#include "math/math.h"
#include "random/random.h"
-//#include "visual/visual.h"
+#include "list/list.h"
/* datatypes */
t_3dvec f; /* forces */
int element; /* number of element in pse */
double mass; /* atom mass */
- //t_list vicinity /* verlet neighbour list */
} t_atom;
+typedef struct s_linkcell {
+ int listfd;
+ int nx,ny,nz;
+ int cells;
+ double x,y,z;
+ t_list *subcell;
+} t_linkcell;
+
+#include "visual/visual.h"
+
typedef struct s_moldyn {
/* atoms, amount, dimensions */
int count;
t_atom *atom;
t_3dvec dim;
/* potential, force & parameters */
- double (*potential)(struct s_moldyn *moldyn);
- int (*force)(struct s_moldyn *moldyn);
+ int (*potential_force_function)(struct s_moldyn *moldyn);
void *pot_params;
+ /* cut off radius */
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];
char dfb[64];
int dfd;
unsigned int vwrite;
+ char vfb[64];
void *visual;
/* moldyn general status */
unsigned char status;
+ /* random */
+ t_random random;
} t_moldyn;
typedef struct s_ho_params {
typedef struct s_lj_params {
double sigma6;
double sigma12;
- double epsilon;
+ 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
*/
#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 */
int moldyn_usage(char **argv);
int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv);
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);
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