2 * This file is part of the GROMACS molecular simulation package.
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.
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.
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.
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.
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.
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.
35 /*! \inpublicapi \file
37 * Implements nblib integrator
39 * \author Victor Holanda <victor.holanda@cscs.ch>
40 * \author Joe Jordan <ejjordan@kth.se>
41 * \author Prashanth Kanduri <kanduri@cscs.ch>
42 * \author Sebastian Keller <keller@cscs.ch>
43 * \author Artem Zhmurov <zhmurov@gmail.com>
45 #ifndef NBLIB_INTEGRATOR_H
46 #define NBLIB_INTEGRATOR_H
50 #include "nblib/box.h"
51 #include "nblib/vector.h"
64 /*! \brief Simple integrator
70 /*! \brief Constructor.
72 * \param[in] topology Topology object to build list of inverse masses.
73 * \param[in] box Box object for ensuring that coordinates remain within bounds
75 LeapFrog(const Topology& topology, const Box& box);
79 * Integrates the equation of motion using Leap-Frog algorithm.
80 * Updates coordinates and velocities.
82 * \param[in] dt Timestep.
83 * \param[out] coordinates Coordinate array that would be modified in-place.
84 * \param[out] velocities Velocity array that would be modified in-place.
85 * \param[in] forces Force array to be read.
88 void integrate(real dt,
89 gmx::ArrayRef<Vec3> coordinates,
90 gmx::ArrayRef<Vec3> velocities,
91 gmx::ArrayRef<const Vec3> forces);
94 //! 1/mass for all atoms
95 std::vector<real> inverseMasses_;
96 //! Box for PBC conformity
102 #endif // NBLIB_INTEGRATOR_H