From 0d71b08d4382b23b8217342caf138cfce36226cc Mon Sep 17 00:00:00 2001
From: hackbard <hackbard>
Date: Fri, 17 Nov 2006 10:19:50 +0000
Subject: [PATCH] began rewrite ...

---
 moldyn.c | 24 ++++++++++++++++++------
 moldyn.h | 47 +++++++++++++++++++++++++++++++----------------
 2 files changed, 49 insertions(+), 22 deletions(-)

diff --git a/moldyn.c b/moldyn.c
index ad0f9a3..f92ce55 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -481,7 +481,7 @@ int link_cell_update(t_moldyn *moldyn) {
 	for(i=0;i<lc->cells;i++)
 		list_destroy(&(moldyn->lc.subcell[i]));
 	
-	for(count=0;count<moldyn->count;count++) {
+	for(count=0;count<moedyn->count;count++) {
 		i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
 		j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
 		k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
@@ -995,12 +995,16 @@ int tersoff(t_moldyn *moldyn) {
 
 			/* 2 body stuff */
 
+			/* we need: f_c, df_c, f_r, df_r */
+
 			v3_sub(&dist_ij,btom,&(atom[i]));
 			d_ij=v3_norm(&dist_ij);
 			if(d_ij<=S) {
 
-				S=;
-				R=;
+				/* determine the tersoff parameters */
+				if(atom[i].element!=btom->element) {
+				S=sqrt(TERSOFF_S[e1]*TERSOFF_S[e2]);
+				R=R_m;
 				A=;
 				lambda=;
 				B=;
@@ -1010,8 +1014,10 @@ int tersoff(t_moldyn *moldyn) {
 				betaN=;
 
 				if(d_ij<=R) {
-					f_c=1.0;
-					df_c=0.0;
+					df_r=-lambda*A*exp(-lambda*d_ij)/d_ij;
+					v3_scale(&force,&dist_ij,df_r);
+					v3_add(&(atom[i].f),&(atom[i].f),
+						&force);
 				}
 				else {
 					s_r=S-R;
@@ -1019,7 +1025,11 @@ int tersoff(t_moldyn *moldyn) {
 					f_c=0.5+0.5*cos(arg1);
 					df_c=-0.5*sin(arg1)*(PI/(s_r*d_ij));
 					f_r=A*exp(-lambda*d_ij);
-					f_a=-B*exp(-mu*d_ij);
+					df_r=-lambda*f_r/d_ij;
+					scale=df_c*f_r+df_r*f_c;
+					v3_scale(&force,&dist_ij,scale);
+					v3_add(&(atom[i].f),&(atom[i].f),
+					       &force);
 				}
 			}
 			else 
@@ -1084,6 +1094,8 @@ int tersoff(t_moldyn *moldyn) {
 					v3_sub(&distance_jk,ktom,btom);
 					cos_theta=(d_ij2+d_ik*d_ik-d_jk*d_jk)/\
 					          (2*d_ij*d_ik);
+					sin_theta=sqrt(1.0/\
+					          (cos_theta*cos_theta));
 					theta=arccos(cos_theta);
 
 					
diff --git a/moldyn.h b/moldyn.h
index 49ca0b2..c6712ba 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -12,35 +12,50 @@
 #include "random/random.h"
 #include "list/list.h"
 
+
 /* datatypes */
 
+
+/* the atom of the md simulation */
+
 typedef struct s_atom {
-	t_3dvec r;	/* positions */
-	t_3dvec v;	/* velocities */
-	t_3dvec f;	/* forces */
-	int element;	/* number of element in pse */
-	double mass;	/* atom mass */
+	t_3dvec r;		/* position */
+	t_3dvec v;		/* velocity */
+	t_3dvec f;		/* force */
+	int element;		/* number of element in pse */
+	double mass;		/* atom mass */
+	unsigned char attr;	/* attributes */
 } t_atom;
 
+#define ATOM_ATTR_FP	0x01	/* fixed position (bulk material) */
+#define ATOM_ATTR_HB	0x02	/* coupled to heat bath (velocity scaling) */
+
+/* cell lists */
+
 typedef struct s_linkcell {
-	int listfd;
-	int nx,ny,nz;
-	int cells;
-	double x,y,z;
-	t_list *subcell;
+	int nx,ny,nz;		/* amount of cells in x, y and z direction */
+	int cells;		/* total amount of cells */
+	double len;		/* prefered cell edge length */
+	double x,y,z;		/* the actual cell lengthes */
+	t_list *subcell;	/* pointer to the cell lists */
+	int dnlc;		/* direct neighbour lists counter */
 } t_linkcell;
 
 #include "visual/visual.h"
 
+# moldyn properties structure */
+
 typedef struct s_moldyn {
-	/* atoms, amount, dimensions */
-	int count;
-	t_atom *atom;
-	t_3dvec dim;
+
+	int count;		/* total amount of atoms */
+	t_atom *atom;		/* pointer to the atoms */
+	t_3dvec dim;		/* dimensions of the simulation volume */
 	/* potential, force & parameters */
+
+	/* potential force funtion created by the user */
 	int (*potential_force_function)(struct s_moldyn *moldyn);
-	void *pot_params;
-	/* cut off radius */
+	void *pot_params;	/* parameters describing the potential */ 
+
 	double cutoff;
 	double cutoff_square;
 	/* linked list / cell method */
-- 
2.39.2