X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=b14037219f7ddcdf5b34adf4deb173d78636510a;hb=e25ff194682ff5fac86c60701343103e74973bed;hp=e9f1495355df4dad8a44f3779f678649b328a99d;hpb=e6f456c0fa807b86e1b25996e70efcdcfe390ea5;p=physik%2Fposic.git

diff --git a/moldyn.h b/moldyn.h
index e9f1495..b140372 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -12,150 +12,345 @@
 #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;
-	double x,y,z;
-	t_list *subcell;
+	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"
 
-typedef struct s_moldyn {
-	/* atoms, amount, dimensions */
+/* moldyn schedule structure */
+typedef struct s_moldyn_schedule {
 	int count;
-	t_atom *atom;
-	t_3dvec dim;
-	/* potential, force & parameters */
-	int (*potential_force_function)(struct s_moldyn *moldyn);
+	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 */
+	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 (*func2b_post)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+	int (*func3b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,
+	              u8 bck);
 	void *pot_params;
-	/* cut off radius */
-	double cutoff;
-	double cutoff_square;
-	/* linked list / cell method */
-	t_linkcell lc;
-	/* temperature */
-	double t;
-	/* integration of newtons equations */
+	//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 list interface */
+
+	double t_ref;		/* reference temperature */
+	double t;		/* actual temperature */
+
+	double p_ref;		/* reference pressure */
+	double p;		/* actual pressure (computed by virial) */
+	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;
-	double tau;
-	double tau_square;
-	/* energy */
-	double energy;
-	/* logging & visualization */
-	unsigned char lvstat;
-	unsigned int ewrite;
-	char efb[64];
-	int efd;
-	unsigned int mwrite;
-	char mfb[64];
-	int mfd;
-	unsigned int swrite;
-	char sfb[64];
-	int sfd;
-	unsigned int dwrite;
-	char dfb[64];
-	int dfd;
-	unsigned int vwrite;
-	char vfb[64];
-	void *visual;
-	/* moldyn general status */
-	unsigned char status;
-} t_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 */
 
-typedef struct s_ho_params {
-	double spring_constant;
-	double equilibrium_distance;
-} t_ho_params;
+	double energy;		/* potential energy */
+	double ekin;		/* kinetic energy */
 
-typedef struct s_lj_params {
-	double sigma6;
-	double sigma12;
-	double epsilon4;
-} t_lj_params;
+	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 */
+	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 pfd;		/* gnuplot script file descriptor */
+
+	u8 status;		/* general moldyn properties */
+
+	t_random random;	/* random interface */
+
+	double debug;		/* debugging stuff, ignore */
+} t_moldyn;
 
 /*
+ *
  *  defines
+ *
  */
 
-/* general 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_LVSTAT_TOTAL_E		0x01
-#define MOLDYN_LVSTAT_TOTAL_M		0x02
-#define MOLDYN_LVSTAT_SAVE		0x04
-#define MOLDYN_LVSTAT_DUMP		0x08
-#define MOLDYN_LVSTAT_VISUAL		0x10
-#define MOLDYN_LVSTAT_INITIALIZED	0x80
+#define MOLDYN_PSCALE			0x08	/* size controlled by piston */
 
-#define MOLDYN_STAT_POTENTIAL		0x01
-#define MOLDYN_STAT_FORCE		0x02
+#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
+ *
+ * - 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 ATM	((1.0133e5*PASCAL))			/* N / A^2 */
 
 #define MOLDYN_TEMP			273.0
-#define MOLDYN_TAU			1.0e-15
+#define MOLDYN_TAU			1.0
+#define MOLDYN_CUTOFF			10.0
 #define MOLDYN_RUNS			1000000
 
 #define MOLDYN_INTEGRATE_VERLET		0x00
-#define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
+#define MOLDYN_INTEGRATE_DEFAULT 	MOLDYN_INTEGRATE_VERLET
 
 #define MOLDYN_POTENTIAL_HO		0x00
 #define MOLDYN_POTENTIAL_LJ		0x01
-#define MOLDYN_POTENTIAL_DEFAULT MOLDYN_POTENTIAL_LJ
+#define MOLDYN_POTENTIAL_TM		0x02
+
+#define LOG_TOTAL_ENERGY		0x01
+#define LOG_TOTAL_MOMENTUM		0x02
+#define SAVE_STEP			0x04
+#define VISUAL_STEP			0x08
+#define CREATE_REPORT			0x10
+
+#define TRUE				1
+#define FALSE				0
 
-/* phsical values */
+#define VERBOSE				1
+#define QUIET				0
+
+/*
+ *
+ * phsical values / constants
+ *
+ *
+ */
 
-#define K_BOLTZMANN		1.3807e-27			/* Nm/K */
-#define AMU			1.660540e-27			/* kg */
+#define ONE_THIRD		(1.0/3.0)
 
-#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_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			(2.7e-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
 
-/* function prototypes */
+#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
+ */
 
-int moldyn_usage(char **argv);
-int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv);
-int moldyn_log_init(t_moldyn *moldyn,void *v);
+#define CUBIC			0x01
+#define FCC			0x02
+#define DIAMOND			0x04
+
+
+/*
+ *
+ * function prototypes
+ *
+ */
+
+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 create_lattice(unsigned char type,int element,double mass,double lc,
-                   int a,int b,int c,t_atom **atom);
-int destroy_lattice(t_atom *atom);
-int thermal_init(t_moldyn *moldyn,t_random *random);
-int scale_velocity(t_moldyn *moldyn);
-double get_e_kin(t_atom *atom,int count);
-double get_e_pot(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_potential2b_post(t_moldyn *moldyn,pf_func2b_post func);
+int set_potential3b(t_moldyn *moldyn,pf_func3b func);
+int set_potential_params(t_moldyn *moldyn,void *params);
+
+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);
+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 temperature_calc(t_moldyn *moldyn);
+double get_temperature(t_moldyn *moldyn);
+int scale_velocity(t_moldyn *moldyn,u8 equi_init);
+double pressure_calc(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,double scale,u8 x,u8 y,u8 z);
+int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z);
+
+double get_e_kin(t_moldyn *moldyn);
+double update_e_kin(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_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);
 
-int harmonic_oscillator(t_moldyn *moldyn);
-int lennard_jones(t_moldyn *moldyn);
+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));
+
+int moldyn_bc_check(t_moldyn *moldyn);
 
 #endif