X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=707fe032e2e51f87a13800e717f33a461f5e85b7;hb=c38fe34069adb9697683235f8b1e2311a3122e8f;hp=6e76bc0c5be072ad40f4fbe88b90fae57adb594a;hpb=177cf8b5cb5a3c59e2330327b628937540f123ac;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 6e76bc0..707fe03 100644
--- 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));