From: Roland Schulz Date: Tue, 22 Jan 2019 19:45:01 +0000 (-0800) Subject: Renamed listed-forces to listed_forces X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=7c1764b2c763c8f0483d43f919f12e1218c9f004;p=alexxy%2Fgromacs.git Renamed listed-forces to listed_forces There should be consistency in naming. _ is used in almost all cases (2744 to 122 in src/gromacs not counting files changed here). Follow up changes will change the remaining files. Change-Id: Iea57accfd94d7ede180b9becd7d607425a8df7f6 --- diff --git a/docs/doxygen/cycle-suppressions.txt b/docs/doxygen/cycle-suppressions.txt index 0f7e243b6b..09410e82d6 100644 --- a/docs/doxygen/cycle-suppressions.txt +++ b/docs/doxygen/cycle-suppressions.txt @@ -7,7 +7,7 @@ domdec -> ewald domdec -> mdlib domdec -> pulling fileio -> gmxlib -gmxlib -> listed-forces +gmxlib -> listed_forces mdlib -> essentialdynamics mdlib -> imd mdlib -> ewald @@ -15,4 +15,4 @@ mdlib -> pulling mdlib -> awh simd -> hardware gpu_utils -> hardware -listed-forces -> mdlib +listed_forces -> mdlib diff --git a/src/gromacs/CMakeLists.txt b/src/gromacs/CMakeLists.txt index 71dceb857f..4e242f1cc7 100644 --- a/src/gromacs/CMakeLists.txt +++ b/src/gromacs/CMakeLists.txt @@ -96,7 +96,7 @@ endfunction() add_subdirectory(gmxlib) add_subdirectory(mdlib) add_subdirectory(applied-forces) -add_subdirectory(listed-forces) +add_subdirectory(listed_forces) add_subdirectory(commandline) add_subdirectory(domdec) add_subdirectory(ewald) diff --git a/src/gromacs/domdec/domdec.cpp b/src/gromacs/domdec/domdec.cpp index 48c3f84963..6ed75fbeaa 100644 --- a/src/gromacs/domdec/domdec.cpp +++ b/src/gromacs/domdec/domdec.cpp @@ -1,7 +1,7 @@ /* * 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, by the GROMACS development team, led by + * Copyright (c) 2005,2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, 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. @@ -60,7 +60,7 @@ #include "gromacs/gmxlib/nrnb.h" #include "gromacs/gpu_utils/gpu_utils.h" #include "gromacs/hardware/hw_info.h" -#include "gromacs/listed-forces/manage-threading.h" +#include "gromacs/listed_forces/manage-threading.h" #include "gromacs/math/vec.h" #include "gromacs/math/vectypes.h" #include "gromacs/mdlib/calc_verletbuf.h" diff --git a/src/gromacs/gmxana/anadih.cpp b/src/gromacs/gmxana/anadih.cpp index cf7869ced0..7b94925c0e 100644 --- a/src/gromacs/gmxana/anadih.cpp +++ b/src/gromacs/gmxana/anadih.cpp @@ -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, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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. @@ -46,7 +46,7 @@ #include "gromacs/fileio/trxio.h" #include "gromacs/fileio/xvgr.h" #include "gromacs/gmxana/gstat.h" -#include "gromacs/listed-forces/bonded.h" +#include "gromacs/listed_forces/bonded.h" #include "gromacs/math/functions.h" #include "gromacs/math/units.h" #include "gromacs/math/vec.h" diff --git a/src/gromacs/gmxana/gmx_dipoles.cpp b/src/gromacs/gmxana/gmx_dipoles.cpp index 095aa2da37..de453d4a29 100644 --- a/src/gromacs/gmxana/gmx_dipoles.cpp +++ b/src/gromacs/gmxana/gmx_dipoles.cpp @@ -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, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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. @@ -52,7 +52,7 @@ #include "gromacs/fileio/xvgr.h" #include "gromacs/gmxana/gmx_ana.h" #include "gromacs/linearalgebra/nrjac.h" -#include "gromacs/listed-forces/bonded.h" +#include "gromacs/listed_forces/bonded.h" #include "gromacs/math/functions.h" #include "gromacs/math/units.h" #include "gromacs/math/vec.h" diff --git a/src/gromacs/gmxana/gmx_disre.cpp b/src/gromacs/gmxana/gmx_disre.cpp index bb5438df7e..389188933c 100644 --- a/src/gromacs/gmxana/gmx_disre.cpp +++ b/src/gromacs/gmxana/gmx_disre.cpp @@ -53,7 +53,7 @@ #include "gromacs/gmxana/gmx_ana.h" #include "gromacs/gmxana/gstat.h" #include "gromacs/gmxlib/nrnb.h" -#include "gromacs/listed-forces/disre.h" +#include "gromacs/listed_forces/disre.h" #include "gromacs/math/do_fit.h" #include "gromacs/math/functions.h" #include "gromacs/math/vec.h" diff --git a/src/gromacs/gmxana/gmx_eneconv.cpp b/src/gromacs/gmxana/gmx_eneconv.cpp index 8ef0a06129..fd439e1003 100644 --- a/src/gromacs/gmxana/gmx_eneconv.cpp +++ b/src/gromacs/gmxana/gmx_eneconv.cpp @@ -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, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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. @@ -46,7 +46,7 @@ #include "gromacs/fileio/enxio.h" #include "gromacs/fileio/trxio.h" #include "gromacs/gmxana/gmx_ana.h" -#include "gromacs/listed-forces/disre.h" +#include "gromacs/listed_forces/disre.h" #include "gromacs/math/functions.h" #include "gromacs/math/vec.h" #include "gromacs/mdtypes/md_enums.h" diff --git a/src/gromacs/gmxana/hxprops.cpp b/src/gromacs/gmxana/hxprops.cpp index 4e29b849bd..94a6671d87 100644 --- a/src/gromacs/gmxana/hxprops.cpp +++ b/src/gromacs/gmxana/hxprops.cpp @@ -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, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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. @@ -43,7 +43,7 @@ #include -#include "gromacs/listed-forces/bonded.h" +#include "gromacs/listed_forces/bonded.h" #include "gromacs/math/functions.h" #include "gromacs/math/units.h" #include "gromacs/math/vec.h" diff --git a/src/gromacs/gmxana/nrama.cpp b/src/gromacs/gmxana/nrama.cpp index b721117b2a..689f6c17ee 100644 --- a/src/gromacs/gmxana/nrama.cpp +++ b/src/gromacs/gmxana/nrama.cpp @@ -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, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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. @@ -43,7 +43,7 @@ #include -#include "gromacs/listed-forces/bonded.h" +#include "gromacs/listed_forces/bonded.h" #include "gromacs/pbcutil/rmpbc.h" #include "gromacs/utility/cstringutil.h" #include "gromacs/utility/fatalerror.h" diff --git a/src/gromacs/gmxlib/nonbonded/nonbonded.cpp b/src/gromacs/gmxlib/nonbonded/nonbonded.cpp index 8ca8aa9ef6..cde937b75a 100644 --- a/src/gromacs/gmxlib/nonbonded/nonbonded.cpp +++ b/src/gromacs/gmxlib/nonbonded/nonbonded.cpp @@ -51,7 +51,7 @@ #include "gromacs/gmxlib/nonbonded/nb_generic.h" #include "gromacs/gmxlib/nonbonded/nb_generic_cg.h" #include "gromacs/gmxlib/nonbonded/nb_kernel.h" -#include "gromacs/listed-forces/bonded.h" +#include "gromacs/listed_forces/bonded.h" #include "gromacs/math/utilities.h" #include "gromacs/math/vec.h" #include "gromacs/mdtypes/enerdata.h" diff --git a/src/gromacs/gmxpreprocess/x2top.cpp b/src/gromacs/gmxpreprocess/x2top.cpp index 568f88540e..fdbe302c14 100644 --- a/src/gromacs/gmxpreprocess/x2top.cpp +++ b/src/gromacs/gmxpreprocess/x2top.cpp @@ -54,7 +54,7 @@ #include "gromacs/gmxpreprocess/pdb2top.h" #include "gromacs/gmxpreprocess/toppush.h" #include "gromacs/gmxpreprocess/toputil.h" -#include "gromacs/listed-forces/bonded.h" +#include "gromacs/listed_forces/bonded.h" #include "gromacs/math/units.h" #include "gromacs/math/utilities.h" #include "gromacs/math/vec.h" diff --git a/src/gromacs/listed-forces/CMakeLists.txt b/src/gromacs/listed_forces/CMakeLists.txt similarity index 95% rename from src/gromacs/listed-forces/CMakeLists.txt rename to src/gromacs/listed_forces/CMakeLists.txt index 4339a190fe..bd97c81fe1 100644 --- a/src/gromacs/listed-forces/CMakeLists.txt +++ b/src/gromacs/listed_forces/CMakeLists.txt @@ -1,7 +1,7 @@ # # This file is part of the GROMACS molecular simulation package. # -# Copyright (c) 2014,2015,2016,2018, by the GROMACS development team, led by +# Copyright (c) 2014,2015,2016,2018,2019, 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. @@ -36,7 +36,7 @@ gmx_add_libgromacs_sources( bonded.cpp disre.cpp gpubonded-impl.cpp - listed-forces.cpp + listed_forces.cpp listed-internal.cpp manage-threading.cpp orires.cpp diff --git a/src/gromacs/listed-forces/bonded.cpp b/src/gromacs/listed_forces/bonded.cpp similarity index 99% rename from src/gromacs/listed-forces/bonded.cpp rename to src/gromacs/listed_forces/bonded.cpp index cbf89ad421..0ae06d19af 100644 --- a/src/gromacs/listed-forces/bonded.cpp +++ b/src/gromacs/listed_forces/bonded.cpp @@ -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, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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. @@ -41,7 +41,7 @@ * * \author Mark Abraham * - * \ingroup module_listed-forces + * \ingroup module_listed_forces */ #include "gmxpre.h" @@ -54,7 +54,7 @@ #include -#include "gromacs/listed-forces/pairs.h" +#include "gromacs/listed_forces/pairs.h" #include "gromacs/math/functions.h" #include "gromacs/math/units.h" #include "gromacs/math/utilities.h" diff --git a/src/gromacs/listed-forces/bonded.h b/src/gromacs/listed_forces/bonded.h similarity index 99% rename from src/gromacs/listed-forces/bonded.h rename to src/gromacs/listed_forces/bonded.h index 814f4d0807..9a139f035d 100644 --- a/src/gromacs/listed-forces/bonded.h +++ b/src/gromacs/listed_forces/bonded.h @@ -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, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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. @@ -41,7 +41,7 @@ * * \author Mark Abraham * \inlibraryapi - * \ingroup module_listed-forces + * \ingroup module_listed_forces */ #ifndef GMX_LISTED_FORCES_BONDED_H diff --git a/src/gromacs/listed-forces/disre.cpp b/src/gromacs/listed_forces/disre.cpp similarity index 99% rename from src/gromacs/listed-forces/disre.cpp rename to src/gromacs/listed_forces/disre.cpp index 408601c06a..f827ada753 100644 --- a/src/gromacs/listed-forces/disre.cpp +++ b/src/gromacs/listed_forces/disre.cpp @@ -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, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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 --git a/src/gromacs/listed-forces/disre.h b/src/gromacs/listed_forces/disre.h similarity index 96% rename from src/gromacs/listed-forces/disre.h rename to src/gromacs/listed_forces/disre.h index 211700d984..7cbce33908 100644 --- a/src/gromacs/listed-forces/disre.h +++ b/src/gromacs/listed_forces/disre.h @@ -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, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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. @@ -39,7 +39,7 @@ * Declares functions for handling distance restraints. * * \inlibraryapi - * \ingroup module_listed-forces + * \ingroup module_listed_forces */ #ifndef GMX_LISTED_FORCES_DISRE_H #define GMX_LISTED_FORCES_DISRE_H diff --git a/src/gromacs/listed-forces/gpubonded-impl.cpp b/src/gromacs/listed_forces/gpubonded-impl.cpp similarity index 97% rename from src/gromacs/listed-forces/gpubonded-impl.cpp rename to src/gromacs/listed_forces/gpubonded-impl.cpp index 998ad7a5c8..77c3256510 100644 --- a/src/gromacs/listed-forces/gpubonded-impl.cpp +++ b/src/gromacs/listed_forces/gpubonded-impl.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2018, by the GROMACS development team, led by + * Copyright (c) 2018,2019, 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. @@ -38,7 +38,7 @@ * * \author Mark Abraham * - * \ingroup module_listed-forces + * \ingroup module_listed_forces */ #include "gmxpre.h" @@ -47,7 +47,7 @@ #include -#include "gromacs/listed-forces/gpubonded.h" +#include "gromacs/listed_forces/gpubonded.h" #include "gromacs/mdtypes/inputrec.h" #include "gromacs/topology/topology.h" #include "gromacs/utility/stringutil.h" diff --git a/src/gromacs/listed-forces/gpubonded-impl.cu b/src/gromacs/listed_forces/gpubonded-impl.cu similarity index 98% rename from src/gromacs/listed-forces/gpubonded-impl.cu rename to src/gromacs/listed_forces/gpubonded-impl.cu index 9df0a2d215..8da1a9ffd0 100644 --- a/src/gromacs/listed-forces/gpubonded-impl.cu +++ b/src/gromacs/listed_forces/gpubonded-impl.cu @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2018, by the GROMACS development team, led by + * Copyright (c) 2018,2019, 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. @@ -40,7 +40,7 @@ * \author Szilárd Páll * \author Mark Abraham * - * \ingroup module_listed-forces + * \ingroup module_listed_forces */ #include "gmxpre.h" @@ -52,7 +52,7 @@ #include "gromacs/gpu_utils/gpu_vec.cuh" #include "gromacs/gpu_utils/gputraits.cuh" #include "gromacs/gpu_utils/hostallocator.h" -#include "gromacs/listed-forces/gpubonded.h" +#include "gromacs/listed_forces/gpubonded.h" #include "gromacs/mdtypes/enerdata.h" #include "gromacs/topology/forcefieldparameters.h" #include "gromacs/topology/idef.h" diff --git a/src/gromacs/listed-forces/gpubonded-impl.h b/src/gromacs/listed_forces/gpubonded-impl.h similarity index 98% rename from src/gromacs/listed-forces/gpubonded-impl.h rename to src/gromacs/listed_forces/gpubonded-impl.h index 3720fe23fa..79c0ad157e 100644 --- a/src/gromacs/listed-forces/gpubonded-impl.h +++ b/src/gromacs/listed_forces/gpubonded-impl.h @@ -43,7 +43,7 @@ * \author Szilárd Páll * \author Mark Abraham * - * \ingroup module_listed-forces + * \ingroup module_listed_forces */ #ifndef GMX_LISTED_FORCES_GPUBONDED_IMPL_H #define GMX_LISTED_FORCES_GPUBONDED_IMPL_H @@ -51,7 +51,7 @@ #include "gromacs/gpu_utils/gpu_vec.cuh" #include "gromacs/gpu_utils/gputraits.cuh" #include "gromacs/gpu_utils/hostallocator.h" -#include "gromacs/listed-forces/gpubonded.h" +#include "gromacs/listed_forces/gpubonded.h" #include "gromacs/topology/idef.h" struct gmx_ffparams_t; diff --git a/src/gromacs/listed-forces/gpubonded.h b/src/gromacs/listed_forces/gpubonded.h similarity index 97% rename from src/gromacs/listed-forces/gpubonded.h rename to src/gromacs/listed_forces/gpubonded.h index e2c49f4660..442e42041f 100644 --- a/src/gromacs/listed-forces/gpubonded.h +++ b/src/gromacs/listed_forces/gpubonded.h @@ -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 * 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. @@ -43,7 +43,7 @@ * \author Mark Abraham * * \inlibraryapi - * \ingroup module_listed-forces + * \ingroup module_listed_forces */ #ifndef GMX_LISTED_FORCES_GPUBONDED_H #define GMX_LISTED_FORCES_GPUBONDED_H diff --git a/src/gromacs/listed-forces/gpubondedkernels.cu b/src/gromacs/listed_forces/gpubondedkernels.cu similarity index 99% rename from src/gromacs/listed-forces/gpubondedkernels.cu rename to src/gromacs/listed_forces/gpubondedkernels.cu index ea494f0144..2f78486340 100644 --- a/src/gromacs/listed-forces/gpubondedkernels.cu +++ b/src/gromacs/listed_forces/gpubondedkernels.cu @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2018, by the GROMACS development team, led by + * Copyright (c) 2018,2019, 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. @@ -43,7 +43,7 @@ * \author Alan Gray * \author Mark Abraham * - * \ingroup module_listed-forces + * \ingroup module_listed_forces */ #include "gmxpre.h" @@ -54,8 +54,8 @@ #include "gromacs/gpu_utils/devicebuffer.h" #include "gromacs/gpu_utils/gpu_vec.cuh" #include "gromacs/gpu_utils/gputraits.cuh" -#include "gromacs/listed-forces/gpubonded.h" -#include "gromacs/listed-forces/listed-forces.h" +#include "gromacs/listed_forces/gpubonded.h" +#include "gromacs/listed_forces/listed_forces.h" #include "gromacs/math/units.h" #include "gromacs/mdlib/force_flags.h" #include "gromacs/mdtypes/enerdata.h" diff --git a/src/gromacs/listed-forces/listed-internal.cpp b/src/gromacs/listed_forces/listed-internal.cpp similarity index 94% rename from src/gromacs/listed-forces/listed-internal.cpp rename to src/gromacs/listed_forces/listed-internal.cpp index a753f76cc7..2161bff3c5 100644 --- a/src/gromacs/listed-forces/listed-internal.cpp +++ b/src/gromacs/listed_forces/listed-internal.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014,2017,2018, by the GROMACS development team, led by + * Copyright (c) 2014,2017,2018,2019, 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. @@ -37,7 +37,7 @@ * \brief This file defines functions needed internally by the module. * * \author Mark Abraham - * \ingroup module_listed-forces + * \ingroup module_listed_forces */ #include "gmxpre.h" diff --git a/src/gromacs/listed-forces/listed-internal.h b/src/gromacs/listed_forces/listed-internal.h similarity index 99% rename from src/gromacs/listed-forces/listed-internal.h rename to src/gromacs/listed_forces/listed-internal.h index 01b11aa255..ad4f3f680f 100644 --- a/src/gromacs/listed-forces/listed-internal.h +++ b/src/gromacs/listed_forces/listed-internal.h @@ -38,7 +38,7 @@ * internally by the module. * * \author Mark Abraham - * \ingroup module_listed-forces + * \ingroup module_listed_forces */ #ifndef GMX_LISTED_FORCES_LISTED_INTERNAL_H #define GMX_LISTED_FORCES_LISTED_INTERNAL_H diff --git a/src/gromacs/listed-forces/listed-forces.cpp b/src/gromacs/listed_forces/listed_forces.cpp similarity index 98% rename from src/gromacs/listed-forces/listed-forces.cpp rename to src/gromacs/listed_forces/listed_forces.cpp index fd5f9b76c5..97255fe9a9 100644 --- a/src/gromacs/listed-forces/listed-forces.cpp +++ b/src/gromacs/listed_forces/listed_forces.cpp @@ -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 * 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. @@ -39,11 +39,11 @@ * * \author Mark Abraham * - * \ingroup module_listed-forces + * \ingroup module_listed_forces */ #include "gmxpre.h" -#include "listed-forces.h" +#include "listed_forces.h" #include @@ -52,11 +52,11 @@ #include "gromacs/gmxlib/network.h" #include "gromacs/gmxlib/nrnb.h" -#include "gromacs/listed-forces/bonded.h" -#include "gromacs/listed-forces/disre.h" -#include "gromacs/listed-forces/orires.h" -#include "gromacs/listed-forces/pairs.h" -#include "gromacs/listed-forces/position-restraints.h" +#include "gromacs/listed_forces/bonded.h" +#include "gromacs/listed_forces/disre.h" +#include "gromacs/listed_forces/orires.h" +#include "gromacs/listed_forces/pairs.h" +#include "gromacs/listed_forces/position-restraints.h" #include "gromacs/math/vec.h" #include "gromacs/mdlib/force.h" #include "gromacs/mdlib/force_flags.h" diff --git a/src/gromacs/listed-forces/listed-forces.h b/src/gromacs/listed_forces/listed_forces.h similarity index 97% rename from src/gromacs/listed-forces/listed-forces.h rename to src/gromacs/listed_forces/listed_forces.h index 9c1d452616..165ebffc7d 100644 --- a/src/gromacs/listed-forces/listed-forces.h +++ b/src/gromacs/listed_forces/listed_forces.h @@ -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 * 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. @@ -32,7 +32,7 @@ * To help us fund GROMACS development, we humbly ask that you cite * the research papers on the package. Check out http://www.gromacs.org. */ -/*! \defgroup module_listed-forces Interactions between lists of particles +/*! \defgroup module_listed_forces Interactions between lists of particles * \ingroup group_mdrun * * \brief Handles computing energies and forces for listed @@ -61,7 +61,7 @@ * \author Mark Abraham * * \inlibraryapi - * \ingroup module_listed-forces + * \ingroup module_listed_forces */ #ifndef GMX_LISTED_FORCES_LISTED_FORCES_H #define GMX_LISTED_FORCES_LISTED_FORCES_H diff --git a/src/gromacs/listed-forces/manage-threading.cpp b/src/gromacs/listed_forces/manage-threading.cpp similarity index 99% rename from src/gromacs/listed-forces/manage-threading.cpp rename to src/gromacs/listed_forces/manage-threading.cpp index c1fc232fc8..5aa96feb88 100644 --- a/src/gromacs/listed-forces/manage-threading.cpp +++ b/src/gromacs/listed_forces/manage-threading.cpp @@ -39,7 +39,7 @@ * interactions. * * \author Mark Abraham - * \ingroup module_listed-forces + * \ingroup module_listed_forces */ #include "gmxpre.h" @@ -55,7 +55,7 @@ #include #include -#include "gromacs/listed-forces/gpubonded.h" +#include "gromacs/listed_forces/gpubonded.h" #include "gromacs/mdlib/gmx_omp_nthreads.h" #include "gromacs/pbcutil/ishift.h" #include "gromacs/topology/ifunc.h" diff --git a/src/gromacs/listed-forces/manage-threading.h b/src/gromacs/listed_forces/manage-threading.h similarity index 96% rename from src/gromacs/listed-forces/manage-threading.h rename to src/gromacs/listed_forces/manage-threading.h index a395956d15..f50e98e4d0 100644 --- a/src/gromacs/listed-forces/manage-threading.h +++ b/src/gromacs/listed_forces/manage-threading.h @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2013,2014,2015,2016,2018, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015,2016,2018,2019, 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. @@ -39,7 +39,7 @@ * * \author Mark Abraham * \inlibraryapi - * \ingroup module_listed-forces + * \ingroup module_listed_forces */ #ifndef GMX_LISTED_FORCES_MANAGE_THREADING_H #define GMX_LISTED_FORCES_MANAGE_THREADING_H diff --git a/src/gromacs/listed-forces/orires.cpp b/src/gromacs/listed_forces/orires.cpp similarity index 100% rename from src/gromacs/listed-forces/orires.cpp rename to src/gromacs/listed_forces/orires.cpp diff --git a/src/gromacs/listed-forces/orires.h b/src/gromacs/listed_forces/orires.h similarity index 97% rename from src/gromacs/listed-forces/orires.h rename to src/gromacs/listed_forces/orires.h index d7066e1380..83e8b13e25 100644 --- a/src/gromacs/listed-forces/orires.h +++ b/src/gromacs/listed_forces/orires.h @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2010,2014,2015,2017,2018, by the GROMACS development team, led by + * Copyright (c) 2010,2014,2015,2017,2018,2019, 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. @@ -39,7 +39,7 @@ * Declares functions for handling orientation restraints. * * \inlibraryapi - * \ingroup module_listed-forces + * \ingroup module_listed_forces */ #ifndef GMX_LISTED_FORCES_ORIRES_H #define GMX_LISTED_FORCES_ORIRES_H diff --git a/src/gromacs/listed-forces/pairs.cpp b/src/gromacs/listed_forces/pairs.cpp similarity index 99% rename from src/gromacs/listed-forces/pairs.cpp rename to src/gromacs/listed_forces/pairs.cpp index 8de6b30d4a..e910e59227 100644 --- a/src/gromacs/listed-forces/pairs.cpp +++ b/src/gromacs/listed_forces/pairs.cpp @@ -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 * 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. @@ -39,7 +39,7 @@ * * \author Mark Abraham * - * \ingroup module_listed-forces + * \ingroup module_listed_forces */ #include "gmxpre.h" diff --git a/src/gromacs/listed-forces/pairs.h b/src/gromacs/listed_forces/pairs.h similarity index 95% rename from src/gromacs/listed-forces/pairs.h rename to src/gromacs/listed_forces/pairs.h index 88af8347c4..31f8b61d64 100644 --- a/src/gromacs/listed-forces/pairs.h +++ b/src/gromacs/listed_forces/pairs.h @@ -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 * 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. @@ -39,7 +39,7 @@ * * \author Mark Abraham * \inlibraryapi - * \ingroup module_listed-forces + * \ingroup module_listed_forces */ #ifndef GMX_LISTED_FORCES_PAIRS_H #define GMX_LISTED_FORCES_PAIRS_H diff --git a/src/gromacs/listed-forces/position-restraints.cpp b/src/gromacs/listed_forces/position-restraints.cpp similarity index 99% rename from src/gromacs/listed-forces/position-restraints.cpp rename to src/gromacs/listed_forces/position-restraints.cpp index 0fa2a2fed8..f6c865b30b 100644 --- a/src/gromacs/listed-forces/position-restraints.cpp +++ b/src/gromacs/listed_forces/position-restraints.cpp @@ -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 * 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. @@ -39,7 +39,7 @@ * * \author Mark Abraham * - * \ingroup module_listed-forces + * \ingroup module_listed_forces */ #include "gmxpre.h" diff --git a/src/gromacs/listed-forces/position-restraints.h b/src/gromacs/listed_forces/position-restraints.h similarity index 96% rename from src/gromacs/listed-forces/position-restraints.h rename to src/gromacs/listed_forces/position-restraints.h index a02cae0524..79387ecb41 100644 --- a/src/gromacs/listed-forces/position-restraints.h +++ b/src/gromacs/listed_forces/position-restraints.h @@ -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, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015,2017,2019, 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. @@ -42,7 +42,7 @@ * * \author Mark Abraham * \inlibraryapi - * \ingroup module_listed-forces + * \ingroup module_listed_forces */ #ifndef GMX_LISTED_FORCES_POSITION_RESTRAINTS_H diff --git a/src/gromacs/listed-forces/restcbt.cpp b/src/gromacs/listed_forces/restcbt.cpp similarity index 99% rename from src/gromacs/listed-forces/restcbt.cpp rename to src/gromacs/listed_forces/restcbt.cpp index f264029e43..6e88355ff2 100644 --- a/src/gromacs/listed-forces/restcbt.cpp +++ b/src/gromacs/listed_forces/restcbt.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by + * Copyright (c) 2014,2015,2017,2019, 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. @@ -41,7 +41,7 @@ * * \author Nicolae Goga * - * \ingroup module_listed-forces + * \ingroup module_listed_forces */ #include "gmxpre.h" diff --git a/src/gromacs/listed-forces/restcbt.h b/src/gromacs/listed_forces/restcbt.h similarity index 99% rename from src/gromacs/listed-forces/restcbt.h rename to src/gromacs/listed_forces/restcbt.h index 7b6cabd816..56dca730fe 100644 --- a/src/gromacs/listed-forces/restcbt.h +++ b/src/gromacs/listed_forces/restcbt.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014,2015, by the GROMACS development team, led by + * Copyright (c) 2014,2015,2019, 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. @@ -43,7 +43,7 @@ * * \author Nicolae Goga * - * \ingroup module_listed-forces + * \ingroup module_listed_forces */ #ifndef GMX_LISTED_FORCES_RESTCBT_H diff --git a/src/gromacs/listed-forces/tests/CMakeLists.txt b/src/gromacs/listed_forces/tests/CMakeLists.txt similarity index 93% rename from src/gromacs/listed-forces/tests/CMakeLists.txt rename to src/gromacs/listed_forces/tests/CMakeLists.txt index 254fc1b936..e987e69a4b 100644 --- a/src/gromacs/listed-forces/tests/CMakeLists.txt +++ b/src/gromacs/listed_forces/tests/CMakeLists.txt @@ -1,7 +1,7 @@ # # This file is part of the GROMACS molecular simulation package. # -# Copyright (c) 2016, by the GROMACS development team, led by +# Copyright (c) 2016,2019, 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. @@ -32,6 +32,6 @@ # To help us fund GROMACS development, we humbly ask that you cite # the research papers on the package. Check out http://www.gromacs.org. -gmx_add_unit_test(ListedForcesTest listed-forces-test +gmx_add_unit_test(ListedForcesTest listed_forces-test bonded.cpp) diff --git a/src/gromacs/listed-forces/tests/bonded.cpp b/src/gromacs/listed_forces/tests/bonded.cpp similarity index 98% rename from src/gromacs/listed-forces/tests/bonded.cpp rename to src/gromacs/listed_forces/tests/bonded.cpp index 21130615a2..11541a522b 100644 --- a/src/gromacs/listed-forces/tests/bonded.cpp +++ b/src/gromacs/listed_forces/tests/bonded.cpp @@ -37,11 +37,11 @@ * Implements test of bonded force routines * * \author David van der Spoel - * \ingroup module_listed-forces + * \ingroup module_listed_forces */ #include "gmxpre.h" -#include "gromacs/listed-forces/bonded.h" +#include "gromacs/listed_forces/bonded.h" #include @@ -49,7 +49,7 @@ #include -#include "gromacs/listed-forces/listed-forces.h" +#include "gromacs/listed_forces/listed_forces.h" #include "gromacs/math/units.h" #include "gromacs/math/vec.h" #include "gromacs/math/vectypes.h" diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_0.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_0.xml similarity index 100% rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_0.xml rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_0.xml diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_1.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_1.xml similarity index 100% rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_1.xml rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_1.xml diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_2.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_2.xml similarity index 100% rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_2.xml rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_2.xml diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_3.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_3.xml similarity index 100% rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_3.xml rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_3.xml diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_4.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_4.xml similarity index 100% rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_4.xml rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_4.xml diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_5.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_5.xml similarity index 100% rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_5.xml rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_5.xml diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_6.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_6.xml similarity index 100% rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_6.xml rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_6.xml diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_7.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_7.xml similarity index 100% rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_7.xml rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_7.xml diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_8.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_8.xml similarity index 100% rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_8.xml rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_8.xml diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_0.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_0.xml similarity index 100% rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_0.xml rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_0.xml diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_1.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_1.xml similarity index 100% rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_1.xml rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_1.xml diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_2.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_2.xml similarity index 100% rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_2.xml rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_2.xml diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_3.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_3.xml similarity index 100% rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_3.xml rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_3.xml diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_4.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_4.xml similarity index 100% rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_4.xml rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_4.xml diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_5.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_5.xml similarity index 100% rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_5.xml rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_5.xml diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_6.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_6.xml similarity index 100% rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_6.xml rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_6.xml diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_7.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_7.xml similarity index 100% rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_7.xml rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_7.xml diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_8.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_8.xml similarity index 100% rename from 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src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_0.xml rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_0.xml diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_1.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_1.xml similarity index 100% rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_1.xml rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_1.xml diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_2.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_2.xml similarity index 100% rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_2.xml rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_2.xml diff --git 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src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_5.xml diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_6.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_6.xml similarity index 100% rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_6.xml rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_6.xml diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_7.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_7.xml similarity index 100% rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_7.xml rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_7.xml diff --git a/src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_8.xml b/src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_8.xml similarity index 100% rename from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_8.xml rename to src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_8.xml diff --git a/src/gromacs/listed-forces/utilities.h b/src/gromacs/listed_forces/utilities.h similarity index 95% rename from src/gromacs/listed-forces/utilities.h rename to src/gromacs/listed_forces/utilities.h index 96ab324b41..c652fa5ae3 100644 --- a/src/gromacs/listed-forces/utilities.h +++ b/src/gromacs/listed_forces/utilities.h @@ -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 * 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. @@ -39,7 +39,7 @@ * * \author Mark Abraham * - * \ingroup module_listed-forces + * \ingroup module_listed_forces */ #ifndef GMX_LISTED_FORCES_UTILITIES_H #define GMX_LISTED_FORCES_UTILITIES_H diff --git a/src/gromacs/mdlib/expanded.cpp b/src/gromacs/mdlib/expanded.cpp index 7e70646bd5..5e0c61b0fd 100644 --- a/src/gromacs/mdlib/expanded.cpp +++ b/src/gromacs/mdlib/expanded.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, 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. @@ -48,8 +48,8 @@ #include "gromacs/gmxlib/chargegroup.h" #include "gromacs/gmxlib/network.h" #include "gromacs/gmxlib/nrnb.h" -#include "gromacs/listed-forces/disre.h" -#include "gromacs/listed-forces/orires.h" +#include "gromacs/listed_forces/disre.h" +#include "gromacs/listed_forces/orires.h" #include "gromacs/math/functions.h" #include "gromacs/math/units.h" #include "gromacs/math/vec.h" diff --git a/src/gromacs/mdlib/force.cpp b/src/gromacs/mdlib/force.cpp index e86d4eee61..7847aaa8cc 100644 --- a/src/gromacs/mdlib/force.cpp +++ b/src/gromacs/mdlib/force.cpp @@ -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, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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. @@ -52,7 +52,7 @@ #include "gromacs/gmxlib/network.h" #include "gromacs/gmxlib/nrnb.h" #include "gromacs/gmxlib/nonbonded/nonbonded.h" -#include "gromacs/listed-forces/listed-forces.h" +#include "gromacs/listed_forces/listed_forces.h" #include "gromacs/math/vec.h" #include "gromacs/math/vecdump.h" #include "gromacs/mdlib/force_flags.h" diff --git a/src/gromacs/mdlib/forcerec.cpp b/src/gromacs/mdlib/forcerec.cpp index f43b13e7a2..c231eace7b 100644 --- a/src/gromacs/mdlib/forcerec.cpp +++ b/src/gromacs/mdlib/forcerec.cpp @@ -58,9 +58,9 @@ #include "gromacs/gmxlib/nonbonded/nonbonded.h" #include "gromacs/gpu_utils/gpu_utils.h" #include "gromacs/hardware/hw_info.h" -#include "gromacs/listed-forces/gpubonded.h" -#include "gromacs/listed-forces/manage-threading.h" -#include "gromacs/listed-forces/pairs.h" +#include "gromacs/listed_forces/gpubonded.h" +#include "gromacs/listed_forces/manage-threading.h" +#include "gromacs/listed_forces/pairs.h" #include "gromacs/math/functions.h" #include "gromacs/math/units.h" #include "gromacs/math/utilities.h" diff --git a/src/gromacs/mdlib/mdebin.cpp b/src/gromacs/mdlib/mdebin.cpp index 3ff4978346..6477842305 100644 --- a/src/gromacs/mdlib/mdebin.cpp +++ b/src/gromacs/mdlib/mdebin.cpp @@ -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, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, 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. @@ -49,8 +49,8 @@ #include "gromacs/fileio/gmxfio.h" #include "gromacs/fileio/xvgr.h" #include "gromacs/gmxlib/network.h" -#include "gromacs/listed-forces/disre.h" -#include "gromacs/listed-forces/orires.h" +#include "gromacs/listed_forces/disre.h" +#include "gromacs/listed_forces/orires.h" #include "gromacs/math/functions.h" #include "gromacs/math/units.h" #include "gromacs/math/vec.h" diff --git a/src/gromacs/mdlib/mdsetup.cpp b/src/gromacs/mdlib/mdsetup.cpp index 62558c8552..5a5bb53164 100644 --- a/src/gromacs/mdlib/mdsetup.cpp +++ b/src/gromacs/mdlib/mdsetup.cpp @@ -39,7 +39,7 @@ #include "gromacs/domdec/domdec.h" #include "gromacs/domdec/domdec_struct.h" #include "gromacs/ewald/pme.h" -#include "gromacs/listed-forces/manage-threading.h" +#include "gromacs/listed_forces/manage-threading.h" #include "gromacs/mdlib/constr.h" #include "gromacs/mdlib/mdatoms.h" #include "gromacs/mdlib/shellfc.h" diff --git a/src/gromacs/mdlib/sim_util.cpp b/src/gromacs/mdlib/sim_util.cpp index 8e7af55869..c6c02e77a0 100644 --- a/src/gromacs/mdlib/sim_util.cpp +++ b/src/gromacs/mdlib/sim_util.cpp @@ -61,11 +61,11 @@ #include "gromacs/gmxlib/nonbonded/nonbonded.h" #include "gromacs/gpu_utils/gpu_utils.h" #include "gromacs/imd/imd.h" -#include "gromacs/listed-forces/bonded.h" -#include "gromacs/listed-forces/disre.h" -#include "gromacs/listed-forces/gpubonded.h" -#include "gromacs/listed-forces/manage-threading.h" -#include "gromacs/listed-forces/orires.h" +#include "gromacs/listed_forces/bonded.h" +#include "gromacs/listed_forces/disre.h" +#include "gromacs/listed_forces/gpubonded.h" +#include "gromacs/listed_forces/manage-threading.h" +#include "gromacs/listed_forces/orires.h" #include "gromacs/math/arrayrefwithpadding.h" #include "gromacs/math/functions.h" #include "gromacs/math/units.h" diff --git a/src/gromacs/mdlib/update.cpp b/src/gromacs/mdlib/update.cpp index e6f39df9bc..311d162298 100644 --- a/src/gromacs/mdlib/update.cpp +++ b/src/gromacs/mdlib/update.cpp @@ -48,8 +48,8 @@ #include "gromacs/fileio/confio.h" #include "gromacs/gmxlib/network.h" #include "gromacs/gmxlib/nrnb.h" -#include "gromacs/listed-forces/disre.h" -#include "gromacs/listed-forces/orires.h" +#include "gromacs/listed_forces/disre.h" +#include "gromacs/listed_forces/orires.h" #include "gromacs/math/functions.h" #include "gromacs/math/invertmatrix.h" #include "gromacs/math/paddedvector.h" diff --git a/src/gromacs/mdrun/md.cpp b/src/gromacs/mdrun/md.cpp index 82923ab02b..86c7bea16a 100644 --- a/src/gromacs/mdrun/md.cpp +++ b/src/gromacs/mdrun/md.cpp @@ -67,7 +67,7 @@ #include "gromacs/gmxlib/nrnb.h" #include "gromacs/gpu_utils/gpu_utils.h" #include "gromacs/imd/imd.h" -#include "gromacs/listed-forces/manage-threading.h" +#include "gromacs/listed_forces/manage-threading.h" #include "gromacs/math/functions.h" #include "gromacs/math/utilities.h" #include "gromacs/math/vec.h" diff --git a/src/gromacs/mdrun/mimic.cpp b/src/gromacs/mdrun/mimic.cpp index dc315a49e3..aaec3bbf1f 100644 --- a/src/gromacs/mdrun/mimic.cpp +++ b/src/gromacs/mdrun/mimic.cpp @@ -66,7 +66,7 @@ #include "gromacs/gmxlib/nrnb.h" #include "gromacs/gpu_utils/gpu_utils.h" #include "gromacs/imd/imd.h" -#include "gromacs/listed-forces/manage-threading.h" +#include "gromacs/listed_forces/manage-threading.h" #include "gromacs/math/functions.h" #include "gromacs/math/utilities.h" #include "gromacs/math/vec.h" diff --git a/src/gromacs/mdrun/minimize.cpp b/src/gromacs/mdrun/minimize.cpp index 7a11fdbbb6..d7f720018e 100644 --- a/src/gromacs/mdrun/minimize.cpp +++ b/src/gromacs/mdrun/minimize.cpp @@ -65,7 +65,7 @@ #include "gromacs/gmxlib/nrnb.h" #include "gromacs/imd/imd.h" #include "gromacs/linearalgebra/sparsematrix.h" -#include "gromacs/listed-forces/manage-threading.h" +#include "gromacs/listed_forces/manage-threading.h" #include "gromacs/math/functions.h" #include "gromacs/math/vec.h" #include "gromacs/mdlib/constr.h" diff --git a/src/gromacs/mdrun/rerun.cpp b/src/gromacs/mdrun/rerun.cpp index a8ae9395ff..6ca622a2a1 100644 --- a/src/gromacs/mdrun/rerun.cpp +++ b/src/gromacs/mdrun/rerun.cpp @@ -67,7 +67,7 @@ #include "gromacs/gmxlib/nrnb.h" #include "gromacs/gpu_utils/gpu_utils.h" #include "gromacs/imd/imd.h" -#include "gromacs/listed-forces/manage-threading.h" +#include "gromacs/listed_forces/manage-threading.h" #include "gromacs/math/functions.h" #include "gromacs/math/utilities.h" #include "gromacs/math/vec.h" diff --git a/src/gromacs/mdrun/runner.cpp b/src/gromacs/mdrun/runner.cpp index f553e9f7bb..7dfeb1293a 100644 --- a/src/gromacs/mdrun/runner.cpp +++ b/src/gromacs/mdrun/runner.cpp @@ -74,9 +74,9 @@ #include "gromacs/hardware/cpuinfo.h" #include "gromacs/hardware/detecthardware.h" #include "gromacs/hardware/printhardware.h" -#include "gromacs/listed-forces/disre.h" -#include "gromacs/listed-forces/gpubonded.h" -#include "gromacs/listed-forces/orires.h" +#include "gromacs/listed_forces/disre.h" +#include "gromacs/listed_forces/gpubonded.h" +#include "gromacs/listed_forces/orires.h" #include "gromacs/math/functions.h" #include "gromacs/math/utilities.h" #include "gromacs/math/vec.h"