Fix bug in logic of setupBoundary.

This commit is contained in:
Jan Eitzinger 2020-08-14 13:51:01 +02:00
parent 9e7cbf5687
commit 24a2e87e7e

View File

@ -65,24 +65,6 @@ static int NmaxGhost;
static int *BorderMap;
static int *PBCx, *PBCy, *PBCz;
typedef enum {
LEFT = 0,
RIGHT,
FRONT,
BACK,
TOP,
BOTTOM,
TOPRIGHTBACK,
TOPLEFTBACK,
TOPRIGHTFRONT,
TOPLEFTFRONT,
BOTTOMRIGHTBACK,
BOTTOMLEFTBACK,
BOTTOMRIGHTFRONT,
BOTTOMLEFTFRONT,
DCOUNT
} direction;
typedef struct {
int* numneigh;
int* neighbors;
@ -571,90 +553,6 @@ void growarray()
}
}
int setupGhostAtom(int i, int lastidx)
{
/* Setup ghost atoms */
if (x[i] < Cutneigh) { /* left plane */
x[lastidx+1] = x[i] + xprd;
y[lastidx+1] = y[i];
z[lastidx+1] = z[i];
lastidx++; Nghost++;
/* treat corners */
if (y[i] < Cutneigh && z[i] < Cutneigh) { /* bottom left front corner */
x[lastidx+1] = x[i] + xprd;
y[lastidx+1] = y[i] + yprd;
z[lastidx+1] = z[i] + zprd;
lastidx++; Nghost++;
} else if (y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { /* bottom left back corner */
x[lastidx+1] = x[i] + xprd;
y[lastidx+1] = y[i] - yprd;
z[lastidx+1] = z[i] + zprd;
lastidx++; Nghost++;
} else if (y[i] < Cutneigh && z[i] >= (zprd-Cutneigh)) { /* top left front corner */
x[lastidx+1] = x[i] + xprd;
y[lastidx+1] = y[i] + yprd;
z[lastidx+1] = z[i] - zprd;
lastidx++; Nghost++;
} else if (y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { /* top left back corner */
x[lastidx+1] = x[i] + xprd;
y[lastidx+1] = y[i] - yprd;
z[lastidx+1] = z[i] - zprd;
lastidx++; Nghost++;
}
} else if (x[i] >= (xprd-Cutneigh)) { /* right plane */
x[lastidx+1] = x[i] - xprd;
y[lastidx+1] = y[i];
z[lastidx+1] = z[i];
lastidx++; Nghost++;
/* treat corners */
if (y[i] < Cutneigh && z[i] < Cutneigh) { /* bottom right front corner */
x[lastidx+1] = x[i] - xprd;
y[lastidx+1] = y[i] + yprd;
z[lastidx+1] = z[i] + zprd;
lastidx++; Nghost++;
} else if (y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { /* bottom right back corner */
x[lastidx+1] = x[i] - xprd;
y[lastidx+1] = y[i] - yprd;
z[lastidx+1] = z[i] + zprd;
lastidx++; Nghost++;
} else if (y[i] < Cutneigh && z[i] >= (zprd-Cutneigh)) { /* top right front corner */
x[lastidx+1] = x[i] - xprd;
y[lastidx+1] = y[i] + yprd;
z[lastidx+1] = z[i] - zprd;
lastidx++; Nghost++;
} else if (y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { /* top right back corner */
x[lastidx+1] = x[i] - xprd;
y[lastidx+1] = y[i] - yprd;
z[lastidx+1] = z[i] - zprd;
lastidx++; Nghost++;
}
} else if (y[i] < Cutneigh) { /* front plane */
x[lastidx+1] = x[i];
y[lastidx+1] = y[i] + yprd;
z[lastidx+1] = z[i];
lastidx++; Nghost++;
} else if (y[i] >= (yprd-Cutneigh)) { /* back plane */
x[lastidx+1] = x[i];
y[lastidx+1] = y[i] - yprd;
z[lastidx+1] = z[i];
lastidx++; Nghost++;
} else if (z[i] < Cutneigh) { /* bottom plane */
x[lastidx+1] = x[i];
y[lastidx+1] = y[i];
z[lastidx+1] = z[i] + zprd;
lastidx++; Nghost++;
} else if (z[i] >= (zprd-Cutneigh)) { /* top plane */
x[lastidx+1] = x[i];
y[lastidx+1] = y[i];
z[lastidx+1] = z[i] - zprd;
lastidx++; Nghost++;
}
return lastidx;
}
void updateBorders()
{
for(int i = 0; i < Nghost; i++) {
@ -691,8 +589,9 @@ void updateAtomLocations()
void setupBordersNew()
{
int nghostprev;
Nghost = -1;
int lastidx = 0;
int nghostprev = 0;
Nghost = 0;
for (int i = 0; i < Nlocal; i++) {
@ -700,59 +599,45 @@ void setupBordersNew()
growarray();
}
if (Nghost + 1 >= NmaxGhost) {
growBoundary();
}
if (x[i] < Cutneigh) {
Nghost++;
BorderMap[Nghost] = i;
PBCx[Nghost] = +1; PBCy[Nghost] = 0; PBCz[Nghost] = 0;
x[i+lastidx] = x[i] + xprd;
y[i+lastidx] = y[i];
z[i+lastidx] = z[i];
lastidx++;
} else if (x[i] >= xprd - Cutneigh) {
Nghost++;
BorderMap[Nghost] = i;
PBCx[Nghost] = -1; PBCy[Nghost] = 0; PBCz[Nghost] = 0;
x[i+lastidx] = x[i] - xprd;
y[i+lastidx] = y[i];
z[i+lastidx] = z[i];
lastidx++;
}
}
nghostprev = Nghost+1;
printf("nghost 1 %d\n", nghostprev);
for (int i = 0; i < Nlocal + nghostprev; i++) {
for (int i = 0; i < Nlocal + nghostprev ; i++) {
if (Nlocal + Nghost + 1 >= Nmax) {
growarray();
}
if (Nghost + 1 >= NmaxGhost) {
growBoundary();
}
if (y[i] < Cutneigh) {
if (i >= Nlocal) {
Nghost++;
BorderMap[Nghost] = BorderMap[i - Nlocal];
PBCx[Nghost] = 0; PBCy[Nghost] = +1; PBCz[Nghost] = 0;
} else {
Nghost++;
BorderMap[Nghost] = i;
PBCx[Nghost] = 0; PBCy[Nghost] = +1; PBCz[Nghost] = 0;
}
x[i+lastidx] = x[i];
y[i+lastidx] = y[i] + yprd;
z[i+lastidx] = z[i];
lastidx++;
} else if (y[i] >= yprd - Cutneigh) {
if (i >= Nlocal) {
Nghost++;
BorderMap[Nghost] = BorderMap[i - Nlocal];
PBCx[Nghost] = 0; PBCy[Nghost] = -1; PBCz[Nghost] = 0;
} else {
Nghost++;
BorderMap[Nghost] = i;
PBCx[Nghost] = 0; PBCy[Nghost] = -1; PBCz[Nghost] = 0;
}
x[i+lastidx] = x[i];
y[i+lastidx] = y[i] - yprd;
z[i+lastidx] = z[i];
lastidx++;
}
}
nghostprev = Nghost+1;
printf("nghost 2 %d\n", nghostprev);
for (int i = 0; i < Nlocal + nghostprev; i++) {
@ -760,31 +645,18 @@ void setupBordersNew()
growarray();
}
if (Nghost + 1 >= NmaxGhost) {
growBoundary();
}
if (z[i] < Cutneigh) {
if (i >= Nlocal) {
Nghost++;
BorderMap[Nghost] = BorderMap[i - Nlocal];
PBCx[Nghost] = 0; PBCy[Nghost] = 0; PBCz[Nghost] = +1;
} else {
Nghost++;
BorderMap[Nghost] = i;
PBCx[Nghost] = 0; PBCy[Nghost] = 0; PBCz[Nghost] = +1;
}
x[i+lastidx] = x[i];
y[i+lastidx] = y[i];
z[i+lastidx] = z[i] + zprd;
lastidx++;
} else if(z[i] >= zprd - Cutneigh) {
if (i >= Nlocal) {
Nghost++;
BorderMap[Nghost] = BorderMap[i - Nlocal];
PBCx[Nghost] = 0; PBCy[Nghost] = 0; PBCz[Nghost] = -1;
} else {
Nghost++;
BorderMap[Nghost] = i;
PBCx[Nghost] = 0; PBCy[Nghost] = 0; PBCz[Nghost] = -1;
}
x[i+lastidx] = x[i];
y[i+lastidx] = y[i];
z[i+lastidx] = z[i] - zprd;
lastidx++;
}
}
@ -803,11 +675,11 @@ void setupBorders()
for(int i = 0; i < Nlocal; i++) {
if (Nlocal + Nghost + 1 >= Nmax) {
if (Nlocal + Nghost + 7 >= Nmax) {
growarray();
}
if (Nghost + 1 >= NmaxGhost) {
if (Nghost + 7 >= NmaxGhost) {
growBoundary();
}
@ -822,18 +694,25 @@ void setupBorders()
if (y[i] < Cutneigh) { /* bottom left front corner */
ADDGHOST(+1,+1,+1);
}
} else if (y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { /* bottom left back corner */
}
if (y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { /* bottom left back corner */
ADDGHOST(+1,-1,+1);
} else if (z[i] >= (zprd-Cutneigh)) { /* top left edge */
}
if (z[i] >= (zprd-Cutneigh)) { /* top left edge */
ADDGHOST(+1,0,-1);
if (y[i] < Cutneigh) { /* bottom left front corner */
ADDGHOST(+1,+1,-1);
}
} else if (y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { /* top left back corner */
}
if (y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { /* top left back corner */
ADDGHOST(+1,-1,-1);
}
} else if (x[i] >= (xprd-Cutneigh)) { /* right plane */
}
if (x[i] >= (xprd-Cutneigh)) { /* right plane */
ADDGHOST(-1,0,0);
/* treat edges and corners */
@ -843,53 +722,65 @@ void setupBorders()
if (y[i] < Cutneigh) { /* bottom right front corner */
ADDGHOST(-1,+1,+1);
}
} else if (y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { /* bottom right back corner */
}
if (y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { /* bottom right back corner */
ADDGHOST(-1,-1,+1);
} else if (z[i] >= (zprd-Cutneigh)) { /* top right edge */
}
if (z[i] >= (zprd-Cutneigh)) { /* top right edge */
ADDGHOST(-1,0,-1);
if (y[i] < Cutneigh) { /* top right front corner */
ADDGHOST(-1,+1,-1);
}
} else if (y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { /* top right back corner */
}
if (y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { /* top right back corner */
ADDGHOST(-1,-1,-1);
}
} else if (y[i] < Cutneigh) { /* front plane */
}
if (y[i] < Cutneigh) { /* front plane */
ADDGHOST(0,+1,0);
if (z[i] < Cutneigh) { /* bottom front edge */
ADDGHOST(0,+1,+1);
} else if (z[i] >= (zprd-Cutneigh)) { /* top front edge */
}
if (z[i] >= (zprd-Cutneigh)) { /* top front edge */
ADDGHOST(0,+1,-1);
}
if (x[i] < Cutneigh) { /* left front edge */
ADDGHOST(+1,+1,0);
} else if (x[i] >= (xprd-Cutneigh)) { /* right front edge */
}
if (x[i] >= (xprd-Cutneigh)) { /* right front edge */
ADDGHOST(+1,-1,0);
}
} else if (y[i] >= (yprd-Cutneigh)) { /* back plane */
}
if (y[i] >= (yprd-Cutneigh)) { /* back plane */
ADDGHOST(0,-1,0);
if (z[i] < Cutneigh) { /* bottom back edge */
ADDGHOST(0,-1,+1);
} else if (z[i] >= (zprd-Cutneigh)) { /* top back edge */
}
if (z[i] >= (zprd-Cutneigh)) { /* top back edge */
ADDGHOST(0,-1,-1);
}
if (x[i] < Cutneigh) { /* left back edge */
ADDGHOST(-1,+1,0);
} else if (x[i] >= (xprd-Cutneigh)) { /* right back edge */
}
if (x[i] >= (xprd-Cutneigh)) { /* right back edge */
ADDGHOST(-1,-1,0);
}
} else if (z[i] < Cutneigh) { /* bottom plane */
}
if (z[i] < Cutneigh) { /* bottom plane */
ADDGHOST(0,0,+1);
} else if (z[i] >= (zprd-Cutneigh)) { /* top plane */
}
if (z[i] >= (zprd-Cutneigh)) { /* top plane */
ADDGHOST(0,0,-1);
}
}
// increase by one to make it the ghost count
// increase by one to make it the ghost atom count
Nghost++;
}
@ -1171,6 +1062,8 @@ void thermoCompute(int iflag, Parameter *param, Thermo *thermo)
void initialIntegrate(Parameter *param)
{
/* printf("dtforce %f dt %f\n",param->dtforce, param->dt); */
for(int i = 0; i < Nlocal; i++) {
vx[i] += param->dtforce * fx[i];
vy[i] += param->dtforce * fy[i];
@ -1295,6 +1188,7 @@ int main (int argc, char** argv)
initialIntegrate(&param);
updateBorders();
printf("x = %f %f %f\n", x[0], y[0], z[0]);
if(!((n + 1) % neighbor.every)) {
printf("Reneighbor at %d\n",n);
updateAtomLocations();
@ -1310,7 +1204,6 @@ int main (int argc, char** argv)
if(thermo.nstat) {
thermoCompute(n + 1, &param, &thermo);
}
printf("x = %f %f %f\n", x[0], y[0], z[0]);
}
thermoCompute(-1, &param, &thermo);