X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=blobdiff_plain;f=moldyn.c;h=aec87f66dc31fd845a73e9466de17fa95dc9e021;hb=390cbe35b27e4fb6766827a5e6b85903142e8a65;hp=08901c783452a006b638787351b735e20e2a56c3;hpb=3961d57b84198e336085fd79263fec40837066a0;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 08901c7..aec87f6 100644
--- 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);
@@ -198,10 +214,11 @@ int moldyn_integrate(t_moldyn *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;
@@ -232,7 +249,7 @@ 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 */
@@ -254,6 +271,72 @@ 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) {
@@ -321,7 +404,7 @@ int force_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);