began rewrite ...

[physik/posic.git] / moldyn.h

diff --git a/moldyn.h b/moldyn.h
index 266436b..c6712ba 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -10,38 +10,67 @@
 
 #include "math/math.h"
 #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_list vicinity       /* verlet neighbour list */
+       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 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 */
-       double (*potential)(struct s_moldyn *moldyn);
-       int (*force)(struct s_moldyn *moldyn);
-       void *pot_params;
+
+       /* potential force funtion created by the user */
+       int (*potential_force_function)(struct s_moldyn *moldyn);
+       void *pot_params;       /* parameters describing the potential */ 
+
        double cutoff;
        double cutoff_square;
+       /* linked list / cell method */
+       t_linkcell lc;
        /* temperature */
        double t;
        /* integration of newtons equations */
        int (*integrate)(struct s_moldyn *moldyn);
        int time_steps;
        double tau;
+       double tau_square;
+       /* energy */
+       double energy;
        /* logging & visualization */
+       t_visual vis;
        unsigned char lvstat;
        unsigned int ewrite;
        char efb[64];
@@ -60,6 +89,8 @@ typedef struct s_moldyn {
        void *visual;
        /* moldyn general status */
        unsigned char status;
+       /* random */
+       t_random random;
 } t_moldyn;
 
 typedef struct s_ho_params {
@@ -73,6 +104,15 @@ typedef struct s_lj_params {
        double epsilon4;
 } t_lj_params;
 
+typedef struct s_tersoff_params {
+       double l_1,l_2;
+       double m_1,m_2;
+       double a_1,a_2;
+       double b_1,b_2;
+       double r_1,r_2;
+       double s_1,s_2;
+} t_tersoff_params;
+
 /*
  *  defines
  */
@@ -91,8 +131,16 @@ typedef struct s_lj_params {
 
 #define MOLDYN_TEMP                    273.0
 #define MOLDYN_TAU                     1.0e-15
+#define MOLDYN_CUTOFF                  10.0e-9
 #define MOLDYN_RUNS                    1000000
 
+#define MOLDYN_INTEGRATE_VERLET                0x00
+#define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
+
+#define MOLDYN_POTENTIAL_HO            0x00
+#define MOLDYN_POTENTIAL_LJ            0x01
+#define MOLDYN_POTENTIAL_DEFAULT MOLDYN_POTENTIAL_LJ
+
 /* phsical values */
 
 #define K_BOLTZMANN            1.3807e-27                      /* Nm/K */
@@ -114,14 +162,15 @@ typedef struct s_lj_params {
 
 int moldyn_usage(char **argv);
 int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv);
-int moldyn_log_init(t_moldyn *moldyn,void *v);
+int moldyn_log_init(t_moldyn *moldyn);
+int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
 int moldyn_shutdown(t_moldyn *moldyn);
 
 int create_lattice(unsigned char type,int element,double mass,double lc,
                    int a,int b,int c,t_atom **atom);
 int destroy_lattice(t_atom *atom);
-int thermal_init(t_moldyn *moldyn,t_random *random,int count);
-int scale_velocity(t_moldyn *moldyn,int count);
+int thermal_init(t_moldyn *moldyn);
+int scale_velocity(t_moldyn *moldyn);
 double get_e_kin(t_atom *atom,int count);
 double get_e_pot(t_moldyn *moldyn);
 double get_total_energy(t_moldyn *moldyn);
@@ -129,12 +178,15 @@ t_3dvec get_total_p(t_atom *atom,int count);
 
 double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t);
 
+int link_cell_init(t_moldyn *moldyn);
+int link_cell_update(t_moldyn *moldyn);
+int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
+int link_cell_shutdown(t_moldyn *moldyn);
+
 int moldyn_integrate(t_moldyn *moldyn);
 int velocity_verlet(t_moldyn *moldyn);
 
-double potential_harmonic_oscillator(t_moldyn *moldyn);
-int force_harmonic_oscillator(t_moldyn *moldyn);
-double potential_lennard_jones(t_moldyn *moldyn);
-int force_lennard_jones(t_moldyn *moldyn);
+int harmonic_oscillator(t_moldyn *moldyn);
+int lennard_jones(t_moldyn *moldyn);
 
 #endif