/* 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 */
/* potential force function and parameter pointers */
int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
int (*func2b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
- int (*func2b_post)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
- int (*func3b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,
- u8 bck);
+ int (*func3b_j1)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+ int (*func3b_j2)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+ int (*func3b_j3)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+ int (*func3b_k1)(struct s_moldyn *moldyn,
+ t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
+ int (*func3b_k2)(struct s_moldyn *moldyn,
+ t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
void *pot_params;
- //int (*potential_force_function)(struct s_moldyn *moldyn);
+ unsigned char run3bp;
double cutoff; /* cutoff radius */
double cutoff_square; /* square of the cutoff radius */
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 t_avg; /* average value of t */
+
+ 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; /* 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 */
double tau; /* delta t */
double time; /* absolute time */
double tau_square; /* delta t squared */
- double elapsed; /* total elapsed time */
+ 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 */
int efd; /* fd for energy log */
unsigned int mwrite; /* how often to log momentum */
int mfd; /* fd for momentum log */
+ unsigned int pwrite; /* how often to log pressure */
+ int pfd; /* fd for pressure log */
+ unsigned int twrite; /* how often to log temperature */
+ int tfd; /* fd for temperature log */
unsigned int vwrite; /* how often to visualize atom information */
unsigned int swrite; /* how often to create a save file */
int rfd; /* report file descriptor */
char rtitle[64]; /* report title */
char rauthor[64]; /* report author */
- int pfd; /* gnuplot script file descriptor */
+ int epfd; /* energy gnuplot script file descriptor */
+ int ppfd; /* pressure gnuplot script file descriptor */
+ int tpfd; /* temperature gnuplot script file descriptor */
u8 status; /* general moldyn properties */
#define P_SCALE_DIRECT 0x08 /* direct p control */
/*
- * default values
+ * default values & units
*
* - length unit: 1 A (1 A = 1e-10 m)
* - time unit: 1 fs (1 fs = 1e-15 s)
#define KILOGRAM (1.0/AMU) /* amu */
#define NEWTON (METER*KILOGRAM/(SECOND*SECOND)) /* A amu / fs^2 */
#define PASCAL (NEWTON/(METER*METER)) /* N / A^2 */
-#define ATM ((1.0133e5*PASCAL)) /* 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
#define LOG_TOTAL_ENERGY 0x01
#define LOG_TOTAL_MOMENTUM 0x02
-#define SAVE_STEP 0x04
-#define VISUAL_STEP 0x08
-#define CREATE_REPORT 0x10
+#define LOG_PRESSURE 0x04
+#define LOG_TEMPERATURE 0x08
+#define SAVE_STEP 0x10
+#define VISUAL_STEP 0x20
+#define CREATE_REPORT 0x40
#define TRUE 1
#define FALSE 0
#define VERBOSE 1
#define QUIET 0
+#define SCALE_UP 'u'
+#define SCALE_DOWN 'd'
+#define SCALE_DIRECT 'D'
+
/*
- *
- * phsical values / constants
- *
+ * potential related phsical values / constants
*
*/
#define ONE_THIRD (1.0/3.0)
-#define K_BOLTZMANN (1.380650524e-23*METER*NEWTON) /* NA/K */
-#define EV (1.6021765314e-19*METER*NEWTON) /* NA */
-
#define C 0x06
+#define LC_C 3.567 /* A */
#define M_C 12.011 /* amu */
#define SI 0x0e
-#define LC_SI (0.543105e-9*METER) /* A */
+#define LC_SI 5.43105 /* A */
#define M_SI 28.08553 /* amu */
+#define LC_3C_SIC 4.3596 /* A */
+
#define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* A */
//#define LJ_SIGMA_SI (LC_SI/1.122462) /* A */
-//#define LJ_SIGMA_SI (0.5*sqrt(2.0)*LC_SI/1.122462) /* A */
+//#define LJ_SIGMA_SI (0.5*sqrt(2.0)*LC_SI/1.122462) /* A */
#define LJ_EPSILON_SI (2.1678*EV) /* NA */
-#define TM_R_SI (2.7e-10*METER) /* A */
-#define TM_S_SI (3.0e-10*METER) /* A */
+#define TM_R_SI 2.7 /* A */
+#define TM_S_SI 3.0 /* A */
#define TM_A_SI (1830.8*EV) /* NA */
#define TM_B_SI (471.18*EV) /* NA */
-#define TM_LAMBDA_SI (2.4799e10/METER) /* 1/A */
-#define TM_MU_SI (1.7322e10/METER) /* 1/A */
+#define TM_LAMBDA_SI 2.4799 /* 1/A */
+#define TM_MU_SI 1.7322 /* 1/A */
#define TM_BETA_SI 1.1000e-6
#define TM_N_SI 0.78734
#define TM_C_SI 1.0039e5
#define TM_D_SI 16.217
#define TM_H_SI -0.59825
-#define TM_R_C (1.8e-10*METER) /* A */
-#define TM_S_C (2.1e-10*METER) /* A */
+#define TM_R_C 1.8 /* A */
+#define TM_S_C 2.1 /* A */
#define TM_A_C (1393.6*EV) /* NA */
#define TM_B_C (346.7*EV) /* NA */
-#define TM_LAMBDA_C (3.4879e10/METER) /* 1/A */
-#define TM_MU_C (2.2119e10/METER) /* 1/A */
+#define TM_LAMBDA_C 3.4879 /* 1/A */
+#define TM_MU_C 2.2119 /* 1/A */
#define TM_BETA_C 1.5724e-7
#define TM_N_C 0.72751
#define TM_C_C 3.8049e4
#define TM_CHI_SIC 0.9776
+#define TM_LC_SIC 4.32 /* A */
+
+#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_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_GAMMA_SI 0.114354
+#define ALBE_C_SI 2.00494
+#define ALBE_D_SI 0.81472
+#define ALBE_H_SI 0.259
+
+#define ALBE_LC_SI 5.429
+
+#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_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_GAMMA_C 0.11233
+#define ALBE_C_C 181.910
+#define ALBE_D_C 6.28433
+#define ALBE_H_C 0.5556
+
+#define ALBE_LC_C 3.566
+
+#define ALBE_R_SIC (2.40-0.20)
+#define ALBE_S_SIC (2.40+0.10)
+#define ALBE_A_SIC (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 ALBE_GAMMA_SIC 0.011877
+#define ALBE_C_SIC 273987
+#define ALBE_D_SIC 180.314
+#define ALBE_H_SIC 0.68
+
+#define ALBE_LC_SIC 4.359
+
+
/*
- * lattice constants
+ * lattice types
*/
#define CUBIC 0x01
*
*/
-typedef int (*pf_func1b)(t_moldyn *,t_atom *ai);
-typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8 bc);
-typedef int (*pf_func2b_post)(t_moldyn *,t_atom *,t_atom *,u8 bc);
-typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8 bc);
+typedef int (*pf_func1b)(t_moldyn *,t_atom *);
+typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8);
+typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8);
int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
int moldyn_shutdown(t_moldyn *moldyn);
int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
int set_potential1b(t_moldyn *moldyn,pf_func1b func);
int set_potential2b(t_moldyn *moldyn,pf_func2b func);
-int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func);
-int set_potential3b(t_moldyn *moldyn,pf_func3b func);
+int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func);
+int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func);
+int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func);
+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);
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);
+ u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin);
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 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);
-int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z);
-int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z);
+int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
+int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
-double get_e_kin(t_moldyn *moldyn);
-double update_e_kin(t_moldyn *moldyn);
+double e_kin_calc(t_moldyn *moldyn);
double get_total_energy(t_moldyn *moldyn);
t_3dvec get_total_p(t_moldyn *moldyn);
int moldyn_bc_check(t_moldyn *moldyn);
+int get_line(int fd,char *line,int max);
+
#endif
projects / physik / posic.git / blobdiff