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
61 /* special list structure for low mem approach */
62 typedef struct s_lowmem_list {
68 typedef struct s_linkcell {
69 int nx,ny,nz; /* amount of cells in x, y and z direction */
70 int cells; /* total amount of cells */
71 double len; /* prefered cell edge length */
72 double x,y,z; /* the actual cell lengthes */
74 int **subcell; /* pointer to the cell lists */
76 t_lowmem_list *subcell; /* low mem approach list */
78 t_list *subcell; /* pointer to the cell lists */
80 int dnlc; /* direct neighbour lists counter */
83 #define MAX_ATOMS_PER_LIST 20
85 /* moldyn schedule structure */
86 typedef struct s_moldyn_schedule {
91 int (*hook)(void *moldyn,void *hook_params);
95 /* visualization structure */
96 typedef struct s_visual {
97 int fd; /* rasmol script file descriptor */
98 char fb[128]; /* basename of the save files */
99 t_3dvec dim; /* dimensions of the simulation cell */
102 /* moldyn main structure */
103 typedef struct s_moldyn {
104 int argc; /* number of arguments */
105 char **args; /* pointer to arguments */
107 int count; /* total amount of atoms */
108 double mass; /* total system mass */
109 t_atom *atom; /* pointer to the atoms */
111 t_3dvec dim; /* dimensions of the simulation volume */
112 double volume; /* volume of sim cell (dim.x*dim.y*dim.z) */
114 /* potential force function and parameter pointers */
115 int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
116 int (*func2b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
117 int (*func3b_j1)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
118 int (*func3b_j2)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
119 int (*func3b_j3)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
120 int (*func3b_k1)(struct s_moldyn *moldyn,
121 t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
122 int (*func3b_k2)(struct s_moldyn *moldyn,
123 t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
125 unsigned char run3bp;
127 double cutoff; /* cutoff radius */
128 double cutoff_square; /* square of the cutoff radius */
129 double nnd; /* nearest neighbour distance (optional) */
131 t_linkcell lc; /* linked cell list interface */
133 int avg_skip; /* amount of steps without average calc */
135 double t_ref; /* reference temperature */
136 double t; /* actual temperature */
137 double t_sum; /* sum over all t */
138 double t_avg; /* average value of t */
141 t_virial gvir; /* global virial (absolute coordinates) */
149 // gp stuff exchanged by kinetic energies
150 //double gp; /* pressure computed from global virial */
151 //double gp_sum; /* sum over all gp */
152 //double gp_avg; /* average value of gp */
157 t_virial vir; /* actual virial */
159 double virial_sum; /* sum over all calculated virials */
160 double virial_avg; /* average of virial */
162 double p_ref; /* reference pressure */
163 double p; /* actual pressure (computed by virial) */
164 double px,py,pz; /* components of pressure */
165 double p_sum; /* sum over all p */
166 double p_avg; /* average value of p */
168 double tp; /* thermodynamic pressure dU/dV */
169 double tp_sum; /* sum over dU/dV pressure */
170 double tp_avg; /* average value of dU/dV pressure */
171 int tp_cnt; /* how often to do thermodynamic p calc */
173 /* pressure and temperature control (velocity/volume scaling) */
174 /* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */
175 unsigned char pt_scale; /* type of p and t scaling */
176 double t_tc; /* t berendsen control time constant */
177 double p_tc; /* p berendsen control time constant */
179 /* simulation schedule */
180 t_moldyn_schedule schedule;
181 int current; /* current position in schedule */
183 /* integration function pointer */
184 int (*integrate)(struct s_moldyn *moldyn);
185 int time_steps; /* amount of iterations */
186 double tau; /* delta t */
187 double time; /* absolute time */
188 double tau_square; /* delta t squared */
189 int total_steps; /* total steps */
192 double energy; /* potential energy */
193 double ekin; /* kinetic energy */
195 /* energy averages & fluctuations */
196 double k_sum; /* sum of kinetic energy */
197 double v_sum; /* sum of potential energy */
198 double k_avg; /* average of kinetic energy */
199 double v_avg; /* average of potential energy */
200 double k2_sum; /* sum of kinetic energy squared */
201 double v2_sum; /* sum of potential energy squared */
202 double k2_avg; /* average of kinetic energy squared */
203 double v2_avg; /* average of potential energy squared */
204 double dk2_avg; /* mean square kinetic energy fluctuations */
205 double dv2_avg; /* mean square potential energy fluctuations */
207 /* response functions */
208 double c_v_nve; /* constant volume heat capacity (nve) */
209 double c_v_nvt; /* constant volume heat capacity (nvt) */
211 char vlsdir[128]; /* visualization/log/save directory */
212 t_visual vis; /* visualization interface structure */
213 u8 vlsprop; /* log/vis/save properties */
214 unsigned int ewrite; /* how often to log energy */
215 int efd; /* fd for energy log */
216 unsigned int mwrite; /* how often to log momentum */
217 int mfd; /* fd for momentum log */
218 unsigned int pwrite; /* how often to log pressure */
219 int pfd; /* fd for pressure log */
220 unsigned int twrite; /* how often to log temperature */
221 int tfd; /* fd for temperature log */
222 unsigned int vwrite; /* how often to log volume */
223 int vfd; /* fd for volume log */
224 unsigned int awrite; /* how often to visualize atom information */
225 unsigned int swrite; /* how often to create a save file */
226 int rfd; /* report file descriptor */
227 char rtitle[64]; /* report title */
228 char rauthor[64]; /* report author */
229 int epfd; /* energy gnuplot script file descriptor */
230 int ppfd; /* pressure gnuplot script file descriptor */
231 int tpfd; /* temperature gnuplot script file descriptor */
233 u8 status; /* general moldyn properties */
235 t_random random; /* random interface */
237 double debug; /* debugging stuff, ignore */
239 /* potential 2 body check function */
240 int (*check_2b_bond)(struct s_moldyn *moldyn,
241 t_atom *itom,t_atom *jtom,u8 bc);
244 typedef struct s_pcc {
251 typedef struct s_ba {
257 typedef struct s_vb {
261 typedef struct s_part_vals {
267 #define PART_INSIDE_R 1
268 #define PART_OUTSIDE_R 2
269 #define PART_INSIDE_D 3
270 #define PART_OUTSIDE_D 4
278 #define MOLDYN_STAT_PBX 0x01 /* periodic boudaries in x */
279 #define MOLDYN_STAT_PBY 0x02 /* y */
280 #define MOLDYN_STAT_PBZ 0x04 /* and z direction */
282 #define MOLDYN_PSCALE 0x08 /* size controlled by piston */
284 #define MOLDYN_1BP 0x10 /* care about single */
285 #define MOLDYN_2BP 0x20 /* 2 body */
286 #define MOLDYN_3BP 0x40 /* and 3 body particle pots */
288 #define T_SCALE_NONE 0x00
289 #define T_SCALE_BERENDSEN 0x01 /* berendsen t control */
290 #define T_SCALE_DIRECT 0x02 /* direct t control */
291 #define T_SCALE_MASK 0x03
293 #define P_SCALE_NONE 0x00
294 #define P_SCALE_BERENDSEN 0x04 /* berendsen p control */
295 #define P_SCALE_DIRECT 0x08 /* direct p control */
296 #define P_SCALE_MASK 0x0c
299 * default values & units
301 * - length unit: 1 A (1 A = 1e-10 m)
302 * - time unit: 1 fs (1 fs = 1e-15 s)
303 * - mass unit: 1 amu (1 amu = 1.6605388628e-27 kg )
305 * fyi: in the following 1 N = (amu*A)/(fs*fs)
309 #define METER 1e10 /* A */
310 #define SECOND 1e15 /* fs */
311 #define AMU 1.6605388628e-27 /* kg */
312 #define KILOGRAM (1.0/AMU) /* amu */
313 #define NEWTON (METER*KILOGRAM/(SECOND*SECOND)) /* A amu / fs^2 */
314 #define PASCAL (NEWTON/(METER*METER)) /* N / A^2 */
315 #define GPA (1e9*PASCAL) /* N / A^2 */
316 #define BAR ((1.0e5*PASCAL)) /* N / A^2 */
317 #define K_BOLTZMANN (1.380650524e-23*METER*NEWTON) /* NA/K */
318 #define K_B2 (K_BOLTZMANN*K_BOLTZMANN) /* (NA)^2/K^2 */
319 #define EV (1.6021765314e-19*METER*NEWTON) /* NA */
320 #define JOULE (NEWTON*METER) /* NA */
322 #define MOLDYN_TEMP 273.0
323 #define MOLDYN_TAU 1.0
324 #define MOLDYN_CUTOFF 10.0
325 #define MOLDYN_RUNS 1000000
327 #define MOLDYN_INTEGRATE_VERLET 0x00
328 #define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
330 #define MOLDYN_POTENTIAL_HO 0x00
331 #define MOLDYN_POTENTIAL_LJ 0x01
332 #define MOLDYN_POTENTIAL_TM 0x02
333 #define MOLDYN_POTENTIAL_AM 0x03
335 #define LOG_TOTAL_ENERGY 0x01
336 #define LOG_TOTAL_MOMENTUM 0x02
337 #define LOG_PRESSURE 0x04
338 #define LOG_TEMPERATURE 0x08
339 #define LOG_VOLUME 0x10
340 #define SAVE_STEP 0x20
341 #define VISUAL_STEP 0x40
342 #define CREATE_REPORT 0x80
351 #define SCALE_DOWN 'd'
352 #define SCALE_DIRECT 'D'
358 #define ONE_THIRD (1.0/3.0)
361 * element specific defines
365 #define LC_C 3.567 /* A */
366 #define M_C 12.011 /* amu */
369 #define LC_SI 5.43105 /* A */
370 #define M_SI 28.08553 /* amu */
372 #define LC_3C_SIC 4.3596 /* A */
381 #define ZINCBLENDE 0x08
392 * function prototypes
396 int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
397 int moldyn_shutdown(t_moldyn *moldyn);
399 int set_int_alg(t_moldyn *moldyn,u8 algo);
400 int set_cutoff(t_moldyn *moldyn,double cutoff);
401 int set_temperature(t_moldyn *moldyn,double t_ref);
402 int set_pressure(t_moldyn *moldyn,double p_ref);
403 int set_p_scale(t_moldyn *moldyn,u8 ptype,double ptc);
404 int set_t_scale(t_moldyn *moldyn,u8 ttype,double ttc);
405 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc);
406 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize);
407 int set_nn_dist(t_moldyn *moldyn,double dist);
408 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
409 int set_potential(t_moldyn *moldyn,u8 type);
411 int set_avg_skip(t_moldyn *moldyn,int skip);
413 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
414 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title);
415 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer);
416 int moldyn_log_shutdown(t_moldyn *moldyn);
418 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
419 u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin,
420 u8 p_type,t_part_vals *p_vals);
421 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
422 t_3dvec *r,t_3dvec *v);
423 int del_atom(t_moldyn *moldyn,int tag);
424 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
425 u8 p_type,t_part_vals *p_vals);
426 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
427 u8 p_type,t_part_vals *p_vals);
428 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
429 u8 p_type,t_part_vals *p_vals);
430 int destroy_atoms(t_moldyn *moldyn);
432 int thermal_init(t_moldyn *moldyn,u8 equi_init);
433 double total_mass_calc(t_moldyn *moldyn);
434 double temperature_calc(t_moldyn *moldyn);
435 double get_temperature(t_moldyn *moldyn);
436 int scale_velocity(t_moldyn *moldyn,u8 equi_init);
437 double virial_sum(t_moldyn *moldyn);
438 double pressure_calc(t_moldyn *moldyn);
439 int average_reset(t_moldyn *moldyn);
440 int average_and_fluctuation_calc(t_moldyn *moldyn);
441 int get_heat_capacity(t_moldyn *moldyn);
442 double thermodynamic_pressure_calc(t_moldyn *moldyn);
443 double get_pressure(t_moldyn *moldyn);
444 int scale_volume(t_moldyn *moldyn);
445 int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
446 int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
448 double e_kin_calc(t_moldyn *moldyn);
449 double get_total_energy(t_moldyn *moldyn);
450 t_3dvec get_total_p(t_moldyn *moldyn);
452 double estimate_time_step(t_moldyn *moldyn,double nn_dist);
454 int link_cell_init(t_moldyn *moldyn,u8 vol);
455 int link_cell_update(t_moldyn *moldyn);
457 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int **cell);
459 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int *cell);
461 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
463 int link_cell_shutdown(t_moldyn *moldyn);
465 typedef int (*set_hook)(void *,void *);
467 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau);
468 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params);
470 int moldyn_integrate(t_moldyn *moldyn);
471 int velocity_verlet(t_moldyn *moldyn);
473 int potential_force_calc(t_moldyn *moldyn);
474 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d);
475 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d)
476 // __attribute__((always_inline));
477 int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
478 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
479 // __attribute__((always_inline));
481 int moldyn_bc_check(t_moldyn *moldyn);
483 int moldyn_read_save_file(t_moldyn *moldyn,char *file);
484 int moldyn_free_save_file(t_moldyn *moldyn);
485 int moldyn_load(t_moldyn *moldyn);
486 int process_2b_bonds(t_moldyn *moldyn,void *data,
487 int (*process)(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
489 int process_neighbours(t_moldyn *moldyn,void *data,t_atom *atom,
490 int (*process)(t_moldyn *moldyn,t_atom *atom,t_atom *natom,
493 int get_line(int fd,char *line,int max);
495 int pair_correlation_init(t_moldyn *moldyn,double dr);
496 int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc);
497 int calculate_pair_correlation_process(t_moldyn *moldyn,t_atom *itom,
498 t_atom *jtom,void *data,u8 bc);
499 int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr);
500 int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
502 int bond_analyze(t_moldyn *moldyn,double *quality);
504 int visual_init(t_moldyn *moldyn,char *filebase);
505 int visual_bonds_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
508 void *visual_atoms(void *ptr);
510 int visual_atoms(t_moldyn *moldyn);
513 int fpu_set_rtd(void);