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 double virial; /* actual virial */
141 double virial_sum; /* sum over all calculated virials */
142 double virial_avg; /* average of virial */
144 double p_ref; /* reference pressure */
145 double p; /* actual pressure (computed by virial) */
146 double p_sum; /* sum over all p */
147 double p_avg; /* average value of p */
149 t_3dvec tp; /* thermodynamic pressure dU/dV */
150 double dv; /* dV for thermodynamic pressure calc */
152 /* pressure and temperature control (velocity/volume scaling) */
153 /* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */
154 unsigned char pt_scale; /* type of p and t scaling */
155 double t_tc; /* t berendsen control time constant */
156 double p_tc; /* p berendsen control time constant */
158 /* simulation schedule */
159 t_moldyn_schedule schedule;
160 int current; /* current position in schedule */
162 /* integration function pointer */
163 int (*integrate)(struct s_moldyn *moldyn);
164 int time_steps; /* amount of iterations */
165 double tau; /* delta t */
166 double time; /* absolute time */
167 double tau_square; /* delta t squared */
168 int total_steps; /* total steps */
171 double energy; /* potential energy */
172 double ekin; /* kinetic energy */
174 /* energy averages & fluctuations */
175 double k_sum; /* sum of kinetic energy */
176 double v_sum; /* sum of potential energy */
177 double k_avg; /* average of kinetic energy */
178 double v_avg; /* average of potential energy */
179 double k2_sum; /* sum of kinetic energy squared */
180 double v2_sum; /* sum of potential energy squared */
181 double k2_avg; /* average of kinetic energy squared */
182 double v2_avg; /* average of potential energy squared */
183 double dk2_avg; /* mean square kinetic energy fluctuations */
184 double dv2_avg; /* mean square potential energy fluctuations */
186 /* response functions */
187 double c_v_nve; /* constant volume heat capacity (nve) */
188 double c_v_nvt; /* constant volume heat capacity (nvt) */
190 char vlsdir[128]; /* visualization/log/save directory */
191 t_visual vis; /* visualization interface structure */
192 u8 vlsprop; /* log/vis/save properties */
193 unsigned int ewrite; /* how often to log energy */
194 int efd; /* fd for energy log */
195 unsigned int mwrite; /* how often to log momentum */
196 int mfd; /* fd for momentum log */
197 unsigned int pwrite; /* how often to log pressure */
198 int pfd; /* fd for pressure log */
199 unsigned int twrite; /* how often to log temperature */
200 int tfd; /* fd for temperature log */
201 unsigned int vwrite; /* how often to visualize atom information */
202 unsigned int swrite; /* how often to create a save file */
203 int rfd; /* report file descriptor */
204 char rtitle[64]; /* report title */
205 char rauthor[64]; /* report author */
206 int epfd; /* energy gnuplot script file descriptor */
207 int ppfd; /* pressure gnuplot script file descriptor */
208 int tpfd; /* temperature gnuplot script file descriptor */
210 u8 status; /* general moldyn properties */
212 t_random random; /* random interface */
214 double debug; /* debugging stuff, ignore */
223 #define MOLDYN_STAT_PBX 0x01 /* periodic boudaries in x */
224 #define MOLDYN_STAT_PBY 0x02 /* y */
225 #define MOLDYN_STAT_PBZ 0x04 /* and z direction */
227 #define MOLDYN_PSCALE 0x08 /* size controlled by piston */
229 #define MOLDYN_1BP 0x10 /* care about single */
230 #define MOLDYN_2BP 0x20 /* 2 body */
231 #define MOLDYN_3BP 0x40 /* and 3 body particle pots */
233 #define T_SCALE_BERENDSEN 0x01 /* berendsen t control */
234 #define T_SCALE_DIRECT 0x02 /* direct t control */
235 #define P_SCALE_BERENDSEN 0x04 /* berendsen p control */
236 #define P_SCALE_DIRECT 0x08 /* direct p control */
239 * default values & units
241 * - length unit: 1 A (1 A = 1e-10 m)
242 * - time unit: 1 fs (1 fs = 1e-15 s)
243 * - mass unit: 1 amu (1 amu = 1.6605388628e-27 kg )
245 * fyi: in the following 1 N = (amu*A)/(fs*fs)
249 #define METER 1e10 /* A */
250 #define SECOND 1e15 /* fs */
251 #define AMU 1.6605388628e-27 /* kg */
252 #define KILOGRAM (1.0/AMU) /* amu */
253 #define NEWTON (METER*KILOGRAM/(SECOND*SECOND)) /* A amu / fs^2 */
254 #define PASCAL (NEWTON/(METER*METER)) /* N / A^2 */
255 #define BAR ((1.0e5*PASCAL)) /* N / A^2 */
256 #define K_BOLTZMANN (1.380650524e-23*METER*NEWTON) /* NA/K */
257 #define K_B2 (K_BOLTZMANN*K_BOLTZMANN) /* (NA)^2/K^2 */
258 #define EV (1.6021765314e-19*METER*NEWTON) /* NA */
259 #define JOULE (NEWTON*METER) /* NA */
261 #define MOLDYN_TEMP 273.0
262 #define MOLDYN_TAU 1.0
263 #define MOLDYN_CUTOFF 10.0
264 #define MOLDYN_RUNS 1000000
266 #define MOLDYN_INTEGRATE_VERLET 0x00
267 #define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
269 #define MOLDYN_POTENTIAL_HO 0x00
270 #define MOLDYN_POTENTIAL_LJ 0x01
271 #define MOLDYN_POTENTIAL_TM 0x02
273 #define LOG_TOTAL_ENERGY 0x01
274 #define LOG_TOTAL_MOMENTUM 0x02
275 #define LOG_PRESSURE 0x04
276 #define LOG_TEMPERATURE 0x08
277 #define SAVE_STEP 0x10
278 #define VISUAL_STEP 0x20
279 #define CREATE_REPORT 0x40
288 #define SCALE_DOWN 'd'
289 #define SCALE_DIRECT 'D'
292 * potential related phsical values / constants
296 #define ONE_THIRD (1.0/3.0)
299 #define LC_C 3.567 /* A */
300 #define M_C 12.011 /* amu */
303 #define LC_SI 5.43105 /* A */
304 #define M_SI 28.08553 /* amu */
306 #define LC_3C_SIC 4.3596 /* A */
308 #define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* A */
309 //#define LJ_SIGMA_SI (LC_SI/1.122462) /* A */
310 //#define LJ_SIGMA_SI (0.5*sqrt(2.0)*LC_SI/1.122462) /* A */
311 #define LJ_EPSILON_SI (2.1678*EV) /* NA */
313 #define TM_R_SI 2.7 /* A */
314 #define TM_S_SI 3.0 /* A */
315 #define TM_A_SI (1830.8*EV) /* NA */
316 #define TM_B_SI (471.18*EV) /* NA */
317 #define TM_LAMBDA_SI 2.4799 /* 1/A */
318 #define TM_MU_SI 1.7322 /* 1/A */
319 #define TM_BETA_SI 1.1000e-6
320 #define TM_N_SI 0.78734
321 #define TM_C_SI 1.0039e5
322 #define TM_D_SI 16.217
323 #define TM_H_SI -0.59825
325 #define TM_R_C 1.8 /* A */
326 #define TM_S_C 2.1 /* A */
327 #define TM_A_C (1393.6*EV) /* NA */
328 #define TM_B_C (346.7*EV) /* NA */
329 #define TM_LAMBDA_C 3.4879 /* 1/A */
330 #define TM_MU_C 2.2119 /* 1/A */
331 #define TM_BETA_C 1.5724e-7
332 #define TM_N_C 0.72751
333 #define TM_C_C 3.8049e4
335 #define TM_H_C -0.57058
337 #define TM_CHI_SIC 0.9776
339 #define TM_LC_SIC 4.32 /* A */
341 #define ALBE_R_SI (2.82-0.14)
342 #define ALBE_S_SI (2.82+0.14)
343 #define ALBE_A_SI (3.24*EV/0.842)
344 #define ALBE_B_SI (-1.842*3.24*EV/0.842)
345 #define ALBE_R0_SI 2.232
346 #define ALBE_LAMBDA_SI (1.4761*sqrt(2.0*1.842))
347 #define ALBE_MU_SI (1.4761*sqrt(2.0/1.842))
348 #define ALBE_GAMMA_SI 0.114354
349 #define ALBE_C_SI 2.00494
350 #define ALBE_D_SI 0.81472
351 #define ALBE_H_SI 0.259
353 #define ALBE_LC_SI 5.429
355 #define ALBE_R_C (2.00-0.15)
356 #define ALBE_S_C (2.00+0.15)
357 #define ALBE_A_C (6.00*EV/1.167)
358 #define ALBE_B_C (-2.167*6.00*EV/1.167)
359 #define ALBE_R0_C 1.4276
360 #define ALBE_LAMBDA_C (2.0099*sqrt(2.0*2.167))
361 #define ALBE_MU_C (2.0099*sqrt(2.0/2.167))
362 #define ALBE_GAMMA_C 0.11233
363 #define ALBE_C_C 181.910
364 #define ALBE_D_C 6.28433
365 #define ALBE_H_C 0.5556
367 #define ALBE_LC_C 3.566
369 #define ALBE_R_SIC (2.40-0.20)
370 #define ALBE_S_SIC (2.40+0.20)
371 #define ALBE_A_SIC (4.36*EV/0.847)
372 #define ALBE_B_SIC (-1.847*4.36*EV/0.847)
373 #define ALBE_R0_SIC 1.79
374 #define ALBE_LAMBDA_SIC (1.6991*sqrt(2.0*1.847))
375 #define ALBE_MU_SIC (1.6991*sqrt(2.0/1.847))
376 #define ALBE_GAMMA_SIC 0.011877
377 #define ALBE_C_SIC 273987
378 #define ALBE_D_SIC 180.314
379 #define ALBE_H_SIC 0.68
381 #define ALBE_LC_SIC 4.359
394 * function prototypes
398 typedef int (*pf_func1b)(t_moldyn *,t_atom *);
399 typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8);
400 typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8);
402 int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
403 int moldyn_shutdown(t_moldyn *moldyn);
405 int set_int_alg(t_moldyn *moldyn,u8 algo);
406 int set_cutoff(t_moldyn *moldyn,double cutoff);
407 int set_bondlen(t_moldyn *moldyn,double b0,double b1,double bm);
408 int set_temperature(t_moldyn *moldyn,double t_ref);
409 int set_pressure(t_moldyn *moldyn,double p_ref);
410 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc);
411 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize);
412 int set_nn_dist(t_moldyn *moldyn,double dist);
413 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
414 int set_potential1b(t_moldyn *moldyn,pf_func1b func);
415 int set_potential2b(t_moldyn *moldyn,pf_func2b func);
416 int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func);
417 int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func);
418 int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func);
419 int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func);
420 int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func);
421 int set_potential_params(t_moldyn *moldyn,void *params);
423 int set_avg_skip(t_moldyn *moldyn,int skip);
425 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
426 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title);
427 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer);
428 int moldyn_log_shutdown(t_moldyn *moldyn);
430 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
431 u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin);
432 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
433 t_3dvec *r,t_3dvec *v);
434 int del_atom(t_moldyn *moldyn,int tag);
435 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
436 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
437 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
438 int destroy_atoms(t_moldyn *moldyn);
440 int thermal_init(t_moldyn *moldyn,u8 equi_init);
441 double total_mass_calc(t_moldyn *moldyn);
442 double temperature_calc(t_moldyn *moldyn);
443 double get_temperature(t_moldyn *moldyn);
444 int scale_velocity(t_moldyn *moldyn,u8 equi_init);
445 double virial_sum(t_moldyn *moldyn);
446 double pressure_calc(t_moldyn *moldyn);
447 int average_reset(t_moldyn *moldyn);
448 int average_and_fluctuation_calc(t_moldyn *moldyn);
449 int get_heat_capacity(t_moldyn *moldyn);
450 double thermodynamic_pressure_calc(t_moldyn *moldyn);
451 double get_pressure(t_moldyn *moldyn);
452 int scale_volume(t_moldyn *moldyn);
453 int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
454 int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
456 double e_kin_calc(t_moldyn *moldyn);
457 double get_total_energy(t_moldyn *moldyn);
458 t_3dvec get_total_p(t_moldyn *moldyn);
460 double estimate_time_step(t_moldyn *moldyn,double nn_dist);
462 int link_cell_init(t_moldyn *moldyn,u8 vol);
463 int link_cell_update(t_moldyn *moldyn);
465 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int **cell);
467 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
469 int link_cell_shutdown(t_moldyn *moldyn);
471 typedef int (*set_hook)(void *,void *);
473 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau);
474 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params);
476 int moldyn_integrate(t_moldyn *moldyn);
477 int velocity_verlet(t_moldyn *moldyn);
479 int potential_force_calc(t_moldyn *moldyn);
480 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d);
481 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d)
482 // __attribute__((always_inline));
483 int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
484 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
485 // __attribute__((always_inline));
487 int moldyn_bc_check(t_moldyn *moldyn);
489 int moldyn_read_save_file(t_moldyn *moldyn,char *file);
490 int moldyn_load(t_moldyn *moldyn);
491 int get_line(int fd,char *line,int max);
493 int pair_correlation_init(t_moldyn *moldyn,double dr);
494 int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr);
496 int visual_init(t_moldyn *moldyn,char *filebase);
497 int visual_atoms(t_moldyn *moldyn);