#define MOLDYN_H
#include "math/math.h"
+#include "random/random.h"
+#include "list/list.h"
+
/* datatypes */
+typedef unsigned char u8;
+
+/* 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 */
+ u8 bnum; /* brand number */
+ u8 attr; /* attributes */
} t_atom;
+#define ATOM_ATTR_FP 0x01 /* fixed position (bulk material) */
+#define ATOM_ATTR_HB 0x02 /* coupled to heat bath (velocity scaling) */
+
+#define ATOM_ATTR_1BP 0x10 /* single paricle potential */
+#define ATOM_ATTR_2BP 0x20 /* pair potential */
+#define ATOM_ATTR_3BP 0x40 /* 3 body potential */
+
+/* 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 */
+ int countn; /* amount of neighbours */
+} t_linkcell;
+
+#include "visual/visual.h"
+
+# moldyn structure */
+
+typedef struct s_moldyn {
+
+ int count; /* total amount of atoms */
+ t_atom *atom; /* pointer to the atoms */
+
+ t_3dvec dim; /* dimensions of the simulation volume */
+
+ /* potential force function and parameter pointers */
+ int (*pf_func1b)(struct s_moldyn *,t_atom *);
+ void *pot1b_params;
+ int (*pf_func2b)(struct s_moldyn *,t_atom *,t_atom *);
+ void *pot2b_params;
+ int (*pf_func3b)(struct s_moldyn *,t_atom *,t_atom *,t_atom *);
+ void *pot3b_params;
+ //int (*potential_force_function)(struct s_moldyn *moldyn);
+
+ double cutoff; /* cutoff radius */
+ double cutoff_square; /* square of the cutoff radius */
+
+ t_linkcell lc; /* linked cell method */
+
+ double t; /* temperature */
+
+ /* integration function pointer */
+ int (*integrate)(struct s_moldyn *moldyn);
+ int time_steps; /* amount of iterations */
+ double tau; /* delta t */
+ double tau_square; /* delta t squared */
+
+ double energy; /* energy */
+
+ t_visual vis; /* visualization/log/save interface structure */
+ u8 lvstat; /* log & vis properties */
+ unsigned int ewrite; /* how often to log energy */
+ char efb[64]; /* energy log filename */
+ int efd; /* fd for energy log */
+ unsigned int mwrite; /* how often to log momentum */
+ char mfb[64]; /* momentum log filename */
+ int mfd; /* fd for momentum log */
+ unsigned int vwrite; /* how often to visualize atom information */
+ char vfb[64]; /* visualization file name base */
+ void *visual; /* pointer (hack!) */
+ unsigned int swrite; /* how often to create a save file */
+
+ u8 status; /* general moldyn properties */
+
+ t_random random; /* random interface */
+} t_moldyn;
+
+#define MOLDYN_LVSTAT_TOTAL_E 0x01
+#define MOLDYN_LVSTAT_TOTAL_M 0x02
+#define MOLDYN_LVSTAT_SAVE 0x04
+#define MOLDYN_LVSTAT_VISUAL 0x08
+#define MOLDYN_LVSTAT_INITIALIZED 0x10
+
+#define MOLDYN_STAT_PBX 0x08 /* periodic boudaries in x */
+#define MOLDYN_STAT_PBY 0x10 /* y */
+#define MOLDYN_STAT_PBZ 0x20 /* and z direction */
+
+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;
+
+/* tersoff exchange structure to exchange 2bp and 3bp calculated values */
-/* defines */
+typedef struct s_tersoff_exchange {
+ double f_c,df_c;
+
+ t_3dvec dist_ij;
+ double d_ij;
+ double d_ij2;
+
+ double chi;
+
+ double *B;
+ double *mu;
+
+ double *beta;
+ double *n;
+ double *c;
+ double *d;
+ double *h;
+
+ double c2;
+ double d2;
+ double c2d2;
+ double betan;
+
+ u8 run3bp;
+} t_tersoff_exchange;
+
+/* tersoff multi (2!) potential parameters */
+
+typedef struct s_tersoff_mult_params {
+ double S[2]; /* tersoff cutoff radii */
+ double R[2]; /* tersoff cutoff radii */
+ double Smixed; /* mixed S radius */
+ double Rmixed; /* mixed R radius */
+ double A[2]; /* factor of tersoff attractive part */
+ double B[2]; /* factor of tersoff repulsive part */
+ double Amixed; /* mixed A factor */
+ double Bmixed; /* mixed B factor */
+ double lambda[2]; /* tersoff lambda */
+ double lambda_m; /* mixed lambda */
+ double mu[2]; /* tersoff mu */
+ double mu_m; /* mixed mu */
+
+ double chi;
+
+ double beta[2];
+ double n[2];
+ double c[2];
+ double d[2];
+ double h[2];
+
+ t_tersoff_exchange exchange; /* exchange between 2bp and 3bp calc */
+} t_tersoff_params;
+
+/*
+ * defines
+ */
+
+/* general 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 */
+#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 create_lattice(unsigned char type,int element,double mass,double lc,
- t_3dvec *dim,t_atom **atom);
+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(u8 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);
+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