X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=72a672ac500591dc39694549377cae6c4157d5b3;hb=45b27e01673a6cc5bebecb49c51d7f587917483e;hp=e96cdd4bd66e32632087321d07d12173024bec24;hpb=b040d775deb32173e6536464a3e2ad95a6a5bd55;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index e96cdd4..72a672a 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -9,9 +9,12 @@
 
 #include <stdio.h>
 #include <stdlib.h>
+#include <math.h>
 
 #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,
@@ -63,37 +66,351 @@ 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;
+	}
+
+	/* 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);
 	}
 
-	c=sqrt((2.0*e)/(3.0*count*K_BOLTZMANN));
+	/* 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++)
-		v3_scale(&(atom[count].v),&(atom[count].v),(1.0/c));
+		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[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;
+}
+
+double get_e_pot(t_moldyn *moldyn) {
+
+	return(moldyn->potential(moldyn));
+}
+
+double get_total_energy(t_moldyn *moldyn) {
+
+	double e;
+
+	e=get_e_kin(moldyn->atom,moldyn->count);
+	e+=get_e_pot(moldyn);
+
+	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 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;	
+}
+
+
+/*
+ *
+ * 'integration of newtons equation' - algorithms
+ *
+ */
+
+/* start the integration */
+
+int moldyn_integrate(t_moldyn *moldyn) {
+
+	int i;
+	int write;
+
+	write=moldyn->write;
+
+	/* calculate initial forces */
+	moldyn->force(moldyn);
+
+	for(i=0;i<moldyn->time_steps;i++) {
+		/* integration step */
+		moldyn->integrate(moldyn);
+
+		/* check for visualiziation */
+		if(!(i%write)) {
+			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].v),&(atom[i].v),&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
+ * 
+ */
+
+/* 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) {
+
+	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=moldyn->pot_params;
+	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=1.0/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;
+}
+
+int force_lennard_jones(t_moldyn *moldyn) {
+
+	t_lj_params *params;
+	int i,j,count;
+	t_atom *atom;
+	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++) {
+			v3_sub(&distance,&(atom[j].r),&(atom[i].r));
+			v3_per_bound(&distance,&(moldyn->dim));
+			d=v3_absolute_square(&distance);
+			if(d<=moldyn->cutoff_square) {
+				h1=1.0/d;			/* 1/r^2 */
+				d=h1*h1;			/* 1/r^4 */
+				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);
+			}
+		}
+	}
 
 	return 0;
 }