X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=36e701ea0877d88118d4d6441d963b5c1cbac803;hb=684bf7c398cdfa98549b0c7a1fa37e6dc5b35bea;hp=484c45605529657c396d12fad349dff7f05c24a7;hpb=58fd691b276fbe87593036714f26dbfe7486cbeb;p=physik%2Fposic.git

diff --git a/moldyn.h b/moldyn.h
index 484c456..36e701e 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -33,11 +33,13 @@ typedef struct s_virial {
 
 /* the atom of the md simulation */
 typedef struct s_atom {
+	t_3dvec r_0;		/* initial position */
 	t_3dvec r;		/* position */
 	t_3dvec v;		/* velocity */
 	t_3dvec f;		/* force */
 	t_virial virial;	/* virial */
 	double e;		/* site energy */
+	double ekin;		/* kinetic energy */
 	int element;		/* number of element in pse */
 	double mass;		/* atom mass */
 	u8 brand;		/* brand id */
@@ -76,7 +78,11 @@ typedef struct s_moldyn_schedule {
 
 /* moldyn main structure */
 typedef struct s_moldyn {
+	int argc;		/* number of arguments */
+	char **args;		/* pointer to arguments */
+
 	int count;		/* total amount of atoms */
+	double mass;		/* total system mass */
 	t_atom *atom;		/* pointer to the atoms */
 
 	t_3dvec dim;		/* dimensions of the simulation volume */
@@ -101,23 +107,31 @@ typedef struct s_moldyn {
 
 	t_linkcell lc;		/* linked cell list interface */
 
+	int avg_skip;		/* amount of steps without average calc */
+
 	double t_ref;		/* reference temperature */
 	double t;		/* actual temperature */
 	double t_sum;		/* sum over all t */
-	double mean_t;		/* mean value of t */
+	double t_avg;		/* average value of t */
+
+	t_virial gvir;		/* global virial (absolute coordinates) */
+	double gv;
+	double gv_sum;
+	double gv_avg;
 
-	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 gp_avg;		/* average value of gp */
 
-	double mean_v;		/* mean of virial */
+	double virial;		/* actual virial */
 	double virial_sum;	/* sum over all calculated virials */
+	double virial_avg;	/* average of virial */
 
 	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 */
+	double p_avg;		/* average value of p */
+
 	t_3dvec tp;		/* thermodynamic pressure dU/dV */
 	double dv;		/* dV for thermodynamic pressure calc */
 
@@ -144,12 +158,16 @@ typedef struct s_moldyn {
 	double ekin;		/* kinetic energy */
 
 	/* energy averages & fluctuations */
-	double k_m;
-	double p_m;
-	double t_m;
-	double dk2_m;		/* mean square kinetic energy fluctuations */
-	double dp2_m;		/* mean square potential energy fluctuations */
-	double dt2_m;		/* mean square fluctuations in total energy */
+	double k_sum;		/* sum of kinetic energy */
+	double v_sum;		/* sum of potential energy */
+	double k_avg;		/* average of kinetic energy */
+	double v_avg;		/* average of potential energy */
+	double k2_sum;		/* sum of kinetic energy squared */
+	double v2_sum;		/* sum of potential energy squared */
+	double k2_avg;		/* average of kinetic energy squared */
+	double v2_avg;		/* average of potential energy squared */
+	double dk2_avg;		/* mean square kinetic energy fluctuations */
+	double dv2_avg;		/* mean square potential energy fluctuations */
 	
 	/* response functions */
 	double c_v_nve;		/* constant volume heat capacity (nve) */
@@ -304,12 +322,12 @@ typedef struct s_moldyn {
 
 #define TM_CHI_SIC		0.9776
 
-#define TM_LC_3C_SIC		(0.432e-9*METER)		/* A */
+#define TM_LC_SIC		4.32				/* A */
 
 #define ALBE_R_SI		(2.82-0.14)
 #define ALBE_S_SI		(2.82+0.14)
 #define ALBE_A_SI		(3.24*EV/0.842)
-#define ALBE_B_SI		(1.842*3.24*EV/0.842)
+#define ALBE_B_SI		(-1.842*3.24*EV/0.842)
 #define ALBE_R0_SI		2.232
 #define ALBE_LAMBDA_SI		(1.4761*sqrt(2.0*1.842))
 #define ALBE_MU_SI		(1.4761*sqrt(2.0/1.842))
@@ -318,12 +336,12 @@ typedef struct s_moldyn {
 #define ALBE_D_SI		0.81472
 #define ALBE_H_SI		0.259
 
-#define LC_SI_ALBE		5.429
+#define ALBE_LC_SI		5.429
 
 #define ALBE_R_C		(2.00-0.15)
 #define ALBE_S_C		(2.00+0.15)
 #define ALBE_A_C		(6.00*EV/1.167)
-#define ALBE_B_C		(2.167*6.00*EV/1.167)
+#define ALBE_B_C		(-2.167*6.00*EV/1.167)
 #define ALBE_R0_C		1.4276
 #define ALBE_LAMBDA_C		(2.0099*sqrt(2.0*2.167))
 #define ALBE_MU_C		(2.0099*sqrt(2.0/2.167))
@@ -332,12 +350,12 @@ typedef struct s_moldyn {
 #define ALBE_D_C		6.28433
 #define ALBE_H_C		0.5556
 
-#define LC_C_ALBE		3.566
+#define ALBE_LC_C		3.566
 
 #define ALBE_R_SIC		(2.40-0.20)
-#define ALBE_S_SIC		(2.40+0.10)
+#define ALBE_S_SIC		(2.40+0.20)
 #define ALBE_A_SIC		(4.36*EV/0.847)
-#define ALBE_B_SIC		(1.847*4.36*EV/0.847)
+#define ALBE_B_SIC		(-1.847*4.36*EV/0.847)
 #define ALBE_R0_SIC		1.79
 #define ALBE_LAMBDA_SIC		(1.6991*sqrt(2.0*1.847))
 #define ALBE_MU_SIC		(1.6991*sqrt(2.0/1.847))
@@ -346,7 +364,7 @@ typedef struct s_moldyn {
 #define ALBE_D_SIC		180.314
 #define ALBE_H_SIC		0.68
 
-#define LC_SIC_ALBE		4.359
+#define ALBE_LC_SIC		4.359
 
 
 /*
@@ -388,6 +406,8 @@ 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 set_avg_skip(t_moldyn *moldyn,int skip);
+
 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);
@@ -395,18 +415,22 @@ 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,t_3dvec *origin);
+int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
+             t_3dvec *r,t_3dvec *v);
 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 total_mass_calc(t_moldyn *moldyn);
 double temperature_calc(t_moldyn *moldyn);
 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 get_heat_capacity(t_moldyn *moldyn);
 double thermodynamic_pressure_calc(t_moldyn *moldyn);
 double get_pressure(t_moldyn *moldyn);
 int scale_volume(t_moldyn *moldyn);
@@ -443,7 +467,5 @@ int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
 int moldyn_bc_check(t_moldyn *moldyn);
 
 int get_line(int fd,char *line,int max);
-int calc_fluctuations(double start,double end,t_moldyn *moldyn);
-int get_heat_capacity(t_moldyn *moldyn);
 
 #endif