X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=a7fa60a2311a4487712ef3f646adbb950430c180;hb=1097ea2efb575855edd332c28a9cd8f807cd0716;hp=cbfc17302fb04806d21d4b68085b27bb9309a79c;hpb=792f14f95b47989f7f12df0ea70b54619be016ee;p=physik%2Fposic.git

diff --git a/moldyn.h b/moldyn.h
index cbfc173..a7fa60a 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -10,88 +10,237 @@
 
 #include "math/math.h"
 #include "random/random.h"
-//#include "visual/visual.h"
+#include "list/list.h"
 
-/* datatypes */
 
+/*
+ * 
+ * datatypes
+ *
+ */
+
+/* general */
+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_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 */
+	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 schedule structure */
+typedef struct s_moldyn_schedule {
+	int content_count;
+	int *runs;
+	double *tau;
+	int (*hook)(t_moldyn *,void *);
+	void *hook_params;
+} t_moldyn_schedule;
+
+/* moldyn main 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 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 */
+
+	/* simulation schedule */
+	t_moldyn_schedule schedule;
+	int current;		/* current position in schedule */
+
+	/* 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 elapsed;		/* total elapsed time */
+
+	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 */
+
+
+/*
+ *
+ * potential parameter structures
+ *
+ */
+
+/*
+ * harmonic oscillator potential parameter structure
+ */
+
 typedef struct s_ho_params {
 	double spring_constant;
 	double equilibrium_distance;
 } t_ho_params;
 
+/*
+ * lennard jones potential parameter structure
+ */
+
 typedef struct s_lj_params {
 	double sigma6;
 	double sigma12;
-	double epsilon;
+	double epsilon4;
 } t_lj_params;
 
 /*
- *  defines
+ * tersoff 
  */
 
-/* general defines */
+/* tersoff exchange structure to exchange 2bp and 3bp calculated values */
+typedef struct s_tersoff_exchange {
+	double f_c,df_c;
 
-#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
+	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
+ *
+ */
 
-#define MOLDYN_STAT_POTENTIAL		0x01
-#define MOLDYN_STAT_FORCE		0x02
+/* default values */
 
 #define MOLDYN_TEMP			273.0
 #define MOLDYN_TAU			1.0e-15
+#define MOLDYN_CUTOFF			1.0e-9
 #define MOLDYN_RUNS			1000000
 
-/* phsical values */
+#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_TM		0x02
+
+#define MOLDYN_SET_POTENTIAL		0x00
+#define MOLDYN_SET_TEMPERATURE		0x01
+#define MOLDYN_SET_
+#define MOLDYN_SET_
+
+/*
+ *
+ * phsical values / constants
+ *
+ */
 
 #define K_BOLTZMANN		1.3807e-27			/* Nm/K */
 #define AMU			1.660540e-27			/* kg */
@@ -108,17 +257,24 @@ typedef struct s_lj_params {
 #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 */
+
+/*
+ *
+ * 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,
+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,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);
@@ -126,12 +282,15 @@ 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);
 
-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