src/gromacs/mdlib/wholemoleculetransform.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2020, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  35 /*! \libinternal \file
  36  *
  37  * \brief Declares the WholeMolecules class for generating whole molecules
  38  *
  39  * \author Berk Hess <hess@kth.se>
  40  * \ingroup module_mdlib
  41  * \inlibraryapi
  42  */
  43 #ifndef GMX_MDLIB_WHOLEMOLECULETRANSFORM_H
  44 #define GMX_MDLIB_WHOLEMOLECULETRANSFORM_H
  45
  46 #include <vector>
  47
  48 #include "gromacs/math/vectypes.h"
  49 #include "gromacs/pbcutil/mshift.h"
  50 #include "gromacs/utility/arrayref.h"
  51
  52 struct gmx_mtop_t;
  53 enum class PbcType : int;
  54
  55 namespace gmx
  56 {
  57
  58 /*! \libinternal
  59  * \brief This class manages a coordinate buffer with molecules not split
  60  * over periodic boundary conditions for use in force calculations
  61  * which require whole molecules.
  62  *
  63  * Note: This class should not be used for computation of forces which
  64  *       have virial contributions through shift forces.
  65  */
  66 class WholeMoleculeTransform
  67 {
  68 public:
  69     /*! \brief Constructor */
  70     WholeMoleculeTransform(const gmx_mtop_t& mtop, PbcType pbcType);
  71
  72     /*! \brief Updates the graph when atoms have been shifted by periodic vectors */
  73     void updateForAtomPbcJumps(ArrayRef<const RVec> x, const matrix box);
  74
  75     /*! \brief Create and return coordinates with whole molecules for input coordinates \p x
  76      *
  77      * \param[in] x  Input coordinates, should not have periodic displacement compared
  78      *               with the coordinates passed in the last call to \p updateForAtomPbcJumps().
  79      * \param[in] box  The current periodic image vectors
  80      *
  81      * Note: this operation is not free. If you need whole molecules coordinates
  82      * more than once during the force calculation, store the result and reuse it.
  83      */
  84     ArrayRef<const RVec> wholeMoleculeCoordinates(ArrayRef<const RVec> x, const matrix box);
  85
  86 private:
  87     //! The type of PBC
  88     PbcType pbcType_;
  89     //! The graph
  90     t_graph graph_;
  91     //! Buffer for storing coordinates for whole molecules
  92     std::vector<RVec> wholeMoleculeCoordinates_;
  93 };
  94
  95 } // namespace gmx
  96
  97 #endif