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 (*func_i0)(struct s_moldyn *moldyn,t_atom *ai);
108 int (*func_j0)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
109 int (*func_j0_k0)(struct s_moldyn *moldyn,
110 t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
111 int (*func_j0e)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
112 int (*func_j1)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
113 int (*func_j1_k0)(struct s_moldyn *moldyn,
114 t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
115 int (*func_j1c)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
116 int (*func_j1_k1)(struct s_moldyn *moldyn,
117 t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
118 int (*func_j1e)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
120 unsigned char run3bp;
122 double cutoff; /* cutoff radius */
123 double cutoff_square; /* square of the cutoff radius */
124 double nnd; /* nearest neighbour distance (optional) */
126 t_linkcell lc; /* linked cell list interface */
128 int avg_skip; /* amount of steps without average calc */
130 double t_ref; /* reference temperature */
131 double t; /* actual temperature */
132 double t_sum; /* sum over all t */
133 double t_avg; /* average value of t */
135 t_virial gvir; /* global virial (absolute coordinates) */
140 double gp; /* pressure computed from global virial */
141 double gp_sum; /* sum over all gp */
142 double gp_avg; /* average value of gp */
144 t_virial vir; /* actual virial */
146 double virial_sum; /* sum over all calculated virials */
147 double virial_avg; /* average of virial */
149 double p_ref; /* reference pressure */
150 double p; /* actual pressure (computed by virial) */
151 double px,py,pz; /* components of pressure */
152 double p_sum; /* sum over all p */
153 double p_avg; /* average value of p */
155 double tp; /* thermodynamic pressure dU/dV */
156 double tp_sum; /* sum over dU/dV pressure */
157 double tp_avg; /* average value of dU/dV pressure */
158 int tp_cnt; /* how often to do thermodynamic p calc */
160 /* pressure and temperature control (velocity/volume scaling) */
161 /* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */
162 unsigned char pt_scale; /* type of p and t scaling */
163 double t_tc; /* t berendsen control time constant */
164 double p_tc; /* p berendsen control time constant */
166 /* simulation schedule */
167 t_moldyn_schedule schedule;
168 int current; /* current position in schedule */
170 /* integration function pointer */
171 int (*integrate)(struct s_moldyn *moldyn);
172 int time_steps; /* amount of iterations */
173 double tau; /* delta t */
174 double time; /* absolute time */
175 double tau_square; /* delta t squared */
176 int total_steps; /* total steps */
179 double energy; /* potential energy */
180 double ekin; /* kinetic energy */
182 /* energy averages & fluctuations */
183 double k_sum; /* sum of kinetic energy */
184 double v_sum; /* sum of potential energy */
185 double k_avg; /* average of kinetic energy */
186 double v_avg; /* average of potential energy */
187 double k2_sum; /* sum of kinetic energy squared */
188 double v2_sum; /* sum of potential energy squared */
189 double k2_avg; /* average of kinetic energy squared */
190 double v2_avg; /* average of potential energy squared */
191 double dk2_avg; /* mean square kinetic energy fluctuations */
192 double dv2_avg; /* mean square potential energy fluctuations */
194 /* response functions */
195 double c_v_nve; /* constant volume heat capacity (nve) */
196 double c_v_nvt; /* constant volume heat capacity (nvt) */
198 char vlsdir[128]; /* visualization/log/save directory */
199 t_visual vis; /* visualization interface structure */
200 u8 vlsprop; /* log/vis/save properties */
201 unsigned int ewrite; /* how often to log energy */
202 int efd; /* fd for energy log */
203 unsigned int mwrite; /* how often to log momentum */
204 int mfd; /* fd for momentum log */
205 unsigned int pwrite; /* how often to log pressure */
206 int pfd; /* fd for pressure log */
207 unsigned int twrite; /* how often to log temperature */
208 int tfd; /* fd for temperature log */
209 unsigned int vwrite; /* how often to log volume */
210 int vfd; /* fd for volume log */
211 unsigned int awrite; /* how often to visualize atom information */
212 unsigned int swrite; /* how often to create a save file */
213 int rfd; /* report file descriptor */
214 char rtitle[64]; /* report title */
215 char rauthor[64]; /* report author */
216 int epfd; /* energy gnuplot script file descriptor */
217 int ppfd; /* pressure gnuplot script file descriptor */
218 int tpfd; /* temperature gnuplot script file descriptor */
220 u8 status; /* general moldyn properties */
222 t_random random; /* random interface */
224 double debug; /* debugging stuff, ignore */
226 /* potential 2 body check function */
227 int (*check_2b_bond)(struct s_moldyn *moldyn,
228 t_atom *itom,t_atom *jtom,u8 bc);
231 typedef struct s_pcc {
238 typedef struct s_ba {
244 typedef struct s_vb {
254 #define MOLDYN_STAT_PBX 0x01 /* periodic boudaries in x */
255 #define MOLDYN_STAT_PBY 0x02 /* y */
256 #define MOLDYN_STAT_PBZ 0x04 /* and z direction */
258 #define MOLDYN_PSCALE 0x08 /* size controlled by piston */
260 #define MOLDYN_1BP 0x10 /* care about single */
261 #define MOLDYN_2BP 0x20 /* 2 body */
262 #define MOLDYN_3BP 0x40 /* and 3 body particle pots */
264 #define T_SCALE_NONE 0x00
265 #define T_SCALE_BERENDSEN 0x01 /* berendsen t control */
266 #define T_SCALE_DIRECT 0x02 /* direct t control */
267 #define T_SCALE_MASK 0x03
269 #define P_SCALE_NONE 0x00
270 #define P_SCALE_BERENDSEN 0x04 /* berendsen p control */
271 #define P_SCALE_DIRECT 0x08 /* direct p control */
272 #define P_SCALE_MASK 0x0c
275 * default values & units
277 * - length unit: 1 A (1 A = 1e-10 m)
278 * - time unit: 1 fs (1 fs = 1e-15 s)
279 * - mass unit: 1 amu (1 amu = 1.6605388628e-27 kg )
281 * fyi: in the following 1 N = (amu*A)/(fs*fs)
285 #define METER 1e10 /* A */
286 #define SECOND 1e15 /* fs */
287 #define AMU 1.6605388628e-27 /* kg */
288 #define KILOGRAM (1.0/AMU) /* amu */
289 #define NEWTON (METER*KILOGRAM/(SECOND*SECOND)) /* A amu / fs^2 */
290 #define PASCAL (NEWTON/(METER*METER)) /* N / A^2 */
291 #define GPA (1e9*PASCAL) /* N / A^2 */
292 #define BAR ((1.0e5*PASCAL)) /* N / A^2 */
293 #define K_BOLTZMANN (1.380650524e-23*METER*NEWTON) /* NA/K */
294 #define K_B2 (K_BOLTZMANN*K_BOLTZMANN) /* (NA)^2/K^2 */
295 #define EV (1.6021765314e-19*METER*NEWTON) /* NA */
296 #define JOULE (NEWTON*METER) /* NA */
298 #define MOLDYN_TEMP 273.0
299 #define MOLDYN_TAU 1.0
300 #define MOLDYN_CUTOFF 10.0
301 #define MOLDYN_RUNS 1000000
303 #define MOLDYN_INTEGRATE_VERLET 0x00
304 #define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
306 #define MOLDYN_POTENTIAL_HO 0x00
307 #define MOLDYN_POTENTIAL_LJ 0x01
308 #define MOLDYN_POTENTIAL_TM 0x02
309 #define MOLDYN_POTENTIAL_AM 0x03
310 #define MOLDYN_POTENTIAL_AO 0x04
312 #define LOG_TOTAL_ENERGY 0x01
313 #define LOG_TOTAL_MOMENTUM 0x02
314 #define LOG_PRESSURE 0x04
315 #define LOG_TEMPERATURE 0x08
316 #define LOG_VOLUME 0x10
317 #define SAVE_STEP 0x20
318 #define VISUAL_STEP 0x40
319 #define CREATE_REPORT 0x80
328 #define SCALE_DOWN 'd'
329 #define SCALE_DIRECT 'D'
335 #define ONE_THIRD (1.0/3.0)
338 * element specific defines
342 #define LC_C 3.567 /* A */
343 #define M_C 12.011 /* amu */
346 #define LC_SI 5.43105 /* A */
347 #define M_SI 28.08553 /* amu */
349 #define LC_3C_SIC 4.3596 /* A */
358 #define ZINCBLENDE 0x08
368 * function prototypes
372 int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
373 int moldyn_shutdown(t_moldyn *moldyn);
375 int set_int_alg(t_moldyn *moldyn,u8 algo);
376 int set_cutoff(t_moldyn *moldyn,double cutoff);
377 int set_temperature(t_moldyn *moldyn,double t_ref);
378 int set_pressure(t_moldyn *moldyn,double p_ref);
379 int set_p_scale(t_moldyn *moldyn,u8 ptype,double ptc);
380 int set_t_scale(t_moldyn *moldyn,u8 ttype,double ttc);
381 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc);
382 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize);
383 int set_nn_dist(t_moldyn *moldyn,double dist);
384 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
385 int set_potential(t_moldyn *moldyn,u8 type);
387 int set_avg_skip(t_moldyn *moldyn,int skip);
389 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
390 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title);
391 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer);
392 int moldyn_log_shutdown(t_moldyn *moldyn);
394 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
395 u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin);
396 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
397 t_3dvec *r,t_3dvec *v);
398 int del_atom(t_moldyn *moldyn,int tag);
399 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
400 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
401 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
402 int destroy_atoms(t_moldyn *moldyn);
404 int thermal_init(t_moldyn *moldyn,u8 equi_init);
405 double total_mass_calc(t_moldyn *moldyn);
406 double temperature_calc(t_moldyn *moldyn);
407 double get_temperature(t_moldyn *moldyn);
408 int scale_velocity(t_moldyn *moldyn,u8 equi_init);
409 double virial_sum(t_moldyn *moldyn);
410 double pressure_calc(t_moldyn *moldyn);
411 int average_reset(t_moldyn *moldyn);
412 int average_and_fluctuation_calc(t_moldyn *moldyn);
413 int get_heat_capacity(t_moldyn *moldyn);
414 double thermodynamic_pressure_calc(t_moldyn *moldyn);
415 double get_pressure(t_moldyn *moldyn);
416 int scale_volume(t_moldyn *moldyn);
417 int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
418 int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
420 double e_kin_calc(t_moldyn *moldyn);
421 double get_total_energy(t_moldyn *moldyn);
422 t_3dvec get_total_p(t_moldyn *moldyn);
424 double estimate_time_step(t_moldyn *moldyn,double nn_dist);
426 int link_cell_init(t_moldyn *moldyn,u8 vol);
427 int link_cell_update(t_moldyn *moldyn);
429 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int **cell);
431 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 moldyn_read_save_file(t_moldyn *moldyn,char *file);
454 int moldyn_free_save_file(t_moldyn *moldyn);
455 int moldyn_load(t_moldyn *moldyn);
456 int process_2b_bonds(t_moldyn *moldyn,void *data,
457 int (*process)(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
459 int get_line(int fd,char *line,int max);
461 int pair_correlation_init(t_moldyn *moldyn,double dr);
462 int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc);
463 int calculate_pair_correlation_process(t_moldyn *moldyn,t_atom *itom,
464 t_atom *jtom,void *data,u8 bc);
465 int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr);
466 int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
468 int bond_analyze(t_moldyn *moldyn,double *quality);
470 int visual_init(t_moldyn *moldyn,char *filebase);
471 int visual_bonds_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
473 int visual_atoms(t_moldyn *moldyn);