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[gromacs.git] / src / gromacs / trajectory / trajectoryframe.h
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39 /* The gmx_bools indicate whether a field was read from the trajectory.
40 * Do not try to use a pointer when its gmx_bool is FALSE, as memory might
41 * not be allocated.
43 #ifndef GMX_TRAJECTORY_TRX_H
44 #define GMX_TRAJECTORY_TRX_H
46 #include <cstdio>
48 #include <array>
50 #include "gromacs/math/vectypes.h"
51 #include "gromacs/utility/arrayref.h"
52 #include "gromacs/utility/basedefinitions.h"
53 #include "gromacs/utility/real.h"
55 struct t_atoms;
57 typedef struct t_trxframe // NOLINT (clang-analyzer-optin.performance.Padding)
59 int not_ok; /* integrity flags */
60 gmx_bool bDouble; /* Double precision? */
61 int natoms; /* number of atoms (atoms, x, v, f, index) */
62 gmx_bool bStep;
63 int64_t step; /* MD step number */
64 gmx_bool bTime;
65 real time; /* time of the frame */
66 gmx_bool bLambda;
67 gmx_bool bFepState; /* does it contain fep_state? */
68 real lambda; /* free energy perturbation lambda */
69 int fep_state; /* which fep state are we in? */
70 gmx_bool bAtoms;
71 t_atoms* atoms; /* atoms struct (natoms) */
72 gmx_bool bPrec;
73 real prec; /* precision of x, fraction of 1 nm */
74 gmx_bool bX;
75 rvec* x; /* coordinates (natoms) */
76 gmx_bool bV;
77 rvec* v; /* velocities (natoms) */
78 gmx_bool bF;
79 rvec* f; /* forces (natoms) */
80 gmx_bool bBox;
81 matrix box; /* the 3 box vectors */
82 gmx_bool bPBC;
83 int ePBC; /* the type of pbc */
84 gmx_bool bIndex;
85 int* index; /* atom indices of contained coordinates */
86 } t_trxframe;
88 void comp_frame(FILE* fp, t_trxframe* fr1, t_trxframe* fr2, gmx_bool bRMSD, real ftol, real abstol);
90 void done_frame(t_trxframe* frame);
92 namespace gmx
95 /*!\brief A 3x3 matrix data type useful for simulation boxes
97 * \todo Implement a full replacement for C-style real[DIM][DIM] */
98 using BoxMatrix = std::array<std::array<real, DIM>, DIM>;
100 /*! \internal
101 * \brief Contains a valid trajectory frame.
103 * Valid frames have a step and time, but need not have any particular
104 * other fields.
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.
111 * \todo Consider a std::optional work-alike type for expressing that
112 * a field may or may not have content. */
113 class TrajectoryFrame
115 public:
116 /*! \brief Constructor
118 * \throws APIError If \c frame lacks either step or time.
120 explicit TrajectoryFrame(const t_trxframe& frame);
121 /*! \brief Return a string that helps users identify this frame, containing time and step number.
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;
142 private:
143 //! Handle to trajectory data
144 const t_trxframe& frame_;
145 //! Box matrix data from the frame_.
146 BoxMatrix box_;
149 } // namespace gmx
151 #endif