fixed (dank rolf)

[physik/posic.git] / moldyn.c

diff --git a/moldyn.c b/moldyn.c
index 6e76bc0..707fe03 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -456,8 +456,8 @@ int link_cell_init(t_moldyn *moldyn) {
        printf("initializing linked cells (%d)\n",lc->cells);
 
        for(i=0;i<lc->cells;i++)
-               //list_init(&(lc->subcell[i]),1);
-               list_init(&(lc->subcell[i]),lc->listfd);
+               list_init(&(lc->subcell[i]),1);
+               //list_init(&(lc->subcell[i]),lc->listfd);
 
        link_cell_update(moldyn);
        
@@ -478,13 +478,13 @@ int link_cell_update(t_moldyn *moldyn) {
        ny=lc->ny;
        nz=lc->nz;
 
-       for(i=0;i<nx*ny*nz;i++)
+       for(i=0;i<lc->cells;i++)
                list_destroy(&(moldyn->lc.subcell[i]));
        
        for(count=0;count<moldyn->count;count++) {
-               i=atom[count].r.x/lc->x;
-               j=atom[count].r.y/lc->y;
-               k=atom[count].r.z/lc->z;
+               i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
+               j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
+               k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
                list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
                                       &(atom[count]));
        }
@@ -510,7 +510,9 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
        count2=27;
        a=nx*ny;
 
+
        cell[0]=lc->subcell[i+j*nx+k*a];
+       printf("%d\n",i+j*nx+k*a);
        for(ci=-1;ci<=1;ci++) {
                bx=0;
                x=i+ci;
@@ -532,12 +534,17 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
                                        z=(z+nz)%nz;
                                        bz=1;
                                }
-                               if(!(x|y|z)) continue;
+                               if(!(ci|cj|ck)) continue;
+                               printf(" %d %d %d \n",x,y,z);
                                if(bx|by|bz) {
                                        cell[--count2]=lc->subcell[x+y*nx+z*a];
+                                       printf("%d\n",x+y*nx+z*a);
+                                       printf("--- %d\n",count2);
                                }
                                else {
                                        cell[count1++]=lc->subcell[x+y*nx+z*a];
+                                       printf("%d\n",x+y*nx+z*a);
+                                       printf("--- %d\n",count1);
                                }
                        }
                }
@@ -598,8 +605,6 @@ int moldyn_integrate(t_moldyn *moldyn) {
        moldyn->potential_force_function(moldyn);
 
        for(i=0;i<moldyn->time_steps;i++) {
-               /* show runs */
-               printf(".");
 
                /* neighbour list update */
                link_cell_update(moldyn);
@@ -642,9 +647,12 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
                }
                if(v) {
-                       if(!(i%v))
+                       if(!(i%v)) {
                                visual_atoms(moldyn->visual,i*moldyn->tau,
                                             moldyn->atom,moldyn->count);
+                               printf("\rsteps: %d",i);
+                               fflush(stdout);
+                       }
                }
        }
 
@@ -722,9 +730,10 @@ int harmonic_oscillator(t_moldyn *moldyn) {
        u=0.0;
        for(i=0;i<count;i++) {
                /* determine cell + neighbours */
-               ni=atom[i].r.x/lc->x;
-               nj=atom[i].r.y/lc->y;
-               nk=atom[i].r.z/lc->z;
+               ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
+               nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
+               nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
+               printf("%d %d %d\n",ni,nj,nk);
                c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
 
                /* processing cell of atom i */
@@ -818,10 +827,15 @@ int lennard_jones(t_moldyn *moldyn) {
        u=0.0;
        for(i=0;i<count;i++) {
                /* determine cell + neighbours */
-               ni=atom[i].r.x/lc->x;
-               nj=atom[i].r.y/lc->y;
-               nk=atom[i].r.z/lc->z;
+               ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
+               nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
+               nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
+                       printf("hier atom = %08x\n",&(atom[i]));
                c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
+                       printf("da atom = %08x\n",&(atom[i]));
+                       printf("da atom = %08x\n",&(moldyn->atom[i]));
+
+               printf("c = %d (%d %d %d)\n",c,ni,nj,nk);
 
                /* processing cell of atom i */
                this=&(neighbour[0]);
@@ -830,7 +844,9 @@ int lennard_jones(t_moldyn *moldyn) {
                        btom=this->current->data;
                        if(btom==&(atom[i]))
                                continue;
+               puts("foo");
                        v3_sub(&distance,&(atom[i].r),&(btom->r));
+               puts("foo");
                        d=1.0/v3_absolute_square(&distance); /* 1/r^2 */
                        h1=d*d;         /* 1/r^4 */
                        h2*=d;          /* 1/r^6 */
@@ -844,6 +860,7 @@ int lennard_jones(t_moldyn *moldyn) {
                        d*=eps;
                        v3_scale(&force,&distance,d);
                        v3_add(&(atom[i].f),&(atom[i].f),&force);
+                       printf("test!!\n");
                } while(list_next(this)!=L_NO_NEXT_ELEMENT);
 
                /* neighbours not doing boundary condition overflow */
@@ -853,6 +870,7 @@ int lennard_jones(t_moldyn *moldyn) {
                        if(this->start!=NULL) {
 
                        do {
+                               printf("in bound: %d\n",j);
                                btom=this->current->data;
                                v3_sub(&distance,&(atom[i].r),&(btom->r));
                                d=v3_absolute_square(&distance); /* r^2 */
@@ -884,6 +902,7 @@ int lennard_jones(t_moldyn *moldyn) {
                        if(this->start!=NULL) {
 
                        do {
+                               printf("out bound: %d\n",j);
                                btom=this->current->data;
                                v3_sub(&distance,&(atom[i].r),&(btom->r));
                                v3_per_bound(&distance,&(moldyn->dim));