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 double mass; /* total system mass */
81 t_atom *atom; /* pointer to the atoms */
83 t_3dvec dim; /* dimensions of the simulation volume */
84 double volume; /* volume of sim cell (dim.x*dim.y*dim.z) */
86 /* potential force function and parameter pointers */
87 int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
88 int (*func2b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
89 int (*func3b_j1)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
90 int (*func3b_j2)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
91 int (*func3b_j3)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
92 int (*func3b_k1)(struct s_moldyn *moldyn,
93 t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
94 int (*func3b_k2)(struct s_moldyn *moldyn,
95 t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
99 double cutoff; /* cutoff radius */
100 double cutoff_square; /* square of the cutoff radius */
101 double nnd; /* nearest neighbour distance (optional) */
103 t_linkcell lc; /* linked cell list interface */
105 double t_ref; /* reference temperature */
106 double t; /* actual temperature */
107 double t_sum; /* sum over all t */
108 double mean_t; /* mean value of t */
110 t_virial virial; /* global virial (absolute coordinates) */
111 double gp; /* pressure computed from global virial */
112 double gp_sum; /* sum over all gp */
113 double mean_gp; /* mean value of gp */
115 double mean_v; /* mean of virial */
116 double virial_sum; /* sum over all calculated virials */
118 double p_ref; /* reference pressure */
119 double p; /* actual pressure (computed by virial) */
120 double p_sum; /* sum over all p */
121 double mean_p; /* mean value of p */
122 t_3dvec tp; /* thermodynamic pressure dU/dV */
123 double dv; /* dV for thermodynamic pressure calc */
125 /* pressure and temperature control (velocity/volume scaling) */
126 /* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */
127 unsigned char pt_scale; /* type of p and t scaling */
128 double t_tc; /* t berendsen control time constant */
129 double p_tc; /* p berendsen control time constant */
131 /* simulation schedule */
132 t_moldyn_schedule schedule;
133 int current; /* current position in schedule */
135 /* integration function pointer */
136 int (*integrate)(struct s_moldyn *moldyn);
137 int time_steps; /* amount of iterations */
138 double tau; /* delta t */
139 double time; /* absolute time */
140 double tau_square; /* delta t squared */
141 int total_steps; /* total steps */
144 double energy; /* potential energy */
145 double ekin; /* kinetic energy */
147 /* energy averages & fluctuations */
148 double k_sum; /* sum of kinetic energy */
149 double v_sum; /* sum of potential energy */
150 double k_mean; /* average of kinetic energy */
151 double v_mean; /* average of potential energy */
152 double k2_sum; /* sum of kinetic energy squared */
153 double v2_sum; /* sum of potential energy squared */
154 double k2_mean; /* average of kinetic energy squared */
155 double v2_mean; /* average of potential energy squared */
156 double dk2_mean; /* mean square kinetic energy fluctuations */
157 double dv2_mean; /* mean square potential energy fluctuations */
159 /* response functions */
160 double c_v_nve; /* constant volume heat capacity (nve) */
161 double c_v_nvt; /* constant volume heat capacity (nvt) */
163 char vlsdir[128]; /* visualization/log/save directory */
164 t_visual vis; /* visualization interface structure */
165 u8 vlsprop; /* log/vis/save properties */
166 unsigned int ewrite; /* how often to log energy */
167 int efd; /* fd for energy log */
168 unsigned int mwrite; /* how often to log momentum */
169 int mfd; /* fd for momentum log */
170 unsigned int pwrite; /* how often to log pressure */
171 int pfd; /* fd for pressure log */
172 unsigned int twrite; /* how often to log temperature */
173 int tfd; /* fd for temperature log */
174 unsigned int vwrite; /* how often to visualize atom information */
175 unsigned int swrite; /* how often to create a save file */
176 int rfd; /* report file descriptor */
177 char rtitle[64]; /* report title */
178 char rauthor[64]; /* report author */
179 int epfd; /* energy gnuplot script file descriptor */
180 int ppfd; /* pressure gnuplot script file descriptor */
181 int tpfd; /* temperature gnuplot script file descriptor */
183 u8 status; /* general moldyn properties */
185 t_random random; /* random interface */
187 double debug; /* debugging stuff, ignore */
196 #define MOLDYN_STAT_PBX 0x01 /* periodic boudaries in x */
197 #define MOLDYN_STAT_PBY 0x02 /* y */
198 #define MOLDYN_STAT_PBZ 0x04 /* and z direction */
200 #define MOLDYN_PSCALE 0x08 /* size controlled by piston */
202 #define MOLDYN_1BP 0x10 /* care about single */
203 #define MOLDYN_2BP 0x20 /* 2 body */
204 #define MOLDYN_3BP 0x40 /* and 3 body particle pots */
206 #define T_SCALE_BERENDSEN 0x01 /* berendsen t control */
207 #define T_SCALE_DIRECT 0x02 /* direct t control */
208 #define P_SCALE_BERENDSEN 0x04 /* berendsen p control */
209 #define P_SCALE_DIRECT 0x08 /* direct p control */
212 * default values & units
214 * - length unit: 1 A (1 A = 1e-10 m)
215 * - time unit: 1 fs (1 fs = 1e-15 s)
216 * - mass unit: 1 amu (1 amu = 1.6605388628e-27 kg )
218 * fyi: in the following 1 N = (amu*A)/(fs*fs)
222 #define METER 1e10 /* A */
223 #define SECOND 1e15 /* fs */
224 #define AMU 1.6605388628e-27 /* kg */
225 #define KILOGRAM (1.0/AMU) /* amu */
226 #define NEWTON (METER*KILOGRAM/(SECOND*SECOND)) /* A amu / fs^2 */
227 #define PASCAL (NEWTON/(METER*METER)) /* N / A^2 */
228 #define BAR ((1.0e5*PASCAL)) /* N / A^2 */
229 #define K_BOLTZMANN (1.380650524e-23*METER*NEWTON) /* NA/K */
230 #define K_B2 (K_BOLTZMANN*K_BOLTZMANN) /* (NA)^2/K^2 */
231 #define EV (1.6021765314e-19*METER*NEWTON) /* NA */
232 #define JOULE (NEWTON*METER) /* NA */
234 #define MOLDYN_TEMP 273.0
235 #define MOLDYN_TAU 1.0
236 #define MOLDYN_CUTOFF 10.0
237 #define MOLDYN_RUNS 1000000
239 #define MOLDYN_INTEGRATE_VERLET 0x00
240 #define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
242 #define MOLDYN_POTENTIAL_HO 0x00
243 #define MOLDYN_POTENTIAL_LJ 0x01
244 #define MOLDYN_POTENTIAL_TM 0x02
246 #define LOG_TOTAL_ENERGY 0x01
247 #define LOG_TOTAL_MOMENTUM 0x02
248 #define LOG_PRESSURE 0x04
249 #define LOG_TEMPERATURE 0x08
250 #define SAVE_STEP 0x10
251 #define VISUAL_STEP 0x20
252 #define CREATE_REPORT 0x40
261 #define SCALE_DOWN 'd'
262 #define SCALE_DIRECT 'D'
265 * potential related phsical values / constants
269 #define ONE_THIRD (1.0/3.0)
272 #define LC_C 3.567 /* A */
273 #define M_C 12.011 /* amu */
276 #define LC_SI 5.43105 /* A */
277 #define M_SI 28.08553 /* amu */
279 #define LC_3C_SIC 4.3596 /* A */
281 #define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* A */
282 //#define LJ_SIGMA_SI (LC_SI/1.122462) /* A */
283 //#define LJ_SIGMA_SI (0.5*sqrt(2.0)*LC_SI/1.122462) /* A */
284 #define LJ_EPSILON_SI (2.1678*EV) /* NA */
286 #define TM_R_SI 2.7 /* A */
287 #define TM_S_SI 3.0 /* A */
288 #define TM_A_SI (1830.8*EV) /* NA */
289 #define TM_B_SI (471.18*EV) /* NA */
290 #define TM_LAMBDA_SI 2.4799 /* 1/A */
291 #define TM_MU_SI 1.7322 /* 1/A */
292 #define TM_BETA_SI 1.1000e-6
293 #define TM_N_SI 0.78734
294 #define TM_C_SI 1.0039e5
295 #define TM_D_SI 16.217
296 #define TM_H_SI -0.59825
298 #define TM_R_C 1.8 /* A */
299 #define TM_S_C 2.1 /* A */
300 #define TM_A_C (1393.6*EV) /* NA */
301 #define TM_B_C (346.7*EV) /* NA */
302 #define TM_LAMBDA_C 3.4879 /* 1/A */
303 #define TM_MU_C 2.2119 /* 1/A */
304 #define TM_BETA_C 1.5724e-7
305 #define TM_N_C 0.72751
306 #define TM_C_C 3.8049e4
308 #define TM_H_C -0.57058
310 #define TM_CHI_SIC 0.9776
312 #define TM_LC_3C_SIC (0.432e-9*METER) /* A */
314 #define ALBE_R_SI (2.82-0.14)
315 #define ALBE_S_SI (2.82+0.14)
316 #define ALBE_A_SI (3.24*EV/0.842)
317 #define ALBE_B_SI (1.842*3.24*EV/0.842)
318 #define ALBE_R0_SI 2.232
319 #define ALBE_LAMBDA_SI (1.4761*sqrt(2.0*1.842))
320 #define ALBE_MU_SI (1.4761*sqrt(2.0/1.842))
321 #define ALBE_GAMMA_SI 0.114354
322 #define ALBE_C_SI 2.00494
323 #define ALBE_D_SI 0.81472
324 #define ALBE_H_SI 0.259
326 #define LC_SI_ALBE 5.429
328 #define ALBE_R_C (2.00-0.15)
329 #define ALBE_S_C (2.00+0.15)
330 #define ALBE_A_C (6.00*EV/1.167)
331 #define ALBE_B_C (2.167*6.00*EV/1.167)
332 #define ALBE_R0_C 1.4276
333 #define ALBE_LAMBDA_C (2.0099*sqrt(2.0*2.167))
334 #define ALBE_MU_C (2.0099*sqrt(2.0/2.167))
335 #define ALBE_GAMMA_C 0.11233
336 #define ALBE_C_C 181.910
337 #define ALBE_D_C 6.28433
338 #define ALBE_H_C 0.5556
340 #define LC_C_ALBE 3.566
342 #define ALBE_R_SIC (2.40-0.20)
343 #define ALBE_S_SIC (2.40+0.10)
344 #define ALBE_A_SIC (4.36*EV/0.847)
345 #define ALBE_B_SIC (1.847*4.36*EV/0.847)
346 #define ALBE_R0_SIC 1.79
347 #define ALBE_LAMBDA_SIC (1.6991*sqrt(2.0*1.847))
348 #define ALBE_MU_SIC (1.6991*sqrt(2.0/1.847))
349 #define ALBE_GAMMA_SIC 0.011877
350 #define ALBE_C_SIC 273987
351 #define ALBE_D_SIC 180.314
352 #define ALBE_H_SIC 0.68
354 #define LC_SIC_ALBE 4.359
368 * function prototypes
372 typedef int (*pf_func1b)(t_moldyn *,t_atom *);
373 typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8);
374 typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8);
376 int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
377 int moldyn_shutdown(t_moldyn *moldyn);
379 int set_int_alg(t_moldyn *moldyn,u8 algo);
380 int set_cutoff(t_moldyn *moldyn,double cutoff);
381 int set_temperature(t_moldyn *moldyn,double t_ref);
382 int set_pressure(t_moldyn *moldyn,double p_ref);
383 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc);
384 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize);
385 int set_nn_dist(t_moldyn *moldyn,double dist);
386 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
387 int set_potential1b(t_moldyn *moldyn,pf_func1b func);
388 int set_potential2b(t_moldyn *moldyn,pf_func2b func);
389 int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func);
390 int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func);
391 int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func);
392 int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func);
393 int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func);
394 int set_potential_params(t_moldyn *moldyn,void *params);
396 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
397 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title);
398 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer);
399 int moldyn_log_shutdown(t_moldyn *moldyn);
401 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
402 u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin);
403 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
404 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
405 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
406 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
407 t_3dvec *r,t_3dvec *v);
408 int destroy_atoms(t_moldyn *moldyn);
410 int thermal_init(t_moldyn *moldyn,u8 equi_init);
411 double total_mass_calc(t_moldyn *moldyn);
412 double temperature_calc(t_moldyn *moldyn);
413 double get_temperature(t_moldyn *moldyn);
414 int scale_velocity(t_moldyn *moldyn,u8 equi_init);
415 double pressure_calc(t_moldyn *moldyn);
416 int energy_fluctuation_calc(t_moldyn *moldyn);
417 int get_heat_capacity(t_moldyn *moldyn);
418 double thermodynamic_pressure_calc(t_moldyn *moldyn);
419 double get_pressure(t_moldyn *moldyn);
420 int scale_volume(t_moldyn *moldyn);
421 int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
422 int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
424 double e_kin_calc(t_moldyn *moldyn);
425 double get_total_energy(t_moldyn *moldyn);
426 t_3dvec get_total_p(t_moldyn *moldyn);
428 double estimate_time_step(t_moldyn *moldyn,double nn_dist);
430 int link_cell_init(t_moldyn *moldyn,u8 vol);
431 int link_cell_update(t_moldyn *moldyn);
432 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
433 int link_cell_shutdown(t_moldyn *moldyn);
435 typedef int (*set_hook)(void *,void *);
437 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau);
438 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params);
440 int moldyn_integrate(t_moldyn *moldyn);
441 int velocity_verlet(t_moldyn *moldyn);
443 int potential_force_calc(t_moldyn *moldyn);
444 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d);
445 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d)
446 // __attribute__((always_inline));
447 int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
448 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
449 // __attribute__((always_inline));
451 int moldyn_bc_check(t_moldyn *moldyn);
453 int get_line(int fd,char *line,int max);