#include <stdio.h>
#include <stdlib.h>
+#include <math.h>
#include "math/math.h"
#include "init/init.h"
+#include "random/random.h"
int create_lattice(unsigned char type,int element,double mass,double lc,
return ret;
}
-int thermal_init(t_atom *atom,int count,double t) {
+int destroy_lattice(t_atom *atom) {
+
+ if(atom) free(atom);
+
+ return 0;
+}
+
+int thermal_init(t_atom *atom,t_random *random,int count,double t) {
/*
* - gaussian distribution of velocities
+ * - zero total momentum
* - velocity scaling (E = 3/2 N k T), E: kinetic energy
*/
int i;
- double e,c,v;
-
- e=.0;
+ double v,sigma;
+ t_3dvec p_total,delta;
+ /* gaussian distribution of velocities */
+ v3_zero(&p_total);
for(i=0;i<count;i++) {
+ sigma=sqrt(2.0*K_BOLTZMANN*t/atom[i].mass);
/* x direction */
- v=gauss_rand();
- atom[count].v.x=v;
- e+=0.5*atom[count].mass*v*v;
+ v=sigma*rand_get_gauss(random);
+ atom[i].v.x=v;
+ p_total.x+=atom[i].mass*v;
/* y direction */
- v=gauss_rand();
- atom[count].v.y=v;
- e+=0.5*atom[count].mass*v*v;
+ v=sigma*rand_get_gauss(random);
+ atom[i].v.y=v;
+ p_total.y+=atom[i].mass*v;
/* z direction */
- v=gauss_rand();
- atom[count].v.z=v;
- e+=0.5*atom[count].mass*v*v;
+ v=sigma*rand_get_gauss(random);
+ atom[i].v.z=v;
+ p_total.z+=atom[i].mass*v;
}
- c=sqrt((2.0*e)/(3.0*count*K_BOLTZMANN));
+ /* zero total momentum */
+ v3_scale(&p_total,&p_total,1.0/count);
+ for(i=0;i<count;i++) {
+ v3_scale(&delta,&p_total,1.0/atom[i].mass);
+ v3_sub(&(atom[i].v),&(atom[i].v),&delta);
+ }
+
+ /* velocity scaling */
+ scale_velocity(atom,count,t);
+
+ return 0;
+}
+
+int scale_velocity(t_atom *atom,int count,double t) {
+
+ int i;
+ double e,c;
+ /*
+ * - velocity scaling (E = 3/2 N k T), E: kinetic energy
+ */
+ e=0.0;
+ for(i=0;i<count;i++)
+ e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+ c=sqrt((2.0*e)/(3.0*count*K_BOLTZMANN*t));
for(i=0;i<count;i++)
- v3_scale(&(atom[count].v),&(atom[count].v),(1.0/c));
+ v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
return 0;
}
+double get_e_kin(t_atom *atom,int count) {
+
+ int i;
+ double e;
+
+ e=0.0;
+
+ for(i=0;i<count;i++) {
+ e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+ }
+
+ return e;
+}
+
+t_3dvec get_total_p(t_atom *atom, int count) {
+
+ t_3dvec p,p_total;
+ int i;
+
+ v3_zero(&p_total);
+ for(i=0;i<count;i++) {
+ v3_scale(&p,&(atom[i].v),atom[i].mass);
+ v3_add(&p_total,&p_total,&p);
+ }
+
+ return p_total;
+}
+
+double potential_lennard_jones_2(t_moldyn *moldyn,void *ptr) {
+
+ t_lj_params *params;
+ t_atom *atom;
+ int i,j;
+ int count;
+ t_3dvec distance;
+ double d,help;
+ double u;
+ double eps,sig6,sig12;
+
+ params=ptr;
+ atom=moldyn->atom;
+ count=moldyn->count;
+ eps=params->epsilon;
+ sig6=params->sigma6;
+ sig12=params->sigma12;
+
+ u=0.0;
+ for(i=0;i<count;i++) {
+ for(j=0;j<i;j++) {
+ v3_sub(&distance,&(atom[j].r),&(atom[i].r));
+ d=v3_absolute_square(&distance); /* 1/r^2 */
+ help=d*d; /* 1/r^4 */
+ help*=d; /* 1/r^6 */
+ d=help*help; /* 1/r^12 */
+ u+=eps*(sig12*d-sig6*help);
+ }
+ }
+
+ return u;
+}
+
+