X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=blobdiff_plain;f=moldyn.c;h=82749b2f10abf978c9636e213585e21c8393741a;hb=85abe46fecc79a3d7885ff6124186b2be2ca96ac;hp=b507d65354dabcf690628bc8bc31846962542fe3;hpb=3ffe2a08e25fc091b6241885055450009267e2d8;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index b507d65..82749b2 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -87,25 +87,26 @@ int thermal_init(t_atom *atom,t_random *random,int count,double t) {
 	/* gaussian distribution of velocities */
 	v3_zero(&p_total);
 	for(i=0;i<count;i++) {
-		sigma=sqrt(2.0*K_BOLTZMANN*t/atom[count].mass);
+		sigma=sqrt(2.0*K_BOLTZMANN*t/atom[i].mass);
 		/* x direction */
 		v=sigma*rand_get_gauss(random);
-		atom[count].v.x=v;
-		p_total.x+=atom[count].mass*v;
+		atom[i].v.x=v;
+		p_total.x+=atom[i].mass*v;
 		/* y direction */
 		v=sigma*rand_get_gauss(random);
-		atom[count].v.y=v;
-		p_total.x+=atom[count].mass*v;
+		atom[i].v.y=v;
+		p_total.y+=atom[i].mass*v;
 		/* z direction */
 		v=sigma*rand_get_gauss(random);
-		atom[count].v.z=v;
-		p_total.x+=atom[count].mass*v;
+		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[count].mass);
-		v3_sub(&(atom[count].v),&(atom[count].v),&delta);
+		v3_scale(&delta,&p_total,1.0/atom[i].mass);
+		v3_sub(&(atom[i].v),&(atom[i].v),&delta);
 	}
 
 	/* velocity scaling */
@@ -124,10 +125,10 @@ int scale_velocity(t_atom *atom,int count,double t) {
 	 */
 	e=0.0;
 	for(i=0;i<count;i++)
-		e+=0.5*atom[count].mass*v3_absolute_square(&(atom[count].v));
+		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;
 }
@@ -139,9 +140,112 @@ double get_e_kin(t_atom *atom,int count) {
 
 	e=0.0;
 
-	for(i=0;i<count;i++)
-		e+=0.5*atom[count].mass*v3_absolute_square(&(atom[count].v));
+	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;
+}
+
+
+/*
+ *
+ * potentials & corresponding forces
+ * 
+ */
+
+/* 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;
+
+	atom=moldyn->atom;	
+	count=moldyn->count;
+	params=moldyn->pot_params;
+
+	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 */
+			}
+		}
+	}
+
+	return 0;
+}
+