2 * moldyn.h - molecular dynamics library header file
4 * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
11 #include "math/math.h"
12 #include "random/random.h"
13 #include "list/list.h"
23 typedef unsigned char u8;
25 /* the atom of the md simulation */
26 typedef struct s_atom {
27 t_3dvec r; /* position */
28 t_3dvec v; /* velocity */
29 t_3dvec f; /* force */
30 int element; /* number of element in pse */
31 double mass; /* atom mass */
32 u8 bnum; /* brand number */
33 u8 attr; /* attributes */
36 #define ATOM_ATTR_FP 0x01 /* fixed position (bulk material) */
37 #define ATOM_ATTR_HB 0x02 /* coupled to heat bath (velocity scaling) */
39 #define ATOM_ATTR_1BP 0x10 /* single paricle potential */
40 #define ATOM_ATTR_2BP 0x20 /* pair potential */
41 #define ATOM_ATTR_3BP 0x40 /* 3 body potential */
44 typedef struct s_linkcell {
45 int nx,ny,nz; /* amount of cells in x, y and z direction */
46 int cells; /* total amount of cells */
47 double len; /* prefered cell edge length */
48 double x,y,z; /* the actual cell lengthes */
49 t_list *subcell; /* pointer to the cell lists */
50 int dnlc; /* direct neighbour lists counter */
51 int countn; /* amount of neighbours */
54 #include "visual/visual.h"
56 /* moldyn schedule structure */
57 typedef struct s_moldyn_schedule {
61 int (*hook)(void *moldyn,void *hook);
65 /* moldyn main structure */
66 typedef struct s_moldyn {
67 int count; /* total amount of atoms */
68 t_atom *atom; /* pointer to the atoms */
70 t_3dvec dim; /* dimensions of the simulation volume */
72 /* potential force function and parameter pointers */
73 int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
75 int (*func2b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
77 int (*func3b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,
80 //int (*potential_force_function)(struct s_moldyn *moldyn);
82 double cutoff; /* cutoff radius */
83 double cutoff_square; /* square of the cutoff radius */
84 double nnd; /* nearest neighbour distance (optional) */
86 t_linkcell lc; /* linked cell list interface */
88 double t; /* temperature */
90 /* simulation schedule */
91 t_moldyn_schedule schedule;
92 int current; /* current position in schedule */
94 /* integration function pointer */
95 int (*integrate)(struct s_moldyn *moldyn);
96 int time_steps; /* amount of iterations */
97 double tau; /* delta t */
98 double time; /* absolute time */
99 double tau_square; /* delta t squared */
100 double elapsed; /* total elapsed time */
102 double energy; /* potential energy */
103 double ekin; /* kinetic energy */
105 t_visual vis; /* visualization/log/save interface structure */
106 u8 lvstat; /* log & vis properties */
107 unsigned int ewrite; /* how often to log energy */
108 int efd; /* fd for energy log */
109 unsigned int mwrite; /* how often to log momentum */
110 int mfd; /* fd for momentum log */
111 unsigned int vwrite; /* how often to visualize atom information */
112 char vfb[64]; /* visualization file name base */
113 //void *visual; /* pointer (hack!) */
114 unsigned int swrite; /* how often to create a save file */
115 char sfb[64]; /* visualization file name base */
117 u8 status; /* general moldyn properties */
119 t_random random; /* random interface */
122 #define MOLDYN_STAT_PBX 0x08 /* periodic boudaries in x */
123 #define MOLDYN_STAT_PBY 0x10 /* y */
124 #define MOLDYN_STAT_PBZ 0x20 /* and z direction */
126 #define MOLDYN_1BP 0x00 /* care about single */
127 #define MOLDYN_2BP 0x01 /* 2 body */
128 #define MOLDYN_3BP 0x02 /* and 3 body particle pots */
130 #define VSCALE_INIT_EQUI 0x00 /* initial, eq positions */
131 #define VSCALE_BERENDSEN 0x01 /* berendsen control */
136 * potential parameter structures
141 * harmonic oscillator potential parameter structure
144 typedef struct s_ho_params {
145 double spring_constant;
146 double equilibrium_distance;
150 * lennard jones potential parameter structure
153 typedef struct s_lj_params {
163 /* tersoff exchange structure to exchange 2bp and 3bp calculated values */
164 typedef struct s_tersoff_exchange {
189 } t_tersoff_exchange;
191 /* tersoff multi (2!) potential parameters */
192 typedef struct s_tersoff_mult_params {
193 double S[2]; /* tersoff cutoff radii */
194 double R[2]; /* tersoff cutoff radii */
195 double Smixed; /* mixed S radius */
196 double Rmixed; /* mixed R radius */
197 double A[2]; /* factor of tersoff attractive part */
198 double B[2]; /* factor of tersoff repulsive part */
199 double Amixed; /* mixed A factor */
200 double Bmixed; /* mixed B factor */
201 double lambda[2]; /* tersoff lambda */
202 double lambda_m; /* mixed lambda */
203 double mu[2]; /* tersoff mu */
204 double mu_m; /* mixed mu */
214 t_tersoff_exchange exchange; /* exchange between 2bp and 3bp calc */
215 } t_tersoff_mult_params;
227 #define MOLDYN_TEMP 273.0
228 #define MOLDYN_TAU 1.0e-15
229 #define MOLDYN_CUTOFF 1.0e-9
230 #define MOLDYN_RUNS 1000000
232 #define MOLDYN_CRITICAL_EST_TEMP 5.0
234 #define MOLDYN_INTEGRATE_VERLET 0x00
235 #define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
237 #define MOLDYN_POTENTIAL_HO 0x00
238 #define MOLDYN_POTENTIAL_LJ 0x01
239 #define MOLDYN_POTENTIAL_TM 0x02
241 #define LOG_TOTAL_ENERGY 0x01
242 #define LOG_TOTAL_MOMENTUM 0x02
243 #define SAVE_STEP 0x04
244 #define VISUAL_STEP 0x08
251 * phsical values / constants
255 #define K_BOLTZMANN 1.3807e-27 /* Nm/K */
256 #define AMU 1.660540e-27 /* kg */
257 #define EV 1.60217733e-19 /* Nm */
263 #define M_C (12.011*AMU)
266 #define LC_SI 0.543105e-9 /* m */
267 #define M_SI (28.085*AMU) /* kg */
268 #define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* m */
269 #define LJ_EPSILON_SI (2.1678*1.60e-19) /* Nm */
271 #define TM_R_SI 2.7e-10 /* m */
272 #define TM_S_SI 3.0e-10 /* m */
273 #define TM_A_SI (1830.8*EV) /* Nm */
274 #define TM_B_SI (471.18*EV) /* Nm */
275 #define TM_LAMBDA_SI 2.4799e10 /* 1/m */
276 #define TM_MU_SI 1.7322e10 /* 1/m */
277 #define TM_BETA_SI 1.1000e-6
278 #define TM_N_SI 0.78734
279 #define TM_C_SI 1.0039e5
280 #define TM_D_SI 1.62170
281 #define TM_H_SI (-0.59825)
283 #define TM_R_C 1.8e-10 /* m */
284 #define TM_S_C 2.1e-10 /* m */
285 #define TM_A_C (1393.6*EV) /* Nm */
286 #define TM_B_C (346.7*EV) /* Nm */
287 #define TM_LAMBDA_C 3.4879e10 /* 1/m */
288 #define TM_MU_C 2.2119e10 /* 1/m */
289 #define TM_BETA_C 1.5724e-7
290 #define TM_N_C 0.72751
291 #define TM_C_C 3.8049e4
293 #define TM_H_C (-0.57058)
295 #define TM_CHI_SIC 0.9776
300 * function prototypes
304 typedef int (*pf_func1b)(t_moldyn *,t_atom *ai);
305 typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8 bc);
306 typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8 bc);
308 int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
309 int moldyn_shutdown(t_moldyn *moldyn);
311 int set_int_alg(t_moldyn *moldyn,u8 algo);
312 int set_cutoff(t_moldyn *moldyn,double cutoff);
313 int set_temperature(t_moldyn *moldyn,double t);
314 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize);
315 int set_nn_dist(t_moldyn *moldyn,double dist);
316 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
317 int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params);
318 int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params);
319 int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params);
321 int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer);
322 int moldyn_log_shutdown(t_moldyn *moldyn);
324 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
325 u8 attr,u8 bnum,int a,int b,int c);
326 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
327 t_3dvec *r,t_3dvec *v);
328 int destroy_atoms(t_moldyn *moldyn);
330 int thermal_init(t_moldyn *moldyn);
331 int scale_velocity(t_moldyn *moldyn,u8 type);
333 double get_e_kin(t_moldyn *moldyn);
334 double get_e_pot(t_moldyn *moldyn);
335 double get_total_energy(t_moldyn *moldyn);
336 t_3dvec get_total_p(t_moldyn *moldyn);
338 double estimate_time_step(t_moldyn *moldyn,double nn_dist);
340 int link_cell_init(t_moldyn *moldyn);
341 int link_cell_update(t_moldyn *moldyn);
342 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
343 int link_cell_shutdown(t_moldyn *moldyn);
345 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau);
346 int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params);
348 int moldyn_integrate(t_moldyn *moldyn);
349 int velocity_verlet(t_moldyn *moldyn);
351 int potential_force_calc(t_moldyn *moldyn);
352 int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
353 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
354 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
355 int tersoff_mult_complete_params(t_tersoff_mult_params *p);
356 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai);
357 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
358 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc);