X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=d52fcd3868c2481e70cbc804b5a9cdf92542708d;hb=180ff86ae35ca0ea6ee857e92e56120e65315d17;hp=a9785413ab55eec8ef5c4f6ba46e7a6f1f8b3726;hpb=56fe12b9eabe0cfa493e2f1b1d0d7d219ae8705b;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index a978541..d52fcd3 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);
 
@@ -93,6 +93,13 @@ int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
 	return 0;
 }
 
+int set_nn_dist(t_moldyn *moldyn,double dist) {
+
+	moldyn->nnd=dist;
+
+	return 0;
+}
+
 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 
 	if(x)
@@ -171,9 +178,10 @@ 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;
 }
@@ -184,17 +192,15 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	int count;
 	int ret;
 	t_3dvec origin;
-	t_atom *atom;
 
 	count=a*b*c;
-	atom=moldyn->atom;
 
 	if(type==FCC) count*=4;
 
 	if(type==DIAMOND) count*=8;
 
-	atom=malloc(count*sizeof(t_atom));
-	if(atom==NULL) {
+	moldyn->atom=malloc(count*sizeof(t_atom));
+	if(moldyn->atom==NULL) {
 		perror("malloc (atoms)");
 		return -1;
 	}
@@ -203,10 +209,10 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 
 	switch(type) {
 		case FCC:
-			ret=fcc_init(a,b,c,lc,atom,&origin);
+			ret=fcc_init(a,b,c,lc,moldyn->atom,&origin);
 			break;
 		case DIAMOND:
-			ret=diamond_init(a,b,c,lc,atom,&origin);
+			ret=diamond_init(a,b,c,lc,moldyn->atom,&origin);
 			break;
 		default:
 			printf("unknown lattice type (%02x)\n",type);
@@ -222,12 +228,13 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	}
 
 	moldyn->count=count;
+	printf("[moldyn] created lattice with %d atoms\n",count);
 
 	while(count) {
-		atom[count-1].element=element;
-		atom[count-1].mass=mass;
-		atom[count-1].attr=attr;
-		atom[count-1].bnum=bnum;
+		moldyn->atom[count-1].element=element;
+		moldyn->atom[count-1].mass=mass;
+		moldyn->atom[count-1].attr=attr;
+		moldyn->atom[count-1].bnum=bnum;
 		count-=1;
 	}
 
@@ -312,15 +319,15 @@ int thermal_init(t_moldyn *moldyn) {
 	}
 
 	/* velocity scaling */
-	scale_velocity(moldyn);
+	scale_velocity(moldyn,VSCALE_INIT_EQUI);
 
 	return 0;
 }
 
-int scale_velocity(t_moldyn *moldyn) {
+int scale_velocity(t_moldyn *moldyn,u8 type) {
 
 	int i;
-	double e,c;
+	double e,scale;
 	t_atom *atom;
 
 	atom=moldyn->atom;
@@ -329,17 +336,14 @@ 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));
-	c=sqrt((2.0*e)/(3.0*moldyn->count*K_BOLTZMANN*moldyn->t));
+	scale=(1.5*moldyn->count*K_BOLTZMANN*moldyn->t)/e;
+	if(type&VSCALE_INIT_EQUI) scale*=2.0; /* equipartition theorem */
+	scale=sqrt(scale);
 	for(i=0;i<moldyn->count;i++)
-		v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
+		v3_scale(&(atom[i].v),&(atom[i].v),scale);
 
 	return 0;
 }
@@ -595,9 +599,9 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	t_3dvec p;
 	t_moldyn_schedule *schedule;
 	t_atom *atom;
-
 	int fd;
 	char fb[128];
+	double ds;
 
 	schedule=&(moldyn->schedule);
 	atom=moldyn->atom;
@@ -618,9 +622,16 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	/* calculate initial forces */
 	potential_force_calc(moldyn);
 
-	/* accuracy check */
-	ds=0.5*moldyn->tau_square*v3_norm(&(atom[0].f))/atom[0].mass;
-	if(ds>moldyn->lc.
+	/* do some checks before we actually start calculating bullshit */
+	if(moldyn->cutoff>0.5*moldyn->dim.x)
+		printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
+	if(moldyn->cutoff>0.5*moldyn->dim.y)
+		printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
+	if(moldyn->cutoff>0.5*moldyn->dim.z)
+		printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
+	ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
+	if(ds>0.05*moldyn->nnd)
+		printf("[moldyn] warning: forces too high / tau too small!\n");
 
 	/* zero absolute time */
 	moldyn->time=0.0;