First working code. Clean up.
This commit is contained in:
Jan Eitzinger
parent
49cd67f82f
commit
b20b71ca0b
209
src/main.c
209
src/main.c
@ -58,8 +58,6 @@ static double zlo, zhi;
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static double *x, *y, *z;
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static double *vx, *vy, *vz;
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static double *fx, *fy, *fz;
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static double eng_vdwl;
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static double virial;
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static int NmaxGhost;
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static int *BorderMap;
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@ -116,7 +114,6 @@ typedef struct {
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double p_act;
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double e_act;
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int mstat;
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int nstat;
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} Thermo;
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/* Park/Miller RNG w/out MASKING, so as to be like f90s version */
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@ -129,21 +126,15 @@ typedef struct {
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double myrandom(int* idum)
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{
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int k;
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int k= (*idum) / IQ;
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double ans;
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k = (*idum) / IQ;
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*idum = IA * (*idum - k * IQ) - IR * k;
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if(*idum < 0) *idum += IM;
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ans = AM * (*idum);
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return ans;
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}
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// Neighbor list related subroutines
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// convert atom coordinates in bin index
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int coord2bin(Neighbor* neighbor, double xin, double yin, double zin)
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{
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int ix, iy, iz;
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@ -181,9 +172,6 @@ int coord2bin(Neighbor* neighbor, double xin, double yin, double zin)
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return (iz * neighbor->mbiny * neighbor->mbinx + iy * neighbor->mbinx + ix + 1);
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}
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// Sort atoms in bins. All bins can hold the same number of max atoms
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// If one bin is exceeded reallocate and start over.
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void binatoms(Neighbor *neighbor)
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{
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int* bincount = neighbor->bincount;
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@ -217,7 +205,6 @@ void binatoms(Neighbor *neighbor)
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}
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}
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/* compute closest distance between central bin (0,0,0) and bin (i,j,k) */
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double bindist(Neighbor *neighbor, int i, int j, int k)
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{
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double delx, dely, delz;
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@ -387,40 +374,30 @@ void setup(Neighbor *neighbor, Parameter *param)
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neighbor->bininvy = 1.0 / neighbor->binsizey;
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neighbor->bininvz = 1.0 / neighbor->binsizez;
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// x coordinate
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coord = xlo - Cutneigh - SMALL * xprd;
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neighbor->mbinxlo = (int) (coord * neighbor->bininvx);
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if (coord < 0.0) {
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neighbor->mbinxlo = neighbor->mbinxlo - 1;
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}
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coord = xhi + Cutneigh + SMALL * xprd;
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mbinxhi = (int) (coord * neighbor->bininvx);
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// y coordinate
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coord = ylo - Cutneigh - SMALL * yprd;
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neighbor->mbinylo = (int) (coord * neighbor->bininvy);
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if (coord < 0.0) {
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neighbor->mbinylo = neighbor->mbinylo - 1;
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}
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coord = yhi + Cutneigh + SMALL * yprd;
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mbinyhi = (int) (coord * neighbor->bininvy);
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// z coordinate
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coord = zlo - Cutneigh - SMALL * zprd;
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neighbor->mbinzlo = (int) (coord * neighbor->bininvz);
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if (coord < 0.0) {
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neighbor->mbinzlo = neighbor->mbinzlo - 1;
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}
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coord = zhi + Cutneigh + SMALL * zprd;
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mbinzhi = (int) (coord * neighbor->bininvz);
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neighbor->mbinxlo = neighbor->mbinxlo - 1;
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mbinxhi = mbinxhi + 1;
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neighbor->mbinx = mbinxhi - neighbor->mbinxlo + 1;
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@ -463,12 +440,6 @@ void setup(Neighbor *neighbor, Parameter *param)
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}
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}
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/* printf("STENCIL %d \n", neighbor->nstencil); */
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/* for (int i=0; i<neighbor->nstencil; i++) { */
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/* printf("%d ", neighbor->stencil[i]); */
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/* } */
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/* printf("\n"); */
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neighbor->mbins = neighbor->mbinx * neighbor->mbiny * neighbor->mbinz;
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if (neighbor->bincount) {
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@ -485,13 +456,11 @@ void setup(Neighbor *neighbor, Parameter *param)
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double* myrealloc(double *ptr, int n, int nold) {
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double* newarray;
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newarray = (double*) malloc(n * sizeof(double));
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if(nold) {
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memcpy(newarray, ptr, nold * sizeof(double));
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}
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if(ptr) {
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free(ptr);
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}
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@ -508,7 +477,6 @@ int* myreallocInt(int *ptr, int n, int nold) {
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if(nold) {
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memcpy(newarray, ptr, nold * sizeof(int));
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}
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if(ptr) {
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free(ptr);
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}
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@ -536,15 +504,9 @@ void growarray()
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int nold = Nmax;
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Nmax += DELTA;
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x = myrealloc(x, Nmax, nold);
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y = myrealloc(y, Nmax, nold);
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z = myrealloc(z, Nmax, nold);
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vx = myrealloc(vx, Nmax, nold);
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vy = myrealloc(vy, Nmax, nold);
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vz = myrealloc(vz, Nmax, nold);
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fx = myrealloc(fx, Nmax, nold);
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fy = myrealloc(fy, Nmax, nold);
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fz = myrealloc(fz, Nmax, nold);
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x = myrealloc(x, Nmax, nold); y = myrealloc(y, Nmax, nold); z = myrealloc(z, Nmax, nold);
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vx = myrealloc(vx, Nmax, nold); vy = myrealloc(vy, Nmax, nold); vz = myrealloc(vz, Nmax, nold);
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fx = myrealloc(fx, Nmax, nold); fy = myrealloc(fy, Nmax, nold); fz = myrealloc(fz, Nmax, nold);
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if(x == NULL || y == NULL || z == NULL ||
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vx == NULL || vy == NULL || vz == NULL ||
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@ -566,7 +528,6 @@ void updateAtomLocations()
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{
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for(int i = 0; i < Nlocal; i++) {
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/* Relocate atoms that have left the domain */
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if(x[i] < 0.0) {
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x[i] += xprd;
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} else if(x[i] >= xprd) {
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@ -664,11 +625,6 @@ void setupBordersNew()
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}
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#define ADDGHOST(dx,dy,dz) Nghost++; BorderMap[Nghost] = i; PBCx[Nghost] = dx; PBCy[Nghost] = dy; PBCz[Nghost] = dz;
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/* Enforce periodic boundary conditions
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* Relocate atoms that have left domain for
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* 6 planes (and 8 corners (diagonal))
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* Setup ghost atoms at boundaries*/
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void setupBorders()
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{
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Nghost = -1;
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@ -678,7 +634,6 @@ void setupBorders()
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if (Nlocal + Nghost + 7 >= Nmax) {
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growarray();
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}
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if (Nghost + 7 >= NmaxGhost) {
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growBoundary();
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}
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@ -714,12 +669,10 @@ void setupBorders()
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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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Nghost++;
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}
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/* place atoms in the same bin consecutive in memory */
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void sortAtoms(Neighbor *neighbor)
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{
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binatoms(neighbor);
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@ -740,12 +693,8 @@ void sortAtoms(Neighbor *neighbor)
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double* new_vy = (double*) malloc(Nmax * sizeof(double));
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double* new_vz = (double*) malloc(Nmax * sizeof(double));
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double* old_x = x;
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double* old_y = y;
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double* old_z = z;
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double* old_vx = vx;
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double* old_vy = vy;
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double* old_vz = vz;
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double* old_x = x; double* old_y = y; double* old_z = z;
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double* old_vx = vx; double* old_vy = vy; double* old_vz = vz;
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for(int mybin = 0; mybin<mbins; mybin++) {
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int start = mybin>0?binpos[mybin-1]:0;
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@ -765,23 +714,14 @@ void sortAtoms(Neighbor *neighbor)
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free(x); free(y); free(z);
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free(vx); free(vy); free(vz);
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x = new_x;
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y = new_y;
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z = new_z;
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vx = new_vx;
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vy = new_vy;
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vz = new_vz;
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x = new_x; y = new_y; z = new_z;
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vx = new_vx; vy = new_vy; vz = new_vz;
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}
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void create_atoms(Parameter *param)
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{
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/* total # of atoms */
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Natoms = 4 * param->nx * param->ny * param->nz;
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Nlocal = 0;
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/* determine loop bounds of lattice subsection that overlaps my sub-box
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insure loop bounds do not exceed nx,ny,nz */
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double alat = pow((4.0 / param->rho), (1.0 / 3.0));
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int ilo = (int) (xlo / (0.5 * alat) - 1);
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int ihi = (int) (xhi / (0.5 * alat) + 1);
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@ -797,9 +737,6 @@ void create_atoms(Parameter *param)
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klo = MAX(klo, 0);
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khi = MIN(khi, 2 * param->nz - 1);
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/* printf("CA alat=%f ilo=%d ihi=%d jlo=%d jhi=%d klo=%d khi=%d\n", */
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/* alat, ilo, ihi, jlo, jhi, klo, khi); */
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double xtmp, ytmp, ztmp, vxtmp, vytmp, vztmp;
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int i, j, k, m, n;
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int sx = 0; int sy = 0; int sz = 0;
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@ -848,49 +785,22 @@ void create_atoms(Parameter *param)
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growarray();
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}
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/* printf("%d %f %f %f\n",Nlocal, xtmp, ytmp, ztmp); */
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x[Nlocal] = xtmp;
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y[Nlocal] = ytmp;
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z[Nlocal] = ztmp;
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vx[Nlocal] = vxtmp;
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vy[Nlocal] = vytmp;
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vz[Nlocal] = vztmp;
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x[Nlocal] = xtmp; y[Nlocal] = ytmp; z[Nlocal] = ztmp;
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vx[Nlocal] = vxtmp; vy[Nlocal] = vytmp; vz[Nlocal] = vztmp;
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Nlocal++;
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}
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}
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sx++;
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if(sx == subboxdim) {
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sx = 0;
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sy++;
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}
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if(sy == subboxdim) {
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sy = 0;
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sz++;
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}
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if(sz == subboxdim) {
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sz = 0;
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ox++;
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}
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if(ox * subboxdim > ihi) {
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ox = 0;
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oy++;
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}
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if(oy * subboxdim > jhi) {
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oy = 0;
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oz++;
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}
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if(sx == subboxdim) { sx = 0; sy++; }
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if(sy == subboxdim) { sy = 0; sz++; }
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if(sz == subboxdim) { sz = 0; ox++; }
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if(ox * subboxdim > ihi) { ox = 0; oy++; }
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if(oy * subboxdim > jhi) { oy = 0; oz++; }
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}
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}
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void adjustVelocity(Parameter *param, Thermo *thermo)
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{
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/* zero center-of-mass motion */
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@ -914,7 +824,6 @@ void adjustVelocity(Parameter *param, Thermo *thermo)
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vz[i] -= vztot;
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}
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/* rescale velocities, including old ones */
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thermo->t_act = 0;
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double t = 0.0;
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@ -947,32 +856,19 @@ void thermoSetup(Parameter *param, Thermo *thermo)
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thermo->p_scale = 1.0 / 3 / xprd / yprd / zprd;
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thermo->e_scale = 0.5;
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eng_vdwl = 0.0;
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virial = 0.0;
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printf("step\ttemp\t\tpressure\n");
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}
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void thermoCompute(int iflag, Parameter *param, Thermo *thermo)
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{
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double t, eng, p;
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if(iflag > 0 && iflag % param->nstat){
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return;
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}
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if(iflag == -1 && param->nstat > 0 && param->ntimes % param->nstat == 0)
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{
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return;
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}
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t = 0.0;
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double t = 0.0, p;
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for(int i = 0; i < Nlocal; i++) {
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t += (vx[i] * vx[i] + vy[i] * vy[i] + vz[i] * vz[i]) * param->mass;
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}
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t = t * thermo->t_scale;
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eng = eng_vdwl * thermo->e_scale / Natoms;
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p = (t * thermo->dof_boltz) * thermo->p_scale;
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int istep = iflag;
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@ -980,35 +876,27 @@ void thermoCompute(int iflag, Parameter *param, Thermo *thermo)
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if(iflag == -1){
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istep = param->ntimes;
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}
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if(iflag == 0){
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thermo->mstat = 0;
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}
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thermo->steparr[thermo->mstat] = istep;
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thermo->tmparr[thermo->mstat] = t;
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thermo->engarr[thermo->mstat] = eng;
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thermo->prsarr[thermo->mstat] = p;
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thermo->mstat++;
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fprintf(stdout, "%i %e %e %e\n", istep, t, eng, p);
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fprintf(stdout, "%i\t%e\t%e\n", istep, t, p);
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}
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void initialIntegrate(Parameter *param)
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{
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/* printf("dtforce %f dt %f\n",param->dtforce, param->dt); */
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for(int i = 0; i < Nlocal; i++) {
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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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@ -1026,8 +914,6 @@ void computeForce(Neighbor *neighbor, Parameter *param)
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double cutforcesq = param->cutforce * param->cutforce;
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double sigma6 = param->sigma6;
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double epsilon = param->epsilon;
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double t_eng_vdwl = 0.0;
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double t_virial = 0.0;
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for(int i = 0; i < Nlocal; i++) {
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fx[i] = 0.0;
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@ -1035,8 +921,6 @@ void computeForce(Neighbor *neighbor, Parameter *param)
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fz[i] = 0.0;
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}
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// loop over all neighbors of my atoms
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// store force on atom i
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for(int i = 0; i < Nlocal; i++) {
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neighs = &neighbor->neighbors[i * neighbor->maxneighs];
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int numneighs = neighbor->numneigh[i];
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@ -1047,69 +931,28 @@ void computeForce(Neighbor *neighbor, Parameter *param)
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double fix = 0;
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double fiy = 0;
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double fiz = 0;
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/* printf("%d %d: ", i, numneighs); */
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for(int k = 0; k < numneighs; k++) {
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int j = neighs[k];
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/* printf("%d ", j); */
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double delx = xtmp - x[j];
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double dely = ytmp - y[j];
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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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fx[i] += fix;
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fy[i] += fiy;
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fz[i] += fiz;
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}
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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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{
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||||
printf("Atom counts: Natoms=%d Nlocal=%d Nghost=%d Nmax=%d\n",
|
||||
Natoms, Nlocal, Nghost, Nmax);
|
||||
|
||||
int nall = Nlocal + Nghost;
|
||||
double min = -Cutneigh;
|
||||
double max = xprd + Cutneigh;
|
||||
|
||||
/* for (int i=0; i<nall; i++) { */
|
||||
/* printf("%d %f %f %f\n", i, x[i], y[i], z[i]); */
|
||||
|
||||
/* if ( x[i] < min || x[i] > max || */
|
||||
/* y[i] < min || y[i] > max || */
|
||||
/* z[i] < min || z[i] > max) { */
|
||||
/* printf("OOB!!\n"); */
|
||||
/* } */
|
||||
/* } */
|
||||
}
|
||||
|
||||
int main (int argc, char** argv)
|
||||
@ -1125,36 +968,28 @@ int main (int argc, char** argv)
|
||||
adjustVelocity(¶m, &thermo);
|
||||
setupBorders();
|
||||
updateBorders();
|
||||
/* printAtomState(); */
|
||||
/* exit(EXIT_SUCCESS); */
|
||||
buildNeighborlist(&neighbor);
|
||||
thermoCompute(0, ¶m, &thermo);
|
||||
computeForce(&neighbor, ¶m);
|
||||
|
||||
for(int n = 0; n < param.ntimes; n++) {
|
||||
|
||||
/* printf("A x = %f %f %f maps %d\n", x[176962], y[176962], z[176962], BorderMap[176962-Nlocal]); */
|
||||
/* printf("A x = %f %f %f\n", x[129212], y[129212], z[129212]); */
|
||||
initialIntegrate(¶m);
|
||||
|
||||
printf("x = %f %f %f\n", x[0], y[0], z[0]);
|
||||
if(!((n + 1) % neighbor.every)) {
|
||||
printf("Reneighbor at %d\n",n);
|
||||
if((n + 1) % neighbor.every) {
|
||||
updateBorders();
|
||||
} else {
|
||||
updateAtomLocations();
|
||||
setupBorders();
|
||||
updateBorders();
|
||||
/* sortAtoms(&neighbor); */
|
||||
buildNeighborlist(&neighbor);
|
||||
} else {
|
||||
updateBorders();
|
||||
}
|
||||
/* printf("B x = %f %f %f\n", x[129212], y[129212], z[129212]); */
|
||||
/* printf("B x = %f %f %f\n", x[176962], y[176962], z[176962]); */
|
||||
|
||||
computeForce(&neighbor, ¶m);
|
||||
finalIntegrate(¶m);
|
||||
|
||||
if(thermo.nstat) {
|
||||
if(!((n + 1) % param.nstat) && (n+1) < param.ntimes) {
|
||||
thermoCompute(n + 1, ¶m, &thermo);
|
||||
}
|
||||
}
|
||||
|
||||
Loading…
Reference in New Issue
Block a user