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Fix bug in logic of setupBoundary.

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This commit is contained in:
Jan Eitzinger 2020-08-14 13:51:01 +02:00
parent 9e7cbf5687
commit 24a2e87e7e
1 changed files with 68 additions and 175 deletions
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243
src/main.c
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@ -65,24 +65,6 @@ static int NmaxGhost;
static int *BorderMap; static int *BorderMap;
static int *PBCx, *PBCy, *PBCz; 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 { typedef struct {
int* numneigh; int* numneigh;
int* neighbors; 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() void updateBorders()
{ {
for(int i = 0; i < Nghost; i++) { for(int i = 0; i < Nghost; i++) {
@ -691,8 +589,9 @@ void updateAtomLocations()
void setupBordersNew() void setupBordersNew()
{ {
int nghostprev; int lastidx = 0;
Nghost = -1; int nghostprev = 0;
Nghost = 0;
for (int i = 0; i < Nlocal; i++) { for (int i = 0; i < Nlocal; i++) {
@ -700,59 +599,45 @@ void setupBordersNew()
growarray(); growarray();
} }
if (Nghost + 1 >= NmaxGhost) {
growBoundary();
}
if (x[i] < Cutneigh) { if (x[i] < Cutneigh) {
Nghost++; Nghost++;
BorderMap[Nghost] = i; x[i+lastidx] = x[i] + xprd;
PBCx[Nghost] = +1; PBCy[Nghost] = 0; PBCz[Nghost] = 0; y[i+lastidx] = y[i];
z[i+lastidx] = z[i];
lastidx++;
} else if (x[i] >= xprd - Cutneigh) { } else if (x[i] >= xprd - Cutneigh) {
Nghost++; Nghost++;
BorderMap[Nghost] = i; x[i+lastidx] = x[i] - xprd;
PBCx[Nghost] = -1; PBCy[Nghost] = 0; PBCz[Nghost] = 0; y[i+lastidx] = y[i];
z[i+lastidx] = z[i];
lastidx++;
} }
} }
nghostprev = Nghost+1; 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) { if (Nlocal + Nghost + 1 >= Nmax) {
growarray(); growarray();
} }
if (Nghost + 1 >= NmaxGhost) {
growBoundary();
}
if (y[i] < Cutneigh) { if (y[i] < Cutneigh) {
if (i >= Nlocal) {
Nghost++; Nghost++;
BorderMap[Nghost] = BorderMap[i - Nlocal]; x[i+lastidx] = x[i];
PBCx[Nghost] = 0; PBCy[Nghost] = +1; PBCz[Nghost] = 0; y[i+lastidx] = y[i] + yprd;
} else { z[i+lastidx] = z[i];
Nghost++; lastidx++;
BorderMap[Nghost] = i;
PBCx[Nghost] = 0; PBCy[Nghost] = +1; PBCz[Nghost] = 0;
}
} else if (y[i] >= yprd - Cutneigh) { } else if (y[i] >= yprd - Cutneigh) {
if (i >= Nlocal) {
Nghost++; Nghost++;
BorderMap[Nghost] = BorderMap[i - Nlocal]; x[i+lastidx] = x[i];
PBCx[Nghost] = 0; PBCy[Nghost] = -1; PBCz[Nghost] = 0; y[i+lastidx] = y[i] - yprd;
} else { z[i+lastidx] = z[i];
Nghost++; lastidx++;
BorderMap[Nghost] = i;
PBCx[Nghost] = 0; PBCy[Nghost] = -1; PBCz[Nghost] = 0;
}
} }
} }
nghostprev = Nghost+1; nghostprev = Nghost+1;
printf("nghost 2 %d\n", nghostprev);
for (int i = 0; i < Nlocal + nghostprev; i++) { for (int i = 0; i < Nlocal + nghostprev; i++) {
@ -760,31 +645,18 @@ void setupBordersNew()
growarray(); growarray();
} }
if (Nghost + 1 >= NmaxGhost) {
growBoundary();
}
if (z[i] < Cutneigh) { if (z[i] < Cutneigh) {
if (i >= Nlocal) {
Nghost++; Nghost++;
BorderMap[Nghost] = BorderMap[i - Nlocal]; x[i+lastidx] = x[i];
PBCx[Nghost] = 0; PBCy[Nghost] = 0; PBCz[Nghost] = +1; y[i+lastidx] = y[i];
} else { z[i+lastidx] = z[i] + zprd;
Nghost++; lastidx++;
BorderMap[Nghost] = i;
PBCx[Nghost] = 0; PBCy[Nghost] = 0; PBCz[Nghost] = +1;
}
} else if(z[i] >= zprd - Cutneigh) { } else if(z[i] >= zprd - Cutneigh) {
if (i >= Nlocal) {
Nghost++; Nghost++;
BorderMap[Nghost] = BorderMap[i - Nlocal]; x[i+lastidx] = x[i];
PBCx[Nghost] = 0; PBCy[Nghost] = 0; PBCz[Nghost] = -1; y[i+lastidx] = y[i];
} else { z[i+lastidx] = z[i] - zprd;
Nghost++; lastidx++;
BorderMap[Nghost] = i;
PBCx[Nghost] = 0; PBCy[Nghost] = 0; PBCz[Nghost] = -1;
}
} }
} }
@ -803,11 +675,11 @@ void setupBorders()
for(int i = 0; i < Nlocal; i++) { for(int i = 0; i < Nlocal; i++) {
if (Nlocal + Nghost + 1 >= Nmax) { if (Nlocal + Nghost + 7 >= Nmax) {
growarray(); growarray();
} }
if (Nghost + 1 >= NmaxGhost) { if (Nghost + 7 >= NmaxGhost) {
growBoundary(); growBoundary();
} }
@ -822,18 +694,25 @@ void setupBorders()
if (y[i] < Cutneigh) { /* bottom left front corner */ if (y[i] < Cutneigh) { /* bottom left front corner */
ADDGHOST(+1,+1,+1); 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); 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); ADDGHOST(+1,0,-1);
if (y[i] < Cutneigh) { /* bottom left front corner */ if (y[i] < Cutneigh) { /* bottom left front corner */
ADDGHOST(+1,+1,-1); 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); ADDGHOST(+1,-1,-1);
} }
} else if (x[i] >= (xprd-Cutneigh)) { /* right plane */ }
if (x[i] >= (xprd-Cutneigh)) { /* right plane */
ADDGHOST(-1,0,0); ADDGHOST(-1,0,0);
/* treat edges and corners */ /* treat edges and corners */
@ -843,53 +722,65 @@ void setupBorders()
if (y[i] < Cutneigh) { /* bottom right front corner */ if (y[i] < Cutneigh) { /* bottom right front corner */
ADDGHOST(-1,+1,+1); 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); 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); ADDGHOST(-1,0,-1);
if (y[i] < Cutneigh) { /* top right front corner */ if (y[i] < Cutneigh) { /* top right front corner */
ADDGHOST(-1,+1,-1); 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); ADDGHOST(-1,-1,-1);
} }
} else if (y[i] < Cutneigh) { /* front plane */ }
if (y[i] < Cutneigh) { /* front plane */
ADDGHOST(0,+1,0); ADDGHOST(0,+1,0);
if (z[i] < Cutneigh) { /* bottom front edge */ if (z[i] < Cutneigh) { /* bottom front edge */
ADDGHOST(0,+1,+1); 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); ADDGHOST(0,+1,-1);
} }
if (x[i] < Cutneigh) { /* left front edge */ if (x[i] < Cutneigh) { /* left front edge */
ADDGHOST(+1,+1,0); 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); ADDGHOST(+1,-1,0);
} }
} else if (y[i] >= (yprd-Cutneigh)) { /* back plane */ }
if (y[i] >= (yprd-Cutneigh)) { /* back plane */
ADDGHOST(0,-1,0); ADDGHOST(0,-1,0);
if (z[i] < Cutneigh) { /* bottom back edge */ if (z[i] < Cutneigh) { /* bottom back edge */
ADDGHOST(0,-1,+1); 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); ADDGHOST(0,-1,-1);
} }
if (x[i] < Cutneigh) { /* left back edge */ if (x[i] < Cutneigh) { /* left back edge */
ADDGHOST(-1,+1,0); 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); ADDGHOST(-1,-1,0);
} }
} else if (z[i] < Cutneigh) { /* bottom plane */ }
if (z[i] < Cutneigh) { /* bottom plane */
ADDGHOST(0,0,+1); ADDGHOST(0,0,+1);
} else if (z[i] >= (zprd-Cutneigh)) { /* top plane */ }
if (z[i] >= (zprd-Cutneigh)) { /* top plane */
ADDGHOST(0,0,-1); ADDGHOST(0,0,-1);
} }
} }
// increase by one to make it the ghost count // increase by one to make it the ghost atom count
Nghost++; Nghost++;
} }
@ -1171,6 +1062,8 @@ void thermoCompute(int iflag, Parameter *param, Thermo *thermo)
void initialIntegrate(Parameter *param) void initialIntegrate(Parameter *param)
{ {
/* printf("dtforce %f dt %f\n",param->dtforce, param->dt); */
for(int i = 0; i < Nlocal; i++) { for(int i = 0; i < Nlocal; i++) {
vx[i] += param->dtforce * fx[i]; vx[i] += param->dtforce * fx[i];
vy[i] += param->dtforce * fy[i]; vy[i] += param->dtforce * fy[i];
@ -1295,6 +1188,7 @@ int main (int argc, char** argv)
initialIntegrate(&param); initialIntegrate(&param);
updateBorders(); updateBorders();
printf("x = %f %f %f\n", x[0], y[0], z[0]);
if(!((n + 1) % neighbor.every)) { if(!((n + 1) % neighbor.every)) {
printf("Reneighbor at %d\n",n); printf("Reneighbor at %d\n",n);
updateAtomLocations(); updateAtomLocations();
@ -1310,7 +1204,6 @@ int main (int argc, char** argv)
if(thermo.nstat) { if(thermo.nstat) {
thermoCompute(n + 1, &param, &thermo); thermoCompute(n + 1, &param, &thermo);
} }
printf("x = %f %f %f\n", x[0], y[0], z[0]);
} }
thermoCompute(-1, &param, &thermo); thermoCompute(-1, &param, &thermo);