vel scaling issues, tersoff still segfaulting!

[physik/posic.git] / moldyn.c

diff --git a/moldyn.c b/moldyn.c
index 26f298f..80f4fa1 100644 (file)
--- 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;
 }