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 "visual/visual.h"
17 typedef struct s_atom {
18 t_3dvec r; /* positions */
19 t_3dvec v; /* velocities */
20 t_3dvec f; /* forces */
21 int element; /* number of element in pse */
22 double mass; /* atom mass */
23 //t_list vicinity /* verlet neighbour list */
26 typedef struct s_moldyn {
29 double (*potential)(struct s_moldyn *moldyn);
31 int (*force)(struct s_moldyn *moldyn);
35 int (*integrate)(struct s_moldyn *moldyn);
43 typedef struct s_ho_params {
44 double spring_constant;
45 double equilibrium_distance;
48 typedef struct s_lj_params {
60 #define MOLDYN_STAT_POTENTIAL 0x01
61 #define MOLDYN_STAT_FORCE 0x02
65 #define K_BOLTZMANN 1.3807e-27 /* Nm/K */
66 #define AMU 1.660540e-27 /* kg */
72 #define M_C (12.011*AMU)
75 #define LC_SI 0.543105e-9 /* m */
76 #define M_SI (28.085*AMU) /* kg */
77 #define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* m */
78 #define LJ_EPSILON_SI (2.1678*1.60e-19) /* Nm */
80 /* function prototypes */
82 int create_lattice(unsigned char type,int element,double mass,double lc,
83 int a,int b,int c,t_atom **atom);
84 int destroy_lattice(t_atom *atom);
85 int thermal_init(t_atom *atom,t_random *random,int count,double t);
86 int scale_velocity(t_atom *atom,int count,double t);
87 double get_e_kin(t_atom *atom,int count);
88 double get_e_pot(t_moldyn *moldyn);
89 double get_total_energy(t_moldyn *moldyn);
90 t_3dvec get_total_p(t_atom *atom,int count);
92 double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t);
94 int moldyn_integrate(t_moldyn *moldyn);
95 int velocity_verlet(t_moldyn *moldyn);
97 double potential_harmonic_oscillator(t_moldyn *moldyn);
98 int force_harmonic_oscillator(t_moldyn *moldyn);
99 double potential_lennard_jones(t_moldyn *moldyn);
100 int force_lennard_jones(t_moldyn *moldyn);