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"
17 typedef struct s_atom {
18 t_3dvec r; /* positions */
19 t_3dvec v; /* velocities */
20 t_3dvec f; /* forces */
21 t_3dvec dr; /* delta r for verlet list updates */
22 int element; /* number of element in pse */
23 double mass; /* atom mass */
24 t_list verlet; /* verlet neighbour list */
27 typedef struct s_linkcell {
33 #include "visual/visual.h"
35 typedef struct s_moldyn {
36 /* atoms, amount, dimensions */
40 /* potential, force & parameters */
41 double (*potential)(struct s_moldyn *moldyn);
42 int (*force)(struct s_moldyn *moldyn);
44 /* cut off radius, verlet list & co */
50 /* linked list / cell method */
54 /* integration of newtons equations */
55 int (*integrate)(struct s_moldyn *moldyn);
58 /* logging & visualization */
75 /* moldyn general status */
79 typedef struct s_ho_params {
80 double spring_constant;
81 double equilibrium_distance;
84 typedef struct s_lj_params {
96 #define MOLDYN_LVSTAT_TOTAL_E 0x01
97 #define MOLDYN_LVSTAT_TOTAL_M 0x02
98 #define MOLDYN_LVSTAT_SAVE 0x04
99 #define MOLDYN_LVSTAT_DUMP 0x08
100 #define MOLDYN_LVSTAT_VISUAL 0x10
101 #define MOLDYN_LVSTAT_INITIALIZED 0x80
103 #define MOLDYN_STAT_POTENTIAL 0x01
104 #define MOLDYN_STAT_FORCE 0x02
106 #define MOLDYN_TEMP 273.0
107 #define MOLDYN_TAU 1.0e-15
108 #define MOLDYN_RUNS 1000000
112 #define K_BOLTZMANN 1.3807e-27 /* Nm/K */
113 #define AMU 1.660540e-27 /* kg */
119 #define M_C (12.011*AMU)
122 #define LC_SI 0.543105e-9 /* m */
123 #define M_SI (28.085*AMU) /* kg */
124 #define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* m */
125 #define LJ_EPSILON_SI (2.1678*1.60e-19) /* Nm */
127 /* function prototypes */
129 int moldyn_usage(char **argv);
130 int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv);
131 int moldyn_log_init(t_moldyn *moldyn,void *v);
132 int moldyn_shutdown(t_moldyn *moldyn);
134 int create_lattice(unsigned char type,int element,double mass,double lc,
135 int a,int b,int c,t_atom **atom);
136 int destroy_lattice(t_atom *atom);
137 int thermal_init(t_moldyn *moldyn,t_random *random,int count);
138 int scale_velocity(t_moldyn *moldyn,int count);
139 double get_e_kin(t_atom *atom,int count);
140 double get_e_pot(t_moldyn *moldyn);
141 double get_total_energy(t_moldyn *moldyn);
142 t_3dvec get_total_p(t_atom *atom,int count);
144 double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t);
146 int verlet_list_init(t_moldyn *moldyn);
147 int link_cell_init(t_moldyn *moldyn);
148 int verlet_list_update(t_moldyn *moldyn);
149 int link_cell_update(t_moldyn *moldyn);
150 int verlet_list_shutdown(t_moldyn *moldyn);
151 int link_cell_shutdown(t_moldyn *moldyn);
153 int moldyn_integrate(t_moldyn *moldyn);
154 int velocity_verlet(t_moldyn *moldyn);
156 double potential_harmonic_oscillator(t_moldyn *moldyn);
157 int force_harmonic_oscillator(t_moldyn *moldyn);
158 double potential_lennard_jones(t_moldyn *moldyn);
159 int force_lennard_jones(t_moldyn *moldyn);