/* 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 */
#define ATOM_ATTR_FP 0x01 /* fixed position (bulk material) */
#define ATOM_ATTR_HB 0x02 /* coupled to heat bath (velocity scaling) */
+#define ATOM_ATTR_VA 0x04 /* visualize this atom */
+#define ATOM_ATTR_VB 0x08 /* visualize the bond of this atom */
#define ATOM_ATTR_1BP 0x10 /* single paricle potential */
#define ATOM_ATTR_2BP 0x20 /* pair potential */
int dnlc; /* direct neighbour lists counter */
} t_linkcell;
-#include "visual/visual.h"
-
/* moldyn schedule structure */
typedef struct s_moldyn_schedule {
int count;
void *hook_params;
} t_moldyn_schedule;
+/* visualization structure */
+typedef struct s_visual {
+ int fd; /* rasmol script file descriptor */
+ char fb[128]; /* basename of the save files */
+ t_3dvec dim; /* dimensions of the simulation cell */
+} t_visual;
+
/* 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 */
double cutoff; /* cutoff radius */
double cutoff_square; /* square of the cutoff radius */
double nnd; /* nearest neighbour distance (optional) */
+ double bondlen[3]; /* bond lengthes (only 2 atomic systems) */
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 */
/* 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) */
#define ALBE_R_SI (2.82-0.14)
#define ALBE_S_SI (2.82+0.14)
#define ALBE_A_SI (3.24*EV/0.842)
-#define ALBE_B_SI (1.842*3.24*EV/0.842)
+#define ALBE_B_SI (-1.842*3.24*EV/0.842)
#define ALBE_R0_SI 2.232
#define ALBE_LAMBDA_SI (1.4761*sqrt(2.0*1.842))
#define ALBE_MU_SI (1.4761*sqrt(2.0/1.842))
#define ALBE_R_C (2.00-0.15)
#define ALBE_S_C (2.00+0.15)
#define ALBE_A_C (6.00*EV/1.167)
-#define ALBE_B_C (2.167*6.00*EV/1.167)
+#define ALBE_B_C (-2.167*6.00*EV/1.167)
#define ALBE_R0_C 1.4276
#define ALBE_LAMBDA_C (2.0099*sqrt(2.0*2.167))
#define ALBE_MU_C (2.0099*sqrt(2.0/2.167))
#define ALBE_LC_C 3.566
#define ALBE_R_SIC (2.40-0.20)
-#define ALBE_S_SIC (2.40+0.10)
+#define ALBE_S_SIC (2.40+0.20)
#define ALBE_A_SIC (4.36*EV/0.847)
-#define ALBE_B_SIC (1.847*4.36*EV/0.847)
+#define ALBE_B_SIC (-1.847*4.36*EV/0.847)
#define ALBE_R0_SIC 1.79
#define ALBE_LAMBDA_SIC (1.6991*sqrt(2.0*1.847))
#define ALBE_MU_SIC (1.6991*sqrt(2.0/1.847))
#define FCC 0x02
#define DIAMOND 0x04
-
/*
*
* function prototypes
int set_int_alg(t_moldyn *moldyn,u8 algo);
int set_cutoff(t_moldyn *moldyn,double cutoff);
+int set_bondlen(t_moldyn *moldyn,double b0,double b1,double bm);
int set_temperature(t_moldyn *moldyn,double t_ref);
int set_pressure(t_moldyn *moldyn,double p_ref);
int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc);
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);
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 del_atom(t_moldyn *moldyn,int tag);
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);
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);
int get_line(int fd,char *line,int max);
+int visual_init(t_moldyn *moldyn,char *filebase);
+int visual_atoms(t_moldyn *moldyn);
+
#endif
+