#include "math/math.h"
#include "random/random.h"
-//#include "visual/visual.h"
+#include "list/list.h"
/* datatypes */
t_3dvec r; /* positions */
t_3dvec v; /* velocities */
t_3dvec f; /* forces */
+ t_3dvec dr; /* delta r for verlet list updates */
int element; /* number of element in pse */
double mass; /* atom mass */
+ t_list verlet; /* verlet neighbour list */
} t_atom;
+typedef struct s_linkcell {
+ int nx,ny,nz;
+ 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);
- void *pot_params;
int (*force)(struct s_moldyn *moldyn);
+ void *pot_params;
+ /* cut off radius, verlet list & co */
+ double cutoff;
double cutoff_square;
- t_3dvec dim;
+ double r_verlet;
+ double dr_max1;
+ double dr_max2;
+ /* 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;
+ /* logging & visualization */
+ unsigned char lvstat;
+ unsigned int ewrite;
+ char efb[64];
+ int efd;
+ unsigned int mwrite;
+ char mfb[64];
+ int mfd;
+ unsigned int swrite;
+ char sfb[64];
+ int sfd;
+ unsigned int dwrite;
+ char dfb[64];
+ int dfd;
+ unsigned int vwrite;
+ char vfb[64];
void *visual;
+ /* moldyn general status */
unsigned char status;
} t_moldyn;
+typedef struct s_ho_params {
+ double spring_constant;
+ double equilibrium_distance;
+} t_ho_params;
+
typedef struct s_lj_params {
double sigma6;
double sigma12;
- double epsilon;
+ double epsilon4;
} t_lj_params;
/*
/* general defines */
+#define MOLDYN_LVSTAT_TOTAL_E 0x01
+#define MOLDYN_LVSTAT_TOTAL_M 0x02
+#define MOLDYN_LVSTAT_SAVE 0x04
+#define MOLDYN_LVSTAT_DUMP 0x08
+#define MOLDYN_LVSTAT_VISUAL 0x10
+#define MOLDYN_LVSTAT_INITIALIZED 0x80
+
#define MOLDYN_STAT_POTENTIAL 0x01
#define MOLDYN_STAT_FORCE 0x02
+#define MOLDYN_TEMP 273.0
+#define MOLDYN_TAU 1.0e-15
+#define MOLDYN_RUNS 1000000
+
/* phsical values */
-//#define K_BOLTZMANN 1.3807E-23
-#define K_BOLTZMANN 1.0
+#define K_BOLTZMANN 1.3807e-27 /* Nm/K */
+#define AMU 1.660540e-27 /* kg */
#define FCC 0x01
#define DIAMOND 0x02
#define C 0x06
-#define M_C 6.0
+#define M_C (12.011*AMU)
-#define Si 0x0e
-#define M_SI 14.0
-#define LC_SI 5.43105
+#define SI 0x0e
+#define LC_SI 0.543105e-9 /* m */
+#define M_SI (28.085*AMU) /* kg */
+#define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* m */
+#define LJ_EPSILON_SI (2.1678*1.60e-19) /* Nm */
/* function prototypes */
+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_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_atom *atom,t_random *random,int count,double t);
-int scale_velocity(t_atom *atom,int count,double t);
+int thermal_init(t_moldyn *moldyn,t_random *random,int count);
+int scale_velocity(t_moldyn *moldyn,int count);
double get_e_kin(t_atom *atom,int count);
double get_e_pot(t_moldyn *moldyn);
double get_total_energy(t_moldyn *moldyn);
t_3dvec get_total_p(t_atom *atom,int count);
+double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t);
+
+int verlet_list_init(t_moldyn *moldyn);
+int link_cell_init(t_moldyn *moldyn);
+int verlet_list_update(t_moldyn *moldyn);
+int link_cell_update(t_moldyn *moldyn);
+int verlet_list_shutdown(t_moldyn *moldyn);
+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);