return p_total;
}
+double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
+
+ 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);
+
+ return tau;
+}
+
/*
*
int moldyn_integrate(t_moldyn *moldyn) {
int i;
+ int write;
+
+ write=moldyn->write;
/* calculate initial forces */
moldyn->force(moldyn);
moldyn->integrate(moldyn);
/* check for visualiziation */
- // to be continued ...
- if(!(i%100))
+ if(!(i%write)) {
visual_atoms(moldyn->visual,i*moldyn->tau,
moldyn->atom,moldyn->count);
+ printf("finished %d / %d\n",i,moldyn->time_steps);
+ }
}
return 0;
/* velocities */
v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
- v3_add(&(atom[i].r),&(atom[i].r),&delta);
+ v3_add(&(atom[i].v),&(atom[i].v),&delta);
}
/* forces depending on chosen potential */
*
*/
+/* harmonic oscillator potential and force */
+
+double potential_harmonic_oscillator(t_moldyn *moldyn) {
+
+ t_ho_params *params;
+ t_atom *atom;
+ int i,j;
+ int count;
+ t_3dvec distance;
+ double d,u;
+ double sc,equi_dist;
+
+ params=moldyn->pot_params;
+ atom=moldyn->atom;
+ sc=params->spring_constant;
+ equi_dist=params->equilibrium_distance;
+ count=moldyn->count;
+
+ u=0.0;
+ for(i=0;i<count;i++) {
+ for(j=0;j<i;j++) {
+ v3_sub(&distance,&(atom[i].r),&(atom[j].r));
+ d=v3_norm(&distance);
+ u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
+ }
+ }
+
+ return u;
+}
+
+int force_harmonic_oscillator(t_moldyn *moldyn) {
+
+ t_ho_params *params;
+ int i,j,count;
+ t_atom *atom;
+ t_3dvec distance;
+ t_3dvec force;
+ double d;
+ double sc,equi_dist;
+
+ atom=moldyn->atom;
+ count=moldyn->count;
+ params=moldyn->pot_params;
+ sc=params->spring_constant;
+ equi_dist=params->equilibrium_distance;
+
+ for(i=0;i<count;i++) v3_zero(&(atom[i].f));
+
+ for(i=0;i<count;i++) {
+ for(j=0;j<i;j++) {
+ v3_sub(&distance,&(atom[i].r),&(atom[j].r));
+ v3_per_bound(&distance,&(moldyn->dim));
+ d=v3_norm(&distance);
+ if(d<=moldyn->cutoff) {
+ v3_scale(&force,&distance,
+ (-sc*(1.0-(equi_dist/d))));
+ v3_add(&(atom[i].f),&(atom[i].f),&force);
+ v3_sub(&(atom[j].f),&(atom[j].f),&force);
+ }
+ }
+ }
+
+ return 0;
+}
+
+
/* lennard jones potential & force for one sort of atoms */
double potential_lennard_jones(t_moldyn *moldyn) {
h1*=h2; /* 1/r^14 */
h1*=sig12;
h2*=sig6;
- d=-12.0*h1+6.0*h2;
+ d=12.0*h1-6.0*h2;
d*=eps;
v3_scale(&force,&distance,d);
v3_add(&(atom[j].f),&(atom[j].f),&force);