/* 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 cells; /* total amount of cells */
double len; /* prefered cell edge length */
double x,y,z; /* the actual cell lengthes */
+#ifdef STATIC_LISTS
+ int **subcell; /* pointer to the cell lists */
+#else
t_list *subcell; /* pointer to the cell lists */
+#endif
int dnlc; /* direct neighbour lists counter */
} t_linkcell;
-#include "visual/visual.h"
+#define MAX_ATOMS_PER_LIST 20
/* moldyn schedule structure */
typedef struct s_moldyn_schedule {
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 */
t_3dvec dim; /* dimensions of the simulation volume */
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 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 */
+
+ t_virial vir; /* actual virial */
+ double 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 */
- t_3dvec tp; /* thermodynamic pressure dU/dV */
- double dv; /* dV for thermodynamic pressure calc */
+ double p_avg; /* average value of p */
+
+ double tp; /* thermodynamic pressure dU/dV */
+ double tp_sum; /* sum over dU/dV pressure */
+ double tp_avg; /* average value of dU/dV pressure */
+ int tp_cnt; /* how often to do thermodynamic p calc */
/* pressure and temperature control (velocity/volume scaling) */
/* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */
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 */
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 vwrite; /* how often to log volume */
+ int vfd; /* fd for volume log */
+ unsigned int awrite; /* 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 */
#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 GPA (1e9*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_MOMENTUM 0x02
#define LOG_PRESSURE 0x04
#define LOG_TEMPERATURE 0x08
-#define SAVE_STEP 0x10
-#define VISUAL_STEP 0x20
-#define CREATE_REPORT 0x40
+#define LOG_VOLUME 0x10
+#define SAVE_STEP 0x20
+#define VISUAL_STEP 0x40
+#define CREATE_REPORT 0x80
#define TRUE 1
#define FALSE 0
#define VERBOSE 1
#define QUIET 0
+#define SCALE_UP 'u'
+#define SCALE_DOWN 'd'
+#define SCALE_DIRECT 'D'
+
/*
* potential related phsical values / constants
*
#define ONE_THIRD (1.0/3.0)
#define C 0x06
-#define LC_C (0.3567e-9*METER) /* A */
+#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 (0.43596e-9*METER) /* A */
+#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_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)
+#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+0.20)
+#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
#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_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 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 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 average_reset(t_moldyn *moldyn);
+int average_and_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 e_kin_calc(t_moldyn *moldyn);
double get_total_energy(t_moldyn *moldyn);
int link_cell_init(t_moldyn *moldyn,u8 vol);
int link_cell_update(t_moldyn *moldyn);
+#ifdef STATIC_LISTS
+int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int **cell);
+#else
int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
+#endif
int link_cell_shutdown(t_moldyn *moldyn);
typedef int (*set_hook)(void *,void *);
int moldyn_bc_check(t_moldyn *moldyn);
+int moldyn_read_save_file(t_moldyn *moldyn,char *file);
+int moldyn_load(t_moldyn *moldyn);
+int get_line(int fd,char *line,int max);
+
+int pair_correlation_init(t_moldyn *moldyn,double dr);
+int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc);
+int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr);
+
+int visual_init(t_moldyn *moldyn,char *filebase);
+int visual_atoms(t_moldyn *moldyn);
+
#endif
+
projects / physik / posic.git / blobdiff