#include "math/math.h"
#include "random/random.h"
+#include "list/list.h"
-/* datatypes */
+/*
+ *
+ * datatypes
+ *
+ */
+
+/* general */
+typedef unsigned char u8;
+
+/* the atom of the md simulation */
typedef struct s_atom {
- t_3dvec r; /* positions */
- t_3dvec v; /* velocities */
- t_3dvec f; /* forces */
- int element; /* number of element in pse */
- double mass; /* atom mass */
+ t_3dvec r; /* position */
+ t_3dvec v; /* velocity */
+ t_3dvec f; /* force */
+ int element; /* number of element in pse */
+ double mass; /* atom mass */
+ u8 bnum; /* brand number */
+ 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 */
+
+/* cell lists */
+typedef struct s_linkcell {
+ int nx,ny,nz; /* amount of cells in x, y and z direction */
+ int cells; /* total amount of cells */
+ double len; /* prefered cell edge length */
+ double x,y,z; /* the actual cell lengthes */
+ t_list *subcell; /* pointer to the cell lists */
+ int dnlc; /* direct neighbour lists counter */
+} t_linkcell;
+
+#include "visual/visual.h"
+
+/* moldyn schedule structure */
+typedef struct s_moldyn_schedule {
+ int content_count;
+ int *runs;
+ double *tau;
+ int (*hook)(void *moldyn,void *hook);
+ void *hook_params;
+} t_moldyn_schedule;
+
+/* moldyn main structure */
typedef struct s_moldyn {
- int count;
- t_atom *atom;
- double (*potential)(struct s_moldyn *moldyn);
- void *pot_params;
- int (*force)(struct s_moldyn *moldyn);
- double cutoff_square;
- t_3dvec dim;
- unsigned char status;
+ int count; /* total amount of atoms */
+ 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);
+ void *pot1b_params;
+ 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 (*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 */
+
+ double t_ref; /* reference temperature */
+ double t; /* actual temperature */
+
+ double p_ref; /* reference pressure */
+ double p; /* actual pressure */
+
+ /* pressure and temperature control (velocity/volume scaling) */
+ /* (in units of tau!) */
+ 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 current; /* current position in schedule */
+
+ /* integration function pointer */
+ 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; /* potential energy */
+ double ekin; /* kinetic energy */
+
+ 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 */
+ unsigned int swrite; /* how often to create a save file */
+
+ u8 status; /* general moldyn properties */
+
+ t_random random; /* random interface */
+
+ 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_1BP 0x00 /* care about single */
+#define MOLDYN_2BP 0x01 /* 2 body */
+#define MOLDYN_3BP 0x02 /* 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 */
+
+
+/*
+ *
+ * potential parameter structures
+ *
+ */
+
+/*
+ * harmonic oscillator potential parameter structure
+ */
+
+typedef struct s_ho_params {
+ double spring_constant;
+ double equilibrium_distance;
+} t_ho_params;
+
+/*
+ * lennard jones potential parameter structure
+ */
+
typedef struct s_lj_params {
double sigma6;
double sigma12;
- double epsilon;
+ double epsilon4;
} t_lj_params;
/*
+ * tersoff
+ */
+
+/* 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 chi;
+
+ 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 R[2]; /* tersoff cutoff radii */
+ double Smixed; /* mixed S radius */
+ double Rmixed; /* mixed R radius */
+ double A[2]; /* factor of tersoff attractive part */
+ double B[2]; /* factor of tersoff repulsive part */
+ double Amixed; /* mixed A factor */
+ double Bmixed; /* mixed B factor */
+ double lambda[2]; /* tersoff lambda */
+ double lambda_m; /* mixed lambda */
+ double mu[2]; /* tersoff mu */
+ double mu_m; /* mixed mu */
+
+ double chi;
+
+ double beta[2];
+ double n[2];
+ double c[2];
+ double d[2];
+ double h[2];
+
+ t_tersoff_exchange exchange; /* exchange between 2bp and 3bp calc */
+} t_tersoff_mult_params;
+
+
+
+/*
+ *
* defines
+ *
+ */
+
+/*
+ * 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 )
*/
-/* general defines */
+#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 MOLDYN_TEMP 273.0
+#define MOLDYN_TAU 1.0
+#define MOLDYN_CUTOFF 10.0
+#define MOLDYN_RUNS 1000000
+
+#define MOLDYN_INTEGRATE_VERLET 0x00
+#define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
+
+#define MOLDYN_POTENTIAL_HO 0x00
+#define MOLDYN_POTENTIAL_LJ 0x01
+#define MOLDYN_POTENTIAL_TM 0x02
-#define MOLDYN_STAT_POTENTIAL 0x01
-#define MOLDYN_STAT_FORCE 0x02
+#define LOG_TOTAL_ENERGY 0x01
+#define LOG_TOTAL_MOMENTUM 0x02
+#define SAVE_STEP 0x04
+#define VISUAL_STEP 0x08
-/* phsical values */
+#define TRUE 1
+#define FALSE 0
-//#define K_BOLTZMANN 1.3807E-23
-#define K_BOLTZMANN 1.0
+/*
+ *
+ * phsical values / constants
+ *
+ */
+
+#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 SI 0x0e
+#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 FCC 0x01
#define DIAMOND 0x02
-#define C 0x06
-#define M_C 6.0
-#define Si 0x0e
-#define M_SI 14.0
-#define LC_SI 5.43105
+/*
+ *
+ * function prototypes
+ *
+ */
+
+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 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_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_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 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);
-/* function prototypes */
+int thermal_init(t_moldyn *moldyn,u8 equi_init);
+int scale_velocity(t_moldyn *moldyn,u8 equi_init);
-int create_lattice(unsigned char 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_atom *atom,t_random *random,int count,double t);
-int scale_velocity(t_atom *atom,int count,double t);
-double get_e_kin(t_atom *atom,int count);
+double get_e_kin(t_moldyn *moldyn);
double get_e_pot(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);
+
+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);
+
+int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau);
+int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params);
+
+int moldyn_integrate(t_moldyn *moldyn);
+int velocity_verlet(t_moldyn *moldyn);
+
+int potential_force_calc(t_moldyn *moldyn);
+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);
+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);
-double potential_lennard_jones(t_moldyn *moldyn);
-int force_lennard_jones(t_moldyn *moldyn);
+int moldyn_bc_check(t_moldyn *moldyn);
#endif
projects / physik / posic.git / blobdiff