#define MOLDYN_H
#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_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 {
-/* defines */
+ int count; /* total amount of atoms */
+ t_atom *atom; /* pointer to the atoms */
+ t_3dvec dim; /* dimensions of the simulation volume */
+ /* potential, force & parameters */
+
+ /* 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];
+ 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;
+ /* random */
+ t_random random;
+} 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 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
+ */
+
+/* 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_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 */
+#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);
+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,
- t_3dvec *dim,t_atom **atom);
+ int a,int b,int c,t_atom **atom);
+int destroy_lattice(t_atom *atom);
+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);
+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);
+
+int harmonic_oscillator(t_moldyn *moldyn);
+int lennard_jones(t_moldyn *moldyn);
#endif
projects / physik / posic.git / blobdiff