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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
43 #ifndef GMX_TRAJECTORY_TRX_H
44 #define GMX_TRAJECTORY_TRX_H
50 #include "gromacs/math/vectypes.h"
51 #include "gromacs/utility/arrayref.h"
52 #include "gromacs/utility/basedefinitions.h"
53 #include "gromacs/utility/real.h"
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) */
63 int64_t step
; /* MD step number */
65 real time
; /* time of the frame */
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? */
71 t_atoms
* atoms
; /* atoms struct (natoms) */
73 real prec
; /* precision of x, fraction of 1 nm */
75 rvec
* x
; /* coordinates (natoms) */
77 rvec
* v
; /* velocities (natoms) */
79 rvec
* f
; /* forces (natoms) */
81 matrix box
; /* the 3 box vectors */
83 int ePBC
; /* the type of pbc */
85 int* index
; /* atom indices of contained coordinates */
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
);
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
>;
101 * \brief Contains a valid trajectory frame.
103 * Valid frames have a step and time, but need not have any particular
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
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.
129 //! The PBC characteristics of the box.
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.
139 //! Return a handle to the frame's box, which is all zero if the frame has no box.
140 const BoxMatrix
& box() const;
143 //! Handle to trajectory data
144 const t_trxframe
& frame_
;
145 //! Box matrix data from the frame_.