx[Nghost] = 0; PBCy[Nghost] = -1; PBCz[Nghost] = 0;
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}
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x[i+lastidx] = x[i];
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y[i+lastidx] = y[i] - yprd;
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z[i+lastidx] = z[i];
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lastidx++;
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}
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}
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nghostprev = Nghost+1;
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printf("nghost 2 %d\n", nghostprev);
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for (int i = 0; i < Nlocal + nghostprev; i++) {
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@ -760,31 +645,18 @@ void setupBordersNew()
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growarray();
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}
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if (Nghost + 1 >= NmaxGhost) {
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growBoundary();
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}
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if (z[i] < Cutneigh) {
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if (i >= Nlocal) {
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Nghost++;
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BorderMap[Nghost] = BorderMap[i - Nlocal];
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PBCx[Nghost] = 0; PBCy[Nghost] = 0; PBCz[Nghost] = +1;
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} else {
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Nghost++;
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BorderMap[Nghost] = i;
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PBCx[Nghost] = 0; PBCy[Nghost] = 0; PBCz[Nghost] = +1;
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}
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x[i+lastidx] = x[i];
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y[i+lastidx] = y[i];
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z[i+lastidx] = z[i] + zprd;
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lastidx++;
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} else if(z[i] >= zprd - Cutneigh) {
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if (i >= Nlocal) {
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Nghost++;
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BorderMap[Nghost] = BorderMap[i - Nlocal];
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PBCx[Nghost] = 0; PBCy[Nghost] = 0; PBCz[Nghost] = -1;
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} else {
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Nghost++;
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BorderMap[Nghost] = i;
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PBCx[Nghost] = 0; PBCy[Nghost] = 0; PBCz[Nghost] = -1;
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}
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x[i+lastidx] = x[i];
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y[i+lastidx] = y[i];
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z[i+lastidx] = z[i] - zprd;
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lastidx++;
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}
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}
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@ -803,11 +675,11 @@ void setupBorders()
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for(int i = 0; i < Nlocal; i++) {
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if (Nlocal + Nghost + 1 >= Nmax) {
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if (Nlocal + Nghost + 7 >= Nmax) {
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growarray();
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}
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if (Nghost + 1 >= NmaxGhost) {
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if (Nghost + 7 >= NmaxGhost) {
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growBoundary();
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}
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@ -822,18 +694,25 @@ void setupBorders()
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if (y[i] < Cutneigh) { /* bottom left front corner */
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ADDGHOST(+1,+1,+1);
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}
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} else if (y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { /* bottom left back corner */
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}
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if (y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { /* bottom left back corner */
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ADDGHOST(+1,-1,+1);
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} else if (z[i] >= (zprd-Cutneigh)) { /* top left edge */
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}
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if (z[i] >= (zprd-Cutneigh)) { /* top left edge */
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ADDGHOST(+1,0,-1);
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if (y[i] < Cutneigh) { /* bottom left front corner */
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ADDGHOST(+1,+1,-1);
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}
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} else if (y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { /* top left back corner */
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}
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if (y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { /* top left back corner */
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ADDGHOST(+1,-1,-1);
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}
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} else if (x[i] >= (xprd-Cutneigh)) { /* right plane */
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}
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if (x[i] >= (xprd-Cutneigh)) { /* right plane */
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ADDGHOST(-1,0,0);
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/* treat edges and corners */
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@ -843,53 +722,65 @@ void setupBorders()
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if (y[i] < Cutneigh) { /* bottom right front corner */
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ADDGHOST(-1,+1,+1);
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}
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} else if (y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { /* bottom right back corner */
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}
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if (y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { /* bottom right back corner */
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ADDGHOST(-1,-1,+1);
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} else if (z[i] >= (zprd-Cutneigh)) { /* top right edge */
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}
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if (z[i] >= (zprd-Cutneigh)) { /* top right edge */
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ADDGHOST(-1,0,-1);
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if (y[i] < Cutneigh) { /* top right front corner */
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ADDGHOST(-1,+1,-1);
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}
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} else if (y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { /* top right back corner */
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}
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if (y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { /* top right back corner */
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ADDGHOST(-1,-1,-1);
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}
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} else if (y[i] < Cutneigh) { /* front plane */
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}
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if (y[i] < Cutneigh) { /* front plane */
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ADDGHOST(0,+1,0);
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if (z[i] < Cutneigh) { /* bottom front edge */
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ADDGHOST(0,+1,+1);
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} else if (z[i] >= (zprd-Cutneigh)) { /* top front edge */
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}
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if (z[i] >= (zprd-Cutneigh)) { /* top front edge */
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ADDGHOST(0,+1,-1);
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}
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if (x[i] < Cutneigh) { /* left front edge */
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ADDGHOST(+1,+1,0);
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} else if (x[i] >= (xprd-Cutneigh)) { /* right front edge */
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}
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if (x[i] >= (xprd-Cutneigh)) { /* right front edge */
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ADDGHOST(+1,-1,0);
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}
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} else if (y[i] >= (yprd-Cutneigh)) { /* back plane */
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}
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if (y[i] >= (yprd-Cutneigh)) { /* back plane */
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ADDGHOST(0,-1,0);
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if (z[i] < Cutneigh) { /* bottom back edge */
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ADDGHOST(0,-1,+1);
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} else if (z[i] >= (zprd-Cutneigh)) { /* top back edge */
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}
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if (z[i] >= (zprd-Cutneigh)) { /* top back edge */
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ADDGHOST(0,-1,-1);
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}
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if (x[i] < Cutneigh) { /* left back edge */
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ADDGHOST(-1,+1,0);
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} else if (x[i] >= (xprd-Cutneigh)) { /* right back edge */
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}
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if (x[i] >= (xprd-Cutneigh)) { /* right back edge */
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ADDGHOST(-1,-1,0);
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}
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} else if (z[i] < Cutneigh) { /* bottom plane */
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}
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if (z[i] < Cutneigh) { /* bottom plane */
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ADDGHOST(0,0,+1);
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} else if (z[i] >= (zprd-Cutneigh)) { /* top plane */
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}
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if (z[i] >= (zprd-Cutneigh)) { /* top plane */
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ADDGHOST(0,0,-1);
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}
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}
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// increase by one to make it the ghost count
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// increase by one to make it the ghost atom count
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Nghost++;
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}
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@ -1171,6 +1062,8 @@ void thermoCompute(int iflag, Parameter *param, Thermo *thermo)
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void initialIntegrate(Parameter *param)
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{
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/* printf("dtforce %f dt %f\n",param->dtforce, param->dt); */
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for(int i = 0; i < Nlocal; i++) {
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vx[i] += param->dtforce * fx[i];
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vy[i] += param->dtforce * fy[i];
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@ -1295,6 +1188,7 @@ int main (int argc, char** argv)
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initialIntegrate(¶m);
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updateBorders();
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printf("x = %f %f %f\n", x[0], y[0], z[0]);
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if(!((n + 1) % neighbor.every)) {
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printf("Reneighbor at %d\n",n);
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updateAtomLocations();
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@ -1310,7 +1204,6 @@ int main (int argc, char** argv)
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if(thermo.nstat) {
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thermoCompute(n + 1, ¶m, &thermo);
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}
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printf("x = %f %f %f\n", x[0], y[0], z[0]);
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}
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thermoCompute(-1, ¶m, &thermo);
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