still full of bugs ...

[physik/posic.git] / moldyn.h

diff --git a/moldyn.h b/moldyn.h
index b4f71d6..c5cc064 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -22,16 +22,27 @@
 /* general */
 typedef unsigned char u8;
 
+/* virial */
+typedef struct s_virial {
+       double xx;      /*                      | xx     xy     xz |    */
+       double yy;      /*      V       =       | yx     yy     yz |    */
+       double zz;      /*                      | zx     zy     zz |    */
+       double xy;      /*                                              */
+       double xz;      /*      with:   xy=yx, xz=zx, yz=zy             */
+       double yz;      /*                                              */
+} t_virial;
+
 /* the atom of the md simulation */
 typedef struct s_atom {
        t_3dvec r;              /* position */
        t_3dvec v;              /* velocity */
        t_3dvec f;              /* force */
-       t_3dvec virial;         /* virial */
+       t_virial virial;        /* virial */
        double e;               /* site energy */
        int element;            /* number of element in pse */
        double mass;            /* atom mass */
-       u8 bnum;                /* brand number */
+       u8 brand;               /* brand id */
+       int tag;                /* atom unique id (number of atom) */
        u8 attr;                /* attributes */
 } t_atom;
 
@@ -56,7 +67,8 @@ typedef struct s_linkcell {
 
 /* moldyn schedule structure */
 typedef struct s_moldyn_schedule {
-       int content_count;
+       int count;
+       int total_sched;
        int *runs;
        double *tau;
        int (*hook)(void *moldyn,void *hook);
@@ -70,6 +82,7 @@ typedef struct s_moldyn {
 
        t_3dvec dim;            /* dimensions of the simulation volume */
        double volume;          /* volume of sim cell (dim.x*dim.y*dim.z) */
+       double vt1,vt2;
 
        /* potential force function and parameter pointers */
        int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
@@ -171,6 +184,7 @@ typedef struct s_lj_params {
        double sigma6;
        double sigma12;
        double epsilon4;
+       double uc;
 } t_lj_params;
 
 /*
@@ -183,6 +197,7 @@ typedef struct s_tersoff_exchange {
        double f_a,df_a;
 
        t_3dvec dist_ij;
+       double d_ij2;
        double d_ij;
 
        double chi;
@@ -220,8 +235,10 @@ typedef struct s_tersoff_exchange {
 /* tersoff multi (2!) potential parameters */
 typedef struct s_tersoff_mult_params {
        double S[2];            /* tersoff cutoff radii */
+       double S2[2];           /* tersoff cutoff radii squared */
        double R[2];            /* tersoff cutoff radii */
        double Smixed;          /* mixed S radius */
+       double S2mixed;         /* mixed S radius squared */
        double Rmixed;          /* mixed R radius */
        double A[2];            /* factor of tersoff attractive part */
        double B[2];            /* factor of tersoff repulsive part */
@@ -308,6 +325,7 @@ typedef struct s_tersoff_mult_params {
 #define SI                     0x0e
 #define LC_SI                  (0.543105e-9*METER)             /* A */
 #define M_SI                   28.08553                        /* amu */
+
 #define LJ_SIGMA_SI            ((0.25*sqrt(3.0)*LC_SI)/1.122462)       /* A */
 #define LJ_EPSILON_SI          (2.1678*EV)                             /* NA */
 
@@ -377,19 +395,23 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer);
 int moldyn_log_shutdown(t_moldyn *moldyn);
 
 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
-                   u8 attr,u8 bnum,int a,int b,int c);
+                   u8 attr,u8 brand,int a,int b,int c);
 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 bnum,u8 attr,
+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 temperature_calc(t_moldyn *moldyn);
+double get_temperature(t_moldyn *moldyn);
 int scale_velocity(t_moldyn *moldyn,u8 equi_init);
+double pressure_calc(t_moldyn *moldyn);
+double get_pressure(t_moldyn *moldyn);
 int scale_volume(t_moldyn *moldyn);
 
 double get_e_kin(t_moldyn *moldyn);
-double get_e_pot(t_moldyn *moldyn);
+double update_e_kin(t_moldyn *moldyn);
 double get_total_energy(t_moldyn *moldyn);
 t_3dvec get_total_p(t_moldyn *moldyn);
 
@@ -407,9 +429,10 @@ int moldyn_integrate(t_moldyn *moldyn);
 int velocity_verlet(t_moldyn *moldyn);
 
 int potential_force_calc(t_moldyn *moldyn);
+inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d)
+       __attribute__((always_inline));
 inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
        __attribute__((always_inline));
-int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
 int tersoff_mult_complete_params(t_tersoff_mult_params *p);