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_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 unsigned char pt_scale; /* type of p and t scaling */
96 double t_tc; /* t berendsen control time constant */
97 double p_tc; /* p berendsen control time constant */
99 /* simulation schedule */
100 t_moldyn_schedule schedule;
101 int current; /* current position in schedule */
103 /* integration function pointer */
104 int (*integrate)(struct s_moldyn *moldyn);
105 int time_steps; /* amount of iterations */
106 double tau; /* delta t */
107 double time; /* absolute time */
108 double tau_square; /* delta t squared */
109 double elapsed; /* total elapsed time */
111 double energy; /* potential energy */
112 double ekin; /* kinetic energy */
114 t_visual vis; /* visualization/log/save interface structure */
115 u8 lvstat; /* log & vis properties */
116 unsigned int ewrite; /* how often to log energy */
117 int efd; /* fd for energy log */
118 unsigned int mwrite; /* how often to log momentum */
119 int mfd; /* fd for momentum log */
120 unsigned int vwrite; /* how often to visualize atom information */
121 char vfb[64]; /* visualization file name base */
122 //void *visual; /* pointer (hack!) */
123 unsigned int swrite; /* how often to create a save file */
124 char sfb[64]; /* visualization file name base */
126 u8 status; /* general moldyn properties */
128 t_random random; /* random interface */
131 #define MOLDYN_STAT_PBX 0x08 /* periodic boudaries in x */
132 #define MOLDYN_STAT_PBY 0x10 /* y */
133 #define MOLDYN_STAT_PBZ 0x20 /* and z direction */
135 #define MOLDYN_1BP 0x00 /* care about single */
136 #define MOLDYN_2BP 0x01 /* 2 body */
137 #define MOLDYN_3BP 0x02 /* and 3 body particle pots */
139 #define T_SCALE_BERENDSEN 0x01 /* berendsen t control */
140 #define T_SCALE_DIRECT 0x02 /* direct t control */
141 #define P_SCALE_BERENDSEN 0x04 /* berendsen p control */
142 #define P_SCALE_DIRECT 0x08 /* direct p control */
147 * potential parameter structures
152 * harmonic oscillator potential parameter structure
155 typedef struct s_ho_params {
156 double spring_constant;
157 double equilibrium_distance;
161 * lennard jones potential parameter structure
164 typedef struct s_lj_params {
174 /* tersoff exchange structure to exchange 2bp and 3bp calculated values */
175 typedef struct s_tersoff_exchange {
200 } t_tersoff_exchange;
202 /* tersoff multi (2!) potential parameters */
203 typedef struct s_tersoff_mult_params {
204 double S[2]; /* tersoff cutoff radii */
205 double R[2]; /* tersoff cutoff radii */
206 double Smixed; /* mixed S radius */
207 double Rmixed; /* mixed R radius */
208 double A[2]; /* factor of tersoff attractive part */
209 double B[2]; /* factor of tersoff repulsive part */
210 double Amixed; /* mixed A factor */
211 double Bmixed; /* mixed B factor */
212 double lambda[2]; /* tersoff lambda */
213 double lambda_m; /* mixed lambda */
214 double mu[2]; /* tersoff mu */
215 double mu_m; /* mixed mu */
225 t_tersoff_exchange exchange; /* exchange between 2bp and 3bp calc */
226 } t_tersoff_mult_params;
238 #define MOLDYN_TEMP 273.0
239 #define MOLDYN_TAU 1.0e-15
240 #define MOLDYN_CUTOFF 1.0e-9
241 #define MOLDYN_RUNS 1000000
243 #define MOLDYN_CRITICAL_EST_TEMP 5.0
245 #define MOLDYN_INTEGRATE_VERLET 0x00
246 #define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
248 #define MOLDYN_POTENTIAL_HO 0x00
249 #define MOLDYN_POTENTIAL_LJ 0x01
250 #define MOLDYN_POTENTIAL_TM 0x02
252 #define LOG_TOTAL_ENERGY 0x01
253 #define LOG_TOTAL_MOMENTUM 0x02
254 #define SAVE_STEP 0x04
255 #define VISUAL_STEP 0x08
262 * phsical values / constants
266 #define K_BOLTZMANN 1.3807e-27 /* Nm/K */
267 #define AMU 1.660540e-27 /* kg */
268 #define EV 1.60217733e-19 /* Nm */
274 #define M_C (12.011*AMU)
277 #define LC_SI 0.543105e-9 /* m */
278 #define M_SI (28.085*AMU) /* kg */
279 #define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* m */
280 #define LJ_EPSILON_SI (2.1678*1.60e-19) /* Nm */
282 #define TM_R_SI 2.7e-10 /* m */
283 #define TM_S_SI 3.0e-10 /* m */
284 #define TM_A_SI (1830.8*EV) /* Nm */
285 #define TM_B_SI (471.18*EV) /* Nm */
286 #define TM_LAMBDA_SI 2.4799e10 /* 1/m */
287 #define TM_MU_SI 1.7322e10 /* 1/m */
288 #define TM_BETA_SI 1.1000e-6
289 #define TM_N_SI 0.78734
290 #define TM_C_SI 1.0039e5
291 #define TM_D_SI 1.62170
292 #define TM_H_SI (-0.59825)
294 #define TM_R_C 1.8e-10 /* m */
295 #define TM_S_C 2.1e-10 /* m */
296 #define TM_A_C (1393.6*EV) /* Nm */
297 #define TM_B_C (346.7*EV) /* Nm */
298 #define TM_LAMBDA_C 3.4879e10 /* 1/m */
299 #define TM_MU_C 2.2119e10 /* 1/m */
300 #define TM_BETA_C 1.5724e-7
301 #define TM_N_C 0.72751
302 #define TM_C_C 3.8049e4
304 #define TM_H_C (-0.57058)
306 #define TM_CHI_SIC 0.9776
311 * function prototypes
315 typedef int (*pf_func1b)(t_moldyn *,t_atom *ai);
316 typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8 bc);
317 typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8 bc);
319 int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
320 int moldyn_shutdown(t_moldyn *moldyn);
322 int set_int_alg(t_moldyn *moldyn,u8 algo);
323 int set_cutoff(t_moldyn *moldyn,double cutoff);
324 int set_temperature(t_moldyn *moldyn,double t_ref);
325 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc);
326 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize);
327 int set_nn_dist(t_moldyn *moldyn,double dist);
328 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
329 int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params);
330 int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params);
331 int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params);
333 int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer);
334 int moldyn_log_shutdown(t_moldyn *moldyn);
336 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
337 u8 attr,u8 bnum,int a,int b,int c);
338 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
339 t_3dvec *r,t_3dvec *v);
340 int destroy_atoms(t_moldyn *moldyn);
342 int thermal_init(t_moldyn *moldyn,u8 equi_init);
343 int scale_velocity(t_moldyn *moldyn,u8 equi_init);
345 double get_e_kin(t_moldyn *moldyn);
346 double get_e_pot(t_moldyn *moldyn);
347 double get_total_energy(t_moldyn *moldyn);
348 t_3dvec get_total_p(t_moldyn *moldyn);
350 double estimate_time_step(t_moldyn *moldyn,double nn_dist);
352 int link_cell_init(t_moldyn *moldyn);
353 int link_cell_update(t_moldyn *moldyn);
354 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
355 int link_cell_shutdown(t_moldyn *moldyn);
357 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau);
358 int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params);
360 int moldyn_integrate(t_moldyn *moldyn);
361 int velocity_verlet(t_moldyn *moldyn);
363 int potential_force_calc(t_moldyn *moldyn);
364 int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
365 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
366 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
367 int tersoff_mult_complete_params(t_tersoff_mult_params *p);
368 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai);
369 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
370 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc);