Fix bug in ghost atom setup.
This commit is contained in:
Jan Eitzinger
parent
24a2e87e7e
commit
49cd67f82f
143
src/main.c
143
src/main.c
@ -684,100 +684,35 @@ void setupBorders()
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}
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/* Setup ghost atoms */
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if (x[i] < Cutneigh) { /* left plane */
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ADDGHOST(+1,0,0);
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/* treat edges and corners */
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if (z[i] < Cutneigh) { /* bottom left edge */
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ADDGHOST(+1,0,+1);
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if (y[i] < Cutneigh) { /* bottom left front corner */
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ADDGHOST(+1,+1,+1);
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}
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}
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if (y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { /* bottom left back corner */
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ADDGHOST(+1,-1,+1);
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}
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if (z[i] >= (zprd-Cutneigh)) { /* top left edge */
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ADDGHOST(+1,0,-1);
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if (y[i] < Cutneigh) { /* bottom left front corner */
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ADDGHOST(+1,+1,-1);
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}
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}
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if (y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { /* top left back corner */
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ADDGHOST(+1,-1,-1);
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}
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}
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if (x[i] >= (xprd-Cutneigh)) { /* right plane */
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ADDGHOST(-1,0,0);
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/* treat edges and corners */
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if (z[i] < Cutneigh) { /* bottom right edge */
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ADDGHOST(-1,0,+1);
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if (y[i] < Cutneigh) { /* bottom right front corner */
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ADDGHOST(-1,+1,+1);
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}
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}
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if (y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { /* bottom right back corner */
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ADDGHOST(-1,-1,+1);
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}
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if (z[i] >= (zprd-Cutneigh)) { /* top right edge */
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ADDGHOST(-1,0,-1);
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if (y[i] < Cutneigh) { /* top right front corner */
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ADDGHOST(-1,+1,-1);
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}
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}
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if (y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { /* top right back corner */
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ADDGHOST(-1,-1,-1);
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}
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}
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if (y[i] < Cutneigh) { /* front plane */
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ADDGHOST(0,+1,0);
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if (z[i] < Cutneigh) { /* bottom front edge */
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ADDGHOST(0,+1,+1);
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}
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if (z[i] >= (zprd-Cutneigh)) { /* top front edge */
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ADDGHOST(0,+1,-1);
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}
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if (x[i] < Cutneigh) { /* left front edge */
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ADDGHOST(+1,+1,0);
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}
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if (x[i] >= (xprd-Cutneigh)) { /* right front edge */
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ADDGHOST(+1,-1,0);
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}
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}
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if (y[i] >= (yprd-Cutneigh)) { /* back plane */
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ADDGHOST(0,-1,0);
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if (z[i] < Cutneigh) { /* bottom back edge */
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ADDGHOST(0,-1,+1);
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}
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if (z[i] >= (zprd-Cutneigh)) { /* top back edge */
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ADDGHOST(0,-1,-1);
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}
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if (x[i] < Cutneigh) { /* left back edge */
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ADDGHOST(-1,+1,0);
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}
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if (x[i] >= (xprd-Cutneigh)) { /* right back edge */
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ADDGHOST(-1,-1,0);
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}
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}
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if (z[i] < Cutneigh) { /* bottom plane */
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ADDGHOST(0,0,+1);
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}
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if (z[i] >= (zprd-Cutneigh)) { /* top plane */
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ADDGHOST(0,0,-1);
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}
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/* 6 planes */
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if (x[i] < Cutneigh) { ADDGHOST(+1,0,0); }
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if (x[i] >= (xprd-Cutneigh)) { ADDGHOST(-1,0,0); }
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if (y[i] < Cutneigh) { ADDGHOST(0,+1,0); }
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if (y[i] >= (yprd-Cutneigh)) { ADDGHOST(0,-1,0); }
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if (z[i] < Cutneigh) { ADDGHOST(0,0,+1); }
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if (z[i] >= (zprd-Cutneigh)) { ADDGHOST(0,0,-1); }
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/* 8 corners */
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if (x[i] < Cutneigh && y[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(+1,+1,+1); }
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if (x[i] < Cutneigh && y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(+1,-1,+1); }
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if (x[i] < Cutneigh && y[i] >= Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(+1,+1,-1); }
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if (x[i] < Cutneigh && y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(+1,-1,-1); }
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if (x[i] >= (xprd-Cutneigh) && y[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(-1,+1,+1); }
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if (x[i] >= (xprd-Cutneigh) && y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(-1,-1,+1); }
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if (x[i] >= (xprd-Cutneigh) && y[i] < Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(-1,+1,-1); }
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if (x[i] >= (xprd-Cutneigh) && y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(-1,-1,-1); }
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/* 12 edges */
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if (x[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(+1,0,+1); }
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if (x[i] < Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(+1,0,-1); }
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if (x[i] >= (xprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(-1,0,+1); }
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if (x[i] >= (xprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(-1,0,-1); }
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if (y[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(0,+1,+1); }
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if (y[i] < Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(0,+1,-1); }
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if (y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(0,-1,+1); }
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if (y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(0,-1,-1); }
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if (y[i] < Cutneigh && x[i] < Cutneigh) { ADDGHOST(+1,+1,0); }
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if (y[i] < Cutneigh && x[i] >= (xprd-Cutneigh)) { ADDGHOST(-1,+1,0); }
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if (y[i] >= (yprd-Cutneigh) && x[i] < Cutneigh) { ADDGHOST(+1,-1,0); }
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if (y[i] >= (yprd-Cutneigh) && x[i] >= (xprd-Cutneigh)) { ADDGHOST(-1,-1,0); }
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}
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// increase by one to make it the ghost atom count
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@ -1068,10 +1003,12 @@ void initialIntegrate(Parameter *param)
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vx[i] += param->dtforce * fx[i];
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vy[i] += param->dtforce * fy[i];
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vz[i] += param->dtforce * fz[i];
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/* if (i==129212) printf("f %f %f %f v %f %f %f\n",fx[i], fy[i], fz[i], vx[i], vy[i], vz[i] ); */
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x[i] += param->dt * vx[i];
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y[i] += param->dt * vy[i];
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z[i] += param->dt * vz[i];
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}
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/* printf("C x = %f %f %f\n", x[129212], y[129212], z[129212]); */
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}
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void finalIntegrate(Parameter *param)
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@ -1120,17 +1057,27 @@ void computeForce(Neighbor *neighbor, Parameter *param)
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double delz = ztmp - z[j];
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double rsq = delx * delx + dely * dely + delz * delz;
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if(rsq < cutforcesq) {
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double sr2 = 1.0 / rsq;
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double sr6 = sr2 * sr2 * sr2 * sigma6;
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double force = 48.0 * sr6 * (sr6 - 0.5) * sr2 * epsilon;
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/* if (i==129212){ */
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/* printf("%d %f %f %f r %f",j, x[j],y[j],z[j],rsq); */
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/* } */
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/* if (i==129212){ */
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/* printf("f %f", force); */
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/* } */
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fix += delx * force;
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fiy += dely * force;
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fiz += delz * force;
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t_eng_vdwl += sr6 * (sr6 - 1.0) * epsilon;
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t_virial += (delx * delx + dely * dely + delz * delz) * force;
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/* if (i==129212){ */
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/* printf("\n"); */
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/* } */
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}
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}
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/* printf("\n"); */
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@ -1142,6 +1089,7 @@ void computeForce(Neighbor *neighbor, Parameter *param)
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eng_vdwl += (4.0 * t_eng_vdwl);
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virial += (0.5 * t_virial);
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/* exit(EXIT_SUCCESS); */
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}
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void printAtomState()
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@ -1185,8 +1133,9 @@ int main (int argc, char** argv)
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for(int n = 0; n < param.ntimes; n++) {
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/* printf("A x = %f %f %f maps %d\n", x[176962], y[176962], z[176962], BorderMap[176962-Nlocal]); */
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/* printf("A x = %f %f %f\n", x[129212], y[129212], z[129212]); */
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initialIntegrate(¶m);
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updateBorders();
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printf("x = %f %f %f\n", x[0], y[0], z[0]);
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if(!((n + 1) % neighbor.every)) {
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@ -1196,7 +1145,11 @@ int main (int argc, char** argv)
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updateBorders();
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/* sortAtoms(&neighbor); */
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buildNeighborlist(&neighbor);
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} else {
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updateBorders();
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}
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/* printf("B x = %f %f %f\n", x[129212], y[129212], z[129212]); */
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/* printf("B x = %f %f %f\n", x[176962], y[176962], z[176962]); */
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computeForce(&neighbor, ¶m);
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finalIntegrate(¶m);
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