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 */
53 #include "visual/visual.h"
55 /* moldyn schedule structure */
56 typedef struct s_moldyn_schedule {
60 int (*hook)(void *moldyn,void *hook);
64 /* moldyn main structure */
65 typedef struct s_moldyn {
66 int count; /* total amount of atoms */
67 t_atom *atom; /* pointer to the atoms */
69 t_3dvec dim; /* dimensions of the simulation volume */
71 /* potential force function and parameter pointers */
72 int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
74 int (*func2b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
75 int (*func2b_post)(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_ref; /* reference temperature */
89 double t; /* actual temperature */
91 double p_ref; /* reference pressure */
92 double p; /* actual pressure */
94 /* pressure and temperature control (velocity/volume scaling) */
95 /* (in units of tau!) */
96 unsigned char pt_scale; /* type of p and t scaling */
97 double t_tc; /* t berendsen control time constant */
98 double p_tc; /* p berendsen control time constant */
100 /* simulation schedule */
101 t_moldyn_schedule schedule;
102 int current; /* current position in schedule */
104 /* integration function pointer */
105 int (*integrate)(struct s_moldyn *moldyn);
106 int time_steps; /* amount of iterations */
107 double tau; /* delta t */
108 double time; /* absolute time */
109 double tau_square; /* delta t squared */
110 double elapsed; /* total elapsed time */
112 double energy; /* potential energy */
113 double ekin; /* kinetic energy */
115 char vlsdir[128]; /* visualization/log/save directory */
116 t_visual vis; /* visualization interface structure */
117 u8 vlsprop; /* log/vis/save properties */
118 unsigned int ewrite; /* how often to log energy */
119 int efd; /* fd for energy log */
120 unsigned int mwrite; /* how often to log momentum */
121 int mfd; /* fd for momentum log */
122 unsigned int vwrite; /* how often to visualize atom information */
123 unsigned int swrite; /* how often to create a save file */
125 u8 status; /* general moldyn properties */
127 t_random random; /* random interface */
129 int debug; /* debugging stuff, ignore */
132 #define MOLDYN_STAT_PBX 0x08 /* periodic boudaries in x */
133 #define MOLDYN_STAT_PBY 0x10 /* y */
134 #define MOLDYN_STAT_PBZ 0x20 /* and z direction */
136 #define MOLDYN_1BP 0x00 /* care about single */
137 #define MOLDYN_2BP 0x01 /* 2 body */
138 #define MOLDYN_3BP 0x02 /* and 3 body particle pots */
140 #define T_SCALE_BERENDSEN 0x01 /* berendsen t control */
141 #define T_SCALE_DIRECT 0x02 /* direct t control */
142 #define P_SCALE_BERENDSEN 0x04 /* berendsen p control */
143 #define P_SCALE_DIRECT 0x08 /* direct p control */
148 * potential parameter structures
153 * harmonic oscillator potential parameter structure
156 typedef struct s_ho_params {
157 double spring_constant;
158 double equilibrium_distance;
162 * lennard jones potential parameter structure
165 typedef struct s_lj_params {
175 /* tersoff exchange structure to exchange 2bp and 3bp calculated values */
176 typedef struct s_tersoff_exchange {
213 } t_tersoff_exchange;
215 /* tersoff multi (2!) potential parameters */
216 typedef struct s_tersoff_mult_params {
217 double S[2]; /* tersoff cutoff radii */
218 double R[2]; /* tersoff cutoff radii */
219 double Smixed; /* mixed S radius */
220 double Rmixed; /* mixed R radius */
221 double A[2]; /* factor of tersoff attractive part */
222 double B[2]; /* factor of tersoff repulsive part */
223 double Amixed; /* mixed A factor */
224 double Bmixed; /* mixed B factor */
225 double lambda[2]; /* tersoff lambda */
226 double lambda_m; /* mixed lambda */
227 double mu[2]; /* tersoff mu */
228 double mu_m; /* mixed mu */
238 t_tersoff_exchange exchange; /* exchange between 2bp and 3bp calc */
239 } t_tersoff_mult_params;
252 * - length unit: 1 A (1 A = 1e-10 m)
253 * - time unit: 1 fs (1 fs = 1e-15 s)
254 * - mass unit: 1 amu (1 amu = 1.6605388628e-27 kg )
257 #define METER 1e10 /* A */
258 #define SECOND 1e15 /* fs */
259 #define AMU 1.6605388628e-27 /* kg */
260 #define KILOGRAM (1.0/AMU) /* amu */
261 #define NEWTON (METER*KILOGRAM/(SECOND*SECOND)) /* A amu / fs^2 */
263 #define MOLDYN_TEMP 273.0
264 #define MOLDYN_TAU 1.0
265 #define MOLDYN_CUTOFF 10.0
266 #define MOLDYN_RUNS 1000000
268 #define MOLDYN_INTEGRATE_VERLET 0x00
269 #define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
271 #define MOLDYN_POTENTIAL_HO 0x00
272 #define MOLDYN_POTENTIAL_LJ 0x01
273 #define MOLDYN_POTENTIAL_TM 0x02
275 #define LOG_TOTAL_ENERGY 0x01
276 #define LOG_TOTAL_MOMENTUM 0x02
277 #define SAVE_STEP 0x04
278 #define VISUAL_STEP 0x08
285 * phsical values / constants
289 #define K_BOLTZMANN (1.380650524e-23*METER*NEWTON) /* NA/K */
290 #define EV (1.6021765314e-19*METER*NEWTON) /* NA */
293 #define M_C 12.011 /* amu */
296 #define LC_SI (0.543105e-9*METER) /* A */
297 #define M_SI 28.08553 /* amu */
298 #define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* A */
299 #define LJ_EPSILON_SI (2.1678*EV) /* NA */
301 #define TM_R_SI (2.7e-10*METER) /* A */
302 #define TM_S_SI (3.0e-10*METER) /* A */
303 #define TM_A_SI (1830.8*EV) /* NA */
304 #define TM_B_SI (471.18*EV) /* NA */
305 #define TM_LAMBDA_SI (2.4799e10/METER) /* 1/A */
306 #define TM_MU_SI (1.7322e10/METER) /* 1/A */
307 #define TM_BETA_SI 1.1000e-6
308 #define TM_N_SI 0.78734
309 #define TM_C_SI 1.0039e5
310 #define TM_D_SI 16.217
311 #define TM_H_SI -0.59825
313 #define TM_R_C (1.8e-10*METER) /* A */
314 #define TM_S_C (2.1e-10*METER) /* A */
315 #define TM_A_C (1393.6*EV) /* NA */
316 #define TM_B_C (346.7*EV) /* NA */
317 #define TM_LAMBDA_C (3.4879e10/METER) /* 1/A */
318 #define TM_MU_C (2.2119e10/METER) /* 1/A */
319 #define TM_BETA_C 1.5724e-7
320 #define TM_N_C 0.72751
321 #define TM_C_C 3.8049e4
323 #define TM_H_C -0.57058
325 #define TM_CHI_SIC 0.9776
337 * function prototypes
341 typedef int (*pf_func1b)(t_moldyn *,t_atom *ai);
342 typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8 bc);
343 typedef int (*pf_func2b_post)(t_moldyn *,t_atom *,t_atom *,u8 bc);
344 typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8 bc);
346 int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
347 int moldyn_shutdown(t_moldyn *moldyn);
349 int set_int_alg(t_moldyn *moldyn,u8 algo);
350 int set_cutoff(t_moldyn *moldyn,double cutoff);
351 int set_temperature(t_moldyn *moldyn,double t_ref);
352 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc);
353 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize);
354 int set_nn_dist(t_moldyn *moldyn,double dist);
355 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
356 int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params);
357 int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params);
358 int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params);
359 int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params);
361 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
362 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer);
363 int moldyn_log_shutdown(t_moldyn *moldyn);
365 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
366 u8 attr,u8 bnum,int a,int b,int c);
367 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
368 t_3dvec *r,t_3dvec *v);
369 int destroy_atoms(t_moldyn *moldyn);
371 int thermal_init(t_moldyn *moldyn,u8 equi_init);
372 int scale_velocity(t_moldyn *moldyn,u8 equi_init);
374 double get_e_kin(t_moldyn *moldyn);
375 double get_e_pot(t_moldyn *moldyn);
376 double get_total_energy(t_moldyn *moldyn);
377 t_3dvec get_total_p(t_moldyn *moldyn);
379 double estimate_time_step(t_moldyn *moldyn,double nn_dist);
381 int link_cell_init(t_moldyn *moldyn);
382 int link_cell_update(t_moldyn *moldyn);
383 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
384 int link_cell_shutdown(t_moldyn *moldyn);
386 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau);
387 int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params);
389 int moldyn_integrate(t_moldyn *moldyn);
390 int velocity_verlet(t_moldyn *moldyn);
392 int potential_force_calc(t_moldyn *moldyn);
393 int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
394 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
395 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
396 int tersoff_mult_complete_params(t_tersoff_mult_params *p);
397 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai);
398 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
399 int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
400 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc);
402 int moldyn_bc_check(t_moldyn *moldyn);