src/gromacs/trajectory/trajectoryframe.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
   7  * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
   8  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   9  * and including many others, as listed in the AUTHORS file in the
  10  * top-level source directory and at http://www.gromacs.org.
  11  *
  12  * GROMACS is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU Lesser General Public License
  14  * as published by the Free Software Foundation; either version 2.1
  15  * of the License, or (at your option) any later version.
  16  *
  17  * GROMACS is distributed in the hope that it will be useful,
  18  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  19  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  20  * Lesser General Public License for more details.
  21  *
  22  * You should have received a copy of the GNU Lesser General Public
  23  * License along with GROMACS; if not, see
  24  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  25  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  26  *
  27  * If you want to redistribute modifications to GROMACS, please
  28  * consider that scientific software is very special. Version
  29  * control is crucial - bugs must be traceable. We will be happy to
  30  * consider code for inclusion in the official distribution, but
  31  * derived work must not be called official GROMACS. Details are found
  32  * in the README & COPYING files - if they are missing, get the
  33  * official version at http://www.gromacs.org.
  34  *
  35  * To help us fund GROMACS development, we humbly ask that you cite
  36  * the research papers on the package. Check out http://www.gromacs.org.
  37  */
  38
  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.
  42  */
  43 #ifndef GMX_TRAJECTORY_TRX_H
  44 #define GMX_TRAJECTORY_TRX_H
  45
  46 #include <cstdio>
  47
  48 #include <array>
  49
  50 #include "gromacs/math/vectypes.h"
  51 #include "gromacs/utility/arrayref.h"
  52 #include "gromacs/utility/basedefinitions.h"
  53 #include "gromacs/utility/real.h"
  54
  55 struct t_atoms;
  56 enum class PbcType : int;
  57
  58 typedef struct t_trxframe // NOLINT (clang-analyzer-optin.performance.Padding)
  59 {
  60     int      not_ok;  /* integrity flags                  */
  61     gmx_bool bDouble; /* Double precision?                */
  62     int      natoms;  /* number of atoms (atoms, x, v, f, index) */
  63     gmx_bool bStep;
  64     int64_t  step; /* MD step number                   */
  65     gmx_bool bTime;
  66     real     time; /* time of the frame                */
  67     gmx_bool bLambda;
  68     gmx_bool bFepState; /* does it contain fep_state?       */
  69     real     lambda;    /* free energy perturbation lambda  */
  70     int      fep_state; /* which fep state are we in? */
  71     gmx_bool bAtoms;
  72     t_atoms* atoms; /* atoms struct (natoms)            */
  73     gmx_bool bPrec;
  74     real     prec; /* precision of x, fraction of 1 nm */
  75     gmx_bool bX;
  76     rvec*    x; /* coordinates (natoms)             */
  77     gmx_bool bV;
  78     rvec*    v; /* velocities (natoms)              */
  79     gmx_bool bF;
  80     rvec*    f; /* forces (natoms)                  */
  81     gmx_bool bBox;
  82     matrix   box; /* the 3 box vectors                */
  83     gmx_bool bPBC;
  84     PbcType  pbcType; /* the type of pbc                  */
  85     gmx_bool bIndex;
  86     int*     index; /* atom indices of contained coordinates */
  87 } t_trxframe;
  88
  89 void comp_frame(FILE* fp, t_trxframe* fr1, t_trxframe* fr2, gmx_bool bRMSD, real ftol, real abstol);
  90
  91 void done_frame(t_trxframe* frame);
  92
  93 namespace gmx
  94 {
  95
  96 /*!\brief A 3x3 matrix data type useful for simulation boxes
  97  *
  98  * \todo Implement a full replacement for C-style real[DIM][DIM] */
  99 using BoxMatrix = std::array<std::array<real, DIM>, DIM>;
 100
 101 /*! \internal
 102  * \brief Contains a valid trajectory frame.
 103  *
 104  * Valid frames have a step and time, but need not have any particular
 105  * other fields.
 106  *
 107  * \todo Eventually t_trxframe should be replaced by a class such as
 108  * this. Currently we need to introduce BoxMatrix so that we can have
 109  * a normal C++ getter that returns the contents of a box matrix,
 110  * since you cannot use a real[DIM][DIM] as a function return type.
 111  *
 112  * \todo Consider a std::optional work-alike type for expressing that
 113  * a field may or may not have content. */
 114 class TrajectoryFrame
 115 {
 116 public:
 117     /*! \brief Constructor
 118      *
 119      * \throws APIError If \c frame lacks either step or time.
 120      */
 121     explicit TrajectoryFrame(const t_trxframe& frame);
 122     /*! \brief Return a string that helps users identify this frame, containing time and step number.
 123      *
 124      * \throws std::bad_alloc  when out of memory */
 125     std::string frameName() const;
 126     //! Step number read from the trajectory file frame.
 127     std::int64_t step() const;
 128     //! Time read from the trajectory file frame.
 129     double time() const;
 130     //! The PBC characteristics of the box.
 131     PbcType pbc() const;
 132     //! Get a view of position coordinates of the frame (which could be empty).
 133     ArrayRef<const RVec> x() const;
 134     //! Get a view of velocity coordinates of the frame (which could be empty).
 135     ArrayRef<const RVec> v() const;
 136     //! Get a view of force coordinates of the frame (which could be empty).
 137     ArrayRef<const RVec> f() const;
 138     //! Return whether the frame has a box.
 139     bool hasBox() const;
 140     //! Return a handle to the frame's box, which is all zero if the frame has no box.
 141     const BoxMatrix& box() const;
 142
 143 private:
 144     //! Handle to trajectory data
 145     const t_trxframe& frame_;
 146     //! Box matrix data from the frame_.
 147     BoxMatrix box_;
 148 };
 149
 150 } // namespace gmx
 151
 152 #endif