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 t_3dvec virial; /* virial (v_xx, v_yy, v_zz) */
31 double e; /* site energy */
32 int element; /* number of element in pse */
33 double mass; /* atom mass */
34 u8 brand; /* brand id */
35 int tag; /* atom unique id (number of atom) */
36 u8 attr; /* attributes */
39 #define ATOM_ATTR_FP 0x01 /* fixed position (bulk material) */
40 #define ATOM_ATTR_HB 0x02 /* coupled to heat bath (velocity scaling) */
42 #define ATOM_ATTR_1BP 0x10 /* single paricle potential */
43 #define ATOM_ATTR_2BP 0x20 /* pair potential */
44 #define ATOM_ATTR_3BP 0x40 /* 3 body potential */
47 typedef struct s_linkcell {
48 int nx,ny,nz; /* amount of cells in x, y and z direction */
49 int cells; /* total amount of cells */
50 double len; /* prefered cell edge length */
51 double x,y,z; /* the actual cell lengthes */
52 t_list *subcell; /* pointer to the cell lists */
53 int dnlc; /* direct neighbour lists counter */
56 #include "visual/visual.h"
58 /* moldyn schedule structure */
59 typedef struct s_moldyn_schedule {
64 int (*hook)(void *moldyn,void *hook);
68 /* moldyn main structure */
69 typedef struct s_moldyn {
70 int count; /* total amount of atoms */
71 t_atom *atom; /* pointer to the atoms */
73 t_3dvec dim; /* dimensions of the simulation volume */
74 double volume; /* volume of sim cell (dim.x*dim.y*dim.z) */
76 /* potential force function and parameter pointers */
77 int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
79 int (*func2b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
80 int (*func2b_post)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
82 int (*func3b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,
85 //int (*potential_force_function)(struct s_moldyn *moldyn);
87 double cutoff; /* cutoff radius */
88 double cutoff_square; /* square of the cutoff radius */
89 double nnd; /* nearest neighbour distance (optional) */
91 t_linkcell lc; /* linked cell list interface */
93 double t_ref; /* reference temperature */
94 double t; /* actual temperature */
96 double p_ref; /* reference pressure */
97 double p; /* actual pressure */
99 /* pressure and temperature control (velocity/volume scaling) */
100 /* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */
101 unsigned char pt_scale; /* type of p and t scaling */
102 double t_tc; /* t berendsen control time constant */
103 double p_tc; /* p berendsen control time constant */
105 /* simulation schedule */
106 t_moldyn_schedule schedule;
107 int current; /* current position in schedule */
109 /* integration function pointer */
110 int (*integrate)(struct s_moldyn *moldyn);
111 int time_steps; /* amount of iterations */
112 double tau; /* delta t */
113 double time; /* absolute time */
114 double tau_square; /* delta t squared */
115 double elapsed; /* total elapsed time */
117 double energy; /* potential energy */
118 double ekin; /* kinetic energy */
120 char vlsdir[128]; /* visualization/log/save directory */
121 t_visual vis; /* visualization interface structure */
122 u8 vlsprop; /* log/vis/save properties */
123 unsigned int ewrite; /* how often to log energy */
124 int efd; /* fd for energy log */
125 unsigned int mwrite; /* how often to log momentum */
126 int mfd; /* fd for momentum log */
127 unsigned int vwrite; /* how often to visualize atom information */
128 unsigned int swrite; /* how often to create a save file */
130 u8 status; /* general moldyn properties */
132 t_random random; /* random interface */
134 int debug; /* debugging stuff, ignore */
137 #define MOLDYN_STAT_PBX 0x01 /* periodic boudaries in x */
138 #define MOLDYN_STAT_PBY 0x02 /* y */
139 #define MOLDYN_STAT_PBZ 0x04 /* and z direction */
141 #define MOLDYN_PSCALE 0x08 /* size controlled by piston */
143 #define MOLDYN_1BP 0x10 /* care about single */
144 #define MOLDYN_2BP 0x20 /* 2 body */
145 #define MOLDYN_3BP 0x40 /* and 3 body particle pots */
147 #define T_SCALE_BERENDSEN 0x01 /* berendsen t control */
148 #define T_SCALE_DIRECT 0x02 /* direct t control */
149 #define P_SCALE_BERENDSEN 0x04 /* berendsen p control */
150 #define P_SCALE_DIRECT 0x08 /* direct p control */
155 * potential parameter structures
160 * harmonic oscillator potential parameter structure
163 typedef struct s_ho_params {
164 double spring_constant;
165 double equilibrium_distance;
169 * lennard jones potential parameter structure
172 typedef struct s_lj_params {
182 /* tersoff exchange structure to exchange 2bp and 3bp calculated values */
183 typedef struct s_tersoff_exchange {
220 } t_tersoff_exchange;
222 /* tersoff multi (2!) potential parameters */
223 typedef struct s_tersoff_mult_params {
224 double S[2]; /* tersoff cutoff radii */
225 double R[2]; /* tersoff cutoff radii */
226 double Smixed; /* mixed S radius */
227 double Rmixed; /* mixed R radius */
228 double A[2]; /* factor of tersoff attractive part */
229 double B[2]; /* factor of tersoff repulsive part */
230 double Amixed; /* mixed A factor */
231 double Bmixed; /* mixed B factor */
232 double lambda[2]; /* tersoff lambda */
233 double lambda_m; /* mixed lambda */
234 double mu[2]; /* tersoff mu */
235 double mu_m; /* mixed mu */
245 t_tersoff_exchange exchange; /* exchange between 2bp and 3bp calc */
246 } t_tersoff_mult_params;
256 #define ONE_THIRD (1.0/3.0)
261 * - length unit: 1 A (1 A = 1e-10 m)
262 * - time unit: 1 fs (1 fs = 1e-15 s)
263 * - mass unit: 1 amu (1 amu = 1.6605388628e-27 kg )
265 * fyi: in the following 1 N = (amu*A)/(fs*fs)
269 #define METER 1e10 /* A */
270 #define SECOND 1e15 /* fs */
271 #define AMU 1.6605388628e-27 /* kg */
272 #define KILOGRAM (1.0/AMU) /* amu */
273 #define NEWTON (METER*KILOGRAM/(SECOND*SECOND)) /* A amu / fs^2 */
274 #define PASCAL (NEWTON/(METER*METER)) /* N / A^2 */
275 #define ATM (1.0133e5*PASCAL) /* N / A^2 */
277 #define MOLDYN_TEMP 273.0
278 #define MOLDYN_TAU 1.0
279 #define MOLDYN_CUTOFF 10.0
280 #define MOLDYN_RUNS 1000000
282 #define MOLDYN_INTEGRATE_VERLET 0x00
283 #define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
285 #define MOLDYN_POTENTIAL_HO 0x00
286 #define MOLDYN_POTENTIAL_LJ 0x01
287 #define MOLDYN_POTENTIAL_TM 0x02
289 #define LOG_TOTAL_ENERGY 0x01
290 #define LOG_TOTAL_MOMENTUM 0x02
291 #define SAVE_STEP 0x04
292 #define VISUAL_STEP 0x08
299 * phsical values / constants
304 #define K_BOLTZMANN (1.380650524e-23*METER*NEWTON) /* NA/K */
305 #define EV (1.6021765314e-19*METER*NEWTON) /* NA */
308 #define M_C 12.011 /* amu */
311 #define LC_SI (0.543105e-9*METER) /* A */
312 #define M_SI 28.08553 /* amu */
313 #define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* A */
314 #define LJ_EPSILON_SI (2.1678*EV) /* NA */
316 #define TM_R_SI (2.7e-10*METER) /* A */
317 #define TM_S_SI (3.0e-10*METER) /* A */
318 #define TM_A_SI (1830.8*EV) /* NA */
319 #define TM_B_SI (471.18*EV) /* NA */
320 #define TM_LAMBDA_SI (2.4799e10/METER) /* 1/A */
321 #define TM_MU_SI (1.7322e10/METER) /* 1/A */
322 #define TM_BETA_SI 1.1000e-6
323 #define TM_N_SI 0.78734
324 #define TM_C_SI 1.0039e5
325 #define TM_D_SI 16.217
326 #define TM_H_SI -0.59825
328 #define TM_R_C (1.8e-10*METER) /* A */
329 #define TM_S_C (2.1e-10*METER) /* A */
330 #define TM_A_C (1393.6*EV) /* NA */
331 #define TM_B_C (346.7*EV) /* NA */
332 #define TM_LAMBDA_C (3.4879e10/METER) /* 1/A */
333 #define TM_MU_C (2.2119e10/METER) /* 1/A */
334 #define TM_BETA_C 1.5724e-7
335 #define TM_N_C 0.72751
336 #define TM_C_C 3.8049e4
338 #define TM_H_C -0.57058
340 #define TM_CHI_SIC 0.9776
352 * function prototypes
356 typedef int (*pf_func1b)(t_moldyn *,t_atom *ai);
357 typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8 bc);
358 typedef int (*pf_func2b_post)(t_moldyn *,t_atom *,t_atom *,u8 bc);
359 typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8 bc);
361 int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
362 int moldyn_shutdown(t_moldyn *moldyn);
364 int set_int_alg(t_moldyn *moldyn,u8 algo);
365 int set_cutoff(t_moldyn *moldyn,double cutoff);
366 int set_temperature(t_moldyn *moldyn,double t_ref);
367 int set_pressure(t_moldyn *moldyn,double p_ref);
368 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc);
369 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize);
370 int set_nn_dist(t_moldyn *moldyn,double dist);
371 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
372 int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params);
373 int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params);
374 int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params);
375 int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params);
377 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
378 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer);
379 int moldyn_log_shutdown(t_moldyn *moldyn);
381 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
382 u8 attr,u8 brand,int a,int b,int c);
383 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
384 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
385 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
386 t_3dvec *r,t_3dvec *v);
387 int destroy_atoms(t_moldyn *moldyn);
389 int thermal_init(t_moldyn *moldyn,u8 equi_init);
390 int scale_velocity(t_moldyn *moldyn,u8 equi_init);
391 int scale_volume(t_moldyn *moldyn);
393 double get_e_kin(t_moldyn *moldyn);
394 double get_e_pot(t_moldyn *moldyn);
395 double get_total_energy(t_moldyn *moldyn);
396 t_3dvec get_total_p(t_moldyn *moldyn);
398 double estimate_time_step(t_moldyn *moldyn,double nn_dist);
400 int link_cell_init(t_moldyn *moldyn);
401 int link_cell_update(t_moldyn *moldyn);
402 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
403 int link_cell_shutdown(t_moldyn *moldyn);
405 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau);
406 int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params);
408 int moldyn_integrate(t_moldyn *moldyn);
409 int velocity_verlet(t_moldyn *moldyn);
411 int potential_force_calc(t_moldyn *moldyn);
412 inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
413 __attribute__((always_inline));
414 int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
415 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
416 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
417 int tersoff_mult_complete_params(t_tersoff_mult_params *p);
418 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai);
419 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
420 int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
421 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc);
423 int moldyn_bc_check(t_moldyn *moldyn);