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"
15 #include "report/report.h"
24 typedef unsigned char u8;
27 typedef struct s_virial {
28 double xx; /* | xx xy xz | */
29 double yy; /* V = | yx yy yz | */
30 double zz; /* | zx zy zz | */
32 double xz; /* with: xy=yx, xz=zx, yz=zy */
36 /* the atom of the md simulation */
37 typedef struct s_atom {
38 t_3dvec r; /* position */
39 t_3dvec v; /* velocity */
40 t_3dvec f; /* force */
41 t_virial virial; /* virial */
42 double e; /* site 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 count; /* total amount of atoms */
82 t_atom *atom; /* pointer to the atoms */
84 t_3dvec dim; /* dimensions of the simulation volume */
85 double volume; /* volume of sim cell (dim.x*dim.y*dim.z) */
87 /* potential force function and parameter pointers */
88 int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
90 int (*func2b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
91 int (*func2b_post)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
93 int (*func3b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,
96 //int (*potential_force_function)(struct s_moldyn *moldyn);
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 */
107 double p_ref; /* reference pressure */
108 double p; /* actual pressure (computed by virial) */
109 t_3dvec tp; /* thermodynamic pressure dU/dV */
110 double dv; /* dV for thermodynamic pressure calc */
112 /* pressure and temperature control (velocity/volume scaling) */
113 /* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */
114 unsigned char pt_scale; /* type of p and t scaling */
115 double t_tc; /* t berendsen control time constant */
116 double p_tc; /* p berendsen control time constant */
118 /* simulation schedule */
119 t_moldyn_schedule schedule;
120 int current; /* current position in schedule */
122 /* integration function pointer */
123 int (*integrate)(struct s_moldyn *moldyn);
124 int time_steps; /* amount of iterations */
125 double tau; /* delta t */
126 double time; /* absolute time */
127 double tau_square; /* delta t squared */
128 double elapsed; /* total elapsed time */
130 double energy; /* potential energy */
131 double ekin; /* kinetic energy */
133 char vlsdir[128]; /* visualization/log/save directory */
134 t_visual vis; /* visualization interface structure */
135 u8 vlsprop; /* log/vis/save properties */
136 unsigned int ewrite; /* how often to log energy */
137 int efd; /* fd for energy log */
138 unsigned int mwrite; /* how often to log momentum */
139 int mfd; /* fd for momentum log */
140 unsigned int vwrite; /* how often to visualize atom information */
141 unsigned int swrite; /* how often to create a save file */
142 int rfd; /* report file descriptor */
143 char rtitle[64]; /* report title */
144 char rauthor[64]; /* report author */
145 int pfd; /* gnuplot script file descriptor */
147 u8 status; /* general moldyn properties */
149 t_random random; /* random interface */
151 int debug; /* debugging stuff, ignore */
154 #define MOLDYN_STAT_PBX 0x01 /* periodic boudaries in x */
155 #define MOLDYN_STAT_PBY 0x02 /* y */
156 #define MOLDYN_STAT_PBZ 0x04 /* and z direction */
158 #define MOLDYN_PSCALE 0x08 /* size controlled by piston */
160 #define MOLDYN_1BP 0x10 /* care about single */
161 #define MOLDYN_2BP 0x20 /* 2 body */
162 #define MOLDYN_3BP 0x40 /* and 3 body particle pots */
164 #define T_SCALE_BERENDSEN 0x01 /* berendsen t control */
165 #define T_SCALE_DIRECT 0x02 /* direct t control */
166 #define P_SCALE_BERENDSEN 0x04 /* berendsen p control */
167 #define P_SCALE_DIRECT 0x08 /* direct p control */
171 * potential parameter structures
176 * harmonic oscillator potential parameter structure
179 typedef struct s_ho_params {
180 double spring_constant;
181 double equilibrium_distance;
185 * lennard jones potential parameter structure
188 typedef struct s_lj_params {
199 /* tersoff exchange structure to exchange 2bp and 3bp calculated values */
200 typedef struct s_tersoff_exchange {
238 } t_tersoff_exchange;
240 /* tersoff multi (2!) potential parameters */
241 typedef struct s_tersoff_mult_params {
242 double S[2]; /* tersoff cutoff radii */
243 double S2[2]; /* tersoff cutoff radii squared */
244 double R[2]; /* tersoff cutoff radii */
245 double Smixed; /* mixed S radius */
246 double S2mixed; /* mixed S radius squared */
247 double Rmixed; /* mixed R radius */
248 double A[2]; /* factor of tersoff attractive part */
249 double B[2]; /* factor of tersoff repulsive part */
250 double Amixed; /* mixed A factor */
251 double Bmixed; /* mixed B factor */
252 double lambda[2]; /* tersoff lambda */
253 double lambda_m; /* mixed lambda */
254 double mu[2]; /* tersoff mu */
255 double mu_m; /* mixed mu */
265 t_tersoff_exchange exchange; /* exchange between 2bp and 3bp calc */
266 } t_tersoff_mult_params;
276 #define ONE_THIRD (1.0/3.0)
281 * - length unit: 1 A (1 A = 1e-10 m)
282 * - time unit: 1 fs (1 fs = 1e-15 s)
283 * - mass unit: 1 amu (1 amu = 1.6605388628e-27 kg )
285 * fyi: in the following 1 N = (amu*A)/(fs*fs)
289 #define METER 1e10 /* A */
290 #define SECOND 1e15 /* fs */
291 #define AMU 1.6605388628e-27 /* kg */
292 #define KILOGRAM (1.0/AMU) /* amu */
293 #define NEWTON (METER*KILOGRAM/(SECOND*SECOND)) /* A amu / fs^2 */
294 #define PASCAL (NEWTON/(METER*METER)) /* N / A^2 */
295 #define ATM (1.0133e5*PASCAL) /* N / A^2 */
297 #define MOLDYN_TEMP 273.0
298 #define MOLDYN_TAU 1.0
299 #define MOLDYN_CUTOFF 10.0
300 #define MOLDYN_RUNS 1000000
302 #define MOLDYN_INTEGRATE_VERLET 0x00
303 #define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
305 #define MOLDYN_POTENTIAL_HO 0x00
306 #define MOLDYN_POTENTIAL_LJ 0x01
307 #define MOLDYN_POTENTIAL_TM 0x02
309 #define LOG_TOTAL_ENERGY 0x01
310 #define LOG_TOTAL_MOMENTUM 0x02
311 #define SAVE_STEP 0x04
312 #define VISUAL_STEP 0x08
313 #define CREATE_REPORT 0x10
320 * phsical values / constants
325 #define K_BOLTZMANN (1.380650524e-23*METER*NEWTON) /* NA/K */
326 #define EV (1.6021765314e-19*METER*NEWTON) /* NA */
329 #define M_C 12.011 /* amu */
332 #define LC_SI (0.543105e-9*METER) /* A */
333 #define M_SI 28.08553 /* amu */
335 #define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* A */
336 #define LJ_EPSILON_SI (2.1678*EV) /* NA */
338 #define TM_R_SI (2.7e-10*METER) /* A */
339 #define TM_S_SI (3.0e-10*METER) /* A */
340 #define TM_A_SI (1830.8*EV) /* NA */
341 #define TM_B_SI (471.18*EV) /* NA */
342 #define TM_LAMBDA_SI (2.4799e10/METER) /* 1/A */
343 #define TM_MU_SI (1.7322e10/METER) /* 1/A */
344 #define TM_BETA_SI 1.1000e-6
345 #define TM_N_SI 0.78734
346 #define TM_C_SI 1.0039e5
347 #define TM_D_SI 16.217
348 #define TM_H_SI -0.59825
350 #define TM_R_C (1.8e-10*METER) /* A */
351 #define TM_S_C (2.1e-10*METER) /* A */
352 #define TM_A_C (1393.6*EV) /* NA */
353 #define TM_B_C (346.7*EV) /* NA */
354 #define TM_LAMBDA_C (3.4879e10/METER) /* 1/A */
355 #define TM_MU_C (2.2119e10/METER) /* 1/A */
356 #define TM_BETA_C 1.5724e-7
357 #define TM_N_C 0.72751
358 #define TM_C_C 3.8049e4
360 #define TM_H_C -0.57058
362 #define TM_CHI_SIC 0.9776
375 * function prototypes
379 typedef int (*pf_func1b)(t_moldyn *,t_atom *ai);
380 typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8 bc);
381 typedef int (*pf_func2b_post)(t_moldyn *,t_atom *,t_atom *,u8 bc);
382 typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8 bc);
384 int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
385 int moldyn_shutdown(t_moldyn *moldyn);
387 int set_int_alg(t_moldyn *moldyn,u8 algo);
388 int set_cutoff(t_moldyn *moldyn,double cutoff);
389 int set_temperature(t_moldyn *moldyn,double t_ref);
390 int set_pressure(t_moldyn *moldyn,double p_ref);
391 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc);
392 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize);
393 int set_nn_dist(t_moldyn *moldyn,double dist);
394 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
395 int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params);
396 int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params);
397 int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params);
398 int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params);
400 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
401 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title);
402 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer);
403 int moldyn_log_shutdown(t_moldyn *moldyn);
405 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
406 u8 attr,u8 brand,int a,int b,int c);
407 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
408 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
409 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
410 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
411 t_3dvec *r,t_3dvec *v);
412 int destroy_atoms(t_moldyn *moldyn);
414 int thermal_init(t_moldyn *moldyn,u8 equi_init);
415 double temperature_calc(t_moldyn *moldyn);
416 double get_temperature(t_moldyn *moldyn);
417 int scale_velocity(t_moldyn *moldyn,u8 equi_init);
418 double pressure_calc(t_moldyn *moldyn);
419 double thermodynamic_pressure_calc(t_moldyn *moldyn);
420 double get_pressure(t_moldyn *moldyn);
421 int scale_volume(t_moldyn *moldyn);
422 int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z);
423 int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z);
425 double get_e_kin(t_moldyn *moldyn);
426 double update_e_kin(t_moldyn *moldyn);
427 double get_total_energy(t_moldyn *moldyn);
428 t_3dvec get_total_p(t_moldyn *moldyn);
430 double estimate_time_step(t_moldyn *moldyn,double nn_dist);
432 int link_cell_init(t_moldyn *moldyn);
433 int link_cell_update(t_moldyn *moldyn);
434 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
435 int link_cell_shutdown(t_moldyn *moldyn);
437 typedef int (*set_hook)(void *,void *);
439 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau);
440 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params);
442 int moldyn_integrate(t_moldyn *moldyn);
443 int velocity_verlet(t_moldyn *moldyn);
445 int potential_force_calc(t_moldyn *moldyn);
446 inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d)
447 __attribute__((always_inline));
448 inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
449 __attribute__((always_inline));
450 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
451 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
452 int tersoff_mult_complete_params(t_tersoff_mult_params *p);
453 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai);
454 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
455 int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
456 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc);
458 int moldyn_bc_check(t_moldyn *moldyn);