some checkins

[physik/posic.git] / moldyn.h

diff --git a/moldyn.h b/moldyn.h
index 87c8948..a1866a9 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -45,6 +45,7 @@ typedef struct s_atom {
        u8 brand;               /* brand id */
        int tag;                /* atom unique id (number of atom) */
        u8 attr;                /* attributes */
+       int pbc[3];             /* pb crossing in x, y and z direction */
 } t_atom;
 
 #define ATOM_ATTR_FP   0x01    /* fixed position (bulk material) */
@@ -137,14 +138,22 @@ typedef struct s_moldyn {
        double t_sum;           /* sum over all t */
        double t_avg;           /* average value of t */
 
+       /* for sale! */
        t_virial gvir;          /* global virial (absolute coordinates) */
-       double gv;
-       double gv_sum;
-       double gv_avg;
-
-       double gp;              /* pressure computed from global virial */
-       double gp_sum;          /* sum over all gp */
-       double gp_avg;          /* average value of gp */
+       //double gv;
+       //double gv_sum;
+       //double gv_avg;
+       double sale1;
+       double sale2;
+       double sale3;
+
+       // gp stuff exchanged by kinetic energies
+       //double gp;            /* pressure computed from global virial */
+       //double gp_sum;                /* sum over all gp */
+       //double gp_avg;                /* average value of gp */
+       double ekinx;
+       double ekiny;
+       double ekinz;
 
        t_virial vir;           /* actual virial */
        double virial;
@@ -250,6 +259,43 @@ typedef struct s_vb {
        int fd;
 } t_vb;
 
+typedef struct s_part_params {
+       u8 type;
+       double r;
+       t_3dvec p;
+       t_3dvec d;
+} t_part_params;
+
+#define PART_INSIDE_R   1
+#define PART_OUTSIDE_R  2
+#define PART_INSIDE_D   3
+#define PART_OUTSIDE_D  4
+
+typedef struct s_defect_params {
+       u8 type;
+       u8 stype;
+       double od;
+       double dd;
+       int element;
+       u8 brand;
+       u8 attr;
+} t_defect_params;
+
+#define DEFECT_TYPE_0D 1
+#define DEFECT_TYPE_1D 2
+#define DEFECT_TYPE_2D 3
+#define DEFECT_TYPE_3D 4
+
+#define DEFECT_STYPE_DB_X      1
+#define DEFECT_STYPE_DB_Y      2
+#define DEFECT_STYPE_DB_Z      3
+#define DEFECT_STYPE_DB_R      4
+
+typedef struct s_offset_params {
+       t_3dvec o;
+       u8 use;
+} t_offset_params;
+
 /*
  *
  *  defines
@@ -396,14 +442,19 @@ int moldyn_set_report(t_moldyn *moldyn,char *author,char *title);
 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer);
 int moldyn_log_shutdown(t_moldyn *moldyn);
 
-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,
+int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,
+                   u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin,
+                   t_part_params *p_params,t_defect_params *d_params,
+                   t_offset_params *o_params);
+int add_atom(t_moldyn *moldyn,int element,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);
+int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
+               t_part_params *p_params,t_defect_params *d_params);
+int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
+             t_part_params *p_params,t_defect_params *d_params);
+int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
+                 t_part_params *p_params,t_defect_params *d_params);
 int destroy_atoms(t_moldyn *moldyn);
 
 int thermal_init(t_moldyn *moldyn,u8 equi_init);
@@ -452,6 +503,7 @@ int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d);
 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d)
 //     __attribute__((always_inline));
 int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
+int check_per_bound_and_care_for_pbc(t_moldyn *moldyn,t_atom *a);
 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
 //     __attribute__((always_inline));
 
@@ -471,6 +523,7 @@ int get_line(int fd,char *line,int max);
 
 int pair_correlation_init(t_moldyn *moldyn,double dr);
 int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc);
+int calculate_msd(t_moldyn *moldyn,double *msd);
 int calculate_pair_correlation_process(t_moldyn *moldyn,t_atom *itom,
                                        t_atom *jtom,void *data,u8 bc);
 int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr);
@@ -481,7 +534,11 @@ int bond_analyze(t_moldyn *moldyn,double *quality);
 int visual_init(t_moldyn *moldyn,char *filebase);
 int visual_bonds_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
                          void *data,u8 bc);
+#ifdef VISUAL_THREAD
+void *visual_atoms(void *ptr);
+#else
 int visual_atoms(t_moldyn *moldyn);
+#endif
 
 int fpu_set_rtd(void);