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; /* position */
37 t_3dvec v; /* velocity */
38 t_3dvec f; /* force */
39 t_virial virial; /* virial */
40 double e; /* site energy */
41 int element; /* number of element in pse */
42 double mass; /* atom mass */
43 u8 brand; /* brand id */
44 int tag; /* atom unique id (number of atom) */
45 u8 attr; /* attributes */
48 #define ATOM_ATTR_FP 0x01 /* fixed position (bulk material) */
49 #define ATOM_ATTR_HB 0x02 /* coupled to heat bath (velocity scaling) */
51 #define ATOM_ATTR_1BP 0x10 /* single paricle potential */
52 #define ATOM_ATTR_2BP 0x20 /* pair potential */
53 #define ATOM_ATTR_3BP 0x40 /* 3 body potential */
56 typedef struct s_linkcell {
57 int nx,ny,nz; /* amount of cells in x, y and z direction */
58 int cells; /* total amount of cells */
59 double len; /* prefered cell edge length */
60 double x,y,z; /* the actual cell lengthes */
61 t_list *subcell; /* pointer to the cell lists */
62 int dnlc; /* direct neighbour lists counter */
65 #include "visual/visual.h"
67 /* moldyn schedule structure */
68 typedef struct s_moldyn_schedule {
73 int (*hook)(void *moldyn,void *hook_params);
77 /* moldyn main structure */
78 typedef struct s_moldyn {
79 int count; /* total amount of atoms */
80 t_atom *atom; /* pointer to the atoms */
82 t_3dvec dim; /* dimensions of the simulation volume */
83 double volume; /* volume of sim cell (dim.x*dim.y*dim.z) */
85 /* potential force function and parameter pointers */
86 int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
87 int (*func2b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
88 int (*func2b_post)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
89 int (*func3b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,
92 //int (*potential_force_function)(struct s_moldyn *moldyn);
94 double cutoff; /* cutoff radius */
95 double cutoff_square; /* square of the cutoff radius */
96 double nnd; /* nearest neighbour distance (optional) */
98 t_linkcell lc; /* linked cell list interface */
100 double t_ref; /* reference temperature */
101 double t; /* actual temperature */
103 double p_ref; /* reference pressure */
104 double p; /* actual pressure (computed by virial) */
105 t_3dvec tp; /* thermodynamic pressure dU/dV */
106 double dv; /* dV for thermodynamic pressure calc */
108 /* pressure and temperature control (velocity/volume scaling) */
109 /* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */
110 unsigned char pt_scale; /* type of p and t scaling */
111 double t_tc; /* t berendsen control time constant */
112 double p_tc; /* p berendsen control time constant */
114 /* simulation schedule */
115 t_moldyn_schedule schedule;
116 int current; /* current position in schedule */
118 /* integration function pointer */
119 int (*integrate)(struct s_moldyn *moldyn);
120 int time_steps; /* amount of iterations */
121 double tau; /* delta t */
122 double time; /* absolute time */
123 double tau_square; /* delta t squared */
124 double elapsed; /* total elapsed time */
126 double energy; /* potential energy */
127 double ekin; /* kinetic energy */
129 char vlsdir[128]; /* visualization/log/save directory */
130 t_visual vis; /* visualization interface structure */
131 u8 vlsprop; /* log/vis/save properties */
132 unsigned int ewrite; /* how often to log energy */
133 int efd; /* fd for energy log */
134 unsigned int mwrite; /* how often to log momentum */
135 int mfd; /* fd for momentum log */
136 unsigned int pwrite; /* how often to log pressure */
137 int pfd; /* fd for pressure log */
138 unsigned int twrite; /* how often to log temperature */
139 int tfd; /* fd for temperature log */
140 unsigned int vwrite; /* how often to visualize atom information */
141 unsigned int swrite; /* how often to create a save file */
142 int rfd; /* report file descriptor */
143 char rtitle[64]; /* report title */
144 char rauthor[64]; /* report author */
145 int epfd; /* energy gnuplot script file descriptor */
146 int ppfd; /* pressure gnuplot script file descriptor */
147 int tpfd; /* temperature gnuplot script file descriptor */
149 u8 status; /* general moldyn properties */
151 t_random random; /* random interface */
153 double debug; /* debugging stuff, ignore */
162 #define MOLDYN_STAT_PBX 0x01 /* periodic boudaries in x */
163 #define MOLDYN_STAT_PBY 0x02 /* y */
164 #define MOLDYN_STAT_PBZ 0x04 /* and z direction */
166 #define MOLDYN_PSCALE 0x08 /* size controlled by piston */
168 #define MOLDYN_1BP 0x10 /* care about single */
169 #define MOLDYN_2BP 0x20 /* 2 body */
170 #define MOLDYN_3BP 0x40 /* and 3 body particle pots */
172 #define T_SCALE_BERENDSEN 0x01 /* berendsen t control */
173 #define T_SCALE_DIRECT 0x02 /* direct t control */
174 #define P_SCALE_BERENDSEN 0x04 /* berendsen p control */
175 #define P_SCALE_DIRECT 0x08 /* direct p control */
180 * - length unit: 1 A (1 A = 1e-10 m)
181 * - time unit: 1 fs (1 fs = 1e-15 s)
182 * - mass unit: 1 amu (1 amu = 1.6605388628e-27 kg )
184 * fyi: in the following 1 N = (amu*A)/(fs*fs)
188 #define METER 1e10 /* A */
189 #define SECOND 1e15 /* fs */
190 #define AMU 1.6605388628e-27 /* kg */
191 #define KILOGRAM (1.0/AMU) /* amu */
192 #define NEWTON (METER*KILOGRAM/(SECOND*SECOND)) /* A amu / fs^2 */
193 #define PASCAL (NEWTON/(METER*METER)) /* N / A^2 */
194 #define ATM ((1.0133e5*PASCAL)) /* N / A^2 */
196 #define MOLDYN_TEMP 273.0
197 #define MOLDYN_TAU 1.0
198 #define MOLDYN_CUTOFF 10.0
199 #define MOLDYN_RUNS 1000000
201 #define MOLDYN_INTEGRATE_VERLET 0x00
202 #define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
204 #define MOLDYN_POTENTIAL_HO 0x00
205 #define MOLDYN_POTENTIAL_LJ 0x01
206 #define MOLDYN_POTENTIAL_TM 0x02
208 #define LOG_TOTAL_ENERGY 0x01
209 #define LOG_TOTAL_MOMENTUM 0x02
210 #define LOG_PRESSURE 0x04
211 #define LOG_TEMPERATURE 0x08
212 #define SAVE_STEP 0x10
213 #define VISUAL_STEP 0x20
214 #define CREATE_REPORT 0x40
224 * phsical values / constants
229 #define ONE_THIRD (1.0/3.0)
231 #define K_BOLTZMANN (1.380650524e-23*METER*NEWTON) /* NA/K */
232 #define EV (1.6021765314e-19*METER*NEWTON) /* NA */
235 #define M_C 12.011 /* amu */
238 #define LC_SI (0.543105e-9*METER) /* A */
239 #define M_SI 28.08553 /* amu */
241 #define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* A */
242 //#define LJ_SIGMA_SI (LC_SI/1.122462) /* A */
243 //#define LJ_SIGMA_SI (0.5*sqrt(2.0)*LC_SI/1.122462) /* A */
244 #define LJ_EPSILON_SI (2.1678*EV) /* NA */
246 #define TM_R_SI (2.7e-10*METER) /* A */
247 #define TM_S_SI (3.0e-10*METER) /* A */
248 #define TM_A_SI (1830.8*EV) /* NA */
249 #define TM_B_SI (471.18*EV) /* NA */
250 #define TM_LAMBDA_SI (2.4799e10/METER) /* 1/A */
251 #define TM_MU_SI (1.7322e10/METER) /* 1/A */
252 #define TM_BETA_SI 1.1000e-6
253 #define TM_N_SI 0.78734
254 #define TM_C_SI 1.0039e5
255 #define TM_D_SI 16.217
256 #define TM_H_SI -0.59825
258 #define TM_R_C (1.8e-10*METER) /* A */
259 #define TM_S_C (2.1e-10*METER) /* A */
260 #define TM_A_C (1393.6*EV) /* NA */
261 #define TM_B_C (346.7*EV) /* NA */
262 #define TM_LAMBDA_C (3.4879e10/METER) /* 1/A */
263 #define TM_MU_C (2.2119e10/METER) /* 1/A */
264 #define TM_BETA_C 1.5724e-7
265 #define TM_N_C 0.72751
266 #define TM_C_C 3.8049e4
268 #define TM_H_C -0.57058
270 #define TM_CHI_SIC 0.9776
283 * function prototypes
287 typedef int (*pf_func1b)(t_moldyn *,t_atom *ai);
288 typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8 bc);
289 typedef int (*pf_func2b_post)(t_moldyn *,t_atom *,t_atom *,u8 bc);
290 typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8 bc);
292 int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
293 int moldyn_shutdown(t_moldyn *moldyn);
295 int set_int_alg(t_moldyn *moldyn,u8 algo);
296 int set_cutoff(t_moldyn *moldyn,double cutoff);
297 int set_temperature(t_moldyn *moldyn,double t_ref);
298 int set_pressure(t_moldyn *moldyn,double p_ref);
299 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc);
300 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize);
301 int set_nn_dist(t_moldyn *moldyn,double dist);
302 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
303 int set_potential1b(t_moldyn *moldyn,pf_func1b func);
304 int set_potential2b(t_moldyn *moldyn,pf_func2b func);
305 int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func);
306 int set_potential3b(t_moldyn *moldyn,pf_func3b func);
307 int set_potential_params(t_moldyn *moldyn,void *params);
309 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
310 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title);
311 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer);
312 int moldyn_log_shutdown(t_moldyn *moldyn);
314 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
315 u8 attr,u8 brand,int a,int b,int c);
316 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
317 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
318 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
319 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
320 t_3dvec *r,t_3dvec *v);
321 int destroy_atoms(t_moldyn *moldyn);
323 int thermal_init(t_moldyn *moldyn,u8 equi_init);
324 double temperature_calc(t_moldyn *moldyn);
325 double get_temperature(t_moldyn *moldyn);
326 int scale_velocity(t_moldyn *moldyn,u8 equi_init);
327 double pressure_calc(t_moldyn *moldyn);
328 double thermodynamic_pressure_calc(t_moldyn *moldyn);
329 double get_pressure(t_moldyn *moldyn);
330 int scale_volume(t_moldyn *moldyn);
331 int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z);
332 int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z);
334 double get_e_kin(t_moldyn *moldyn);
335 double update_e_kin(t_moldyn *moldyn);
336 double get_total_energy(t_moldyn *moldyn);
337 t_3dvec get_total_p(t_moldyn *moldyn);
339 double estimate_time_step(t_moldyn *moldyn,double nn_dist);
341 int link_cell_init(t_moldyn *moldyn,u8 vol);
342 int link_cell_update(t_moldyn *moldyn);
343 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
344 int link_cell_shutdown(t_moldyn *moldyn);
346 typedef int (*set_hook)(void *,void *);
348 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau);
349 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params);
351 int moldyn_integrate(t_moldyn *moldyn);
352 int velocity_verlet(t_moldyn *moldyn);
354 int potential_force_calc(t_moldyn *moldyn);
355 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d);
356 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d)
357 // __attribute__((always_inline));
358 int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
359 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
360 // __attribute__((always_inline));
362 int moldyn_bc_check(t_moldyn *moldyn);