began rewrite ...

diff --git a/moldyn.c b/moldyn.c
index ad0f9a3..f92ce55 100644 (file)
--- 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 (file)
--- 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 */