int moldyn_shutdown(t_moldyn *moldyn) {
+ moldyn_log_shutdown(moldyn);
link_cell_shutdown(moldyn);
moldyn_log_shutdown(moldyn);
rand_close(&(moldyn->random));
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;
}
/*
* - 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));
return p_total;
}
-double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
+double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
double tau;
- tau=0.05*nn_dist/(sqrt(3.0*K_BOLTZMANN*t/moldyn->atom[0].mass));
- tau*=1.0E-9;
- if(tau<moldyn->tau)
- printf("[moldyn] warning: time step (%f > %.15f)\n",
- moldyn->tau,tau);
+ /* nn_dist is the nearest neighbour distance */
+
+ if(moldyn->t==5.0) {
+ printf("[moldyn] i do not estimate timesteps below %f K!\n",
+ MOLDYN_CRITICAL_EST_TEMP);
+ return 23.42;
+ }
+
+ tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
return tau;
}
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);
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);
/* 2 body pair potential/force */
if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
-
+
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,
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) {
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;