src/gromacs/trajectory/trajectoryframe.h

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  37
  38 /* The gmx_bools indicate whether a field was read from the trajectory.
  39  * Do not try to use a pointer when its gmx_bool is FALSE, as memory might
  40  * not be allocated.
  41  */
  42 #ifndef GMX_TRAJECTORY_TRX_H
  43 #define GMX_TRAJECTORY_TRX_H
  44
  45 #include <cstdio>
  46
  47 #include <array>
  48
  49 #include "gromacs/math/vectypes.h"
  50 #include "gromacs/utility/arrayref.h"
  51 #include "gromacs/utility/basedefinitions.h"
  52 #include "gromacs/utility/real.h"
  53
  54 struct t_atoms;
  55
  56 typedef struct t_trxframe      // NOLINT (clang-analyzer-optin.performance.Padding)
  57 {
  58     int             not_ok;    /* integrity flags                  */
  59     gmx_bool        bDouble;   /* Double precision?                */
  60     int             natoms;    /* number of atoms (atoms, x, v, f, index) */
  61     gmx_bool        bStep;
  62     int64_t         step;      /* MD step number                   */
  63     gmx_bool        bTime;
  64     real            time;      /* time of the frame                */
  65     gmx_bool        bLambda;
  66     gmx_bool        bFepState; /* does it contain fep_state?       */
  67     real            lambda;    /* free energy perturbation lambda  */
  68     int             fep_state; /* which fep state are we in? */
  69     gmx_bool        bAtoms;
  70     t_atoms        *atoms;     /* atoms struct (natoms)            */
  71     gmx_bool        bPrec;
  72     real            prec;      /* precision of x, fraction of 1 nm */
  73     gmx_bool        bX;
  74     rvec           *x;         /* coordinates (natoms)             */
  75     gmx_bool        bV;
  76     rvec           *v;         /* velocities (natoms)              */
  77     gmx_bool        bF;
  78     rvec           *f;         /* forces (natoms)                  */
  79     gmx_bool        bBox;
  80     matrix          box;       /* the 3 box vectors                */
  81     gmx_bool        bPBC;
  82     int             ePBC;      /* the type of pbc                  */
  83     gmx_bool        bIndex;
  84     int            *index;     /* atom indices of contained coordinates */
  85 } t_trxframe;
  86
  87 void comp_frame(FILE *fp, t_trxframe *fr1, t_trxframe *fr2,
  88                 gmx_bool bRMSD, real ftol, real abstol);
  89
  90 void done_frame(t_trxframe *frame);
  91
  92 namespace gmx
  93 {
  94
  95 /*!\brief A 3x3 matrix data type useful for simulation boxes
  96  *
  97  * \todo Implement a full replacement for C-style real[DIM][DIM] */
  98 using BoxMatrix = std::array <std::array<real, DIM>, DIM>;
  99
 100 /*! \internal
 101  * \brief Contains a valid trajectory frame.
 102  *
 103  * Valid frames have a step and time, but need not have any particular
 104  * other fields.
 105  *
 106  * \todo Eventually t_trxframe should be replaced by a class such as
 107  * this. Currently we need to introduce BoxMatrix so that we can have
 108  * a normal C++ getter that returns the contents of a box matrix,
 109  * since you cannot use a real[DIM][DIM] as a function return type.
 110  *
 111  * \todo Consider a std::optional work-alike type for expressing that
 112  * a field may or may not have content. */
 113 class TrajectoryFrame
 114 {
 115     public:
 116         /*! \brief Constructor
 117          *
 118          * \throws APIError If \c frame lacks either step or time.
 119          */
 120         explicit TrajectoryFrame(const t_trxframe &frame);
 121         /*! \brief Return a string that helps users identify this frame, containing time and step number.
 122          *
 123          * \throws std::bad_alloc  when out of memory */
 124         std::string frameName() const;
 125         //! Step number read from the trajectory file frame.
 126         std::int64_t step() const;
 127         //! Time read from the trajectory file frame.
 128         double time() const;
 129         //! The PBC characteristics of the box.
 130         int pbc() const;
 131         //! Get a view of position coordinates of the frame (which could be empty).
 132         ArrayRef<const RVec> x() const;
 133         //! Get a view of velocity coordinates of the frame (which could be empty).
 134         ArrayRef<const RVec> v() const;
 135         //! Get a view of force coordinates of the frame (which could be empty).
 136         ArrayRef<const RVec> f() const;
 137         //! Return whether the frame has a box.
 138         bool hasBox() const;
 139         //! Return a handle to the frame's box, which is all zero if the frame has no box.
 140         const BoxMatrix &box() const;
 141     private:
 142         //! Handle to trajectory data
 143         const t_trxframe &frame_;
 144         //! Box matrix data from the frame_.
 145         BoxMatrix         box_;
 146 };
 147
 148 } // namespace gmx
 149
 150 #endif