From: Roland Schulz Date: Sat, 2 Feb 2019 18:05:23 +0000 (-0800) Subject: Rename all source files from - to _ for consistency. X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=90aa21a73ccf42dda058d3dd3278f9cdcab2a50f;p=alexxy%2Fgromacs.git Rename all source files from - to _ for consistency. Refs #2839 Change-Id: I3a1af667b2b266b1fd65586445b5e7a8a1b6b618 --- diff --git a/docs/dev-manual/build-system.rst b/docs/dev-manual/build-system.rst index 020a35fec0..fbdbedb2f4 100644 --- a/docs/dev-manual/build-system.rst +++ b/docs/dev-manual/build-system.rst @@ -543,6 +543,6 @@ The build system uses a few different mechanisms to influence the compilation: Additionally, the following file is generated by the build system: :file:`baseversion-gen.cpp` - Provides definitions for declarations in :file:`baseversion-gen.h` for + Provides definitions for declarations in :file:`baseversion_gen.h` for version info output. The contents are generated either from Git version info, or from static version info if not building from a git repository. diff --git a/docs/dev-manual/gmxtree.rst b/docs/dev-manual/gmxtree.rst index 2fc13566cd..f09a9ba45a 100644 --- a/docs/dev-manual/gmxtree.rst +++ b/docs/dev-manual/gmxtree.rst @@ -90,7 +90,7 @@ module and documenting it. modules, using ``gmx_install_headers()``. * All source files must include "gmxpre.h" as the first header. * A source/header file should include "config.h," "gromacs/simd/simd.h", - or "gromacs/ewald/pme-simd.h" if and only if it uses a macro declared + or "gromacs/ewald/pme_simd.h" if and only if it uses a macro declared in such files. * If the file has a git attribute to identify it as a candidate for include sorting, the include sorter described below should not produce any diff --git a/docs/dev-manual/naming.rst b/docs/dev-manual/naming.rst index 8a839d26f5..a9ba6d0ccf 100644 --- a/docs/dev-manual/naming.rst +++ b/docs/dev-manual/naming.rst @@ -20,9 +20,9 @@ Files readability and/or usability of the API, but this should then be clearly documented. - There can also be a :file:`{file}-impl.h` file that declares classes or + There can also be a :file:`{file}_impl.h` file that declares classes or functions that are not accessible outside the module. If the whole file only - declares symbols internal to the module, then the :file:`-impl.h` suffix is + declares symbols internal to the module, then the :file:`_impl.h` suffix is omitted. In most cases, declarations that are not used outside a single source file diff --git a/docs/doxygen/gmxtree.py b/docs/doxygen/gmxtree.py index b9f9be7c76..8f0dc41f22 100644 --- a/docs/doxygen/gmxtree.py +++ b/docs/doxygen/gmxtree.py @@ -2,7 +2,7 @@ # # 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. @@ -1079,5 +1079,5 @@ class GromacsTree(object): be checked.""" return (self._files['src/config.h'], self._files['src/gromacs/simd/simd.h'], - self._files['src/gromacs/ewald/pme-simd.h'], + self._files['src/gromacs/ewald/pme_simd.h'], self._files['src/gromacs/mdlib/nbnxn_simd.h']) diff --git a/docs/doxygen/lib/simd.md b/docs/doxygen/lib/simd.md index cbdbf3bd9a..1363f3728f 100644 --- a/docs/doxygen/lib/simd.md +++ b/docs/doxygen/lib/simd.md @@ -589,7 +589,7 @@ performance problem if the code does not correctly include `make check-source` checks the whole code for the use of symbols defined in `gromacs/simd/simd.h` and requires that files using those symbols do the correct include. Similar checking is done for higher-level -SIMD-management headers, e.g. `gromacs/ewald/pme-simd.h`. +SIMD-management headers, e.g. `gromacs/ewald/pme_simd.h`. The SIMD math library diff --git a/docs/doxygen/suppressions.txt b/docs/doxygen/suppressions.txt index dcbf13ce0a..3bfccc1c80 100644 --- a/docs/doxygen/suppressions.txt +++ b/docs/doxygen/suppressions.txt @@ -15,10 +15,10 @@ src/gromacs/utility/baseversion-gen.cpp: warning: does not include "gmxpre.h" fi # Exclude header files that are used for inlining code; the responsibility for # making the right #includes should be on the source file that uses these. # TODO: # Stop using the preprocessor for meta-programming! -src/gromacs/ewald/pme-simd4.h: warning: should include "pme-simd.h" -src/gromacs/ewald/pme-spline-work.cpp: warning: includes "simd.h" unnecessarily -src/gromacs/ewald/pme-spline-work.h: warning: includes "simd.h" unnecessarily -src/gromacs/ewald/pme-spread.cpp: warning: includes "simd.h" unnecessarily +src/gromacs/ewald/pme_simd4.h: warning: should include "pme_simd.h" +src/gromacs/ewald/pme_spline_work.cpp: warning: includes "simd.h" unnecessarily +src/gromacs/ewald/pme_spline_work.h: warning: includes "simd.h" unnecessarily +src/gromacs/ewald/pme_spread.cpp: warning: includes "simd.h" unnecessarily src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h: warning: should include "simd.h" src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h: warning: should include "simd.h" src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h: warning: should include "simd.h" diff --git a/src/api/cpp/context.cpp b/src/api/cpp/context.cpp index d11571e878..9c2398179c 100644 --- a/src/api/cpp/context.cpp +++ b/src/api/cpp/context.cpp @@ -70,9 +70,9 @@ #include "gmxapi/status.h" #include "gmxapi/version.h" -#include "context-impl.h" +#include "context_impl.h" #include "createsession.h" -#include "session-impl.h" +#include "session_impl.h" #include "workflow.h" namespace gmxapi diff --git a/src/api/cpp/context-impl.h b/src/api/cpp/context_impl.h similarity index 98% rename from src/api/cpp/context-impl.h rename to src/api/cpp/context_impl.h index 7b8ca47aae..0d90d1587c 100644 --- a/src/api/cpp/context-impl.h +++ b/src/api/cpp/context_impl.h @@ -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. diff --git a/src/api/cpp/md.cpp b/src/api/cpp/md.cpp index 5d235301f0..6ac41b7be2 100644 --- a/src/api/cpp/md.cpp +++ b/src/api/cpp/md.cpp @@ -42,7 +42,7 @@ #include "gmxapi/gmxapi.h" #include "gmxapi/md/mdmodule.h" -#include "md-impl.h" +#include "md_impl.h" namespace gmxapi { diff --git a/src/api/cpp/md-impl.h b/src/api/cpp/md_impl.h similarity index 97% rename from src/api/cpp/md-impl.h rename to src/api/cpp/md_impl.h index aa2a70d9ea..8eeda00d9e 100644 --- a/src/api/cpp/md-impl.h +++ b/src/api/cpp/md_impl.h @@ -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. diff --git a/src/api/cpp/mdsignals.h b/src/api/cpp/mdsignals.h index 2ebdd17f85..f5717a3f10 100644 --- a/src/api/cpp/mdsignals.h +++ b/src/api/cpp/mdsignals.h @@ -53,7 +53,7 @@ #include "gmxapi/session.h" #include "gmxapi/md/mdsignals.h" -#include "session-impl.h" +#include "session_impl.h" namespace gmxapi { diff --git a/src/api/cpp/session.cpp b/src/api/cpp/session.cpp index a5bfd0d624..d1abc69eb1 100644 --- a/src/api/cpp/session.cpp +++ b/src/api/cpp/session.cpp @@ -56,7 +56,7 @@ #include "createsession.h" #include "mdsignals.h" -#include "session-impl.h" +#include "session_impl.h" #include "sessionresources.h" namespace gmxapi diff --git a/src/api/cpp/session-impl.h b/src/api/cpp/session_impl.h similarity index 98% rename from src/api/cpp/session-impl.h rename to src/api/cpp/session_impl.h index 8c0d7488df..2f93738826 100644 --- a/src/api/cpp/session-impl.h +++ b/src/api/cpp/session_impl.h @@ -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. @@ -59,7 +59,7 @@ namespace gmxapi // Forward declaration class MpiContextManager; // Locally defined in session.cpp class ContextImpl; // locally defined in context.cpp -class SignalManager; // defined in mdsignals-impl.h +class SignalManager; // defined in mdsignals_impl.h /*! * \brief Implementation class for executing sessions. diff --git a/src/api/cpp/system.cpp b/src/api/cpp/system.cpp index 2493b0b8e3..666a14f4c4 100644 --- a/src/api/cpp/system.cpp +++ b/src/api/cpp/system.cpp @@ -47,7 +47,7 @@ #include "gmxapi/status.h" #include "gmxapi/system.h" -#include "system-impl.h" +#include "system_impl.h" #include "workflow.h" namespace gmxapi diff --git a/src/api/cpp/system-impl.h b/src/api/cpp/system_impl.h similarity index 97% rename from src/api/cpp/system-impl.h rename to src/api/cpp/system_impl.h index 26e400af1b..109de3f638 100644 --- a/src/api/cpp/system-impl.h +++ b/src/api/cpp/system_impl.h @@ -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. diff --git a/src/api/cpp/workflow.cpp b/src/api/cpp/workflow.cpp index cf90d806fb..5996d509dd 100644 --- a/src/api/cpp/workflow.cpp +++ b/src/api/cpp/workflow.cpp @@ -39,7 +39,7 @@ #include "gromacs/utility/gmxassert.h" -#include "workflow-impl.h" +#include "workflow_impl.h" namespace gmxapi { diff --git a/src/api/cpp/workflow/tests/workflow.cpp b/src/api/cpp/workflow/tests/workflow.cpp index ec04474bb4..75a92a8713 100644 --- a/src/api/cpp/workflow/tests/workflow.cpp +++ b/src/api/cpp/workflow/tests/workflow.cpp @@ -36,7 +36,7 @@ #include #include "api/cpp/workflow.h" -#include "api/cpp/workflow-impl.h" +#include "api/cpp/workflow_impl.h" #include "api/cpp/include/gmxapi/context.h" #include "api/cpp/include/gmxapi/status.h" #include "api/cpp/include/gmxapi/system.h" diff --git a/src/api/cpp/workflow-impl.h b/src/api/cpp/workflow_impl.h similarity index 97% rename from src/api/cpp/workflow-impl.h rename to src/api/cpp/workflow_impl.h index 57c6161d25..20efb36b33 100644 --- a/src/api/cpp/workflow-impl.h +++ b/src/api/cpp/workflow_impl.h @@ -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. diff --git a/src/gromacs/CMakeLists.txt b/src/gromacs/CMakeLists.txt index 4e242f1cc7..b4eb9e476f 100644 --- a/src/gromacs/CMakeLists.txt +++ b/src/gromacs/CMakeLists.txt @@ -95,7 +95,7 @@ endfunction() add_subdirectory(gmxlib) add_subdirectory(mdlib) -add_subdirectory(applied-forces) +add_subdirectory(applied_forces) add_subdirectory(listed_forces) add_subdirectory(commandline) add_subdirectory(domdec) @@ -435,12 +435,12 @@ if(GMX_USE_OPENCL) # Install the PME source and headers file(GLOB OPENCL_INSTALLED_FILES - ewald/pme-spread.clh - ewald/pme-solve.clh - ewald/pme-gather.clh - ewald/pme-gpu-utils.clh - ewald/pme-program.cl - ewald/pme-gpu-types.h + ewald/pme_spread.clh + ewald/pme_solve.clh + ewald/pme_gather.clh + ewald/pme_gpu_utils.clh + ewald/pme_program.cl + ewald/pme_gpu_types.h ) install(FILES ${OPENCL_INSTALLED_FILES} DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/ewald diff --git a/src/gromacs/applied-forces/CMakeLists.txt b/src/gromacs/applied_forces/CMakeLists.txt similarity index 95% rename from src/gromacs/applied-forces/CMakeLists.txt rename to src/gromacs/applied_forces/CMakeLists.txt index 702e776e0f..1bb3b7033f 100644 --- a/src/gromacs/applied-forces/CMakeLists.txt +++ b/src/gromacs/applied_forces/CMakeLists.txt @@ -1,7 +1,7 @@ # # This file is part of the GROMACS molecular simulation package. # -# Copyright (c) 2015,2016, by the GROMACS development team, led by +# Copyright (c) 2015,2016,2019, 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. diff --git a/src/gromacs/applied-forces/electricfield.cpp b/src/gromacs/applied_forces/electricfield.cpp similarity index 99% rename from src/gromacs/applied-forces/electricfield.cpp rename to src/gromacs/applied_forces/electricfield.cpp index 730aa55c43..5b6678f8f6 100644 --- a/src/gromacs/applied-forces/electricfield.cpp +++ b/src/gromacs/applied_forces/electricfield.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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/applied-forces/electricfield.h b/src/gromacs/applied_forces/electricfield.h similarity index 97% rename from src/gromacs/applied-forces/electricfield.h rename to src/gromacs/applied_forces/electricfield.h index a5d0f8f951..a68d48840b 100644 --- a/src/gromacs/applied-forces/electricfield.h +++ b/src/gromacs/applied_forces/electricfield.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by + * Copyright (c) 2015,2016,2017,2019, 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. diff --git a/src/gromacs/applied-forces/tests/CMakeLists.txt b/src/gromacs/applied_forces/tests/CMakeLists.txt similarity index 92% rename from src/gromacs/applied-forces/tests/CMakeLists.txt rename to src/gromacs/applied_forces/tests/CMakeLists.txt index 3788986961..d0c94c0ed3 100644 --- a/src/gromacs/applied-forces/tests/CMakeLists.txt +++ b/src/gromacs/applied_forces/tests/CMakeLists.txt @@ -1,7 +1,7 @@ # # This file is part of the GROMACS molecular simulation package. # -# Copyright (c) 2015,2016, by the GROMACS development team, led by +# Copyright (c) 2015,2016,2019, 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(AppliedForcesUnitTest applied-forces-test +gmx_add_unit_test(AppliedForcesUnitTest applied_forces-test electricfield.cpp ) diff --git a/src/gromacs/applied-forces/tests/electricfield.cpp b/src/gromacs/applied_forces/tests/electricfield.cpp similarity index 97% rename from src/gromacs/applied-forces/tests/electricfield.cpp rename to src/gromacs/applied_forces/tests/electricfield.cpp index f9ba3950a8..82c983e0ef 100644 --- a/src/gromacs/applied-forces/tests/electricfield.cpp +++ b/src/gromacs/applied_forces/tests/electricfield.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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 @@ */ #include "gmxpre.h" -#include "gromacs/applied-forces/electricfield.h" +#include "gromacs/applied_forces/electricfield.h" #include diff --git a/src/gromacs/awh/awh.cpp b/src/gromacs/awh/awh.cpp index 1e731a6fd8..87bc0812a2 100644 --- a/src/gromacs/awh/awh.cpp +++ b/src/gromacs/awh/awh.cpp @@ -57,12 +57,12 @@ #include "gromacs/fileio/enxio.h" #include "gromacs/gmxlib/network.h" #include "gromacs/math/units.h" -#include "gromacs/mdtypes/awh-history.h" -#include "gromacs/mdtypes/awh-params.h" +#include "gromacs/mdtypes/awh_history.h" +#include "gromacs/mdtypes/awh_params.h" #include "gromacs/mdtypes/commrec.h" #include "gromacs/mdtypes/forceoutput.h" #include "gromacs/mdtypes/inputrec.h" -#include "gromacs/mdtypes/pull-params.h" +#include "gromacs/mdtypes/pull_params.h" #include "gromacs/mdtypes/state.h" #include "gromacs/pbcutil/pbc.h" #include "gromacs/pulling/pull.h" diff --git a/src/gromacs/awh/bias.cpp b/src/gromacs/awh/bias.cpp index 3c39990acb..ecba420798 100644 --- a/src/gromacs/awh/bias.cpp +++ b/src/gromacs/awh/bias.cpp @@ -60,8 +60,8 @@ #include "gromacs/gmxlib/network.h" #include "gromacs/math/functions.h" #include "gromacs/math/utilities.h" -#include "gromacs/mdtypes/awh-history.h" -#include "gromacs/mdtypes/awh-params.h" +#include "gromacs/mdtypes/awh_history.h" +#include "gromacs/mdtypes/awh_params.h" #include "gromacs/mdtypes/commrec.h" #include "gromacs/utility/exceptions.h" #include "gromacs/utility/gmxassert.h" diff --git a/src/gromacs/awh/biasparams.cpp b/src/gromacs/awh/biasparams.cpp index f4db497002..a02f4e4d8d 100644 --- a/src/gromacs/awh/biasparams.cpp +++ b/src/gromacs/awh/biasparams.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -51,7 +51,7 @@ #include #include "gromacs/math/functions.h" -#include "gromacs/mdtypes/awh-params.h" +#include "gromacs/mdtypes/awh_params.h" #include "gromacs/utility/arrayref.h" #include "gromacs/utility/exceptions.h" #include "gromacs/utility/gmxassert.h" diff --git a/src/gromacs/awh/biassharing.cpp b/src/gromacs/awh/biassharing.cpp index 0dfe8acec3..ca752a9845 100644 --- a/src/gromacs/awh/biassharing.cpp +++ b/src/gromacs/awh/biassharing.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -48,7 +48,7 @@ #include #include "gromacs/gmxlib/network.h" -#include "gromacs/mdtypes/awh-params.h" +#include "gromacs/mdtypes/awh_params.h" #include "gromacs/mdtypes/commrec.h" #include "gromacs/utility/exceptions.h" #include "gromacs/utility/stringutil.h" diff --git a/src/gromacs/awh/biasstate.cpp b/src/gromacs/awh/biasstate.cpp index c45f8f19b5..26ac4af4f3 100644 --- a/src/gromacs/awh/biasstate.cpp +++ b/src/gromacs/awh/biasstate.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -58,8 +58,8 @@ #include "gromacs/fileio/xvgr.h" #include "gromacs/gmxlib/network.h" #include "gromacs/math/utilities.h" -#include "gromacs/mdtypes/awh-history.h" -#include "gromacs/mdtypes/awh-params.h" +#include "gromacs/mdtypes/awh_history.h" +#include "gromacs/mdtypes/awh_params.h" #include "gromacs/mdtypes/commrec.h" #include "gromacs/simd/simd.h" #include "gromacs/simd/simd_math.h" diff --git a/src/gromacs/awh/biaswriter.cpp b/src/gromacs/awh/biaswriter.cpp index cc45086a6e..d31ac315c1 100644 --- a/src/gromacs/awh/biaswriter.cpp +++ b/src/gromacs/awh/biaswriter.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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 @@ #include #include "gromacs/awh/awh.h" -#include "gromacs/mdtypes/awh-params.h" +#include "gromacs/mdtypes/awh_params.h" #include "gromacs/mdtypes/commrec.h" #include "gromacs/trajectory/energyframe.h" #include "gromacs/utility/gmxassert.h" diff --git a/src/gromacs/awh/coordstate.cpp b/src/gromacs/awh/coordstate.cpp index efd58c3397..8173431b96 100644 --- a/src/gromacs/awh/coordstate.cpp +++ b/src/gromacs/awh/coordstate.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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 #include "gromacs/math/utilities.h" -#include "gromacs/mdtypes/awh-history.h" -#include "gromacs/mdtypes/awh-params.h" +#include "gromacs/mdtypes/awh_history.h" +#include "gromacs/mdtypes/awh_params.h" #include "gromacs/random/threefry.h" #include "gromacs/random/uniformrealdistribution.h" #include "gromacs/utility/arrayref.h" diff --git a/src/gromacs/awh/correlationhistory.cpp b/src/gromacs/awh/correlationhistory.cpp index 47ecb44a27..195e3d265e 100644 --- a/src/gromacs/awh/correlationhistory.cpp +++ b/src/gromacs/awh/correlationhistory.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -50,7 +50,7 @@ #include #include "gromacs/gmxlib/network.h" -#include "gromacs/mdtypes/awh-correlation-history.h" +#include "gromacs/mdtypes/awh_correlation_history.h" #include "gromacs/mdtypes/commrec.h" #include "gromacs/utility/arrayref.h" #include "gromacs/utility/exceptions.h" diff --git a/src/gromacs/awh/grid.cpp b/src/gromacs/awh/grid.cpp index 6cebf587fe..b9a188d841 100644 --- a/src/gromacs/awh/grid.cpp +++ b/src/gromacs/awh/grid.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -54,7 +54,7 @@ #include "gromacs/math/functions.h" #include "gromacs/math/utilities.h" -#include "gromacs/mdtypes/awh-params.h" +#include "gromacs/mdtypes/awh_params.h" #include "gromacs/utility/cstringutil.h" #include "gromacs/utility/exceptions.h" #include "gromacs/utility/gmxassert.h" diff --git a/src/gromacs/awh/histogramsize.cpp b/src/gromacs/awh/histogramsize.cpp index ffcae4e481..2810229ee1 100644 --- a/src/gromacs/awh/histogramsize.cpp +++ b/src/gromacs/awh/histogramsize.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -52,8 +52,8 @@ #include -#include "gromacs/mdtypes/awh-history.h" -#include "gromacs/mdtypes/awh-params.h" +#include "gromacs/mdtypes/awh_history.h" +#include "gromacs/mdtypes/awh_params.h" #include "gromacs/utility/gmxassert.h" #include "gromacs/utility/stringutil.h" diff --git a/src/gromacs/awh/pointstate.h b/src/gromacs/awh/pointstate.h index 414d644ba0..2215344418 100644 --- a/src/gromacs/awh/pointstate.h +++ b/src/gromacs/awh/pointstate.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -52,8 +52,8 @@ #include -#include "gromacs/mdtypes/awh-history.h" -#include "gromacs/mdtypes/awh-params.h" +#include "gromacs/mdtypes/awh_history.h" +#include "gromacs/mdtypes/awh_params.h" #include "gromacs/utility/gmxassert.h" #include "biasparams.h" diff --git a/src/gromacs/awh/read-params.cpp b/src/gromacs/awh/read_params.cpp similarity index 99% rename from src/gromacs/awh/read-params.cpp rename to src/gromacs/awh/read_params.cpp index db83a07584..a02b54fc4a 100644 --- a/src/gromacs/awh/read-params.cpp +++ b/src/gromacs/awh/read_params.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. @@ -36,7 +36,7 @@ */ #include "gmxpre.h" -#include "read-params.h" +#include "read_params.h" #include "gromacs/awh/awh.h" #include "gromacs/fileio/readinp.h" @@ -44,10 +44,10 @@ #include "gromacs/math/units.h" #include "gromacs/math/utilities.h" #include "gromacs/math/vec.h" -#include "gromacs/mdtypes/awh-params.h" +#include "gromacs/mdtypes/awh_params.h" #include "gromacs/mdtypes/inputrec.h" #include "gromacs/mdtypes/md_enums.h" -#include "gromacs/mdtypes/pull-params.h" +#include "gromacs/mdtypes/pull_params.h" #include "gromacs/pbcutil/pbc.h" #include "gromacs/pulling/pull.h" #include "gromacs/random/seed.h" diff --git a/src/gromacs/awh/read-params.h b/src/gromacs/awh/read_params.h similarity index 97% rename from src/gromacs/awh/read-params.h rename to src/gromacs/awh/read_params.h index 5c5be7a4f9..fa953974ea 100644 --- a/src/gromacs/awh/read-params.h +++ b/src/gromacs/awh/read_params.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * 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/awh/tests/bias.cpp b/src/gromacs/awh/tests/bias.cpp index 8e4475ed5c..4477b7239d 100644 --- a/src/gromacs/awh/tests/bias.cpp +++ b/src/gromacs/awh/tests/bias.cpp @@ -47,7 +47,7 @@ #include "gromacs/awh/correlationgrid.h" #include "gromacs/awh/pointstate.h" -#include "gromacs/mdtypes/awh-params.h" +#include "gromacs/mdtypes/awh_params.h" #include "gromacs/utility/stringutil.h" #include "testutils/refdata.h" diff --git a/src/gromacs/awh/tests/biasstate.cpp b/src/gromacs/awh/tests/biasstate.cpp index 06c871608d..2d65d5be68 100644 --- a/src/gromacs/awh/tests/biasstate.cpp +++ b/src/gromacs/awh/tests/biasstate.cpp @@ -47,7 +47,7 @@ #include "gromacs/awh/grid.h" #include "gromacs/awh/pointstate.h" #include "gromacs/math/functions.h" -#include "gromacs/mdtypes/awh-params.h" +#include "gromacs/mdtypes/awh_params.h" #include "gromacs/utility/smalloc.h" #include "testutils/testasserts.h" diff --git a/src/gromacs/awh/tests/grid.cpp b/src/gromacs/awh/tests/grid.cpp index 772490e0a1..04adccf90a 100644 --- a/src/gromacs/awh/tests/grid.cpp +++ b/src/gromacs/awh/tests/grid.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -44,7 +44,7 @@ #include #include -#include "gromacs/mdtypes/awh-params.h" +#include "gromacs/mdtypes/awh_params.h" #include "gromacs/utility/gmxassert.h" #include "testutils/testasserts.h" diff --git a/src/gromacs/commandline/cmdlinehelpmodule.h b/src/gromacs/commandline/cmdlinehelpmodule.h index 497d87d700..8ff0bdeb82 100644 --- a/src/gromacs/commandline/cmdlinehelpmodule.h +++ b/src/gromacs/commandline/cmdlinehelpmodule.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2012,2013,2014,2015,2018, by the GROMACS development team, led by + * Copyright (c) 2012,2013,2014,2015,2018,2019, 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/onlinehelp/ihelptopic.h" #include "gromacs/utility/classhelpers.h" -#include "cmdlinemodulemanager-impl.h" +#include "cmdlinemodulemanager_impl.h" namespace gmx { diff --git a/src/gromacs/commandline/cmdlinemodulemanager.cpp b/src/gromacs/commandline/cmdlinemodulemanager.cpp index d9ff26e43c..85e88e344b 100644 --- a/src/gromacs/commandline/cmdlinemodulemanager.cpp +++ b/src/gromacs/commandline/cmdlinemodulemanager.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. @@ -66,7 +66,7 @@ #include "gromacs/utility/sysinfo.h" #include "cmdlinehelpmodule.h" -#include "cmdlinemodulemanager-impl.h" +#include "cmdlinemodulemanager_impl.h" namespace gmx { diff --git a/src/gromacs/commandline/cmdlinemodulemanager-impl.h b/src/gromacs/commandline/cmdlinemodulemanager_impl.h similarity index 98% rename from src/gromacs/commandline/cmdlinemodulemanager-impl.h rename to src/gromacs/commandline/cmdlinemodulemanager_impl.h index 53b54c8664..0141f24138 100644 --- a/src/gromacs/commandline/cmdlinemodulemanager-impl.h +++ b/src/gromacs/commandline/cmdlinemodulemanager_impl.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by + * Copyright (c) 2012,2013,2014,2015,2019, 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. diff --git a/src/gromacs/domdec/domdec.cpp b/src/gromacs/domdec/domdec.cpp index d4a5169b6c..3a7a230a66 100644 --- a/src/gromacs/domdec/domdec.cpp +++ b/src/gromacs/domdec/domdec.cpp @@ -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/ewald/CMakeLists.txt b/src/gromacs/ewald/CMakeLists.txt index 05654eda2d..318a36c6c3 100644 --- a/src/gromacs/ewald/CMakeLists.txt +++ b/src/gromacs/ewald/CMakeLists.txt @@ -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. @@ -33,55 +33,55 @@ # the research papers on the package. Check out http://www.gromacs.org. gmx_add_libgromacs_sources( - calculate-spline-moduli.cpp + calculate_spline_moduli.cpp ewald.cpp - ewald-utils.cpp - long-range-correction.cpp + ewald_utils.cpp + long_range_correction.cpp pme.cpp - pme-gather.cpp - pme-grid.cpp - pme-load-balancing.cpp - pme-only.cpp - pme-pp.cpp - pme-redistribute.cpp - pme-solve.cpp - pme-spline-work.cpp - pme-spread.cpp + pme_gather.cpp + pme_grid.cpp + pme_load_balancing.cpp + pme_only.cpp + pme_pp.cpp + pme_redistribute.cpp + pme_solve.cpp + pme_spline_work.cpp + pme_spread.cpp # Files that implement stubs - pme-gpu-program.cpp + pme_gpu_program.cpp ) if (GMX_USE_CUDA) gmx_add_libgromacs_sources( # CUDA-specific sources - pme-gather.cu - pme-gpu-3dfft.cu - pme-solve.cu - pme-spread.cu - pme-gpu-program-impl.cu + pme_gather.cu + pme_gpu_3dfft.cu + pme_solve.cu + pme_spread.cu + pme_gpu_program_impl.cu # GPU-specific sources - pme-gpu.cpp - pme-gpu-internal.cpp - pme-gpu-timings.cpp + pme_gpu.cpp + pme_gpu_internal.cpp + pme_gpu_timings.cpp ) gmx_compile_cpp_as_cuda( - pme-gpu-internal.cpp - pme-gpu-program.cpp - pme-gpu-timings.cpp + pme_gpu_internal.cpp + pme_gpu_program.cpp + pme_gpu_timings.cpp ) elseif (GMX_USE_OPENCL) gmx_add_libgromacs_sources( # OpenCL-specific sources - pme-gpu-3dfft-ocl.cpp - pme-gpu-program-impl-ocl.cpp + pme_gpu_3dfft_ocl.cpp + pme_gpu_program_impl_ocl.cpp # GPU-specific sources - pme-gpu.cpp - pme-gpu-internal.cpp - pme-gpu-timings.cpp + pme_gpu.cpp + pme_gpu_internal.cpp + pme_gpu_timings.cpp ) else() gmx_add_libgromacs_sources( # Files that implement stubs - pme-gpu-program-impl.cpp + pme_gpu_program_impl.cpp ) endif() diff --git a/src/gromacs/ewald/calculate-spline-moduli.cpp b/src/gromacs/ewald/calculate_spline_moduli.cpp similarity index 97% rename from src/gromacs/ewald/calculate-spline-moduli.cpp rename to src/gromacs/ewald/calculate_spline_moduli.cpp index d25620e9cb..ac2136e5c0 100644 --- a/src/gromacs/ewald/calculate-spline-moduli.cpp +++ b/src/gromacs/ewald/calculate_spline_moduli.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, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015,2016,2017,2019, 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. @@ -36,7 +36,7 @@ */ #include "gmxpre.h" -#include "calculate-spline-moduli.h" +#include "calculate_spline_moduli.h" #include @@ -48,7 +48,7 @@ #include "gromacs/utility/gmxassert.h" #include "gromacs/utility/smalloc.h" -#include "pme-internal.h" +#include "pme_internal.h" static void make_dft_mod(real *mod, const double *data, int splineOrder, int ndata) diff --git a/src/gromacs/ewald/calculate-spline-moduli.h b/src/gromacs/ewald/calculate_spline_moduli.h similarity index 95% rename from src/gromacs/ewald/calculate-spline-moduli.h rename to src/gromacs/ewald/calculate_spline_moduli.h index 3e33e6a053..35746f60e5 100644 --- a/src/gromacs/ewald/calculate-spline-moduli.h +++ b/src/gromacs/ewald/calculate_spline_moduli.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, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015,2019, 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. @@ -37,7 +37,7 @@ #ifndef GMX_EWALD_CALCULATE_SPLINE_MODULI_H #define GMX_EWALD_CALCULATE_SPLINE_MODULI_H -#include "pme-internal.h" +#include "pme_internal.h" /* Calulate plain SPME B-spline interpolation */ void make_bspline_moduli(splinevec bsp_mod, diff --git a/src/gromacs/ewald/ewald.cpp b/src/gromacs/ewald/ewald.cpp index 696a47c9d3..a16f0599ab 100644 --- a/src/gromacs/ewald/ewald.cpp +++ b/src/gromacs/ewald/ewald.cpp @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2013,2014,2015,2017,2018, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015,2017,2018,2019, 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. @@ -55,7 +55,7 @@ #include -#include "gromacs/ewald/ewald-utils.h" +#include "gromacs/ewald/ewald_utils.h" #include "gromacs/math/functions.h" #include "gromacs/math/gmxcomplex.h" #include "gromacs/math/units.h" diff --git a/src/gromacs/ewald/ewald-utils.cpp b/src/gromacs/ewald/ewald_utils.cpp similarity index 96% rename from src/gromacs/ewald/ewald-utils.cpp rename to src/gromacs/ewald/ewald_utils.cpp index 5bab76eadc..be6727af06 100644 --- a/src/gromacs/ewald/ewald-utils.cpp +++ b/src/gromacs/ewald/ewald_utils.cpp @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2013,2014,2015,2017, 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. @@ -36,7 +36,7 @@ */ #include "gmxpre.h" -#include "ewald-utils.h" +#include "ewald_utils.h" #include diff --git a/src/gromacs/ewald/ewald-utils.h b/src/gromacs/ewald/ewald_utils.h similarity index 98% rename from src/gromacs/ewald/ewald-utils.h rename to src/gromacs/ewald/ewald_utils.h index 39ca3e81b3..ab760f8efb 100644 --- a/src/gromacs/ewald/ewald-utils.h +++ b/src/gromacs/ewald/ewald_utils.h @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2013,2014,2017, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2017,2019, 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. diff --git a/src/gromacs/ewald/long-range-correction.cpp b/src/gromacs/ewald/long_range_correction.cpp similarity index 99% rename from src/gromacs/ewald/long-range-correction.cpp rename to src/gromacs/ewald/long_range_correction.cpp index 0a83727190..6a93d0a57d 100644 --- a/src/gromacs/ewald/long-range-correction.cpp +++ b/src/gromacs/ewald/long_range_correction.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. @@ -36,11 +36,11 @@ */ #include "gmxpre.h" -#include "long-range-correction.h" +#include "long_range_correction.h" #include -#include "gromacs/ewald/ewald-utils.h" +#include "gromacs/ewald/ewald_utils.h" #include "gromacs/math/functions.h" #include "gromacs/math/units.h" #include "gromacs/math/utilities.h" @@ -52,7 +52,7 @@ #include "gromacs/utility/fatalerror.h" #include "gromacs/utility/gmxassert.h" -#include "pme-internal.h" +#include "pme_internal.h" /* There's nothing special to do here if just masses are perturbed, * but if either charge or type is perturbed then the implementation diff --git a/src/gromacs/ewald/long-range-correction.h b/src/gromacs/ewald/long_range_correction.h similarity index 97% rename from src/gromacs/ewald/long-range-correction.h rename to src/gromacs/ewald/long_range_correction.h index 37108de07f..c060deb764 100644 --- a/src/gromacs/ewald/long-range-correction.h +++ b/src/gromacs/ewald/long_range_correction.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. diff --git a/src/gromacs/ewald/pme.cpp b/src/gromacs/ewald/pme.cpp index fab7970464..f906a04e45 100644 --- a/src/gromacs/ewald/pme.cpp +++ b/src/gromacs/ewald/pme.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. @@ -83,7 +83,7 @@ #include #include "gromacs/domdec/domdec.h" -#include "gromacs/ewald/ewald-utils.h" +#include "gromacs/ewald/ewald_utils.h" #include "gromacs/fft/parallel_3dfft.h" #include "gromacs/fileio/pdbio.h" #include "gromacs/gmxlib/network.h" @@ -115,15 +115,15 @@ #include "gromacs/utility/stringutil.h" #include "gromacs/utility/unique_cptr.h" -#include "calculate-spline-moduli.h" -#include "pme-gather.h" -#include "pme-gpu-internal.h" -#include "pme-grid.h" -#include "pme-internal.h" -#include "pme-redistribute.h" -#include "pme-solve.h" -#include "pme-spline-work.h" -#include "pme-spread.h" +#include "calculate_spline_moduli.h" +#include "pme_gather.h" +#include "pme_gpu_internal.h" +#include "pme_grid.h" +#include "pme_internal.h" +#include "pme_redistribute.h" +#include "pme_solve.h" +#include "pme_spline_work.h" +#include "pme_spread.h" /*! \brief Help build a descriptive message in \c error if there are * \c errorReasons why PME on GPU is not supported. diff --git a/src/gromacs/ewald/pme.cuh b/src/gromacs/ewald/pme.cuh index fd18de2c0d..3994a84d83 100644 --- a/src/gromacs/ewald/pme.cuh +++ b/src/gromacs/ewald/pme.cuh @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -45,9 +45,9 @@ #include "gromacs/math/vectypes.h" // for DIM -#include "pme-gpu-constants.h" -#include "pme-gpu-internal.h" // for GridOrdering -#include "pme-gpu-types.h" +#include "pme_gpu_constants.h" +#include "pme_gpu_internal.h" // for GridOrdering +#include "pme_gpu_types.h" /*! \brief \internal * A single structure encompassing all the PME data used in CUDA kernels. diff --git a/src/gromacs/ewald/pme-gather.clh b/src/gromacs/ewald/pme_gather.clh similarity index 98% rename from src/gromacs/ewald/pme-gather.clh rename to src/gromacs/ewald/pme_gather.clh index e795d4dd70..8b19f474a5 100644 --- a/src/gromacs/ewald/pme-gather.clh +++ b/src/gromacs/ewald/pme_gather.clh @@ -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. @@ -37,7 +37,7 @@ * \brief Implements PME OpenCL force gathering kernel. * When including this and other PME OpenCL kernel files, plenty of common * constants/macros are expected to be defined (such as "order" which is PME interpolation order). - * For details, please see how pme-program.cl is compiled in pme-gpu-program-impl-ocl.cpp. + * For details, please see how pme_program.cl is compiled in pme_gpu_program_impl_ocl.cpp. * * This file's kernels specifically expect the following definitions: * @@ -51,8 +51,8 @@ * \author Aleksei Iupinov */ -#include "pme-gpu-types.h" -#include "pme-gpu-utils.clh" +#include "pme_gpu_types.h" +#include "pme_gpu_utils.clh" #ifndef COMPILE_GATHER_HELPERS_ONCE #define COMPILE_GATHER_HELPERS_ONCE diff --git a/src/gromacs/ewald/pme-gather.cpp b/src/gromacs/ewald/pme_gather.cpp similarity index 98% rename from src/gromacs/ewald/pme-gather.cpp rename to src/gromacs/ewald/pme_gather.cpp index b939468ab6..0802005eab 100644 --- a/src/gromacs/ewald/pme-gather.cpp +++ b/src/gromacs/ewald/pme_gather.cpp @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2013,2014,2015,2017,2018, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015,2017,2018,2019, 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. @@ -37,7 +37,7 @@ #include "gmxpre.h" -#include "pme-gather.h" +#include "pme_gather.h" #include "gromacs/math/vec.h" #include "gromacs/simd/simd.h" @@ -46,9 +46,9 @@ #include "gromacs/utility/smalloc.h" #include "gromacs/utility/typetraits.h" -#include "pme-internal.h" -#include "pme-simd.h" -#include "pme-spline-work.h" +#include "pme_internal.h" +#include "pme_simd.h" +#include "pme_spline_work.h" using namespace gmx; // TODO: Remove when this file is moved into gmx namespace diff --git a/src/gromacs/ewald/pme-gather.cu b/src/gromacs/ewald/pme_gather.cu similarity index 99% rename from src/gromacs/ewald/pme-gather.cu rename to src/gromacs/ewald/pme_gather.cu index b8297c4d68..e9775a5dd0 100644 --- a/src/gromacs/ewald/pme-gather.cu +++ b/src/gromacs/ewald/pme_gather.cu @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -44,7 +44,7 @@ #include #include "pme.cuh" -#include "pme-gpu-utils.h" +#include "pme_gpu_utils.h" /*! \brief * An inline CUDA function: unroll the dynamic index accesses to the constant grid sizes to avoid local memory operations. diff --git a/src/gromacs/ewald/pme-gather.h b/src/gromacs/ewald/pme_gather.h similarity index 94% rename from src/gromacs/ewald/pme-gather.h rename to src/gromacs/ewald/pme_gather.h index 864eda3be2..384c72598d 100644 --- a/src/gromacs/ewald/pme-gather.h +++ b/src/gromacs/ewald/pme_gather.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014,2015,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -37,7 +37,7 @@ #include "gromacs/utility/real.h" -#include "pme-internal.h" +#include "pme_internal.h" void gather_f_bsplines(const struct gmx_pme_t *pme, const real *grid, diff --git a/src/gromacs/ewald/pme-gpu.cpp b/src/gromacs/ewald/pme_gpu.cpp similarity index 98% rename from src/gromacs/ewald/pme-gpu.cpp rename to src/gromacs/ewald/pme_gpu.cpp index 40c653bb83..efe4a60235 100644 --- a/src/gromacs/ewald/pme-gpu.cpp +++ b/src/gromacs/ewald/pme_gpu.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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 -#include "gromacs/ewald/ewald-utils.h" +#include "gromacs/ewald/ewald_utils.h" #include "gromacs/ewald/pme.h" #include "gromacs/fft/parallel_3dfft.h" #include "gromacs/math/invertmatrix.h" @@ -59,10 +59,10 @@ #include "gromacs/utility/gmxassert.h" #include "gromacs/utility/stringutil.h" -#include "pme-gpu-internal.h" -#include "pme-grid.h" -#include "pme-internal.h" -#include "pme-solve.h" +#include "pme_gpu_internal.h" +#include "pme_grid.h" +#include "pme_internal.h" +#include "pme_solve.h" void pme_gpu_reset_timings(const gmx_pme_t *pme) { diff --git a/src/gromacs/ewald/pme-gpu-3dfft.cu b/src/gromacs/ewald/pme_gpu_3dfft.cu similarity index 96% rename from src/gromacs/ewald/pme-gpu-3dfft.cu rename to src/gromacs/ewald/pme_gpu_3dfft.cu index 4445e2475d..c36d440b14 100644 --- a/src/gromacs/ewald/pme-gpu-3dfft.cu +++ b/src/gromacs/ewald/pme_gpu_3dfft.cu @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -42,15 +42,15 @@ #include "gmxpre.h" -#include "pme-gpu-3dfft.h" +#include "pme_gpu_3dfft.h" #include "gromacs/utility/fatalerror.h" #include "gromacs/utility/gmxassert.h" #include "pme.cuh" -#include "pme-gpu-types.h" -#include "pme-gpu-types-host.h" -#include "pme-gpu-types-host-impl.h" +#include "pme_gpu_types.h" +#include "pme_gpu_types_host.h" +#include "pme_gpu_types_host_impl.h" static void handleCufftError(cufftResult_t status, const char *msg) { diff --git a/src/gromacs/ewald/pme-gpu-3dfft.h b/src/gromacs/ewald/pme_gpu_3dfft.h similarity index 97% rename from src/gromacs/ewald/pme-gpu-3dfft.h rename to src/gromacs/ewald/pme_gpu_3dfft.h index 6da6b86d85..cee64552e8 100644 --- a/src/gromacs/ewald/pme-gpu-3dfft.h +++ b/src/gromacs/ewald/pme_gpu_3dfft.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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/ewald/pme-gpu-3dfft-ocl.cpp b/src/gromacs/ewald/pme_gpu_3dfft_ocl.cpp similarity index 97% rename from src/gromacs/ewald/pme-gpu-3dfft-ocl.cpp rename to src/gromacs/ewald/pme_gpu_3dfft_ocl.cpp index 729a32a07d..e2019ba558 100644 --- a/src/gromacs/ewald/pme-gpu-3dfft-ocl.cpp +++ b/src/gromacs/ewald/pme_gpu_3dfft_ocl.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -48,10 +48,10 @@ #include "gromacs/utility/gmxassert.h" #include "gromacs/utility/stringutil.h" -#include "pme-gpu-3dfft.h" -#include "pme-gpu-internal.h" -#include "pme-gpu-types.h" -#include "pme-gpu-types-host-impl.h" +#include "pme_gpu_3dfft.h" +#include "pme_gpu_internal.h" +#include "pme_gpu_types.h" +#include "pme_gpu_types_host_impl.h" //! Throws the exception on clFFT error static void handleClfftError(clfftStatus status, const char *msg) diff --git a/src/gromacs/ewald/pme-gpu-constants.h b/src/gromacs/ewald/pme_gpu_constants.h similarity index 99% rename from src/gromacs/ewald/pme-gpu-constants.h rename to src/gromacs/ewald/pme_gpu_constants.h index ca108915e2..695a9e220c 100644 --- a/src/gromacs/ewald/pme-gpu-constants.h +++ b/src/gromacs/ewald/pme_gpu_constants.h @@ -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. diff --git a/src/gromacs/ewald/pme-gpu-internal.cpp b/src/gromacs/ewald/pme_gpu_internal.cpp similarity index 99% rename from src/gromacs/ewald/pme-gpu-internal.cpp rename to src/gromacs/ewald/pme_gpu_internal.cpp index a8d98e96cf..27da475ac8 100644 --- a/src/gromacs/ewald/pme-gpu-internal.cpp +++ b/src/gromacs/ewald/pme_gpu_internal.cpp @@ -47,7 +47,7 @@ #include "gmxpre.h" -#include "pme-gpu-internal.h" +#include "pme_gpu_internal.h" #include "config.h" @@ -55,7 +55,7 @@ #include #include -#include "gromacs/ewald/ewald-utils.h" +#include "gromacs/ewald/ewald_utils.h" #include "gromacs/gpu_utils/gpu_utils.h" #include "gromacs/math/invertmatrix.h" #include "gromacs/math/units.h" @@ -76,17 +76,17 @@ #include "gromacs/ewald/pme.h" -#include "pme-gpu-3dfft.h" -#include "pme-gpu-constants.h" -#include "pme-gpu-program-impl.h" -#include "pme-gpu-timings.h" -#include "pme-gpu-types.h" -#include "pme-gpu-types-host.h" -#include "pme-gpu-types-host-impl.h" -#include "pme-gpu-utils.h" -#include "pme-grid.h" -#include "pme-internal.h" -#include "pme-solve.h" +#include "pme_gpu_3dfft.h" +#include "pme_gpu_constants.h" +#include "pme_gpu_program_impl.h" +#include "pme_gpu_timings.h" +#include "pme_gpu_types.h" +#include "pme_gpu_types_host.h" +#include "pme_gpu_types_host_impl.h" +#include "pme_gpu_utils.h" +#include "pme_grid.h" +#include "pme_internal.h" +#include "pme_solve.h" /*! \internal \brief * Wrapper for getting a pointer to the plain C++ part of the GPU kernel parameters structure. diff --git a/src/gromacs/ewald/pme-gpu-internal.h b/src/gromacs/ewald/pme_gpu_internal.h similarity index 98% rename from src/gromacs/ewald/pme-gpu-internal.h rename to src/gromacs/ewald/pme_gpu_internal.h index 652c7f7aa5..afe3bf65ab 100644 --- a/src/gromacs/ewald/pme-gpu-internal.h +++ b/src/gromacs/ewald/pme_gpu_internal.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -37,7 +37,7 @@ * * \brief This file contains internal function definitions for performing the PME calculations on GPU. * These are not meant to be exposed outside of the PME GPU code. - * As of now, their bodies are still in the common pme-gpu.cpp files. + * As of now, their bodies are still in the common pme_gpu.cpp files. * * \author Aleksei Iupinov * \ingroup module_ewald @@ -50,7 +50,7 @@ #include "gromacs/gpu_utils/gpu_macros.h" // for the GPU_FUNC_ macros #include "gromacs/utility/arrayref.h" -#include "pme-gpu-types-host.h" // for the inline functions accessing PmeGpu members +#include "pme_gpu_types_host.h" // for the inline functions accessing PmeGpu members struct gmx_hw_info_t; struct gmx_gpu_opt_t; @@ -356,7 +356,7 @@ void pme_gpu_reinit_3dfft(const PmeGpu *pmeGpu); */ void pme_gpu_destroy_3dfft(const PmeGpu *pmeGpu); -/* Several GPU event-based timing functions that live in pme-gpu-timings.cpp */ +/* Several GPU event-based timing functions that live in pme_gpu_timings.cpp */ /*! \libinternal \brief * Finalizes all the active PME GPU stage timings for the current computation. Should be called at the end of every computation. @@ -529,7 +529,7 @@ inline bool pme_gpu_is_testing(const PmeGpu *pmeGpu) return pmeGpu->settings.copyAllOutputs; } -/* A block of C++ functions that live in pme-gpu-internal.cpp */ +/* A block of C++ functions that live in pme_gpu_internal.cpp */ /*! \libinternal \brief * Returns the energy and virial GPU outputs, useful for testing. diff --git a/src/gromacs/ewald/pme-gpu-program.cpp b/src/gromacs/ewald/pme_gpu_program.cpp similarity index 97% rename from src/gromacs/ewald/pme-gpu-program.cpp rename to src/gromacs/ewald/pme_gpu_program.cpp index fbb1a8eeb7..67e6a4e1c9 100644 --- a/src/gromacs/ewald/pme-gpu-program.cpp +++ b/src/gromacs/ewald/pme_gpu_program.cpp @@ -45,11 +45,11 @@ #include "gmxpre.h" -#include "pme-gpu-program.h" +#include "pme_gpu_program.h" #include -#include "pme-gpu-program-impl.h" +#include "pme_gpu_program_impl.h" PmeGpuProgram::PmeGpuProgram(const gmx_device_info_t *deviceInfo) : impl_(std::make_unique(deviceInfo)) diff --git a/src/gromacs/ewald/pme-gpu-program.h b/src/gromacs/ewald/pme_gpu_program.h similarity index 97% rename from src/gromacs/ewald/pme-gpu-program.h rename to src/gromacs/ewald/pme_gpu_program.h index 76045e32bf..de4eb562a6 100644 --- a/src/gromacs/ewald/pme-gpu-program.h +++ b/src/gromacs/ewald/pme_gpu_program.h @@ -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. diff --git a/src/gromacs/ewald/pme-gpu-program-impl.cpp b/src/gromacs/ewald/pme_gpu_program_impl.cpp similarity index 95% rename from src/gromacs/ewald/pme-gpu-program-impl.cpp rename to src/gromacs/ewald/pme_gpu_program_impl.cpp index 47297e3ece..cb993bea8b 100644 --- a/src/gromacs/ewald/pme-gpu-program-impl.cpp +++ b/src/gromacs/ewald/pme_gpu_program_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. @@ -43,7 +43,7 @@ #include "gmxpre.h" -#include "pme-gpu-program-impl.h" +#include "pme_gpu_program_impl.h" PmeGpuProgramImpl::PmeGpuProgramImpl(const gmx_device_info_t * /*unused*/) : warpSize(0), diff --git a/src/gromacs/ewald/pme-gpu-program-impl.cu b/src/gromacs/ewald/pme_gpu_program_impl.cu similarity index 95% rename from src/gromacs/ewald/pme-gpu-program-impl.cu rename to src/gromacs/ewald/pme_gpu_program_impl.cu index db2f1b178d..087d85f50e 100644 --- a/src/gromacs/ewald/pme-gpu-program-impl.cu +++ b/src/gromacs/ewald/pme_gpu_program_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. @@ -43,11 +43,11 @@ */ #include "gmxpre.h" -#include "pme-gpu-program-impl.h" +#include "pme_gpu_program_impl.h" -#include "pme-gpu-constants.h" -#include "pme-gpu-internal.h" // for GridOrdering enum -#include "pme-gpu-types-host.h" +#include "pme_gpu_constants.h" +#include "pme_gpu_internal.h" // for GridOrdering enum +#include "pme_gpu_types_host.h" // PME interpolation order constexpr int c_pmeOrder = 4; diff --git a/src/gromacs/ewald/pme-gpu-program-impl.h b/src/gromacs/ewald/pme_gpu_program_impl.h similarity index 98% rename from src/gromacs/ewald/pme-gpu-program-impl.h rename to src/gromacs/ewald/pme_gpu_program_impl.h index 2f2bf68564..f1c114115f 100644 --- a/src/gromacs/ewald/pme-gpu-program-impl.h +++ b/src/gromacs/ewald/pme_gpu_program_impl.h @@ -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. diff --git a/src/gromacs/ewald/pme-gpu-program-impl-ocl.cpp b/src/gromacs/ewald/pme_gpu_program_impl_ocl.cpp similarity index 96% rename from src/gromacs/ewald/pme-gpu-program-impl-ocl.cpp rename to src/gromacs/ewald/pme_gpu_program_impl_ocl.cpp index 16bfac9aad..a355800560 100644 --- a/src/gromacs/ewald/pme-gpu-program-impl-ocl.cpp +++ b/src/gromacs/ewald/pme_gpu_program_impl_ocl.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. @@ -47,11 +47,11 @@ #include "gromacs/gpu_utils/ocl_compiler.h" #include "gromacs/utility/stringutil.h" -#include "pme-gpu-constants.h" -#include "pme-gpu-internal.h" // for GridOrdering enum -#include "pme-gpu-program-impl.h" -#include "pme-gpu-types-host.h" -#include "pme-grid.h" +#include "pme_gpu_constants.h" +#include "pme_gpu_internal.h" // for GridOrdering enum +#include "pme_gpu_program_impl.h" +#include "pme_gpu_types_host.h" +#include "pme_grid.h" PmeGpuProgramImpl::PmeGpuProgramImpl(const gmx_device_info_t *deviceInfo) { @@ -145,9 +145,9 @@ void PmeGpuProgramImpl::compileKernels(const gmx_device_info_t *deviceInfo) "-Dorder=%d " "-DatomsPerWarp=%zd " "-DthreadsPerAtom=%d " - // forwarding from pme-grid.h, used for spline computation table sizes only + // forwarding from pme_grid.h, used for spline computation table sizes only "-Dc_pmeMaxUnitcellShift=%f " - // forwarding PME behavior constants from pme-gpu-constants.h + // forwarding PME behavior constants from pme_gpu_constants.h "-Dc_usePadding=%d " "-Dc_skipNeutralAtoms=%d " "-Dc_virialAndEnergyCount=%d " @@ -177,7 +177,7 @@ void PmeGpuProgramImpl::compileKernels(const gmx_device_info_t *deviceInfo) the log output here should be written there */ program = gmx::ocl::compileProgram(stderr, "gromacs/ewald", - "pme-program.cl", + "pme_program.cl", commonDefines, context, deviceInfo->ocl_gpu_id.ocl_device_id, @@ -218,7 +218,7 @@ void PmeGpuProgramImpl::compileKernels(const gmx_device_info_t *deviceInfo) GMX_THROW(gmx::InternalError(errorString)); } - // The names below must correspond to those defined in pme-program.cl + // The names below must correspond to those defined in pme_program.cl // TODO use a map with string key instead? if (!strcmp(kernelNamesBuffer.data(), "pmeSplineKernel")) { diff --git a/src/gromacs/ewald/pme-gpu-timings.cpp b/src/gromacs/ewald/pme_gpu_timings.cpp similarity index 96% rename from src/gromacs/ewald/pme-gpu-timings.cpp rename to src/gromacs/ewald/pme_gpu_timings.cpp index 5c218c1410..58361a59f0 100644 --- a/src/gromacs/ewald/pme-gpu-timings.cpp +++ b/src/gromacs/ewald/pme_gpu_timings.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -42,13 +42,13 @@ #include "gmxpre.h" -#include "pme-gpu-timings.h" +#include "pme_gpu_timings.h" #include "gromacs/utility/gmxassert.h" -#include "pme-gpu-internal.h" -#include "pme-gpu-types-host.h" -#include "pme-gpu-types-host-impl.h" +#include "pme_gpu_internal.h" +#include "pme_gpu_types_host.h" +#include "pme_gpu_types_host_impl.h" /*! \brief * Tells if CUDA-based performance tracking is enabled for PME. diff --git a/src/gromacs/ewald/pme-gpu-timings.h b/src/gromacs/ewald/pme_gpu_timings.h similarity index 97% rename from src/gromacs/ewald/pme-gpu-timings.h rename to src/gromacs/ewald/pme_gpu_timings.h index 08ee83d42d..df8c80398b 100644 --- a/src/gromacs/ewald/pme-gpu-timings.h +++ b/src/gromacs/ewald/pme_gpu_timings.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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/ewald/pme-gpu-types.h b/src/gromacs/ewald/pme_gpu_types.h similarity index 99% rename from src/gromacs/ewald/pme-gpu-types.h rename to src/gromacs/ewald/pme_gpu_types.h index 6fb6cae827..0598aacbbf 100644 --- a/src/gromacs/ewald/pme-gpu-types.h +++ b/src/gromacs/ewald/pme_gpu_types.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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/ewald/pme-gpu-types-host.h b/src/gromacs/ewald/pme_gpu_types_host.h similarity index 99% rename from src/gromacs/ewald/pme-gpu-types-host.h rename to src/gromacs/ewald/pme_gpu_types_host.h index 5a780ecba2..eacc911dfb 100644 --- a/src/gromacs/ewald/pme-gpu-types-host.h +++ b/src/gromacs/ewald/pme_gpu_types_host.h @@ -54,7 +54,7 @@ #include #include "gromacs/ewald/pme.h" -#include "gromacs/ewald/pme-gpu-program.h" +#include "gromacs/ewald/pme_gpu_program.h" #include "gromacs/gpu_utils/gpu_utils.h" // for GpuApiCallBehavior #include "gromacs/gpu_utils/hostallocator.h" #include "gromacs/math/vectypes.h" diff --git a/src/gromacs/ewald/pme-gpu-types-host-impl.h b/src/gromacs/ewald/pme_gpu_types_host_impl.h similarity index 98% rename from src/gromacs/ewald/pme-gpu-types-host-impl.h rename to src/gromacs/ewald/pme_gpu_types_host_impl.h index e005552400..6949bde60f 100644 --- a/src/gromacs/ewald/pme-gpu-types-host-impl.h +++ b/src/gromacs/ewald/pme_gpu_types_host_impl.h @@ -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. @@ -35,7 +35,7 @@ /*! \internal \file * \brief Defines the host-side PME GPU data structure, which is dependent on the GPU types. - * It's included by pointer in the general PmeGpu host structure in pme-gpu-types-host.h. + * It's included by pointer in the general PmeGpu host structure in pme_gpu_types_host.h. * * \author Aleksei Iupinov * \ingroup module_ewald diff --git a/src/gromacs/ewald/pme-gpu-utils.clh b/src/gromacs/ewald/pme_gpu_utils.clh similarity index 96% rename from src/gromacs/ewald/pme-gpu-utils.clh rename to src/gromacs/ewald/pme_gpu_utils.clh index fe0531dc49..5f611e9510 100644 --- a/src/gromacs/ewald/pme-gpu-utils.clh +++ b/src/gromacs/ewald/pme_gpu_utils.clh @@ -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. @@ -37,11 +37,11 @@ /*! \internal \file * \brief This file defines the small PME OpenCL inline device functions. - * This closely mirrors pme-gpu-utils.h (which is used in CUDA and unit tests), except with no templates. + * This closely mirrors pme_gpu_utils.h (which is used in CUDA and unit tests), except with no templates. * Instead of templated parameters this file expects following defines during compilation: * - order - PME interpolation order; * - atomsPerWarp - number of atoms processed by a warp (fixed for spread and gather kernels to be the same); - * - c_usePadding and c_skipNeutralAtoms - same as in pme-gpu-constants.h. + * - c_usePadding and c_skipNeutralAtoms - same as in pme_gpu_constants.h. * * \author Aleksei Iupinov * \ingroup module_ewald diff --git a/src/gromacs/ewald/pme-gpu-utils.h b/src/gromacs/ewald/pme_gpu_utils.h similarity index 97% rename from src/gromacs/ewald/pme-gpu-utils.h rename to src/gromacs/ewald/pme_gpu_utils.h index e576a56045..c706f071ec 100644 --- a/src/gromacs/ewald/pme-gpu-utils.h +++ b/src/gromacs/ewald/pme_gpu_utils.h @@ -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 @@ /*! \internal \file * \brief This file defines small PME GPU inline host/device functions. * Note that OpenCL device-side functions can't use C++ features, so they are - * located in a similar file pme-gpu-utils.clh. + * located in a similar file pme_gpu_utils.clh. * Be sure to keep the logic in sync in both files when changing it! * * \author Aleksei Iupinov @@ -49,7 +49,7 @@ #include -#include "pme-gpu-constants.h" +#include "pme_gpu_constants.h" //! A macro for inline GPU functions. #if GMX_GPU == GMX_GPU_CUDA diff --git a/src/gromacs/ewald/pme-grid.cpp b/src/gromacs/ewald/pme_grid.cpp similarity index 99% rename from src/gromacs/ewald/pme-grid.cpp rename to src/gromacs/ewald/pme_grid.cpp index a2a0dfaff0..2f1b16d720 100644 --- a/src/gromacs/ewald/pme-grid.cpp +++ b/src/gromacs/ewald/pme_grid.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. @@ -37,7 +37,7 @@ /* TODO find out what this file should be called */ #include "gmxpre.h" -#include "pme-grid.h" +#include "pme_grid.h" #include "config.h" @@ -50,7 +50,7 @@ #include "gromacs/utility/fatalerror.h" #include "gromacs/utility/smalloc.h" -#include "pme-internal.h" +#include "pme_internal.h" #ifdef DEBUG_PME #include "gromacs/fileio/pdbio.h" @@ -58,7 +58,7 @@ #include "gromacs/utility/futil.h" #endif -#include "pme-simd.h" +#include "pme_simd.h" /* GMX_CACHE_SEP should be a multiple of the SIMD and SIMD4 register size * to preserve alignment. diff --git a/src/gromacs/ewald/pme-grid.h b/src/gromacs/ewald/pme_grid.h similarity index 97% rename from src/gromacs/ewald/pme-grid.h rename to src/gromacs/ewald/pme_grid.h index f861997595..52fd095ca4 100644 --- a/src/gromacs/ewald/pme-grid.h +++ b/src/gromacs/ewald/pme_grid.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. diff --git a/src/gromacs/ewald/pme-internal.h b/src/gromacs/ewald/pme_internal.h similarity index 99% rename from src/gromacs/ewald/pme-internal.h rename to src/gromacs/ewald/pme_internal.h index 9dcfdf38c8..76aa3c090f 100644 --- a/src/gromacs/ewald/pme-internal.h +++ b/src/gromacs/ewald/pme_internal.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. @@ -59,7 +59,7 @@ #include "gromacs/utility/basedefinitions.h" #include "gromacs/utility/gmxmpi.h" -#include "pme-gpu-types-host.h" +#include "pme_gpu_types_host.h" //! A repeat of typedef from parallel_3dfft.h typedef struct gmx_parallel_3dfft *gmx_parallel_3dfft_t; diff --git a/src/gromacs/ewald/pme-load-balancing.cpp b/src/gromacs/ewald/pme_load_balancing.cpp similarity index 99% rename from src/gromacs/ewald/pme-load-balancing.cpp rename to src/gromacs/ewald/pme_load_balancing.cpp index a975b49788..8ff5939072 100644 --- a/src/gromacs/ewald/pme-load-balancing.cpp +++ b/src/gromacs/ewald/pme_load_balancing.cpp @@ -43,7 +43,7 @@ */ #include "gmxpre.h" -#include "pme-load-balancing.h" +#include "pme_load_balancing.h" #include #include @@ -55,7 +55,7 @@ #include "gromacs/domdec/domdec_network.h" #include "gromacs/domdec/domdec_struct.h" #include "gromacs/domdec/partition.h" -#include "gromacs/ewald/ewald-utils.h" +#include "gromacs/ewald/ewald_utils.h" #include "gromacs/ewald/pme.h" #include "gromacs/fft/calcgrid.h" #include "gromacs/gmxlib/network.h" @@ -79,7 +79,7 @@ #include "gromacs/utility/smalloc.h" #include "gromacs/utility/strconvert.h" -#include "pme-internal.h" +#include "pme_internal.h" /*! \brief Parameters and settings for one PP-PME setup */ struct pme_setup_t { diff --git a/src/gromacs/ewald/pme-load-balancing.h b/src/gromacs/ewald/pme_load_balancing.h similarity index 97% rename from src/gromacs/ewald/pme-load-balancing.h rename to src/gromacs/ewald/pme_load_balancing.h index b660ef3970..11ea28cb86 100644 --- a/src/gromacs/ewald/pme-load-balancing.h +++ b/src/gromacs/ewald/pme_load_balancing.h @@ -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. diff --git a/src/gromacs/ewald/pme-only.cpp b/src/gromacs/ewald/pme_only.cpp similarity index 99% rename from src/gromacs/ewald/pme-only.cpp rename to src/gromacs/ewald/pme_only.cpp index e448d45426..9fd7a138e9 100644 --- a/src/gromacs/ewald/pme-only.cpp +++ b/src/gromacs/ewald/pme_only.cpp @@ -92,9 +92,9 @@ #include "gromacs/utility/gmxomp.h" #include "gromacs/utility/smalloc.h" -#include "pme-gpu-internal.h" -#include "pme-internal.h" -#include "pme-pp-communication.h" +#include "pme_gpu_internal.h" +#include "pme_internal.h" +#include "pme_pp_communication.h" //! Contains information about the PP ranks that partner this PME rank. struct PpRanks diff --git a/src/gromacs/ewald/pme-pp.cpp b/src/gromacs/ewald/pme_pp.cpp similarity index 98% rename from src/gromacs/ewald/pme-pp.cpp rename to src/gromacs/ewald/pme_pp.cpp index fcad69f0af..a15e1b57cd 100644 --- a/src/gromacs/ewald/pme-pp.cpp +++ b/src/gromacs/ewald/pme_pp.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. @@ -66,8 +66,8 @@ #include "gromacs/utility/gmxmpi.h" #include "gromacs/utility/smalloc.h" -#include "pme-internal.h" -#include "pme-pp-communication.h" +#include "pme_internal.h" +#include "pme_pp_communication.h" /*! \brief Block to wait for communication to PME ranks to complete * diff --git a/src/gromacs/ewald/pme-pp-communication.h b/src/gromacs/ewald/pme_pp_communication.h similarity index 98% rename from src/gromacs/ewald/pme-pp-communication.h rename to src/gromacs/ewald/pme_pp_communication.h index 5d66cf3d5d..31c0bb717d 100644 --- a/src/gromacs/ewald/pme-pp-communication.h +++ b/src/gromacs/ewald/pme_pp_communication.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. diff --git a/src/gromacs/ewald/pme-program.cl b/src/gromacs/ewald/pme_program.cl similarity index 92% rename from src/gromacs/ewald/pme-program.cl rename to src/gromacs/ewald/pme_program.cl index afbf17273d..58fa2c6c31 100644 --- a/src/gromacs/ewald/pme-program.cl +++ b/src/gromacs/ewald/pme_program.cl @@ -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 @@ * This file includes all the PME OpenCL kernel files multiple times, with additional defines. * Plenty of common constants/macros are also expected to be already defined by the compiler * (such as "order" which is PME interpolation order). - * For details, please see how pme-program.cl is compiled in pme-gpu-program-impl-ocl.cpp. + * For details, please see how pme_program.cl is compiled in pme_gpu_program_impl_ocl.cpp. * * This file specifically expects the following work size definitions: * @@ -63,7 +63,7 @@ #define computeSplines 1 #define spreadCharges 1 #define CUSTOMIZED_KERNEL_NAME(x) pmeSplineAndSpreadKernel -#include "pme-spread.clh" +#include "pme_spread.clh" #undef computeSplines #undef spreadCharges #undef CUSTOMIZED_KERNEL_NAME @@ -72,7 +72,7 @@ #define computeSplines 1 #define spreadCharges 0 #define CUSTOMIZED_KERNEL_NAME(x) pmeSplineKernel -#include "pme-spread.clh" +#include "pme_spread.clh" #undef computeSplines #undef spreadCharges #undef CUSTOMIZED_KERNEL_NAME @@ -81,7 +81,7 @@ #define computeSplines 0 #define spreadCharges 1 #define CUSTOMIZED_KERNEL_NAME(x) pmeSpreadKernel -#include "pme-spread.clh" +#include "pme_spread.clh" #undef computeSplines #undef spreadCharges #undef CUSTOMIZED_KERNEL_NAME @@ -97,14 +97,14 @@ // gather #define overwriteForces 1 #define CUSTOMIZED_KERNEL_NAME(x) pmeGatherKernel -#include "pme-gather.clh" +#include "pme_gather.clh" #undef overwriteForces #undef CUSTOMIZED_KERNEL_NAME // gather with reduction #define overwriteForces 0 #define CUSTOMIZED_KERNEL_NAME(x) pmeGatherReduceWithInputKernel -#include "pme-gather.clh" +#include "pme_gather.clh" #undef overwriteForces #undef CUSTOMIZED_KERNEL_NAME @@ -121,7 +121,7 @@ #define gridOrdering YZX #define computeEnergyAndVirial 0 #define CUSTOMIZED_KERNEL_NAME(x) pmeSolveYZXKernel -#include "pme-solve.clh" +#include "pme_solve.clh" #undef gridOrdering #undef computeEnergyAndVirial #undef CUSTOMIZED_KERNEL_NAME @@ -130,7 +130,7 @@ #define gridOrdering YZX #define computeEnergyAndVirial 1 #define CUSTOMIZED_KERNEL_NAME(x) pmeSolveYZXEnergyKernel -#include "pme-solve.clh" +#include "pme_solve.clh" #undef gridOrdering #undef computeEnergyAndVirial #undef CUSTOMIZED_KERNEL_NAME @@ -139,7 +139,7 @@ #define gridOrdering XYZ #define computeEnergyAndVirial 0 #define CUSTOMIZED_KERNEL_NAME(x) pmeSolveXYZKernel -#include "pme-solve.clh" +#include "pme_solve.clh" #undef gridOrdering #undef computeEnergyAndVirial #undef CUSTOMIZED_KERNEL_NAME @@ -148,7 +148,7 @@ #define gridOrdering XYZ #define computeEnergyAndVirial 1 #define CUSTOMIZED_KERNEL_NAME(x) pmeSolveXYZEnergyKernel -#include "pme-solve.clh" +#include "pme_solve.clh" #undef gridOrdering #undef computeEnergyAndVirial #undef CUSTOMIZED_KERNEL_NAME diff --git a/src/gromacs/ewald/pme-redistribute.cpp b/src/gromacs/ewald/pme_redistribute.cpp similarity index 98% rename from src/gromacs/ewald/pme-redistribute.cpp rename to src/gromacs/ewald/pme_redistribute.cpp index bbef6bf975..3db06d32d8 100644 --- a/src/gromacs/ewald/pme-redistribute.cpp +++ b/src/gromacs/ewald/pme_redistribute.cpp @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2013,2014,2015,2016,2018, 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. @@ -36,7 +36,7 @@ */ #include "gmxpre.h" -#include "pme-redistribute.h" +#include "pme_redistribute.h" #include "config.h" @@ -49,8 +49,8 @@ #include "gromacs/utility/gmxmpi.h" #include "gromacs/utility/smalloc.h" -#include "pme-internal.h" -#include "pme-simd.h" +#include "pme_internal.h" +#include "pme_simd.h" static void pme_calc_pidx(int start, int end, matrix recipbox, rvec x[], diff --git a/src/gromacs/ewald/pme-redistribute.h b/src/gromacs/ewald/pme_redistribute.h similarity index 95% rename from src/gromacs/ewald/pme-redistribute.h rename to src/gromacs/ewald/pme_redistribute.h index 2508611039..dc30592b84 100644 --- a/src/gromacs/ewald/pme-redistribute.h +++ b/src/gromacs/ewald/pme_redistribute.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014,2015,2018, by the GROMACS development team, led by + * Copyright (c) 2014,2015,2018,2019, 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. @@ -35,7 +35,7 @@ #ifndef GMX_EWALD_PME_REDISTRIBUTE_H #define GMX_EWALD_PME_REDISTRIBUTE_H -#include "pme-internal.h" +#include "pme_internal.h" void pme_realloc_atomcomm_things(pme_atomcomm_t *atc); diff --git a/src/gromacs/ewald/pme-simd.h b/src/gromacs/ewald/pme_simd.h similarity index 97% rename from src/gromacs/ewald/pme-simd.h rename to src/gromacs/ewald/pme_simd.h index 7bbbc25b83..2e4475e346 100644 --- a/src/gromacs/ewald/pme-simd.h +++ b/src/gromacs/ewald/pme_simd.h @@ -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. diff --git a/src/gromacs/ewald/pme-simd4.h b/src/gromacs/ewald/pme_simd4.h similarity index 98% rename from src/gromacs/ewald/pme-simd4.h rename to src/gromacs/ewald/pme_simd4.h index d1d40bd825..0fdc3170b1 100644 --- a/src/gromacs/ewald/pme-simd4.h +++ b/src/gromacs/ewald/pme_simd4.h @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by + * Copyright (c) 2012,2013,2014,2015,2017,2018,2019, 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. diff --git a/src/gromacs/ewald/pme-solve.clh b/src/gromacs/ewald/pme_solve.clh similarity index 98% rename from src/gromacs/ewald/pme-solve.clh rename to src/gromacs/ewald/pme_solve.clh index b85b1ecc24..a4b877e0dd 100644 --- a/src/gromacs/ewald/pme-solve.clh +++ b/src/gromacs/ewald/pme_solve.clh @@ -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. @@ -37,7 +37,7 @@ * \brief Implements PME OpenCL solving kernel. * When including this and other PME OpenCL kernel files, plenty of common * constants/macros are expected to be defined. - * For details, please see how pme-program.cl is compiled in pme-gpu-program-impl-ocl.cpp. + * For details, please see how pme_program.cl is compiled in pme_gpu_program_impl_ocl.cpp. * * This file's solving kernel specifically expects the following definitions for its flavors: * @@ -49,7 +49,7 @@ * \author Aleksei Iupinov */ -#include "pme-gpu-types.h" +#include "pme_gpu_types.h" #include "gromacs/gpu_utils/vectype_ops.clh" /*! \brief diff --git a/src/gromacs/ewald/pme-solve.cpp b/src/gromacs/ewald/pme_solve.cpp similarity index 99% rename from src/gromacs/ewald/pme-solve.cpp rename to src/gromacs/ewald/pme_solve.cpp index 863b81ccee..1e944bce10 100644 --- a/src/gromacs/ewald/pme-solve.cpp +++ b/src/gromacs/ewald/pme_solve.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. @@ -37,7 +37,7 @@ #include "gmxpre.h" -#include "pme-solve.h" +#include "pme_solve.h" #include @@ -51,7 +51,7 @@ #include "gromacs/utility/exceptions.h" #include "gromacs/utility/smalloc.h" -#include "pme-internal.h" +#include "pme_internal.h" #if GMX_SIMD_HAVE_REAL /* Turn on arbitrary width SIMD intrinsics for PME solve */ diff --git a/src/gromacs/ewald/pme-solve.cu b/src/gromacs/ewald/pme_solve.cu similarity index 99% rename from src/gromacs/ewald/pme-solve.cu rename to src/gromacs/ewald/pme_solve.cu index c00ec9df0e..3aec442c7b 100644 --- a/src/gromacs/ewald/pme-solve.cu +++ b/src/gromacs/ewald/pme_solve.cu @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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/ewald/pme-solve.h b/src/gromacs/ewald/pme_solve.h similarity index 97% rename from src/gromacs/ewald/pme-solve.h rename to src/gromacs/ewald/pme_solve.h index 0252fd5adf..ed6457dcdd 100644 --- a/src/gromacs/ewald/pme-solve.h +++ b/src/gromacs/ewald/pme_solve.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. diff --git a/src/gromacs/ewald/pme-spline-work.cpp b/src/gromacs/ewald/pme_spline_work.cpp similarity index 95% rename from src/gromacs/ewald/pme-spline-work.cpp rename to src/gromacs/ewald/pme_spline_work.cpp index ef2da9253e..09f9ebdc07 100644 --- a/src/gromacs/ewald/pme-spline-work.cpp +++ b/src/gromacs/ewald/pme_spline_work.cpp @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2013,2014,2015,2017,2018, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015,2017,2018,2019, 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. @@ -37,7 +37,7 @@ #include "gmxpre.h" -#include "pme-spline-work.h" +#include "pme_spline_work.h" #include "gromacs/simd/simd.h" #include "gromacs/utility/alignedallocator.h" @@ -45,7 +45,7 @@ #include "gromacs/utility/real.h" #include "gromacs/utility/smalloc.h" -#include "pme-simd.h" +#include "pme_simd.h" using namespace gmx; // TODO: Remove when this file is moved into gmx namespace diff --git a/src/gromacs/ewald/pme-spline-work.h b/src/gromacs/ewald/pme_spline_work.h similarity index 95% rename from src/gromacs/ewald/pme-spline-work.h rename to src/gromacs/ewald/pme_spline_work.h index 6e77f6cdf0..1d0ad410a7 100644 --- a/src/gromacs/ewald/pme-spline-work.h +++ b/src/gromacs/ewald/pme_spline_work.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014,2015,2018, by the GROMACS development team, led by + * Copyright (c) 2014,2015,2018,2019, 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 @@ #include "gromacs/simd/simd.h" -#include "pme-simd.h" +#include "pme_simd.h" struct pme_spline_work { diff --git a/src/gromacs/ewald/pme-spread.clh b/src/gromacs/ewald/pme_spread.clh similarity index 99% rename from src/gromacs/ewald/pme-spread.clh rename to src/gromacs/ewald/pme_spread.clh index 5916e162c3..2b140133c1 100644 --- a/src/gromacs/ewald/pme-spread.clh +++ b/src/gromacs/ewald/pme_spread.clh @@ -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. @@ -37,7 +37,7 @@ * \brief Implements PME OpenCL spline parameter computation and charge spread kernels. * When including this and other PME OpenCL kernel files, plenty of common * constants/macros are expected to be defined (such as "order" which is PME interpolation order). - * For details, please see how pme-program.cl is compiled in pme-gpu-program-impl-ocl.cpp. + * For details, please see how pme_program.cl is compiled in pme_gpu_program_impl_ocl.cpp. * * This file's kernels specifically expect the following definitions: * @@ -51,8 +51,8 @@ * \author Aleksei Iupinov */ -#include "pme-gpu-types.h" -#include "pme-gpu-utils.clh" +#include "pme_gpu_types.h" +#include "pme_gpu_utils.clh" #include "gromacs/gpu_utils/vectype_ops.clh" /* diff --git a/src/gromacs/ewald/pme-spread.cpp b/src/gromacs/ewald/pme_spread.cpp similarity index 99% rename from src/gromacs/ewald/pme-spread.cpp rename to src/gromacs/ewald/pme_spread.cpp index 6ee5381967..deed63f025 100644 --- a/src/gromacs/ewald/pme-spread.cpp +++ b/src/gromacs/ewald/pme_spread.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. @@ -36,7 +36,7 @@ */ #include "gmxpre.h" -#include "pme-spread.h" +#include "pme_spread.h" #include "config.h" @@ -52,10 +52,10 @@ #include "gromacs/utility/fatalerror.h" #include "gromacs/utility/smalloc.h" -#include "pme-grid.h" -#include "pme-internal.h" -#include "pme-simd.h" -#include "pme-spline-work.h" +#include "pme_grid.h" +#include "pme_internal.h" +#include "pme_simd.h" +#include "pme_spline_work.h" /* TODO consider split of pme-spline from this file */ @@ -377,7 +377,7 @@ static void spread_coefficients_bsplines_thread(const pmegrid_t #define PME_SPREAD_SIMD4_ALIGNED #define PME_ORDER 4 #endif -#include "pme-simd4.h" +#include "pme_simd4.h" #else DO_BSPLINE(4); #endif @@ -386,7 +386,7 @@ static void spread_coefficients_bsplines_thread(const pmegrid_t #ifdef PME_SIMD4_SPREAD_GATHER #define PME_SPREAD_SIMD4_ALIGNED #define PME_ORDER 5 -#include "pme-simd4.h" +#include "pme_simd4.h" #else DO_BSPLINE(5); #endif diff --git a/src/gromacs/ewald/pme-spread.cu b/src/gromacs/ewald/pme_spread.cu similarity index 99% rename from src/gromacs/ewald/pme-spread.cu rename to src/gromacs/ewald/pme_spread.cu index 030367fd30..728300c815 100644 --- a/src/gromacs/ewald/pme-spread.cu +++ b/src/gromacs/ewald/pme_spread.cu @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2013-2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 2013-2016,2017,2018,2019, 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/gpu_utils/cuda_kernel_utils.cuh" #include "pme.cuh" -#include "pme-gpu-utils.h" -#include "pme-grid.h" +#include "pme_gpu_utils.h" +#include "pme_grid.h" /* * This define affects the spline calculation behaviour in the kernel. diff --git a/src/gromacs/ewald/pme-spread.h b/src/gromacs/ewald/pme_spread.h similarity index 95% rename from src/gromacs/ewald/pme-spread.h rename to src/gromacs/ewald/pme_spread.h index 78d8fbef69..23e0731853 100644 --- a/src/gromacs/ewald/pme-spread.h +++ b/src/gromacs/ewald/pme_spread.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. @@ -39,7 +39,7 @@ #include "gromacs/utility/real.h" -#include "pme-internal.h" +#include "pme_internal.h" void spread_on_grid(const gmx_pme_t *pme, diff --git a/src/gromacs/ewald/tests/pmebsplinetest.cpp b/src/gromacs/ewald/tests/pmebsplinetest.cpp index b57d2dd91b..c7a952a714 100644 --- a/src/gromacs/ewald/tests/pmebsplinetest.cpp +++ b/src/gromacs/ewald/tests/pmebsplinetest.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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 -#include "gromacs/ewald/pme-internal.h" +#include "gromacs/ewald/pme_internal.h" #include "gromacs/math/vectypes.h" #include "gromacs/mdtypes/inputrec.h" #include "gromacs/utility/stringutil.h" diff --git a/src/gromacs/ewald/tests/pmetestcommon.cpp b/src/gromacs/ewald/tests/pmetestcommon.cpp index 6fa0627777..625a077afa 100644 --- a/src/gromacs/ewald/tests/pmetestcommon.cpp +++ b/src/gromacs/ewald/tests/pmetestcommon.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -48,12 +48,12 @@ #include #include "gromacs/domdec/domdec.h" -#include "gromacs/ewald/pme-gather.h" -#include "gromacs/ewald/pme-gpu-internal.h" -#include "gromacs/ewald/pme-grid.h" -#include "gromacs/ewald/pme-internal.h" -#include "gromacs/ewald/pme-solve.h" -#include "gromacs/ewald/pme-spread.h" +#include "gromacs/ewald/pme_gather.h" +#include "gromacs/ewald/pme_gpu_internal.h" +#include "gromacs/ewald/pme_grid.h" +#include "gromacs/ewald/pme_internal.h" +#include "gromacs/ewald/pme_solve.h" +#include "gromacs/ewald/pme_spread.h" #include "gromacs/fft/parallel_3dfft.h" #include "gromacs/gpu_utils/gpu_utils.h" #include "gromacs/math/invertmatrix.h" diff --git a/src/gromacs/ewald/tests/pmetestcommon.h b/src/gromacs/ewald/tests/pmetestcommon.h index d4f4027e2f..3b353b026a 100644 --- a/src/gromacs/ewald/tests/pmetestcommon.h +++ b/src/gromacs/ewald/tests/pmetestcommon.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -49,7 +49,7 @@ #include #include "gromacs/ewald/pme.h" -#include "gromacs/ewald/pme-gpu-internal.h" +#include "gromacs/ewald/pme_gpu_internal.h" #include "gromacs/math/gmxcomplex.h" #include "gromacs/utility/arrayref.h" #include "gromacs/utility/unique_cptr.h" diff --git a/src/gromacs/ewald/tests/testhardwarecontexts.h b/src/gromacs/ewald/tests/testhardwarecontexts.h index f364c466d4..f733e23095 100644 --- a/src/gromacs/ewald/tests/testhardwarecontexts.h +++ b/src/gromacs/ewald/tests/testhardwarecontexts.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -48,7 +48,7 @@ #include -#include "gromacs/ewald/pme-gpu-program.h" +#include "gromacs/ewald/pme_gpu_program.h" #include "gromacs/hardware/gpu_hw_info.h" struct gmx_hw_info_t; diff --git a/src/gromacs/fileio/checkpoint.cpp b/src/gromacs/fileio/checkpoint.cpp index a3a7a09493..555c6e790b 100644 --- a/src/gromacs/fileio/checkpoint.cpp +++ b/src/gromacs/fileio/checkpoint.cpp @@ -57,15 +57,15 @@ #include "buildinfo.h" #include "gromacs/fileio/filetypes.h" #include "gromacs/fileio/gmxfio.h" -#include "gromacs/fileio/gmxfio-xdr.h" +#include "gromacs/fileio/gmxfio_xdr.h" #include "gromacs/fileio/xdr_datatype.h" #include "gromacs/fileio/xdrf.h" #include "gromacs/gmxlib/network.h" #include "gromacs/math/vec.h" #include "gromacs/math/vecdump.h" #include "gromacs/math/vectypes.h" -#include "gromacs/mdtypes/awh-correlation-history.h" -#include "gromacs/mdtypes/awh-history.h" +#include "gromacs/mdtypes/awh_correlation_history.h" +#include "gromacs/mdtypes/awh_history.h" #include "gromacs/mdtypes/commrec.h" #include "gromacs/mdtypes/df_history.h" #include "gromacs/mdtypes/edsamhistory.h" diff --git a/src/gromacs/fileio/enxio.cpp b/src/gromacs/fileio/enxio.cpp index dc0a177c9f..cc2ac96df4 100644 --- a/src/gromacs/fileio/enxio.cpp +++ b/src/gromacs/fileio/enxio.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. @@ -44,7 +44,7 @@ #include #include "gromacs/fileio/gmxfio.h" -#include "gromacs/fileio/gmxfio-xdr.h" +#include "gromacs/fileio/gmxfio_xdr.h" #include "gromacs/fileio/xdrf.h" #include "gromacs/math/functions.h" #include "gromacs/math/vec.h" diff --git a/src/gromacs/fileio/gmxfio.cpp b/src/gromacs/fileio/gmxfio.cpp index bf7749b9f7..a9fc9c0b05 100644 --- a/src/gromacs/fileio/gmxfio.cpp +++ b/src/gromacs/fileio/gmxfio.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. @@ -62,7 +62,7 @@ #include "gromacs/utility/mutex.h" #include "gromacs/utility/smalloc.h" -#include "gmxfio-impl.h" +#include "gmxfio_impl.h" /* This is the new improved and thread safe version of gmxfio. */ diff --git a/src/gromacs/fileio/gmxfio-impl.h b/src/gromacs/fileio/gmxfio_impl.h similarity index 97% rename from src/gromacs/fileio/gmxfio-impl.h rename to src/gromacs/fileio/gmxfio_impl.h index 0b455979dd..1cc7d40b31 100644 --- a/src/gromacs/fileio/gmxfio-impl.h +++ b/src/gromacs/fileio/gmxfio_impl.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, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015,2019, 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. diff --git a/src/gromacs/fileio/gmxfio-xdr.cpp b/src/gromacs/fileio/gmxfio_xdr.cpp similarity index 99% rename from src/gromacs/fileio/gmxfio-xdr.cpp rename to src/gromacs/fileio/gmxfio_xdr.cpp index 87a672112e..9a40af48dd 100644 --- a/src/gromacs/fileio/gmxfio-xdr.cpp +++ b/src/gromacs/fileio/gmxfio_xdr.cpp @@ -36,7 +36,7 @@ */ #include "gmxpre.h" -#include "gmxfio-xdr.h" +#include "gmxfio_xdr.h" #include #include @@ -47,7 +47,7 @@ #include "gromacs/utility/gmxassert.h" #include "gromacs/utility/smalloc.h" -#include "gmxfio-impl.h" +#include "gmxfio_impl.h" /* Enumerated for data types in files */ enum { diff --git a/src/gromacs/fileio/gmxfio-xdr.h b/src/gromacs/fileio/gmxfio_xdr.h similarity index 98% rename from src/gromacs/fileio/gmxfio-xdr.h rename to src/gromacs/fileio/gmxfio_xdr.h index 848e936c80..27811f3030 100644 --- a/src/gromacs/fileio/gmxfio-xdr.h +++ b/src/gromacs/fileio/gmxfio_xdr.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. diff --git a/src/gromacs/fileio/mtxio.cpp b/src/gromacs/fileio/mtxio.cpp index 7a48bc64ff..542a6ae082 100644 --- a/src/gromacs/fileio/mtxio.cpp +++ b/src/gromacs/fileio/mtxio.cpp @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by + * Copyright (c) 2012,2013,2014,2015,2017,2019, 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. @@ -44,7 +44,7 @@ */ #include "gromacs/fileio/gmxfio.h" -#include "gromacs/fileio/gmxfio-xdr.h" +#include "gromacs/fileio/gmxfio_xdr.h" #include "gromacs/linearalgebra/sparsematrix.h" #include "gromacs/utility/baseversion.h" #include "gromacs/utility/fatalerror.h" diff --git a/src/gromacs/fileio/tpxio.cpp b/src/gromacs/fileio/tpxio.cpp index 8891f103cd..fb04ec0ee2 100644 --- a/src/gromacs/fileio/tpxio.cpp +++ b/src/gromacs/fileio/tpxio.cpp @@ -50,14 +50,14 @@ #include "gromacs/fileio/filetypes.h" #include "gromacs/fileio/gmxfio.h" -#include "gromacs/fileio/gmxfio-xdr.h" +#include "gromacs/fileio/gmxfio_xdr.h" #include "gromacs/math/units.h" #include "gromacs/math/vec.h" -#include "gromacs/mdtypes/awh-history.h" -#include "gromacs/mdtypes/awh-params.h" +#include "gromacs/mdtypes/awh_history.h" +#include "gromacs/mdtypes/awh_params.h" #include "gromacs/mdtypes/inputrec.h" #include "gromacs/mdtypes/md_enums.h" -#include "gromacs/mdtypes/pull-params.h" +#include "gromacs/mdtypes/pull_params.h" #include "gromacs/mdtypes/state.h" #include "gromacs/pbcutil/boxutilities.h" #include "gromacs/pbcutil/pbc.h" diff --git a/src/gromacs/fileio/trrio.cpp b/src/gromacs/fileio/trrio.cpp index 2fe6ff8afb..b69811cb86 100644 --- a/src/gromacs/fileio/trrio.cpp +++ b/src/gromacs/fileio/trrio.cpp @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2013,2014,2015,2016,2018, 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. @@ -41,7 +41,7 @@ #include #include "gromacs/fileio/gmxfio.h" -#include "gromacs/fileio/gmxfio-xdr.h" +#include "gromacs/fileio/gmxfio_xdr.h" #include "gromacs/mdtypes/md_enums.h" #include "gromacs/utility/fatalerror.h" #include "gromacs/utility/futil.h" diff --git a/src/gromacs/fileio/trxio.cpp b/src/gromacs/fileio/trxio.cpp index f655a3cb26..f9a33fefac 100644 --- a/src/gromacs/fileio/trxio.cpp +++ b/src/gromacs/fileio/trxio.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. @@ -49,7 +49,7 @@ #include "gromacs/fileio/filetypes.h" #include "gromacs/fileio/g96io.h" #include "gromacs/fileio/gmxfio.h" -#include "gromacs/fileio/gmxfio-xdr.h" +#include "gromacs/fileio/gmxfio_xdr.h" #include "gromacs/fileio/groio.h" #include "gromacs/fileio/oenv.h" #include "gromacs/fileio/pdbio.h" diff --git a/src/gromacs/fileio/xtcio.cpp b/src/gromacs/fileio/xtcio.cpp index bd705f2b76..09f0d8cab7 100644 --- a/src/gromacs/fileio/xtcio.cpp +++ b/src/gromacs/fileio/xtcio.cpp @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2013,2014,2015,2016,2018, 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. @@ -41,7 +41,7 @@ #include #include "gromacs/fileio/gmxfio.h" -#include "gromacs/fileio/gmxfio-xdr.h" +#include "gromacs/fileio/gmxfio_xdr.h" #include "gromacs/fileio/xdrf.h" #include "gromacs/math/vec.h" #include "gromacs/utility/fatalerror.h" diff --git a/src/gromacs/gmxana/gmx_awh.cpp b/src/gromacs/gmxana/gmx_awh.cpp index e17343a925..1d7463bdaa 100644 --- a/src/gromacs/gmxana/gmx_awh.cpp +++ b/src/gromacs/gmxana/gmx_awh.cpp @@ -60,7 +60,7 @@ #include "gromacs/fileio/xvgr.h" #include "gromacs/gmxana/gmx_ana.h" #include "gromacs/math/units.h" -#include "gromacs/mdtypes/awh-params.h" +#include "gromacs/mdtypes/awh_params.h" #include "gromacs/mdtypes/inputrec.h" #include "gromacs/topology/mtop_util.h" #include "gromacs/topology/topology.h" diff --git a/src/gromacs/gmxana/gmx_pme_error.cpp b/src/gromacs/gmxana/gmx_pme_error.cpp index 48ed788268..bc87405672 100644 --- a/src/gromacs/gmxana/gmx_pme_error.cpp +++ b/src/gromacs/gmxana/gmx_pme_error.cpp @@ -41,7 +41,7 @@ #include #include "gromacs/commandline/pargs.h" -#include "gromacs/ewald/ewald-utils.h" +#include "gromacs/ewald/ewald_utils.h" #include "gromacs/ewald/pme.h" #include "gromacs/fft/calcgrid.h" #include "gromacs/fileio/checkpoint.h" diff --git a/src/gromacs/gmxana/gmx_wham.cpp b/src/gromacs/gmxana/gmx_wham.cpp index 307a04485c..12d9d1d227 100644 --- a/src/gromacs/gmxana/gmx_wham.cpp +++ b/src/gromacs/gmxana/gmx_wham.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. @@ -63,7 +63,7 @@ #include "gromacs/math/vec.h" #include "gromacs/mdtypes/inputrec.h" #include "gromacs/mdtypes/md_enums.h" -#include "gromacs/mdtypes/pull-params.h" +#include "gromacs/mdtypes/pull_params.h" #include "gromacs/mdtypes/state.h" #include "gromacs/pulling/pull.h" #include "gromacs/random/tabulatednormaldistribution.h" diff --git a/src/gromacs/gmxlib/conformation-utilities.cpp b/src/gromacs/gmxlib/conformation_utilities.cpp similarity index 97% rename from src/gromacs/gmxlib/conformation-utilities.cpp rename to src/gromacs/gmxlib/conformation_utilities.cpp index 5f93fd7573..c3d6dbd118 100644 --- a/src/gromacs/gmxlib/conformation-utilities.cpp +++ b/src/gromacs/gmxlib/conformation_utilities.cpp @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2012,2014,2015,2018, by the GROMACS development team, led by + * Copyright (c) 2012,2014,2015,2018,2019, 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 @@ /* This file is completely threadsafe - keep it that way! */ #include "gmxpre.h" -#include "conformation-utilities.h" +#include "conformation_utilities.h" #include diff --git a/src/gromacs/gmxlib/conformation-utilities.h b/src/gromacs/gmxlib/conformation_utilities.h similarity index 96% rename from src/gromacs/gmxlib/conformation-utilities.h rename to src/gromacs/gmxlib/conformation_utilities.h index 9c20592da6..b3dbc96f39 100644 --- a/src/gromacs/gmxlib/conformation-utilities.h +++ b/src/gromacs/gmxlib/conformation_utilities.h @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2010,2014,2018, by the GROMACS development team, led by + * Copyright (c) 2010,2014,2018,2019, 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/gmxpreprocess/add_par.cpp b/src/gromacs/gmxpreprocess/add_par.cpp index aca94d8a2d..741452d69a 100644 --- a/src/gromacs/gmxpreprocess/add_par.cpp +++ b/src/gromacs/gmxpreprocess/add_par.cpp @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2011,2014,2015,2017,2018, by the GROMACS development team, led by + * Copyright (c) 2011,2014,2015,2017,2018,2019, 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. @@ -43,7 +43,7 @@ #include -#include "gromacs/gmxpreprocess/grompp-impl.h" +#include "gromacs/gmxpreprocess/grompp_impl.h" #include "gromacs/gmxpreprocess/hackblock.h" #include "gromacs/gmxpreprocess/notset.h" #include "gromacs/gmxpreprocess/toputil.h" diff --git a/src/gromacs/gmxpreprocess/convparm.cpp b/src/gromacs/gmxpreprocess/convparm.cpp index a28d9918da..df6889d52a 100644 --- a/src/gromacs/gmxpreprocess/convparm.cpp +++ b/src/gromacs/gmxpreprocess/convparm.cpp @@ -46,7 +46,7 @@ #include #include "gromacs/gmxpreprocess/gpp_atomtype.h" -#include "gromacs/gmxpreprocess/grompp-impl.h" +#include "gromacs/gmxpreprocess/grompp_impl.h" #include "gromacs/gmxpreprocess/topio.h" #include "gromacs/gmxpreprocess/toputil.h" #include "gromacs/math/functions.h" diff --git a/src/gromacs/gmxpreprocess/editconf.cpp b/src/gromacs/gmxpreprocess/editconf.cpp index 58347b87a8..dcbd52a49d 100644 --- a/src/gromacs/gmxpreprocess/editconf.cpp +++ b/src/gromacs/gmxpreprocess/editconf.cpp @@ -51,7 +51,7 @@ #include "gromacs/fileio/tpxio.h" #include "gromacs/fileio/trxio.h" #include "gromacs/gmxana/princ.h" -#include "gromacs/gmxlib/conformation-utilities.h" +#include "gromacs/gmxlib/conformation_utilities.h" #include "gromacs/math/functions.h" #include "gromacs/math/units.h" #include "gromacs/math/vec.h" diff --git a/src/gromacs/gmxpreprocess/gen_ad.cpp b/src/gromacs/gmxpreprocess/gen_ad.cpp index c77553fb31..6711476243 100644 --- a/src/gromacs/gmxpreprocess/gen_ad.cpp +++ b/src/gromacs/gmxpreprocess/gen_ad.cpp @@ -48,7 +48,7 @@ #include "gromacs/fileio/confio.h" #include "gromacs/gmxpreprocess/gpp_nextnb.h" -#include "gromacs/gmxpreprocess/grompp-impl.h" +#include "gromacs/gmxpreprocess/grompp_impl.h" #include "gromacs/gmxpreprocess/hackblock.h" #include "gromacs/gmxpreprocess/notset.h" #include "gromacs/gmxpreprocess/pgutil.h" diff --git a/src/gromacs/gmxpreprocess/gen_vsite.cpp b/src/gromacs/gmxpreprocess/gen_vsite.cpp index b55d8a37f4..1bc33529d7 100644 --- a/src/gromacs/gmxpreprocess/gen_vsite.cpp +++ b/src/gromacs/gmxpreprocess/gen_vsite.cpp @@ -50,7 +50,7 @@ #include "gromacs/gmxpreprocess/add_par.h" #include "gromacs/gmxpreprocess/fflibutil.h" #include "gromacs/gmxpreprocess/gpp_atomtype.h" -#include "gromacs/gmxpreprocess/grompp-impl.h" +#include "gromacs/gmxpreprocess/grompp_impl.h" #include "gromacs/gmxpreprocess/hackblock.h" #include "gromacs/gmxpreprocess/notset.h" #include "gromacs/gmxpreprocess/resall.h" diff --git a/src/gromacs/gmxpreprocess/gpp_atomtype.cpp b/src/gromacs/gmxpreprocess/gpp_atomtype.cpp index a5b905f6ef..3fe7003ccd 100644 --- a/src/gromacs/gmxpreprocess/gpp_atomtype.cpp +++ b/src/gromacs/gmxpreprocess/gpp_atomtype.cpp @@ -42,7 +42,7 @@ #include #include -#include "gromacs/gmxpreprocess/grompp-impl.h" +#include "gromacs/gmxpreprocess/grompp_impl.h" #include "gromacs/gmxpreprocess/notset.h" #include "gromacs/gmxpreprocess/topdirs.h" #include "gromacs/gmxpreprocess/toputil.h" diff --git a/src/gromacs/gmxpreprocess/gpp_nextnb.cpp b/src/gromacs/gmxpreprocess/gpp_nextnb.cpp index 66ef693a6b..74c2fa3226 100644 --- a/src/gromacs/gmxpreprocess/gpp_nextnb.cpp +++ b/src/gromacs/gmxpreprocess/gpp_nextnb.cpp @@ -41,7 +41,7 @@ #include -#include "gromacs/gmxpreprocess/grompp-impl.h" +#include "gromacs/gmxpreprocess/grompp_impl.h" #include "gromacs/gmxpreprocess/toputil.h" #include "gromacs/topology/ifunc.h" #include "gromacs/utility/fatalerror.h" diff --git a/src/gromacs/gmxpreprocess/grompp.cpp b/src/gromacs/gmxpreprocess/grompp.cpp index 4e0922fd84..08ce54c750 100644 --- a/src/gromacs/gmxpreprocess/grompp.cpp +++ b/src/gromacs/gmxpreprocess/grompp.cpp @@ -49,9 +49,9 @@ #include -#include "gromacs/awh/read-params.h" +#include "gromacs/awh/read_params.h" #include "gromacs/commandline/pargs.h" -#include "gromacs/ewald/ewald-utils.h" +#include "gromacs/ewald/ewald_utils.h" #include "gromacs/ewald/pme.h" #include "gromacs/fft/calcgrid.h" #include "gromacs/fileio/confio.h" @@ -63,7 +63,7 @@ #include "gromacs/gmxpreprocess/convparm.h" #include "gromacs/gmxpreprocess/gen_maxwell_velocities.h" #include "gromacs/gmxpreprocess/gpp_atomtype.h" -#include "gromacs/gmxpreprocess/grompp-impl.h" +#include "gromacs/gmxpreprocess/grompp_impl.h" #include "gromacs/gmxpreprocess/notset.h" #include "gromacs/gmxpreprocess/readir.h" #include "gromacs/gmxpreprocess/tomorse.h" diff --git a/src/gromacs/gmxpreprocess/grompp-impl.h b/src/gromacs/gmxpreprocess/grompp_impl.h similarity index 100% rename from src/gromacs/gmxpreprocess/grompp-impl.h rename to src/gromacs/gmxpreprocess/grompp_impl.h diff --git a/src/gromacs/gmxpreprocess/insert-molecules.cpp b/src/gromacs/gmxpreprocess/insert_molecules.cpp similarity index 99% rename from src/gromacs/gmxpreprocess/insert-molecules.cpp rename to src/gromacs/gmxpreprocess/insert_molecules.cpp index 268b56e125..572c385516 100644 --- a/src/gromacs/gmxpreprocess/insert-molecules.cpp +++ b/src/gromacs/gmxpreprocess/insert_molecules.cpp @@ -36,7 +36,7 @@ */ #include "gmxpre.h" -#include "insert-molecules.h" +#include "insert_molecules.h" #include #include @@ -48,7 +48,7 @@ #include "gromacs/fileio/confio.h" #include "gromacs/fileio/filetypes.h" #include "gromacs/fileio/xvgr.h" -#include "gromacs/gmxlib/conformation-utilities.h" +#include "gromacs/gmxlib/conformation_utilities.h" #include "gromacs/gmxpreprocess/makeexclusiondistances.h" #include "gromacs/math/functions.h" #include "gromacs/math/utilities.h" diff --git a/src/gromacs/gmxpreprocess/insert-molecules.h b/src/gromacs/gmxpreprocess/insert_molecules.h similarity index 96% rename from src/gromacs/gmxpreprocess/insert-molecules.h rename to src/gromacs/gmxpreprocess/insert_molecules.h index 8392f92277..37601f2748 100644 --- a/src/gromacs/gmxpreprocess/insert-molecules.h +++ b/src/gromacs/gmxpreprocess/insert_molecules.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014,2015,2018, by the GROMACS development team, led by + * Copyright (c) 2014,2015,2018,2019, 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/gmxpreprocess/nm2type.cpp b/src/gromacs/gmxpreprocess/nm2type.cpp index 836cec2227..3926d6137a 100644 --- a/src/gromacs/gmxpreprocess/nm2type.cpp +++ b/src/gromacs/gmxpreprocess/nm2type.cpp @@ -49,7 +49,7 @@ #include "gromacs/gmxpreprocess/fflibutil.h" #include "gromacs/gmxpreprocess/gpp_atomtype.h" #include "gromacs/gmxpreprocess/gpp_nextnb.h" -#include "gromacs/gmxpreprocess/grompp-impl.h" +#include "gromacs/gmxpreprocess/grompp_impl.h" #include "gromacs/gmxpreprocess/notset.h" #include "gromacs/gmxpreprocess/pdb2top.h" #include "gromacs/gmxpreprocess/toppush.h" diff --git a/src/gromacs/gmxpreprocess/pdb2gmx.cpp b/src/gromacs/gmxpreprocess/pdb2gmx.cpp index cab4521a43..6f613f901c 100644 --- a/src/gromacs/gmxpreprocess/pdb2gmx.cpp +++ b/src/gromacs/gmxpreprocess/pdb2gmx.cpp @@ -53,10 +53,10 @@ #include "gromacs/fileio/filetypes.h" #include "gromacs/fileio/gmxfio.h" #include "gromacs/fileio/pdbio.h" -#include "gromacs/gmxlib/conformation-utilities.h" +#include "gromacs/gmxlib/conformation_utilities.h" #include "gromacs/gmxpreprocess/fflibutil.h" #include "gromacs/gmxpreprocess/genhydro.h" -#include "gromacs/gmxpreprocess/grompp-impl.h" +#include "gromacs/gmxpreprocess/grompp_impl.h" #include "gromacs/gmxpreprocess/h_db.h" #include "gromacs/gmxpreprocess/hackblock.h" #include "gromacs/gmxpreprocess/hizzie.h" diff --git a/src/gromacs/gmxpreprocess/pdb2top.cpp b/src/gromacs/gmxpreprocess/pdb2top.cpp index ecb7f264a8..292397645c 100644 --- a/src/gromacs/gmxpreprocess/pdb2top.cpp +++ b/src/gromacs/gmxpreprocess/pdb2top.cpp @@ -53,7 +53,7 @@ #include "gromacs/gmxpreprocess/gen_ad.h" #include "gromacs/gmxpreprocess/gen_vsite.h" #include "gromacs/gmxpreprocess/gpp_nextnb.h" -#include "gromacs/gmxpreprocess/grompp-impl.h" +#include "gromacs/gmxpreprocess/grompp_impl.h" #include "gromacs/gmxpreprocess/h_db.h" #include "gromacs/gmxpreprocess/hackblock.h" #include "gromacs/gmxpreprocess/notset.h" diff --git a/src/gromacs/gmxpreprocess/readir.cpp b/src/gromacs/gmxpreprocess/readir.cpp index 9e6a9d1ee2..1960170bb0 100644 --- a/src/gromacs/gmxpreprocess/readir.cpp +++ b/src/gromacs/gmxpreprocess/readir.cpp @@ -46,7 +46,7 @@ #include #include -#include "gromacs/awh/read-params.h" +#include "gromacs/awh/read_params.h" #include "gromacs/fileio/readinp.h" #include "gromacs/fileio/warninp.h" #include "gromacs/gmxlib/chargegroup.h" @@ -60,7 +60,7 @@ #include "gromacs/mdrunutility/mdmodules.h" #include "gromacs/mdtypes/inputrec.h" #include "gromacs/mdtypes/md_enums.h" -#include "gromacs/mdtypes/pull-params.h" +#include "gromacs/mdtypes/pull_params.h" #include "gromacs/options/options.h" #include "gromacs/options/treesupport.h" #include "gromacs/pbcutil/pbc.h" diff --git a/src/gromacs/gmxpreprocess/readpull.cpp b/src/gromacs/gmxpreprocess/readpull.cpp index f910615911..16f00271e7 100644 --- a/src/gromacs/gmxpreprocess/readpull.cpp +++ b/src/gromacs/gmxpreprocess/readpull.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. @@ -49,7 +49,7 @@ #include "gromacs/mdlib/mdrun.h" #include "gromacs/mdtypes/inputrec.h" #include "gromacs/mdtypes/md_enums.h" -#include "gromacs/mdtypes/pull-params.h" +#include "gromacs/mdtypes/pull_params.h" #include "gromacs/pbcutil/pbc.h" #include "gromacs/pulling/pull.h" #include "gromacs/topology/topology.h" diff --git a/src/gromacs/gmxpreprocess/resall.cpp b/src/gromacs/gmxpreprocess/resall.cpp index 0c67d5abd6..ea89de540a 100644 --- a/src/gromacs/gmxpreprocess/resall.cpp +++ b/src/gromacs/gmxpreprocess/resall.cpp @@ -48,7 +48,7 @@ #include "gromacs/gmxpreprocess/fflibutil.h" #include "gromacs/gmxpreprocess/gpp_atomtype.h" -#include "gromacs/gmxpreprocess/grompp-impl.h" +#include "gromacs/gmxpreprocess/grompp_impl.h" #include "gromacs/gmxpreprocess/hackblock.h" #include "gromacs/gmxpreprocess/notset.h" #include "gromacs/gmxpreprocess/pgutil.h" diff --git a/src/gromacs/gmxpreprocess/solvate.cpp b/src/gromacs/gmxpreprocess/solvate.cpp index 40405d5670..60fa35e97c 100644 --- a/src/gromacs/gmxpreprocess/solvate.cpp +++ b/src/gromacs/gmxpreprocess/solvate.cpp @@ -46,7 +46,7 @@ #include "gromacs/commandline/pargs.h" #include "gromacs/fileio/confio.h" #include "gromacs/fileio/pdbio.h" -#include "gromacs/gmxlib/conformation-utilities.h" +#include "gromacs/gmxlib/conformation_utilities.h" #include "gromacs/gmxpreprocess/makeexclusiondistances.h" #include "gromacs/math/functions.h" #include "gromacs/math/units.h" diff --git a/src/gromacs/gmxpreprocess/ter_db.cpp b/src/gromacs/gmxpreprocess/ter_db.cpp index 866f810368..6f78669d25 100644 --- a/src/gromacs/gmxpreprocess/ter_db.cpp +++ b/src/gromacs/gmxpreprocess/ter_db.cpp @@ -47,7 +47,7 @@ #include "gromacs/fileio/gmxfio.h" #include "gromacs/gmxpreprocess/fflibutil.h" #include "gromacs/gmxpreprocess/gpp_atomtype.h" -#include "gromacs/gmxpreprocess/grompp-impl.h" +#include "gromacs/gmxpreprocess/grompp_impl.h" #include "gromacs/gmxpreprocess/h_db.h" #include "gromacs/gmxpreprocess/hackblock.h" #include "gromacs/gmxpreprocess/notset.h" diff --git a/src/gromacs/gmxpreprocess/tests/CMakeLists.txt b/src/gromacs/gmxpreprocess/tests/CMakeLists.txt index f3d52e3237..ecb8c960dd 100644 --- a/src/gromacs/gmxpreprocess/tests/CMakeLists.txt +++ b/src/gromacs/gmxpreprocess/tests/CMakeLists.txt @@ -34,7 +34,7 @@ gmx_add_unit_test(GmxPreprocessTests gmxpreprocess-test genconf.cpp - insert-molecules.cpp + insert_molecules.cpp readir.cpp solvate.cpp topdirs.cpp diff --git a/src/gromacs/gmxpreprocess/tests/insert-molecules.cpp b/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp similarity index 96% rename from src/gromacs/gmxpreprocess/tests/insert-molecules.cpp rename to src/gromacs/gmxpreprocess/tests/insert_molecules.cpp index ff603a6e1d..39699fdb15 100644 --- a/src/gromacs/gmxpreprocess/tests/insert-molecules.cpp +++ b/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015,2016,2019, 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. @@ -41,7 +41,7 @@ */ #include "gmxpre.h" -#include "gromacs/gmxpreprocess/insert-molecules.h" +#include "gromacs/gmxpreprocess/insert_molecules.h" #include "testutils/cmdlinetest.h" #include "testutils/refdata.h" diff --git a/src/gromacs/gmxpreprocess/tomorse.cpp b/src/gromacs/gmxpreprocess/tomorse.cpp index 7cef8dfee7..90b2962746 100644 --- a/src/gromacs/gmxpreprocess/tomorse.cpp +++ b/src/gromacs/gmxpreprocess/tomorse.cpp @@ -45,7 +45,7 @@ #include #include "gromacs/gmxpreprocess/gpp_atomtype.h" -#include "gromacs/gmxpreprocess/grompp-impl.h" +#include "gromacs/gmxpreprocess/grompp_impl.h" #include "gromacs/gmxpreprocess/toputil.h" #include "gromacs/topology/ifunc.h" #include "gromacs/utility/cstringutil.h" diff --git a/src/gromacs/gmxpreprocess/topdirs.cpp b/src/gromacs/gmxpreprocess/topdirs.cpp index 87da79bf20..89f4374b1f 100644 --- a/src/gromacs/gmxpreprocess/topdirs.cpp +++ b/src/gromacs/gmxpreprocess/topdirs.cpp @@ -49,7 +49,7 @@ #include "gromacs/utility/fatalerror.h" #include "gromacs/utility/smalloc.h" -/* Must correspond to the Directive enum in grompp-impl.h */ +/* Must correspond to the Directive enum in grompp_impl.h */ static gmx::EnumerationArray directive_names = { { "defaults", diff --git a/src/gromacs/gmxpreprocess/topio.cpp b/src/gromacs/gmxpreprocess/topio.cpp index 10f6d39b9c..97a5ff7f99 100644 --- a/src/gromacs/gmxpreprocess/topio.cpp +++ b/src/gromacs/gmxpreprocess/topio.cpp @@ -57,7 +57,7 @@ #include "gromacs/gmxpreprocess/gpp_atomtype.h" #include "gromacs/gmxpreprocess/gpp_bond_atomtype.h" #include "gromacs/gmxpreprocess/gpp_nextnb.h" -#include "gromacs/gmxpreprocess/grompp-impl.h" +#include "gromacs/gmxpreprocess/grompp_impl.h" #include "gromacs/gmxpreprocess/readir.h" #include "gromacs/gmxpreprocess/topdirs.h" #include "gromacs/gmxpreprocess/toppush.h" diff --git a/src/gromacs/gmxpreprocess/toppush.cpp b/src/gromacs/gmxpreprocess/toppush.cpp index 6828bb0703..abf5722ddf 100644 --- a/src/gromacs/gmxpreprocess/toppush.cpp +++ b/src/gromacs/gmxpreprocess/toppush.cpp @@ -49,7 +49,7 @@ #include "gromacs/fileio/warninp.h" #include "gromacs/gmxpreprocess/gpp_atomtype.h" #include "gromacs/gmxpreprocess/gpp_bond_atomtype.h" -#include "gromacs/gmxpreprocess/grompp-impl.h" +#include "gromacs/gmxpreprocess/grompp_impl.h" #include "gromacs/gmxpreprocess/notset.h" #include "gromacs/gmxpreprocess/readir.h" #include "gromacs/gmxpreprocess/topdirs.h" diff --git a/src/gromacs/gmxpreprocess/topshake.cpp b/src/gromacs/gmxpreprocess/topshake.cpp index 93ae99953c..5c54f19db7 100644 --- a/src/gromacs/gmxpreprocess/topshake.cpp +++ b/src/gromacs/gmxpreprocess/topshake.cpp @@ -42,7 +42,7 @@ #include #include -#include "gromacs/gmxpreprocess/grompp-impl.h" +#include "gromacs/gmxpreprocess/grompp_impl.h" #include "gromacs/gmxpreprocess/notset.h" #include "gromacs/gmxpreprocess/readir.h" #include "gromacs/gmxpreprocess/topdirs.h" diff --git a/src/gromacs/gmxpreprocess/toputil.cpp b/src/gromacs/gmxpreprocess/toputil.cpp index facc152e5a..c5a69f6014 100644 --- a/src/gromacs/gmxpreprocess/toputil.cpp +++ b/src/gromacs/gmxpreprocess/toputil.cpp @@ -45,7 +45,7 @@ #include #include "gromacs/gmxpreprocess/gpp_atomtype.h" -#include "gromacs/gmxpreprocess/grompp-impl.h" +#include "gromacs/gmxpreprocess/grompp_impl.h" #include "gromacs/gmxpreprocess/notset.h" #include "gromacs/gmxpreprocess/topdirs.h" #include "gromacs/topology/block.h" diff --git a/src/gromacs/gmxpreprocess/vsite_parm.cpp b/src/gromacs/gmxpreprocess/vsite_parm.cpp index 9917af8b91..548456d453 100644 --- a/src/gromacs/gmxpreprocess/vsite_parm.cpp +++ b/src/gromacs/gmxpreprocess/vsite_parm.cpp @@ -46,7 +46,7 @@ #include "gromacs/gmxpreprocess/add_par.h" #include "gromacs/gmxpreprocess/gpp_atomtype.h" -#include "gromacs/gmxpreprocess/grompp-impl.h" +#include "gromacs/gmxpreprocess/grompp_impl.h" #include "gromacs/gmxpreprocess/notset.h" #include "gromacs/gmxpreprocess/resall.h" #include "gromacs/gmxpreprocess/toputil.h" diff --git a/src/gromacs/gmxpreprocess/x2top.cpp b/src/gromacs/gmxpreprocess/x2top.cpp index fdbe302c14..22a84e45bf 100644 --- a/src/gromacs/gmxpreprocess/x2top.cpp +++ b/src/gromacs/gmxpreprocess/x2top.cpp @@ -47,7 +47,7 @@ #include "gromacs/gmxpreprocess/gen_ad.h" #include "gromacs/gmxpreprocess/gpp_atomtype.h" #include "gromacs/gmxpreprocess/gpp_nextnb.h" -#include "gromacs/gmxpreprocess/grompp-impl.h" +#include "gromacs/gmxpreprocess/grompp_impl.h" #include "gromacs/gmxpreprocess/hackblock.h" #include "gromacs/gmxpreprocess/nm2type.h" #include "gromacs/gmxpreprocess/notset.h" diff --git a/src/gromacs/gmxpreprocess/xlate.cpp b/src/gromacs/gmxpreprocess/xlate.cpp index be603334b5..da4df8ca2c 100644 --- a/src/gromacs/gmxpreprocess/xlate.cpp +++ b/src/gromacs/gmxpreprocess/xlate.cpp @@ -45,7 +45,7 @@ #include #include "gromacs/gmxpreprocess/fflibutil.h" -#include "gromacs/gmxpreprocess/grompp-impl.h" +#include "gromacs/gmxpreprocess/grompp_impl.h" #include "gromacs/gmxpreprocess/hackblock.h" #include "gromacs/topology/residuetypes.h" #include "gromacs/topology/symtab.h" diff --git a/src/gromacs/gpu_utils/tests/hostallocator.cpp b/src/gromacs/gpu_utils/tests/hostallocator.cpp index 203fac3422..c7613dd184 100644 --- a/src/gromacs/gpu_utils/tests/hostallocator.cpp +++ b/src/gromacs/gpu_utils/tests/hostallocator.cpp @@ -381,4 +381,4 @@ TYPED_TEST_CASE(AllocatorTest, AllocatorTypesToTest); } // namespace gmx // Includes tests common to all allocation policies. -#include "gromacs/utility/tests/alignedallocator-impl.h" +#include "gromacs/utility/tests/alignedallocator_impl.h" diff --git a/src/gromacs/listed_forces/CMakeLists.txt b/src/gromacs/listed_forces/CMakeLists.txt index bd97c81fe1..22936e1e5b 100644 --- a/src/gromacs/listed_forces/CMakeLists.txt +++ b/src/gromacs/listed_forces/CMakeLists.txt @@ -35,19 +35,19 @@ gmx_add_libgromacs_sources( bonded.cpp disre.cpp - gpubonded-impl.cpp + gpubonded_impl.cpp listed_forces.cpp - listed-internal.cpp - manage-threading.cpp + listed_internal.cpp + manage_threading.cpp orires.cpp pairs.cpp - position-restraints.cpp + position_restraints.cpp restcbt.cpp ) if(GMX_USE_CUDA) gmx_add_libgromacs_sources( - gpubonded-impl.cu + gpubonded_impl.cu gpubondedkernels.cu ) endif() diff --git a/src/gromacs/listed_forces/bonded.cpp b/src/gromacs/listed_forces/bonded.cpp index 0ae06d19af..8c03e0a29a 100644 --- a/src/gromacs/listed_forces/bonded.cpp +++ b/src/gromacs/listed_forces/bonded.cpp @@ -63,7 +63,7 @@ #include "gromacs/pbcutil/ishift.h" #include "gromacs/pbcutil/mshift.h" #include "gromacs/pbcutil/pbc.h" -#include "gromacs/pbcutil/pbc-simd.h" +#include "gromacs/pbcutil/pbc_simd.h" #include "gromacs/simd/simd.h" #include "gromacs/simd/simd_math.h" #include "gromacs/simd/vector_operations.h" @@ -72,7 +72,7 @@ #include "gromacs/utility/real.h" #include "gromacs/utility/smalloc.h" -#include "listed-internal.h" +#include "listed_internal.h" #include "restcbt.h" using namespace gmx; // TODO: Remove when this file is moved into gmx namespace diff --git a/src/gromacs/listed_forces/gpubonded-impl.cpp b/src/gromacs/listed_forces/gpubonded_impl.cpp similarity index 100% rename from src/gromacs/listed_forces/gpubonded-impl.cpp rename to src/gromacs/listed_forces/gpubonded_impl.cpp diff --git a/src/gromacs/listed_forces/gpubonded-impl.cu b/src/gromacs/listed_forces/gpubonded_impl.cu similarity index 99% rename from src/gromacs/listed_forces/gpubonded-impl.cu rename to src/gromacs/listed_forces/gpubonded_impl.cu index 8da1a9ffd0..40f2c6dd18 100644 --- a/src/gromacs/listed_forces/gpubonded-impl.cu +++ b/src/gromacs/listed_forces/gpubonded_impl.cu @@ -45,7 +45,7 @@ #include "gmxpre.h" -#include "gpubonded-impl.h" +#include "gpubonded_impl.h" #include "gromacs/gpu_utils/cudautils.cuh" #include "gromacs/gpu_utils/devicebuffer.h" diff --git a/src/gromacs/listed_forces/gpubonded-impl.h b/src/gromacs/listed_forces/gpubonded_impl.h similarity index 100% rename from src/gromacs/listed_forces/gpubonded-impl.h rename to src/gromacs/listed_forces/gpubonded_impl.h diff --git a/src/gromacs/listed_forces/gpubondedkernels.cu b/src/gromacs/listed_forces/gpubondedkernels.cu index 2f78486340..a804553d1f 100644 --- a/src/gromacs/listed_forces/gpubondedkernels.cu +++ b/src/gromacs/listed_forces/gpubondedkernels.cu @@ -69,7 +69,7 @@ #include "gromacs/topology/ifunc.h" #include "gromacs/utility/gmxassert.h" -#include "gpubonded-impl.h" +#include "gpubonded_impl.h" #if defined(_MSVC) #include diff --git a/src/gromacs/listed_forces/listed_forces.cpp b/src/gromacs/listed_forces/listed_forces.cpp index 97255fe9a9..d99dcfe8c8 100644 --- a/src/gromacs/listed_forces/listed_forces.cpp +++ b/src/gromacs/listed_forces/listed_forces.cpp @@ -56,7 +56,7 @@ #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/position_restraints.h" #include "gromacs/math/vec.h" #include "gromacs/mdlib/force.h" #include "gromacs/mdlib/force_flags.h" @@ -74,7 +74,7 @@ #include "gromacs/utility/fatalerror.h" #include "gromacs/utility/smalloc.h" -#include "listed-internal.h" +#include "listed_internal.h" #include "utilities.h" struct BondedInteractions diff --git a/src/gromacs/listed_forces/listed-internal.cpp b/src/gromacs/listed_forces/listed_internal.cpp similarity index 98% rename from src/gromacs/listed_forces/listed-internal.cpp rename to src/gromacs/listed_forces/listed_internal.cpp index 2161bff3c5..fe883968e8 100644 --- a/src/gromacs/listed_forces/listed-internal.cpp +++ b/src/gromacs/listed_forces/listed_internal.cpp @@ -41,7 +41,7 @@ */ #include "gmxpre.h" -#include "listed-internal.h" +#include "listed_internal.h" #include diff --git a/src/gromacs/listed_forces/listed-internal.h b/src/gromacs/listed_forces/listed_internal.h similarity index 100% rename from src/gromacs/listed_forces/listed-internal.h rename to src/gromacs/listed_forces/listed_internal.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 5aa96feb88..9b1ff77f69 100644 --- a/src/gromacs/listed_forces/manage-threading.cpp +++ b/src/gromacs/listed_forces/manage_threading.cpp @@ -43,7 +43,7 @@ */ #include "gmxpre.h" -#include "manage-threading.h" +#include "manage_threading.h" #include "config.h" @@ -64,7 +64,7 @@ #include "gromacs/utility/gmxassert.h" #include "gromacs/utility/smalloc.h" -#include "listed-internal.h" +#include "listed_internal.h" #include "utilities.h" /*! \brief struct for passing all data required for a function type */ diff --git a/src/gromacs/listed_forces/manage-threading.h b/src/gromacs/listed_forces/manage_threading.h similarity index 100% rename from src/gromacs/listed_forces/manage-threading.h rename to src/gromacs/listed_forces/manage_threading.h diff --git a/src/gromacs/listed_forces/pairs.cpp b/src/gromacs/listed_forces/pairs.cpp index e910e59227..283c7cbb70 100644 --- a/src/gromacs/listed_forces/pairs.cpp +++ b/src/gromacs/listed_forces/pairs.cpp @@ -55,7 +55,7 @@ #include "gromacs/pbcutil/ishift.h" #include "gromacs/pbcutil/mshift.h" #include "gromacs/pbcutil/pbc.h" -#include "gromacs/pbcutil/pbc-simd.h" +#include "gromacs/pbcutil/pbc_simd.h" #include "gromacs/simd/simd.h" #include "gromacs/simd/simd_math.h" #include "gromacs/simd/vector_operations.h" @@ -64,7 +64,7 @@ #include "gromacs/utility/fatalerror.h" #include "gromacs/utility/gmxassert.h" -#include "listed-internal.h" +#include "listed_internal.h" using namespace gmx; // TODO: Remove when this file is moved into gmx namespace 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 f6c865b30b..9e1a41c994 100644 --- a/src/gromacs/listed_forces/position-restraints.cpp +++ b/src/gromacs/listed_forces/position_restraints.cpp @@ -44,7 +44,7 @@ #include "gmxpre.h" -#include "position-restraints.h" +#include "position_restraints.h" #include #include diff --git a/src/gromacs/listed_forces/position-restraints.h b/src/gromacs/listed_forces/position_restraints.h similarity index 100% rename from src/gromacs/listed_forces/position-restraints.h rename to src/gromacs/listed_forces/position_restraints.h diff --git a/src/gromacs/mdlib/broadcaststructs.cpp b/src/gromacs/mdlib/broadcaststructs.cpp index 61768551a7..51fd02767e 100644 --- a/src/gromacs/mdlib/broadcaststructs.cpp +++ b/src/gromacs/mdlib/broadcaststructs.cpp @@ -47,11 +47,11 @@ #include "gromacs/math/vec.h" #include "gromacs/mdlib/mdrun.h" #include "gromacs/mdlib/tgroup.h" -#include "gromacs/mdtypes/awh-params.h" +#include "gromacs/mdtypes/awh_params.h" #include "gromacs/mdtypes/commrec.h" #include "gromacs/mdtypes/inputrec.h" #include "gromacs/mdtypes/md_enums.h" -#include "gromacs/mdtypes/pull-params.h" +#include "gromacs/mdtypes/pull_params.h" #include "gromacs/mdtypes/state.h" #include "gromacs/topology/mtop_util.h" #include "gromacs/topology/symtab.h" diff --git a/src/gromacs/mdlib/calc_verletbuf.cpp b/src/gromacs/mdlib/calc_verletbuf.cpp index 0807282c85..fd07917451 100644 --- a/src/gromacs/mdlib/calc_verletbuf.cpp +++ b/src/gromacs/mdlib/calc_verletbuf.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. @@ -41,7 +41,7 @@ #include -#include "gromacs/ewald/ewald-utils.h" +#include "gromacs/ewald/ewald_utils.h" #include "gromacs/math/functions.h" #include "gromacs/math/units.h" #include "gromacs/math/vec.h" diff --git a/src/gromacs/mdlib/compute_io.cpp b/src/gromacs/mdlib/compute_io.cpp index ec5b613b24..4849bcfe28 100644 --- a/src/gromacs/mdlib/compute_io.cpp +++ b/src/gromacs/mdlib/compute_io.cpp @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2012,2014,2015,2017,2018, by the GROMACS development team, led by + * Copyright (c) 2012,2014,2015,2017,2018,2019, 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. @@ -43,7 +43,7 @@ #include "gromacs/mdtypes/inputrec.h" #include "gromacs/mdtypes/md_enums.h" -#include "gromacs/mdtypes/pull-params.h" +#include "gromacs/mdtypes/pull_params.h" #include "gromacs/topology/topology.h" static int div_nsteps(int nsteps, int nst) diff --git a/src/gromacs/mdlib/force.cpp b/src/gromacs/mdlib/force.cpp index 7847aaa8cc..09f54fc4f8 100644 --- a/src/gromacs/mdlib/force.cpp +++ b/src/gromacs/mdlib/force.cpp @@ -47,7 +47,7 @@ #include "gromacs/domdec/domdec.h" #include "gromacs/domdec/domdec_struct.h" #include "gromacs/ewald/ewald.h" -#include "gromacs/ewald/long-range-correction.h" +#include "gromacs/ewald/long_range_correction.h" #include "gromacs/ewald/pme.h" #include "gromacs/gmxlib/network.h" #include "gromacs/gmxlib/nrnb.h" @@ -56,7 +56,7 @@ #include "gromacs/math/vec.h" #include "gromacs/math/vecdump.h" #include "gromacs/mdlib/force_flags.h" -#include "gromacs/mdlib/forcerec-threading.h" +#include "gromacs/mdlib/forcerec_threading.h" #include "gromacs/mdlib/mdrun.h" #include "gromacs/mdlib/ns.h" #include "gromacs/mdlib/qmmm.h" diff --git a/src/gromacs/mdlib/forcerec.cpp b/src/gromacs/mdlib/forcerec.cpp index dec8a2a022..5d7872a3ff 100644 --- a/src/gromacs/mdlib/forcerec.cpp +++ b/src/gromacs/mdlib/forcerec.cpp @@ -52,21 +52,21 @@ #include "gromacs/domdec/domdec.h" #include "gromacs/domdec/domdec_struct.h" #include "gromacs/ewald/ewald.h" -#include "gromacs/ewald/ewald-utils.h" +#include "gromacs/ewald/ewald_utils.h" #include "gromacs/fileio/filetypes.h" #include "gromacs/gmxlib/network.h" #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/manage_threading.h" #include "gromacs/listed_forces/pairs.h" #include "gromacs/math/functions.h" #include "gromacs/math/units.h" #include "gromacs/math/utilities.h" #include "gromacs/math/vec.h" #include "gromacs/mdlib/force.h" -#include "gromacs/mdlib/forcerec-threading.h" +#include "gromacs/mdlib/forcerec_threading.h" #include "gromacs/mdlib/gmx_omp_nthreads.h" #include "gromacs/mdlib/md_support.h" #include "gromacs/mdlib/nb_verlet.h" diff --git a/src/gromacs/mdlib/forcerec-threading.h b/src/gromacs/mdlib/forcerec_threading.h similarity index 96% rename from src/gromacs/mdlib/forcerec-threading.h rename to src/gromacs/mdlib/forcerec_threading.h index 9bf01ceade..26d40570a0 100644 --- a/src/gromacs/mdlib/forcerec-threading.h +++ b/src/gromacs/mdlib/forcerec_threading.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014,2015,2018, by the GROMACS development team, led by + * Copyright (c) 2014,2015,2018,2019, 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/mdlib/lincs.cpp b/src/gromacs/mdlib/lincs.cpp index 44f1415c07..ac37a7b54e 100644 --- a/src/gromacs/mdlib/lincs.cpp +++ b/src/gromacs/mdlib/lincs.cpp @@ -69,7 +69,7 @@ #include "gromacs/mdtypes/md_enums.h" #include "gromacs/mdtypes/mdatom.h" #include "gromacs/pbcutil/pbc.h" -#include "gromacs/pbcutil/pbc-simd.h" +#include "gromacs/pbcutil/pbc_simd.h" #include "gromacs/simd/simd.h" #include "gromacs/simd/simd_math.h" #include "gromacs/simd/vector_operations.h" diff --git a/src/gromacs/mdlib/mdsetup.cpp b/src/gromacs/mdlib/mdsetup.cpp index 5a5bb53164..c3dffae4f5 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/resethandler.cpp b/src/gromacs/mdlib/resethandler.cpp index 17bd7df8e3..0e1e06993f 100644 --- a/src/gromacs/mdlib/resethandler.cpp +++ b/src/gromacs/mdlib/resethandler.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. @@ -46,7 +46,7 @@ #include "gromacs/domdec/domdec.h" #include "gromacs/ewald/pme.h" -#include "gromacs/ewald/pme-load-balancing.h" +#include "gromacs/ewald/pme_load_balancing.h" #include "gromacs/gmxlib/nrnb.h" #include "gromacs/gpu_utils/gpu_utils.h" #include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h" diff --git a/src/gromacs/mdlib/settle.cpp b/src/gromacs/mdlib/settle.cpp index 8bcbfd1008..3263c0ddd2 100644 --- a/src/gromacs/mdlib/settle.cpp +++ b/src/gromacs/mdlib/settle.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. @@ -58,7 +58,7 @@ #include "gromacs/mdtypes/mdatom.h" #include "gromacs/pbcutil/ishift.h" #include "gromacs/pbcutil/pbc.h" -#include "gromacs/pbcutil/pbc-simd.h" +#include "gromacs/pbcutil/pbc_simd.h" #include "gromacs/simd/simd.h" #include "gromacs/simd/simd_math.h" #include "gromacs/topology/idef.h" diff --git a/src/gromacs/mdlib/sim_util.cpp b/src/gromacs/mdlib/sim_util.cpp index c6c02e77a0..5e3656bd0c 100644 --- a/src/gromacs/mdlib/sim_util.cpp +++ b/src/gromacs/mdlib/sim_util.cpp @@ -64,7 +64,7 @@ #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/manage_threading.h" #include "gromacs/listed_forces/orires.h" #include "gromacs/math/arrayrefwithpadding.h" #include "gromacs/math/functions.h" diff --git a/src/gromacs/mdrun/md.cpp b/src/gromacs/mdrun/md.cpp index 1825b36b1b..8d38a7c068 100644 --- a/src/gromacs/mdrun/md.cpp +++ b/src/gromacs/mdrun/md.cpp @@ -60,13 +60,13 @@ #include "gromacs/domdec/partition.h" #include "gromacs/essentialdynamics/edsam.h" #include "gromacs/ewald/pme.h" -#include "gromacs/ewald/pme-load-balancing.h" +#include "gromacs/ewald/pme_load_balancing.h" #include "gromacs/fileio/trxio.h" #include "gromacs/gmxlib/network.h" #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" @@ -100,8 +100,8 @@ #include "gromacs/mdlib/update.h" #include "gromacs/mdlib/vcm.h" #include "gromacs/mdlib/vsite.h" -#include "gromacs/mdtypes/awh-history.h" -#include "gromacs/mdtypes/awh-params.h" +#include "gromacs/mdtypes/awh_history.h" +#include "gromacs/mdtypes/awh_params.h" #include "gromacs/mdtypes/commrec.h" #include "gromacs/mdtypes/df_history.h" #include "gromacs/mdtypes/energyhistory.h" diff --git a/src/gromacs/mdrun/mimic.cpp b/src/gromacs/mdrun/mimic.cpp index ffa3117749..c77e5637a5 100644 --- a/src/gromacs/mdrun/mimic.cpp +++ b/src/gromacs/mdrun/mimic.cpp @@ -59,13 +59,13 @@ #include "gromacs/domdec/partition.h" #include "gromacs/essentialdynamics/edsam.h" #include "gromacs/ewald/pme.h" -#include "gromacs/ewald/pme-load-balancing.h" +#include "gromacs/ewald/pme_load_balancing.h" #include "gromacs/fileio/trxio.h" #include "gromacs/gmxlib/network.h" #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" @@ -99,8 +99,8 @@ #include "gromacs/mdlib/update.h" #include "gromacs/mdlib/vcm.h" #include "gromacs/mdlib/vsite.h" -#include "gromacs/mdtypes/awh-history.h" -#include "gromacs/mdtypes/awh-params.h" +#include "gromacs/mdtypes/awh_history.h" +#include "gromacs/mdtypes/awh_params.h" #include "gromacs/mdtypes/commrec.h" #include "gromacs/mdtypes/df_history.h" #include "gromacs/mdtypes/energyhistory.h" diff --git a/src/gromacs/mdrun/minimize.cpp b/src/gromacs/mdrun/minimize.cpp index d7f720018e..ee8c8ac0de 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 aba3f6fc95..53bcd23b84 100644 --- a/src/gromacs/mdrun/rerun.cpp +++ b/src/gromacs/mdrun/rerun.cpp @@ -60,13 +60,13 @@ #include "gromacs/domdec/partition.h" #include "gromacs/essentialdynamics/edsam.h" #include "gromacs/ewald/pme.h" -#include "gromacs/ewald/pme-load-balancing.h" +#include "gromacs/ewald/pme_load_balancing.h" #include "gromacs/fileio/trxio.h" #include "gromacs/gmxlib/network.h" #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" @@ -100,8 +100,8 @@ #include "gromacs/mdlib/update.h" #include "gromacs/mdlib/vcm.h" #include "gromacs/mdlib/vsite.h" -#include "gromacs/mdtypes/awh-history.h" -#include "gromacs/mdtypes/awh-params.h" +#include "gromacs/mdtypes/awh_history.h" +#include "gromacs/mdtypes/awh_params.h" #include "gromacs/mdtypes/commrec.h" #include "gromacs/mdtypes/df_history.h" #include "gromacs/mdtypes/energyhistory.h" diff --git a/src/gromacs/mdrun/runner.cpp b/src/gromacs/mdrun/runner.cpp index 5f38a12d47..92ac8c69b3 100644 --- a/src/gromacs/mdrun/runner.cpp +++ b/src/gromacs/mdrun/runner.cpp @@ -60,9 +60,9 @@ #include "gromacs/domdec/domdec.h" #include "gromacs/domdec/domdec_struct.h" #include "gromacs/domdec/localatomsetmanager.h" -#include "gromacs/ewald/ewald-utils.h" +#include "gromacs/ewald/ewald_utils.h" #include "gromacs/ewald/pme.h" -#include "gromacs/ewald/pme-gpu-program.h" +#include "gromacs/ewald/pme_gpu_program.h" #include "gromacs/fileio/checkpoint.h" #include "gromacs/fileio/gmxfio.h" #include "gromacs/fileio/oenv.h" diff --git a/src/gromacs/mdrun/tpi.cpp b/src/gromacs/mdrun/tpi.cpp index 5aaf23de06..cebc50de14 100644 --- a/src/gromacs/mdrun/tpi.cpp +++ b/src/gromacs/mdrun/tpi.cpp @@ -59,7 +59,7 @@ #include "gromacs/fileio/trxio.h" #include "gromacs/fileio/xvgr.h" #include "gromacs/gmxlib/chargegroup.h" -#include "gromacs/gmxlib/conformation-utilities.h" +#include "gromacs/gmxlib/conformation_utilities.h" #include "gromacs/gmxlib/network.h" #include "gromacs/gmxlib/nrnb.h" #include "gromacs/math/units.h" diff --git a/src/gromacs/mdrunutility/mdmodules.cpp b/src/gromacs/mdrunutility/mdmodules.cpp index 039a11e774..f0eab395c7 100644 --- a/src/gromacs/mdrunutility/mdmodules.cpp +++ b/src/gromacs/mdrunutility/mdmodules.cpp @@ -38,7 +38,7 @@ #include -#include "gromacs/applied-forces/electricfield.h" +#include "gromacs/applied_forces/electricfield.h" #include "gromacs/mdtypes/iforceprovider.h" #include "gromacs/mdtypes/imdmodule.h" #include "gromacs/mdtypes/imdoutputprovider.h" diff --git a/src/gromacs/mdrunutility/tests/CMakeLists.txt b/src/gromacs/mdrunutility/tests/CMakeLists.txt index b765917e95..97b3f48513 100644 --- a/src/gromacs/mdrunutility/tests/CMakeLists.txt +++ b/src/gromacs/mdrunutility/tests/CMakeLists.txt @@ -1,7 +1,7 @@ # # This file is part of the GROMACS molecular simulation package. # -# Copyright (c) 2016,2017, by the GROMACS development team, led by +# Copyright (c) 2016,2017,2019, 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. @@ -40,5 +40,5 @@ gmx_add_unit_test(MdrunUtilityUnitTests mdrunutility-test $) gmx_add_mpi_unit_test(MdrunUtilityMpiUnitTests mdrunutility-mpi-test 4 - threadaffinity-mpi.cpp + threadaffinity_mpi.cpp $) diff --git a/src/gromacs/mdrunutility/tests/threadaffinity-mpi.cpp b/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp similarity index 99% rename from src/gromacs/mdrunutility/tests/threadaffinity-mpi.cpp rename to src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp index 7ed0397a8c..c0bb431f8f 100644 --- a/src/gromacs/mdrunutility/tests/threadaffinity-mpi.cpp +++ b/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2016,2017, by the GROMACS development team, led by + * Copyright (c) 2016,2017,2019, 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. diff --git a/src/gromacs/mdtypes/awh-correlation-history.h b/src/gromacs/mdtypes/awh_correlation_history.h similarity index 98% rename from src/gromacs/mdtypes/awh-correlation-history.h rename to src/gromacs/mdtypes/awh_correlation_history.h index b0d8b58231..56fd442648 100644 --- a/src/gromacs/mdtypes/awh-correlation-history.h +++ b/src/gromacs/mdtypes/awh_correlation_history.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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/mdtypes/awh-history.h b/src/gromacs/mdtypes/awh_history.h similarity index 97% rename from src/gromacs/mdtypes/awh-history.h rename to src/gromacs/mdtypes/awh_history.h index ad00f270d0..b33f7e5a33 100644 --- a/src/gromacs/mdtypes/awh-history.h +++ b/src/gromacs/mdtypes/awh_history.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -49,7 +49,7 @@ #include -#include "gromacs/mdtypes/awh-correlation-history.h" +#include "gromacs/mdtypes/awh_correlation_history.h" #include "gromacs/utility/basedefinitions.h" namespace gmx diff --git a/src/gromacs/mdtypes/awh-params.h b/src/gromacs/mdtypes/awh_params.h similarity index 98% rename from src/gromacs/mdtypes/awh-params.h rename to src/gromacs/mdtypes/awh_params.h index 6eef443fda..f01286deb1 100644 --- a/src/gromacs/mdtypes/awh-params.h +++ b/src/gromacs/mdtypes/awh_params.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * 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/mdtypes/inputrec.cpp b/src/gromacs/mdtypes/inputrec.cpp index 6edc255c4f..46d58cf502 100644 --- a/src/gromacs/mdtypes/inputrec.cpp +++ b/src/gromacs/mdtypes/inputrec.cpp @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2010, The GROMACS development team. - * Copyright (c) 2012,2014,2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 2012,2014,2015,2016,2017,2018,2019, 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. @@ -46,9 +46,9 @@ #include "gromacs/math/veccompare.h" #include "gromacs/math/vecdump.h" -#include "gromacs/mdtypes/awh-params.h" +#include "gromacs/mdtypes/awh_params.h" #include "gromacs/mdtypes/md_enums.h" -#include "gromacs/mdtypes/pull-params.h" +#include "gromacs/mdtypes/pull_params.h" #include "gromacs/pbcutil/pbc.h" #include "gromacs/utility/compare.h" #include "gromacs/utility/cstringutil.h" diff --git a/src/gromacs/mdtypes/pull-params.h b/src/gromacs/mdtypes/pull_params.h similarity index 98% rename from src/gromacs/mdtypes/pull-params.h rename to src/gromacs/mdtypes/pull_params.h index ab58be708f..3ec189d076 100644 --- a/src/gromacs/mdtypes/pull-params.h +++ b/src/gromacs/mdtypes/pull_params.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2016,2018, by the GROMACS development team, led by + * Copyright (c) 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. diff --git a/src/gromacs/mdtypes/state.cpp b/src/gromacs/mdtypes/state.cpp index 10ae4e9d29..ef9956a9c8 100644 --- a/src/gromacs/mdtypes/state.cpp +++ b/src/gromacs/mdtypes/state.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. @@ -46,11 +46,11 @@ #include "gromacs/math/paddedvector.h" #include "gromacs/math/vec.h" #include "gromacs/math/veccompare.h" -#include "gromacs/mdtypes/awh-history.h" +#include "gromacs/mdtypes/awh_history.h" #include "gromacs/mdtypes/df_history.h" #include "gromacs/mdtypes/inputrec.h" #include "gromacs/mdtypes/md_enums.h" -#include "gromacs/mdtypes/pull-params.h" +#include "gromacs/mdtypes/pull_params.h" #include "gromacs/mdtypes/swaphistory.h" #include "gromacs/pbcutil/boxutilities.h" #include "gromacs/pbcutil/pbc.h" diff --git a/src/gromacs/onlinehelp-doc.h b/src/gromacs/onlinehelp_doc.h similarity index 97% rename from src/gromacs/onlinehelp-doc.h rename to src/gromacs/onlinehelp_doc.h index 13acaaa2f9..a83e61f3fe 100644 --- a/src/gromacs/onlinehelp-doc.h +++ b/src/gromacs/onlinehelp_doc.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015, by the GROMACS development team, led by + * Copyright (c) 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. diff --git a/src/gromacs/options/abstractsection.cpp b/src/gromacs/options/abstractsection.cpp index bb056cf8d7..8f3fe770a7 100644 --- a/src/gromacs/options/abstractsection.cpp +++ b/src/gromacs/options/abstractsection.cpp @@ -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. @@ -43,7 +43,7 @@ #include "abstractsection.h" -#include "options-impl.h" +#include "options_impl.h" namespace gmx { diff --git a/src/gromacs/options/options.cpp b/src/gromacs/options/options.cpp index c8de6e435a..79fbb16c30 100644 --- a/src/gromacs/options/options.cpp +++ b/src/gromacs/options/options.cpp @@ -54,7 +54,7 @@ #include "gromacs/utility/gmxassert.h" #include "gromacs/utility/stringutil.h" -#include "options-impl.h" +#include "options_impl.h" namespace gmx { diff --git a/src/gromacs/options/options-impl.h b/src/gromacs/options/options_impl.h similarity index 98% rename from src/gromacs/options/options-impl.h rename to src/gromacs/options/options_impl.h index acaccc8c26..d95dc90c67 100644 --- a/src/gromacs/options/options-impl.h +++ b/src/gromacs/options/options_impl.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2018, by the GROMACS development team, led by + * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2018,2019, 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. diff --git a/src/gromacs/options/optionsassigner.cpp b/src/gromacs/options/optionsassigner.cpp index f9cb896873..d2b9856e96 100644 --- a/src/gromacs/options/optionsassigner.cpp +++ b/src/gromacs/options/optionsassigner.cpp @@ -51,7 +51,7 @@ #include "gromacs/utility/exceptions.h" #include "gromacs/utility/gmxassert.h" -#include "options-impl.h" +#include "options_impl.h" namespace gmx { diff --git a/src/gromacs/options/optionsvisitor.cpp b/src/gromacs/options/optionsvisitor.cpp index c628d3a5a1..cb950a37fb 100644 --- a/src/gromacs/options/optionsvisitor.cpp +++ b/src/gromacs/options/optionsvisitor.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2010,2012,2014,2015,2016,2018, by the GROMACS development team, led by + * Copyright (c) 2010,2012,2014,2015,2016,2018,2019, 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. @@ -47,7 +47,7 @@ #include "gromacs/options/options.h" #include "gromacs/options/optionsection.h" -#include "options-impl.h" +#include "options_impl.h" namespace gmx { diff --git a/src/gromacs/pbcutil/pbc-simd.cpp b/src/gromacs/pbcutil/pbc_simd.cpp similarity index 97% rename from src/gromacs/pbcutil/pbc-simd.cpp rename to src/gromacs/pbcutil/pbc_simd.cpp index fb9addd565..92700e830f 100644 --- a/src/gromacs/pbcutil/pbc-simd.cpp +++ b/src/gromacs/pbcutil/pbc_simd.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by + * Copyright (c) 2015,2016,2017,2019, 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 @@ */ #include "gmxpre.h" -#include "pbc-simd.h" +#include "pbc_simd.h" #include "gromacs/math/vec.h" #include "gromacs/pbcutil/pbc.h" diff --git a/src/gromacs/pbcutil/pbc-simd.h b/src/gromacs/pbcutil/pbc_simd.h similarity index 98% rename from src/gromacs/pbcutil/pbc-simd.h rename to src/gromacs/pbcutil/pbc_simd.h index 2040b8efa0..e5e64d9d23 100644 --- a/src/gromacs/pbcutil/pbc-simd.h +++ b/src/gromacs/pbcutil/pbc_simd.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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/pulling/pull.h b/src/gromacs/pulling/pull.h index 9fd108e3fb..9ae87394d0 100644 --- a/src/gromacs/pulling/pull.h +++ b/src/gromacs/pulling/pull.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. @@ -54,7 +54,7 @@ #include "gromacs/math/vectypes.h" #include "gromacs/mdlib/mdrun.h" -#include "gromacs/mdtypes/pull-params.h" +#include "gromacs/mdtypes/pull_params.h" #include "gromacs/utility/arrayref.h" #include "gromacs/utility/basedefinitions.h" #include "gromacs/utility/real.h" diff --git a/src/gromacs/pulling/pull_internal.h b/src/gromacs/pulling/pull_internal.h index 9084b07714..b6351a9d52 100644 --- a/src/gromacs/pulling/pull_internal.h +++ b/src/gromacs/pulling/pull_internal.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. @@ -54,7 +54,7 @@ #include #include "gromacs/domdec/localatomset.h" -#include "gromacs/mdtypes/pull-params.h" +#include "gromacs/mdtypes/pull_params.h" #include "gromacs/utility/gmxmpi.h" /*! \brief Determines up to what local atom count a pull group gets processed single-threaded. diff --git a/src/gromacs/restraint/restraintmdmodule.cpp b/src/gromacs/restraint/restraintmdmodule.cpp index 590516dfc0..32c0d01861 100644 --- a/src/gromacs/restraint/restraintmdmodule.cpp +++ b/src/gromacs/restraint/restraintmdmodule.cpp @@ -42,7 +42,7 @@ #include "gromacs/mdtypes/forceoutput.h" #include "gromacs/mdtypes/iforceprovider.h" -#include "restraintmdmodule-impl.h" +#include "restraintmdmodule_impl.h" namespace gmx { diff --git a/src/gromacs/restraint/restraintmdmodule-impl.h b/src/gromacs/restraint/restraintmdmodule_impl.h similarity index 99% rename from src/gromacs/restraint/restraintmdmodule-impl.h rename to src/gromacs/restraint/restraintmdmodule_impl.h index 67cce4a59a..3895c3c19b 100644 --- a/src/gromacs/restraint/restraintmdmodule-impl.h +++ b/src/gromacs/restraint/restraintmdmodule_impl.h @@ -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. diff --git a/src/gromacs/selection/compiler.cpp b/src/gromacs/selection/compiler.cpp index 8438dbe00c..5e35fc407e 100644 --- a/src/gromacs/selection/compiler.cpp +++ b/src/gromacs/selection/compiler.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -289,7 +289,7 @@ #include "keywords.h" #include "mempool.h" #include "poscalc.h" -#include "selectioncollection-impl.h" +#include "selectioncollection_impl.h" #include "selelem.h" #include "selmethod.h" diff --git a/src/gromacs/selection/evaluate.cpp b/src/gromacs/selection/evaluate.cpp index c5659dbb2b..59a4aa27f3 100644 --- a/src/gromacs/selection/evaluate.cpp +++ b/src/gromacs/selection/evaluate.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -68,7 +68,7 @@ #include "mempool.h" #include "poscalc.h" -#include "selectioncollection-impl.h" +#include "selectioncollection_impl.h" #include "selelem.h" #include "selmethod.h" diff --git a/src/gromacs/selection/parsetree.cpp b/src/gromacs/selection/parsetree.cpp index 6f2596c113..1b504071cc 100644 --- a/src/gromacs/selection/parsetree.cpp +++ b/src/gromacs/selection/parsetree.cpp @@ -240,7 +240,7 @@ #include "keywords.h" #include "poscalc.h" #include "scanner.h" -#include "selectioncollection-impl.h" +#include "selectioncollection_impl.h" #include "selelem.h" #include "selmethod.h" #include "symrec.h" diff --git a/src/gromacs/selection/scanner_internal.cpp b/src/gromacs/selection/scanner_internal.cpp index b04366c880..abb96a5d6c 100644 --- a/src/gromacs/selection/scanner_internal.cpp +++ b/src/gromacs/selection/scanner_internal.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2009,2010,2011,2012,2014,2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 2009,2010,2011,2012,2014,2015,2016,2017,2018,2019, 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. @@ -69,7 +69,7 @@ #include "parser.h" #include "parsetree.h" #include "scanner.h" -#include "selectioncollection-impl.h" +#include "selectioncollection_impl.h" #include "selelem.h" #include "selmethod.h" #include "symrec.h" diff --git a/src/gromacs/selection/selectioncollection.cpp b/src/gromacs/selection/selectioncollection.cpp index c2a6218fb8..bd45bcb90d 100644 --- a/src/gromacs/selection/selectioncollection.cpp +++ b/src/gromacs/selection/selectioncollection.cpp @@ -71,7 +71,7 @@ #include "parser.h" #include "poscalc.h" #include "scanner.h" -#include "selectioncollection-impl.h" +#include "selectioncollection_impl.h" #include "selelem.h" #include "selmethod.h" #include "symrec.h" diff --git a/src/gromacs/selection/selectioncollection-impl.h b/src/gromacs/selection/selectioncollection_impl.h similarity index 98% rename from src/gromacs/selection/selectioncollection-impl.h rename to src/gromacs/selection/selectioncollection_impl.h index 56d62fc327..c8028af48f 100644 --- a/src/gromacs/selection/selectioncollection-impl.h +++ b/src/gromacs/selection/selectioncollection_impl.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by + * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2019, 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. diff --git a/src/gromacs/selection/selmethod.cpp b/src/gromacs/selection/selmethod.cpp index bf9b2ee572..8aecaaa4ae 100644 --- a/src/gromacs/selection/selmethod.cpp +++ b/src/gromacs/selection/selmethod.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2009,2010,2011,2012,2014,2015,2017,2018, by the GROMACS development team, led by + * Copyright (c) 2009,2010,2011,2012,2014,2015,2017,2018,2019, 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. @@ -51,7 +51,7 @@ #include "gromacs/utility/exceptions.h" #include "gromacs/utility/stringutil.h" -#include "selmethod-impl.h" +#include "selmethod_impl.h" #include "symrec.h" /*! \internal \brief diff --git a/src/gromacs/selection/selmethod-impl.h b/src/gromacs/selection/selmethod_impl.h similarity index 98% rename from src/gromacs/selection/selmethod-impl.h rename to src/gromacs/selection/selmethod_impl.h index 184d8ae2fc..12af47cfda 100644 --- a/src/gromacs/selection/selmethod-impl.h +++ b/src/gromacs/selection/selmethod_impl.h @@ -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. diff --git a/src/gromacs/selection/sm_distance.cpp b/src/gromacs/selection/sm_distance.cpp index ca0d1ad38b..0bb0831018 100644 --- a/src/gromacs/selection/sm_distance.cpp +++ b/src/gromacs/selection/sm_distance.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -51,7 +51,7 @@ #include "gromacs/utility/exceptions.h" #include "selmethod.h" -#include "selmethod-impl.h" +#include "selmethod_impl.h" /*! \internal * \brief diff --git a/src/gromacs/selection/sm_insolidangle.cpp b/src/gromacs/selection/sm_insolidangle.cpp index cd5cc97d5c..fd90c036f3 100644 --- a/src/gromacs/selection/sm_insolidangle.cpp +++ b/src/gromacs/selection/sm_insolidangle.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -132,7 +132,7 @@ #include "selelem.h" #include "selmethod.h" -#include "selmethod-impl.h" +#include "selmethod_impl.h" using std::min; using std::max; diff --git a/src/gromacs/selection/sm_merge.cpp b/src/gromacs/selection/sm_merge.cpp index 26298901c1..e681239e24 100644 --- a/src/gromacs/selection/sm_merge.cpp +++ b/src/gromacs/selection/sm_merge.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -49,7 +49,7 @@ #include "gromacs/utility/smalloc.h" #include "selmethod.h" -#include "selmethod-impl.h" +#include "selmethod_impl.h" /*! \internal \brief * Data structure for the merging selection modifiers. diff --git a/src/gromacs/selection/sm_permute.cpp b/src/gromacs/selection/sm_permute.cpp index 0b942e5445..a90e00cf0d 100644 --- a/src/gromacs/selection/sm_permute.cpp +++ b/src/gromacs/selection/sm_permute.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -49,7 +49,7 @@ #include "gromacs/utility/stringutil.h" #include "selmethod.h" -#include "selmethod-impl.h" +#include "selmethod_impl.h" /*! \internal \brief * Data structure for the \p permute selection modifier. diff --git a/src/gromacs/selection/sm_position.cpp b/src/gromacs/selection/sm_position.cpp index 569957c700..dad8060cd8 100644 --- a/src/gromacs/selection/sm_position.cpp +++ b/src/gromacs/selection/sm_position.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -51,7 +51,7 @@ #include "poscalc.h" #include "selelem.h" #include "selmethod.h" -#include "selmethod-impl.h" +#include "selmethod_impl.h" /*! \internal \brief * Data structure for position keyword evaluation. diff --git a/src/gromacs/selection/sm_same.cpp b/src/gromacs/selection/sm_same.cpp index ec4beace5e..26d7c5d16c 100644 --- a/src/gromacs/selection/sm_same.cpp +++ b/src/gromacs/selection/sm_same.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -52,7 +52,7 @@ #include "parsetree.h" #include "selelem.h" #include "selmethod.h" -#include "selmethod-impl.h" +#include "selmethod_impl.h" /*! \internal * \brief diff --git a/src/gromacs/selection/sm_simple.cpp b/src/gromacs/selection/sm_simple.cpp index a61cd5e73f..6e3440d9c3 100644 --- a/src/gromacs/selection/sm_simple.cpp +++ b/src/gromacs/selection/sm_simple.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -51,7 +51,7 @@ #include "gromacs/utility/gmxassert.h" #include "selmethod.h" -#include "selmethod-impl.h" +#include "selmethod_impl.h" /** Evaluates the \p all selection keyword. */ static void diff --git a/src/gromacs/tools/report-methods.cpp b/src/gromacs/tools/report_methods.cpp similarity index 99% rename from src/gromacs/tools/report-methods.cpp rename to src/gromacs/tools/report_methods.cpp index 253895ea73..882e18d08a 100644 --- a/src/gromacs/tools/report-methods.cpp +++ b/src/gromacs/tools/report_methods.cpp @@ -34,7 +34,7 @@ */ #include "gmxpre.h" -#include "report-methods.h" +#include "report_methods.h" #include "gromacs/commandline/cmdlineoptionsmodule.h" #include "gromacs/fileio/confio.h" diff --git a/src/gromacs/tools/report-methods.h b/src/gromacs/tools/report_methods.h similarity index 98% rename from src/gromacs/tools/report-methods.h rename to src/gromacs/tools/report_methods.h index 221cdf2e4f..dc918badc7 100644 --- a/src/gromacs/tools/report-methods.h +++ b/src/gromacs/tools/report_methods.h @@ -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. diff --git a/src/gromacs/tools/tests/CMakeLists.txt b/src/gromacs/tools/tests/CMakeLists.txt index d543a8ce81..9eee06a2f6 100644 --- a/src/gromacs/tools/tests/CMakeLists.txt +++ b/src/gromacs/tools/tests/CMakeLists.txt @@ -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. @@ -33,5 +33,5 @@ # the research papers on the package. Check out http://www.gromacs.org. gmx_add_unit_test(ToolUnitTests tool-test - report-methods.cpp) + report_methods.cpp) diff --git a/src/gromacs/tools/tests/report-methods.cpp b/src/gromacs/tools/tests/report_methods.cpp similarity index 98% rename from src/gromacs/tools/tests/report-methods.cpp rename to src/gromacs/tools/tests/report_methods.cpp index d84fb3328b..74bb402a40 100644 --- a/src/gromacs/tools/tests/report-methods.cpp +++ b/src/gromacs/tools/tests/report_methods.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. @@ -40,7 +40,7 @@ */ #include "gmxpre.h" -#include "gromacs/tools/report-methods.h" +#include "gromacs/tools/report_methods.h" #include "gromacs/fileio/tpxio.h" #include "gromacs/gmxpreprocess/grompp.h" diff --git a/src/gromacs/trajectoryanalysis/analysissettings.cpp b/src/gromacs/trajectoryanalysis/analysissettings.cpp index 165c010976..c54d3801f7 100644 --- a/src/gromacs/trajectoryanalysis/analysissettings.cpp +++ b/src/gromacs/trajectoryanalysis/analysissettings.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -48,7 +48,7 @@ #include "gromacs/utility/arrayref.h" #include "gromacs/utility/gmxassert.h" -#include "analysissettings-impl.h" +#include "analysissettings_impl.h" namespace gmx { diff --git a/src/gromacs/trajectoryanalysis/analysissettings-impl.h b/src/gromacs/trajectoryanalysis/analysissettings_impl.h similarity index 97% rename from src/gromacs/trajectoryanalysis/analysissettings-impl.h rename to src/gromacs/trajectoryanalysis/analysissettings_impl.h index 4bd75f2cd0..edc2b3c5b3 100644 --- a/src/gromacs/trajectoryanalysis/analysissettings-impl.h +++ b/src/gromacs/trajectoryanalysis/analysissettings_impl.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2010,2011,2012,2014,2015, by the GROMACS development team, led by + * Copyright (c) 2010,2011,2012,2014,2015,2019, 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. diff --git a/src/gromacs/trajectoryanalysis/runnercommon.cpp b/src/gromacs/trajectoryanalysis/runnercommon.cpp index 3341d04096..93e47cec84 100644 --- a/src/gromacs/trajectoryanalysis/runnercommon.cpp +++ b/src/gromacs/trajectoryanalysis/runnercommon.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -71,7 +71,7 @@ #include "gromacs/utility/smalloc.h" #include "gromacs/utility/stringutil.h" -#include "analysissettings-impl.h" +#include "analysissettings_impl.h" namespace gmx { diff --git a/src/gromacs/utility/baseversion-gen.cpp.cmakein b/src/gromacs/utility/baseversion-gen.cpp.cmakein index 441cefebd3..17daa56644 100644 --- a/src/gromacs/utility/baseversion-gen.cpp.cmakein +++ b/src/gromacs/utility/baseversion-gen.cpp.cmakein @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2010,2012,2014,2015,2018, by the GROMACS development team, led by + * Copyright (c) 2010,2012,2014,2015,2018,2019, 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. */ -#include "gromacs/utility/baseversion-gen.h" +#include "gromacs/utility/baseversion_gen.h" const char _gmx_ver_string[] = "@GMX_VERSION_STRING_FULL@"; const char _gmx_full_git_hash[] = "@GMX_VERSION_FULL_HASH@"; diff --git a/src/gromacs/utility/baseversion.cpp b/src/gromacs/utility/baseversion.cpp index 1cf7cc0652..ee195b2b3f 100644 --- a/src/gromacs/utility/baseversion.cpp +++ b/src/gromacs/utility/baseversion.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014,2015,2018, by the GROMACS development team, led by + * Copyright (c) 2014,2015,2018,2019, 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 @@ #include "config.h" -#include "baseversion-gen.h" +#include "baseversion_gen.h" const char *gmx_version() { diff --git a/src/gromacs/utility/baseversion-gen.h b/src/gromacs/utility/baseversion_gen.h similarity index 96% rename from src/gromacs/utility/baseversion-gen.h rename to src/gromacs/utility/baseversion_gen.h index 1efca7a64e..ee793533a5 100644 --- a/src/gromacs/utility/baseversion-gen.h +++ b/src/gromacs/utility/baseversion_gen.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2010,2012,2013,2014,2015,2018, by the GROMACS development team, led by + * Copyright (c) 2010,2012,2013,2014,2015,2018,2019, 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/utility/tests/CMakeLists.txt b/src/gromacs/utility/tests/CMakeLists.txt index c88bf29fce..39fdf059ab 100644 --- a/src/gromacs/utility/tests/CMakeLists.txt +++ b/src/gromacs/utility/tests/CMakeLists.txt @@ -52,5 +52,5 @@ gmx_add_unit_test(UtilityUnitTests utility-test ) gmx_add_mpi_unit_test(UtilityMpiUnitTests utility-mpi-test 4 - physicalnodecommunicator-mpi.cpp + physicalnodecommunicator_mpi.cpp ) diff --git a/src/gromacs/utility/tests/alignedallocator.cpp b/src/gromacs/utility/tests/alignedallocator.cpp index d046a24c6b..7e21cc933a 100644 --- a/src/gromacs/utility/tests/alignedallocator.cpp +++ b/src/gromacs/utility/tests/alignedallocator.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -70,7 +70,7 @@ TYPED_TEST_CASE(AllocatorTest, AllocatorTypesToTest); } // namespace gmx // Includes tests common to all allocation policies. -#include "gromacs/utility/tests/alignedallocator-impl.h" +#include "gromacs/utility/tests/alignedallocator_impl.h" namespace gmx { diff --git a/src/gromacs/utility/tests/alignedallocator-impl.h b/src/gromacs/utility/tests/alignedallocator_impl.h similarity index 98% rename from src/gromacs/utility/tests/alignedallocator-impl.h rename to src/gromacs/utility/tests/alignedallocator_impl.h index 045da902c4..8d240fec74 100644 --- a/src/gromacs/utility/tests/alignedallocator-impl.h +++ b/src/gromacs/utility/tests/alignedallocator_impl.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. diff --git a/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp b/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp similarity index 96% rename from src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp rename to src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp index b88421aca7..a97e344a88 100644 --- a/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp +++ b/src/gromacs/utility/tests/physicalnodecommunicator_mpi.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. diff --git a/src/programs/legacymodules.cpp b/src/programs/legacymodules.cpp index 4e33812166..e3a6f1cb19 100644 --- a/src/programs/legacymodules.cpp +++ b/src/programs/legacymodules.cpp @@ -52,14 +52,14 @@ #include "gromacs/gmxpreprocess/genion.h" #include "gromacs/gmxpreprocess/genrestr.h" #include "gromacs/gmxpreprocess/grompp.h" -#include "gromacs/gmxpreprocess/insert-molecules.h" +#include "gromacs/gmxpreprocess/insert_molecules.h" #include "gromacs/gmxpreprocess/pdb2gmx.h" #include "gromacs/gmxpreprocess/solvate.h" #include "gromacs/gmxpreprocess/x2top.h" #include "gromacs/tools/check.h" #include "gromacs/tools/convert_tpr.h" #include "gromacs/tools/dump.h" -#include "gromacs/tools/report-methods.h" +#include "gromacs/tools/report_methods.h" #include "mdrun/mdrun_main.h" #include "view/view.h" diff --git a/src/testutils/CMakeLists.txt b/src/testutils/CMakeLists.txt index 5bcc6993b6..0747669960 100644 --- a/src/testutils/CMakeLists.txt +++ b/src/testutils/CMakeLists.txt @@ -1,7 +1,7 @@ # # This file is part of the GROMACS molecular simulation package. # -# Copyright (c) 2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by +# Copyright (c) 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. @@ -44,10 +44,10 @@ set(TESTUTILS_SOURCES filematchers.cpp interactivetest.cpp loggertest.cpp - mpi-printer.cpp + mpi_printer.cpp mpitest.cpp refdata.cpp - refdata-xml.cpp + refdata_xml.cpp simulationdatabase.cpp stdiohelper.cpp stringtest.cpp diff --git a/src/testutils/mpi-printer.cpp b/src/testutils/mpi_printer.cpp similarity index 98% rename from src/testutils/mpi-printer.cpp rename to src/testutils/mpi_printer.cpp index 1d09b365b2..a193d12763 100644 --- a/src/testutils/mpi-printer.cpp +++ b/src/testutils/mpi_printer.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by + * Copyright (c) 2013,2014,2015,2016,2019, 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. @@ -34,7 +34,7 @@ */ #include "gmxpre.h" -#include "mpi-printer.h" +#include "mpi_printer.h" #include "config.h" diff --git a/src/testutils/mpi-printer.h b/src/testutils/mpi_printer.h similarity index 97% rename from src/testutils/mpi-printer.h rename to src/testutils/mpi_printer.h index f771049020..434fabd5da 100644 --- a/src/testutils/mpi-printer.h +++ b/src/testutils/mpi_printer.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2013, by the GROMACS development team, led by + * Copyright (c) 2013,2019, 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/testutils/refdata.cpp b/src/testutils/refdata.cpp index 98043304be..1e22a71f7b 100644 --- a/src/testutils/refdata.cpp +++ b/src/testutils/refdata.cpp @@ -62,9 +62,9 @@ #include "gromacs/utility/real.h" #include "gromacs/utility/stringutil.h" -#include "testutils/refdata-checkers.h" -#include "testutils/refdata-impl.h" -#include "testutils/refdata-xml.h" +#include "testutils/refdata_checkers.h" +#include "testutils/refdata_impl.h" +#include "testutils/refdata_xml.h" #include "testutils/testasserts.h" #include "testutils/testexceptions.h" #include "testutils/testfilemanager.h" diff --git a/src/testutils/refdata-checkers.h b/src/testutils/refdata_checkers.h similarity index 98% rename from src/testutils/refdata-checkers.h rename to src/testutils/refdata_checkers.h index 32656d27fd..0d3fda7aab 100644 --- a/src/testutils/refdata-checkers.h +++ b/src/testutils/refdata_checkers.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 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. @@ -55,7 +55,7 @@ #include "gromacs/utility/strconvert.h" #include "gromacs/utility/stringutil.h" -#include "testutils/refdata-impl.h" +#include "testutils/refdata_impl.h" #include "testutils/testasserts.h" #include "testutils/testexceptions.h" diff --git a/src/testutils/refdata-impl.h b/src/testutils/refdata_impl.h similarity index 100% rename from src/testutils/refdata-impl.h rename to src/testutils/refdata_impl.h diff --git a/src/testutils/refdata-xml.cpp b/src/testutils/refdata_xml.cpp similarity index 98% rename from src/testutils/refdata-xml.cpp rename to src/testutils/refdata_xml.cpp index 0b7a826944..50e2e6f4e8 100644 --- a/src/testutils/refdata-xml.cpp +++ b/src/testutils/refdata_xml.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by + * Copyright (c) 2015,2016,2017,2019, 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. @@ -42,13 +42,13 @@ */ #include "gmxpre.h" -#include "refdata-xml.h" +#include "refdata_xml.h" #include #include "gromacs/utility/exceptions.h" -#include "testutils/refdata-impl.h" +#include "testutils/refdata_impl.h" #include "testutils/testexceptions.h" namespace gmx diff --git a/src/testutils/refdata-xml.h b/src/testutils/refdata_xml.h similarity index 96% rename from src/testutils/refdata-xml.h rename to src/testutils/refdata_xml.h index ef8c703e99..fd56e34652 100644 --- a/src/testutils/refdata-xml.h +++ b/src/testutils/refdata_xml.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2016, by the GROMACS development team, led by + * Copyright (c) 2015,2016,2019, 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. @@ -44,7 +44,7 @@ #include -#include "testutils/refdata-impl.h" +#include "testutils/refdata_impl.h" namespace gmx { diff --git a/src/testutils/testinit.cpp b/src/testutils/testinit.cpp index e87b9ea88f..5acb455869 100644 --- a/src/testutils/testinit.cpp +++ b/src/testutils/testinit.cpp @@ -67,7 +67,7 @@ #include "gromacs/utility/programcontext.h" #include "gromacs/utility/textwriter.h" -#include "testutils/mpi-printer.h" +#include "testutils/mpi_printer.h" #include "testutils/refdata.h" #include "testutils/testfilemanager.h" #include "testutils/testoptions.h" diff --git a/src/testutils/testutils-doc.h b/src/testutils/testutils_doc.h similarity index 96% rename from src/testutils/testutils-doc.h rename to src/testutils/testutils_doc.h index eb111256d0..f59a1aaebc 100644 --- a/src/testutils/testutils-doc.h +++ b/src/testutils/testutils_doc.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2017, by the GROMACS development team, led by + * Copyright (c) 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. @@ -82,12 +82,12 @@ * - gmx::test::StdioTestHelper provides a helper class for tests that need to * execute legacy code where `stdin` reading cannot be easily mocked. * - * Additionally, testinit.h and mpi-printer.h, and their corresponding source + * Additionally, testinit.h and mpi_printer.h, and their corresponding source * files, provide functionality that is not visible on the API level: they * provide initialization routines for the above functionality, which are * automatically called by the %main() function provided in unittest_main.cpp. * - * mpi-printer.h provides a Google Test listener that is installed when the + * mpi_printer.h provides a Google Test listener that is installed when the * tests are compiled with MPI. This listener allows the test binary to be run * on multiple MPI ranks, and synchronizes the execution and output from the * test cases, as well as makes the test fail on even if an assertion fails