1 /* 2 * This file is part of the GROMACS molecular simulation package. 3 * 4 * Copyright (c) 2020,2021, 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 /*! \inpublicapi \file 36 * \brief 37 * Implements nblib utilities for system setup 38 * 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> 44 */ 45 46 #ifndef NBLIB_UTIL_SETUP_H 47 #define NBLIB_UTIL_SETUP_H 48 49 #include <functional> 50 #include <iostream> 51 #include <sstream> 52 #include <string> 53 #include <tuple> 54 #include <type_traits> 55 #include <vector> 56 57 #include "nblib/basicdefinitions.h" 58 #include "nblib/vector.h" 59 60 namespace gmx 61 { 62 template<typename T> 63 class ArrayRef; 64 } // namespace gmx 65 66 namespace nblib 67 { 68 69 /*! \brief Generate velocities from a Maxwell Boltzmann distribution 70 * 71 * masses should be the same as the ones specified for the Topology object 72 */ 73 std::vector<Vec3> generateVelocity(real Temperature, unsigned int seed, std::vector<real> const& masses); 74 75 //! \brief Check within the container of gmx::RVecs for a NaN or inf 76 bool isRealValued(gmx::ArrayRef<const Vec3> values); 77 78 //! \brief Zero a cartesian buffer 79 void zeroCartesianArray(gmx::ArrayRef<Vec3> cartesianArray); 80 81 } // namespace nblib 82 83 #endif // NBLIB_UTIL_SETUP_H 84