Serial md code

/* system.h - defines the system_t type and its mpi type */
#ifndef SYSTEMH
#define SYSTEMH
#include <stddef.h>
#include <stdbool.h>

typedef struct system_t {
    long long Ntot;      /* number of particles in the full domain (parameter) */
    double    rho;       /* density of the system (parameter)*/
    double    T0;        /* initial temperature (parameter) */
    double    runtime;   /* how long to run (parameter) */
    double    dt;        /* duration of single time step (parameter) */
    long      seed;      /* global random seed (parameter) */
    double    equil;     /* when to start measuring energies etc. (parameter)*/
    bool      usecells;  /* 1 if cells are to be used (parameter) */
    double    L;         /* length of the box (derived parameter) */
    int       N;         /* number of particles in the subdomain*/
    double    K;         /* kinetic energy in the subdomain*/
    double    U;         /* potential energy in the subdomain */
    /* for cell structure: */
    int       totnc[3];  /* total number of cells in the whole system */
    int       nc[3];     /* number of cells in the subdomain in each direction */
    int       ncprod;    /* product of nc[3], i.e., total number of cells in this subdomain */
    int       minc[3];   /* first cell index in 3 dimensions in the subdomain */
    int       maxc[3];   /* last cell index in 3 dimensions in the subdomain */
    double    cellsize[3]; /* size of the cells in each direction */
    int*      start_of_cell; /* position in atom[] of the first particles in each cell (1d using a super index) */
    int*      n_in_cell; /* number of particles in each cell (1d using a super index) (i.e., subsequent n_in_cell-1 particles are also in that cell */
} system_t;

bool sanity_check(system_t* sys, double rc, bool verbose);

#endif