X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=blobdiff_plain;ds=sidebyside;f=moldyn.c;h=707fe032e2e51f87a13800e717f33a461f5e85b7;hb=c38fe34069adb9697683235f8b1e2311a3122e8f;hp=4b580890f3eaab417494fa497130f53570130ce4;hpb=e6f456c0fa807b86e1b25996e70efcdcfe390ea5;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 4b58089..707fe03 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -35,6 +35,7 @@ int moldyn_usage(char **argv) {
 	printf("--- physics options ---\n");
 	printf("-T <temperature> [K] (%f)\n",MOLDYN_TEMP);
 	printf("-t <timestep tau> [s] (%.15f)\n",MOLDYN_TAU);
+	printf("-C <cutoff radius> [m] (%.15f)\n",MOLDYN_CUTOFF);
 	printf("-R <runs> (%d)\n",MOLDYN_RUNS);
 	printf(" -- integration algo --\n");
 	printf("  -I <number> (%d)\n",MOLDYN_INTEGRATE_DEFAULT);
@@ -98,6 +99,9 @@ int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
 				case 't':
 					moldyn->tau=atof(argv[++i]);
 					break;
+				case 'C':
+					moldyn->cutoff=atof(argv[++i]);
+					break;
 				case 'R':
 					moldyn->time_steps=atoi(argv[++i]);
 					break;
@@ -153,12 +157,12 @@ int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
 	return 0;
 }
 
-int moldyn_log_init(t_moldyn *moldyn,void *v) {
+int moldyn_log_init(t_moldyn *moldyn) {
 
 	moldyn->lvstat=0;
 	t_visual *vis;
 
-	vis=v;
+	vis=&(moldyn->vis);
 
 	if(moldyn->ewrite) {
 		moldyn->efd=open(moldyn->efb,O_WRONLY|O_CREAT|O_TRUNC);
@@ -204,7 +208,7 @@ int moldyn_log_init(t_moldyn *moldyn,void *v) {
 	return 0;
 }
 
-int moldyn_shutdown(t_moldyn *moldyn) {
+int moldyn_log_shutdown(t_moldyn *moldyn) {
 
 	if(moldyn->efd) close(moldyn->efd);
 	if(moldyn->mfd) close(moldyn->efd);
@@ -214,6 +218,33 @@ int moldyn_shutdown(t_moldyn *moldyn) {
 	return 0;
 }
 
+int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
+
+	int ret;
+
+	ret=moldyn_parse_argv(moldyn,argc,argv);
+	if(ret<0) return ret;
+
+	ret=moldyn_log_init(moldyn);
+	if(ret<0) return ret;
+
+	rand_init(&(moldyn->random),NULL,1);
+	moldyn->random.status|=RAND_STAT_VERBOSE;
+
+	moldyn->status=0;
+
+	return 0;
+}
+
+int moldyn_shutdown(t_moldyn *moldyn) {
+
+	moldyn_log_shutdown(moldyn);
+	rand_close(&(moldyn->random));
+	free(moldyn->atom);
+
+	return 0;
+}
+
 int create_lattice(unsigned char type,int element,double mass,double lc,
                    int a,int b,int c,t_atom **atom) {
 
@@ -270,7 +301,7 @@ int destroy_lattice(t_atom *atom) {
 	return 0;
 }
 
-int thermal_init(t_moldyn *moldyn,t_random *random) {
+int thermal_init(t_moldyn *moldyn) {
 
 	/*
 	 * - gaussian distribution of velocities
@@ -282,8 +313,10 @@ int thermal_init(t_moldyn *moldyn,t_random *random) {
 	double v,sigma;
 	t_3dvec p_total,delta;
 	t_atom *atom;
+	t_random *random;
 
 	atom=moldyn->atom;
+	random=&(moldyn->random);
 
 	/* gaussian distribution of velocities */
 	v3_zero(&p_total);
@@ -402,9 +435,13 @@ double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
 int link_cell_init(t_moldyn *moldyn) {
 
 	t_linkcell *lc;
+	int i;
 
 	lc=&(moldyn->lc);
 
+	/* list log fd */
+	lc->listfd=open("/dev/null",O_WRONLY);
+
 	/* partitioning the md cell */
 	lc->nx=moldyn->dim.x/moldyn->cutoff;
 	lc->x=moldyn->dim.x/lc->nx;
@@ -413,7 +450,14 @@ int link_cell_init(t_moldyn *moldyn) {
 	lc->nz=moldyn->dim.z/moldyn->cutoff;
 	lc->z=moldyn->dim.z/lc->nz;
 
-	lc->subcell=malloc(lc->nx*lc->ny*lc->nz*sizeof(t_list));
+	lc->cells=lc->nx*lc->ny*lc->nz;
+	lc->subcell=malloc(lc->cells*sizeof(t_list));
+
+	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);
 
  	link_cell_update(moldyn);
 	
@@ -434,13 +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]));
 	}
@@ -461,12 +505,14 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 	lc=&(moldyn->lc);
 	nx=lc->nx;
 	ny=lc->ny;
-	nx=lc->nz;
+	nz=lc->nz;
 	count1=1;
 	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;
@@ -488,12 +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);
 				}
 			}
 		}
@@ -512,6 +563,8 @@ int link_cell_shutdown(t_moldyn *moldyn) {
 	for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
 		list_shutdown(&(moldyn->lc.subcell[i]));
 
+	if(lc->listfd) close(lc->listfd);
+
 	return 0;
 }
 
@@ -548,15 +601,10 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	moldyn->tau_square=moldyn->tau*moldyn->tau;
 	moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 
-	/* create the neighbour list */
-	link_cell_update(moldyn);
-
 	/* calculate initial forces */
 	moldyn->potential_force_function(moldyn);
 
 	for(i=0;i<moldyn->time_steps;i++) {
-		/* show runs */
-		printf(".");
 
 		/* neighbour list update */
 		link_cell_update(moldyn);
@@ -599,9 +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);
+			}
 		}
 	}
 
@@ -679,9 +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 */
@@ -775,10 +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]);
@@ -787,7 +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 */
@@ -801,6 +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 */
@@ -810,6 +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 */
@@ -841,6 +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));