X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=9d782d657fbc89c5ab800ed7705de48c87739a1e;hb=76f807f6dda48b6d606309cea79005e612e4f665;hp=2f274c2da8fb7fcaeec9344f21bec718cb8585a8;hpb=8e98c9cbbddf1c9c852874f956b0dbe2f9a4a922;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 2f274c2..9d782d6 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -41,9 +41,9 @@ int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 
 int moldyn_shutdown(t_moldyn *moldyn) {
 
+	printf("[moldyn] shutdown\n");
 	moldyn_log_shutdown(moldyn);
 	link_cell_shutdown(moldyn);
-	moldyn_log_shutdown(moldyn);
 	rand_close(&(moldyn->random));
 	free(moldyn->atom);
 
@@ -171,9 +171,10 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
 
 int moldyn_log_shutdown(t_moldyn *moldyn) {
 
+	printf("[moldyn] log shutdown\n");
 	if(moldyn->efd) close(moldyn->efd);
 	if(moldyn->mfd) close(moldyn->mfd);
-	if(moldyn->visual) visual_tini(moldyn->visual);
+	if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
 
 	return 0;
 }
@@ -252,11 +253,12 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
 	moldyn->atom=ptr;
 
 	atom=moldyn->atom;
-	atom->r=*r;
-	atom->v=*v;
-	atom->element=element;
-	atom->bnum=bnum;
-	atom->attr=attr;
+	atom[count-1].r=*r;
+	atom[count-1].v=*v;
+	atom[count-1].element=element;
+	atom[count-1].mass=mass;
+	atom[count-1].bnum=bnum;
+	atom[count-1].attr=attr;
 
 	return 0;
 }
@@ -327,6 +329,12 @@ int scale_velocity(t_moldyn *moldyn) {
 	/*
 	 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 	 */
+
+	if(moldyn->t==0.0) {
+		printf("[moldyn] no velocity scaling for T = 0 K\n");
+		return -1;
+	}
+
 	e=0.0;
 	for(i=0;i<moldyn->count;i++)
 		e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
@@ -587,11 +595,13 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	unsigned int e,m,s,v;
 	t_3dvec p;
 	t_moldyn_schedule *schedule;
+	t_atom *atom;
 
 	int fd;
 	char fb[128];
 
 	schedule=&(moldyn->schedule);
+	atom=moldyn->atom;
 
 	/* initialize linked cell method */
 	link_cell_init(moldyn);
@@ -700,7 +710,7 @@ int velocity_verlet(t_moldyn *moldyn) {
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
 		v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
-		v3_per_bound(&(atom[i].r),&(moldyn->dim));
+		check_per_bound(moldyn,&(atom[i].r));
 
 		/* velocities */
 		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
@@ -749,7 +759,6 @@ 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 */
@@ -762,7 +771,6 @@ printf("DEBUG: count = %d\n",count);
 		/* 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,
@@ -772,7 +780,6 @@ printf("DEBUG: processing atom %d\n",i);
 			countn=lc->countn;
 			dnlc=lc->dnlc;
 
-printf("DEBUG: countn = %d - dnslc = %d\n",countn,dnlc);
 			for(j=0;j<countn;j++) {
 
 				this=&(neighbour[j]);
@@ -791,7 +798,6 @@ printf("DEBUG: countn = %d - dnslc = %d\n",countn,dnlc);
 
 					if((btom->attr&ATOM_ATTR_2BP)&
 					   (atom[i].attr&ATOM_ATTR_2BP))
-printf("DEBUG: calling func2b\n");
 						moldyn->func2b(moldyn,
 						               &(atom[i]),
 						               btom,
@@ -898,7 +904,6 @@ int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
 	v3_sub(&distance,&(ai->r),&(aj->r));
 	
-	v3_per_bound(&distance,&(moldyn->dim));
 	if(bc) check_per_bound(moldyn,&distance);
 	d=v3_norm(&distance);
 	if(d<=moldyn->cutoff) {
@@ -942,7 +947,7 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 		d=+h1-h2;
 		d*=eps;
 		v3_scale(&force,&distance,d);
-		v3_add(&(ai->f),&(aj->f),&force);
+		v3_add(&(ai->f),&(ai->f),&force);
 	}
 
 	return 0;