diff --git a/src/main.c b/src/main.c index f16752c..39cf9bb 100644 --- a/src/main.c +++ b/src/main.c @@ -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(¶m); 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, ¶m, &thermo); } - printf("x = %f %f %f\n", x[0], y[0], z[0]); } thermoCompute(-1, ¶m, &thermo);