#include "random/random.h"
#include "list/list.h"
+#include "report/report.h"
/*
*
/* 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_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;
#define ATOM_ATTR_FP 0x01 /* fixed position (bulk material) */
#define ATOM_ATTR_HB 0x02 /* coupled to heat bath (velocity scaling) */
-#define ATOM_ATTR_1BP 0x10 /* single paricle potential */
-#define ATOM_ATTR_2BP 0x20 /* pair potential */
-#define ATOM_ATTR_3BP 0x40 /* 3 body potential */
+#define ATOM_ATTR_1BP 0x10 /* single paricle potential */
+#define ATOM_ATTR_2BP 0x20 /* pair potential */
+#define ATOM_ATTR_3BP 0x40 /* 3 body potential */
/* cell lists */
typedef struct s_linkcell {
double x,y,z; /* the actual cell lengthes */
t_list *subcell; /* pointer to the cell lists */
int dnlc; /* direct neighbour lists counter */
- int countn; /* amount of neighbours */
} t_linkcell;
#include "visual/visual.h"
-# moldyn schedule structure */
+/* moldyn schedule structure */
typedef struct s_moldyn_schedule {
- int content_count;
+ int count;
+ int total_sched;
int *runs;
- int *tau;
- int (*hook)(t_moldyn *,void *);
+ double *tau;
+ int (*hook)(void *moldyn,void *hook_params);
void *hook_params;
} t_moldyn_schedule;
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 (*pf_func1b)(struct s_moldyn *,t_atom *);
+ int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
void *pot1b_params;
- int (*pf_func2b)(struct s_moldyn *,t_atom *,t_atom *);
+ 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);
void *pot2b_params;
- int (*pf_func3b)(struct s_moldyn *,t_atom *,t_atom *,t_atom *);
+ int (*func3b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,
+ u8 bck);
void *pot3b_params;
//int (*potential_force_function)(struct s_moldyn *moldyn);
double cutoff; /* cutoff radius */
double cutoff_square; /* square of the cutoff radius */
+ double nnd; /* nearest neighbour distance (optional) */
+
+ t_linkcell lc; /* linked cell list interface */
- t_linkcell lc; /* linked cell method */
+ double t_ref; /* reference temperature */
+ double t; /* actual temperature */
- double t; /* temperature */
+ double p_ref; /* reference pressure */
+ double p; /* actual pressure (computed by virial) */
+ t_3dvec tp; /* thermodynamic pressure dU/dV */
+ double dv; /* dV for thermodynamic pressure calc */
+
+ /* 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 */
/* simulation schedule */
t_moldyn_schedule schedule;
int (*integrate)(struct s_moldyn *moldyn);
int time_steps; /* amount of iterations */
double tau; /* delta t */
+ double time; /* absolute time */
double tau_square; /* delta t squared */
double elapsed; /* total elapsed time */
- double energy; /* energy */
+ 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 */
- char efb[64]; /* energy log filename */
int efd; /* fd for energy log */
unsigned int mwrite; /* how often to log momentum */
- char mfb[64]; /* momentum log filename */
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 */
+ int rfd; /* report file descriptor */
+ char rtitle[64]; /* report title */
+ char rauthor[64]; /* report author */
+ int pfd; /* gnuplot script file descriptor */
u8 status; /* general moldyn properties */
t_random random; /* random interface */
+
+ int debug; /* debugging stuff, ignore */
} t_moldyn;
-#define MOLDYN_LVSTAT_TOTAL_E 0x01
-#define MOLDYN_LVSTAT_TOTAL_M 0x02
-#define MOLDYN_LVSTAT_SAVE 0x04
-#define MOLDYN_LVSTAT_VISUAL 0x08
-#define MOLDYN_LVSTAT_INITIALIZED 0x10
+#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_STAT_PBX 0x08 /* periodic boudaries in x */
-#define MOLDYN_STAT_PBY 0x10 /* y */
-#define MOLDYN_STAT_PBZ 0x20 /* and z direction */
+#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 */
+#define P_SCALE_BERENDSEN 0x04 /* berendsen p control */
+#define P_SCALE_DIRECT 0x08 /* direct p control */
/*
*
double sigma6;
double sigma12;
double epsilon4;
+ double uc;
} t_lj_params;
/*
/* tersoff exchange structure to exchange 2bp and 3bp calculated values */
typedef struct s_tersoff_exchange {
double f_c,df_c;
+ double f_a,df_a;
t_3dvec dist_ij;
- double d_ij;
double d_ij2;
+ double d_ij;
double chi;
- double *B;
- double *mu;
-
- double *beta;
- double *n;
- double *c;
- double *d;
- double *h;
-
- double c2;
- double d2;
- double c2d2;
- double 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;
+
+ double zeta_ij;
+ double zeta_ji;
+ t_3dvec dzeta_ij;
+ t_3dvec dzeta_ji;
} t_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 */
double h[2];
t_tersoff_exchange exchange; /* exchange between 2bp and 3bp calc */
-} t_tersoff_params;
+} t_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_INTEGRATE_VERLET 0x00
#define MOLDYN_POTENTIAL_LJ 0x01
#define MOLDYN_POTENTIAL_TM 0x02
-#define MOLDYN_SET_POTENTIAL 0x00
-#define MOLDYN_SET_TEMPERATURE 0x01
-#define MOLDYN_SET_
-#define MOLDYN_SET_
+#define LOG_TOTAL_ENERGY 0x01
+#define LOG_TOTAL_MOMENTUM 0x02
+#define SAVE_STEP 0x04
+#define VISUAL_STEP 0x08
+#define CREATE_REPORT 0x10
+
+#define TRUE 1
+#define FALSE 0
/*
*
* phsical values / constants
*
+ *
*/
-#define K_BOLTZMANN 1.3807e-27 /* Nm/K */
-#define AMU 1.660540e-27 /* kg */
-
-#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*1.60e-19) /* Nm */
+#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*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_CHI_SIC 0.9776
+
+/*
+ * lattice constants
+ */
+
+#define CUBIC 0x01
+#define FCC 0x02
+#define DIAMOND 0x04
/*
*
*/
-int moldyn_usage(char **argv);
-int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv);
-int moldyn_log_init(t_moldyn *moldyn);
+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);
+
int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
int moldyn_shutdown(t_moldyn *moldyn);
-int create_lattice(u8 type,int element,double mass,double lc,
- int a,int b,int c,t_atom **atom);
-int destroy_lattice(t_atom *atom);
-int thermal_init(t_moldyn *moldyn);
-int scale_velocity(t_moldyn *moldyn);
-double get_e_kin(t_atom *atom,int count);
-double get_e_pot(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);
+int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
+int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params);
+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_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);
+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 pressure_calc(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);
+
+double get_e_kin(t_moldyn *moldyn);
+double update_e_kin(t_moldyn *moldyn);
double get_total_energy(t_moldyn *moldyn);
-t_3dvec get_total_p(t_atom *atom,int count);
+t_3dvec get_total_p(t_moldyn *moldyn);
-double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t);
+double estimate_time_step(t_moldyn *moldyn,double nn_dist);
int link_cell_init(t_moldyn *moldyn);
int link_cell_update(t_moldyn *moldyn);
int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
int link_cell_shutdown(t_moldyn *moldyn);
+typedef int (*set_hook)(void *,void *);
+
+int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau);
+int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params);
+
int moldyn_integrate(t_moldyn *moldyn);
int velocity_verlet(t_moldyn *moldyn);
-int harmonic_oscillator(t_moldyn *moldyn);
-int lennard_jones(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 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);
+int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai);
+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
projects / physik / posic.git / blobdiff