fixed create_lattice routine

[physik/posic.git] / moldyn.c

diff --git a/moldyn.c b/moldyn.c
index a978541..515a273 100644 (file)
--- 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);
 
@@ -171,9 +171,10 @@ 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 +185,15 @@ 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 +202,10 @@ 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);
@@ -224,10 +223,10 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
        moldyn->count=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;
        }
 
@@ -618,10 +617,6 @@ 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.
-
        /* zero absolute time */
        moldyn->time=0.0;