From: Paul Bauer Date: Tue, 7 Jan 2020 10:01:22 +0000 (+0100) Subject: Merge commit d30f2cb6 from release-2020 into master X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=343c908495c27277ba46f21b66c26da8fe7e808a;p=alexxy%2Fgromacs.git Merge commit d30f2cb6 from release-2020 into master Merging the release-2020 branch in stages to allow update to TPR format to be cherry-picked in. Change-Id: I36c0861d0cb6f17a3f4ff739fa868867844f2944 --- 343c908495c27277ba46f21b66c26da8fe7e808a diff --cc admin/copyright.py index 0b349861cc,8d57385a11..7b817430ef --- a/admin/copyright.py +++ b/admin/copyright.py @@@ -2,7 -2,7 +2,7 @@@ # # This file is part of the GROMACS molecular simulation package. # --# Copyright (c) 2013,2014,2015,2016,2018,2019, by the GROMACS development team, led by ++# Copyright (c) 2013,2014,2015,2016,2018,2019,2020, by the GROMACS development team, led by # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # and including many others, as listed in the AUTHORS file in the # top-level source directory and at http://www.gromacs.org. diff --cc cmake/gmxCPackUtilities.cmake index 5a5c267c41,3a788950fa..11e1bac0bb --- a/cmake/gmxCPackUtilities.cmake +++ b/cmake/gmxCPackUtilities.cmake @@@ -1,7 -1,7 +1,7 @@@ # # This file is part of the GROMACS molecular simulation package. # - # Copyright (c) 2014,2015,2016,2017,2018, by the GROMACS development team, led by -# Copyright (c) 2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by ++# Copyright (c) 2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # and including many others, as listed in the AUTHORS file in the # top-level source directory and at http://www.gromacs.org. diff --cc cmake/gmxVersionInfo.cmake index 880363dba7,6c7925b0e8..42f59adeab --- a/cmake/gmxVersionInfo.cmake +++ b/cmake/gmxVersionInfo.cmake @@@ -1,7 -1,7 +1,7 @@@ # # This file is part of the GROMACS molecular simulation package. # --# Copyright (c) 2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by ++# Copyright (c) 2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # and including many others, as listed in the AUTHORS file in the # top-level source directory and at http://www.gromacs.org. diff --cc docs/CMakeLists.txt index 568c798c46,32636d3dd1..99310f3417 --- a/docs/CMakeLists.txt +++ b/docs/CMakeLists.txt @@@ -1,7 -1,7 +1,7 @@@ # # This file is part of the GROMACS molecular simulation package. # --# Copyright (c) 2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by ++# Copyright (c) 2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # and including many others, as listed in the AUTHORS file in the # top-level source directory and at http://www.gromacs.org. diff --cc docs/conf.py index 8a50bd1f91,929a34c051..1dd0bb1b2e --- a/docs/conf.py +++ b/docs/conf.py @@@ -1,7 -1,7 +1,7 @@@ # # This file is part of the GROMACS molecular simulation package. # --# Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by ++# Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # and including many others, as listed in the AUTHORS file in the # top-level source directory and at http://www.gromacs.org. diff --cc python_packaging/documentation/conf.py index 4f93335501,860b6c58af..3fdaf484bb --- a/python_packaging/documentation/conf.py +++ b/python_packaging/documentation/conf.py @@@ -1,3 -1,37 +1,37 @@@ + # + # This file is part of the GROMACS molecular simulation package. + # -# Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by ++# Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by + # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, + # and including many others, as listed in the AUTHORS file in the + # top-level source directory and at http://www.gromacs.org. + # + # GROMACS is free software; you can redistribute it and/or + # modify it under the terms of the GNU Lesser General Public License + # as published by the Free Software Foundation; either version 2.1 + # of the License, or (at your option) any later version. + # + # GROMACS is distributed in the hope that it will be useful, + # but WITHOUT ANY WARRANTY; without even the implied warranty of + # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + # Lesser General Public License for more details. + # + # You should have received a copy of the GNU Lesser General Public + # License along with GROMACS; if not, see + # http://www.gnu.org/licenses, or write to the Free Software Foundation, + # Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + # + # If you want to redistribute modifications to GROMACS, please + # consider that scientific software is very special. Version + # control is crucial - bugs must be traceable. We will be happy to + # consider code for inclusion in the official distribution, but + # derived work must not be called official GROMACS. Details are found + # in the README & COPYING files - if they are missing, get the + # official version at http://www.gromacs.org. + # + # To help us fund GROMACS development, we humbly ask that you cite + # the research papers on the package. Check out http://www.gromacs.org. + # Configuration file for the Sphinx documentation builder. # # This file only contains a selection of the most common options. For a full diff --cc python_packaging/src/gmxapi/_logging.py index 3c24083cc3,890f225d22..2304e5a4b0 --- a/python_packaging/src/gmxapi/_logging.py +++ b/python_packaging/src/gmxapi/_logging.py @@@ -1,7 -1,7 +1,7 @@@ # # This file is part of the GROMACS molecular simulation package. # --# Copyright (c) 2019, by the GROMACS development team, led by ++# Copyright (c) 2019,2020, by the GROMACS development team, led by # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # and including many others, as listed in the AUTHORS file in the # top-level source directory and at http://www.gromacs.org. diff --cc python_packaging/src/gmxapi/commandline.py index 11b2e1fa5f,b881e67b7f..378de8c6d6 --- a/python_packaging/src/gmxapi/commandline.py +++ b/python_packaging/src/gmxapi/commandline.py @@@ -1,7 -1,7 +1,7 @@@ # # This file is part of the GROMACS molecular simulation package. # --# Copyright (c) 2019, by the GROMACS development team, led by ++# Copyright (c) 2019,2020, by the GROMACS development team, led by # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # and including many others, as listed in the AUTHORS file in the # top-level source directory and at http://www.gromacs.org. @@@ -31,6 -31,6 +31,7 @@@ # # To help us fund GROMACS development, we humbly ask that you cite # the research papers on the package. Check out http://www.gromacs.org. ++ """ Provide command line operation. """ diff --cc python_packaging/src/gmxapi/datamodel.py index 96a94d1d8a,ee308f90b8..c9af75092c --- a/python_packaging/src/gmxapi/datamodel.py +++ b/python_packaging/src/gmxapi/datamodel.py @@@ -1,7 -1,7 +1,7 @@@ # # This file is part of the GROMACS molecular simulation package. # --# Copyright (c) 2019, by the GROMACS development team, led by ++# Copyright (c) 2019,2020, by the GROMACS development team, led by # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # and including many others, as listed in the AUTHORS file in the # top-level source directory and at http://www.gromacs.org. diff --cc python_packaging/src/gmxapi/export_tprfile.cpp index 58e48728fe,6be962bfaa..85387acd87 --- a/python_packaging/src/gmxapi/export_tprfile.cpp +++ b/python_packaging/src/gmxapi/export_tprfile.cpp @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2019, by the GROMACS development team, led by ++ * Copyright (c) 2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc python_packaging/src/gmxapi/operation.py index 9468136e20,4ed554bf02..5e36d9ff1a --- a/python_packaging/src/gmxapi/operation.py +++ b/python_packaging/src/gmxapi/operation.py @@@ -1,7 -1,7 +1,7 @@@ # # This file is part of the GROMACS molecular simulation package. # --# Copyright (c) 2019, by the GROMACS development team, led by ++# Copyright (c) 2019,2020, by the GROMACS development team, led by # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # and including many others, as listed in the AUTHORS file in the # top-level source directory and at http://www.gromacs.org. diff --cc python_packaging/src/gmxapi/version.py index f4161966c6,5a4e929b66..f08e8a9ee2 --- a/python_packaging/src/gmxapi/version.py +++ b/python_packaging/src/gmxapi/version.py @@@ -1,7 -1,7 +1,7 @@@ # # This file is part of the GROMACS molecular simulation package. # --# Copyright (c) 2019, by the GROMACS development team, led by ++# Copyright (c) 2019,2020, by the GROMACS development team, led by # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # and including many others, as listed in the AUTHORS file in the # top-level source directory and at http://www.gromacs.org. diff --cc python_packaging/src/setup.py index 9ea6464095,c4a2c48748..d906933e1b --- a/python_packaging/src/setup.py +++ b/python_packaging/src/setup.py @@@ -1,7 -1,7 +1,7 @@@ # # This file is part of the GROMACS molecular simulation package. # --# Copyright (c) 2019, by the GROMACS development team, led by ++# Copyright (c) 2019,2020, by the GROMACS development team, led by # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # and including many others, as listed in the AUTHORS file in the # top-level source directory and at http://www.gromacs.org. diff --cc src/api/CMakeLists.txt index c3b3f3ba51,124b8dbc9d..8b824e0461 --- a/src/api/CMakeLists.txt +++ b/src/api/CMakeLists.txt @@@ -1,7 -1,7 +1,7 @@@ # # This file is part of the GROMACS molecular simulation package. # --# Copyright (c) 2018,2019, by the GROMACS development team, led by ++# Copyright (c) 2018,2019,2020, by the GROMACS development team, led by # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # and including many others, as listed in the AUTHORS file in the # top-level source directory and at http://www.gromacs.org. diff --cc src/api/cpp/CMakeLists.txt index 273d8382b8,f22edbbbe8..1f6e172060 --- a/src/api/cpp/CMakeLists.txt +++ b/src/api/cpp/CMakeLists.txt @@@ -1,7 -1,7 +1,7 @@@ # # This file is part of the GROMACS molecular simulation package. # --# Copyright (c) 2018,2019, by the GROMACS development team, led by ++# Copyright (c) 2018,2019,2020, by the GROMACS development team, led by # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # and including many others, as listed in the AUTHORS file in the # top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/applied_forces/densityfittingforceprovider.cpp index 106831562d,535b418a61..57f9e5a6a9 --- a/src/gromacs/applied_forces/densityfittingforceprovider.cpp +++ b/src/gromacs/applied_forces/densityfittingforceprovider.cpp @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2019, by the GROMACS development team, led by ++ * Copyright (c) 2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/domdec/domdec.cpp index 3f93013309,de3fc3c4b3..3e8a3d87c9 --- a/src/gromacs/domdec/domdec.cpp +++ b/src/gromacs/domdec/domdec.cpp @@@ -2,7 -2,7 +2,7 @@@ * This file is part of the GROMACS molecular simulation package. * * Copyright (c) 2005,2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, by the. -- * Copyright (c) 2019, by the GROMACS development team, led by ++ * Copyright (c) 2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/domdec/domdec.h index 78c321d624,9fb46bc060..cf91516868 --- a/src/gromacs/domdec/domdec.h +++ b/src/gromacs/domdec/domdec.h @@@ -2,7 -2,7 +2,7 @@@ * This file is part of the GROMACS molecular simulation package. * * Copyright (c) 2005 - 2014, The GROMACS development team. -- * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/ewald/pme_load_balancing.cpp index 98d0d9e2fc,e0431a76cd..19eca520de --- a/src/gromacs/ewald/pme_load_balancing.cpp +++ b/src/gromacs/ewald/pme_load_balancing.cpp @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2012-2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/ewald/pme_load_balancing.h index 929188917a,1e6682d46c..b163d349ec --- a/src/gromacs/ewald/pme_load_balancing.h +++ b/src/gromacs/ewald/pme_load_balancing.h @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2012-2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/ewald/pme_only.cpp index a4ec150656,4e66664ae2..6c8077bbab --- a/src/gromacs/ewald/pme_only.cpp +++ b/src/gromacs/ewald/pme_only.cpp @@@ -3,7 -3,7 +3,7 @@@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. -- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/ewald/tests/pmetestcommon.cpp index a57195d1f6,fc68e96f41..57bed345c4 --- a/src/gromacs/ewald/tests/pmetestcommon.cpp +++ b/src/gromacs/ewald/tests/pmetestcommon.cpp @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/fileio/pdbio.cpp index 3466d8d4f1,f431614cc8..c842577de6 --- a/src/gromacs/fileio/pdbio.cpp +++ b/src/gromacs/fileio/pdbio.cpp @@@ -3,7 -3,7 +3,7 @@@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. -- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/gmxana/anadih.cpp index b76f99dc1a,bfe16bede1..2731d4a11d --- a/src/gromacs/gmxana/anadih.cpp +++ b/src/gromacs/gmxana/anadih.cpp @@@ -3,7 -3,7 +3,7 @@@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. -- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/gmxana/angle_correction.cpp index 0000000000,3ee9a99542..3bf1507dd7 mode 000000,100644..100644 --- a/src/gromacs/gmxana/angle_correction.cpp +++ b/src/gromacs/gmxana/angle_correction.cpp @@@ -1,0 -1,56 +1,56 @@@ + /* + * This file is part of the GROMACS molecular simulation package. + * - * Copyright (c) 2019, by the GROMACS development team, led by ++ * Copyright (c) 2019,2020, by the GROMACS development team, led by + * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, + * and including many others, as listed in the AUTHORS file in the + * top-level source directory and at http://www.gromacs.org. + * + * GROMACS is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * GROMACS is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with GROMACS; if not, see + * http://www.gnu.org/licenses, or write to the Free Software Foundation, + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + * + * If you want to redistribute modifications to GROMACS, please + * consider that scientific software is very special. Version + * control is crucial - bugs must be traceable. We will be happy to + * consider code for inclusion in the official distribution, but + * derived work must not be called official GROMACS. Details are found + * in the README & COPYING files - if they are missing, get the + * official version at http://www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the research papers on the package. Check out http://www.gromacs.org. + */ + #include "gmxpre.h" + + #include "angle_correction.h" + + #include + + #include "gromacs/math/units.h" + #include "gromacs/math/vec.h" + + real correctRadianAngleRange(const real angle) + { + real correctedAngle = angle; + while (correctedAngle < -M_PI) + { + correctedAngle += 2 * M_PI; + } + while (correctedAngle >= M_PI) + { + correctedAngle -= 2 * M_PI; + } + return correctedAngle; + } diff --cc src/gromacs/gmxana/angle_correction.h index 0000000000,5c68c4df4e..52ab32a3be mode 000000,100644..100644 --- a/src/gromacs/gmxana/angle_correction.h +++ b/src/gromacs/gmxana/angle_correction.h @@@ -1,0 -1,48 +1,48 @@@ + /* + * This file is part of the GROMACS molecular simulation package. + * - * Copyright (c) 2019, by the GROMACS development team, led by ++ * Copyright (c) 2019,2020, by the GROMACS development team, led by + * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, + * and including many others, as listed in the AUTHORS file in the + * top-level source directory and at http://www.gromacs.org. + * + * GROMACS is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * GROMACS is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with GROMACS; if not, see + * http://www.gnu.org/licenses, or write to the Free Software Foundation, + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + * + * If you want to redistribute modifications to GROMACS, please + * consider that scientific software is very special. Version + * control is crucial - bugs must be traceable. We will be happy to + * consider code for inclusion in the official distribution, but + * derived work must not be called official GROMACS. Details are found + * in the README & COPYING files - if they are missing, get the + * official version at http://www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the research papers on the package. Check out http://www.gromacs.org. + */ + #ifndef GMX_GMXANA_ANGLE_CORRECTION_H + #define GMX_GMXANA_ANGLE_CORRECTION_H + + #include "gromacs/math/units.h" + + /*! \brief + * Return the angle in radians after correcting to be within range of -PI < \p angle < PI. + * + * \param[in] angle The angle in radians. + * \returns Angle within range. + */ + real correctRadianAngleRange(real angle); + + #endif diff --cc src/gromacs/gmxana/cmat.cpp index cde327414c,07368d9d41..96f20a86da --- a/src/gromacs/gmxana/cmat.cpp +++ b/src/gromacs/gmxana/cmat.cpp @@@ -3,7 -3,7 +3,7 @@@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. -- * Copyright (c) 2013,2014,2015,2017,2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2013,2014,2015,2017,2018,2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/gmxana/gmx_angle.cpp index 0a92c634d8,e99bee5628..5b6246a96c --- a/src/gromacs/gmxana/gmx_angle.cpp +++ b/src/gromacs/gmxana/gmx_angle.cpp @@@ -3,7 -3,7 +3,7 @@@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. -- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/gmxpreprocess/readir.cpp index d6dbbe240c,8ad44f5300..9a5e6908ed --- a/src/gromacs/gmxpreprocess/readir.cpp +++ b/src/gromacs/gmxpreprocess/readir.cpp @@@ -3,7 -3,7 +3,7 @@@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. -- * Copyright (c) 2013-2019, by the GROMACS development team, led by ++ * Copyright (c) 2013-2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/mdlib/energyoutput.cpp index bb71c96b0f,f2532f3dfe..c692c03f87 --- a/src/gromacs/mdlib/energyoutput.cpp +++ b/src/gromacs/mdlib/energyoutput.cpp @@@ -3,7 -3,7 +3,7 @@@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. -- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/mdlib/energyoutput.h index f8cc196d5e,070b7eeb23..898093092a --- a/src/gromacs/mdlib/energyoutput.h +++ b/src/gromacs/mdlib/energyoutput.h @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2019, by the GROMACS development team, led by ++ * Copyright (c) 2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/mdlib/forcerec.cpp index 9440cf8f08,c8a42aac58..adfb6caf09 --- a/src/gromacs/mdlib/forcerec.cpp +++ b/src/gromacs/mdlib/forcerec.cpp @@@ -3,7 -3,7 +3,7 @@@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. -- * Copyright (c) 2013-2019, by the GROMACS development team, led by ++ * Copyright (c) 2013-2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/mdlib/sim_util.cpp index 8e0541bc86,c8d3cbb713..938e774d5d --- a/src/gromacs/mdlib/sim_util.cpp +++ b/src/gromacs/mdlib/sim_util.cpp @@@ -3,7 -3,7 +3,7 @@@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. -- * Copyright (c) 2013-2019, by the GROMACS development team, led by ++ * Copyright (c) 2013-2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/mdlib/tests/energyoutput.cpp index 32f3993dd9,dae2602959..06f2bf7328 --- a/src/gromacs/mdlib/tests/energyoutput.cpp +++ b/src/gromacs/mdlib/tests/energyoutput.cpp @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/mdlib/trajectory_writing.cpp index dc2cc747fc,e06b416a0a..9cca0c87f1 --- a/src/gromacs/mdlib/trajectory_writing.cpp +++ b/src/gromacs/mdlib/trajectory_writing.cpp @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/mdrun/md.cpp index 4f163faf86,8505f8649d..99421cbd9a --- a/src/gromacs/mdrun/md.cpp +++ b/src/gromacs/mdrun/md.cpp @@@ -3,7 -3,7 +3,7 @@@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. -- * Copyright (c) 2011-2019, by the GROMACS development team, led by ++ * Copyright (c) 2011-2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/mdrun/mimic.cpp index a86999fb3d,65e08ed342..6c2e4e7ba5 --- a/src/gromacs/mdrun/mimic.cpp +++ b/src/gromacs/mdrun/mimic.cpp @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/mdrun/minimize.cpp index cab90eb55d,e20b7e88b0..8afbb528fb --- a/src/gromacs/mdrun/minimize.cpp +++ b/src/gromacs/mdrun/minimize.cpp @@@ -3,7 -3,7 +3,7 @@@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. -- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/mdrun/rerun.cpp index 4ef73be2c0,c75be98e38..bbf7655135 --- a/src/gromacs/mdrun/rerun.cpp +++ b/src/gromacs/mdrun/rerun.cpp @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/mdrun/runner.cpp index b0ee231788,f5b9cb1b7a..95a95f5c24 --- a/src/gromacs/mdrun/runner.cpp +++ b/src/gromacs/mdrun/runner.cpp @@@ -3,7 -3,7 +3,7 @@@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. -- * Copyright (c) 2011-2019, by the GROMACS development team, led by ++ * Copyright (c) 2011-2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/mdtypes/commrec.h index 47973cd7ee,72291ff816..524b76395f --- a/src/gromacs/mdtypes/commrec.h +++ b/src/gromacs/mdtypes/commrec.h @@@ -3,7 -3,7 +3,7 @@@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. -- * Copyright (c) 2013,2014,2015,2017,2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2013,2014,2015,2017,2018,2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/mdtypes/state_propagator_data_gpu.h index c6ae19c589,697f9d2c86..44cbc8d7e5 --- a/src/gromacs/mdtypes/state_propagator_data_gpu.h +++ b/src/gromacs/mdtypes/state_propagator_data_gpu.h @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2019, by the GROMACS development team, led by ++ * Copyright (c) 2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp index 9b201b9376,1e2eadaff4..ae6bcd6c71 --- a/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp +++ b/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2019, by the GROMACS development team, led by ++ * Copyright (c) 2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/mdtypes/state_propagator_data_gpu_impl.h index af073b6284,9ac9711d29..1423277722 --- a/src/gromacs/mdtypes/state_propagator_data_gpu_impl.h +++ b/src/gromacs/mdtypes/state_propagator_data_gpu_impl.h @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2019, by the GROMACS development team, led by ++ * Copyright (c) 2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/mdtypes/state_propagator_data_gpu_impl_gpu.cpp index 9d674afd8f,29821a4313..031327e80d --- a/src/gromacs/mdtypes/state_propagator_data_gpu_impl_gpu.cpp +++ b/src/gromacs/mdtypes/state_propagator_data_gpu_impl_gpu.cpp @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2019, by the GROMACS development team, led by ++ * Copyright (c) 2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@@ -243,15 -255,12 +255,16 @@@ void StatePropagatorDataGpu::Impl::copy AtomLocality atomLocality, CommandStream commandStream) { - GMX_UNUSED_VALUE(dataSize); + GMX_ASSERT(atomLocality < AtomLocality::Count, "Wrong atom locality."); + GMX_ASSERT(dataSize >= 0, "Trying to copy to device buffer before it was allocated."); + GMX_ASSERT(commandStream != nullptr, + "No stream is valid for copying with given atom locality."); + wallcycle_start_nocount(wcycle_, ewcLAUNCH_GPU); + wallcycle_sub_start(wcycle_, ewcsLAUNCH_STATE_PROPAGATOR_DATA); int atomsStartAt, numAtomsToCopy; std::tie(atomsStartAt, numAtomsToCopy) = getAtomRangesFromAtomLocality(atomLocality); @@@ -277,15 -289,12 +293,16 @@@ void StatePropagatorDataGpu::Impl::copy AtomLocality atomLocality, CommandStream commandStream) { - GMX_UNUSED_VALUE(dataSize); + GMX_ASSERT(atomLocality < AtomLocality::Count, "Wrong atom locality."); + GMX_ASSERT(dataSize >= 0, "Trying to copy from device buffer before it was allocated."); + GMX_ASSERT(commandStream != nullptr, + "No stream is valid for copying with given atom locality."); + wallcycle_start_nocount(wcycle_, ewcLAUNCH_GPU); + wallcycle_sub_start(wcycle_, ewcsLAUNCH_STATE_PROPAGATOR_DATA); int atomsStartAt, numAtomsToCopy; std::tie(atomsStartAt, numAtomsToCopy) = getAtomRangesFromAtomLocality(atomLocality); @@@ -321,8 -341,11 +349,11 @@@ void StatePropagatorDataGpu::Impl::copy // TODO: remove this by adding an event-mark free flavor of this function if (GMX_GPU == GMX_GPU_CUDA) { - xReadyOnDevice_[atomLocality].markEvent(commandStream); + xReadyOnDevice_[atomLocality].markEvent(xCopyStreams_[atomLocality]); } + + wallcycle_sub_stop(wcycle_, ewcsLAUNCH_STATE_PROPAGATOR_DATA); + wallcycle_stop(wcycle_, ewcLAUNCH_GPU); } GpuEventSynchronizer* diff --cc src/gromacs/modularsimulator/computeglobalselement.cpp index e902776573,7e8a8199c3..bf6935b20c --- a/src/gromacs/modularsimulator/computeglobalselement.cpp +++ b/src/gromacs/modularsimulator/computeglobalselement.cpp @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2019, by the GROMACS development team, led by ++ * Copyright (c) 2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/modularsimulator/energyelement.cpp index faa84fdc9c,dc8fc3e493..7ae50a6116 --- a/src/gromacs/modularsimulator/energyelement.cpp +++ b/src/gromacs/modularsimulator/energyelement.cpp @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2019, by the GROMACS development team, led by ++ * Copyright (c) 2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/modularsimulator/modularsimulator.cpp index 72c6dfa76b,c785f5d3dd..b116f29b2c --- a/src/gromacs/modularsimulator/modularsimulator.cpp +++ b/src/gromacs/modularsimulator/modularsimulator.cpp @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2019, by the GROMACS development team, led by ++ * Copyright (c) 2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/modularsimulator/modularsimulatorinterfaces.h index a93b2070fb,6d4986d2dd..de1e152718 --- a/src/gromacs/modularsimulator/modularsimulatorinterfaces.h +++ b/src/gromacs/modularsimulator/modularsimulatorinterfaces.h @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2019, by the GROMACS development team, led by ++ * Copyright (c) 2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/modularsimulator/pmeloadbalancehelper.cpp index 718fc2ccbf,54df4768d7..11f9212f7c --- a/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp +++ b/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2019, by the GROMACS development team, led by ++ * Copyright (c) 2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/modularsimulator/statepropagatordata.cpp index c59f6d1e8b,17b8eb47cb..c0ed27be68 --- a/src/gromacs/modularsimulator/statepropagatordata.cpp +++ b/src/gromacs/modularsimulator/statepropagatordata.cpp @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2019, by the GROMACS development team, led by ++ * Copyright (c) 2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/modularsimulator/statepropagatordata.h index eed831f0e7,d6a7fac8d3..71a3d269f3 --- a/src/gromacs/modularsimulator/statepropagatordata.h +++ b/src/gromacs/modularsimulator/statepropagatordata.h @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2019, by the GROMACS development team, led by ++ * Copyright (c) 2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/nbnxm/cuda/nbnxm_buffer_ops_kernels.cuh index a535842e7e,53bd7541ef..efb713c093 --- a/src/gromacs/nbnxm/cuda/nbnxm_buffer_ops_kernels.cuh +++ b/src/gromacs/nbnxm/cuda/nbnxm_buffer_ops_kernels.cuh @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/nbnxm/cuda/nbnxm_cuda.cu index 04d0dfd383,acf3717d8e..2bec5d520b --- a/src/gromacs/nbnxm/cuda/nbnxm_cuda.cu +++ b/src/gromacs/nbnxm/cuda/nbnxm_cuda.cu @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2012-2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/pulling/pull.cpp index c20deec924,a93cda1ea6..b70211fbcd --- a/src/gromacs/pulling/pull.cpp +++ b/src/gromacs/pulling/pull.cpp @@@ -3,7 -3,7 +3,7 @@@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. -- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/pulling/pull.h index 20b8bf1d4c,de6ec28f5a..c9e304e19b --- a/src/gromacs/pulling/pull.h +++ b/src/gromacs/pulling/pull.h @@@ -3,7 -3,7 +3,7 @@@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. -- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/taskassignment/decidegpuusage.cpp index a83b2b82e0,9b069fd890..bfd43291b2 --- a/src/gromacs/taskassignment/decidegpuusage.cpp +++ b/src/gromacs/taskassignment/decidegpuusage.cpp @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/taskassignment/decidegpuusage.h index 08ff410b40,45ba2d333f..573cac02cf --- a/src/gromacs/taskassignment/decidegpuusage.h +++ b/src/gromacs/taskassignment/decidegpuusage.h @@@ -1,7 -1,7 +1,7 @@@ /* * This file is part of the GROMACS molecular simulation package. * -- * Copyright (c) 2017,2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/timing/wallcycle.cpp index 59a55b8bd1,638b8dc475..9c5ff6e63a --- a/src/gromacs/timing/wallcycle.cpp +++ b/src/gromacs/timing/wallcycle.cpp @@@ -3,7 -3,7 +3,7 @@@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2008, The GROMACS development team. -- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/gromacs/timing/wallcycle.h index fa65919c60,c2d5bc8bf5..85bd5b59d5 --- a/src/gromacs/timing/wallcycle.h +++ b/src/gromacs/timing/wallcycle.h @@@ -3,7 -3,7 +3,7 @@@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2008, The GROMACS development team. -- * Copyright (c) 2013,2014,2015,2017,2018,2019, by the GROMACS development team, led by ++ * Copyright (c) 2013,2014,2015,2017,2018,2019,2020, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. diff --cc src/programs/mdrun/tests/CMakeLists.txt index e5869b594c,c6bda33065..beb86b9b3a --- a/src/programs/mdrun/tests/CMakeLists.txt +++ b/src/programs/mdrun/tests/CMakeLists.txt @@@ -1,7 -1,7 +1,7 @@@ # # This file is part of the GROMACS molecular simulation package. # --# Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by ++# Copyright (c) 2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # and including many others, as listed in the AUTHORS file in the # top-level source directory and at http://www.gromacs.org. diff --cc src/programs/mdrun/tests/outputfiles.cpp index 0000000000,5b0db0bfe0..9414b16c9f mode 000000,100644..100644 --- a/src/programs/mdrun/tests/outputfiles.cpp +++ b/src/programs/mdrun/tests/outputfiles.cpp @@@ -1,0 -1,118 +1,118 @@@ + /* + * This file is part of the GROMACS molecular simulation package. + * - * Copyright (c) 2019, by the GROMACS development team, led by ++ * Copyright (c) 2019,2020, by the GROMACS development team, led by + * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, + * and including many others, as listed in the AUTHORS file in the + * top-level source directory and at http://www.gromacs.org. + * + * GROMACS is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * GROMACS is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with GROMACS; if not, see + * http://www.gnu.org/licenses, or write to the Free Software Foundation, + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + * + * If you want to redistribute modifications to GROMACS, please + * consider that scientific software is very special. Version + * control is crucial - bugs must be traceable. We will be happy to + * consider code for inclusion in the official distribution, but + * derived work must not be called official GROMACS. Details are found + * in the README & COPYING files - if they are missing, get the + * official version at http://www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the research papers on the package. Check out http://www.gromacs.org. + */ + + /*! \internal \file + * \brief + * Checks that expected output files are present + * + * \author Pascal Merz + * \ingroup module_mdrun_integration_tests + */ + + #include "gmxpre.h" + + #include "gromacs/utility/path.h" + #include "gromacs/utility/stringutil.h" + + #include "testutils/simulationdatabase.h" + + #include "moduletest.h" + + namespace gmx + { + namespace test + { + namespace + { + + /*! \brief Test fixture base for presence of output files + * + * This test checks that some expected output files are actually written + * in a very simple mdrun call. Currently, it tests for the presence of + * full precision trajectory (.trr), log file (.log), energy trajectory (.edr), + * final configuration (.gro) and checkpoint file (.cpt). + * + * The test only checks whether the files are existing, it does not check + * their contents. + */ + using OutputFilesTestParams = std::tuple; + class OutputFiles : public MdrunTestFixture, public ::testing::WithParamInterface + { + }; + + TEST_P(OutputFiles, FilesArePresent) + { + auto params = GetParam(); + auto simulationName = std::get<0>(params); + auto integrator = std::get<1>(params); + + SCOPED_TRACE( + formatString("Checking for presence of expected output files using " + "simulation '%s' with integrator '%s'", + simulationName.c_str(), integrator.c_str())); + + // Prepare the .tpr file + { + CommandLine caller; + runner_.useTopGroAndNdxFromDatabase(simulationName); + runner_.useStringAsMdpFile(prepareMdpFileContents( + prepareMdpFieldValues(simulationName.c_str(), integrator.c_str(), "no", "no"))); + EXPECT_EQ(0, runner_.callGrompp(caller)); + } + // Do mdrun + { + CommandLine mdrunCaller; + ASSERT_EQ(0, runner_.callMdrun(mdrunCaller)); + } + // Check if expected files are present + { + for (const auto& file : { runner_.fullPrecisionTrajectoryFileName_, runner_.logFileName_, + runner_.edrFileName_, fileManager_.getTemporaryFilePath("state.gro"), + fileManager_.getTemporaryFilePath("state.cpt") }) + { + EXPECT_TRUE(File::exists(file, File::returnFalseOnError)) + << "File " << file << " was not found."; + } + } + } + + INSTANTIATE_TEST_CASE_P(Argon12, + OutputFiles, + ::testing::Combine(::testing::Values("argon12"), + ::testing::Values("md", "md-vv"))); + + } // namespace + } // namespace test + } // namespace gmx diff --cc tests/CMakeLists.txt index de6a5af418,2dbc14b37f..0f0200396f --- a/tests/CMakeLists.txt +++ b/tests/CMakeLists.txt @@@ -1,7 -1,7 +1,7 @@@ # # This file is part of the GROMACS molecular simulation package. # --# Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by ++# Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # and including many others, as listed in the AUTHORS file in the # top-level source directory and at http://www.gromacs.org.