Debug. Runs with wrong temp.
This commit is contained in:
Jan Eitzinger
parent
ff45b07749
commit
fb763f0dfc
194
src/main.c
194
src/main.c
@ -33,9 +33,6 @@
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#include <math.h>
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#include <float.h>
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#include <timing.h>
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#include <allocate.h>
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#define HLINE "----------------------------------------------------------------------------\n"
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#define FACTOR 0.999
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@ -128,7 +125,11 @@ typedef struct {
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double t_scale;
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double p_scale;
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double e_scale;
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double t_act;
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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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@ -156,7 +157,7 @@ double myrandom(int* idum)
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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 x, double y, double z)
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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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double bininvx = neighbor->bininvx;
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@ -166,28 +167,28 @@ int coord2bin(Neighbor* neighbor, double x, double y, double z)
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int mbinylo = neighbor->mbinylo;
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int mbinzlo = neighbor->mbinzlo;
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if(x >= xprd) {
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ix = (int)((x - xprd) * bininvx) + neighbor->nbinx - mbinxlo;
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} else if(x >= 0.0) {
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ix = (int)(x * bininvx) - mbinxlo;
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if(xin >= xprd) {
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ix = (int)((xin - xprd) * bininvx) + neighbor->nbinx - mbinxlo;
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} else if(xin >= 0.0) {
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ix = (int)(xin * bininvx) - mbinxlo;
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} else {
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ix = (int)(x * bininvx) - mbinxlo - 1;
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ix = (int)(xin * bininvx) - mbinxlo - 1;
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}
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if(y >= yprd) {
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iy = (int)((y - yprd) * bininvy) + neighbor->nbiny - mbinylo;
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} else if(y >= 0.0) {
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iy = (int)(y * bininvy) - mbinylo;
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if(yin >= yprd) {
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iy = (int)((yin - yprd) * bininvy) + neighbor->nbiny - mbinylo;
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} else if(yin >= 0.0) {
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iy = (int)(yin * bininvy) - mbinylo;
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} else {
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iy = (int)(y * bininvy) - mbinylo - 1;
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iy = (int)(yin * bininvy) - mbinylo - 1;
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}
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if(z >= zprd) {
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iz = (int)((z - zprd) * bininvz) + neighbor->nbinz - mbinzlo;
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} else if(z >= 0.0) {
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iz = (int)(z * bininvz) - mbinzlo;
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if(zin >= zprd) {
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iz = (int)((zin - zprd) * bininvz) + neighbor->nbinz - mbinzlo;
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} else if(zin >= 0.0) {
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iz = (int)(zin * bininvz) - mbinzlo;
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} else {
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iz = (int)(z * bininvz) - mbinzlo - 1;
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iz = (int)(zin * bininvz) - mbinzlo - 1;
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}
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return (iz * neighbor->mbiny * neighbor->mbinx + iy * neighbor->mbinx + ix + 1);
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@ -267,12 +268,12 @@ void buildNeighborlist(Neighbor *neighbor)
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int nall = Nlocal + Nghost;
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/* extend atom arrays if necessary */
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if(nall > Nmax) {
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Nmax = nall;
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if(nall > neighbor->nmax) {
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neighbor->nmax = nall;
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if(neighbor->numneigh) free(neighbor->numneigh);
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if(neighbor->neighbors) free(neighbor->neighbors);
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neighbor->numneigh = (int*) malloc(Nmax * sizeof(int));
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neighbor->neighbors = (int*) malloc(Nmax * neighbor->maxneighs * sizeof(int*));
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neighbor->numneigh = (int*) malloc(neighbor->nmax * sizeof(int));
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neighbor->neighbors = (int*) malloc(neighbor->nmax * neighbor->maxneighs * sizeof(int*));
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}
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/* bin local & ghost atoms */
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@ -298,6 +299,11 @@ void buildNeighborlist(Neighbor *neighbor)
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for(int m = 0; m < neighbor->bincount[jbin]; m++) {
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int j = loc_bin[m];
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if ( j == i ){
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continue;
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}
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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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@ -354,7 +360,9 @@ void init(Neighbor *neighbor, Parameter *param)
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neighbor->nbinz = neighscale * param->nz;
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neighbor->every = 20;
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neighbor->ncalls = 0;
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neighbor->nmax = 0;
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neighbor->atoms_per_bin = 8;
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neighbor->maxneighs = 100;
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neighbor->cutneigh = param->cutforce + 0.30;
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neighbor->numneigh = NULL;
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neighbor->neighbors = NULL;
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@ -529,7 +537,7 @@ void growarray()
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void processBorders(double cutneigh)
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{
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Nghost = 0;
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int lastidx = Nlocal;
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int lastidx = Nlocal-1;
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for(int i = 0; i < Nlocal; i++) {
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@ -637,23 +645,6 @@ void processBorders(double cutneigh)
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}
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}
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void addatom(double x_in, double y_in, double z_in,
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double vx_in, double vy_in, double vz_in)
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{
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if(Nlocal == Nmax) {
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growarray();
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}
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x[Nlocal] = x_in;
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y[Nlocal] = y_in;
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z[Nlocal] = z_in;
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vx[Nlocal] = vx_in;
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vy[Nlocal] = vy_in;
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vz[Nlocal] = vz_in;
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Nlocal++;
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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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@ -718,12 +709,12 @@ void create_atoms(Parameter *param)
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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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int jlo = (int) ylo / (0.5 * alat) - 1;
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int jhi = (int) yhi / (0.5 * alat) + 1;
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int klo = (int) zlo / (0.5 * alat) - 1;
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int khi = (int) zhi / (0.5 * alat) + 1;
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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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int jlo = (int) (ylo / (0.5 * alat) - 1);
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int jhi = (int) (yhi / (0.5 * alat) + 1);
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int klo = (int) (zlo / (0.5 * alat) - 1);
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int khi = (int) (zhi / (0.5 * alat) + 1);
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ilo = MAX(ilo, 0);
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ihi = MIN(ihi, 2 * param->nx - 1);
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@ -732,12 +723,10 @@ 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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/* each proc generates positions and velocities of atoms on fcc sublattice
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that overlaps its box, only store atoms that fall in my box
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use atom # (generated from lattice coords) as unique seed to generate a
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unique velocity exercise RNG between calls to avoid correlations in adjacent atoms */
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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, vx, vy, vz;
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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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int ox = 0; int oy = 0; int oz = 0;
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@ -762,24 +751,39 @@ void create_atoms(Parameter *param)
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ytmp >= ylo && ytmp < yhi &&
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ztmp >= zlo && ztmp < zhi ) {
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n = k * (2 * param->ny) * (2 * param->nx) + j * (2 * param->nx) + i + 1;
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n = k * (2 * param->ny) * (2 * param->nx) +
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j * (2 * param->nx) +
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i + 1;
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for(m = 0; m < 5; m++) {
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myrandom(&n);
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}
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vx = myrandom(&n);
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vxtmp = myrandom(&n);
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for(m = 0; m < 5; m++){
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myrandom(&n);
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}
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vy = myrandom(&n);
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vytmp = myrandom(&n);
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for(m = 0; m < 5; m++) {
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myrandom(&n);
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}
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vz = myrandom(&n);
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vztmp = myrandom(&n);
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addatom(xtmp, ytmp, ztmp, vx, vy, vz);
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if(Nlocal == Nmax) {
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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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Nlocal++;
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}
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}
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@ -812,6 +816,48 @@ void create_atoms(Parameter *param)
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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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double vxtot = 0.0;
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double vytot = 0.0;
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double vztot = 0.0;
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for(int i = 0; i < Nlocal; i++) {
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vxtot += vx[i];
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vytot += vy[i];
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vztot += vz[i];
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}
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vxtot = vxtot / Natoms;
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vytot = vytot / Natoms;
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vztot = vztot / Natoms;
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for(int i = 0; i < Nlocal; i++) {
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vx[i] -= vxtot;
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vy[i] -= vytot;
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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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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 *= thermo->t_scale;
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double factor = sqrt(param->temp / t);
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for(int i = 0; i < Nlocal; i++) {
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vx[i] *= factor;
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vy[i] *= factor;
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vz[i] *= factor;
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}
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}
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void thermoSetup(Parameter *param, Thermo *thermo)
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{
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int maxstat = param->ntimes / param->nstat + 2;
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@ -923,9 +969,11 @@ 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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@ -944,6 +992,7 @@ void computeForce(Neighbor *neighbor, Parameter *param)
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t_virial += (delx * delx + dely * dely + delz * delz) * force;
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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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@ -954,10 +1003,24 @@ void computeForce(Neighbor *neighbor, Parameter *param)
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virial += (0.5 * t_virial);
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}
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void printState()
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void printAtomState(Neighbor *neighbor)
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{
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printf("Atom counts: Natoms=%d Nlocal=%d Nghost=%d Nmax=%d\n",
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Natoms, Nlocal, Nghost, Nmax);
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int nall = Nlocal + Nghost;
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double min = -neighbor->cutneigh;
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double max = xprd + neighbor->cutneigh;
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for (int i=0; i<nall; i++) {
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printf("%d %f %f %f\n", i, x[i], y[i], z[i]);
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if ( x[i] < min || x[i] > max ||
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y[i] < min || y[i] > max ||
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z[i] < min || z[i] > max) {
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printf("OOB!!\n");
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}
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}
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}
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int main (int argc, char** argv)
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@ -967,15 +1030,15 @@ int main (int argc, char** argv)
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Thermo thermo;
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init(&neighbor, ¶m);
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printState();
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setup(&neighbor, ¶m);
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create_atoms(¶m);
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printState();
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thermoSetup(¶m, &thermo);
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adjustVelocity(¶m, &thermo);
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processBorders(neighbor.cutneigh);
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/* printAtomState(&neighbor); */
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buildNeighborlist(&neighbor);
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printState();
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exit(EXIT_SUCCESS);
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/* printAtomState(); */
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thermoCompute(0, ¶m, &thermo);
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for(int n = 0; n < param.ntimes; n++) {
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@ -983,17 +1046,20 @@ int main (int argc, char** argv)
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if(!((n + 1) % neighbor.every)) {
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processBorders(neighbor.cutneigh);
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sortAtoms(&neighbor);
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/* sortAtoms(&neighbor); */
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buildNeighborlist(&neighbor);
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}
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computeForce(&neighbor, ¶m);
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finalIntegrate(¶m);
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if(param.nstat) {
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if(thermo.nstat) {
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thermoCompute(n + 1, ¶m, &thermo);
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}
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printf("x[0] = %f\n", x[0]);
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}
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thermoCompute(-1, ¶m, &thermo);
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return EXIT_SUCCESS;
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}
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