+ int total_sched;
+ int *runs;
+ double *tau;
+ int (*hook)(void *moldyn,void *hook_params);
+ void *hook_params;
+} t_moldyn_schedule;
+
+/* visualization structure */
+typedef struct s_visual {
+ int fd; /* rasmol script file descriptor */
+ char fb[128]; /* basename of the save files */
+ t_3dvec dim; /* dimensions of the simulation cell */
+} t_visual;
+
+/* moldyn main structure */
+typedef struct s_moldyn {
+ int argc; /* number of arguments */
+ char **args; /* pointer to arguments */
+
+ int count; /* total amount of atoms */
+ double mass; /* total system mass */
+ t_atom *atom; /* pointer to the atoms */
+
+ t_3dvec dim; /* dimensions of the simulation volume */
+ double volume; /* volume of sim cell (dim.x*dim.y*dim.z) */
+
+ /* potential force function and parameter pointers */
+ int (*func_i0)(struct s_moldyn *moldyn,t_atom *ai);
+ int (*func_j0)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+ int (*func_j0_k0)(struct s_moldyn *moldyn,
+ t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
+ int (*func_j0e)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+ int (*func_j1)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+ int (*func_j1_k0)(struct s_moldyn *moldyn,
+ t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
+ int (*func_j1c)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+ int (*func_j1_k1)(struct s_moldyn *moldyn,
+ t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
+ int (*func_j1e)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+ void *pot_params;
+ unsigned char run3bp;
+
+ double cutoff; /* cutoff radius */
+ double cutoff_square; /* square of the cutoff radius */
+ double nnd; /* nearest neighbour distance (optional) */
+
+ t_linkcell lc; /* linked cell list interface */
+
+ int avg_skip; /* amount of steps without average calc */
+
+ double t_ref; /* reference temperature */
+ double t; /* actual temperature */
+ double t_sum; /* sum over all t */
+ double t_avg; /* average value of t */
+
+ t_virial gvir; /* global virial (absolute coordinates) */
+ double gv;
+ double gv_sum;
+ double gv_avg;
+
+ double gp; /* pressure computed from global virial */
+ double gp_sum; /* sum over all gp */
+ double gp_avg; /* average value of gp */
+
+ t_virial vir; /* actual virial */
+ double virial;
+ double virial_sum; /* sum over all calculated virials */
+ double virial_avg; /* average of virial */
+
+ double p_ref; /* reference pressure */
+ double p; /* actual pressure (computed by virial) */
+ double px,py,pz; /* components of pressure */
+ double p_sum; /* sum over all p */
+ double p_avg; /* average value of p */
+
+ double tp; /* thermodynamic pressure dU/dV */
+ double tp_sum; /* sum over dU/dV pressure */
+ double tp_avg; /* average value of dU/dV pressure */
+ int tp_cnt; /* how often to do thermodynamic p calc */
+
+ /* pressure and temperature control (velocity/volume scaling) */
+ /* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */
+ unsigned char pt_scale; /* type of p and t scaling */
+ double t_tc; /* t berendsen control time constant */
+ double p_tc; /* p berendsen control time constant */
+
+ /* simulation schedule */
+ t_moldyn_schedule schedule;
+ int current; /* current position in schedule */
+
+ /* integration function pointer */
+ int (*integrate)(struct s_moldyn *moldyn);
+ int time_steps; /* amount of iterations */
+ double tau; /* delta t */
+ double time; /* absolute time */
+ double tau_square; /* delta t squared */
+ int total_steps; /* total steps */
+
+ /* energy */
+ double energy; /* potential energy */
+ double ekin; /* kinetic energy */
+
+ /* energy averages & fluctuations */
+ double k_sum; /* sum of kinetic energy */
+ double v_sum; /* sum of potential energy */
+ double k_avg; /* average of kinetic energy */
+ double v_avg; /* average of potential energy */
+ double k2_sum; /* sum of kinetic energy squared */
+ double v2_sum; /* sum of potential energy squared */
+ double k2_avg; /* average of kinetic energy squared */
+ double v2_avg; /* average of potential energy squared */
+ double dk2_avg; /* mean square kinetic energy fluctuations */
+ double dv2_avg; /* mean square potential energy fluctuations */
+
+ /* response functions */
+ double c_v_nve; /* constant volume heat capacity (nve) */
+ double c_v_nvt; /* constant volume heat capacity (nvt) */
+
+ char vlsdir[128]; /* visualization/log/save directory */
+ t_visual vis; /* visualization interface structure */
+ u8 vlsprop; /* log/vis/save properties */
+ unsigned int ewrite; /* how often to log energy */
+ int efd; /* fd for energy log */
+ unsigned int mwrite; /* how often to log momentum */
+ int mfd; /* fd for momentum log */
+ unsigned int pwrite; /* how often to log pressure */
+ int pfd; /* fd for pressure log */
+ unsigned int twrite; /* how often to log temperature */
+ int tfd; /* fd for temperature log */
+ unsigned int vwrite; /* how often to log volume */
+ int vfd; /* fd for volume log */
+ unsigned int awrite; /* how often to visualize atom information */
+ unsigned int swrite; /* how often to create a save file */
+ int rfd; /* report file descriptor */
+ char rtitle[64]; /* report title */
+ char rauthor[64]; /* report author */
+ int epfd; /* energy gnuplot script file descriptor */
+ int ppfd; /* pressure gnuplot script file descriptor */
+ int tpfd; /* temperature gnuplot script file descriptor */
+
+ u8 status; /* general moldyn properties */
+
+ t_random random; /* random interface */
+
+ double debug; /* debugging stuff, ignore */
+
+ /* potential 2 body check function */
+ int (*check_2b_bond)(struct s_moldyn *moldyn,
+ t_atom *itom,t_atom *jtom,u8 bc);