X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=c5fed604ff62dbe2c96ee223c395473666bb04b6;hb=ade81aa2afb15f22e98ed9595ff303d4fedfe122;hp=dafd86cb67d415636833bafc147d860dd595850f;hpb=11bf064825efc474fa93c7270870856769a63e84;p=physik%2Fposic.git

diff --git a/moldyn.h b/moldyn.h
index dafd86c..c5fed60 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -36,9 +36,9 @@ typedef struct s_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 */ 
+#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 {
@@ -48,7 +48,6 @@ typedef struct s_linkcell {
 	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"
@@ -70,20 +69,32 @@ 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);
+	int (*func2b_post)(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 */
+	double t_ref;		/* reference temperature */
+	double t;		/* actual temperature */
+
+	double p_ref;		/* reference pressure */
+	double p;		/* actual pressure */
+
+	/* pressure and temperature control (velocity/volume scaling) */
+	unsigned char pt_scale;	/* type of p and t scaling */
+	double t_tc;		/* t berendsen control time constant */
+	double p_tc;		/* p berendsen control time constant */
 
 	/* simulation schedule */
 	t_moldyn_schedule schedule;
@@ -93,6 +104,7 @@ 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 */
 
@@ -107,28 +119,29 @@ typedef struct s_moldyn {
 	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
+	int debug;		/* debugging stuff, ignore */
+} t_moldyn;
 
 #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
-#define MOLDYN_2BP			0x01
-#define MOLDYN_3BP			0x02
+#define MOLDYN_1BP			0x00	/* care about single */
+#define MOLDYN_2BP			0x01	/* 2 body */
+#define MOLDYN_3BP			0x02	/* and 3 body particle pots */
+
+#define T_SCALE_BERENDSEN		0x01	/* berendsen t control */
+#define T_SCALE_DIRECT			0x02	/* direct t control */
+#define P_SCALE_BERENDSEN		0x04	/* berendsen p control */
+#define P_SCALE_DIRECT			0x08	/* direct p control */
 
 
 /*
@@ -163,6 +176,7 @@ 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;
@@ -170,9 +184,6 @@ typedef struct s_tersoff_exchange {
 
 	double chi;
 
-	double *B;
-	double *mu;
-
 	double *beta;
 	double *n;
 	double *c;
@@ -183,8 +194,14 @@ typedef struct s_tersoff_exchange {
 	double d2;
 	double c2d2;
 	double betan;
+	double n_betan;
 
 	u8 run3bp;
+	u8 run2bp_post;
+
+	t_3dvec db_ij;
+	double sum1_3bp;
+	double sum2_3bp;
 } t_tersoff_exchange;
 
 /* tersoff multi (2!) potential parameters */
@@ -211,7 +228,7 @@ 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;
 
 
 
@@ -228,6 +245,8 @@ 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
 
@@ -235,14 +254,16 @@ 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
 
+#define ACCEPTABLE_ERROR		1e-15
+
 /*
  *
  * phsical values / constants
@@ -251,6 +272,7 @@ typedef struct s_tersoff_mult_params {
 
 #define K_BOLTZMANN		1.3807e-27			/* Nm/K */
 #define AMU			1.660540e-27			/* kg */
+#define EV			1.60217733e-19			/* Nm */
 
 #define FCC			0x01
 #define DIAMOND			0x02
@@ -264,6 +286,32 @@ typedef struct s_tersoff_mult_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 */
 
+#define TM_R_SI			2.7e-10				/* m */
+#define TM_S_SI			3.0e-10				/* m */
+#define TM_A_SI			(1830.8*EV)			/* Nm */
+#define TM_B_SI			(471.18*EV)			/* Nm */
+#define TM_LAMBDA_SI		2.4799e10			/* 1/m */
+#define TM_MU_SI		1.7322e10			/* 1/m */
+#define TM_BETA_SI		1.1000e-6
+#define TM_N_SI			0.78734
+#define TM_C_SI			1.0039e5
+#define TM_D_SI			16.217
+#define TM_H_SI			(-0.59825)
+
+#define TM_R_C			1.8e-10				/* m */
+#define TM_S_C			2.1e-10				/* m */
+#define TM_A_C			(1393.6*EV)			/* Nm */
+#define TM_B_C			(346.7*EV)			/* Nm */
+#define TM_LAMBDA_C		3.4879e10			/* 1/m */
+#define TM_MU_C			2.2119e10			/* 1/m */
+#define TM_BETA_C		1.5724e-7
+#define TM_N_C			0.72751
+#define TM_C_C			3.8049e4
+#define TM_D_C			4.384
+#define TM_H_C			(-0.57058)
+
+#define TM_CHI_SIC		0.9776
+
 
 /*
  *
@@ -271,34 +319,44 @@ typedef struct s_tersoff_mult_params {
  *
  */
 
+typedef int (*pf_func1b)(t_moldyn *,t_atom *ai);
+typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8 bc);
+typedef int (*pf_func2b_post)(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 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_temperature(t_moldyn *moldyn,double t_ref);
+int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc);
 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_potential(t_moldyn *moldyn,u8 type,(int *)(func),void *params);
+int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params);
+int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params);
+int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post 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);
-nt moldyn_log_shutdown(t_moldyn *moldyn);
+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);
+             t_3dvec *r,t_3dvec *v);
 int destroy_atoms(t_moldyn *moldyn);
 
-int thermal_init(t_moldyn *moldyn);
-int scale_velocity(t_moldyn *moldyn);
+int thermal_init(t_moldyn *moldyn,u8 equi_init);
+int scale_velocity(t_moldyn *moldyn,u8 equi_init);
 
 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_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);
@@ -313,10 +371,12 @@ int velocity_verlet(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 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_complete_params(t_tersoff_mult_params *p);
 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_post_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