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 212db14..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 */
@@ -109,18 +111,24 @@ typedef struct s_moldyn {
        double t_sum;           /* sum over all t */
        double t_avg;           /* average value of t */
 
-       t_virial virial;        /* global virial (absolute coordinates) */
+       t_virial gvir;          /* global virial (absolute coordinates) */
+       double gv;
+       double gv_sum;
+       double gv_avg;
+
        double gp;              /* pressure computed from global virial */
        double gp_sum;          /* sum over all gp */
        double gp_avg;          /* average value of gp */
 
-       double virial_avg;      /* average 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 p_avg;           /* average value of p */
+
        t_3dvec tp;             /* thermodynamic pressure dU/dV */
        double dv;              /* dV for thermodynamic pressure calc */
 
@@ -404,11 +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);
@@ -416,6 +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);