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) */
52 #define ATOM_ATTR_VA 0x04 /* visualize this atom */
53 #define ATOM_ATTR_VB 0x08 /* visualize the bond of this atom */
55 #define ATOM_ATTR_1BP 0x10 /* single paricle potential */
56 #define ATOM_ATTR_2BP 0x20 /* pair potential */
57 #define ATOM_ATTR_3BP 0x40 /* 3 body potential */
60 typedef struct s_linkcell {
61 int nx,ny,nz; /* amount of cells in x, y and z direction */
62 int cells; /* total amount of cells */
63 double len; /* prefered cell edge length */
64 double x,y,z; /* the actual cell lengthes */
66 int **subcell; /* pointer to the cell lists */
68 t_list *subcell; /* pointer to the cell lists */
70 int dnlc; /* direct neighbour lists counter */
73 #define MAX_ATOMS_PER_LIST 20
75 /* moldyn schedule structure */
76 typedef struct s_moldyn_schedule {
81 int (*hook)(void *moldyn,void *hook_params);
85 /* visualization structure */
86 typedef struct s_visual {
87 int fd; /* rasmol script file descriptor */
88 char fb[128]; /* basename of the save files */
89 t_3dvec dim; /* dimensions of the simulation cell */
92 /* moldyn main structure */
93 typedef struct s_moldyn {
94 int argc; /* number of arguments */
95 char **args; /* pointer to arguments */
97 int count; /* total amount of atoms */
98 double mass; /* total system mass */
99 t_atom *atom; /* pointer to the atoms */
101 t_3dvec dim; /* dimensions of the simulation volume */
102 double volume; /* volume of sim cell (dim.x*dim.y*dim.z) */
104 /* potential force function and parameter pointers */
105 int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
106 int (*func2b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
107 int (*func3b_j1)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
108 int (*func3b_j2)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
109 int (*func3b_j3)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
110 int (*func3b_k1)(struct s_moldyn *moldyn,
111 t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
112 int (*func3b_k2)(struct s_moldyn *moldyn,
113 t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
115 unsigned char run3bp;
117 double cutoff; /* cutoff radius */
118 double cutoff_square; /* square of the cutoff radius */
119 double nnd; /* nearest neighbour distance (optional) */
120 double bondlen[3]; /* bond lengthes (only 2 atomic systems) */
122 t_linkcell lc; /* linked cell list interface */
124 int avg_skip; /* amount of steps without average calc */
126 double t_ref; /* reference temperature */
127 double t; /* actual temperature */
128 double t_sum; /* sum over all t */
129 double t_avg; /* average value of t */
131 t_virial gvir; /* global virial (absolute coordinates) */
136 double gp; /* pressure computed from global virial */
137 double gp_sum; /* sum over all gp */
138 double gp_avg; /* average value of gp */
140 t_virial vir; /* actual virial */
142 double virial_sum; /* sum over all calculated virials */
143 double virial_avg; /* average of virial */
145 double p_ref; /* reference pressure */
146 double p; /* actual pressure (computed by virial) */
147 double p_sum; /* sum over all p */
148 double p_avg; /* average value of p */
150 double tp; /* thermodynamic pressure dU/dV */
151 double tp_sum; /* sum over dU/dV pressure */
152 double tp_avg; /* average value of dU/dV pressure */
153 int tp_cnt; /* how often to do thermodynamic p calc */
155 /* pressure and temperature control (velocity/volume scaling) */
156 /* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */
157 unsigned char pt_scale; /* type of p and t scaling */
158 double t_tc; /* t berendsen control time constant */
159 double p_tc; /* p berendsen control time constant */
161 /* simulation schedule */
162 t_moldyn_schedule schedule;
163 int current; /* current position in schedule */
165 /* integration function pointer */
166 int (*integrate)(struct s_moldyn *moldyn);
167 int time_steps; /* amount of iterations */
168 double tau; /* delta t */
169 double time; /* absolute time */
170 double tau_square; /* delta t squared */
171 int total_steps; /* total steps */
174 double energy; /* potential energy */
175 double ekin; /* kinetic energy */
177 /* energy averages & fluctuations */
178 double k_sum; /* sum of kinetic energy */
179 double v_sum; /* sum of potential energy */
180 double k_avg; /* average of kinetic energy */
181 double v_avg; /* average of potential energy */
182 double k2_sum; /* sum of kinetic energy squared */
183 double v2_sum; /* sum of potential energy squared */
184 double k2_avg; /* average of kinetic energy squared */
185 double v2_avg; /* average of potential energy squared */
186 double dk2_avg; /* mean square kinetic energy fluctuations */
187 double dv2_avg; /* mean square potential energy fluctuations */
189 /* response functions */
190 double c_v_nve; /* constant volume heat capacity (nve) */
191 double c_v_nvt; /* constant volume heat capacity (nvt) */
193 char vlsdir[128]; /* visualization/log/save directory */
194 t_visual vis; /* visualization interface structure */
195 u8 vlsprop; /* log/vis/save properties */
196 unsigned int ewrite; /* how often to log energy */
197 int efd; /* fd for energy log */
198 unsigned int mwrite; /* how often to log momentum */
199 int mfd; /* fd for momentum log */
200 unsigned int pwrite; /* how often to log pressure */
201 int pfd; /* fd for pressure log */
202 unsigned int twrite; /* how often to log temperature */
203 int tfd; /* fd for temperature log */
204 unsigned int vwrite; /* how often to log volume */
205 int vfd; /* fd for volume log */
206 unsigned int awrite; /* how often to visualize atom information */
207 unsigned int swrite; /* how often to create a save file */
208 int rfd; /* report file descriptor */
209 char rtitle[64]; /* report title */
210 char rauthor[64]; /* report author */
211 int epfd; /* energy gnuplot script file descriptor */
212 int ppfd; /* pressure gnuplot script file descriptor */
213 int tpfd; /* temperature gnuplot script file descriptor */
215 u8 status; /* general moldyn properties */
217 t_random random; /* random interface */
219 double debug; /* debugging stuff, ignore */
222 typedef struct s_pcc {
229 typedef struct s_ba {
241 #define MOLDYN_STAT_PBX 0x01 /* periodic boudaries in x */
242 #define MOLDYN_STAT_PBY 0x02 /* y */
243 #define MOLDYN_STAT_PBZ 0x04 /* and z direction */
245 #define MOLDYN_PSCALE 0x08 /* size controlled by piston */
247 #define MOLDYN_1BP 0x10 /* care about single */
248 #define MOLDYN_2BP 0x20 /* 2 body */
249 #define MOLDYN_3BP 0x40 /* and 3 body particle pots */
251 #define T_SCALE_BERENDSEN 0x01 /* berendsen t control */
252 #define T_SCALE_DIRECT 0x02 /* direct t control */
253 #define P_SCALE_BERENDSEN 0x04 /* berendsen p control */
254 #define P_SCALE_DIRECT 0x08 /* direct p control */
257 * default values & units
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 GPA (1e9*PASCAL) /* N / A^2 */
274 #define BAR ((1.0e5*PASCAL)) /* N / A^2 */
275 #define K_BOLTZMANN (1.380650524e-23*METER*NEWTON) /* NA/K */
276 #define K_B2 (K_BOLTZMANN*K_BOLTZMANN) /* (NA)^2/K^2 */
277 #define EV (1.6021765314e-19*METER*NEWTON) /* NA */
278 #define JOULE (NEWTON*METER) /* NA */
280 #define MOLDYN_TEMP 273.0
281 #define MOLDYN_TAU 1.0
282 #define MOLDYN_CUTOFF 10.0
283 #define MOLDYN_RUNS 1000000
285 #define MOLDYN_INTEGRATE_VERLET 0x00
286 #define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
288 #define MOLDYN_POTENTIAL_HO 0x00
289 #define MOLDYN_POTENTIAL_LJ 0x01
290 #define MOLDYN_POTENTIAL_TM 0x02
292 #define LOG_TOTAL_ENERGY 0x01
293 #define LOG_TOTAL_MOMENTUM 0x02
294 #define LOG_PRESSURE 0x04
295 #define LOG_TEMPERATURE 0x08
296 #define LOG_VOLUME 0x10
297 #define SAVE_STEP 0x20
298 #define VISUAL_STEP 0x40
299 #define CREATE_REPORT 0x80
308 #define SCALE_DOWN 'd'
309 #define SCALE_DIRECT 'D'
312 * potential related phsical values / constants
316 #define ONE_THIRD (1.0/3.0)
319 #define LC_C 3.567 /* A */
320 #define M_C 12.011 /* amu */
323 #define LC_SI 5.43105 /* A */
324 #define M_SI 28.08553 /* amu */
326 #define LC_3C_SIC 4.3596 /* A */
328 #define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* A */
329 //#define LJ_SIGMA_SI (LC_SI/1.122462) /* A */
330 //#define LJ_SIGMA_SI (0.5*sqrt(2.0)*LC_SI/1.122462) /* A */
331 #define LJ_EPSILON_SI (2.1678*EV) /* NA */
333 #define TM_R_SI 2.7 /* A */
334 #define TM_S_SI 3.0 /* A */
335 #define TM_A_SI (1830.8*EV) /* NA */
336 #define TM_B_SI (471.18*EV) /* NA */
337 #define TM_LAMBDA_SI 2.4799 /* 1/A */
338 #define TM_MU_SI 1.7322 /* 1/A */
339 #define TM_BETA_SI 1.1000e-6
340 #define TM_N_SI 0.78734
341 #define TM_C_SI 1.0039e5
342 #define TM_D_SI 16.217
343 #define TM_H_SI -0.59825
345 #define TM_R_C 1.8 /* A */
346 #define TM_S_C 2.1 /* A */
347 #define TM_A_C (1393.6*EV) /* NA */
348 #define TM_B_C (346.7*EV) /* NA */
349 #define TM_LAMBDA_C 3.4879 /* 1/A */
350 #define TM_MU_C 2.2119 /* 1/A */
351 #define TM_BETA_C 1.5724e-7
352 #define TM_N_C 0.72751
353 #define TM_C_C 3.8049e4
355 #define TM_H_C -0.57058
357 #define TM_CHI_SIC 0.9776
359 #define TM_LC_SIC 4.32 /* A */
361 #define ALBE_R_SI (2.82-0.14)
362 #define ALBE_S_SI (2.82+0.14)
363 #define ALBE_A_SI (3.24*EV/0.842)
364 #define ALBE_B_SI (-1.842*3.24*EV/0.842)
365 #define ALBE_R0_SI 2.232
366 #define ALBE_LAMBDA_SI (1.4761*sqrt(2.0*1.842))
367 #define ALBE_MU_SI (1.4761*sqrt(2.0/1.842))
368 #define ALBE_GAMMA_SI 0.114354
369 #define ALBE_C_SI 2.00494
370 #define ALBE_D_SI 0.81472
371 #define ALBE_H_SI 0.259
373 #define ALBE_LC_SI 5.429
375 #define ALBE_R_C (2.00-0.15)
376 #define ALBE_S_C (2.00+0.15)
377 #define ALBE_A_C (6.00*EV/1.167)
378 #define ALBE_B_C (-2.167*6.00*EV/1.167)
379 #define ALBE_R0_C 1.4276
380 #define ALBE_LAMBDA_C (2.0099*sqrt(2.0*2.167))
381 #define ALBE_MU_C (2.0099*sqrt(2.0/2.167))
382 #define ALBE_GAMMA_C 0.11233
383 #define ALBE_C_C 181.910
384 #define ALBE_D_C 6.28433
385 #define ALBE_H_C 0.5556
387 #define ALBE_LC_C 3.566
389 #define ALBE_R_SIC (2.40-0.20)
390 #define ALBE_S_SIC (2.40+0.20)
391 #define ALBE_A_SIC (4.36*EV/0.847)
392 #define ALBE_B_SIC (-1.847*4.36*EV/0.847)
393 #define ALBE_R0_SIC 1.79
394 #define ALBE_LAMBDA_SIC (1.6991*sqrt(2.0*1.847))
395 #define ALBE_MU_SIC (1.6991*sqrt(2.0/1.847))
396 #define ALBE_GAMMA_SIC 0.011877
397 #define ALBE_C_SIC 273987
398 #define ALBE_D_SIC 180.314
399 #define ALBE_H_SIC 0.68
401 #define ALBE_LC_SIC 4.359
414 * function prototypes
418 typedef int (*pf_func1b)(t_moldyn *,t_atom *);
419 typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8);
420 typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8);
422 int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
423 int moldyn_shutdown(t_moldyn *moldyn);
425 int set_int_alg(t_moldyn *moldyn,u8 algo);
426 int set_cutoff(t_moldyn *moldyn,double cutoff);
427 int set_bondlen(t_moldyn *moldyn,double b0,double b1,double bm);
428 int set_temperature(t_moldyn *moldyn,double t_ref);
429 int set_pressure(t_moldyn *moldyn,double p_ref);
430 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc);
431 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize);
432 int set_nn_dist(t_moldyn *moldyn,double dist);
433 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
434 int set_potential1b(t_moldyn *moldyn,pf_func1b func);
435 int set_potential2b(t_moldyn *moldyn,pf_func2b func);
436 int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func);
437 int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func);
438 int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func);
439 int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func);
440 int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func);
441 int set_potential_params(t_moldyn *moldyn,void *params);
443 int set_avg_skip(t_moldyn *moldyn,int skip);
445 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
446 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title);
447 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer);
448 int moldyn_log_shutdown(t_moldyn *moldyn);
450 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
451 u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin);
452 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
453 t_3dvec *r,t_3dvec *v);
454 int del_atom(t_moldyn *moldyn,int tag);
455 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
456 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
457 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
458 int destroy_atoms(t_moldyn *moldyn);
460 int thermal_init(t_moldyn *moldyn,u8 equi_init);
461 double total_mass_calc(t_moldyn *moldyn);
462 double temperature_calc(t_moldyn *moldyn);
463 double get_temperature(t_moldyn *moldyn);
464 int scale_velocity(t_moldyn *moldyn,u8 equi_init);
465 double virial_sum(t_moldyn *moldyn);
466 double pressure_calc(t_moldyn *moldyn);
467 int average_reset(t_moldyn *moldyn);
468 int average_and_fluctuation_calc(t_moldyn *moldyn);
469 int get_heat_capacity(t_moldyn *moldyn);
470 double thermodynamic_pressure_calc(t_moldyn *moldyn);
471 double get_pressure(t_moldyn *moldyn);
472 int scale_volume(t_moldyn *moldyn);
473 int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
474 int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
476 double e_kin_calc(t_moldyn *moldyn);
477 double get_total_energy(t_moldyn *moldyn);
478 t_3dvec get_total_p(t_moldyn *moldyn);
480 double estimate_time_step(t_moldyn *moldyn,double nn_dist);
482 int link_cell_init(t_moldyn *moldyn,u8 vol);
483 int link_cell_update(t_moldyn *moldyn);
485 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int **cell);
487 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
489 int link_cell_shutdown(t_moldyn *moldyn);
491 typedef int (*set_hook)(void *,void *);
493 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau);
494 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params);
496 int moldyn_integrate(t_moldyn *moldyn);
497 int velocity_verlet(t_moldyn *moldyn);
499 int potential_force_calc(t_moldyn *moldyn);
500 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d);
501 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d)
502 // __attribute__((always_inline));
503 int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
504 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
505 // __attribute__((always_inline));
507 int moldyn_bc_check(t_moldyn *moldyn);
509 int moldyn_read_save_file(t_moldyn *moldyn,char *file);
510 int moldyn_free_save_file(t_moldyn *moldyn);
511 int moldyn_load(t_moldyn *moldyn);
512 int process_2b_bonds(t_moldyn *moldyn,void *data,
513 int (*process)(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
515 int get_line(int fd,char *line,int max);
517 int pair_correlation_init(t_moldyn *moldyn,double dr);
518 int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc);
519 int calculate_pair_correlation_process(t_moldyn *moldyn,t_atom *itom,
520 t_atom *jtom,void *data,u8 bc);
521 int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr);
522 int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
524 int bond_analyze(t_moldyn *moldyn,double *quality);
526 int visual_init(t_moldyn *moldyn,char *filebase);
527 int visual_atoms(t_moldyn *moldyn);