fixed create_lattice routine

[physik/posic.git] / moldyn.c

diff --git a/moldyn.c b/moldyn.c
index 2f274c2..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;
        }
 
@@ -252,11 +251,12 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
        moldyn->atom=ptr;
 
        atom=moldyn->atom;
-       atom->r=*r;
-       atom->v=*v;
-       atom->element=element;
-       atom->bnum=bnum;
-       atom->attr=attr;
+       atom[count-1].r=*r;
+       atom[count-1].v=*v;
+       atom[count-1].element=element;
+       atom[count-1].mass=mass;
+       atom[count-1].bnum=bnum;
+       atom[count-1].attr=attr;
 
        return 0;
 }
@@ -327,6 +327,12 @@ 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));
@@ -587,11 +593,13 @@ int moldyn_integrate(t_moldyn *moldyn) {
        unsigned int e,m,s,v;
        t_3dvec p;
        t_moldyn_schedule *schedule;
+       t_atom *atom;
 
        int fd;
        char fb[128];
 
        schedule=&(moldyn->schedule);
+       atom=moldyn->atom;
 
        /* initialize linked cell method */
        link_cell_init(moldyn);
@@ -700,7 +708,7 @@ int velocity_verlet(t_moldyn *moldyn) {
                v3_add(&(atom[i].r),&(atom[i].r),&delta);
                v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
                v3_add(&(atom[i].r),&(atom[i].r),&delta);
-               v3_per_bound(&(atom[i].r),&(moldyn->dim));
+               check_per_bound(moldyn,&(atom[i].r));
 
                /* velocities */
                v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
@@ -749,7 +757,6 @@ int potential_force_calc(t_moldyn *moldyn) {
        /* reset energy */
        moldyn->energy=0.0;
 
-printf("DEBUG: count = %d\n",count);
        for(i=0;i<count;i++) {
        
                /* reset force */
@@ -762,7 +769,6 @@ printf("DEBUG: count = %d\n",count);
                /* 2 body pair potential/force */
                if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
        
-printf("DEBUG: processing atom %d\n",i);
                        link_cell_neighbour_index(moldyn,
                                (atom[i].r.x+moldyn->dim.x/2)/lc->x,
                                (atom[i].r.y+moldyn->dim.y/2)/lc->y,
@@ -772,7 +778,6 @@ printf("DEBUG: processing atom %d\n",i);
                        countn=lc->countn;
                        dnlc=lc->dnlc;
 
-printf("DEBUG: countn = %d - dnslc = %d\n",countn,dnlc);
                        for(j=0;j<countn;j++) {
 
                                this=&(neighbour[j]);
@@ -791,7 +796,6 @@ printf("DEBUG: countn = %d - dnslc = %d\n",countn,dnlc);
 
                                        if((btom->attr&ATOM_ATTR_2BP)&
                                           (atom[i].attr&ATOM_ATTR_2BP))
-printf("DEBUG: calling func2b\n");
                                                moldyn->func2b(moldyn,
                                                               &(atom[i]),
                                                               btom,
@@ -898,7 +902,6 @@ int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
        v3_sub(&distance,&(ai->r),&(aj->r));
        
-       v3_per_bound(&distance,&(moldyn->dim));
        if(bc) check_per_bound(moldyn,&distance);
        d=v3_norm(&distance);
        if(d<=moldyn->cutoff) {
@@ -942,7 +945,7 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
                d=+h1-h2;
                d*=eps;
                v3_scale(&force,&distance,d);
-               v3_add(&(ai->f),&(aj->f),&force);
+               v3_add(&(ai->f),&(ai->f),&force);
        }
 
        return 0;