small mods to support site energies and kinetic energies per atom

[physik/posic.git] / moldyn.h

diff --git a/moldyn.h b/moldyn.h
index 2d1a438..a595585 100644 (file)
--- 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 */
@@ -102,23 +104,31 @@ 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 */
 
@@ -147,14 +157,14 @@ 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) */
@@ -309,7 +319,7 @@ 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)
@@ -323,7 +333,7 @@ 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)
@@ -337,7 +347,7 @@ 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)
@@ -351,7 +361,7 @@ 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
 
 
 /*
@@ -393,6 +403,8 @@ 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);
@@ -400,11 +412,11 @@ 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);
@@ -412,6 +424,7 @@ 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);