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"
16 typedef struct s_atom {
17 t_3dvec r; /* positions */
18 t_3dvec v; /* velocities */
19 t_3dvec f; /* forces */
20 int element; /* number of element in pse */
21 double mass; /* atom mass */
22 //t_list vicinity /* verlet neighbour list */
25 #include "visual/visual.h"
27 typedef struct s_moldyn {
28 /* atoms, amount, dimensions */
32 /* potential, force & parameters */
33 double (*potential)(struct s_moldyn *moldyn);
34 int (*force)(struct s_moldyn *moldyn);
40 /* integration of newtons equations */
41 int (*integrate)(struct s_moldyn *moldyn);
44 /* logging & visualization */
61 /* moldyn general status */
65 typedef struct s_ho_params {
66 double spring_constant;
67 double equilibrium_distance;
70 typedef struct s_lj_params {
82 #define MOLDYN_LVSTAT_TOTAL_E 0x01
83 #define MOLDYN_LVSTAT_TOTAL_M 0x02
84 #define MOLDYN_LVSTAT_SAVE 0x04
85 #define MOLDYN_LVSTAT_DUMP 0x08
86 #define MOLDYN_LVSTAT_VISUAL 0x10
87 #define MOLDYN_LVSTAT_INITIALIZED 0x80
89 #define MOLDYN_STAT_POTENTIAL 0x01
90 #define MOLDYN_STAT_FORCE 0x02
92 #define MOLDYN_TEMP 273.0
93 #define MOLDYN_TAU 1.0e-15
94 #define MOLDYN_RUNS 1000000
98 #define K_BOLTZMANN 1.3807e-27 /* Nm/K */
99 #define AMU 1.660540e-27 /* kg */
105 #define M_C (12.011*AMU)
108 #define LC_SI 0.543105e-9 /* m */
109 #define M_SI (28.085*AMU) /* kg */
110 #define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* m */
111 #define LJ_EPSILON_SI (2.1678*1.60e-19) /* Nm */
113 /* function prototypes */
115 int moldyn_usage(char **argv);
116 int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv);
117 int moldyn_log_init(t_moldyn *moldyn,void *v);
118 int moldyn_shutdown(t_moldyn *moldyn);
120 int create_lattice(unsigned char type,int element,double mass,double lc,
121 int a,int b,int c,t_atom **atom);
122 int destroy_lattice(t_atom *atom);
123 int thermal_init(t_moldyn *moldyn,t_random *random,int count);
124 int scale_velocity(t_moldyn *moldyn,int count);
125 double get_e_kin(t_atom *atom,int count);
126 double get_e_pot(t_moldyn *moldyn);
127 double get_total_energy(t_moldyn *moldyn);
128 t_3dvec get_total_p(t_atom *atom,int count);
130 double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t);
132 int moldyn_integrate(t_moldyn *moldyn);
133 int velocity_verlet(t_moldyn *moldyn);
135 double potential_harmonic_oscillator(t_moldyn *moldyn);
136 int force_harmonic_oscillator(t_moldyn *moldyn);
137 double potential_lennard_jones(t_moldyn *moldyn);
138 int force_lennard_jones(t_moldyn *moldyn);