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"
22 typedef unsigned char u8;
25 typedef struct s_virial {
26 double xx; /* | xx xy xz | */
27 double yy; /* V = | yx yy yz | */
28 double zz; /* | zx zy zz | */
30 double xz; /* with: xy=yx, xz=zx, yz=zy */
34 /* the atom of the md simulation */
35 typedef struct s_atom {
36 t_3dvec r_0; /* initial position */
37 t_3dvec r; /* position */
38 t_3dvec v; /* velocity */
39 t_3dvec f; /* force */
40 t_virial virial; /* virial */
41 double e; /* site energy */
42 double ekin; /* kinetic energy */
43 int element; /* number of element in pse */
44 double mass; /* atom mass */
45 u8 brand; /* brand id */
46 int tag; /* atom unique id (number of atom) */
47 u8 attr; /* attributes */
50 #define ATOM_ATTR_FP 0x01 /* fixed position (bulk material) */
51 #define ATOM_ATTR_HB 0x02 /* coupled to heat bath (velocity scaling) */
53 #define ATOM_ATTR_1BP 0x10 /* single paricle potential */
54 #define ATOM_ATTR_2BP 0x20 /* pair potential */
55 #define ATOM_ATTR_3BP 0x40 /* 3 body potential */
58 typedef struct s_linkcell {
59 int nx,ny,nz; /* amount of cells in x, y and z direction */
60 int cells; /* total amount of cells */
61 double len; /* prefered cell edge length */
62 double x,y,z; /* the actual cell lengthes */
63 t_list *subcell; /* pointer to the cell lists */
64 int dnlc; /* direct neighbour lists counter */
67 #include "visual/visual.h"
69 /* moldyn schedule structure */
70 typedef struct s_moldyn_schedule {
75 int (*hook)(void *moldyn,void *hook_params);
79 /* moldyn main structure */
80 typedef struct s_moldyn {
81 int argc; /* number of arguments */
82 char **args; /* pointer to arguments */
84 int count; /* total amount of atoms */
85 double mass; /* total system mass */
86 t_atom *atom; /* pointer to the atoms */
88 t_3dvec dim; /* dimensions of the simulation volume */
89 double volume; /* volume of sim cell (dim.x*dim.y*dim.z) */
91 /* potential force function and parameter pointers */
92 int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
93 int (*func2b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
94 int (*func3b_j1)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
95 int (*func3b_j2)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
96 int (*func3b_j3)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
97 int (*func3b_k1)(struct s_moldyn *moldyn,
98 t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
99 int (*func3b_k2)(struct s_moldyn *moldyn,
100 t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
102 unsigned char run3bp;
104 double cutoff; /* cutoff radius */
105 double cutoff_square; /* square of the cutoff radius */
106 double nnd; /* nearest neighbour distance (optional) */
108 t_linkcell lc; /* linked cell list interface */
110 int avg_skip; /* amount of steps without average calc */
112 double t_ref; /* reference temperature */
113 double t; /* actual temperature */
114 double t_sum; /* sum over all t */
115 double t_avg; /* average value of t */
117 t_virial gvir; /* global virial (absolute coordinates) */
122 double gp; /* pressure computed from global virial */
123 double gp_sum; /* sum over all gp */
124 double gp_avg; /* average value of gp */
126 double virial; /* actual virial */
127 double virial_sum; /* sum over all calculated virials */
128 double virial_avg; /* average of virial */
130 double p_ref; /* reference pressure */
131 double p; /* actual pressure (computed by virial) */
132 double p_sum; /* sum over all p */
133 double p_avg; /* average value of p */
135 t_3dvec tp; /* thermodynamic pressure dU/dV */
136 double dv; /* dV for thermodynamic pressure calc */
138 /* pressure and temperature control (velocity/volume scaling) */
139 /* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */
140 unsigned char pt_scale; /* type of p and t scaling */
141 double t_tc; /* t berendsen control time constant */
142 double p_tc; /* p berendsen control time constant */
144 /* simulation schedule */
145 t_moldyn_schedule schedule;
146 int current; /* current position in schedule */
148 /* integration function pointer */
149 int (*integrate)(struct s_moldyn *moldyn);
150 int time_steps; /* amount of iterations */
151 double tau; /* delta t */
152 double time; /* absolute time */
153 double tau_square; /* delta t squared */
154 int total_steps; /* total steps */
157 double energy; /* potential energy */
158 double ekin; /* kinetic energy */
160 /* energy averages & fluctuations */
161 double k_sum; /* sum of kinetic energy */
162 double v_sum; /* sum of potential energy */
163 double k_avg; /* average of kinetic energy */
164 double v_avg; /* average of potential energy */
165 double k2_sum; /* sum of kinetic energy squared */
166 double v2_sum; /* sum of potential energy squared */
167 double k2_avg; /* average of kinetic energy squared */
168 double v2_avg; /* average of potential energy squared */
169 double dk2_avg; /* mean square kinetic energy fluctuations */
170 double dv2_avg; /* mean square potential energy fluctuations */
172 /* response functions */
173 double c_v_nve; /* constant volume heat capacity (nve) */
174 double c_v_nvt; /* constant volume heat capacity (nvt) */
176 char vlsdir[128]; /* visualization/log/save directory */
177 t_visual vis; /* visualization interface structure */
178 u8 vlsprop; /* log/vis/save properties */
179 unsigned int ewrite; /* how often to log energy */
180 int efd; /* fd for energy log */
181 unsigned int mwrite; /* how often to log momentum */
182 int mfd; /* fd for momentum log */
183 unsigned int pwrite; /* how often to log pressure */
184 int pfd; /* fd for pressure log */
185 unsigned int twrite; /* how often to log temperature */
186 int tfd; /* fd for temperature log */
187 unsigned int vwrite; /* how often to visualize atom information */
188 unsigned int swrite; /* how often to create a save file */
189 int rfd; /* report file descriptor */
190 char rtitle[64]; /* report title */
191 char rauthor[64]; /* report author */
192 int epfd; /* energy gnuplot script file descriptor */
193 int ppfd; /* pressure gnuplot script file descriptor */
194 int tpfd; /* temperature gnuplot script file descriptor */
196 u8 status; /* general moldyn properties */
198 t_random random; /* random interface */
200 double debug; /* debugging stuff, ignore */
209 #define MOLDYN_STAT_PBX 0x01 /* periodic boudaries in x */
210 #define MOLDYN_STAT_PBY 0x02 /* y */
211 #define MOLDYN_STAT_PBZ 0x04 /* and z direction */
213 #define MOLDYN_PSCALE 0x08 /* size controlled by piston */
215 #define MOLDYN_1BP 0x10 /* care about single */
216 #define MOLDYN_2BP 0x20 /* 2 body */
217 #define MOLDYN_3BP 0x40 /* and 3 body particle pots */
219 #define T_SCALE_BERENDSEN 0x01 /* berendsen t control */
220 #define T_SCALE_DIRECT 0x02 /* direct t control */
221 #define P_SCALE_BERENDSEN 0x04 /* berendsen p control */
222 #define P_SCALE_DIRECT 0x08 /* direct p control */
225 * default values & units
227 * - length unit: 1 A (1 A = 1e-10 m)
228 * - time unit: 1 fs (1 fs = 1e-15 s)
229 * - mass unit: 1 amu (1 amu = 1.6605388628e-27 kg )
231 * fyi: in the following 1 N = (amu*A)/(fs*fs)
235 #define METER 1e10 /* A */
236 #define SECOND 1e15 /* fs */
237 #define AMU 1.6605388628e-27 /* kg */
238 #define KILOGRAM (1.0/AMU) /* amu */
239 #define NEWTON (METER*KILOGRAM/(SECOND*SECOND)) /* A amu / fs^2 */
240 #define PASCAL (NEWTON/(METER*METER)) /* N / A^2 */
241 #define BAR ((1.0e5*PASCAL)) /* N / A^2 */
242 #define K_BOLTZMANN (1.380650524e-23*METER*NEWTON) /* NA/K */
243 #define K_B2 (K_BOLTZMANN*K_BOLTZMANN) /* (NA)^2/K^2 */
244 #define EV (1.6021765314e-19*METER*NEWTON) /* NA */
245 #define JOULE (NEWTON*METER) /* NA */
247 #define MOLDYN_TEMP 273.0
248 #define MOLDYN_TAU 1.0
249 #define MOLDYN_CUTOFF 10.0
250 #define MOLDYN_RUNS 1000000
252 #define MOLDYN_INTEGRATE_VERLET 0x00
253 #define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
255 #define MOLDYN_POTENTIAL_HO 0x00
256 #define MOLDYN_POTENTIAL_LJ 0x01
257 #define MOLDYN_POTENTIAL_TM 0x02
259 #define LOG_TOTAL_ENERGY 0x01
260 #define LOG_TOTAL_MOMENTUM 0x02
261 #define LOG_PRESSURE 0x04
262 #define LOG_TEMPERATURE 0x08
263 #define SAVE_STEP 0x10
264 #define VISUAL_STEP 0x20
265 #define CREATE_REPORT 0x40
274 #define SCALE_DOWN 'd'
275 #define SCALE_DIRECT 'D'
278 * potential related phsical values / constants
282 #define ONE_THIRD (1.0/3.0)
285 #define LC_C 3.567 /* A */
286 #define M_C 12.011 /* amu */
289 #define LC_SI 5.43105 /* A */
290 #define M_SI 28.08553 /* amu */
292 #define LC_3C_SIC 4.3596 /* A */
294 #define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* A */
295 //#define LJ_SIGMA_SI (LC_SI/1.122462) /* A */
296 //#define LJ_SIGMA_SI (0.5*sqrt(2.0)*LC_SI/1.122462) /* A */
297 #define LJ_EPSILON_SI (2.1678*EV) /* NA */
299 #define TM_R_SI 2.7 /* A */
300 #define TM_S_SI 3.0 /* A */
301 #define TM_A_SI (1830.8*EV) /* NA */
302 #define TM_B_SI (471.18*EV) /* NA */
303 #define TM_LAMBDA_SI 2.4799 /* 1/A */
304 #define TM_MU_SI 1.7322 /* 1/A */
305 #define TM_BETA_SI 1.1000e-6
306 #define TM_N_SI 0.78734
307 #define TM_C_SI 1.0039e5
308 #define TM_D_SI 16.217
309 #define TM_H_SI -0.59825
311 #define TM_R_C 1.8 /* A */
312 #define TM_S_C 2.1 /* A */
313 #define TM_A_C (1393.6*EV) /* NA */
314 #define TM_B_C (346.7*EV) /* NA */
315 #define TM_LAMBDA_C 3.4879 /* 1/A */
316 #define TM_MU_C 2.2119 /* 1/A */
317 #define TM_BETA_C 1.5724e-7
318 #define TM_N_C 0.72751
319 #define TM_C_C 3.8049e4
321 #define TM_H_C -0.57058
323 #define TM_CHI_SIC 0.9776
325 #define TM_LC_SIC 4.32 /* A */
327 #define ALBE_R_SI (2.82-0.14)
328 #define ALBE_S_SI (2.82+0.14)
329 #define ALBE_A_SI (3.24*EV/0.842)
330 #define ALBE_B_SI (1.842*3.24*EV/0.842)
331 #define ALBE_R0_SI 2.232
332 #define ALBE_LAMBDA_SI (1.4761*sqrt(2.0*1.842))
333 #define ALBE_MU_SI (1.4761*sqrt(2.0/1.842))
334 #define ALBE_GAMMA_SI 0.114354
335 #define ALBE_C_SI 2.00494
336 #define ALBE_D_SI 0.81472
337 #define ALBE_H_SI 0.259
339 #define ALBE_LC_SI 5.429
341 #define ALBE_R_C (2.00-0.15)
342 #define ALBE_S_C (2.00+0.15)
343 #define ALBE_A_C (6.00*EV/1.167)
344 #define ALBE_B_C (2.167*6.00*EV/1.167)
345 #define ALBE_R0_C 1.4276
346 #define ALBE_LAMBDA_C (2.0099*sqrt(2.0*2.167))
347 #define ALBE_MU_C (2.0099*sqrt(2.0/2.167))
348 #define ALBE_GAMMA_C 0.11233
349 #define ALBE_C_C 181.910
350 #define ALBE_D_C 6.28433
351 #define ALBE_H_C 0.5556
353 #define ALBE_LC_C 3.566
355 #define ALBE_R_SIC (2.40-0.20)
356 #define ALBE_S_SIC (2.40+0.20)
357 #define ALBE_A_SIC (4.36*EV/0.847)
358 #define ALBE_B_SIC (1.847*4.36*EV/0.847)
359 #define ALBE_R0_SIC 1.79
360 #define ALBE_LAMBDA_SIC (1.6991*sqrt(2.0*1.847))
361 #define ALBE_MU_SIC (1.6991*sqrt(2.0/1.847))
362 #define ALBE_GAMMA_SIC 0.011877
363 #define ALBE_C_SIC 273987
364 #define ALBE_D_SIC 180.314
365 #define ALBE_H_SIC 0.68
367 #define ALBE_LC_SIC 4.359
381 * function prototypes
385 typedef int (*pf_func1b)(t_moldyn *,t_atom *);
386 typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8);
387 typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8);
389 int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
390 int moldyn_shutdown(t_moldyn *moldyn);
392 int set_int_alg(t_moldyn *moldyn,u8 algo);
393 int set_cutoff(t_moldyn *moldyn,double cutoff);
394 int set_temperature(t_moldyn *moldyn,double t_ref);
395 int set_pressure(t_moldyn *moldyn,double p_ref);
396 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc);
397 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize);
398 int set_nn_dist(t_moldyn *moldyn,double dist);
399 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
400 int set_potential1b(t_moldyn *moldyn,pf_func1b func);
401 int set_potential2b(t_moldyn *moldyn,pf_func2b func);
402 int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func);
403 int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func);
404 int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func);
405 int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func);
406 int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func);
407 int set_potential_params(t_moldyn *moldyn,void *params);
409 int set_avg_skip(t_moldyn *moldyn,int skip);
411 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
412 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title);
413 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer);
414 int moldyn_log_shutdown(t_moldyn *moldyn);
416 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
417 u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin);
418 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
419 t_3dvec *r,t_3dvec *v);
420 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
421 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
422 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
423 int destroy_atoms(t_moldyn *moldyn);
425 int thermal_init(t_moldyn *moldyn,u8 equi_init);
426 double total_mass_calc(t_moldyn *moldyn);
427 double temperature_calc(t_moldyn *moldyn);
428 double get_temperature(t_moldyn *moldyn);
429 int scale_velocity(t_moldyn *moldyn,u8 equi_init);
430 double virial_sum(t_moldyn *moldyn);
431 double pressure_calc(t_moldyn *moldyn);
432 int energy_fluctuation_calc(t_moldyn *moldyn);
433 int get_heat_capacity(t_moldyn *moldyn);
434 double thermodynamic_pressure_calc(t_moldyn *moldyn);
435 double get_pressure(t_moldyn *moldyn);
436 int scale_volume(t_moldyn *moldyn);
437 int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
438 int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
440 double e_kin_calc(t_moldyn *moldyn);
441 double get_total_energy(t_moldyn *moldyn);
442 t_3dvec get_total_p(t_moldyn *moldyn);
444 double estimate_time_step(t_moldyn *moldyn,double nn_dist);
446 int link_cell_init(t_moldyn *moldyn,u8 vol);
447 int link_cell_update(t_moldyn *moldyn);
448 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
449 int link_cell_shutdown(t_moldyn *moldyn);
451 typedef int (*set_hook)(void *,void *);
453 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau);
454 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params);
456 int moldyn_integrate(t_moldyn *moldyn);
457 int velocity_verlet(t_moldyn *moldyn);
459 int potential_force_calc(t_moldyn *moldyn);
460 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d);
461 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d)
462 // __attribute__((always_inline));
463 int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
464 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
465 // __attribute__((always_inline));
467 int moldyn_bc_check(t_moldyn *moldyn);
469 int get_line(int fd,char *line,int max);