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Add boundary ghost layer setup without atom relocation.

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This commit is contained in:
Jan Eitzinger 2020-08-13 09:43:29 +02:00
parent fb763f0dfc
commit a4c2860130
1 changed files with 122 additions and 104 deletions
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224
src/main.c
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@ -50,6 +50,7 @@
#endif #endif
static int Natoms, Nlocal, Nghost, Nmax; static int Natoms, Nlocal, Nghost, Nmax;
static double Cutneigh; // neighbor cutoff
static double xprd, yprd, zprd; static double xprd, yprd, zprd;
static double xlo, xhi; static double xlo, xhi;
static double ylo, yhi; static double ylo, yhi;
@ -83,7 +84,7 @@ typedef struct {
int* neighbors; int* neighbors;
int maxneighs; int maxneighs;
int nbinx, nbiny, nbinz; int nbinx, nbiny, nbinz;
double cutneigh; // neighbor cutoff /* double cutneigh; // neighbor cutoff */
double cutneighsq; // neighbor cutoff squared double cutneighsq; // neighbor cutoff squared
int every; int every;
int ncalls; int ncalls;
@ -354,6 +355,7 @@ void init(Neighbor *neighbor, Parameter *param)
param->mass = 1.0; param->mass = 1.0;
param->dtforce = 0.5 * param->dt; param->dtforce = 0.5 * param->dt;
Cutneigh = param->cutforce + 0.30;
double neighscale = 5.0 / 6.0; double neighscale = 5.0 / 6.0;
neighbor->nbinx = neighscale * param->nx; neighbor->nbinx = neighscale * param->nx;
neighbor->nbiny = neighscale * param->ny; neighbor->nbiny = neighscale * param->ny;
@ -363,7 +365,7 @@ void init(Neighbor *neighbor, Parameter *param)
neighbor->nmax = 0; neighbor->nmax = 0;
neighbor->atoms_per_bin = 8; neighbor->atoms_per_bin = 8;
neighbor->maxneighs = 100; neighbor->maxneighs = 100;
neighbor->cutneigh = param->cutforce + 0.30; /* neighbor->cutneigh = param->cutforce + 0.30; */
neighbor->numneigh = NULL; neighbor->numneigh = NULL;
neighbor->neighbors = NULL; neighbor->neighbors = NULL;
neighbor->stencil = NULL; neighbor->stencil = NULL;
@ -377,7 +379,6 @@ void setup(Neighbor *neighbor, Parameter *param)
double coord; double coord;
int mbinxhi, mbinyhi, mbinzhi; int mbinxhi, mbinyhi, mbinzhi;
int nextx, nexty, nextz; int nextx, nexty, nextz;
double cutneigh = neighbor->cutneigh;
xprd = param->nx * lattice; xprd = param->nx * lattice;
yprd = param->ny * lattice; yprd = param->ny * lattice;
@ -387,7 +388,7 @@ void setup(Neighbor *neighbor, Parameter *param)
ylo = 0.0; yhi = yprd; ylo = 0.0; yhi = yprd;
zlo = 0.0; zhi = zprd; zlo = 0.0; zhi = zprd;
neighbor->cutneighsq = cutneigh * cutneigh; neighbor->cutneighsq = Cutneigh * Cutneigh;
neighbor->binsizex = xprd / neighbor->nbinx; neighbor->binsizex = xprd / neighbor->nbinx;
neighbor->binsizey = yprd / neighbor->nbiny; neighbor->binsizey = yprd / neighbor->nbiny;
neighbor->binsizez = zprd / neighbor->nbinz; neighbor->binsizez = zprd / neighbor->nbinz;
@ -397,36 +398,36 @@ void setup(Neighbor *neighbor, Parameter *param)
neighbor->bininvz = 1.0 / neighbor->binsizez; neighbor->bininvz = 1.0 / neighbor->binsizez;
// x coordinate // x coordinate
coord = xlo - cutneigh - SMALL * xprd; coord = xlo - Cutneigh - SMALL * xprd;
neighbor->mbinxlo = (int) (coord * neighbor->bininvx); neighbor->mbinxlo = (int) (coord * neighbor->bininvx);
if (coord < 0.0) { if (coord < 0.0) {
neighbor->mbinxlo = neighbor->mbinxlo - 1; neighbor->mbinxlo = neighbor->mbinxlo - 1;
} }
coord = xhi + cutneigh + SMALL * xprd; coord = xhi + Cutneigh + SMALL * xprd;
mbinxhi = (int) (coord * neighbor->bininvx); mbinxhi = (int) (coord * neighbor->bininvx);
// y coordinate // y coordinate
coord = ylo - cutneigh - SMALL * yprd; coord = ylo - Cutneigh - SMALL * yprd;
neighbor->mbinylo = (int) (coord * neighbor->bininvy); neighbor->mbinylo = (int) (coord * neighbor->bininvy);
if (coord < 0.0) { if (coord < 0.0) {
neighbor->mbinylo = neighbor->mbinylo - 1; neighbor->mbinylo = neighbor->mbinylo - 1;
} }
coord = yhi + cutneigh + SMALL * yprd; coord = yhi + Cutneigh + SMALL * yprd;
mbinyhi = (int) (coord * neighbor->bininvy); mbinyhi = (int) (coord * neighbor->bininvy);
// z coordinate // z coordinate
coord = zlo - cutneigh - SMALL * zprd; coord = zlo - Cutneigh - SMALL * zprd;
neighbor->mbinzlo = (int) (coord * neighbor->bininvz); neighbor->mbinzlo = (int) (coord * neighbor->bininvz);
if (coord < 0.0) { if (coord < 0.0) {
neighbor->mbinzlo = neighbor->mbinzlo - 1; neighbor->mbinzlo = neighbor->mbinzlo - 1;
} }
coord = zhi + cutneigh + SMALL * zprd; coord = zhi + Cutneigh + SMALL * zprd;
mbinzhi = (int) (coord * neighbor->bininvz); mbinzhi = (int) (coord * neighbor->bininvz);
@ -442,14 +443,14 @@ void setup(Neighbor *neighbor, Parameter *param)
mbinzhi = mbinzhi + 1; mbinzhi = mbinzhi + 1;
neighbor->mbinz = mbinzhi - neighbor->mbinzlo + 1; neighbor->mbinz = mbinzhi - neighbor->mbinzlo + 1;
nextx = (int) (cutneigh * neighbor->bininvx); nextx = (int) (Cutneigh * neighbor->bininvx);
if(nextx * neighbor->binsizex < FACTOR * cutneigh) nextx++; if(nextx * neighbor->binsizex < FACTOR * Cutneigh) nextx++;
nexty = (int) (cutneigh * neighbor->bininvy); nexty = (int) (Cutneigh * neighbor->bininvy);
if(nexty * neighbor->binsizey < FACTOR * cutneigh) nexty++; if(nexty * neighbor->binsizey < FACTOR * Cutneigh) nexty++;
nextz = (int) (cutneigh * neighbor->bininvz); nextz = (int) (Cutneigh * neighbor->bininvz);
if(nextz * neighbor->binsizez < FACTOR * cutneigh) nextz++; if(nextz * neighbor->binsizez < FACTOR * Cutneigh) nextz++;
if (neighbor->stencil) { if (neighbor->stencil) {
free(neighbor->stencil); free(neighbor->stencil);
@ -530,11 +531,105 @@ 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 exchangeBorders()
{
Nghost = 0;
int lastidx = Nlocal-1;
for(int i = 0; i < Nlocal; i++) {
lastidx = setupGhostAtom(i, lastidx);
}
}
/* Enforce periodic boundary conditions /* Enforce periodic boundary conditions
* Relocate atoms that have left domain for * Relocate atoms that have left domain for
* 6 planes (and 8 corners (diagonal)) * 6 planes (and 8 corners (diagonal))
* Setup ghost atoms at boundaries*/ * Setup ghost atoms at boundaries*/
void processBorders(double cutneigh) void processBorders()
{ {
Nghost = 0; Nghost = 0;
int lastidx = Nlocal-1; int lastidx = Nlocal-1;
@ -564,84 +659,7 @@ void processBorders(double cutneigh)
growarray(); growarray();
} }
/* Setup ghost atoms */ lastidx = setupGhostAtom(i, lastidx);
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++;
}
} }
} }
@ -723,8 +741,8 @@ void create_atoms(Parameter *param)
klo = MAX(klo, 0); klo = MAX(klo, 0);
khi = MIN(khi, 2 * param->nz - 1); khi = MIN(khi, 2 * param->nz - 1);
printf("CA alat=%f ilo=%d ihi=%d jlo=%d jhi=%d klo=%d khi=%d\n", /* printf("CA alat=%f ilo=%d ihi=%d jlo=%d jhi=%d klo=%d khi=%d\n", */
alat, ilo, ihi, jlo, jhi, klo, khi); /* alat, ilo, ihi, jlo, jhi, klo, khi); */
double xtmp, ytmp, ztmp, vxtmp, vytmp, vztmp; double xtmp, ytmp, ztmp, vxtmp, vytmp, vztmp;
int i, j, k, m, n; int i, j, k, m, n;
@ -1003,14 +1021,14 @@ void computeForce(Neighbor *neighbor, Parameter *param)
virial += (0.5 * t_virial); virial += (0.5 * t_virial);
} }
void printAtomState(Neighbor *neighbor) void printAtomState()
{ {
printf("Atom counts: Natoms=%d Nlocal=%d Nghost=%d Nmax=%d\n", printf("Atom counts: Natoms=%d Nlocal=%d Nghost=%d Nmax=%d\n",
Natoms, Nlocal, Nghost, Nmax); Natoms, Nlocal, Nghost, Nmax);
int nall = Nlocal + Nghost; int nall = Nlocal + Nghost;
double min = -neighbor->cutneigh; double min = -Cutneigh;
double max = xprd + neighbor->cutneigh; double max = xprd + Cutneigh;
for (int i=0; i<nall; i++) { for (int i=0; i<nall; i++) {
printf("%d %f %f %f\n", i, x[i], y[i], z[i]); printf("%d %f %f %f\n", i, x[i], y[i], z[i]);
@ -1034,18 +1052,18 @@ int main (int argc, char** argv)
create_atoms(&param); create_atoms(&param);
thermoSetup(&param, &thermo); thermoSetup(&param, &thermo);
adjustVelocity(&param, &thermo); adjustVelocity(&param, &thermo);
processBorders(neighbor.cutneigh); processBorders();
/* printAtomState(&neighbor); */ /* printAtomState(&neighbor); */
buildNeighborlist(&neighbor); buildNeighborlist(&neighbor);
/* printAtomState(); */
thermoCompute(0, &param, &thermo); thermoCompute(0, &param, &thermo);
for(int n = 0; n < param.ntimes; n++) { for(int n = 0; n < param.ntimes; n++) {
initialIntegrate(&param); initialIntegrate(&param);
exchangeBorders();
if(!((n + 1) % neighbor.every)) { if(!((n + 1) % neighbor.every)) {
processBorders(neighbor.cutneigh); /* processBorders(); */
/* sortAtoms(&neighbor); */ /* sortAtoms(&neighbor); */
buildNeighborlist(&neighbor); buildNeighborlist(&neighbor);
} }