X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=63dd14f0d45af67c6b8f9782079626f7ca3cfa63;hb=180ff86ae35ca0ea6ee857e92e56120e65315d17;hp=a76b3b4f804c9ad83bad01ab0b445b65066b5b1d;hpb=d3d65b8212c02f787a16cb312bf08b7712e89550;p=physik%2Fposic.git

diff --git a/moldyn.h b/moldyn.h
index a76b3b4..63dd14f 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -53,12 +53,12 @@ typedef struct s_linkcell {
 
 #include "visual/visual.h"
 
-# moldyn schedule structure */
+/* moldyn schedule structure */
 typedef struct s_moldyn_schedule {
 	int content_count;
 	int *runs;
-	int *tau;
-	int (*hook)(t_moldyn *,void *);
+	double *tau;
+	int (*hook)(void *moldyn,void *hook);
 	void *hook_params;
 } t_moldyn_schedule;
 
@@ -70,18 +70,20 @@ typedef struct s_moldyn {
 	t_3dvec dim;		/* dimensions of the simulation volume */
 
 	/* potential force function and parameter pointers */
-	int (*pf_func1b)(struct s_moldyn *,t_atom *);
+	int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
 	void *pot1b_params;
-	int (*pf_func2b)(struct s_moldyn *,t_atom *,t_atom *);
+	int (*func2b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
 	void *pot2b_params;
-	int (*pf_func3b)(struct s_moldyn *,t_atom *,t_atom *,t_atom *);
+	int (*func3b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,
+	              u8 bck);
 	void *pot3b_params;
 	//int (*potential_force_function)(struct s_moldyn *moldyn);
 
 	double cutoff;		/* cutoff radius */
 	double cutoff_square;	/* square of the cutoff radius */
+	double nnd;		/* nearest neighbour distance (optional) */
 
-	t_linkcell lc;		/* linked cell method */
+	t_linkcell lc;		/* linked cell list interface */
 
 	double t;		/* temperature */
 
@@ -93,39 +95,41 @@ typedef struct s_moldyn {
 	int (*integrate)(struct s_moldyn *moldyn);
 	int time_steps;		/* amount of iterations */
 	double tau;		/* delta t */
+	double time;		/* absolute time */
 	double tau_square;	/* delta t squared */
 	double elapsed;		/* total elapsed time */
 
-	double energy;		/* energy */
+	double energy;		/* potential energy */
+	double ekin;		/* kinetic 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!) */
+	//void *visual;		/* pointer (hack!) */
 	unsigned int swrite;	/* how often to create a save file */
+	char sfb[64];		/* visualization file name base */
 
 	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 */
 
+#define MOLDYN_1BP			0x00	/* care about single */
+#define MOLDYN_2BP			0x01	/* 2 body */
+#define MOLDYN_3BP			0x02	/* and 3 body particle pots */
+
+#define VSCALE_INIT_EQUI		0x00	/* initial, eq positions */
+#define VSCALE_BERENDSEN		0x01	/* berendsen control */
+
 
 /*
  *
@@ -159,6 +163,7 @@ typedef struct s_lj_params {
 /* tersoff exchange structure to exchange 2bp and 3bp calculated values */
 typedef struct s_tersoff_exchange {
 	double f_c,df_c;
+	double f_a,df_a;
 
 	t_3dvec dist_ij;
 	double d_ij;
@@ -207,7 +212,7 @@ typedef struct s_tersoff_mult_params {
 	double h[2];
 
 	t_tersoff_exchange exchange;	/* exchange between 2bp and 3bp calc */
-} t_tersoff_params;
+} t_tersoff_mult_params;
 
 
 
@@ -224,6 +229,8 @@ typedef struct s_tersoff_mult_params {
 #define MOLDYN_CUTOFF			1.0e-9
 #define MOLDYN_RUNS			1000000
 
+#define MOLDYN_CRITICAL_EST_TEMP	5.0
+
 #define MOLDYN_INTEGRATE_VERLET		0x00
 #define MOLDYN_INTEGRATE_DEFAULT 	MOLDYN_INTEGRATE_VERLET
 
@@ -231,10 +238,13 @@ typedef struct s_tersoff_mult_params {
 #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_
+#define LOG_TOTAL_ENERGY		0x01
+#define LOG_TOTAL_MOMENTUM		0x02
+#define SAVE_STEP			0x04
+#define VISUAL_STEP			0x08
+
+#define TRUE				1
+#define FALSE				0
 
 /*
  *
@@ -264,33 +274,59 @@ typedef struct s_tersoff_mult_params {
  *
  */
 
-int moldyn_usage(char **argv);
-int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv);
-int moldyn_log_init(t_moldyn *moldyn);
+typedef int (*pf_func1b)(t_moldyn *,t_atom *ai);
+typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8 bc);
+typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8 bc);
+
 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 set_int_alg(t_moldyn *moldyn,u8 algo);
+int set_cutoff(t_moldyn *moldyn,double cutoff);
+int set_temperature(t_moldyn *moldyn,double t);
+int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize);
+int set_nn_dist(t_moldyn *moldyn,double dist);
+int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
+int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params);
+int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params);
+int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params);
+
+int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer);
+int moldyn_log_shutdown(t_moldyn *moldyn);
+
+int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
+                   u8 attr,u8 bnum,int a,int b,int c);
+int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
+             t_3dvec *r,t_3dvec *v);
+int destroy_atoms(t_moldyn *moldyn);
+
 int thermal_init(t_moldyn *moldyn);
-int scale_velocity(t_moldyn *moldyn);
-double get_e_kin(t_atom *atom,int count);
+int scale_velocity(t_moldyn *moldyn,u8 type);
+
+double get_e_kin(t_moldyn *moldyn);
 double get_e_pot(t_moldyn *moldyn);
 double get_total_energy(t_moldyn *moldyn);
-t_3dvec get_total_p(t_atom *atom,int count);
+t_3dvec get_total_p(t_moldyn *moldyn);
 
-double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t);
+double estimate_time_step(t_moldyn *moldyn,double nn_dist);
 
 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_add_schedule(t_moldyn *moldyn,int runs,double tau);
+int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params);
+
 int moldyn_integrate(t_moldyn *moldyn);
 int velocity_verlet(t_moldyn *moldyn);
 
-int harmonic_oscillator(t_moldyn *moldyn);
-int lennard_jones(t_moldyn *moldyn);
+int potential_force_calc(t_moldyn *moldyn);
+int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
+int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai);
+int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc);
 
 #endif