#include "math/math.h"
#include "init/init.h"
#include "random/random.h"
+#include "visual/visual.h"
int create_lattice(unsigned char type,int element,double mass,double lc,
}
+/*
+ *
+ * 'integration of newtons equation' - algorithms
+ *
+ */
+
+/* start the integration */
+
+int moldyn_integrate(t_moldyn *moldyn) {
+
+ int i;
+
+ /* calculate initial forces */
+ moldyn->force(moldyn);
+
+ for(i=0;i<moldyn->time_steps;i++) {
+ /* integration step */
+ moldyn->integrate(moldyn);
+
+ /* check for visualiziation */
+ // to be continued ...
+ if(!(i%100))
+ visual_atoms(moldyn->visual,i*moldyn->tau,
+ moldyn->atom,moldyn->count);
+ }
+
+ return 0;
+}
+
+/* velocity verlet */
+
+int velocity_verlet(t_moldyn *moldyn) {
+
+ int i,count;
+ double tau,tau_square;
+ t_3dvec delta;
+ t_atom *atom;
+
+ atom=moldyn->atom;
+ count=moldyn->count;
+ tau=moldyn->tau;
+
+ tau_square=tau*tau;
+
+ for(i=0;i<count;i++) {
+ /* new positions */
+ v3_scale(&delta,&(atom[i].v),tau);
+ 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));
+
+ /* velocities */
+ v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
+ v3_add(&(atom[i].r),&(atom[i].r),&delta);
+ }
+
+ /* forces depending on chosen potential */
+ moldyn->force(moldyn);
+
+ for(i=0;i<count;i++) {
+ /* again velocities */
+ v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
+ v3_add(&(atom[i].v),&(atom[i].v),&delta);
+ }
+
+ return 0;
+}
+
+
/*
*
* potentials & corresponding forces
t_3dvec distance;
t_3dvec force;
double d,h1,h2;
+ double eps,sig6,sig12;
atom=moldyn->atom;
count=moldyn->count;
params=moldyn->pot_params;
+ eps=params->epsilon;
+ sig6=params->sigma6;
+ sig12=params->sigma12;
+
+ for(i=0;i<count;i++) v3_zero(&(atom[i].f));
for(i=0;i<count;i++) {
for(j=0;j<i;j++) {
h2=d*d; /* 1/r^8 */
h1*=d; /* 1/r^6 */
h1*=h2; /* 1/r^14 */
+ h1*=sig12;
+ h2*=sig6;
+ d=-12.0*h1+6.0*h2;
+ d*=eps;
+ v3_scale(&force,&distance,d);
+ v3_add(&(atom[j].f),&(atom[j].f),&force);
+ v3_sub(&(atom[i].f),&(atom[i].f),&force);
}
}
}