X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=1647c1c314cc71fd17cc57216ae3d732417dc676;hb=2346d076f3d0955fb3a7bfb47f2b17b9eae6dd5b;hp=36e701ea0877d88118d4d6441d963b5c1cbac803;hpb=684bf7c398cdfa98549b0c7a1fa37e6dc5b35bea;p=physik%2Fposic.git

diff --git a/moldyn.h b/moldyn.h
index 36e701e..1647c1c 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -49,6 +49,8 @@ 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_VA	0x04	/* visualize this atom */
+#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 */
@@ -60,11 +62,15 @@ typedef struct s_linkcell {
 	int cells;		/* total amount of cells */
 	double len;		/* prefered cell edge length */
 	double x,y,z;		/* the actual cell lengthes */
+#ifdef STATIC_LISTS
+	int **subcell;		/* pointer to the cell lists */
+#else
 	t_list *subcell;	/* pointer to the cell lists */
+#endif
 	int dnlc;		/* direct neighbour lists counter */
 } t_linkcell;
 
-#include "visual/visual.h"
+#define MAX_ATOMS_PER_LIST	20
 
 /* moldyn schedule structure */
 typedef struct s_moldyn_schedule {
@@ -76,6 +82,13 @@ typedef struct s_moldyn_schedule {
 	void *hook_params;
 } t_moldyn_schedule;
 
+/* visualization structure */
+typedef struct s_visual {
+	int fd;			/* rasmol script file descriptor */
+	char fb[128];		/* basename of the save files */
+	t_3dvec dim;		/* dimensions of the simulation cell */
+} t_visual;
+
 /* moldyn main structure */
 typedef struct s_moldyn {
 	int argc;		/* number of arguments */
@@ -104,6 +117,7 @@ typedef struct s_moldyn {
 	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 */
 
@@ -123,7 +137,8 @@ typedef struct s_moldyn {
 	double gp_sum;		/* sum over all gp */
 	double gp_avg;		/* average value of gp */
 
-	double virial;		/* actual virial */
+	t_virial vir;		/* actual virial */
+	double virial;
 	double virial_sum;	/* sum over all calculated virials */
 	double virial_avg;	/* average of virial */
 
@@ -132,8 +147,10 @@ typedef struct s_moldyn {
 	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.) */
@@ -184,7 +201,9 @@ 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 */
@@ -200,6 +219,19 @@ typedef struct s_moldyn {
 	double debug;		/* debugging stuff, ignore */
 } 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;
+
 /*
  *
  *  defines
@@ -238,6 +270,7 @@ 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 */
@@ -260,9 +293,10 @@ typedef struct s_moldyn {
 #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
@@ -375,7 +409,6 @@ typedef struct s_moldyn {
 #define FCC			0x02
 #define DIAMOND			0x04
 
-
 /*
  *
  * function prototypes
@@ -391,6 +424,7 @@ 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_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc);
@@ -417,6 +451,7 @@ 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,
              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);
@@ -429,7 +464,8 @@ 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);
@@ -445,7 +481,11 @@ 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);
+#ifdef STATIC_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
 int link_cell_shutdown(t_moldyn *moldyn);
 
 typedef int (*set_hook)(void *,void *);
@@ -466,6 +506,25 @@ int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
 
 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 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_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_atoms(t_moldyn *moldyn);
+
 #endif
+