X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=blobdiff_plain;f=moldyn.h;h=c6712ba41d1508fb8e359b627c71082e1307567a;hb=0d71b08d4382b23b8217342caf138cfce36226cc;hp=d94e1936db73727e2638f7b7f1974f814a951c41;hpb=3961d57b84198e336085fd79263fec40837066a0;p=physik%2Fposic.git

diff --git a/moldyn.h b/moldyn.h
index d94e193..c6712ba 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -10,79 +10,183 @@
 
 #include "math/math.h"
 #include "random/random.h"
-//#include "visual/visual.h"
+#include "list/list.h"
+
 
 /* datatypes */
 
+
+/* 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 */
+	int element;		/* number of element in pse */
+	double mass;		/* atom mass */
+	unsigned char attr;	/* attributes */
 } t_atom;
 
+#define ATOM_ATTR_FP	0x01	/* fixed position (bulk material) */
+#define ATOM_ATTR_HB	0x02	/* coupled to heat bath (velocity scaling) */
+
+/* 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 properties structure */
+
 typedef struct s_moldyn {
-	int count;
-	t_atom *atom;
-	double (*potential)(struct s_moldyn *moldyn);
-	void *pot_params;
-	int (*force)(struct s_moldyn *moldyn);
+
+	int count;		/* total amount of atoms */
+	t_atom *atom;		/* pointer to the atoms */
+	t_3dvec dim;		/* dimensions of the simulation volume */
+	/* potential, force & parameters */
+
+	/* potential force funtion created by the user */
+	int (*potential_force_function)(struct s_moldyn *moldyn);
+	void *pot_params;	/* parameters describing the potential */ 
+
+	double cutoff;
 	double cutoff_square;
-	t_3dvec dim;
+	/* linked list / cell method */
+	t_linkcell lc;
+	/* temperature */
+	double t;
+	/* integration of newtons equations */
 	int (*integrate)(struct s_moldyn *moldyn);
 	int time_steps;
 	double tau;
+	double tau_square;
+	/* energy */
+	double energy;
+	/* logging & visualization */
+	t_visual vis;
+	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;
+	/* random */
+	t_random random;
 } t_moldyn;
 
+typedef struct s_ho_params {
+	double spring_constant;
+	double equilibrium_distance;
+} t_ho_params;
+
 typedef struct s_lj_params {
 	double sigma6;
 	double sigma12;
-	double epsilon;
+	double epsilon4;
 } t_lj_params;
 
+typedef struct s_tersoff_params {
+	double l_1,l_2;
+	double m_1,m_2;
+	double a_1,a_2;
+	double b_1,b_2;
+	double r_1,r_2;
+	double s_1,s_2;
+} t_tersoff_params;
+
 /*
  *  defines
  */
 
 /* general defines */
 
+#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_STAT_POTENTIAL		0x01
 #define MOLDYN_STAT_FORCE		0x02
 
+#define MOLDYN_TEMP			273.0
+#define MOLDYN_TAU			1.0e-15
+#define MOLDYN_CUTOFF			10.0e-9
+#define MOLDYN_RUNS			1000000
+
+#define MOLDYN_INTEGRATE_VERLET		0x00
+#define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
+
+#define MOLDYN_POTENTIAL_HO		0x00
+#define MOLDYN_POTENTIAL_LJ		0x01
+#define MOLDYN_POTENTIAL_DEFAULT MOLDYN_POTENTIAL_LJ
+
 /* phsical values */
 
-//#define K_BOLTZMANN		1.3807E-23
-#define K_BOLTZMANN		1.0
+#define K_BOLTZMANN		1.3807e-27			/* Nm/K */
+#define AMU			1.660540e-27			/* kg */
 
 #define FCC			0x01
 #define DIAMOND			0x02
 
 #define C			0x06
-#define M_C			6.0
+#define M_C			(12.011*AMU)
 
-#define Si			0x0e
-#define M_SI			14.0
-#define LC_SI			5.43105
+#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 */
 
 /* function prototypes */
 
+int moldyn_usage(char **argv);
+int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv);
+int moldyn_log_init(t_moldyn *moldyn);
+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_atom *atom,t_random *random,int count,double t);
-int scale_velocity(t_atom *atom,int count,double t);
+int thermal_init(t_moldyn *moldyn);
+int scale_velocity(t_moldyn *moldyn);
 double get_e_kin(t_atom *atom,int count);
 double get_e_pot(t_moldyn *moldyn);
 double get_total_energy(t_moldyn *moldyn);
 t_3dvec get_total_p(t_atom *atom,int count);
 
+double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t);
+
+int link_cell_init(t_moldyn *moldyn);
+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);
+
 int moldyn_integrate(t_moldyn *moldyn);
 int velocity_verlet(t_moldyn *moldyn);
 
-double potential_lennard_jones(t_moldyn *moldyn);
-int force_lennard_jones(t_moldyn *moldyn);
+int harmonic_oscillator(t_moldyn *moldyn);
+int lennard_jones(t_moldyn *moldyn);
 
 #endif