X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=c01bc9f6e5e81da8cca4ca56c8206ea21e4aed81;hb=785f05e0c0ddb57428dc71b0a3f7798673799871;hp=32025fd39a687306a0cb7edb9fb93c7301733937;hpb=0acbade9c8d1ed354c333955dc2c5575540a9236;p=physik%2Fposic.git diff --git a/moldyn.h b/moldyn.h index 32025fd..c01bc9f 100644 --- a/moldyn.h +++ b/moldyn.h @@ -27,6 +27,7 @@ typedef struct s_atom { t_3dvec r; /* position */ t_3dvec v; /* velocity */ t_3dvec f; /* force */ + t_3dvec virial; /* virial */ int element; /* number of element in pse */ double mass; /* atom mass */ u8 bnum; /* brand number */ @@ -67,6 +68,7 @@ typedef struct s_moldyn { t_atom *atom; /* pointer to the atoms */ t_3dvec dim; /* dimensions of the simulation volume */ + double volume; /* volume of sim cell (dim.x*dim.y*dim.z) */ /* potential force function and parameter pointers */ int (*func1b)(struct s_moldyn *moldyn,t_atom *ai); @@ -92,6 +94,7 @@ typedef struct s_moldyn { double p; /* actual pressure */ /* pressure and temperature control (velocity/volume scaling) */ + /* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */ unsigned char pt_scale; /* type of p and t scaling */ double t_tc; /* t berendsen control time constant */ double p_tc; /* p berendsen control time constant */ @@ -111,17 +114,15 @@ typedef struct s_moldyn { double energy; /* potential energy */ double ekin; /* kinetic energy */ - t_visual vis; /* visualization/log/save interface structure */ - u8 lvstat; /* log & vis properties */ + char vlsdir[128]; /* visualization/log/save directory */ + t_visual vis; /* visualization interface structure */ + u8 vlsprop; /* log/vis/save properties */ unsigned int ewrite; /* how often to log energy */ int efd; /* fd for energy log */ unsigned int mwrite; /* how often to log momentum */ int mfd; /* fd for momentum log */ unsigned int vwrite; /* how often to visualize atom information */ - char vfb[64]; /* visualization file name base */ - //void *visual; /* pointer (hack!) */ unsigned int swrite; /* how often to create a save file */ - char sfb[64]; /* visualization file name base */ u8 status; /* general moldyn properties */ @@ -130,13 +131,15 @@ typedef struct s_moldyn { int debug; /* debugging stuff, ignore */ } t_moldyn; -#define MOLDYN_STAT_PBX 0x08 /* periodic boudaries in x */ -#define MOLDYN_STAT_PBY 0x10 /* y */ -#define MOLDYN_STAT_PBZ 0x20 /* and z direction */ +#define MOLDYN_STAT_PBX 0x01 /* periodic boudaries in x */ +#define MOLDYN_STAT_PBY 0x02 /* y */ +#define MOLDYN_STAT_PBZ 0x04 /* and z direction */ -#define MOLDYN_1BP 0x00 /* care about single */ -#define MOLDYN_2BP 0x01 /* 2 body */ -#define MOLDYN_3BP 0x02 /* and 3 body particle pots */ +#define MOLDYN_PSCALE 0x08 /* size controlled by piston */ + +#define MOLDYN_1BP 0x10 /* care about single */ +#define MOLDYN_2BP 0x20 /* 2 body */ +#define MOLDYN_3BP 0x40 /* and 3 body particle pots */ #define T_SCALE_BERENDSEN 0x01 /* berendsen t control */ #define T_SCALE_DIRECT 0x02 /* direct t control */ @@ -183,23 +186,34 @@ typedef struct s_tersoff_exchange { double chi; - double *beta; - double *n; - double *c; - double *d; - double *h; - - double c2; - double d2; - double c2d2; - double betan; - double n_betan; + double *beta_i; + double *beta_j; + double *n_i; + double *n_j; + double *c_i; + double *c_j; + double *d_i; + double *d_j; + double *h_i; + double *h_j; + + double ci2; + double cj2; + double di2; + double dj2; + double ci2di2; + double cj2dj2; + double betaini; + double betajnj; u8 run3bp; u8 run2bp_post; + u8 d_ij_between_rs; - t_3dvec db_ij; - double zeta; + double zeta_ij; + double zeta_ji; + t_3dvec dzeta_ij; + t_3dvec dzeta_ji; } t_tersoff_exchange; /* tersoff multi (2!) potential parameters */ @@ -236,15 +250,32 @@ typedef struct s_tersoff_mult_params { * */ -/* default values */ +#define ONE_THIRD (1.0/3.0) + +/* + * default values + * + * - length unit: 1 A (1 A = 1e-10 m) + * - time unit: 1 fs (1 fs = 1e-15 s) + * - mass unit: 1 amu (1 amu = 1.6605388628e-27 kg ) + * + * fyi: in the following 1 N = (amu*A)/(fs*fs) + * + */ + +#define METER 1e10 /* A */ +#define SECOND 1e15 /* fs */ +#define AMU 1.6605388628e-27 /* kg */ +#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 MOLDYN_TEMP 273.0 -#define MOLDYN_TAU 1.0e-15 -#define MOLDYN_CUTOFF 1.0e-9 +#define MOLDYN_TAU 1.0 +#define MOLDYN_CUTOFF 10.0 #define MOLDYN_RUNS 1000000 -#define MOLDYN_CRITICAL_EST_TEMP 5.0 - #define MOLDYN_INTEGRATE_VERLET 0x00 #define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET @@ -260,56 +291,58 @@ typedef struct s_tersoff_mult_params { #define TRUE 1 #define FALSE 0 -#define ACCEPTABLE_ERROR 1e-15 - /* * * phsical values / constants * + * */ -#define K_BOLTZMANN 1.3807e-27 /* Nm/K */ -#define AMU 1.660540e-27 /* kg */ -#define EV 1.60217733e-19 /* Nm */ - -#define FCC 0x01 -#define DIAMOND 0x02 +#define K_BOLTZMANN (1.380650524e-23*METER*NEWTON) /* NA/K */ +#define EV (1.6021765314e-19*METER*NEWTON) /* NA */ #define C 0x06 -#define M_C (12.011*AMU) +#define M_C 12.011 /* amu */ #define SI 0x0e -#define LC_SI 0.543105e-9 /* m */ -#define M_SI (28.085*AMU) /* kg */ -#define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* m */ -#define LJ_EPSILON_SI (2.1678*EV) /* Nm */ - -#define TM_R_SI 2.7e-10 /* m */ -#define TM_S_SI 3.0e-10 /* m */ -#define TM_A_SI (1830.8*EV) /* Nm */ -#define TM_B_SI (471.18*EV) /* Nm */ -#define TM_LAMBDA_SI 2.4799e10 /* 1/m */ -#define TM_MU_SI 1.7322e10 /* 1/m */ +#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 */ + +#define TM_R_SI (2.7e-10*METER) /* A */ +#define TM_S_SI (3.0e-10*METER) /* 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_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 /* m */ -#define TM_S_C 2.1e-10 /* m */ -#define TM_A_C (1393.6*EV) /* Nm */ -#define TM_B_C (346.7*EV) /* Nm */ -#define TM_LAMBDA_C 3.4879e10 /* 1/m */ -#define TM_MU_C 2.2119e10 /* 1/m */ +#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_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_BETA_C 1.5724e-7 #define TM_N_C 0.72751 #define TM_C_C 3.8049e4 #define TM_D_C 4.384 -#define TM_H_C (-0.57058) +#define TM_H_C -0.57058 #define TM_CHI_SIC 0.9776 +/* + * lattice constants + */ + +#define FCC 0x01 +#define DIAMOND 0x02 + /* * @@ -328,6 +361,7 @@ int moldyn_shutdown(t_moldyn *moldyn); int set_int_alg(t_moldyn *moldyn,u8 algo); int set_cutoff(t_moldyn *moldyn,double cutoff); 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_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize); int set_nn_dist(t_moldyn *moldyn,double dist); @@ -337,17 +371,21 @@ int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params); int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params); int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params); -int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer); +int moldyn_set_log_dir(t_moldyn *moldyn,char *dir); +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); +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, t_3dvec *r,t_3dvec *v); int destroy_atoms(t_moldyn *moldyn); int thermal_init(t_moldyn *moldyn,u8 equi_init); int scale_velocity(t_moldyn *moldyn,u8 equi_init); +int scale_volume(t_moldyn *moldyn); double get_e_kin(t_moldyn *moldyn); double get_e_pot(t_moldyn *moldyn); @@ -368,6 +406,8 @@ int moldyn_integrate(t_moldyn *moldyn); int velocity_verlet(t_moldyn *moldyn); int potential_force_calc(t_moldyn *moldyn); +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); @@ -377,4 +417,6 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc); int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc); int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc); +int moldyn_bc_check(t_moldyn *moldyn); + #endif