#
# 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.
#
# 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.
#
# 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.
#
# 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.
#
# 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.
-# Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ #
+ # This file is part of the GROMACS molecular simulation package.
+ #
++# 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
#
# 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.
#
# 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.
#
# 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.
"""
#
# 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.
/*
* 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.
#
# 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.
#
# 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.
#
# 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.
#
# 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.
#
# 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.
/*
* 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.
* 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.
* 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.
/*
* 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.
/*
* 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.
*
* 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.
/*
* 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.
*
* 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.
*
* 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.
--- /dev/null
- * Copyright (c) 2019, by the GROMACS development team, led by
+ /*
+ * This file is part of the GROMACS molecular simulation package.
+ *
++ * 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 <algorithm>
+
+ #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;
+ }
--- /dev/null
- * Copyright (c) 2019, by the GROMACS development team, led by
+ /*
+ * This file is part of the GROMACS molecular simulation package.
+ *
++ * 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
*
* 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.
*
* 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.
*
* 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.
*
* 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.
/*
* 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.
*
* 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.
*
* 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.
/*
* 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.
/*
* 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.
*
* 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.
/*
* 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.
*
* 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.
/*
* 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.
*
* 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.
*
* 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.
/*
* 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.
/*
* 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.
/*
* 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.
/*
* 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.
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);
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);
// 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*
/*
* 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.
/*
* 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.
/*
* 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.
/*
* 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.
/*
* 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.
/*
* 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.
/*
* 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.
/*
* 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.
/*
* 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.
*
* 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.
*
* 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.
/*
* 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.
/*
* 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.
*
* 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.
*
* 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.
#
# 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.
--- /dev/null
- * Copyright (c) 2019, by the GROMACS development team, led by
+ /*
+ * This file is part of the GROMACS molecular simulation package.
+ *
++ * 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 <pascal.merz@me.com>
+ * \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<std::string, std::string>;
+ class OutputFiles : public MdrunTestFixture, public ::testing::WithParamInterface<OutputFilesTestParams>
+ {
+ };
+
+ 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
#
# 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.
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff