X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=51ad482180fa44ff290109c0118dcb09b0185c09;hb=refs%2Fheads%2Forigin;hp=85bbfd73d894115234476408a66f0fd7747c1164;hpb=b040d775deb32173e6536464a3e2ad95a6a5bd55;p=physik%2Fposic.git

diff --git a/moldyn.h b/moldyn.h
index 85bbfd7..51ad482 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -9,35 +9,458 @@
 #define MOLDYN_H
 
 #include "math/math.h"
+#include "random/random.h"
+#include "list/list.h"
 
-/* datatypes */
+/*
+ * 
+ * datatypes
+ *
+ */
 
+/* general */
+typedef unsigned char u8;
+
+/* virial */
+typedef struct s_virial {
+	double xx;	/*			| xx	 xy	xz |	*/
+	double yy;	/*	V	=	| yx	 yy	yz |	*/
+	double zz;	/*			| zx	 zy	zz |	*/
+	double xy;	/*						*/
+	double xz;	/*	with:	xy=yx, xz=zx, yz=zy		*/
+	double yz;	/*						*/
+} t_virial;
+
+/* 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_3dvec r;		/* position */
+	t_3dvec v;		/* velocity */
+	t_3dvec f;		/* force */
+	t_virial virial;	/* virial */
+	double e;		/* site energy */
+	int element;		/* number of element in pse */
+	double mass;		/* atom mass */
+	u8 brand;		/* brand id */
+	int tag;		/* atom unique id (number of atom) */
+	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 */
+} t_linkcell;
+
+#include "visual/visual.h"
+
+/* moldyn schedule structure */
+typedef struct s_moldyn_schedule {
+	int count;
+	int total_sched;
+	int *runs;
+	double *tau;
+	int (*hook)(void *moldyn,void *hook_params);
+	void *hook_params;
+} t_moldyn_schedule;
+
+/* moldyn main structure */
+typedef struct s_moldyn {
+	int count;		/* total amount of atoms */
+	double mass;		/* total system mass */
+	t_atom *atom;		/* pointer to the atoms */
+
+	t_3dvec dim;		/* dimensions of the simulation volume */
+	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);
+	void *pot_params;
+	unsigned char run3bp;
+
+	double cutoff;		/* cutoff radius */
+	double cutoff_square;	/* square of the cutoff radius */
+	double nnd;		/* nearest neighbour distance (optional) */
+
+	t_linkcell lc;		/* linked cell list interface */
+
+	int avg_skip;		/* amount of steps without average calc */
+
+	double t_ref;		/* reference temperature */
+	double t;		/* actual temperature */
+	double t_sum;		/* sum over all t */
+	double t_avg;		/* average value of t */
+
+	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 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 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 */
+
+	/* pressure and temperature control (velocity/volume scaling) */
+	/* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */
+	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;
+	int current;		/* current position in schedule */
+
+	/* integration function pointer */
+	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 */
+	int total_steps;	/* total steps */
+
+	/* energy */
+	double energy;		/* potential energy */
+	double ekin;		/* kinetic energy */
+
+	/* energy averages & fluctuations */
+	double k_sum;		/* sum of kinetic energy */
+	double v_sum;		/* sum of potential energy */
+	double k_avg;		/* average of kinetic energy */
+	double v_avg;		/* average of potential energy */
+	double k2_sum;		/* sum of kinetic energy squared */
+	double v2_sum;		/* sum of potential energy squared */
+	double k2_avg;		/* average of kinetic energy squared */
+	double v2_avg;		/* average of potential energy squared */
+	double dk2_avg;		/* mean square kinetic energy fluctuations */
+	double dv2_avg;		/* mean square potential energy fluctuations */
+	
+	/* response functions */
+	double c_v_nve;		/* constant volume heat capacity (nve) */
+	double c_v_nvt;		/* constant volume heat capacity (nvt) */
+
+	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 pwrite;	/* how often to log pressure */
+	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 swrite;	/* how often to create a save file */
+	int rfd;		/* report file descriptor */
+	char rtitle[64];	/* report title */
+	char rauthor[64];	/* report author */
+	int epfd;		/* energy gnuplot script file descriptor */
+	int ppfd;		/* pressure gnuplot script file descriptor */
+	int tpfd;		/* temperature gnuplot script file descriptor */
+
+	u8 status;		/* general moldyn properties */
+
+	t_random random;	/* random interface */
+
+	double debug;		/* debugging stuff, ignore */
+} t_moldyn;
+
+/*
+ *
+ *  defines
+ *
+ */
+
+#define MOLDYN_STAT_PBX			0x01	/* periodic boudaries in x */
+#define MOLDYN_STAT_PBY			0x02	/* y */
+#define MOLDYN_STAT_PBZ			0x04	/* and z direction */
+
+#define MOLDYN_PSCALE			0x08	/* size controlled by piston */
+
+#define MOLDYN_1BP			0x10	/* care about single */
+#define MOLDYN_2BP			0x20	/* 2 body */
+#define MOLDYN_3BP			0x40	/* 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 */
+
+/*
+ * default values & units
+ *
+ * - 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 )
+ *
+ * fyi: in the following 1 N = (amu*A)/(fs*fs)
+ *
+ */
+
+#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 PASCAL	(NEWTON/(METER*METER))			/* 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 */
+#define EV		(1.6021765314e-19*METER*NEWTON)	/* NA */
+#define JOULE		(NEWTON*METER)			/* NA */
 
-/* defines */
+#define MOLDYN_TEMP			273.0
+#define MOLDYN_TAU			1.0
+#define MOLDYN_CUTOFF			10.0
+#define MOLDYN_RUNS			1000000
 
-#define K_BOLTZMANN		1.3807E-23;
+#define MOLDYN_INTEGRATE_VERLET		0x00
+#define MOLDYN_INTEGRATE_DEFAULT 	MOLDYN_INTEGRATE_VERLET
 
-#define FCC			0x01
-#define DIAMOND			0x02
+#define MOLDYN_POTENTIAL_HO		0x00
+#define MOLDYN_POTENTIAL_LJ		0x01
+#define MOLDYN_POTENTIAL_TM		0x02
+
+#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 TRUE				1
+#define FALSE				0
+
+#define VERBOSE				1
+#define QUIET				0
+
+#define SCALE_UP			'u'
+#define SCALE_DOWN			'd'
+#define SCALE_DIRECT			'D'
+
+/*
+ * potential related phsical values / constants
+ *
+ */
+
+#define ONE_THIRD		(1.0/3.0)
 
 #define C			0x06
-#define M_C			6.0
+#define LC_C			3.567				/* A */
+#define M_C			12.011				/* amu */
+
+#define SI			0x0e
+#define LC_SI			5.43105				/* A */
+#define M_SI			28.08553			/* amu */
+
+#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+0.10)
+#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
+ */
+
+#define CUBIC			0x01
+#define FCC			0x02
+#define DIAMOND			0x04
+
+
+/*
+ *
+ * function prototypes
+ *
+ */
+
+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_temperature(t_moldyn *moldyn,double t_ref);
+int set_pressure(t_moldyn *moldyn,double p_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);
+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_avg_skip(t_moldyn *moldyn,int skip);
+
+int moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
+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 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 add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
+             t_3dvec *r,t_3dvec *v);
+int destroy_atoms(t_moldyn *moldyn);
+
+int thermal_init(t_moldyn *moldyn,u8 equi_init);
+double total_mass_calc(t_moldyn *moldyn);
+double temperature_calc(t_moldyn *moldyn);
+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 get_heat_capacity(t_moldyn *moldyn);
+double thermodynamic_pressure_calc(t_moldyn *moldyn);
+double get_pressure(t_moldyn *moldyn);
+int scale_volume(t_moldyn *moldyn);
+int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
+int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
+
+double e_kin_calc(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);
+
+int link_cell_init(t_moldyn *moldyn,u8 vol);
+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);
+
+typedef int (*set_hook)(void *,void *);
+
+int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau);
+int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params);
+
+int moldyn_integrate(t_moldyn *moldyn);
+int velocity_verlet(t_moldyn *moldyn);
 
-#define Si			0x0e
-#define M_SI			14.0
-#define LC_SI			5.43105
+int potential_force_calc(t_moldyn *moldyn);
+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);
+//inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
+//	__attribute__((always_inline));
 
-/* function prototypes */
+int moldyn_bc_check(t_moldyn *moldyn);
 
-int create_lattice(unsigned char type,int element,double mass,double lc,
-                   int a,int b,int c,t_atom **atom);
+int get_line(int fd,char *line,int max);
 
 #endif