src/gromacs/mdlib/mdatoms.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) 2010,2014,2015,2016,2017, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  37 #ifndef GMX_MDLIB_MDATOMS_H
  38 #define GMX_MDLIB_MDATOMS_H
  39
  40 #include <cstdio>
  41
  42 #include <memory>
  43 #include <vector>
  44
  45 #include "gromacs/mdtypes/mdatom.h"
  46 #include "gromacs/utility/basedefinitions.h"
  47 #include "gromacs/utility/real.h"
  48 #include "gromacs/utility/unique_cptr.h"
  49
  50 struct gmx_mtop_t;
  51 struct t_inputrec;
  52
  53 namespace gmx
  54 {
  55
  56 /*! \libinternal
  57  * \brief Contains a C-style t_mdatoms while permitting future changes
  58  * to manage some of its memory with C++ vectors with allocators.
  59  *
  60  * The group-scheme kernels need to use a plain C-style t_mdatoms, so
  61  * this type combines that with the memory management needed e.g.for
  62  * efficient PME on GPU transfers.
  63  *
  64  * \todo Refactor this class and rename MDAtoms once the group scheme
  65  * is removed. */
  66 class MDAtoms
  67 {
  68     //! C-style mdatoms struct.
  69     unique_cptr<t_mdatoms> mdatoms_;
  70     public:
  71         // TODO make this private
  72         //! Constructor.
  73         MDAtoms();
  74         //! Getter.
  75         t_mdatoms *mdatoms()
  76         {
  77             return mdatoms_.get();
  78         }
  79         //! Builder function.
  80         friend std::unique_ptr<MDAtoms>
  81         makeMDAtoms(FILE *fp, const gmx_mtop_t &mtop, const t_inputrec &ir);
  82 };
  83
  84 //! Builder function for MdAtomsWrapper.
  85 std::unique_ptr<MDAtoms>
  86 makeMDAtoms(FILE *fp, const gmx_mtop_t &mtop, const t_inputrec &ir);
  87
  88 } // namespace
  89
  90 void atoms2md(const gmx_mtop_t *mtop, const t_inputrec *ir,
  91               int nindex, const int *index,
  92               int homenr,
  93               gmx::MDAtoms *mdAtoms);
  94 /* This routine copies the atoms->atom struct into md.
  95  * If index!=NULL only the indexed atoms are copied.
  96  * For the masses the A-state (lambda=0) mass is used.
  97  * Sets md->lambda = 0.
  98  * In free-energy runs, update_mdatoms() should be called after atoms2md()
  99  * to set the masses corresponding to the value of lambda at each step.
 100  */
 101
 102 void update_mdatoms(t_mdatoms *md, real lambda);
 103 /* When necessary, sets all the mass parameters to values corresponding
 104  * to the free-energy parameter lambda.
 105  * Sets md->lambda = lambda.
 106  */
 107
 108 #endif