X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=eb2c6068caae95cd7efac77c5dff1e7e0eb285b8;hb=3ce21f4433c04699bb6f47f0332a6f0e3c462f5e;hp=505f4960a18037b6d043ddf0d7596625660b328a;hpb=7aface2e184e527132819f17b0fa18a6e1ba4bc3;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 505f496..eb2c606 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));
@@ -251,11 +252,12 @@ 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;
 }
@@ -326,6 +328,12 @@ 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));
@@ -382,15 +390,19 @@ 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;	
 }
@@ -582,11 +594,13 @@ 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);
@@ -695,7 +709,7 @@ 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);
@@ -755,7 +769,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 		/* 2 body pair potential/force */
 		if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
-		
+	
 			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,
@@ -889,7 +903,6 @@ 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) {
@@ -933,7 +946,7 @@ 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;