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 */
140 t_virial gvir; /* global virial (absolute coordinates) */
145 double gp; /* pressure computed from global virial */
146 double gp_sum; /* sum over all gp */
147 double gp_avg; /* average value of gp */
149 t_virial vir; /* actual virial */
151 double virial_sum; /* sum over all calculated virials */
152 double virial_avg; /* average of virial */
154 double p_ref; /* reference pressure */
155 double p; /* actual pressure (computed by virial) */
156 double px,py,pz; /* components of pressure */
157 double p_sum; /* sum over all p */
158 double p_avg; /* average value of p */
160 double tp; /* thermodynamic pressure dU/dV */
161 double tp_sum; /* sum over dU/dV pressure */
162 double tp_avg; /* average value of dU/dV pressure */
163 int tp_cnt; /* how often to do thermodynamic p calc */
165 /* pressure and temperature control (velocity/volume scaling) */
166 /* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */
167 unsigned char pt_scale; /* type of p and t scaling */
168 double t_tc; /* t berendsen control time constant */
169 double p_tc; /* p berendsen control time constant */
171 /* simulation schedule */
172 t_moldyn_schedule schedule;
173 int current; /* current position in schedule */
175 /* integration function pointer */
176 int (*integrate)(struct s_moldyn *moldyn);
177 int time_steps; /* amount of iterations */
178 double tau; /* delta t */
179 double time; /* absolute time */
180 double tau_square; /* delta t squared */
181 int total_steps; /* total steps */
184 double energy; /* potential energy */
185 double ekin; /* kinetic energy */
187 /* energy averages & fluctuations */
188 double k_sum; /* sum of kinetic energy */
189 double v_sum; /* sum of potential energy */
190 double k_avg; /* average of kinetic energy */
191 double v_avg; /* average of potential energy */
192 double k2_sum; /* sum of kinetic energy squared */
193 double v2_sum; /* sum of potential energy squared */
194 double k2_avg; /* average of kinetic energy squared */
195 double v2_avg; /* average of potential energy squared */
196 double dk2_avg; /* mean square kinetic energy fluctuations */
197 double dv2_avg; /* mean square potential energy fluctuations */
199 /* response functions */
200 double c_v_nve; /* constant volume heat capacity (nve) */
201 double c_v_nvt; /* constant volume heat capacity (nvt) */
203 char vlsdir[128]; /* visualization/log/save directory */
204 t_visual vis; /* visualization interface structure */
205 u8 vlsprop; /* log/vis/save properties */
206 unsigned int ewrite; /* how often to log energy */
207 int efd; /* fd for energy log */
208 unsigned int mwrite; /* how often to log momentum */
209 int mfd; /* fd for momentum log */
210 unsigned int pwrite; /* how often to log pressure */
211 int pfd; /* fd for pressure log */
212 unsigned int twrite; /* how often to log temperature */
213 int tfd; /* fd for temperature log */
214 unsigned int vwrite; /* how often to log volume */
215 int vfd; /* fd for volume log */
216 unsigned int awrite; /* how often to visualize atom information */
217 unsigned int swrite; /* how often to create a save file */
218 int rfd; /* report file descriptor */
219 char rtitle[64]; /* report title */
220 char rauthor[64]; /* report author */
221 int epfd; /* energy gnuplot script file descriptor */
222 int ppfd; /* pressure gnuplot script file descriptor */
223 int tpfd; /* temperature gnuplot script file descriptor */
225 u8 status; /* general moldyn properties */
227 t_random random; /* random interface */
229 double debug; /* debugging stuff, ignore */
231 /* potential 2 body check function */
232 int (*check_2b_bond)(struct s_moldyn *moldyn,
233 t_atom *itom,t_atom *jtom,u8 bc);
236 typedef struct s_pcc {
243 typedef struct s_ba {
249 typedef struct s_vb {
259 #define MOLDYN_STAT_PBX 0x01 /* periodic boudaries in x */
260 #define MOLDYN_STAT_PBY 0x02 /* y */
261 #define MOLDYN_STAT_PBZ 0x04 /* and z direction */
263 #define MOLDYN_PSCALE 0x08 /* size controlled by piston */
265 #define MOLDYN_1BP 0x10 /* care about single */
266 #define MOLDYN_2BP 0x20 /* 2 body */
267 #define MOLDYN_3BP 0x40 /* and 3 body particle pots */
269 #define T_SCALE_NONE 0x00
270 #define T_SCALE_BERENDSEN 0x01 /* berendsen t control */
271 #define T_SCALE_DIRECT 0x02 /* direct t control */
272 #define T_SCALE_MASK 0x03
274 #define P_SCALE_NONE 0x00
275 #define P_SCALE_BERENDSEN 0x04 /* berendsen p control */
276 #define P_SCALE_DIRECT 0x08 /* direct p control */
277 #define P_SCALE_MASK 0x0c
280 * default values & units
282 * - length unit: 1 A (1 A = 1e-10 m)
283 * - time unit: 1 fs (1 fs = 1e-15 s)
284 * - mass unit: 1 amu (1 amu = 1.6605388628e-27 kg )
286 * fyi: in the following 1 N = (amu*A)/(fs*fs)
290 #define METER 1e10 /* A */
291 #define SECOND 1e15 /* fs */
292 #define AMU 1.6605388628e-27 /* kg */
293 #define KILOGRAM (1.0/AMU) /* amu */
294 #define NEWTON (METER*KILOGRAM/(SECOND*SECOND)) /* A amu / fs^2 */
295 #define PASCAL (NEWTON/(METER*METER)) /* N / A^2 */
296 #define GPA (1e9*PASCAL) /* N / A^2 */
297 #define BAR ((1.0e5*PASCAL)) /* N / A^2 */
298 #define K_BOLTZMANN (1.380650524e-23*METER*NEWTON) /* NA/K */
299 #define K_B2 (K_BOLTZMANN*K_BOLTZMANN) /* (NA)^2/K^2 */
300 #define EV (1.6021765314e-19*METER*NEWTON) /* NA */
301 #define JOULE (NEWTON*METER) /* NA */
303 #define MOLDYN_TEMP 273.0
304 #define MOLDYN_TAU 1.0
305 #define MOLDYN_CUTOFF 10.0
306 #define MOLDYN_RUNS 1000000
308 #define MOLDYN_INTEGRATE_VERLET 0x00
309 #define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
311 #define MOLDYN_POTENTIAL_HO 0x00
312 #define MOLDYN_POTENTIAL_LJ 0x01
313 #define MOLDYN_POTENTIAL_TM 0x02
314 #define MOLDYN_POTENTIAL_AM 0x03
316 #define LOG_TOTAL_ENERGY 0x01
317 #define LOG_TOTAL_MOMENTUM 0x02
318 #define LOG_PRESSURE 0x04
319 #define LOG_TEMPERATURE 0x08
320 #define LOG_VOLUME 0x10
321 #define SAVE_STEP 0x20
322 #define VISUAL_STEP 0x40
323 #define CREATE_REPORT 0x80
332 #define SCALE_DOWN 'd'
333 #define SCALE_DIRECT 'D'
339 #define ONE_THIRD (1.0/3.0)
342 * element specific defines
346 #define LC_C 3.567 /* A */
347 #define M_C 12.011 /* amu */
350 #define LC_SI 5.43105 /* A */
351 #define M_SI 28.08553 /* amu */
353 #define LC_3C_SIC 4.3596 /* A */
362 #define ZINCBLENDE 0x08
373 * function prototypes
377 int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
378 int moldyn_shutdown(t_moldyn *moldyn);
380 int set_int_alg(t_moldyn *moldyn,u8 algo);
381 int set_cutoff(t_moldyn *moldyn,double cutoff);
382 int set_temperature(t_moldyn *moldyn,double t_ref);
383 int set_pressure(t_moldyn *moldyn,double p_ref);
384 int set_p_scale(t_moldyn *moldyn,u8 ptype,double ptc);
385 int set_t_scale(t_moldyn *moldyn,u8 ttype,double ttc);
386 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc);
387 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize);
388 int set_nn_dist(t_moldyn *moldyn,double dist);
389 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
390 int set_potential(t_moldyn *moldyn,u8 type);
392 int set_avg_skip(t_moldyn *moldyn,int skip);
394 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
395 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title);
396 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer);
397 int moldyn_log_shutdown(t_moldyn *moldyn);
399 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
400 u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin);
401 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
402 t_3dvec *r,t_3dvec *v);
403 int del_atom(t_moldyn *moldyn,int tag);
404 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
405 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
406 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
407 int destroy_atoms(t_moldyn *moldyn);
409 int thermal_init(t_moldyn *moldyn,u8 equi_init);
410 double total_mass_calc(t_moldyn *moldyn);
411 double temperature_calc(t_moldyn *moldyn);
412 double get_temperature(t_moldyn *moldyn);
413 int scale_velocity(t_moldyn *moldyn,u8 equi_init);
414 double virial_sum(t_moldyn *moldyn);
415 double pressure_calc(t_moldyn *moldyn);
416 int average_reset(t_moldyn *moldyn);
417 int average_and_fluctuation_calc(t_moldyn *moldyn);
418 int get_heat_capacity(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,u8 dir,double scale,u8 x,u8 y,u8 z);
423 int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
425 double e_kin_calc(t_moldyn *moldyn);
426 double get_total_energy(t_moldyn *moldyn);
427 t_3dvec get_total_p(t_moldyn *moldyn);
429 double estimate_time_step(t_moldyn *moldyn,double nn_dist);
431 int link_cell_init(t_moldyn *moldyn,u8 vol);
432 int link_cell_update(t_moldyn *moldyn);
434 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int **cell);
436 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int *cell);
438 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
440 int link_cell_shutdown(t_moldyn *moldyn);
442 typedef int (*set_hook)(void *,void *);
444 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau);
445 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params);
447 int moldyn_integrate(t_moldyn *moldyn);
448 int velocity_verlet(t_moldyn *moldyn);
450 int potential_force_calc(t_moldyn *moldyn);
451 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d);
452 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d)
453 // __attribute__((always_inline));
454 int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
455 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
456 // __attribute__((always_inline));
458 int moldyn_bc_check(t_moldyn *moldyn);
460 int moldyn_read_save_file(t_moldyn *moldyn,char *file);
461 int moldyn_free_save_file(t_moldyn *moldyn);
462 int moldyn_load(t_moldyn *moldyn);
463 int process_2b_bonds(t_moldyn *moldyn,void *data,
464 int (*process)(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
466 int process_neighbours(t_moldyn *moldyn,void *data,t_atom *atom,
467 int (*process)(t_moldyn *moldyn,t_atom *atom,t_atom *natom,
470 int get_line(int fd,char *line,int max);
472 int pair_correlation_init(t_moldyn *moldyn,double dr);
473 int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc);
474 int calculate_pair_correlation_process(t_moldyn *moldyn,t_atom *itom,
475 t_atom *jtom,void *data,u8 bc);
476 int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr);
477 int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
479 int bond_analyze(t_moldyn *moldyn,double *quality);
481 int visual_init(t_moldyn *moldyn,char *filebase);
482 int visual_bonds_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
485 void *visual_atoms(void *ptr);
487 int visual_atoms(t_moldyn *moldyn);
490 int fpu_set_rtd(void);