#include "math/math.h"
#include "random/random.h"
-//#include "visual/visual.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 */
+ int countn; /* amount of neighbours */
+} t_linkcell;
+
+#include "visual/visual.h"
+
+# moldyn structure */
+
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);
- void *pot_params;
- double cutoff;
- double cutoff_square;
- /* temperature */
- double t;
- /* integration of newtons equations */
+
+ int count; /* total amount of atoms */
+ t_atom *atom; /* pointer to the atoms */
+
+ t_3dvec dim; /* dimensions of the simulation volume */
+
+ /* potential force function pointer and parameters */
+ int (*pf_func1b)(struct s_moldyn *,t_atom *);
+ int (*pf_func2b)(struct s_moldyn *,t_atom *,t_atom *);
+ int (*pf_func3b)(struct s_moldyn *,t_atom *,t_atom *,t_atom *);
+ //int (*potential_force_function)(struct s_moldyn *moldyn);
+ void *pot_params; /* parameters describing the potential */
+
+ 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;
- 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;
- void *visual;
- /* moldyn general status */
- unsigned char status;
+ 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 */
+ unsigned char 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 */
+
+ unsigned char 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_1BP 0x01
+#define MOLDYN_STAT_2BP 0x02 /* define for pair potentials */
+#define MOLDYN_STAT_3BP 0x04 /* define for 3 body pot */
+#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;
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
*/
/* 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 */
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
projects / physik / posic.git / blobdiff