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Add alternative for setup of ghost atoms.

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This commit is contained in:
Jan Eitzinger 2020-08-14 08:32:36 +02:00
parent a4c2860130
commit 7d0c47da72
1 changed files with 256 additions and 20 deletions
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276
src/main.c
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@ -61,6 +61,10 @@ static double *fx, *fy, *fz;
static double eng_vdwl;
static double virial;
static int NmaxGhost;
static int *BorderMap;
static int *PBCx, *PBCy, *PBCz;
typedef enum {
LEFT = 0,
RIGHT,
@ -341,6 +345,10 @@ void init(Neighbor *neighbor, Parameter *param)
vx = NULL; vy = NULL; vz = NULL;
fx = NULL; fy = NULL; fz = NULL;
NmaxGhost = 0;
BorderMap = NULL;
PBCx = NULL; PBCy = NULL; PBCz = NULL;
param->epsilon = 1.0;
param->sigma6 = 1.0;
param->rho = 0.8442;
@ -509,6 +517,38 @@ double* myrealloc(double *ptr, int n, int nold) {
return newarray;
}
int* myreallocInt(int *ptr, int n, int nold) {
int* newarray;
newarray = (int*) malloc(n * sizeof(int));
if(nold) {
memcpy(newarray, ptr, nold * sizeof(int));
}
if(ptr) {
free(ptr);
}
return newarray;
}
void growBoundary()
{
int nold = NmaxGhost;
NmaxGhost += DELTA;
BorderMap = myreallocInt(BorderMap, NmaxGhost, nold);
PBCx = myreallocInt(PBCx, NmaxGhost, nold);
PBCy = myreallocInt(PBCy, NmaxGhost, nold);
PBCz = myreallocInt(PBCz, NmaxGhost, nold);
if(BorderMap == NULL || PBCx == NULL || PBCy == NULL || PBCz == NULL ) {
printf("ERROR: No memory for Boundary\n");
}
}
void growarray()
{
int nold = Nmax;
@ -615,25 +655,17 @@ int setupGhostAtom(int i, int lastidx)
return lastidx;
}
void exchangeBorders()
void updateBorders()
{
Nghost = 0;
int lastidx = Nlocal-1;
for(int i = 0; i < Nlocal; i++) {
lastidx = setupGhostAtom(i, lastidx);
for(int i = 0; i < Nghost; i++) {
x[Nlocal + i] = x[BorderMap[i]] + PBCx[i] * xprd;
y[Nlocal + i] = y[BorderMap[i]] + PBCy[i] * yprd;
z[Nlocal + i] = z[BorderMap[i]] + PBCz[i] * zprd;
}
}
/* Enforce periodic boundary conditions
* Relocate atoms that have left domain for
* 6 planes (and 8 corners (diagonal))
* Setup ghost atoms at boundaries*/
void processBorders()
void updateAtomLocations()
{
Nghost = 0;
int lastidx = Nlocal-1;
for(int i = 0; i < Nlocal; i++) {
/* Relocate atoms that have left the domain */
@ -654,13 +686,212 @@ void processBorders()
} else if(z[i] >= zprd) {
z[i] -= zprd;
}
}
}
if (lastidx+1 >= Nmax) {
void setupBordersNew()
{
int nghostprev;
Nghost = -1;
for (int i = 0; i < Nlocal; i++) {
if (Nlocal + Nghost + 1 >= Nmax) {
growarray();
}
lastidx = setupGhostAtom(i, lastidx);
if (Nghost + 1 >= NmaxGhost) {
growBoundary();
}
if (x[i] < Cutneigh) {
Nghost++;
BorderMap[Nghost] = i;
PBCx[Nghost] = +1; PBCy[Nghost] = 0; PBCz[Nghost] = 0;
} else if (x[i] >= xprd - Cutneigh) {
Nghost++;
BorderMap[Nghost] = i;
PBCx[Nghost] = -1; PBCy[Nghost] = 0; PBCz[Nghost] = 0;
}
}
nghostprev = Nghost+1;
printf("nghost 1 %d\n", nghostprev);
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;
}
} 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;
}
}
}
nghostprev = Nghost+1;
printf("nghost 2 %d\n", nghostprev);
for (int i = 0; i < Nlocal + nghostprev; i++) {
if (Nlocal + Nghost + 1 >= Nmax) {
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;
}
} 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;
}
}
}
Nghost++;
}
#define ADDGHOST(dx,dy,dz) Nghost++; BorderMap[Nghost] = i; PBCx[Nghost] = dx; PBCy[Nghost] = dy; PBCz[Nghost] = dz;
/* Enforce periodic boundary conditions
* Relocate atoms that have left domain for
* 6 planes (and 8 corners (diagonal))
* Setup ghost atoms at boundaries*/
void setupBorders()
{
Nghost = -1;
for(int i = 0; i < Nlocal; i++) {
if (Nlocal + Nghost + 1 >= Nmax) {
growarray();
}
if (Nghost + 1 >= NmaxGhost) {
growBoundary();
}
/* Setup ghost atoms */
if (x[i] < Cutneigh) { /* left plane */
ADDGHOST(+1,0,0);
/* Nghost++; */
/* BorderMap[Nghost] = i; */
/* PBCx[Nghost] = +1; PBCy[Nghost] = 0; PBCz[Nghost] = 0; */
/* treat edges and corners */
if (z[i] < Cutneigh) { /* bottom left edge */
Nghost++;
BorderMap[Nghost] = i;
PBCx[Nghost] = +1; PBCy[Nghost] = 0; PBCz[Nghost] = +1;
if (y[i] < Cutneigh) { /* bottom left front corner */
Nghost++;
BorderMap[Nghost] = i;
PBCx[Nghost] = +1; PBCy[Nghost] = +1; PBCz[Nghost] = +1;
}
} else if (y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { /* bottom left back corner */
Nghost++;
BorderMap[Nghost] = i;
PBCx[Nghost] = +1; PBCy[Nghost] = -1; PBCz[Nghost] = +1;
} else if (z[i] >= (zprd-Cutneigh)) { /* top left edge */
Nghost++;
BorderMap[Nghost] = i;
PBCx[Nghost] = +1; PBCy[Nghost] = 0; PBCz[Nghost] = -1;
if (y[i] < Cutneigh) { /* bottom left front corner */
Nghost++;
BorderMap[Nghost] = i;
PBCx[Nghost] = +1; PBCy[Nghost] = +1; PBCz[Nghost] = -1;
}
} else if (y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { /* top left back corner */
Nghost++;
BorderMap[Nghost] = i;
PBCx[Nghost] = +1; PBCy[Nghost] = -1; PBCz[Nghost] = -1;
}
} else if (x[i] >= (xprd-Cutneigh)) { /* right plane */
Nghost++;
BorderMap[Nghost] = i;
PBCx[Nghost] = -1; PBCy[Nghost] = 0; PBCz[Nghost] = 0;
/* treat corners */
if (y[i] < Cutneigh && z[i] < Cutneigh) { /* bottom right front corner */
Nghost++;
BorderMap[Nghost] = i;
PBCx[Nghost] = -1; PBCy[Nghost] = +1; PBCz[Nghost] = +1;
} else if (y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { /* bottom right back corner */
Nghost++;
BorderMap[Nghost] = i;
PBCx[Nghost] = -1; PBCy[Nghost] = -1; PBCz[Nghost] = +1;
} else if (y[i] < Cutneigh && z[i] >= (zprd-Cutneigh)) { /* top right front corner */
Nghost++;
BorderMap[Nghost] = i;
PBCx[Nghost] = -1; PBCy[Nghost] = +1; PBCz[Nghost] = -1;
} else if (y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { /* top right back corner */
Nghost++;
BorderMap[Nghost] = i;
PBCx[Nghost] = -1; PBCy[Nghost] = -1; PBCz[Nghost] = -1;
}
} else if (y[i] < Cutneigh) { /* front plane */
Nghost++;
BorderMap[Nghost] = i;
PBCx[Nghost] = 0; PBCy[Nghost] = +1; PBCz[Nghost] = 0;
} else if (y[i] >= (yprd-Cutneigh)) { /* back plane */
Nghost++;
BorderMap[Nghost] = i;
PBCx[Nghost] = 0; PBCy[Nghost] = -1; PBCz[Nghost] = 0;
} else if (z[i] < Cutneigh) { /* bottom plane */
Nghost++;
BorderMap[Nghost] = i;
PBCx[Nghost] = 0; PBCy[Nghost] = 0; PBCz[Nghost] = +1;
} else if (z[i] >= (zprd-Cutneigh)) { /* top plane */
Nghost++;
BorderMap[Nghost] = i;
PBCx[Nghost] = 0; PBCy[Nghost] = 0; PBCz[Nghost] = -1;
}
}
// increase by one to make it the count
Nghost++;
}
/* place atoms in the same bin consecutive in memory */
@ -1052,18 +1283,23 @@ int main (int argc, char** argv)
create_atoms(&param);
thermoSetup(&param, &thermo);
adjustVelocity(&param, &thermo);
processBorders();
/* printAtomState(&neighbor); */
setupBorders();
/* updateBorders(); */
printAtomState();
exit(EXIT_SUCCESS);
buildNeighborlist(&neighbor);
thermoCompute(0, &param, &thermo);
computeForce(&neighbor, &param);
for(int n = 0; n < param.ntimes; n++) {
initialIntegrate(&param);
exchangeBorders();
updateBorders();
if(!((n + 1) % neighbor.every)) {
/* processBorders(); */
updateAtomLocations();
setupBorders();
updateBorders();
/* sortAtoms(&neighbor); */
buildNeighborlist(&neighbor);
}