X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=72ff30bdfb00ab876cce6261360b827298c77043;hb=1d83ceb2ce2ff5150fd079f1066b7f583e38c8f4;hp=947467cf0431d77744bf589fdee2f39562ab61aa;hpb=8e98c9cbbddf1c9c852874f956b0dbe2f9a4a922;p=physik%2Fposic.git

diff --git a/moldyn.h b/moldyn.h
index 947467c..72ff30b 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"
@@ -73,6 +72,7 @@ typedef struct s_moldyn {
 	int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
 	void *pot1b_params;
 	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 (*func3b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,
 	              u8 bck);
@@ -81,10 +81,21 @@ typedef struct s_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) */
+	/* (in units of tau!) */
+	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;
@@ -101,30 +112,35 @@ typedef struct s_moldyn {
 	double energy;		/* potential energy */
 	double ekin;		/* kinetic energy */
 
-	t_visual vis;		/* visualization/log/save interface structure */
-	u8 lvstat;		/* log & vis properties */
+	char vlsdir[128];	/* visualization/log/save directory */
+	t_visual vis;		/* visualization interface structure */
+	u8 vlsprop;		/* log/vis/save properties */
 	unsigned int ewrite;	/* how often to log energy */
 	int efd;		/* fd for energy log */
 	unsigned int mwrite;	/* how often to log momentum */
 	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 */
-	char sfb[64];		/* visualization file name base */
 
 	u8 status;		/* general moldyn properties */
 
 	t_random random;	/* random interface */
+
+	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 */
 
 
 /*
@@ -163,25 +179,37 @@ typedef struct s_tersoff_exchange {
 
 	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;
+	double *beta_i;
+	double *beta_j;
+	double *n_i;
+	double *n_j;
+	double *c_i;
+	double *c_j;
+	double *d_i;
+	double *d_j;
+	double *h_i;
+	double *h_j;
+
+	double ci2;
+	double cj2;
+	double di2;
+	double dj2;
+	double ci2di2;
+	double cj2dj2;
+	double betaini;
+	double betajnj;
 
 	u8 run3bp;
+	u8 run2bp_post;
+	u8 d_ij_between_rs;
+
+	double zeta_ij;
+	double zeta_ji;
+	t_3dvec dzeta_ij;
+	t_3dvec dzeta_ji;
 } t_tersoff_exchange;
 
 /* tersoff multi (2!) potential parameters */
@@ -218,15 +246,25 @@ typedef struct s_tersoff_mult_params {
  *
  */
 
-/* default values */
+/*
+ * default values
+ *
+ * - length unit: 1 A (1 A = 1e-10 m)
+ * - time unit: 1 fs (1 fs = 1e-15 s)
+ * - mass unit: 1 amu (1 amu = 1.6605388628e-27 kg )
+ */
+
+#define METER				1e10			/* A */
+#define SECOND				1e15			/* fs */
+#define AMU				1.6605388628e-27	/* kg */
+#define KILOGRAM			(1.0/AMU)		/* amu */
+#define NEWTON	(METER*KILOGRAM/(SECOND*SECOND))	/* A amu / fs^2 */
 
 #define MOLDYN_TEMP			273.0
-#define MOLDYN_TAU			1.0e-15
-#define MOLDYN_CUTOFF			1.0e-9
+#define MOLDYN_TAU			1.0
+#define MOLDYN_CUTOFF			10.0
 #define MOLDYN_RUNS			1000000
 
-#define MOLDYN_CRITICAL_EST_TEMP	5.0
-
 #define MOLDYN_INTEGRATE_VERLET		0x00
 #define MOLDYN_INTEGRATE_DEFAULT 	MOLDYN_INTEGRATE_VERLET
 
@@ -248,20 +286,50 @@ typedef struct s_tersoff_mult_params {
  *
  */
 
-#define K_BOLTZMANN		1.3807e-27			/* Nm/K */
-#define AMU			1.660540e-27			/* kg */
-
-#define FCC			0x01
-#define DIAMOND			0x02
+#define K_BOLTZMANN		(1.380650524e-23*METER*NEWTON)	/* NA/K */
+#define EV			(1.6021765314e-19*METER*NEWTON)	/* NA */
 
 #define C			0x06
-#define M_C			(12.011*AMU)
+#define M_C			12.011				/* amu */
 
 #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 */
+#define LC_SI			(0.543105e-9*METER)		/* A */
+#define M_SI			28.08553			/* amu */
+#define LJ_SIGMA_SI		((0.25*sqrt(3.0)*LC_SI)/1.122462)	/* A */
+#define LJ_EPSILON_SI		(2.1678*EV)				/* NA */
+
+#define TM_R_SI			(2.7e-10*METER)			/* A */
+#define TM_S_SI			(3.0e-10*METER)			/* A */
+#define TM_A_SI			(1830.8*EV)			/* NA */
+#define TM_B_SI			(471.18*EV)			/* NA */
+#define TM_LAMBDA_SI		(2.4799e10/METER)		/* 1/A */
+#define TM_MU_SI		(1.7322e10/METER)		/* 1/A */
+#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*METER)			/* A */
+#define TM_S_C			(2.1e-10*METER)			/* A */
+#define TM_A_C			(1393.6*EV)			/* NA */
+#define TM_B_C			(346.7*EV)			/* NA */
+#define TM_LAMBDA_C		(3.4879e10/METER)		/* 1/A */
+#define TM_MU_C			(2.2119e10/METER)		/* 1/A */
+#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
+
+/*
+ * lattice constants
+ */
+
+#define FCC			0x01
+#define DIAMOND			0x02
 
 
 /*
@@ -272,6 +340,7 @@ 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);
@@ -279,14 +348,18 @@ 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_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);
+int moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
+int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer);
 int moldyn_log_shutdown(t_moldyn *moldyn);
 
 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
@@ -295,8 +368,8 @@ 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);
+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);
@@ -320,8 +393,12 @@ 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_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);
 
+int moldyn_bc_check(t_moldyn *moldyn);
+
 #endif