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