X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=80f4fa1b7f8cbff28fdb05b3a6e2c4f17c78faaa;hb=4bf9958c9ed62371b6d620c7ca167bd9993d2148;hp=26f298fbb58f2488f048d04dd4fbaad550e9563e;hpb=a33fe7f5d4d7e09b5b52f5f4dadd462cf868ec2f;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 26f298f..80f4fa1 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -72,7 +72,7 @@ int set_cutoff(t_moldyn *moldyn,double cutoff) {
 }
 
 int set_temperature(t_moldyn *moldyn,double t) {
-	
+
 	moldyn->t=t;
 
 	return 0;
@@ -331,6 +331,7 @@ int scale_velocity(t_moldyn *moldyn,u8 type) {
 	int i;
 	double e,scale;
 	t_atom *atom;
+	int count;
 
 	atom=moldyn->atom;
 
@@ -339,13 +340,29 @@ int scale_velocity(t_moldyn *moldyn,u8 type) {
 	 */
 
 	e=0.0;
-	for(i=0;i<moldyn->count;i++)
-		e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
-	scale=(1.5*moldyn->count*K_BOLTZMANN*moldyn->t)/e;
+	count=0;
+	for(i=0;i<moldyn->count;i++) {
+		if(atom[i].attr&ATOM_ATTR_HB) {
+			e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+			count+=1;
+		}
+	}
+
+	/* temporary hack for e,t = 0 */
+	if(e==0.0) {
+		if(moldyn->t!=0.0)
+			thermal_init(moldyn);
+		else
+			return 0;
+	}
+
+	/* direct scaling */
+	scale=(1.5*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),scale);
+		if(atom[i].attr&ATOM_ATTR_HB)
+			v3_scale(&(atom[i].v),&(atom[i].v),scale);
 
 	return 0;
 }