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 */ // TODO
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 */
59 #define DEFAULT_ATOM_ATTR 0x74 // 1,2,3 body interaction + visualize
62 typedef struct s_linkcell {
63 int nx,ny,nz; /* amount of cells in x, y and z direction */
64 int cells; /* total amount of cells */
65 double len; /* prefered cell edge length */
66 double x,y,z; /* the actual cell lengthes */
68 int **subcell; /* pointer to the cell lists */
70 t_list *subcell; /* pointer to the cell lists */
72 int dnlc; /* direct neighbour lists counter */
75 #define MAX_ATOMS_PER_LIST 20
77 /* moldyn schedule structure */
78 typedef struct s_moldyn_schedule {
83 int (*hook)(void *moldyn,void *hook_params);
87 /* visualization structure */
88 typedef struct s_visual {
89 int fd; /* rasmol script file descriptor */
90 char fb[128]; /* basename of the save files */
91 t_3dvec dim; /* dimensions of the simulation cell */
94 /* moldyn main structure */
95 typedef struct s_moldyn {
96 int argc; /* number of arguments */
97 char **args; /* pointer to arguments */
99 int count; /* total amount of atoms */
100 double mass; /* total system mass */
101 t_atom *atom; /* pointer to the atoms */
103 t_3dvec dim; /* dimensions of the simulation volume */
104 double volume; /* volume of sim cell (dim.x*dim.y*dim.z) */
106 /* potential force function and parameter pointers */
107 int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
108 int (*func2b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
109 int (*func3b_j1)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
110 int (*func3b_j2)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
111 int (*func3b_j3)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
112 int (*func3b_k1)(struct s_moldyn *moldyn,
113 t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
114 int (*func3b_k2)(struct s_moldyn *moldyn,
115 t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
117 unsigned char run3bp;
119 double cutoff; /* cutoff radius */
120 double cutoff_square; /* square of the cutoff radius */
121 double nnd; /* nearest neighbour distance (optional) */
123 t_linkcell lc; /* linked cell list interface */
125 int avg_skip; /* amount of steps without average calc */
127 double t_ref; /* reference temperature */
128 double t; /* actual temperature */
129 double t_sum; /* sum over all t */
130 double t_avg; /* average value of t */
132 t_virial gvir; /* global virial (absolute coordinates) */
137 double gp; /* pressure computed from global virial */
138 double gp_sum; /* sum over all gp */
139 double gp_avg; /* average value of gp */
141 t_virial vir; /* actual virial */
143 double virial_sum; /* sum over all calculated virials */
144 double virial_avg; /* average of virial */
146 double p_ref; /* reference pressure */
147 double p; /* actual pressure (computed by virial) */
148 double px,py,pz; /* components of pressure */
149 double p_sum; /* sum over all p */
150 double p_avg; /* average value of p */
152 double tp; /* thermodynamic pressure dU/dV */
153 double tp_sum; /* sum over dU/dV pressure */
154 double tp_avg; /* average value of dU/dV pressure */
155 int tp_cnt; /* how often to do thermodynamic p calc */
157 /* pressure and temperature control (velocity/volume scaling) */
158 /* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */
159 unsigned char pt_scale; /* type of p and t scaling */
160 double t_tc; /* t berendsen control time constant */
161 double p_tc; /* p berendsen control time constant */
163 /* simulation schedule */
164 t_moldyn_schedule schedule;
165 int current; /* current position in schedule */
167 /* integration function pointer */
168 int (*integrate)(struct s_moldyn *moldyn);
169 int time_steps; /* amount of iterations */
170 double tau; /* delta t */
171 double time; /* absolute time */
172 double tau_square; /* delta t squared */
173 int total_steps; /* total steps */
176 double energy; /* potential energy */
177 double ekin; /* kinetic energy */
179 /* energy averages & fluctuations */
180 double k_sum; /* sum of kinetic energy */
181 double v_sum; /* sum of potential energy */
182 double k_avg; /* average of kinetic energy */
183 double v_avg; /* average of potential energy */
184 double k2_sum; /* sum of kinetic energy squared */
185 double v2_sum; /* sum of potential energy squared */
186 double k2_avg; /* average of kinetic energy squared */
187 double v2_avg; /* average of potential energy squared */
188 double dk2_avg; /* mean square kinetic energy fluctuations */
189 double dv2_avg; /* mean square potential energy fluctuations */
191 /* response functions */
192 double c_v_nve; /* constant volume heat capacity (nve) */
193 double c_v_nvt; /* constant volume heat capacity (nvt) */
195 char vlsdir[128]; /* visualization/log/save directory */
196 t_visual vis; /* visualization interface structure */
197 u8 vlsprop; /* log/vis/save properties */
198 unsigned int ewrite; /* how often to log energy */
199 int efd; /* fd for energy log */
200 unsigned int mwrite; /* how often to log momentum */
201 int mfd; /* fd for momentum log */
202 unsigned int pwrite; /* how often to log pressure */
203 int pfd; /* fd for pressure log */
204 unsigned int twrite; /* how often to log temperature */
205 int tfd; /* fd for temperature log */
206 unsigned int vwrite; /* how often to log volume */
207 int vfd; /* fd for volume log */
208 unsigned int awrite; /* how often to visualize atom information */
209 unsigned int swrite; /* how often to create a save file */
210 int rfd; /* report file descriptor */
211 char rtitle[64]; /* report title */
212 char rauthor[64]; /* report author */
213 int epfd; /* energy gnuplot script file descriptor */
214 int ppfd; /* pressure gnuplot script file descriptor */
215 int tpfd; /* temperature gnuplot script file descriptor */
217 u8 status; /* general moldyn properties */
219 t_random random; /* random interface */
221 double debug; /* debugging stuff, ignore */
223 /* potential 2 body check function */
224 int (*check_2b_bond)(struct s_moldyn *moldyn,
225 t_atom *itom,t_atom *jtom,u8 bc);
228 typedef struct s_pcc {
235 typedef struct s_ba {
241 typedef struct s_vb {
251 #define MOLDYN_STAT_PBX 0x01 /* periodic boudaries in x */
252 #define MOLDYN_STAT_PBY 0x02 /* y */
253 #define MOLDYN_STAT_PBZ 0x04 /* and z direction */
255 #define MOLDYN_PSCALE 0x08 /* size controlled by piston */
257 #define MOLDYN_1BP 0x10 /* care about single */
258 #define MOLDYN_2BP 0x20 /* 2 body */
259 #define MOLDYN_3BP 0x40 /* and 3 body particle pots */
261 #define T_SCALE_NONE 0x00
262 #define T_SCALE_BERENDSEN 0x01 /* berendsen t control */
263 #define T_SCALE_DIRECT 0x02 /* direct t control */
264 #define T_SCALE_MASK 0x03
266 #define P_SCALE_NONE 0x00
267 #define P_SCALE_BERENDSEN 0x04 /* berendsen p control */
268 #define P_SCALE_DIRECT 0x08 /* direct p control */
269 #define P_SCALE_MASK 0x0c
272 * default values & units
274 * - length unit: 1 A (1 A = 1e-10 m)
275 * - time unit: 1 fs (1 fs = 1e-15 s)
276 * - mass unit: 1 amu (1 amu = 1.6605388628e-27 kg )
278 * fyi: in the following 1 N = (amu*A)/(fs*fs)
282 #define METER 1e10 /* A */
283 #define SECOND 1e15 /* fs */
284 #define AMU 1.6605388628e-27 /* kg */
285 #define KILOGRAM (1.0/AMU) /* amu */
286 #define NEWTON (METER*KILOGRAM/(SECOND*SECOND)) /* A amu / fs^2 */
287 #define PASCAL (NEWTON/(METER*METER)) /* N / A^2 */
288 #define GPA (1e9*PASCAL) /* N / A^2 */
289 #define BAR ((1.0e5*PASCAL)) /* N / A^2 */
290 #define K_BOLTZMANN (1.380650524e-23*METER*NEWTON) /* NA/K */
291 #define K_B2 (K_BOLTZMANN*K_BOLTZMANN) /* (NA)^2/K^2 */
292 #define EV (1.6021765314e-19*METER*NEWTON) /* NA */
293 #define JOULE (NEWTON*METER) /* NA */
295 #define MOLDYN_TEMP 273.0
296 #define MOLDYN_TAU 1.0
297 #define MOLDYN_CUTOFF 10.0
298 #define MOLDYN_RUNS 1000000
300 #define MOLDYN_INTEGRATE_VERLET 0x00
301 #define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
303 #define MOLDYN_POTENTIAL_HO 0x00
304 #define MOLDYN_POTENTIAL_LJ 0x01
305 #define MOLDYN_POTENTIAL_TM 0x02
306 #define MOLDYN_POTENTIAL_AM 0x03
308 #define LOG_TOTAL_ENERGY 0x01
309 #define LOG_TOTAL_MOMENTUM 0x02
310 #define LOG_PRESSURE 0x04
311 #define LOG_TEMPERATURE 0x08
312 #define LOG_VOLUME 0x10
313 #define SAVE_STEP 0x20
314 #define VISUAL_STEP 0x40
315 #define CREATE_REPORT 0x80
324 #define SCALE_DOWN 'd'
325 #define SCALE_DIRECT 'D'
331 #define ONE_THIRD (1.0/3.0)
334 * element specific defines
338 #define LC_C 3.567 /* A */
339 #define M_C 12.011 /* amu */
342 #define LC_SI 5.43105 /* A */
343 #define M_SI 28.08553 /* amu */
345 #define LC_3C_SIC 4.3596 /* A */
354 #define ZINCBLENDE 0x08
365 * function prototypes
369 int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
370 int moldyn_shutdown(t_moldyn *moldyn);
372 int set_int_alg(t_moldyn *moldyn,u8 algo);
373 int set_cutoff(t_moldyn *moldyn,double cutoff);
374 int set_temperature(t_moldyn *moldyn,double t_ref);
375 int set_pressure(t_moldyn *moldyn,double p_ref);
376 int set_p_scale(t_moldyn *moldyn,u8 ptype,double ptc);
377 int set_t_scale(t_moldyn *moldyn,u8 ttype,double ttc);
378 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc);
379 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize);
380 int set_nn_dist(t_moldyn *moldyn,double dist);
381 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
382 int set_potential(t_moldyn *moldyn,u8 type);
384 int set_avg_skip(t_moldyn *moldyn,int skip);
386 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
387 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title);
388 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer);
389 int moldyn_log_shutdown(t_moldyn *moldyn);
391 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
392 u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin);
393 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
394 t_3dvec *r,t_3dvec *v);
395 int del_atom(t_moldyn *moldyn,int tag);
396 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
397 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
398 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
399 int destroy_atoms(t_moldyn *moldyn);
401 int thermal_init(t_moldyn *moldyn,u8 equi_init);
402 double total_mass_calc(t_moldyn *moldyn);
403 double temperature_calc(t_moldyn *moldyn);
404 double get_temperature(t_moldyn *moldyn);
405 int scale_velocity(t_moldyn *moldyn,u8 equi_init);
406 double virial_sum(t_moldyn *moldyn);
407 double pressure_calc(t_moldyn *moldyn);
408 int average_reset(t_moldyn *moldyn);
409 int average_and_fluctuation_calc(t_moldyn *moldyn);
410 int get_heat_capacity(t_moldyn *moldyn);
411 double thermodynamic_pressure_calc(t_moldyn *moldyn);
412 double get_pressure(t_moldyn *moldyn);
413 int scale_volume(t_moldyn *moldyn);
414 int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
415 int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
417 double e_kin_calc(t_moldyn *moldyn);
418 double get_total_energy(t_moldyn *moldyn);
419 t_3dvec get_total_p(t_moldyn *moldyn);
421 double estimate_time_step(t_moldyn *moldyn,double nn_dist);
423 int link_cell_init(t_moldyn *moldyn,u8 vol);
424 int link_cell_update(t_moldyn *moldyn);
426 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int **cell);
428 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
430 int link_cell_shutdown(t_moldyn *moldyn);
432 typedef int (*set_hook)(void *,void *);
434 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau);
435 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params);
437 int moldyn_integrate(t_moldyn *moldyn);
438 int velocity_verlet(t_moldyn *moldyn);
440 int potential_force_calc(t_moldyn *moldyn);
441 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d);
442 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d)
443 // __attribute__((always_inline));
444 int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
445 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
446 // __attribute__((always_inline));
448 int moldyn_bc_check(t_moldyn *moldyn);
450 int moldyn_read_save_file(t_moldyn *moldyn,char *file);
451 int moldyn_free_save_file(t_moldyn *moldyn);
452 int moldyn_load(t_moldyn *moldyn);
453 int process_2b_bonds(t_moldyn *moldyn,void *data,
454 int (*process)(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
456 int get_line(int fd,char *line,int max);
458 int pair_correlation_init(t_moldyn *moldyn,double dr);
459 int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc);
460 int calculate_pair_correlation_process(t_moldyn *moldyn,t_atom *itom,
461 t_atom *jtom,void *data,u8 bc);
462 int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr);
463 int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
465 int bond_analyze(t_moldyn *moldyn,double *quality);
467 int visual_init(t_moldyn *moldyn,char *filebase);
468 int visual_bonds_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
470 int visual_atoms(t_moldyn *moldyn);