X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=229074361363fb8d2601d92ef642c4825539735e;hb=e1080fc0dd66b0cf5b7715c5e99e7a34ac04a8cf;hp=13f4e9b91a0cfe267a19fc3a5948da208305921a;hpb=d0d09d054c7c358847f366d842919d074788eb00;p=physik%2Fposic.git

diff --git a/moldyn.h b/moldyn.h
index 13f4e9b..2290743 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -49,6 +49,8 @@ typedef struct s_atom {
 
 #define ATOM_ATTR_FP	0x01	/* fixed position (bulk material) */
 #define ATOM_ATTR_HB	0x02	/* coupled to heat bath (velocity scaling) */
+#define ATOM_ATTR_VA	0x04	/* visualize this atom */
+#define ATOM_ATTR_VB	0x08	/* visualize the bond of this atom */
 
 #define ATOM_ATTR_1BP		0x10	/* single paricle potential */
 #define ATOM_ATTR_2BP		0x20	/* pair potential */
@@ -60,11 +62,15 @@ typedef struct s_linkcell {
 	int cells;		/* total amount of cells */
 	double len;		/* prefered cell edge length */
 	double x,y,z;		/* the actual cell lengthes */
+#ifdef STATIC_LISTS
+	int **subcell;		/* pointer to the cell lists */
+#else
 	t_list *subcell;	/* pointer to the cell lists */
+#endif
 	int dnlc;		/* direct neighbour lists counter */
 } t_linkcell;
 
-#include "visual/visual.h"
+#define MAX_ATOMS_PER_LIST	20
 
 /* moldyn schedule structure */
 typedef struct s_moldyn_schedule {
@@ -76,6 +82,13 @@ typedef struct s_moldyn_schedule {
 	void *hook_params;
 } t_moldyn_schedule;
 
+/* visualization structure */
+typedef struct s_visual {
+	int fd;			/* rasmol script file descriptor */
+	char fb[128];		/* basename of the save files */
+	t_3dvec dim;		/* dimensions of the simulation cell */
+} t_visual;
+
 /* moldyn main structure */
 typedef struct s_moldyn {
 	int argc;		/* number of arguments */
@@ -104,6 +117,7 @@ typedef struct s_moldyn {
 	double cutoff;		/* cutoff radius */
 	double cutoff_square;	/* square of the cutoff radius */
 	double nnd;		/* nearest neighbour distance (optional) */
+	double bondlen[3];	/* bond lengthes (only 2 atomic systems) */
 
 	t_linkcell lc;		/* linked cell list interface */
 
@@ -327,7 +341,7 @@ typedef struct s_moldyn {
 #define ALBE_R_SI		(2.82-0.14)
 #define ALBE_S_SI		(2.82+0.14)
 #define ALBE_A_SI		(3.24*EV/0.842)
-#define ALBE_B_SI		(1.842*3.24*EV/0.842)
+#define ALBE_B_SI		(-1.842*3.24*EV/0.842)
 #define ALBE_R0_SI		2.232
 #define ALBE_LAMBDA_SI		(1.4761*sqrt(2.0*1.842))
 #define ALBE_MU_SI		(1.4761*sqrt(2.0/1.842))
@@ -341,7 +355,7 @@ typedef struct s_moldyn {
 #define ALBE_R_C		(2.00-0.15)
 #define ALBE_S_C		(2.00+0.15)
 #define ALBE_A_C		(6.00*EV/1.167)
-#define ALBE_B_C		(2.167*6.00*EV/1.167)
+#define ALBE_B_C		(-2.167*6.00*EV/1.167)
 #define ALBE_R0_C		1.4276
 #define ALBE_LAMBDA_C		(2.0099*sqrt(2.0*2.167))
 #define ALBE_MU_C		(2.0099*sqrt(2.0/2.167))
@@ -355,7 +369,7 @@ typedef struct s_moldyn {
 #define ALBE_R_SIC		(2.40-0.20)
 #define ALBE_S_SIC		(2.40+0.20)
 #define ALBE_A_SIC		(4.36*EV/0.847)
-#define ALBE_B_SIC		(1.847*4.36*EV/0.847)
+#define ALBE_B_SIC		(-1.847*4.36*EV/0.847)
 #define ALBE_R0_SIC		1.79
 #define ALBE_LAMBDA_SIC		(1.6991*sqrt(2.0*1.847))
 #define ALBE_MU_SIC		(1.6991*sqrt(2.0/1.847))
@@ -375,7 +389,6 @@ typedef struct s_moldyn {
 #define FCC			0x02
 #define DIAMOND			0x04
 
-
 /*
  *
  * function prototypes
@@ -391,6 +404,7 @@ int moldyn_shutdown(t_moldyn *moldyn);
 
 int set_int_alg(t_moldyn *moldyn,u8 algo);
 int set_cutoff(t_moldyn *moldyn,double cutoff);
+int set_bondlen(t_moldyn *moldyn,double b0,double b1,double bm);
 int set_temperature(t_moldyn *moldyn,double t_ref);
 int set_pressure(t_moldyn *moldyn,double p_ref);
 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc);
@@ -417,6 +431,7 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
                    u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin);
 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
              t_3dvec *r,t_3dvec *v);
+int del_atom(t_moldyn *moldyn,int tag);
 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
@@ -445,7 +460,11 @@ double estimate_time_step(t_moldyn *moldyn,double nn_dist);
 
 int link_cell_init(t_moldyn *moldyn,u8 vol);
 int link_cell_update(t_moldyn *moldyn);
+#ifdef STATIC_LISTS
+int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int **cell);
+#else
 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
+#endif
 int link_cell_shutdown(t_moldyn *moldyn);
 
 typedef int (*set_hook)(void *,void *);
@@ -466,6 +485,15 @@ int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
 
 int moldyn_bc_check(t_moldyn *moldyn);
 
+int moldyn_read_save_file(t_moldyn *moldyn,char *file);
+int moldyn_load(t_moldyn *moldyn);
 int get_line(int fd,char *line,int max);
 
+int pair_correlation_init(t_moldyn *moldyn,double dr);
+int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr);
+
+int visual_init(t_moldyn *moldyn,char *filebase);
+int visual_atoms(t_moldyn *moldyn);
+
 #endif
+