runtime schedule adding and injection of c atoms

[physik/posic.git] / moldyn.h

diff --git a/moldyn.h b/moldyn.h
index fc9bce7..51ad482 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -77,6 +77,7 @@ typedef struct s_moldyn_schedule {
 /* moldyn main structure */
 typedef struct s_moldyn {
        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 +102,31 @@ 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 */
 
@@ -139,9 +148,26 @@ typedef struct s_moldyn {
        double tau_square;      /* delta t squared */
        int total_steps;        /* total steps */
 
+       /* energy */
        double energy;          /* potential energy */
        double ekin;            /* kinetic energy */
 
+       /* energy averages & fluctuations */
+       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) */
+       double c_v_nvt;         /* constant volume heat capacity (nvt) */
+
        char vlsdir[128];       /* visualization/log/save directory */
        t_visual vis;           /* visualization interface structure */
        u8 vlsprop;             /* log/vis/save properties */
@@ -209,7 +235,9 @@ typedef struct s_moldyn {
 #define PASCAL (NEWTON/(METER*METER))                  /* N / A^2 */
 #define BAR    ((1.0e5*PASCAL))                        /* N / A^2 */
 #define K_BOLTZMANN    (1.380650524e-23*METER*NEWTON)  /* NA/K */
+#define K_B2           (K_BOLTZMANN*K_BOLTZMANN)       /* (NA)^2/K^2 */
 #define EV             (1.6021765314e-19*METER*NEWTON) /* NA */
+#define JOULE          (NEWTON*METER)                  /* NA */
 
 #define MOLDYN_TEMP                    273.0
 #define MOLDYN_TAU                     1.0
@@ -289,7 +317,7 @@ 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)
@@ -303,7 +331,7 @@ 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)
@@ -317,7 +345,7 @@ 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)
@@ -331,7 +359,7 @@ 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
 
 
 /*
@@ -373,6 +401,8 @@ 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);
@@ -388,10 +418,14 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
 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);
@@ -427,7 +461,6 @@ int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
 
 int moldyn_bc_check(t_moldyn *moldyn);
 
-int read_line(int fd,char *line);
-int calc_fluctuations(double start,double end,char *file);
+int get_line(int fd,char *line,int max);
 
 #endif