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);
return 0;
}
+int set_nn_dist(t_moldyn *moldyn,double dist) {
+
+ moldyn->nnd=dist;
+
+ return 0;
+}
+
int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
if(x)
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;
}
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;
}
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);
}
moldyn->count=count;
+ printf("[moldyn] created lattice with %d atoms\n",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;
}
}
/* velocity scaling */
- scale_velocity(moldyn);
+ scale_velocity(moldyn,VSCALE_INIT_EQUI);
return 0;
}
-int scale_velocity(t_moldyn *moldyn) {
+int scale_velocity(t_moldyn *moldyn,u8 type) {
int i;
- double e,c;
+ double e,scale;
t_atom *atom;
atom=moldyn->atom;
* - 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));
- c=sqrt((2.0*e)/(3.0*moldyn->count*K_BOLTZMANN*moldyn->t));
+ scale=(1.5*moldyn->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),(1.0/c));
+ v3_scale(&(atom[i].v),&(atom[i].v),scale);
return 0;
}
t_3dvec p;
t_moldyn_schedule *schedule;
t_atom *atom;
-
int fd;
char fb[128];
+ double ds;
schedule=&(moldyn->schedule);
atom=moldyn->atom;
/* 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.
+ /* do some checks before we actually start calculating bullshit */
+ if(moldyn->cutoff>0.5*moldyn->dim.x)
+ printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
+ if(moldyn->cutoff>0.5*moldyn->dim.y)
+ printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
+ if(moldyn->cutoff>0.5*moldyn->dim.z)
+ printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
+ ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
+ if(ds>0.05*moldyn->nnd)
+ printf("[moldyn] warning: forces too high / tau too small!\n");
/* zero absolute time */
moldyn->time=0.0;