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 {
27 /* atoms, amount, dimensions */
31 /* potential, force & parameters */
32 double (*potential)(struct s_moldyn *moldyn);
33 int (*force)(struct s_moldyn *moldyn);
39 /* integration of newtons equations */
40 int (*integrate)(struct s_moldyn *moldyn);
43 /* logging & visualization */
59 /* moldyn general status */
63 typedef struct s_ho_params {
64 double spring_constant;
65 double equilibrium_distance;
68 typedef struct s_lj_params {
80 #define MOLDYN_LVSTAT_TOTAL_E 0x01
81 #define MOLDYN_LVSTAT_TOTAL_M 0x02
82 #define MOLDYN_LVSTAT_SAVE 0x04
83 #define MOLDYN_LVSTAT_DUMP 0x08
84 #define MOLDYN_LVSTAT_VISUAL 0x10
85 #define MOLDYN_LVSTAT_INITIALIZED 0x80
87 #define MOLDYN_STAT_POTENTIAL 0x01
88 #define MOLDYN_STAT_FORCE 0x02
90 #define MOLDYN_TEMP 273.0
91 #define MOLDYN_TAU 1.0e-15
92 #define MOLDYN_RUNS 1000000
96 #define K_BOLTZMANN 1.3807e-27 /* Nm/K */
97 #define AMU 1.660540e-27 /* kg */
103 #define M_C (12.011*AMU)
106 #define LC_SI 0.543105e-9 /* m */
107 #define M_SI (28.085*AMU) /* kg */
108 #define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* m */
109 #define LJ_EPSILON_SI (2.1678*1.60e-19) /* Nm */
111 /* function prototypes */
113 int moldyn_usage(char **argv);
114 int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv);
115 int moldyn_log_init(t_moldyn *moldyn);
117 int create_lattice(unsigned char type,int element,double mass,double lc,
118 int a,int b,int c,t_atom **atom);
119 int destroy_lattice(t_atom *atom);
120 int thermal_init(t_moldyn *moldyn,t_random *random,int count);
121 int scale_velocity(t_moldyn *moldyn,int count);
122 double get_e_kin(t_atom *atom,int count);
123 double get_e_pot(t_moldyn *moldyn);
124 double get_total_energy(t_moldyn *moldyn);
125 t_3dvec get_total_p(t_atom *atom,int count);
127 double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t);
129 int moldyn_integrate(t_moldyn *moldyn);
130 int velocity_verlet(t_moldyn *moldyn);
132 double potential_harmonic_oscillator(t_moldyn *moldyn);
133 int force_harmonic_oscillator(t_moldyn *moldyn);
134 double potential_lennard_jones(t_moldyn *moldyn);
135 int force_lennard_jones(t_moldyn *moldyn);