more interstitial testing, added bond visualization

[physik/posic.git] / moldyn.h

diff --git a/moldyn.h b/moldyn.h
index a595585..2d4ca48 100644 (file)
--- 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 */
@@ -64,8 +66,6 @@ typedef struct s_linkcell {
        int dnlc;               /* direct neighbour lists counter */
 } t_linkcell;
 
-#include "visual/visual.h"
-
 /* moldyn schedule structure */
 typedef struct s_moldyn_schedule {
        int count;
@@ -76,8 +76,18 @@ 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 */
+       char **args;            /* pointer to arguments */
+
        int count;              /* total amount of atoms */
        double mass;            /* total system mass */
        t_atom *atom;           /* pointer to the atoms */
@@ -101,6 +111,7 @@ 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 */
 
@@ -324,7 +335,7 @@ 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))
@@ -338,7 +349,7 @@ 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))
@@ -350,9 +361,9 @@ typedef struct s_moldyn {
 #define ALBE_LC_C              3.566
 
 #define ALBE_R_SIC             (2.40-0.20)
-#define ALBE_S_SIC             (2.40+0.10)
+#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))
@@ -372,7 +383,6 @@ typedef struct s_moldyn {
 #define FCC                    0x02
 #define DIAMOND                        0x04
 
-
 /*
  *
  * function prototypes
@@ -388,6 +398,7 @@ 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);
@@ -414,6 +425,7 @@ 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);
@@ -465,4 +477,8 @@ int moldyn_bc_check(t_moldyn *moldyn);
 
 int get_line(int fd,char *line,int max);
 
+int visual_init(t_moldyn *moldyn,char *filebase);
+int visual_atoms(t_moldyn *moldyn);
+
 #endif
+