X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=2f274c2da8fb7fcaeec9344f21bec718cb8585a8;hb=8e98c9cbbddf1c9c852874f956b0dbe2f9a4a922;hp=00a9ed9d48d1e24ada50149b06a02284a9b05a1b;hpb=a114a486ccca019135a8cb229545d0e203b61a5b;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 00a9ed9..2f274c2 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -41,6 +41,7 @@ int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 
 int moldyn_shutdown(t_moldyn *moldyn) {
 
+	moldyn_log_shutdown(moldyn);
 	link_cell_shutdown(moldyn);
 	moldyn_log_shutdown(moldyn);
 	rand_close(&(moldyn->random));
@@ -156,7 +157,7 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
 			strncpy(moldyn->sfb,fb,63);
 			break;
 		case VISUAL_STEP:
-			moldyn->mwrite=timer;
+			moldyn->vwrite=timer;
 			strncpy(moldyn->vfb,fb,63);
 			visual_init(&(moldyn->vis),fb);
 			break;
@@ -234,7 +235,7 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 }
 
 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
-             t_3dvec r,t_3dvec v) {
+             t_3dvec *r,t_3dvec *v) {
 
 	t_atom *atom;
 	void *ptr;
@@ -248,10 +249,11 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
 		perror("[moldyn] realloc (add atom)");
 		return -1;
 	}
-	
-	atom=ptr;
-	atom->r=r;
-	atom->v=v;
+	moldyn->atom=ptr;
+
+	atom=moldyn->atom;
+	atom->r=*r;
+	atom->v=*v;
 	atom->element=element;
 	atom->bnum=bnum;
 	atom->attr=attr;
@@ -381,15 +383,19 @@ t_3dvec get_total_p(t_moldyn *moldyn) {
 	return p_total;
 }
 
-double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
+double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 
 	double tau;
 
-	tau=0.05*nn_dist/(sqrt(3.0*K_BOLTZMANN*t/moldyn->atom[0].mass));
-	tau*=1.0E-9;
-	if(tau<moldyn->tau)
-		printf("[moldyn] warning: time step  (%f > %.15f)\n",
-		       moldyn->tau,tau);
+	/* nn_dist is the nearest neighbour distance */
+
+	if(moldyn->t==5.0) {
+		printf("[moldyn] i do not estimate timesteps below %f K!\n",
+		       MOLDYN_CRITICAL_EST_TEMP);
+		return 23.42;
+	}
+
+	tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
 
 	return tau;	
 }
@@ -404,6 +410,9 @@ int link_cell_init(t_moldyn *moldyn) {
 
 	t_linkcell *lc;
 	int i;
+	int fd;
+
+	fd=open("/dev/null",O_WRONLY);
 
 	lc=&(moldyn->lc);
 
@@ -418,10 +427,11 @@ int link_cell_init(t_moldyn *moldyn) {
 	lc->cells=lc->nx*lc->ny*lc->nz;
 	lc->subcell=malloc(lc->cells*sizeof(t_list));
 
-	printf("initializing linked cells (%d)\n",lc->cells);
+	printf("[moldyn] 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]),1);
+		list_init(&(lc->subcell[i]),fd);
 
  	link_cell_update(moldyn);
 	
@@ -541,6 +551,7 @@ int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 		perror("[moldyn] realloc (runs)");
 		return -1;
 	}
+	moldyn->schedule.runs=ptr;
 	moldyn->schedule.runs[count-1]=runs;
 
 	ptr=realloc(schedule->tau,count*sizeof(double));
@@ -548,6 +559,7 @@ int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 		perror("[moldyn] realloc (tau)");
 		return -1;
 	}
+	moldyn->schedule.tau=ptr;
 	moldyn->schedule.tau[count-1]=tau;
 
 	return 0;
@@ -590,11 +602,6 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	s=moldyn->swrite;
 	v=moldyn->vwrite;
 
-	if(!(moldyn->lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
-		printf("[moldyn] warning, lv system not initialized\n");
-		return -1;
-	}
-
 	/* sqaure of some variables */
 	moldyn->tau_square=moldyn->tau*moldyn->tau;
 	moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
@@ -655,18 +662,21 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		}
 		if(v) {
 			if(!(i%v)) {
-				visual_atoms(moldyn->visual,i*moldyn->tau,
+				visual_atoms(&(moldyn->vis),moldyn->time,
 				             moldyn->atom,moldyn->count);
-				printf("\rsteps: %d",i);
+				printf("\rsched: %d, steps: %d",sched,i);
 				fflush(stdout);
 			}
 		}
+
 	}
 
 		/* check for hooks */
 		if(schedule->hook)
 			schedule->hook(moldyn,schedule->hook_params);
 
+	}
+
 	return 0;
 }
 
@@ -698,15 +708,11 @@ int velocity_verlet(t_moldyn *moldyn) {
 	}
 
 	/* neighbour list update */
-printf("list update ...\n");
 	link_cell_update(moldyn);
-printf("done\n");
 
 	/* forces depending on chosen potential */
-printf("calc potential/force ...\n");
 	potential_force_calc(moldyn);
 	//moldyn->potential_force_function(moldyn);
-printf("done\n");
 
 	for(i=0;i<count;i++) {
 		/* again velocities */
@@ -743,6 +749,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 	/* reset energy */
 	moldyn->energy=0.0;
 
+printf("DEBUG: count = %d\n",count);
 	for(i=0;i<count;i++) {
 	
 		/* reset force */
@@ -754,7 +761,8 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 		/* 2 body pair potential/force */
 		if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
-		
+	
+printf("DEBUG: processing atom %d\n",i);
 			link_cell_neighbour_index(moldyn,
 				(atom[i].r.x+moldyn->dim.x/2)/lc->x,
 				(atom[i].r.y+moldyn->dim.y/2)/lc->y,
@@ -764,6 +772,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 			countn=lc->countn;
 			dnlc=lc->dnlc;
 
+printf("DEBUG: countn = %d - dnslc = %d\n",countn,dnlc);
 			for(j=0;j<countn;j++) {
 
 				this=&(neighbour[j]);
@@ -782,6 +791,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 					if((btom->attr&ATOM_ATTR_2BP)&
 					   (atom[i].attr&ATOM_ATTR_2BP))
+printf("DEBUG: calling func2b\n");
 						moldyn->func2b(moldyn,
 						               &(atom[i]),
 						               btom,