X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=5b12048f908f55b3a987475dc8b352f8714ed844;hb=0b96eb313c9bfec6272b1f8de0d99c4ce26d1686;hp=85a4950cc513c9cde9b7dc0cb66f9d49503e3b8f;hpb=ea612b88a0588b8f46fafaebf3b37fb46c83c0cf;p=physik%2Fposic.git

diff --git a/moldyn.h b/moldyn.h
index 85a4950..5b12048 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -85,11 +85,15 @@ typedef struct s_moldyn {
 	/* 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);
+	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;
-	//int (*potential_force_function)(struct s_moldyn *moldyn);
+	unsigned char run3bp;
 
 	double cutoff;		/* cutoff radius */
 	double cutoff_square;	/* square of the cutoff radius */
@@ -99,9 +103,18 @@ typedef struct s_moldyn {
 
 	double t_ref;		/* reference temperature */
 	double t;		/* actual temperature */
+	double t_sum;		/* sum over all t */
+	double mean_t;		/* mean value of t */
+
+	t_virial virial;	/* global virial (absolute coordinates) */
+	double gp;		/* pressure computed from global virial */
+	double gp_sum;		/* sum over all gp */
+	double mean_gp;		/* mean value of gp */
 
 	double p_ref;		/* reference pressure */
 	double p;		/* actual pressure (computed by virial) */
+	double p_sum;		/* sum over all p */
+	double mean_p;		/* mean value of p */
 	t_3dvec tp;		/* thermodynamic pressure dU/dV */
 	double dv;		/* dV for thermodynamic pressure calc */
 
@@ -121,7 +134,7 @@ typedef struct s_moldyn {
 	double tau;		/* delta t */
 	double time;		/* absolute time */
 	double tau_square;	/* delta t squared */
-	double elapsed;		/* total elapsed time */
+	int total_steps;	/* total steps */
 
 	double energy;		/* potential energy */
 	double ekin;		/* kinetic energy */
@@ -175,7 +188,7 @@ typedef struct s_moldyn {
 #define P_SCALE_DIRECT			0x08	/* direct p control */
 
 /*
- * default values
+ * default values & units
  *
  * - length unit: 1 A (1 A = 1e-10 m)
  * - time unit: 1 fs (1 fs = 1e-15 s)
@@ -191,7 +204,9 @@ 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 ATM	((1.0133e5*PASCAL))			/* N / A^2 */
+#define BAR	((1.0e5*PASCAL))			/* N / A^2 */
+#define K_BOLTZMANN	(1.380650524e-23*METER*NEWTON)	/* NA/K */
+#define EV		(1.6021765314e-19*METER*NEWTON)	/* NA */
 
 #define MOLDYN_TEMP			273.0
 #define MOLDYN_TAU			1.0
@@ -220,17 +235,12 @@ typedef struct s_moldyn {
 #define QUIET				0
 
 /*
- *
- * phsical values / constants
- *
+ * potential related phsical values / constants
  *
  */
 
 #define ONE_THIRD		(1.0/3.0)
 
-#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 */
 
@@ -284,10 +294,9 @@ typedef struct s_moldyn {
  *
  */
 
-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);
+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);
@@ -302,8 +311,11 @@ 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_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 moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
@@ -331,8 +343,7 @@ 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 e_kin_calc(t_moldyn *moldyn);
 double get_total_energy(t_moldyn *moldyn);
 t_3dvec get_total_p(t_moldyn *moldyn);