vel scaling issues, tersoff still segfaulting!

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;
 }

diff --git a/sic.c b/sic.c
index 82b3710..fa1cb66 100644 (file)
--- a/sic.c
+++ b/sic.c
@@ -15,7 +15,6 @@
 #include "posic.h"
 
 int main(int argc,char **argv) {
-printf("%d\n",sizeof(t_atom));
        /* main moldyn structure */
        t_moldyn md;
 
@@ -86,7 +85,6 @@ printf("%d\n",sizeof(t_atom));
        /* cutoff radius */
        printf("[sic] setting cutoff radius\n");
        set_cutoff(&md,TM_S_SI);
-       //set_cutoff(&md,1.0*LC_SI);
 
        /* set (initial) dimensions of simulation volume */
        printf("[sic] setting dimensions\n");
@@ -99,8 +97,8 @@ printf("%d\n",sizeof(t_atom));
        /* create the lattice / place atoms */
        printf("[sic] creating atoms\n");
        create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
-                      ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP,
-                      //ATOM_ATTR_2BP,
+                      ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+                      //ATOM_ATTR_2BP|ATOM_ATTR_HB,
                       0,4,4,4);
 
        /* setting a nearest neighbour distance for the moldyn checks */
@@ -108,7 +106,7 @@ printf("%d\n",sizeof(t_atom));
 
        /* set temperature */
        printf("[sic] setting temperature\n");
-       set_temperature(&md,10.0);
+       set_temperature(&md,273.0);
        
        /* initial thermal fluctuations of particles */
        printf("[sic] thermal init\n");
@@ -116,12 +114,12 @@ printf("%d\n",sizeof(t_atom));
 
        /* create the simulation schedule */
        printf("[sic] adding schedule\n");
-       moldyn_add_schedule(&md,1000,1.0e-15);
+       moldyn_add_schedule(&md,100,1.0e-15);
 
        /* activate logging */
        printf("[sic] activate logging\n");
-       moldyn_set_log(&md,LOG_TOTAL_ENERGY,"saves/test-energy",10);
-       moldyn_set_log(&md,VISUAL_STEP,"saves/test-visual",10);
+       moldyn_set_log(&md,LOG_TOTAL_ENERGY,"saves/test-energy",1);
+       moldyn_set_log(&md,VISUAL_STEP,"saves/test-visual",1);
 
        /*
         * let's do the actual md algorithm now