added harmonic potntial + bugfixes + boundings

[physik/posic.git] / moldyn.c

diff --git a/moldyn.c b/moldyn.c
index 3d669d2..72a672a 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -177,6 +177,19 @@ t_3dvec get_total_p(t_atom *atom, int count) {
        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;     
+}
+
 
 /*
  *
@@ -189,6 +202,9 @@ t_3dvec get_total_p(t_atom *atom, int count) {
 int moldyn_integrate(t_moldyn *moldyn) {
 
        int i;
+       int write;
+
+       write=moldyn->write;
 
        /* calculate initial forces */
        moldyn->force(moldyn);
@@ -198,8 +214,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
                moldyn->integrate(moldyn);
 
                /* check for visualiziation */
-               // to be continued ...
-               if(!(i%1)) {
+               if(!(i%write)) {
                        visual_atoms(moldyn->visual,i*moldyn->tau,
                                     moldyn->atom,moldyn->count);
                }
@@ -233,7 +248,7 @@ int velocity_verlet(t_moldyn *moldyn) {
 
                /* 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 */
@@ -255,6 +270,72 @@ int velocity_verlet(t_moldyn *moldyn) {
  * 
  */
 
+/* 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) {