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"
23 typedef unsigned char u8;
25 /* the atom of the md simulation */
26 typedef struct s_atom {
27 t_3dvec r; /* position */
28 t_3dvec v; /* velocity */
29 t_3dvec f; /* force */
30 int element; /* number of element in pse */
31 double mass; /* atom mass */
32 u8 bnum; /* brand number */
33 u8 attr; /* attributes */
36 #define ATOM_ATTR_FP 0x01 /* fixed position (bulk material) */
37 #define ATOM_ATTR_HB 0x02 /* coupled to heat bath (velocity scaling) */
39 #define ATOM_ATTR_1BP 0x10 /* single paricle potential */
40 #define ATOM_ATTR_2BP 0x20 /* pair potential */
41 #define ATOM_ATTR_3BP 0x40 /* 3 body potential */
44 typedef struct s_linkcell {
45 int nx,ny,nz; /* amount of cells in x, y and z direction */
46 int cells; /* total amount of cells */
47 double len; /* prefered cell edge length */
48 double x,y,z; /* the actual cell lengthes */
49 t_list *subcell; /* pointer to the cell lists */
50 int dnlc; /* direct neighbour lists counter */
51 int countn; /* amount of neighbours */
54 #include "visual/visual.h"
56 /* moldyn schedule structure */
57 typedef struct s_moldyn_schedule {
61 int (*hook)(void *moldyn,void *hook);
65 /* moldyn main structure */
66 typedef struct s_moldyn {
67 int count; /* total amount of atoms */
68 t_atom *atom; /* pointer to the atoms */
70 t_3dvec dim; /* dimensions of the simulation volume */
72 /* potential force function and parameter pointers */
73 int (*pf_func1b)(struct s_moldyn *,t_atom *);
75 int (*pf_func2b)(struct s_moldyn *,t_atom *,t_atom *);
77 int (*pf_func3b)(struct s_moldyn *,t_atom *,t_atom *,t_atom *);
79 //int (*potential_force_function)(struct s_moldyn *moldyn);
81 double cutoff; /* cutoff radius */
82 double cutoff_square; /* square of the cutoff radius */
84 t_linkcell lc; /* linked cell method */
86 double t; /* temperature */
88 /* simulation schedule */
89 t_moldyn_schedule schedule;
90 int current; /* current position in schedule */
92 /* integration function pointer */
93 int (*integrate)(struct s_moldyn *moldyn);
94 int time_steps; /* amount of iterations */
95 double tau; /* delta t */
96 double tau_square; /* delta t squared */
97 double elapsed; /* total elapsed time */
99 double energy; /* potential energy */
100 double ekin; /* kinetic energy */
102 t_visual vis; /* visualization/log/save interface structure */
103 u8 lvstat; /* log & vis properties */
104 unsigned int ewrite; /* how often to log energy */
105 int efd; /* fd for energy log */
106 unsigned int mwrite; /* how often to log momentum */
107 int mfd; /* fd for momentum log */
108 unsigned int vwrite; /* how often to visualize atom information */
109 char vfb[64]; /* visualization file name base */
110 void *visual; /* pointer (hack!) */
111 unsigned int swrite; /* how often to create a save file */
112 char sfb[64]; /* visualization file name base */
114 u8 status; /* general moldyn properties */
116 t_random random; /* random interface */
119 #define MOLDYN_LVSTAT_TOTAL_E 0x01
120 #define MOLDYN_LVSTAT_TOTAL_M 0x02
121 #define MOLDYN_LVSTAT_SAVE 0x04
122 #define MOLDYN_LVSTAT_VISUAL 0x08
123 #define MOLDYN_LVSTAT_INITIALIZED 0x10
125 #define MOLDYN_STAT_PBX 0x08 /* periodic boudaries in x */
126 #define MOLDYN_STAT_PBY 0x10 /* y */
127 #define MOLDYN_STAT_PBZ 0x20 /* and z direction */
129 #define MOLDYN_1BP 0x00
130 #define MOLDYN_2BP 0x01
131 #define MOLDYN_3BP 0x02
136 * potential parameter structures
141 * harmonic oscillator potential parameter structure
144 typedef struct s_ho_params {
145 double spring_constant;
146 double equilibrium_distance;
150 * lennard jones potential parameter structure
153 typedef struct s_lj_params {
163 /* tersoff exchange structure to exchange 2bp and 3bp calculated values */
164 typedef struct s_tersoff_exchange {
188 } t_tersoff_exchange;
190 /* tersoff multi (2!) potential parameters */
191 typedef struct s_tersoff_mult_params {
192 double S[2]; /* tersoff cutoff radii */
193 double R[2]; /* tersoff cutoff radii */
194 double Smixed; /* mixed S radius */
195 double Rmixed; /* mixed R radius */
196 double A[2]; /* factor of tersoff attractive part */
197 double B[2]; /* factor of tersoff repulsive part */
198 double Amixed; /* mixed A factor */
199 double Bmixed; /* mixed B factor */
200 double lambda[2]; /* tersoff lambda */
201 double lambda_m; /* mixed lambda */
202 double mu[2]; /* tersoff mu */
203 double mu_m; /* mixed mu */
213 t_tersoff_exchange exchange; /* exchange between 2bp and 3bp calc */
226 #define MOLDYN_TEMP 273.0
227 #define MOLDYN_TAU 1.0e-15
228 #define MOLDYN_CUTOFF 1.0e-9
229 #define MOLDYN_RUNS 1000000
231 #define MOLDYN_INTEGRATE_VERLET 0x00
232 #define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
234 #define MOLDYN_POTENTIAL_HO 0x00
235 #define MOLDYN_POTENTIAL_LJ 0x01
236 #define MOLDYN_POTENTIAL_TM 0x02
238 #define MOLDYN_SET_POTENTIAL 0x00
239 #define MOLDYN_SET_TEMPERATURE 0x01
248 * phsical values / constants
252 #define K_BOLTZMANN 1.3807e-27 /* Nm/K */
253 #define AMU 1.660540e-27 /* kg */
259 #define M_C (12.011*AMU)
262 #define LC_SI 0.543105e-9 /* m */
263 #define M_SI (28.085*AMU) /* kg */
264 #define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* m */
265 #define LJ_EPSILON_SI (2.1678*1.60e-19) /* Nm */
270 * function prototypes
274 int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
275 int moldyn_shutdown(t_moldyn *moldyn);
277 int set_int_alg(t_moldyn *moldyn,u8 algo);
278 int set_cutoff(t_moldyn *moldyn,double cutoff);
279 int set_temperature(t_moldyn *moldyn,double t);
280 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize);
281 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
282 int set_potential(t_moldyn *moldyn,u8 type,(int *)(func),void *params);
284 int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer);
285 nt moldyn_log_shutdown(t_moldyn *moldyn);
287 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
288 u8 attr,u8 bnum,int a,int b,int c);
289 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
290 t_3dvec r,t_3dvec v);
291 int destroy_atoms(t_moldyn *moldyn);
293 int thermal_init(t_moldyn *moldyn);
294 int scale_velocity(t_moldyn *moldyn);
296 double get_e_kin(t_moldyn *moldyn);
297 double get_e_pot(t_moldyn *moldyn);
298 double get_total_energy(t_moldyn *moldyn);
299 t_3dvec get_total_p(t_moldyn *moldyn);
301 double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t);
303 int link_cell_init(t_moldyn *moldyn);
304 int link_cell_update(t_moldyn *moldyn);
305 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
306 int link_cell_shutdown(t_moldyn *moldyn);
308 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau);
309 int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params);
311 int moldyn_integrate(t_moldyn *moldyn);
312 int velocity_verlet(t_moldyn *moldyn);
314 int potential_force_calc(t_moldyn *moldyn);
315 int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
316 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_Atom *aj,u8 bc);
317 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
318 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai);
319 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
320 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc);