X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=9f9d0f71fcd8f44985ab07960bac8d4bb34a51f5;hb=e67bb08cb64bf21a6d4e7e8275007bdc5e769154;hp=868db6267784faa8d684d265e6a976668776f10f;hpb=25c22fe95e80365056c6a7fadc548119360ca8ce;p=physik%2Fposic.git

diff --git a/moldyn.h b/moldyn.h
index 868db62..9f9d0f7 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 */
@@ -76,6 +78,9 @@ 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 */
@@ -102,25 +107,31 @@ typedef struct s_moldyn {
 
 	t_linkcell lc;		/* linked cell list interface */
 
-	int mean_skip;		/* amount of steps without average calc */
+	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 */
 
@@ -149,14 +160,14 @@ typedef struct s_moldyn {
 	/* energy averages & fluctuations */
 	double k_sum;		/* sum of kinetic energy */
 	double v_sum;		/* sum of potential energy */
-	double k_mean;		/* average of kinetic energy */
-	double v_mean;		/* average 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_mean;		/* average of kinetic energy squared */
-	double v2_mean;		/* average of potential energy squared */
-	double dk2_mean;	/* mean square kinetic energy fluctuations */
-	double dv2_mean;	/* mean square potential energy fluctuations */
+	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) */
@@ -395,7 +406,7 @@ 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_mean_skip(t_moldyn *moldyn,int skip);
+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);
@@ -404,11 +415,11 @@ 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);
@@ -416,6 +427,7 @@ 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);