X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=83b3a86d8f41c6560cfe4d829523976dfac3fb6f;hb=a32468230b319b32819f1b20fd28aa9659574d45;hp=2d4ca4873109a80732606ff7f425d764d8b59259;hpb=95cfeec6fbbfa975d5ac5b99ec3f7386ca3d6071;p=physik%2Fposic.git

diff --git a/moldyn.h b/moldyn.h
index 2d4ca48..83b3a86 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -62,10 +62,16 @@ 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;
 
+#define MAX_ATOMS_PER_LIST	20
+
 /* moldyn schedule structure */
 typedef struct s_moldyn_schedule {
 	int count;
@@ -131,7 +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 */
 
@@ -140,8 +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.) */
@@ -192,7 +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 */
@@ -246,6 +257,7 @@ 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 */
@@ -268,9 +280,10 @@ 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
@@ -438,7 +451,8 @@ 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);
@@ -454,7 +468,11 @@ 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 *);
@@ -475,8 +493,14 @@ 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_load(t_moldyn *moldyn);
 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(t_moldyn *moldyn,double dr,void *ptr);
+
 int visual_init(t_moldyn *moldyn,char *filebase);
 int visual_atoms(t_moldyn *moldyn);