src/gromacs/mdlib/lincs_cuda.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2019, 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 Declaration of high-level functions of CUDA implementation of LINCS.
  38  *
  39  * \todo This should only list interfaces needed for libgromacs clients.
  40  *
  41  * \author Artem Zhmurov <zhmurov@gmail.com>
  42  *
  43  * \ingroup module_mdlib
  44  * \inlibraryapi
  45  */
  46 #ifndef GMX_MDLIB_LINCS_CUDA_H
  47 #define GMX_MDLIB_LINCS_CUDA_H
  48
  49
  50 #include "gromacs/mdlib/constr.h"
  51 #include "gromacs/mdtypes/mdatom.h"
  52 #include "gromacs/topology/idef.h"
  53 #include "gromacs/utility/classhelpers.h"
  54
  55 namespace gmx
  56 {
  57
  58 class LincsCuda
  59 {
  60
  61     public:
  62         /*! \brief Constructor.
  63          *
  64          * \param[in] numIterations    Number of iteration for the correction of the projection.
  65          * \param[in] expansionOrder   Order of the matrix inversion algorithm.
  66          */
  67         LincsCuda(int numIterations,
  68                   int expansionOrder);
  69         ~LincsCuda();
  70
  71         /*! \brief Apply LINCS to the coordinates/velocities stored in CPU memory.
  72          *
  73          * This method should not be used in any code-path, where performance is of any value.
  74          * Only suitable for test and will be removed in future patch sets.
  75          * Allocates GPU memory, copies data from CPU, applies LINCS to coordinates and,
  76          * if requested, to velocities, copies the results back, frees GPU memory.
  77          * Method uses this class data structures which should be filled with set() and setPbc()
  78          * methods.
  79          *
  80          * \todo Remove this method
  81          *
  82          * \param[in]     numAtoms          Number of atoms
  83          * \param[in]     h_x               Coordinates before timestep (in CPU memory)
  84          * \param[in,out] h_xp              Coordinates after timestep (in CPU memory). The
  85          *                                  resulting constrained coordinates will be saved here.
  86          * \param[in]     updateVelocities  If the velocities should be updated.
  87          * \param[in,out] h_v               Velocities to update (in CPU memory, can be nullptr
  88          *                                  if not updated)
  89          * \param[in]     invdt             Reciprocal timestep (to scale Lagrange
  90          *                                  multipliers when velocities are updated)
  91          * \param[in]     computeVirial     If virial should be updated.
  92          * \param[in,out] virialScaled      Scaled virial tensor to be updated.
  93          */
  94         void copyApplyCopy(int         numAtoms,
  95                            const rvec *h_x,
  96                            rvec       *h_xp,
  97                            bool        updateVelocities,
  98                            rvec       *h_v,
  99                            real        invdt,
 100                            bool        computeVirial,
 101                            tensor      virialScaled);
 102
 103         /*! \brief
 104          * Update data-structures (e.g. after NB search step).
 105          *
 106          * Updates the constraints data. Should be called if the particles were sorted,
 107          * redistributed between domains, etc.
 108          *
 109          * Information about constraints should be taken from:
 110          *     idef.il[F_CONSTR].iatoms  --- type (T) of constraint and two atom indexes (i1, i2)
 111          *     idef.iparams[T].constr.dA --- target length for constraint of type T
 112          * From t_mdatom, the code should take:
 113          *     md.invmass  --- array of inverse square root of masses for each atom in the system.
 114          *
 115          * \param[in] idef  Local topology data to get information on constraints from.
 116          * \param[in] md    Atoms data to get atom masses from.
 117          */
 118         void set(const t_idef         &idef,
 119                  const t_mdatoms      &md);
 120
 121         /*! \brief
 122          * Update PBC data.
 123          *
 124          * \param[in] pbc  The PBC data in t_pbc format.
 125          */
 126         void setPbc(const t_pbc *pbc);
 127
 128         /*! \brief Class with hardware-specific interfaces and implementations.*/
 129         class Impl;
 130
 131     private:
 132         gmx::PrivateImplPointer<Impl> impl_;
 133
 134 };
 135
 136 } // namespace gmx
 137
 138 #endif