X-Git-Url: https://hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=blobdiff_plain;f=moldyn.h;h=0670f3d19239ada190d6c7d65fd99317392af295;hp=ee452286af3ad5cf1ab44f77e5a558cde03772a1;hb=HEAD;hpb=099c05fce45cacbbd7bbf6a7c5f1067e150d30ac

diff --git a/moldyn.h b/moldyn.h
index ee45228..0670f3d 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -45,16 +45,25 @@ typedef struct s_atom {
 	u8 brand;		/* brand id */
 	int tag;		/* atom unique id (number of atom) */
 	u8 attr;		/* attributes */
+	int pbc[3];		/* pb crossing in x, y and z direction */
 } 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_VA	0x04	/* visualize this atom */
+#define ATOM_ATTR_VA	0x04	/* visualize this atom */ // TODO
 #define ATOM_ATTR_VB	0x08	/* visualize the bond of this atom */
 
-#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 */ 
+
+#define DEFAULT_ATOM_ATTR	0x74	// 1,2,3 body interaction + visualize
+
+/* special list structure for low mem approach */
+typedef struct s_lowmem_list {
+	int *head;
+	int *list;
+} t_lowmem_list;
 
 /* cell lists */
 typedef struct s_linkcell {
@@ -64,13 +73,15 @@ typedef struct s_linkcell {
 	double x,y,z;		/* the actual cell lengthes */
 #ifdef STATIC_LISTS
 	int **subcell;		/* pointer to the cell lists */
+#elif LOWMEM_LISTS
+	t_lowmem_list *subcell; /* low mem approach list */
 #else
 	t_list *subcell;	/* pointer to the cell lists */
 #endif
 	int dnlc;		/* direct neighbour lists counter */
 } t_linkcell;
 
-#define MAX_ATOMS_PER_LIST	10
+#define MAX_ATOMS_PER_LIST	20
 
 /* moldyn schedule structure */
 typedef struct s_moldyn_schedule {
@@ -102,22 +113,24 @@ typedef struct s_moldyn {
 	double volume;		/* volume of sim cell (dim.x*dim.y*dim.z) */
 
 	/* potential force function and parameter pointers */
-	int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
-	int (*func2b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
-	int (*func3b_j1)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
-	int (*func3b_j2)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
-	int (*func3b_j3)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
-	int (*func3b_k1)(struct s_moldyn *moldyn,
-	                 t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
-	int (*func3b_k2)(struct s_moldyn *moldyn,
-	                 t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
+	int (*func_i0)(struct s_moldyn *moldyn,t_atom *ai);
+	int (*func_j0)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+	int (*func_j0_k0)(struct s_moldyn *moldyn,
+	                  t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
+	int (*func_j0e)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+	int (*func_j1)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+	int (*func_j1_k0)(struct s_moldyn *moldyn,
+	                  t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
+	int (*func_j1c)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+	int (*func_j1_k1)(struct s_moldyn *moldyn,
+	                  t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
+	int (*func_j1e)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
 	void *pot_params;
 	unsigned char run3bp;
 
 	double cutoff;		/* cutoff radius */
 	double cutoff_square;	/* square of the cutoff radius */
 	double nnd;		/* nearest neighbour distance (optional) */
-	double bondlen[3];	/* bond lengthes (only 2 atomic systems) */
 
 	t_linkcell lc;		/* linked cell list interface */
 
@@ -128,26 +141,38 @@ typedef struct s_moldyn {
 	double t_sum;		/* sum over all t */
 	double t_avg;		/* average value of t */
 
+	/* for sale! */
 	t_virial gvir;		/* global virial (absolute coordinates) */
-	double gv;
-	double gv_sum;
-	double gv_avg;
-
-	double gp;		/* pressure computed from global virial */
-	double gp_sum;		/* sum over all gp */
-	double gp_avg;		/* average value of gp */
-
-	double virial;		/* actual virial */
+	//double gv;
+	//double gv_sum;
+	//double gv_avg;
+	double sale1;
+	double sale2;
+	double sale3;
+
+	// gp stuff exchanged by kinetic energies
+	//double gp;		/* pressure computed from global virial */
+	//double gp_sum;		/* sum over all gp */
+	//double gp_avg;		/* average value of gp */
+	double ekinx;
+	double ekiny;
+	double ekinz;
+
+	t_virial vir;		/* actual virial */
+	double virial;
 	double virial_sum;	/* sum over all calculated virials */
 	double virial_avg;	/* average of virial */
 
 	double p_ref;		/* reference pressure */
 	double p;		/* actual pressure (computed by virial) */
+	double px,py,pz;	/* components of pressure */
 	double p_sum;		/* sum over all p */
 	double p_avg;		/* average value of p */
 
-	t_3dvec tp;		/* thermodynamic pressure dU/dV */
-	double dv;		/* dV for thermodynamic pressure calc */
+	double tp;		/* thermodynamic pressure dU/dV */
+	double tp_sum;		/* sum over dU/dV pressure */
+	double tp_avg;		/* average value of dU/dV pressure */
+	int tp_cnt;		/* how often to do thermodynamic p calc */
 
 	/* pressure and temperature control (velocity/volume scaling) */
 	/* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */
@@ -198,7 +223,9 @@ typedef struct s_moldyn {
 	int pfd;		/* fd for pressure log */
 	unsigned int twrite;	/* how often to log temperature */
 	int tfd;		/* fd for temperature log */
-	unsigned int vwrite;	/* how often to visualize atom information */
+	unsigned int vwrite;	/* how often to log volume */
+	int vfd;		/* fd for volume log */
+	unsigned int awrite;	/* how often to visualize atom information */
 	unsigned int swrite;	/* how often to create a save file */
 	int rfd;		/* report file descriptor */
 	char rtitle[64];	/* report title */
@@ -212,8 +239,66 @@ typedef struct s_moldyn {
 	t_random random;	/* random interface */
 
 	double debug;		/* debugging stuff, ignore */
+
+	/* potential 2 body check function */
+	int (*check_2b_bond)(struct s_moldyn *moldyn,
+	                     t_atom *itom,t_atom *jtom,u8 bc);
 } t_moldyn;
 
+typedef struct s_pcc {
+	int o1;
+	int o2;
+	double dr;
+	double *stat;
+} t_pcc;
+
+typedef struct s_ba {
+	int *acnt;
+	int *bcnt;
+	int tcnt;
+} t_ba;
+
+typedef struct s_vb {
+	int fd;
+} t_vb;
+
+typedef struct s_part_params {
+	u8 type;
+	double r;
+	t_3dvec p;
+	t_3dvec d;
+} t_part_params;
+
+#define PART_INSIDE_R   1
+#define PART_OUTSIDE_R  2
+#define PART_INSIDE_D   3
+#define PART_OUTSIDE_D  4
+
+typedef struct s_defect_params {
+	u8 type;
+	u8 stype;
+	double od;
+	double dd;
+	int element;
+	u8 brand;
+	u8 attr;
+} t_defect_params;
+
+#define DEFECT_TYPE_0D	1
+#define DEFECT_TYPE_1D	2
+#define DEFECT_TYPE_2D	3
+#define DEFECT_TYPE_3D	4
+
+#define DEFECT_STYPE_DB_X	1
+#define DEFECT_STYPE_DB_Y	2
+#define DEFECT_STYPE_DB_Z	3
+#define DEFECT_STYPE_DB_R	4
+
+typedef struct s_offset_params {
+	t_3dvec o;
+	u8 use;
+} t_offset_params;
+
 /*
  *
  *  defines
@@ -230,10 +315,15 @@ typedef struct s_moldyn {
 #define MOLDYN_2BP			0x20	/* 2 body */
 #define MOLDYN_3BP			0x40	/* and 3 body particle pots */
 
+#define T_SCALE_NONE			0x00
 #define T_SCALE_BERENDSEN		0x01	/* berendsen t control */
 #define T_SCALE_DIRECT			0x02	/* direct t control */
+#define T_SCALE_MASK			0x03
+
+#define P_SCALE_NONE			0x00
 #define P_SCALE_BERENDSEN		0x04	/* berendsen p control */
 #define P_SCALE_DIRECT			0x08	/* direct p control */
+#define P_SCALE_MASK			0x0c
 
 /*
  * default values & units
@@ -252,6 +342,7 @@ typedef struct s_moldyn {
 #define KILOGRAM			(1.0/AMU)		/* amu */
 #define NEWTON	(METER*KILOGRAM/(SECOND*SECOND))	/* A amu / fs^2 */
 #define PASCAL	(NEWTON/(METER*METER))			/* N / A^2 */
+#define GPA	(1e9*PASCAL)				/* N / A^2 */
 #define BAR	((1.0e5*PASCAL))			/* N / A^2 */
 #define K_BOLTZMANN	(1.380650524e-23*METER*NEWTON)	/* NA/K */
 #define K_B2		(K_BOLTZMANN*K_BOLTZMANN)	/* (NA)^2/K^2 */
@@ -269,14 +360,17 @@ typedef struct s_moldyn {
 #define MOLDYN_POTENTIAL_HO		0x00
 #define MOLDYN_POTENTIAL_LJ		0x01
 #define MOLDYN_POTENTIAL_TM		0x02
+#define MOLDYN_POTENTIAL_AM		0x03
+#define MOLDYN_POTENTIAL_AO		0x04
 
 #define LOG_TOTAL_ENERGY		0x01
 #define LOG_TOTAL_MOMENTUM		0x02
 #define LOG_PRESSURE			0x04
 #define LOG_TEMPERATURE			0x08
-#define SAVE_STEP			0x10
-#define VISUAL_STEP			0x20
-#define CREATE_REPORT			0x40
+#define LOG_VOLUME			0x10
+#define SAVE_STEP			0x20
+#define VISUAL_STEP			0x40
+#define CREATE_REPORT			0x80
 
 #define TRUE				1
 #define FALSE				0
@@ -289,12 +383,15 @@ typedef struct s_moldyn {
 #define SCALE_DIRECT			'D'
 
 /*
- * potential related phsical values / constants
- *
+ * usefull constants
  */
 
 #define ONE_THIRD		(1.0/3.0)
 
+/*
+ * element specific defines
+ */
+
 #define C			0x06
 #define LC_C			3.567				/* A */
 #define M_C			12.011				/* amu */
@@ -305,82 +402,6 @@ typedef struct s_moldyn {
 
 #define LC_3C_SIC		4.3596				/* A */
 
-#define LJ_SIGMA_SI		((0.25*sqrt(3.0)*LC_SI)/1.122462)	/* A */
-//#define LJ_SIGMA_SI		(LC_SI/1.122462)			/* A */
-//#define LJ_SIGMA_SI		(0.5*sqrt(2.0)*LC_SI/1.122462)		/* A */
-#define LJ_EPSILON_SI		(2.1678*EV)				/* NA */
-
-#define TM_R_SI			2.7				/* A */
-#define TM_S_SI			3.0				/* A */
-#define TM_A_SI			(1830.8*EV)			/* NA */
-#define TM_B_SI			(471.18*EV)			/* NA */
-#define TM_LAMBDA_SI		2.4799				/* 1/A */
-#define TM_MU_SI		1.7322				/* 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			1.8				/* A */
-#define TM_S_C			2.1				/* A */
-#define TM_A_C			(1393.6*EV)			/* NA */
-#define TM_B_C			(346.7*EV)			/* NA */
-#define TM_LAMBDA_C		3.4879				/* 1/A */
-#define TM_MU_C			2.2119				/* 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
-
-#define TM_LC_SIC		4.32				/* A */
-
-#define ALBE_R_SI		(2.82-0.14)
-#define ALBE_S_SI		(2.82+0.14)
-#define ALBE_A_SI		(3.24*EV/0.842)
-#define ALBE_B_SI		(-1.842*3.24*EV/0.842)
-#define ALBE_R0_SI		2.232
-#define ALBE_LAMBDA_SI		(1.4761*sqrt(2.0*1.842))
-#define ALBE_MU_SI		(1.4761*sqrt(2.0/1.842))
-#define ALBE_GAMMA_SI		0.114354
-#define ALBE_C_SI		2.00494
-#define ALBE_D_SI		0.81472
-#define ALBE_H_SI		0.259
-
-#define ALBE_LC_SI		5.429
-
-#define ALBE_R_C		(2.00-0.15)
-#define ALBE_S_C		(2.00+0.15)
-#define ALBE_A_C		(6.00*EV/1.167)
-#define ALBE_B_C		(-2.167*6.00*EV/1.167)
-#define ALBE_R0_C		1.4276
-#define ALBE_LAMBDA_C		(2.0099*sqrt(2.0*2.167))
-#define ALBE_MU_C		(2.0099*sqrt(2.0/2.167))
-#define ALBE_GAMMA_C		0.11233
-#define ALBE_C_C		181.910
-#define ALBE_D_C		6.28433
-#define ALBE_H_C		0.5556
-
-#define ALBE_LC_C		3.566
-
-#define ALBE_R_SIC		(2.40-0.20)
-#define ALBE_S_SIC		(2.40+0.20)
-#define ALBE_A_SIC		(4.36*EV/0.847)
-#define ALBE_B_SIC		(-1.847*4.36*EV/0.847)
-#define ALBE_R0_SIC		1.79
-#define ALBE_LAMBDA_SIC		(1.6991*sqrt(2.0*1.847))
-#define ALBE_MU_SIC		(1.6991*sqrt(2.0/1.847))
-#define ALBE_GAMMA_SIC		0.011877
-#define ALBE_C_SIC		273987
-#define ALBE_D_SIC		180.314
-#define ALBE_H_SIC		0.68
-
-#define ALBE_LC_SIC		4.359
-
-
 /*
  * lattice types
  */
@@ -388,6 +409,14 @@ typedef struct s_moldyn {
 #define CUBIC			0x01
 #define FCC			0x02
 #define DIAMOND			0x04
+#define ZINCBLENDE		0x08
+#define NONE			0x80
+
+/*
+ * more includes
+ */
+
+//#include "pse.h"
 
 /*
  *
@@ -395,30 +424,20 @@ typedef struct s_moldyn {
  *
  */
 
-typedef int (*pf_func1b)(t_moldyn *,t_atom *);
-typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8);
-typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8);
-
 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_bondlen(t_moldyn *moldyn,double b0,double b1,double bm);
 int set_temperature(t_moldyn *moldyn,double t_ref);
 int set_pressure(t_moldyn *moldyn,double p_ref);
+int set_p_scale(t_moldyn *moldyn,u8 ptype,double ptc);
+int set_t_scale(t_moldyn *moldyn,u8 ttype,double ttc);
 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);
-int set_potential2b(t_moldyn *moldyn,pf_func2b func);
-int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func);
-int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func);
-int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func);
-int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func);
-int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func);
-int set_potential_params(t_moldyn *moldyn,void *params);
+int set_potential(t_moldyn *moldyn,u8 type);
 
 int set_avg_skip(t_moldyn *moldyn,int skip);
 
@@ -427,14 +446,19 @@ int moldyn_set_report(t_moldyn *moldyn,char *author,char *title);
 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,
-                   u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin);
-int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
+int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,
+                   u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin,
+                   t_part_params *p_params,t_defect_params *d_params,
+                   t_offset_params *o_params);
+int add_atom(t_moldyn *moldyn,int element,u8 brand,u8 attr,
              t_3dvec *r,t_3dvec *v);
 int del_atom(t_moldyn *moldyn,int tag);
-int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
-int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
-int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
+int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
+               t_part_params *p_params,t_defect_params *d_params);
+int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
+             t_part_params *p_params,t_defect_params *d_params);
+int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
+                 t_part_params *p_params,t_defect_params *d_params);
 int destroy_atoms(t_moldyn *moldyn);
 
 int thermal_init(t_moldyn *moldyn,u8 equi_init);
@@ -444,7 +468,8 @@ double get_temperature(t_moldyn *moldyn);
 int scale_velocity(t_moldyn *moldyn,u8 equi_init);
 double virial_sum(t_moldyn *moldyn);
 double pressure_calc(t_moldyn *moldyn);
-int energy_fluctuation_calc(t_moldyn *moldyn);
+int average_reset(t_moldyn *moldyn);
+int average_and_fluctuation_calc(t_moldyn *moldyn);
 int get_heat_capacity(t_moldyn *moldyn);
 double thermodynamic_pressure_calc(t_moldyn *moldyn);
 double get_pressure(t_moldyn *moldyn);
@@ -462,6 +487,8 @@ int link_cell_init(t_moldyn *moldyn,u8 vol);
 int link_cell_update(t_moldyn *moldyn);
 #ifdef STATIC_LISTS
 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int **cell);
+#elif LOWMEM_LISTS
+int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int *cell);
 #else
 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
 #endif
@@ -480,20 +507,44 @@ int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d);
 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d)
 //	__attribute__((always_inline));
 int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
+int check_per_bound_and_care_for_pbc(t_moldyn *moldyn,t_atom *a);
 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
 //	__attribute__((always_inline));
 
 int moldyn_bc_check(t_moldyn *moldyn);
 
 int moldyn_read_save_file(t_moldyn *moldyn,char *file);
+int moldyn_free_save_file(t_moldyn *moldyn);
 int moldyn_load(t_moldyn *moldyn);
+int process_2b_bonds(t_moldyn *moldyn,void *data,
+                     int (*process)(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
+                                    void *data,u8 bc));
+int process_neighbours(t_moldyn *moldyn,void *data,t_atom *atom,
+                       int (*process)(t_moldyn *moldyn,t_atom *atom,t_atom *natom,
+                                      void *data,u8 bc));
+
 int get_line(int fd,char *line,int max);
 
 int pair_correlation_init(t_moldyn *moldyn,double dr);
+int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc);
+int calculate_msd(t_moldyn *moldyn,double *msd);
+int calculate_pair_correlation_process(t_moldyn *moldyn,t_atom *itom,
+                                       t_atom *jtom,void *data,u8 bc);
 int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr);
+int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
+                         void *data,u8 bc);
+int bond_analyze(t_moldyn *moldyn,double *quality);
 
 int visual_init(t_moldyn *moldyn,char *filebase);
+int visual_bonds_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
+                         void *data,u8 bc);
+#ifdef VISUAL_THREAD
+void *visual_atoms(void *ptr);
+#else
 int visual_atoms(t_moldyn *moldyn);
+#endif
+
+int fpu_set_rtd(void);
 
 #endif