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 */
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 */
60 typedef struct s_linkcell {
61 int nx,ny,nz; /* amount of cells in x, y and z direction */
62 int cells; /* total amount of cells */
63 double len; /* prefered cell edge length */
64 double x,y,z; /* the actual cell lengthes */
66 int **subcell; /* pointer to the cell lists */
68 t_list *subcell; /* pointer to the cell lists */
70 int dnlc; /* direct neighbour lists counter */
73 #define MAX_ATOMS_PER_LIST 20
75 /* moldyn schedule structure */
76 typedef struct s_moldyn_schedule {
81 int (*hook)(void *moldyn,void *hook_params);
85 /* visualization structure */
86 typedef struct s_visual {
87 int fd; /* rasmol script file descriptor */
88 char fb[128]; /* basename of the save files */
89 t_3dvec dim; /* dimensions of the simulation cell */
92 /* moldyn main structure */
93 typedef struct s_moldyn {
94 int argc; /* number of arguments */
95 char **args; /* pointer to arguments */
97 int count; /* total amount of atoms */
98 double mass; /* total system mass */
99 t_atom *atom; /* pointer to the atoms */
101 t_3dvec dim; /* dimensions of the simulation volume */
102 double volume; /* volume of sim cell (dim.x*dim.y*dim.z) */
104 /* potential force function and parameter pointers */
105 int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
106 int (*func2b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
107 int (*func3b_j1)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
108 int (*func3b_j2)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
109 int (*func3b_j3)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
110 int (*func3b_k1)(struct s_moldyn *moldyn,
111 t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
112 int (*func3b_k2)(struct s_moldyn *moldyn,
113 t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
115 unsigned char run3bp;
117 double cutoff; /* cutoff radius */
118 double cutoff_square; /* square of the cutoff radius */
119 double nnd; /* nearest neighbour distance (optional) */
120 double bondlen[3]; /* bond lengthes (only 2 atomic systems) */
122 t_linkcell lc; /* linked cell list interface */
124 int avg_skip; /* amount of steps without average calc */
126 double t_ref; /* reference temperature */
127 double t; /* actual temperature */
128 double t_sum; /* sum over all t */
129 double t_avg; /* average value of t */
131 t_virial gvir; /* global virial (absolute coordinates) */
136 double gp; /* pressure computed from global virial */
137 double gp_sum; /* sum over all gp */
138 double gp_avg; /* average value of gp */
140 t_virial vir; /* actual virial */
142 double virial_sum; /* sum over all calculated virials */
143 double virial_avg; /* average of virial */
145 double p_ref; /* reference pressure */
146 double p; /* actual pressure (computed by virial) */
147 double p_sum; /* sum over all p */
148 double p_avg; /* average value of p */
150 double tp; /* thermodynamic pressure dU/dV */
151 double tp_sum; /* sum over dU/dV pressure */
152 double tp_avg; /* average value of dU/dV pressure */
153 int tp_cnt; /* how often to do thermodynamic p calc */
155 /* pressure and temperature control (velocity/volume scaling) */
156 /* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */
157 unsigned char pt_scale; /* type of p and t scaling */
158 double t_tc; /* t berendsen control time constant */
159 double p_tc; /* p berendsen control time constant */
161 /* simulation schedule */
162 t_moldyn_schedule schedule;
163 int current; /* current position in schedule */
165 /* integration function pointer */
166 int (*integrate)(struct s_moldyn *moldyn);
167 int time_steps; /* amount of iterations */
168 double tau; /* delta t */
169 double time; /* absolute time */
170 double tau_square; /* delta t squared */
171 int total_steps; /* total steps */
174 double energy; /* potential energy */
175 double ekin; /* kinetic energy */
177 /* energy averages & fluctuations */
178 double k_sum; /* sum of kinetic energy */
179 double v_sum; /* sum of potential energy */
180 double k_avg; /* average of kinetic energy */
181 double v_avg; /* average of potential energy */
182 double k2_sum; /* sum of kinetic energy squared */
183 double v2_sum; /* sum of potential energy squared */
184 double k2_avg; /* average of kinetic energy squared */
185 double v2_avg; /* average of potential energy squared */
186 double dk2_avg; /* mean square kinetic energy fluctuations */
187 double dv2_avg; /* mean square potential energy fluctuations */
189 /* response functions */
190 double c_v_nve; /* constant volume heat capacity (nve) */
191 double c_v_nvt; /* constant volume heat capacity (nvt) */
193 char vlsdir[128]; /* visualization/log/save directory */
194 t_visual vis; /* visualization interface structure */
195 u8 vlsprop; /* log/vis/save properties */
196 unsigned int ewrite; /* how often to log energy */
197 int efd; /* fd for energy log */
198 unsigned int mwrite; /* how often to log momentum */
199 int mfd; /* fd for momentum log */
200 unsigned int pwrite; /* how often to log pressure */
201 int pfd; /* fd for pressure log */
202 unsigned int twrite; /* how often to log temperature */
203 int tfd; /* fd for temperature log */
204 unsigned int vwrite; /* how often to log volume */
205 int vfd; /* fd for volume log */
206 unsigned int awrite; /* how often to visualize atom information */
207 unsigned int swrite; /* how often to create a save file */
208 int rfd; /* report file descriptor */
209 char rtitle[64]; /* report title */
210 char rauthor[64]; /* report author */
211 int epfd; /* energy gnuplot script file descriptor */
212 int ppfd; /* pressure gnuplot script file descriptor */
213 int tpfd; /* temperature gnuplot script file descriptor */
215 u8 status; /* general moldyn properties */
217 t_random random; /* random interface */
219 double debug; /* debugging stuff, ignore */
221 /* potential 2 body check function */
222 int (*check_2b_bond)(struct s_moldyn *moldyn,
223 t_atom *itom,t_atom *jtom,u8 bc);
226 typedef struct s_pcc {
233 typedef struct s_ba {
245 #define MOLDYN_STAT_PBX 0x01 /* periodic boudaries in x */
246 #define MOLDYN_STAT_PBY 0x02 /* y */
247 #define MOLDYN_STAT_PBZ 0x04 /* and z direction */
249 #define MOLDYN_PSCALE 0x08 /* size controlled by piston */
251 #define MOLDYN_1BP 0x10 /* care about single */
252 #define MOLDYN_2BP 0x20 /* 2 body */
253 #define MOLDYN_3BP 0x40 /* and 3 body particle pots */
255 #define T_SCALE_BERENDSEN 0x01 /* berendsen t control */
256 #define T_SCALE_DIRECT 0x02 /* direct t control */
257 #define P_SCALE_BERENDSEN 0x04 /* berendsen p control */
258 #define P_SCALE_DIRECT 0x08 /* direct p control */
261 * default values & units
263 * - length unit: 1 A (1 A = 1e-10 m)
264 * - time unit: 1 fs (1 fs = 1e-15 s)
265 * - mass unit: 1 amu (1 amu = 1.6605388628e-27 kg )
267 * fyi: in the following 1 N = (amu*A)/(fs*fs)
271 #define METER 1e10 /* A */
272 #define SECOND 1e15 /* fs */
273 #define AMU 1.6605388628e-27 /* kg */
274 #define KILOGRAM (1.0/AMU) /* amu */
275 #define NEWTON (METER*KILOGRAM/(SECOND*SECOND)) /* A amu / fs^2 */
276 #define PASCAL (NEWTON/(METER*METER)) /* N / A^2 */
277 #define GPA (1e9*PASCAL) /* N / A^2 */
278 #define BAR ((1.0e5*PASCAL)) /* N / A^2 */
279 #define K_BOLTZMANN (1.380650524e-23*METER*NEWTON) /* NA/K */
280 #define K_B2 (K_BOLTZMANN*K_BOLTZMANN) /* (NA)^2/K^2 */
281 #define EV (1.6021765314e-19*METER*NEWTON) /* NA */
282 #define JOULE (NEWTON*METER) /* NA */
284 #define MOLDYN_TEMP 273.0
285 #define MOLDYN_TAU 1.0
286 #define MOLDYN_CUTOFF 10.0
287 #define MOLDYN_RUNS 1000000
289 #define MOLDYN_INTEGRATE_VERLET 0x00
290 #define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
292 #define MOLDYN_POTENTIAL_HO 0x00
293 #define MOLDYN_POTENTIAL_LJ 0x01
294 #define MOLDYN_POTENTIAL_TM 0x02
295 #define MOLDYN_POTENTIAL_AM 0x03
297 #define LOG_TOTAL_ENERGY 0x01
298 #define LOG_TOTAL_MOMENTUM 0x02
299 #define LOG_PRESSURE 0x04
300 #define LOG_TEMPERATURE 0x08
301 #define LOG_VOLUME 0x10
302 #define SAVE_STEP 0x20
303 #define VISUAL_STEP 0x40
304 #define CREATE_REPORT 0x80
313 #define SCALE_DOWN 'd'
314 #define SCALE_DIRECT 'D'
317 * potential related phsical values / constants
321 #define ONE_THIRD (1.0/3.0)
324 #define LC_C 3.567 /* A */
325 #define M_C 12.011 /* amu */
328 #define LC_SI 5.43105 /* A */
329 #define M_SI 28.08553 /* amu */
331 #define LC_3C_SIC 4.3596 /* A */
333 #define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* A */
334 //#define LJ_SIGMA_SI (LC_SI/1.122462) /* A */
335 //#define LJ_SIGMA_SI (0.5*sqrt(2.0)*LC_SI/1.122462) /* A */
336 #define LJ_EPSILON_SI (2.1678*EV) /* NA */
348 * function prototypes
352 int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
353 int moldyn_shutdown(t_moldyn *moldyn);
355 int set_int_alg(t_moldyn *moldyn,u8 algo);
356 int set_cutoff(t_moldyn *moldyn,double cutoff);
357 int set_bondlen(t_moldyn *moldyn,double b0,double b1,double bm);
358 int set_temperature(t_moldyn *moldyn,double t_ref);
359 int set_pressure(t_moldyn *moldyn,double p_ref);
360 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc);
361 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize);
362 int set_nn_dist(t_moldyn *moldyn,double dist);
363 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
364 int set_potential(t_moldyn *moldyn,u8 type);
366 int set_avg_skip(t_moldyn *moldyn,int skip);
368 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
369 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title);
370 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer);
371 int moldyn_log_shutdown(t_moldyn *moldyn);
373 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
374 u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin);
375 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
376 t_3dvec *r,t_3dvec *v);
377 int del_atom(t_moldyn *moldyn,int tag);
378 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
379 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
380 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
381 int destroy_atoms(t_moldyn *moldyn);
383 int thermal_init(t_moldyn *moldyn,u8 equi_init);
384 double total_mass_calc(t_moldyn *moldyn);
385 double temperature_calc(t_moldyn *moldyn);
386 double get_temperature(t_moldyn *moldyn);
387 int scale_velocity(t_moldyn *moldyn,u8 equi_init);
388 double virial_sum(t_moldyn *moldyn);
389 double pressure_calc(t_moldyn *moldyn);
390 int average_reset(t_moldyn *moldyn);
391 int average_and_fluctuation_calc(t_moldyn *moldyn);
392 int get_heat_capacity(t_moldyn *moldyn);
393 double thermodynamic_pressure_calc(t_moldyn *moldyn);
394 double get_pressure(t_moldyn *moldyn);
395 int scale_volume(t_moldyn *moldyn);
396 int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
397 int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
399 double e_kin_calc(t_moldyn *moldyn);
400 double get_total_energy(t_moldyn *moldyn);
401 t_3dvec get_total_p(t_moldyn *moldyn);
403 double estimate_time_step(t_moldyn *moldyn,double nn_dist);
405 int link_cell_init(t_moldyn *moldyn,u8 vol);
406 int link_cell_update(t_moldyn *moldyn);
408 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int **cell);
410 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
412 int link_cell_shutdown(t_moldyn *moldyn);
414 typedef int (*set_hook)(void *,void *);
416 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau);
417 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params);
419 int moldyn_integrate(t_moldyn *moldyn);
420 int velocity_verlet(t_moldyn *moldyn);
422 int potential_force_calc(t_moldyn *moldyn);
423 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d);
424 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d)
425 // __attribute__((always_inline));
426 int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
427 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
428 // __attribute__((always_inline));
430 int moldyn_bc_check(t_moldyn *moldyn);
432 int moldyn_read_save_file(t_moldyn *moldyn,char *file);
433 int moldyn_free_save_file(t_moldyn *moldyn);
434 int moldyn_load(t_moldyn *moldyn);
435 int process_2b_bonds(t_moldyn *moldyn,void *data,
436 int (*process)(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
438 int get_line(int fd,char *line,int max);
440 int pair_correlation_init(t_moldyn *moldyn,double dr);
441 int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc);
442 int calculate_pair_correlation_process(t_moldyn *moldyn,t_atom *itom,
443 t_atom *jtom,void *data,u8 bc);
444 int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr);
445 int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
447 int bond_analyze(t_moldyn *moldyn,double *quality);
449 int visual_init(t_moldyn *moldyn,char *filebase);
450 int visual_atoms(t_moldyn *moldyn);