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; /* position */
37 t_3dvec v; /* velocity */
38 t_3dvec f; /* force */
39 t_virial virial; /* virial */
40 double e; /* site energy */
41 int element; /* number of element in pse */
42 double mass; /* atom mass */
43 u8 brand; /* brand id */
44 int tag; /* atom unique id (number of atom) */
45 u8 attr; /* attributes */
48 #define ATOM_ATTR_FP 0x01 /* fixed position (bulk material) */
49 #define ATOM_ATTR_HB 0x02 /* coupled to heat bath (velocity scaling) */
51 #define ATOM_ATTR_1BP 0x10 /* single paricle potential */
52 #define ATOM_ATTR_2BP 0x20 /* pair potential */
53 #define ATOM_ATTR_3BP 0x40 /* 3 body potential */
56 typedef struct s_linkcell {
57 int nx,ny,nz; /* amount of cells in x, y and z direction */
58 int cells; /* total amount of cells */
59 double len; /* prefered cell edge length */
60 double x,y,z; /* the actual cell lengthes */
61 t_list *subcell; /* pointer to the cell lists */
62 int dnlc; /* direct neighbour lists counter */
65 #include "visual/visual.h"
67 /* moldyn schedule structure */
68 typedef struct s_moldyn_schedule {
73 int (*hook)(void *moldyn,void *hook_params);
77 /* moldyn main structure */
78 typedef struct s_moldyn {
79 int count; /* total amount of atoms */
80 t_atom *atom; /* pointer to the atoms */
82 t_3dvec dim; /* dimensions of the simulation volume */
83 double volume; /* volume of sim cell (dim.x*dim.y*dim.z) */
85 /* potential force function and parameter pointers */
86 int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
87 int (*func2b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
88 int (*func3b_j1)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
89 int (*func3b_j2)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
90 int (*func3b_j3)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
91 int (*func3b_k1)(struct s_moldyn *moldyn,
92 t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
93 int (*func3b_k2)(struct s_moldyn *moldyn,
94 t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
98 double cutoff; /* cutoff radius */
99 double cutoff_square; /* square of the cutoff radius */
100 double nnd; /* nearest neighbour distance (optional) */
102 t_linkcell lc; /* linked cell list interface */
104 double t_ref; /* reference temperature */
105 double t; /* actual temperature */
106 double t_sum; /* sum over all t */
107 double mean_t; /* mean value of t */
109 t_virial virial; /* global virial (absolute coordinates) */
110 double gp; /* pressure computed from global virial */
111 double gp_sum; /* sum over all gp */
112 double mean_gp; /* mean value of gp */
114 double mean_v; /* mean of virial */
115 double virial_sum; /* sum over all calculated virials */
117 double p_ref; /* reference pressure */
118 double p; /* actual pressure (computed by virial) */
119 double p_sum; /* sum over all p */
120 double mean_p; /* mean value of p */
121 t_3dvec tp; /* thermodynamic pressure dU/dV */
122 double dv; /* dV for thermodynamic pressure calc */
124 /* pressure and temperature control (velocity/volume scaling) */
125 /* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */
126 unsigned char pt_scale; /* type of p and t scaling */
127 double t_tc; /* t berendsen control time constant */
128 double p_tc; /* p berendsen control time constant */
130 /* simulation schedule */
131 t_moldyn_schedule schedule;
132 int current; /* current position in schedule */
134 /* integration function pointer */
135 int (*integrate)(struct s_moldyn *moldyn);
136 int time_steps; /* amount of iterations */
137 double tau; /* delta t */
138 double time; /* absolute time */
139 double tau_square; /* delta t squared */
140 int total_steps; /* total steps */
142 double energy; /* potential energy */
143 double ekin; /* kinetic energy */
145 char vlsdir[128]; /* visualization/log/save directory */
146 t_visual vis; /* visualization interface structure */
147 u8 vlsprop; /* log/vis/save properties */
148 unsigned int ewrite; /* how often to log energy */
149 int efd; /* fd for energy log */
150 unsigned int mwrite; /* how often to log momentum */
151 int mfd; /* fd for momentum log */
152 unsigned int pwrite; /* how often to log pressure */
153 int pfd; /* fd for pressure log */
154 unsigned int twrite; /* how often to log temperature */
155 int tfd; /* fd for temperature log */
156 unsigned int vwrite; /* how often to visualize atom information */
157 unsigned int swrite; /* how often to create a save file */
158 int rfd; /* report file descriptor */
159 char rtitle[64]; /* report title */
160 char rauthor[64]; /* report author */
161 int epfd; /* energy gnuplot script file descriptor */
162 int ppfd; /* pressure gnuplot script file descriptor */
163 int tpfd; /* temperature gnuplot script file descriptor */
165 u8 status; /* general moldyn properties */
167 t_random random; /* random interface */
169 double debug; /* debugging stuff, ignore */
178 #define MOLDYN_STAT_PBX 0x01 /* periodic boudaries in x */
179 #define MOLDYN_STAT_PBY 0x02 /* y */
180 #define MOLDYN_STAT_PBZ 0x04 /* and z direction */
182 #define MOLDYN_PSCALE 0x08 /* size controlled by piston */
184 #define MOLDYN_1BP 0x10 /* care about single */
185 #define MOLDYN_2BP 0x20 /* 2 body */
186 #define MOLDYN_3BP 0x40 /* and 3 body particle pots */
188 #define T_SCALE_BERENDSEN 0x01 /* berendsen t control */
189 #define T_SCALE_DIRECT 0x02 /* direct t control */
190 #define P_SCALE_BERENDSEN 0x04 /* berendsen p control */
191 #define P_SCALE_DIRECT 0x08 /* direct p control */
194 * default values & units
196 * - length unit: 1 A (1 A = 1e-10 m)
197 * - time unit: 1 fs (1 fs = 1e-15 s)
198 * - mass unit: 1 amu (1 amu = 1.6605388628e-27 kg )
200 * fyi: in the following 1 N = (amu*A)/(fs*fs)
204 #define METER 1e10 /* A */
205 #define SECOND 1e15 /* fs */
206 #define AMU 1.6605388628e-27 /* kg */
207 #define KILOGRAM (1.0/AMU) /* amu */
208 #define NEWTON (METER*KILOGRAM/(SECOND*SECOND)) /* A amu / fs^2 */
209 #define PASCAL (NEWTON/(METER*METER)) /* N / A^2 */
210 #define BAR ((1.0e5*PASCAL)) /* N / A^2 */
211 #define K_BOLTZMANN (1.380650524e-23*METER*NEWTON) /* NA/K */
212 #define EV (1.6021765314e-19*METER*NEWTON) /* NA */
214 #define MOLDYN_TEMP 273.0
215 #define MOLDYN_TAU 1.0
216 #define MOLDYN_CUTOFF 10.0
217 #define MOLDYN_RUNS 1000000
219 #define MOLDYN_INTEGRATE_VERLET 0x00
220 #define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
222 #define MOLDYN_POTENTIAL_HO 0x00
223 #define MOLDYN_POTENTIAL_LJ 0x01
224 #define MOLDYN_POTENTIAL_TM 0x02
226 #define LOG_TOTAL_ENERGY 0x01
227 #define LOG_TOTAL_MOMENTUM 0x02
228 #define LOG_PRESSURE 0x04
229 #define LOG_TEMPERATURE 0x08
230 #define SAVE_STEP 0x10
231 #define VISUAL_STEP 0x20
232 #define CREATE_REPORT 0x40
241 #define SCALE_DOWN 'd'
242 #define SCALE_DIRECT 'D'
245 * potential related phsical values / constants
249 #define ONE_THIRD (1.0/3.0)
252 #define LC_C 3.567 /* A */
253 #define M_C 12.011 /* amu */
256 #define LC_SI 5.43105 /* A */
257 #define M_SI 28.08553 /* amu */
259 #define LC_3C_SIC 4.3596 /* A */
261 #define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* A */
262 //#define LJ_SIGMA_SI (LC_SI/1.122462) /* A */
263 //#define LJ_SIGMA_SI (0.5*sqrt(2.0)*LC_SI/1.122462) /* A */
264 #define LJ_EPSILON_SI (2.1678*EV) /* NA */
266 #define TM_R_SI 2.7 /* A */
267 #define TM_S_SI 3.0 /* A */
268 #define TM_A_SI (1830.8*EV) /* NA */
269 #define TM_B_SI (471.18*EV) /* NA */
270 #define TM_LAMBDA_SI 2.4799 /* 1/A */
271 #define TM_MU_SI 1.7322 /* 1/A */
272 #define TM_BETA_SI 1.1000e-6
273 #define TM_N_SI 0.78734
274 #define TM_C_SI 1.0039e5
275 #define TM_D_SI 16.217
276 #define TM_H_SI -0.59825
278 #define TM_R_C 1.8 /* A */
279 #define TM_S_C 2.1 /* A */
280 #define TM_A_C (1393.6*EV) /* NA */
281 #define TM_B_C (346.7*EV) /* NA */
282 #define TM_LAMBDA_C 3.4879 /* 1/A */
283 #define TM_MU_C 2.2119 /* 1/A */
284 #define TM_BETA_C 1.5724e-7
285 #define TM_N_C 0.72751
286 #define TM_C_C 3.8049e4
288 #define TM_H_C -0.57058
290 #define TM_CHI_SIC 0.9776
292 #define TM_LC_3C_SIC (0.432e-9*METER) /* A */
294 #define ALBE_R_SI (2.82-0.14)
295 #define ALBE_S_SI (2.82+0.14)
296 #define ALBE_A_SI (3.24*EV/0.842)
297 #define ALBE_B_SI (1.842*3.24*EV/0.842)
298 #define ALBE_R0_SI 2.232
299 #define ALBE_LAMBDA_SI (1.4761*sqrt(2.0*1.842))
300 #define ALBE_MU_SI (1.4761*sqrt(2.0/1.842))
301 #define ALBE_GAMMA_SI 0.114354
302 #define ALBE_C_SI 2.00494
303 #define ALBE_D_SI 0.81472
304 #define ALBE_H_SI 0.259
306 #define LC_SI_ALBE 5.429
308 #define ALBE_R_C (2.00-0.15)
309 #define ALBE_S_C (2.00+0.15)
310 #define ALBE_A_C (6.00*EV/1.167)
311 #define ALBE_B_C (2.167*6.00*EV/1.167)
312 #define ALBE_R0_C 1.4276
313 #define ALBE_LAMBDA_C (2.0099*sqrt(2.0*2.167))
314 #define ALBE_MU_C (2.0099*sqrt(2.0/2.167))
315 #define ALBE_GAMMA_C 0.11233
316 #define ALBE_C_C 181.910
317 #define ALBE_D_C 6.28433
318 #define ALBE_H_C 0.5556
320 #define LC_C_ALBE 3.566
322 #define ALBE_R_SIC (2.40-0.20)
323 #define ALBE_S_SIC (2.40+0.10)
324 #define ALBE_A_SIC (4.36*EV/0.847)
325 #define ALBE_B_SIC (1.847*4.36*EV/0.847)
326 #define ALBE_R0_SIC 1.79
327 #define ALBE_LAMBDA_SIC (1.6991*sqrt(2.0*1.847))
328 #define ALBE_MU_SIC (1.6991*sqrt(2.0/1.847))
329 #define ALBE_GAMMA_SIC 0.011877
330 #define ALBE_C_SIC 273987
331 #define ALBE_D_SIC 180.314
332 #define ALBE_H_SIC 0.68
334 #define LC_SIC_ALBE 4.359
348 * function prototypes
352 typedef int (*pf_func1b)(t_moldyn *,t_atom *);
353 typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8);
354 typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8);
356 int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
357 int moldyn_shutdown(t_moldyn *moldyn);
359 int set_int_alg(t_moldyn *moldyn,u8 algo);
360 int set_cutoff(t_moldyn *moldyn,double cutoff);
361 int set_temperature(t_moldyn *moldyn,double t_ref);
362 int set_pressure(t_moldyn *moldyn,double p_ref);
363 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc);
364 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize);
365 int set_nn_dist(t_moldyn *moldyn,double dist);
366 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
367 int set_potential1b(t_moldyn *moldyn,pf_func1b func);
368 int set_potential2b(t_moldyn *moldyn,pf_func2b func);
369 int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func);
370 int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func);
371 int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func);
372 int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func);
373 int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func);
374 int set_potential_params(t_moldyn *moldyn,void *params);
376 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
377 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title);
378 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer);
379 int moldyn_log_shutdown(t_moldyn *moldyn);
381 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
382 u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin);
383 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
384 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
385 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
386 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
387 t_3dvec *r,t_3dvec *v);
388 int destroy_atoms(t_moldyn *moldyn);
390 int thermal_init(t_moldyn *moldyn,u8 equi_init);
391 double temperature_calc(t_moldyn *moldyn);
392 double get_temperature(t_moldyn *moldyn);
393 int scale_velocity(t_moldyn *moldyn,u8 equi_init);
394 double pressure_calc(t_moldyn *moldyn);
395 double thermodynamic_pressure_calc(t_moldyn *moldyn);
396 double get_pressure(t_moldyn *moldyn);
397 int scale_volume(t_moldyn *moldyn);
398 int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
399 int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
401 double e_kin_calc(t_moldyn *moldyn);
402 double get_total_energy(t_moldyn *moldyn);
403 t_3dvec get_total_p(t_moldyn *moldyn);
405 double estimate_time_step(t_moldyn *moldyn,double nn_dist);
407 int link_cell_init(t_moldyn *moldyn,u8 vol);
408 int link_cell_update(t_moldyn *moldyn);
409 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
410 int link_cell_shutdown(t_moldyn *moldyn);
412 typedef int (*set_hook)(void *,void *);
414 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau);
415 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params);
417 int moldyn_integrate(t_moldyn *moldyn);
418 int velocity_verlet(t_moldyn *moldyn);
420 int potential_force_calc(t_moldyn *moldyn);
421 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d);
422 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d)
423 // __attribute__((always_inline));
424 int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
425 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
426 // __attribute__((always_inline));
428 int moldyn_bc_check(t_moldyn *moldyn);
430 int read_line(int fd,char *line);
431 int calc_fluctuations(double start,double end,char *file);