From e50071b65ca515d44d7daad490a3bbfa10f565ef Mon Sep 17 00:00:00 2001 From: Roland Schulz Date: Wed, 1 Aug 2018 19:48:12 -0700 Subject: [PATCH] clang-tidy: google tests applicable Change-Id: I32e5dd6226348a162750d272c20c49e116bb94a4 --- docs/dev-manual/formatting.rst | 3 ++- src/.clang-tidy | 5 +++-- src/gromacs/awh/biaswriter.cpp | 2 +- src/gromacs/awh/tests/bias.cpp | 4 ++-- src/gromacs/awh/tests/biasstate.cpp | 4 ++-- src/gromacs/awh/tests/grid.cpp | 4 ++-- src/gromacs/commandline/cmdlinehelpmodule.cpp | 2 +- src/gromacs/compat/make_unique.h | 4 ++-- .../correlationfunctions/tests/autocorr.cpp | 4 ++-- src/gromacs/correlationfunctions/tests/expfit.cpp | 4 ++-- .../tests/manyautocorrelation.cpp | 6 +++--- src/gromacs/essentialdynamics/edsam.cpp | 6 +++--- src/gromacs/ewald/tests/pmebsplinetest.cpp | 6 +++--- src/gromacs/ewald/tests/pmegathertest.cpp | 6 +++--- src/gromacs/ewald/tests/pmesolvetest.cpp | 6 +++--- src/gromacs/ewald/tests/pmesplinespreadtest.cpp | 6 +++--- src/gromacs/ewald/tests/pmetestcommon.cpp | 14 +++++++------- src/gromacs/ewald/tests/pmetestcommon.h | 6 +++--- src/gromacs/ewald/tests/testhardwarecontexts.cpp | 4 ++-- src/gromacs/ewald/tests/testhardwarecontexts.h | 4 ++-- src/gromacs/fileio/tests/readinp.cpp | 4 ++-- src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp | 4 ++-- src/gromacs/gmxpreprocess/tests/readir.cpp | 4 ++-- src/gromacs/gpu_utils/clfftinitializer.cpp | 2 +- src/gromacs/gpu_utils/clfftinitializer.h | 2 +- src/gromacs/gpu_utils/tests/gputest.cpp | 4 ++-- src/gromacs/gpu_utils/tests/gputest.h | 6 +++--- src/gromacs/gpu_utils/tests/hostallocator.cpp | 2 +- src/gromacs/hardware/cpuinfo.cpp | 2 +- src/gromacs/hardware/hardwaretopology.cpp | 2 +- src/gromacs/hardware/hardwaretopology.h | 4 ++-- src/gromacs/hardware/identifyavx512fmaunits.cpp | 4 ++-- src/gromacs/listed-forces/tests/bonded.cpp | 6 +++--- src/gromacs/math/invertmatrix.cpp | 2 +- src/gromacs/math/paddedvector.h | 2 +- src/gromacs/mdlib/boxdeformation.cpp | 2 +- src/gromacs/mdlib/boxdeformation.h | 2 +- src/gromacs/mdlib/constr.cpp | 2 +- src/gromacs/mdlib/constr.h | 2 +- src/gromacs/mdlib/constraintrange.cpp | 2 +- src/gromacs/mdlib/lincs.cpp | 2 +- src/gromacs/mdlib/lincs.h | 2 +- src/gromacs/mdlib/makeconstraints.h | 2 +- src/gromacs/mdlib/mdatoms.cpp | 2 +- src/gromacs/mdlib/mdatoms.h | 2 +- src/gromacs/mdlib/settle.cpp | 2 +- src/gromacs/mdlib/settle.h | 2 +- src/gromacs/mdlib/shake.cpp | 2 +- src/gromacs/mdlib/shake.h | 2 +- src/gromacs/mdlib/simulationsignal.cpp | 2 +- src/gromacs/mdlib/simulationsignal.h | 2 +- src/gromacs/mdlib/tests/calc_verletbuf.cpp | 6 +++--- src/gromacs/mdlib/tests/mdebin.cpp | 6 +++--- src/gromacs/mdlib/tests/settle.cpp | 4 ++-- src/gromacs/mdlib/tests/shake.cpp | 2 +- src/gromacs/mdlib/tests/simulationsignal.cpp | 4 ++-- src/gromacs/mdlib/update.h | 2 +- src/gromacs/mdrun/integrator.cpp | 2 +- src/gromacs/mdrun/runner.cpp | 2 +- src/gromacs/mdtypes/forceoutput.h | 4 ++-- src/gromacs/onlinehelp/rstparser.h | 4 ++-- src/gromacs/options/behaviorcollection.h | 4 ++-- src/gromacs/options/ioptionsbehavior.h | 4 ++-- src/gromacs/options/ioptionscontainer.h | 4 ++-- .../options/ioptionscontainerwithsections.h | 4 ++-- src/gromacs/options/optionsvisitor.cpp | 4 ++-- src/gromacs/pulling/pull_rotation.cpp | 2 +- src/gromacs/pulling/pull_rotation.h | 2 +- src/gromacs/pulling/tests/pull.cpp | 4 ++-- src/gromacs/random/seed.cpp | 2 +- src/gromacs/random/tabulatednormaldistribution.cpp | 2 +- .../random/tests/exponentialdistribution.cpp | 4 ++-- src/gromacs/random/tests/gammadistribution.cpp | 4 ++-- src/gromacs/random/tests/normaldistribution.cpp | 4 ++-- src/gromacs/random/tests/seed.cpp | 4 ++-- .../random/tests/tabulatednormaldistribution.cpp | 4 ++-- src/gromacs/random/tests/threefry.cpp | 4 ++-- .../random/tests/uniformintdistribution.cpp | 4 ++-- .../random/tests/uniformrealdistribution.cpp | 4 ++-- src/gromacs/random/threefry.h | 2 +- src/gromacs/selection/selectionenums.h | 4 ++-- src/gromacs/simd/simd.h | 2 +- src/gromacs/simd/support.cpp | 2 +- src/gromacs/simd/tests/base.cpp | 4 ++-- src/gromacs/simd/tests/base.h | 4 ++-- src/gromacs/simd/tests/scalar.cpp | 6 +++--- src/gromacs/simd/tests/scalar_math.cpp | 8 ++++---- src/gromacs/simd/tests/scalar_util.cpp | 8 ++++---- src/gromacs/simd/tests/simd.cpp | 4 ++-- src/gromacs/simd/tests/simd.h | 4 ++-- src/gromacs/simd/tests/simd4.cpp | 4 ++-- src/gromacs/simd/tests/simd4.h | 4 ++-- src/gromacs/simd/tests/simd4_floatingpoint.cpp | 4 ++-- src/gromacs/simd/tests/simd4_math.cpp | 4 ++-- src/gromacs/simd/tests/simd4_vector_operations.cpp | 6 +++--- src/gromacs/simd/tests/simd_floatingpoint.cpp | 4 ++-- src/gromacs/simd/tests/simd_floatingpoint_util.cpp | 6 +++--- src/gromacs/simd/tests/simd_integer.cpp | 4 ++-- src/gromacs/simd/tests/simd_math.cpp | 4 ++-- src/gromacs/simd/tests/simd_vector_operations.cpp | 6 +++--- src/gromacs/tables/cubicsplinetable.cpp | 2 +- src/gromacs/tables/quadraticsplinetable.cpp | 2 +- src/gromacs/tables/tableinput.h | 4 +++- src/gromacs/taskassignment/decidegpuusage.cpp | 2 +- src/gromacs/taskassignment/decidegpuusage.h | 2 +- src/gromacs/taskassignment/findallgputasks.cpp | 2 +- src/gromacs/taskassignment/findallgputasks.h | 2 +- src/gromacs/taskassignment/reportgpuusage.cpp | 2 +- src/gromacs/taskassignment/reportgpuusage.h | 4 ++-- src/gromacs/taskassignment/resourcedivision.cpp | 2 +- src/gromacs/taskassignment/resourcedivision.h | 2 +- src/gromacs/taskassignment/taskassignment.cpp | 2 +- src/gromacs/taskassignment/taskassignment.h | 2 +- src/gromacs/taskassignment/tests/usergpuids.cpp | 6 +++--- src/gromacs/taskassignment/usergpuids.cpp | 4 ++-- src/gromacs/taskassignment/usergpuids.h | 4 ++-- src/gromacs/topology/block.h | 2 +- src/gromacs/trajectory/energyframe.cpp | 2 +- src/gromacs/trajectory/energyframe.h | 2 +- src/gromacs/trajectoryanalysis/modules/angle.h | 4 ++-- src/gromacs/trajectoryanalysis/tests/clustsize.cpp | 6 +++--- .../trajectoryanalysis/tests/test_selection.cpp | 4 ++-- src/gromacs/utility/coolstuff.cpp | 2 +- src/gromacs/utility/niceheader.cpp | 4 ++-- src/gromacs/utility/niceheader.h | 4 ++-- src/gromacs/utility/physicalnodecommunicator.cpp | 2 +- src/gromacs/utility/physicalnodecommunicator.h | 2 +- src/gromacs/utility/tests/alignedallocator-impl.h | 4 ++-- src/gromacs/utility/tests/alignedallocator.cpp | 10 +++++----- src/gromacs/utility/tests/arrayref.cpp | 2 +- src/gromacs/utility/tests/gmxregex.cpp | 4 ++-- src/gromacs/utility/tests/mutex.cpp | 4 ++-- .../utility/tests/physicalnodecommunicator-mpi.cpp | 2 +- .../utility/tests/physicalnodecommunicator.cpp | 2 +- src/gromacs/utility/tests/stringutil.cpp | 6 +++--- src/gromacs/utility/tests/textreader.cpp | 6 +++--- src/gromacs/utility/tests/typetraits.cpp | 4 ++-- src/programs/mdrun/mdrun.cpp | 2 +- src/programs/mdrun/tests/energycomparison.cpp | 4 ++-- src/programs/mdrun/tests/energycomparison.h | 4 ++-- src/programs/mdrun/tests/energyreader.cpp | 4 ++-- src/programs/mdrun/tests/energyreader.h | 4 ++-- src/programs/mdrun/tests/initialconstraints.cpp | 6 +++--- src/programs/mdrun/tests/moduletest.cpp | 2 +- src/programs/mdrun/tests/multisim.cpp | 4 ++-- src/programs/mdrun/tests/multisimtest.cpp | 4 ++-- src/programs/mdrun/tests/multisimtest.h | 4 ++-- src/programs/mdrun/tests/pmetest.cpp | 6 +++--- src/programs/mdrun/tests/replicaexchange.cpp | 6 +++--- .../mdrun/tests/tabulated_bonded_interactions.cpp | 4 ++-- src/programs/mdrun/tests/termination.cpp | 4 ++-- src/programs/mdrun/tests/terminationhelper.cpp | 4 ++-- src/programs/mdrun/tests/terminationhelper.h | 4 ++-- src/programs/mdrun/tests/tpitest.cpp | 6 +++--- src/programs/mdrun/tests/trajectorycomparison.cpp | 4 ++-- src/programs/mdrun/tests/trajectorycomparison.h | 4 ++-- src/programs/mdrun/tests/trajectoryreader.cpp | 4 ++-- src/programs/mdrun/tests/trajectoryreader.h | 4 ++-- src/testutils/testasserts.cpp | 2 +- src/testutils/testasserts.h | 2 +- src/testutils/testmatchers.cpp | 4 ++-- src/testutils/testmatchers.h | 4 ++-- 162 files changed, 301 insertions(+), 297 deletions(-) diff --git a/docs/dev-manual/formatting.rst b/docs/dev-manual/formatting.rst index d742d97440..e8f0659232 100644 --- a/docs/dev-manual/formatting.rst +++ b/docs/dev-manual/formatting.rst @@ -21,7 +21,8 @@ The following list provides the general formatting/indentation rules for functions in C++ classes, which can be put on a single line. * Use spaces liberally. * ``extern "C"`` and ``namespace`` blocks are not indented, but all others - (including ``class`` and ``switch`` bodies) are. + (including ``class`` and ``switch`` bodies) are. Namespace blocks have + to have a closing comment with the name of it. Additionally: diff --git a/src/.clang-tidy b/src/.clang-tidy index 75da6d7eca..0565928801 100644 --- a/src/.clang-tidy +++ b/src/.clang-tidy @@ -4,9 +4,10 @@ Checks: clang-diagnostic-*,clang-analyzer-*,-clang-analyzer-security.insecureAP -readability-function-size,-readability-else-after-return, modernize-use-nullptr,modernize-use-emplace, modernize-make-unique,modernize-make-shared, - google-readability-casting, cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory, - -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions + -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions, + google-*,-google-build-using-namespace,-google-explicit-constructor, + -google-readability-function-size,-google-readability-todo,-google-runtime-int CheckOptions: - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor diff --git a/src/gromacs/awh/biaswriter.cpp b/src/gromacs/awh/biaswriter.cpp index 6eb5ccadd3..57a635e03e 100644 --- a/src/gromacs/awh/biaswriter.cpp +++ b/src/gromacs/awh/biaswriter.cpp @@ -407,4 +407,4 @@ int BiasWriter::writeToEnergySubblocks(const Bias &bias, return block_.size(); } -} // namepace gmx +} // namespace gmx diff --git a/src/gromacs/awh/tests/bias.cpp b/src/gromacs/awh/tests/bias.cpp index 86e28c0cf0..1c9928adfd 100644 --- a/src/gromacs/awh/tests/bias.cpp +++ b/src/gromacs/awh/tests/bias.cpp @@ -340,5 +340,5 @@ TEST(BiasTest, DetectsCovering) } } -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/awh/tests/biasstate.cpp b/src/gromacs/awh/tests/biasstate.cpp index 1ba40d7c54..c7d2080306 100644 --- a/src/gromacs/awh/tests/biasstate.cpp +++ b/src/gromacs/awh/tests/biasstate.cpp @@ -176,5 +176,5 @@ INSTANTIATE_TEST_CASE_P(WithParameters, BiasStateTest, ::testing::Values("pmf_target_format0.xvg", "pmf_target_format1.xvg")); -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/awh/tests/grid.cpp b/src/gromacs/awh/tests/grid.cpp index e1a883746c..772490e0a1 100644 --- a/src/gromacs/awh/tests/grid.cpp +++ b/src/gromacs/awh/tests/grid.cpp @@ -181,5 +181,5 @@ TEST(gridTest, neighborhood) EXPECT_TRUE(haveCorrectNumNeighbors); } -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/commandline/cmdlinehelpmodule.cpp b/src/gromacs/commandline/cmdlinehelpmodule.cpp index cf006c3908..47110d0ac9 100644 --- a/src/gromacs/commandline/cmdlinehelpmodule.cpp +++ b/src/gromacs/commandline/cmdlinehelpmodule.cpp @@ -538,7 +538,7 @@ class HelpExportReStructuredText : public IHelpExport private: IFileOutputRedirector *outputRedirector_; - const std::string &binaryName_; + const std::string &binaryName_; //NOLINT(google-runtime-member-string-references) HelpLinks links_; // These never release ownership. std::unique_ptr indexFile_; diff --git a/src/gromacs/compat/make_unique.h b/src/gromacs/compat/make_unique.h index 2d89df503d..72242b048b 100644 --- a/src/gromacs/compat/make_unique.h +++ b/src/gromacs/compat/make_unique.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2017, by the GROMACS development team, led by + * Copyright (c) 2017,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -112,7 +112,7 @@ make_unique(Args && ...) = delete; ///\endcond -} // namespace gmx::compat +} // namespace compat } // namespace gmx #endif // header guard diff --git a/src/gromacs/correlationfunctions/tests/autocorr.cpp b/src/gromacs/correlationfunctions/tests/autocorr.cpp index f5b5f2733a..0cf1b4af14 100644 --- a/src/gromacs/correlationfunctions/tests/autocorr.cpp +++ b/src/gromacs/correlationfunctions/tests/autocorr.cpp @@ -230,6 +230,6 @@ TEST_F (AutocorrTest, EacP4) } -} +} // namespace -} +} // namespace gmx diff --git a/src/gromacs/correlationfunctions/tests/expfit.cpp b/src/gromacs/correlationfunctions/tests/expfit.cpp index 4f365f0a35..55e49863c0 100644 --- a/src/gromacs/correlationfunctions/tests/expfit.cpp +++ b/src/gromacs/correlationfunctions/tests/expfit.cpp @@ -209,6 +209,6 @@ TEST_F (ExpfitTest, EffnPRES) { #endif -} +} // namespace -} +} // namespace gmx diff --git a/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp b/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp index 92a8e8534b..a634322371 100644 --- a/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp +++ b/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by + * Copyright (c) 2014,2015,2016,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -81,6 +81,6 @@ TEST_F (ManyAutocorrelationTest, DifferentLength) } #endif -} +} // namespace -} +} // namespace gmx diff --git a/src/gromacs/essentialdynamics/edsam.cpp b/src/gromacs/essentialdynamics/edsam.cpp index 8b3edbf7b4..f242839feb 100644 --- a/src/gromacs/essentialdynamics/edsam.cpp +++ b/src/gromacs/essentialdynamics/edsam.cpp @@ -294,7 +294,7 @@ bool bNeedDoEdsam(const t_edpar &edi) || edi.vecs.radacc.neig || edi.vecs.radcon.neig; } -} +} // namespace /* Multiple ED groups will be labeled with letters instead of numbers @@ -433,7 +433,7 @@ real calc_radius(const t_eigvec &vec) return rad = sqrt(rad); } -} +} // namespace struct t_do_edfit { double **omega; @@ -1533,7 +1533,7 @@ void setup_edvec(t_eigvec *tvec) snew(tvec->fproj, tvec->neig); snew(tvec->refproj, tvec->neig); } -} +} // namespace /* Check if the same atom indices are used for reference and average positions */ diff --git a/src/gromacs/ewald/tests/pmebsplinetest.cpp b/src/gromacs/ewald/tests/pmebsplinetest.cpp index 7549d1aa23..b4c41798ff 100644 --- a/src/gromacs/ewald/tests/pmebsplinetest.cpp +++ b/src/gromacs/ewald/tests/pmebsplinetest.cpp @@ -191,6 +191,6 @@ INSTANTIATE_TEST_CASE_P(SaneInput1, PmeBSplineModuliCorrectnessTest, ::testing:: ::testing::Range(3, 8 + 1), ::testing::Values(ModuliType::PME, ModuliType::P3M) )); -} -} -} +} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/ewald/tests/pmegathertest.cpp b/src/gromacs/ewald/tests/pmegathertest.cpp index 34219cb845..2d86d12feb 100644 --- a/src/gromacs/ewald/tests/pmegathertest.cpp +++ b/src/gromacs/ewald/tests/pmegathertest.cpp @@ -455,6 +455,6 @@ INSTANTIATE_TEST_CASE_P(SaneInput, PmeGatherTest, ::testing::Combine(::testing:: ::testing::Values(PmeForceOutputHandling::Set, PmeForceOutputHandling::ReduceWithInput), ::testing::ValuesIn(atomCounts))); -} -} -} +} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/ewald/tests/pmesolvetest.cpp b/src/gromacs/ewald/tests/pmesolvetest.cpp index 32a296e2ce..148d27ba3b 100644 --- a/src/gromacs/ewald/tests/pmesolvetest.cpp +++ b/src/gromacs/ewald/tests/pmesolvetest.cpp @@ -375,6 +375,6 @@ INSTANTIATE_TEST_CASE_P(DifferentEpsilonR, PmeSolveTest, ::testing::Combine(c_in testing::Values(1.9), c_inputEwaldCoeff_q, c_inputEwaldCoeff_lj, c_inputMethods)); -} -} -} +} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/ewald/tests/pmesplinespreadtest.cpp b/src/gromacs/ewald/tests/pmesplinespreadtest.cpp index aca761a393..105f2ca37a 100644 --- a/src/gromacs/ewald/tests/pmesplinespreadtest.cpp +++ b/src/gromacs/ewald/tests/pmesplinespreadtest.cpp @@ -353,6 +353,6 @@ INSTANTIATE_TEST_CASE_P(SaneInput13, PmeSplineAndSpreadTest, ::testing::Combine( ::testing::Values(c_sampleCoordinates13), ::testing::Values(c_sampleCharges13) )); -} -} -} +} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/ewald/tests/pmetestcommon.cpp b/src/gromacs/ewald/tests/pmetestcommon.cpp index 9bcd6e1704..bb82470c01 100644 --- a/src/gromacs/ewald/tests/pmetestcommon.cpp +++ b/src/gromacs/ewald/tests/pmetestcommon.cpp @@ -207,8 +207,8 @@ static real *pmeGetRealGridInternal(const gmx_pme_t *pme) //! Getting local PME real grid dimensions static void pmeGetRealGridSizesInternal(const gmx_pme_t *pme, CodePath mode, - IVec &gridSize, - IVec &paddedGridSize) + IVec &gridSize, //NOLINT(google-runtime-references) + IVec &paddedGridSize) //NOLINT(google-runtime-references) { const size_t gridIndex = 0; IVec gridOffsetUnused; @@ -236,8 +236,8 @@ static t_complex *pmeGetComplexGridInternal(const gmx_pme_t *pme) //! Getting local PME complex grid dimensions static void pmeGetComplexGridSizesInternal(const gmx_pme_t *pme, - IVec &gridSize, - IVec &paddedGridSize) + IVec &gridSize, //NOLINT(google-runtime-references) + IVec &paddedGridSize) //NOLINT(google-runtime-references) { const size_t gridIndex = 0; IVec gridOffsetUnused, complexOrderUnused; @@ -245,7 +245,7 @@ static void pmeGetComplexGridSizesInternal(const gmx_pme_t *pme, } //! Getting the PME grid memory buffer and its sizes - template definition -template static void pmeGetGridAndSizesInternal(const gmx_pme_t * /*unused*/, CodePath /*unused*/, ValueType * & /*unused*/, IVec & /*unused*/, IVec & /*unused*/) +template static void pmeGetGridAndSizesInternal(const gmx_pme_t * /*unused*/, CodePath /*unused*/, ValueType * & /*unused*/, IVec & /*unused*/, IVec & /*unused*/) //NOLINT(google-runtime-references) { GMX_THROW(InternalError("Deleted function call")); // explicitly deleting general template does not compile in clang/icc, see https://llvm.org/bugs/show_bug.cgi?id=17537 @@ -721,5 +721,5 @@ PmeSolveOutput pmeGetReciprocalEnergyAndVirial(const gmx_pme_t *pme, CodePath mo return std::make_tuple(energy, virial); } -} -} +} // namespace test +} // namespace gmx diff --git a/src/gromacs/ewald/tests/pmetestcommon.h b/src/gromacs/ewald/tests/pmetestcommon.h index 5396cbb13e..cc516f621c 100644 --- a/src/gromacs/ewald/tests/pmetestcommon.h +++ b/src/gromacs/ewald/tests/pmetestcommon.h @@ -142,7 +142,7 @@ void pmePerformSolve(const gmx_pme_t *pme, CodePath mode, GridOrdering gridOrdering, bool computeEnergyAndVirial); //! PME force gathering void pmePerformGather(gmx_pme_t *pme, CodePath mode, - PmeForceOutputHandling inputTreatment, ForcesVector &forces); + PmeForceOutputHandling inputTreatment, ForcesVector &forces); //NOLINT(google-runtime-references) //! PME test finalization before fetching the outputs void pmeFinalizeTest(const gmx_pme_t *pme, CodePath mode); @@ -175,7 +175,7 @@ SparseComplexGridValuesOutput pmeGetComplexGrid(const gmx_pme_t *pme, CodePath m //! Getting the reciprocal energy and virial PmeSolveOutput pmeGetReciprocalEnergyAndVirial(const gmx_pme_t *pme, CodePath mode, PmeSolveAlgorithm method); -} -} +} // namespace test +} // namespace gmx #endif diff --git a/src/gromacs/ewald/tests/testhardwarecontexts.cpp b/src/gromacs/ewald/tests/testhardwarecontexts.cpp index ddea887712..ab7fcb038e 100644 --- a/src/gromacs/ewald/tests/testhardwarecontexts.cpp +++ b/src/gromacs/ewald/tests/testhardwarecontexts.cpp @@ -138,5 +138,5 @@ void PmeTestEnvironment::TearDown() gmx_hardware_info_free(); } -} -} +} // namespace test +} // namespace gmx diff --git a/src/gromacs/ewald/tests/testhardwarecontexts.h b/src/gromacs/ewald/tests/testhardwarecontexts.h index 6d5afe0548..88f45342b9 100644 --- a/src/gromacs/ewald/tests/testhardwarecontexts.h +++ b/src/gromacs/ewald/tests/testhardwarecontexts.h @@ -127,6 +127,6 @@ const PmeTestEnvironment *getPmeTestEnv(); * unit test so that they can use the hardware context. */ void callAddGlobalTestEnvironment(); -} -} +} // namespace test +} // namespace gmx #endif diff --git a/src/gromacs/fileio/tests/readinp.cpp b/src/gromacs/fileio/tests/readinp.cpp index 9206ac3493..6d23b9b525 100644 --- a/src/gromacs/fileio/tests/readinp.cpp +++ b/src/gromacs/fileio/tests/readinp.cpp @@ -132,5 +132,5 @@ TEST_F(ReadTest, get_ereal_WarnsAboutString) ASSERT_TRUE(warning_errors_exist(wi_)); } -} // namespace -} // namespace +} // namespace testing +} // namespace gmx diff --git a/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp b/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp index 412938e3ab..a81d29a6a3 100644 --- a/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp +++ b/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp @@ -177,5 +177,5 @@ INSTANTIATE_TEST_CASE_P(ChainSep, Pdb2gmxTest, } // namespace -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/gmxpreprocess/tests/readir.cpp b/src/gromacs/gmxpreprocess/tests/readir.cpp index b6a721a36d..e9c7f0fa9f 100644 --- a/src/gromacs/gmxpreprocess/tests/readir.cpp +++ b/src/gromacs/gmxpreprocess/tests/readir.cpp @@ -209,5 +209,5 @@ TEST_F(GetIrTest, ImplicitSolventYesWorks) EXPECT_DEATH_IF_SUPPORTED(runTest(inputMdpFile), "Invalid enum"); } -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/gpu_utils/clfftinitializer.cpp b/src/gromacs/gpu_utils/clfftinitializer.cpp index fab5285ab5..f4ccdda703 100644 --- a/src/gromacs/gpu_utils/clfftinitializer.cpp +++ b/src/gromacs/gpu_utils/clfftinitializer.cpp @@ -86,4 +86,4 @@ std::unique_ptr initializeClfftLibrary() return compat::make_unique(); } -} +} // namespace gmx diff --git a/src/gromacs/gpu_utils/clfftinitializer.h b/src/gromacs/gpu_utils/clfftinitializer.h index 80c48f4bc9..18c63eb582 100644 --- a/src/gromacs/gpu_utils/clfftinitializer.h +++ b/src/gromacs/gpu_utils/clfftinitializer.h @@ -94,6 +94,6 @@ class ClfftInitializer */ std::unique_ptr initializeClfftLibrary(); -} +} // namespace gmx #endif diff --git a/src/gromacs/gpu_utils/tests/gputest.cpp b/src/gromacs/gpu_utils/tests/gputest.cpp index 7d7a7536a0..6308a54246 100644 --- a/src/gromacs/gpu_utils/tests/gputest.cpp +++ b/src/gromacs/gpu_utils/tests/gputest.cpp @@ -74,5 +74,5 @@ bool GpuTest::haveValidGpus() const return gpuInfo_->n_dev_compatible > 0; } -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/gpu_utils/tests/gputest.h b/src/gromacs/gpu_utils/tests/gputest.h index eafae6a8ba..ec592cb7df 100644 --- a/src/gromacs/gpu_utils/tests/gputest.h +++ b/src/gromacs/gpu_utils/tests/gputest.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2017, by the GROMACS development team, led by + * Copyright (c) 2017,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and 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 @@ class GpuTest : public ::testing::Test bool haveValidGpus() const; }; -} // namespace -} // namespace +} // namespace test +} // namespace gmx #endif diff --git a/src/gromacs/gpu_utils/tests/hostallocator.cpp b/src/gromacs/gpu_utils/tests/hostallocator.cpp index 7aa7803d4a..72b1e21bcb 100644 --- a/src/gromacs/gpu_utils/tests/hostallocator.cpp +++ b/src/gromacs/gpu_utils/tests/hostallocator.cpp @@ -345,7 +345,7 @@ using AllocatorTypesToTest = ::testing::Types, TYPED_TEST_CASE(AllocatorTest, AllocatorTypesToTest); } // namespace -} // namespace +} // namespace gmx // Includes tests common to all allocation policies. #include "gromacs/utility/tests/alignedallocator-impl.h" diff --git a/src/gromacs/hardware/cpuinfo.cpp b/src/gromacs/hardware/cpuinfo.cpp index 87d32d2a13..ee9955457a 100644 --- a/src/gromacs/hardware/cpuinfo.cpp +++ b/src/gromacs/hardware/cpuinfo.cpp @@ -946,7 +946,7 @@ detectProcCpuInfo(CpuInfo::Vendor * vendor, } } /*! \endcond */ -} // namespace anonymous +} // namespace // static diff --git a/src/gromacs/hardware/hardwaretopology.cpp b/src/gromacs/hardware/hardwaretopology.cpp index 014ae654ce..9fb24b97e4 100644 --- a/src/gromacs/hardware/hardwaretopology.cpp +++ b/src/gromacs/hardware/hardwaretopology.cpp @@ -688,7 +688,7 @@ detectLogicalProcessorCount() return count; } -} // namespace anonymous +} // namespace // static HardwareTopology HardwareTopology::detect() diff --git a/src/gromacs/hardware/hardwaretopology.h b/src/gromacs/hardware/hardwaretopology.h index b2dcf352cb..66abb682de 100644 --- a/src/gromacs/hardware/hardwaretopology.h +++ b/src/gromacs/hardware/hardwaretopology.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) 2015,2016,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -264,6 +264,6 @@ class HardwareTopology bool isThisSystem_; //!< Machine map is real (vs. cached/synthetic) }; -} +} // namespace gmx #endif // GMX_HARDWARE_HARDWARETOPOLOGY_H diff --git a/src/gromacs/hardware/identifyavx512fmaunits.cpp b/src/gromacs/hardware/identifyavx512fmaunits.cpp index e8f18ae6a8..705dcea8a7 100644 --- a/src/gromacs/hardware/identifyavx512fmaunits.cpp +++ b/src/gromacs/hardware/identifyavx512fmaunits.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2017, by the GROMACS development team, led by + * Copyright (c) 2017,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -254,7 +254,7 @@ checkDualAvx512FmaUnits() */ std::mutex initMutex; -} // namespace anonymous +} // namespace int identifyAvx512FmaUnits() diff --git a/src/gromacs/listed-forces/tests/bonded.cpp b/src/gromacs/listed-forces/tests/bonded.cpp index d3d80bd158..973d01bd56 100644 --- a/src/gromacs/listed-forces/tests/bonded.cpp +++ b/src/gromacs/listed-forces/tests/bonded.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) 2016,2017,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -273,6 +273,6 @@ TEST_F (BondedTest, IfuncProperDihedralsPbcXyz) testIfunc(F_PDIHS, iatoms, &iparams, epbcXYZ); } -} +} // namespace -} +} // namespace gmx diff --git a/src/gromacs/math/invertmatrix.cpp b/src/gromacs/math/invertmatrix.cpp index 5c181f672e..b03ce46489 100644 --- a/src/gromacs/math/invertmatrix.cpp +++ b/src/gromacs/math/invertmatrix.cpp @@ -97,4 +97,4 @@ void invertMatrix(const matrix src, matrix dest) dest[ZZ][ZZ] = c*(src[XX][XX]*src[YY][YY]-src[YY][XX]*src[XX][YY]); } -} // namespace +} // namespace gmx diff --git a/src/gromacs/math/paddedvector.h b/src/gromacs/math/paddedvector.h index 9f6da9418c..e38e805346 100644 --- a/src/gromacs/math/paddedvector.h +++ b/src/gromacs/math/paddedvector.h @@ -105,6 +105,6 @@ using PaddedArrayRef = ArrayRef; // TODO These are hacks to avoid littering gmx:: all over code that is // almost all destined to move into the gmx namespace at some point. // An alternative would be about 20 files with using statements. -using gmx::PaddedRVecVector; +using gmx::PaddedRVecVector; //NOLINT(google-global-names-in-headers) #endif diff --git a/src/gromacs/mdlib/boxdeformation.cpp b/src/gromacs/mdlib/boxdeformation.cpp index e55ca702fb..cf84470f92 100644 --- a/src/gromacs/mdlib/boxdeformation.cpp +++ b/src/gromacs/mdlib/boxdeformation.cpp @@ -156,4 +156,4 @@ BoxDeformation::apply(ArrayRef x, } } -} // namespace +} // namespace gmx diff --git a/src/gromacs/mdlib/boxdeformation.h b/src/gromacs/mdlib/boxdeformation.h index ba5bcbe19a..fe1351ee9c 100644 --- a/src/gromacs/mdlib/boxdeformation.h +++ b/src/gromacs/mdlib/boxdeformation.h @@ -98,6 +98,6 @@ prepareBoxDeformation(const matrix &initialBox, t_commrec *cr, const t_inputrec &inputrec); -} // namespace +} // namespace gmx #endif diff --git a/src/gromacs/mdlib/constr.cpp b/src/gromacs/mdlib/constr.cpp index 8d761ad7bd..5e085c375a 100644 --- a/src/gromacs/mdlib/constr.cpp +++ b/src/gromacs/mdlib/constr.cpp @@ -1209,4 +1209,4 @@ bool inter_charge_group_settles(const gmx_mtop_t &mtop) return bInterCG; } -} // namespace +} // namespace gmx diff --git a/src/gromacs/mdlib/constr.h b/src/gromacs/mdlib/constr.h index 6579ba9674..c887bc2754 100644 --- a/src/gromacs/mdlib/constr.h +++ b/src/gromacs/mdlib/constr.h @@ -259,6 +259,6 @@ bool inter_charge_group_constraints(const gmx_mtop_t &mtop); /*! \brief Returns whether there are inter charge group settles */ bool inter_charge_group_settles(const gmx_mtop_t &mtop); -} // namespace +} // namespace gmx #endif diff --git a/src/gromacs/mdlib/constraintrange.cpp b/src/gromacs/mdlib/constraintrange.cpp index 95cf473a8c..a28b955461 100644 --- a/src/gromacs/mdlib/constraintrange.cpp +++ b/src/gromacs/mdlib/constraintrange.cpp @@ -240,4 +240,4 @@ real constr_r_max(FILE *fplog, const gmx_mtop_t *mtop, const t_inputrec *ir) return rmax; } -} // namespace +} // namespace gmx diff --git a/src/gromacs/mdlib/lincs.cpp b/src/gromacs/mdlib/lincs.cpp index 681cf142b4..a5171a3daa 100644 --- a/src/gromacs/mdlib/lincs.cpp +++ b/src/gromacs/mdlib/lincs.cpp @@ -2639,4 +2639,4 @@ bool constrain_lincs(bool computeRmsd, return bOK; } -} // namespace +} // namespace gmx diff --git a/src/gromacs/mdlib/lincs.h b/src/gromacs/mdlib/lincs.h index 096b8e24c9..fe172a4746 100644 --- a/src/gromacs/mdlib/lincs.h +++ b/src/gromacs/mdlib/lincs.h @@ -107,6 +107,6 @@ constrain_lincs(bool computeRmsd, t_nrnb *nrnb, int maxwarn, int *warncount); -} // namespace +} // namespace gmx #endif diff --git a/src/gromacs/mdlib/makeconstraints.h b/src/gromacs/mdlib/makeconstraints.h index 500fbfef0f..65246ecb7b 100644 --- a/src/gromacs/mdlib/makeconstraints.h +++ b/src/gromacs/mdlib/makeconstraints.h @@ -116,6 +116,6 @@ std::unique_ptr makeConstraints(const gmx_mtop_t &mtop, (mtop, ir, std::forward(args) ..., numConstraints, numSettles); } -} // namespace +} // namespace gmx #endif diff --git a/src/gromacs/mdlib/mdatoms.cpp b/src/gromacs/mdlib/mdatoms.cpp index 8df527670f..d0d2c82d67 100644 --- a/src/gromacs/mdlib/mdatoms.cpp +++ b/src/gromacs/mdlib/mdatoms.cpp @@ -198,7 +198,7 @@ makeMDAtoms(FILE *fp, const gmx_mtop_t &mtop, const t_inputrec &ir, return mdAtoms; } -} // namespace +} // namespace gmx void atoms2md(const gmx_mtop_t *mtop, const t_inputrec *ir, int nindex, const int *index, diff --git a/src/gromacs/mdlib/mdatoms.h b/src/gromacs/mdlib/mdatoms.h index b8ecf61345..a77a043f49 100644 --- a/src/gromacs/mdlib/mdatoms.h +++ b/src/gromacs/mdlib/mdatoms.h @@ -102,7 +102,7 @@ std::unique_ptr makeMDAtoms(FILE *fp, const gmx_mtop_t &mtop, const t_inputrec &ir, bool useGpuForPme); -} // namespace +} // namespace gmx void atoms2md(const gmx_mtop_t *mtop, const t_inputrec *ir, int nindex, const int *index, diff --git a/src/gromacs/mdlib/settle.cpp b/src/gromacs/mdlib/settle.cpp index a5a1bec635..fb68c73d72 100644 --- a/src/gromacs/mdlib/settle.cpp +++ b/src/gromacs/mdlib/settle.cpp @@ -901,4 +901,4 @@ void csettle(settledata *settled, } } -} // namespace +} // namespace gmx diff --git a/src/gromacs/mdlib/settle.h b/src/gromacs/mdlib/settle.h index 7c7473d4b5..c5ba5fec36 100644 --- a/src/gromacs/mdlib/settle.h +++ b/src/gromacs/mdlib/settle.h @@ -97,6 +97,6 @@ void settle_proj(settledata *settled, ConstraintVariable econq, rvec *der, rvec *derp, int CalcVirAtomEnd, tensor vir_r_m_dder); -} // namespace +} // namespace gmx #endif diff --git a/src/gromacs/mdlib/shake.cpp b/src/gromacs/mdlib/shake.cpp index c168e04176..8f4b9c3d06 100644 --- a/src/gromacs/mdlib/shake.cpp +++ b/src/gromacs/mdlib/shake.cpp @@ -857,4 +857,4 @@ constrain_shake(FILE *log, return bOK; } -} // namespace +} // namespace gmx diff --git a/src/gromacs/mdlib/shake.h b/src/gromacs/mdlib/shake.h index 40ef291724..62698ce618 100644 --- a/src/gromacs/mdlib/shake.h +++ b/src/gromacs/mdlib/shake.h @@ -107,6 +107,6 @@ void cshake(const int iatom[], int ncon, int *nnit, int maxnit, const real dist2[], real xp[], const real rij[], const real m2[], real omega, const real invmass[], const real tt[], real lagr[], int *nerror); -} // namespace +} // namespace gmx #endif diff --git a/src/gromacs/mdlib/simulationsignal.cpp b/src/gromacs/mdlib/simulationsignal.cpp index aa0a63f137..57cd0043fd 100644 --- a/src/gromacs/mdlib/simulationsignal.cpp +++ b/src/gromacs/mdlib/simulationsignal.cpp @@ -148,4 +148,4 @@ void SimulationSignaller::finalizeSignals() setSignals(); } -} // namespace +} // namespace gmx diff --git a/src/gromacs/mdlib/simulationsignal.h b/src/gromacs/mdlib/simulationsignal.h index 5dc1138fab..4d7ba8bc46 100644 --- a/src/gromacs/mdlib/simulationsignal.h +++ b/src/gromacs/mdlib/simulationsignal.h @@ -159,6 +159,6 @@ class SimulationSignaller std::array mpiBuffer_; }; -} // namespace +} // namespace gmx #endif diff --git a/src/gromacs/mdlib/tests/calc_verletbuf.cpp b/src/gromacs/mdlib/tests/calc_verletbuf.cpp index 9fb809ef95..da90ace13c 100644 --- a/src/gromacs/mdlib/tests/calc_verletbuf.cpp +++ b/src/gromacs/mdlib/tests/calc_verletbuf.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2017, by the GROMACS development team, led by + * Copyright (c) 2017,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -135,6 +135,6 @@ TEST_F(VerletBufferConstraintTest, EqualMasses) GMX_RELEASE_ASSERT(numPointsBeforeMax >= 20 && numPointsAfterMax >= 20, "This test only provides full coverage when we test a sufficient number of points before and after the location of the maximum value for the exact formula."); } -} // namespace anonymous +} // namespace -} // namespace gmx +} // namespace gmx diff --git a/src/gromacs/mdlib/tests/mdebin.cpp b/src/gromacs/mdlib/tests/mdebin.cpp index 7cae684b62..58a6ba1d2b 100644 --- a/src/gromacs/mdlib/tests/mdebin.cpp +++ b/src/gromacs/mdlib/tests/mdebin.cpp @@ -154,6 +154,6 @@ TEST_F(PrintEbin, pr_ebin_HandlesEmptyAverages) checker_.checkString(TextReader::readFileToString(logFilename_), "log"); } -} // namespace -} // namespace -} // namespace +} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/mdlib/tests/settle.cpp b/src/gromacs/mdlib/tests/settle.cpp index 24ee0acdc4..ef9dc06c7f 100644 --- a/src/gromacs/mdlib/tests/settle.cpp +++ b/src/gromacs/mdlib/tests/settle.cpp @@ -315,5 +315,5 @@ INSTANTIATE_TEST_CASE_P(WithParameters, SettleTest, ::testing::Bool(), ::testing::Bool())); -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/mdlib/tests/shake.cpp b/src/gromacs/mdlib/tests/shake.cpp index f1fb6c2c99..294dd7b3e0 100644 --- a/src/gromacs/mdlib/tests/shake.cpp +++ b/src/gromacs/mdlib/tests/shake.cpp @@ -359,4 +359,4 @@ TEST_F(ShakeTest, ConstrainsThreeBondsWithCommonAtoms) } } // namespace -} // namespace +} // namespace gmx diff --git a/src/gromacs/mdlib/tests/simulationsignal.cpp b/src/gromacs/mdlib/tests/simulationsignal.cpp index 591a701d9f..408c511d42 100644 --- a/src/gromacs/mdlib/tests/simulationsignal.cpp +++ b/src/gromacs/mdlib/tests/simulationsignal.cpp @@ -173,5 +173,5 @@ TEST_F(SignalTest, NonLocalSignalPropagatesWhenBothTakePlace) EXPECT_EQ(0, signals_[2].set); } -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/mdlib/update.h b/src/gromacs/mdlib/update.h index d5d41b062d..bf83237c17 100644 --- a/src/gromacs/mdlib/update.h +++ b/src/gromacs/mdlib/update.h @@ -213,7 +213,7 @@ restore_ekinstate_from_state(const t_commrec *cr, gmx_ekindata_t *ekind, const ekinstate_t *ekinstate); void berendsen_tcoupl(const t_inputrec *ir, const gmx_ekindata_t *ekind, real dt, - std::vector &therm_integral); + std::vector &therm_integral); //NOLINT(google-runtime-references) void andersen_tcoupl(t_inputrec *ir, int64_t step, const t_commrec *cr, const t_mdatoms *md, t_state *state, real rate, const gmx_bool *randomize, const real *boltzfac); diff --git a/src/gromacs/mdrun/integrator.cpp b/src/gromacs/mdrun/integrator.cpp index f5158bcae7..658a379a98 100644 --- a/src/gromacs/mdrun/integrator.cpp +++ b/src/gromacs/mdrun/integrator.cpp @@ -92,4 +92,4 @@ void Integrator::run(unsigned int ei) } } -} // namespace +} // namespace gmx diff --git a/src/gromacs/mdrun/runner.cpp b/src/gromacs/mdrun/runner.cpp index 0c0797239c..4cf190406a 100644 --- a/src/gromacs/mdrun/runner.cpp +++ b/src/gromacs/mdrun/runner.cpp @@ -215,7 +215,7 @@ t_commrec *Mdrunner::spawnThreads(int numThreadsToLaunch) const return reinitialize_commrec_for_this_thread(cr); } -} // namespace +} // namespace gmx /*! \brief Initialize variables for Verlet scheme simulation */ static void prepare_verlet_scheme(FILE *fplog, diff --git a/src/gromacs/mdtypes/forceoutput.h b/src/gromacs/mdtypes/forceoutput.h index 60752d7c7e..781392a187 100644 --- a/src/gromacs/mdtypes/forceoutput.h +++ b/src/gromacs/mdtypes/forceoutput.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2017, by the GROMACS development team, led by + * Copyright (c) 2017,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -139,6 +139,6 @@ class ForceWithVirial matrix virial_; //!< Virial accumulation buffer }; -} +} // namespace gmx #endif diff --git a/src/gromacs/onlinehelp/rstparser.h b/src/gromacs/onlinehelp/rstparser.h index c250209166..3bf1b3c734 100644 --- a/src/gromacs/onlinehelp/rstparser.h +++ b/src/gromacs/onlinehelp/rstparser.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) 2015,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -113,7 +113,7 @@ class RstParagraphIterator }; //! The text to iterate over. - const std::string &text_; + const std::string &text_; //NOLINT(google-runtime-member-string-references) //! Start of the current paragraph. size_t begin_; diff --git a/src/gromacs/options/behaviorcollection.h b/src/gromacs/options/behaviorcollection.h index 8652aa963b..2d22ad0857 100644 --- a/src/gromacs/options/behaviorcollection.h +++ b/src/gromacs/options/behaviorcollection.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) 2015,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -96,6 +96,6 @@ class OptionsBehaviorCollection GMX_DISALLOW_COPY_AND_ASSIGN(OptionsBehaviorCollection); }; -} // namespace +} // namespace gmx #endif diff --git a/src/gromacs/options/ioptionsbehavior.h b/src/gromacs/options/ioptionsbehavior.h index 087525e445..09bc9d20d0 100644 --- a/src/gromacs/options/ioptionsbehavior.h +++ b/src/gromacs/options/ioptionsbehavior.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) 2015,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -96,6 +96,6 @@ class IOptionsBehavior virtual void optionsFinished() = 0; }; -} // namespace +} // namespace gmx #endif diff --git a/src/gromacs/options/ioptionscontainer.h b/src/gromacs/options/ioptionscontainer.h index 3cdaafc021..d988f4c3fd 100644 --- a/src/gromacs/options/ioptionscontainer.h +++ b/src/gromacs/options/ioptionscontainer.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) 2015,2016,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -145,6 +145,6 @@ class IOptionsContainer GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer); }; -} // namespace +} // namespace gmx #endif diff --git a/src/gromacs/options/ioptionscontainerwithsections.h b/src/gromacs/options/ioptionscontainerwithsections.h index 198e0caf80..29d8f9754c 100644 --- a/src/gromacs/options/ioptionscontainerwithsections.h +++ b/src/gromacs/options/ioptionscontainerwithsections.h @@ -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) 2016,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -109,6 +109,6 @@ class IOptionsContainerWithSections : public IOptionsContainer GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections); }; -} // namespace +} // namespace gmx #endif diff --git a/src/gromacs/options/optionsvisitor.cpp b/src/gromacs/options/optionsvisitor.cpp index a665803f9f..c628d3a5a1 100644 --- a/src/gromacs/options/optionsvisitor.cpp +++ b/src/gromacs/options/optionsvisitor.cpp @@ -56,12 +56,12 @@ namespace { //! Helper function to call visitOptions() and handle correct indirection. -void visitOption(OptionsVisitor *visitor, OptionInfo &optionInfo) +void visitOption(OptionsVisitor *visitor, OptionInfo &optionInfo) //NOLINT(google-runtime-references) { visitor->visitOption(optionInfo); } //! Helper function to call visitOptions() and handle correct indirection. -void visitOption(OptionsModifyingVisitor *visitor, OptionInfo &optionInfo) +void visitOption(OptionsModifyingVisitor *visitor, OptionInfo &optionInfo) //NOLINT(google-runtime-references) { visitor->visitOption(&optionInfo); } diff --git a/src/gromacs/pulling/pull_rotation.cpp b/src/gromacs/pulling/pull_rotation.cpp index 1e7b3f4838..74fb143114 100644 --- a/src/gromacs/pulling/pull_rotation.cpp +++ b/src/gromacs/pulling/pull_rotation.cpp @@ -316,7 +316,7 @@ gmx_enfrot *EnforcedRotation::getLegacyEnfrot() return &impl_->enforcedRotation_; } -} // namespace +} // namespace gmx /* Activate output of forces for correctness checks */ /* #define PRINT_FORCES */ diff --git a/src/gromacs/pulling/pull_rotation.h b/src/gromacs/pulling/pull_rotation.h index 4e02ddc85f..fe313c3906 100644 --- a/src/gromacs/pulling/pull_rotation.h +++ b/src/gromacs/pulling/pull_rotation.h @@ -87,7 +87,7 @@ class EnforcedRotation PrivateImplPointer impl_; }; -} // namespace +} // namespace gmx /*! \brief Initializes the enforced rotation groups. * diff --git a/src/gromacs/pulling/tests/pull.cpp b/src/gromacs/pulling/tests/pull.cpp index 77ab1a13ad..b56fad0b88 100644 --- a/src/gromacs/pulling/tests/pull.cpp +++ b/src/gromacs/pulling/tests/pull.cpp @@ -196,6 +196,6 @@ TEST_F (PullTest, MaxPullDistanceXySkewedBox) test(epbcXY, box); } -} +} // namespace -} +} // namespace gmx diff --git a/src/gromacs/random/seed.cpp b/src/gromacs/random/seed.cpp index 2b5c855cc8..94a3f83e4d 100644 --- a/src/gromacs/random/seed.cpp +++ b/src/gromacs/random/seed.cpp @@ -60,4 +60,4 @@ makeRandomSeed() return result; } -} +} // namespace gmx diff --git a/src/gromacs/random/tabulatednormaldistribution.cpp b/src/gromacs/random/tabulatednormaldistribution.cpp index 59c01d98a5..e595975f34 100644 --- a/src/gromacs/random/tabulatednormaldistribution.cpp +++ b/src/gromacs/random/tabulatednormaldistribution.cpp @@ -55,4 +55,4 @@ TabulatedNormalDistribution<>::c_table_ = TabulatedNormalDistribution<>::makeTab void TabulatedNormalDistributionDummy(){} #endif -} +} // namespace gmx diff --git a/src/gromacs/random/tests/exponentialdistribution.cpp b/src/gromacs/random/tests/exponentialdistribution.cpp index 759a2c17ee..f2a5202623 100644 --- a/src/gromacs/random/tests/exponentialdistribution.cpp +++ b/src/gromacs/random/tests/exponentialdistribution.cpp @@ -126,6 +126,6 @@ TEST(ExponentialDistributionTest, AltParam) EXPECT_REAL_EQ_TOL(distA(rngA), distB(rngB, paramA), gmx::test::ulpTolerance(0)); } -} // namespace anonymous +} // namespace -} // namespace gmx +} // namespace gmx diff --git a/src/gromacs/random/tests/gammadistribution.cpp b/src/gromacs/random/tests/gammadistribution.cpp index 4cee2ca2a2..1c6fdd154a 100644 --- a/src/gromacs/random/tests/gammadistribution.cpp +++ b/src/gromacs/random/tests/gammadistribution.cpp @@ -120,6 +120,6 @@ TEST(GammaDistributionTest, AltParam) EXPECT_REAL_EQ_TOL(distA(rngA), distB(rngB, paramA), gmx::test::ulpTolerance(0)); } -} // namespace anonymous +} // namespace -} // namespace gmx +} // namespace gmx diff --git a/src/gromacs/random/tests/normaldistribution.cpp b/src/gromacs/random/tests/normaldistribution.cpp index 3ad6af4ab7..97167966cb 100644 --- a/src/gromacs/random/tests/normaldistribution.cpp +++ b/src/gromacs/random/tests/normaldistribution.cpp @@ -132,6 +132,6 @@ TEST(NormalDistributionTest, AltParam) EXPECT_REAL_EQ_TOL(valA, valB, gmx::test::ulpTolerance(0)); } -} // namespace anonymous +} // namespace -} // namespace gmx +} // namespace gmx diff --git a/src/gromacs/random/tests/seed.cpp b/src/gromacs/random/tests/seed.cpp index ac2cb0697c..e97ceb5ace 100644 --- a/src/gromacs/random/tests/seed.cpp +++ b/src/gromacs/random/tests/seed.cpp @@ -66,6 +66,6 @@ TEST(SeedTest, makeRandomSeed) EXPECT_NE(i0, i1); } -} // namespace anonymous +} // namespace -} // namespace gmx +} // namespace gmx diff --git a/src/gromacs/random/tests/tabulatednormaldistribution.cpp b/src/gromacs/random/tests/tabulatednormaldistribution.cpp index 6693d875b4..502c8dfb30 100644 --- a/src/gromacs/random/tests/tabulatednormaldistribution.cpp +++ b/src/gromacs/random/tests/tabulatednormaldistribution.cpp @@ -178,6 +178,6 @@ TEST(TabulatedNormalDistributionTableTest, HasValidProperties) EXPECT_REAL_EQ_TOL(1.0, variance, tolerance) << "Table should have unit variance"; } -} // namespace anonymous +} // namespace -} // namespace gmx +} // namespace gmx diff --git a/src/gromacs/random/tests/threefry.cpp b/src/gromacs/random/tests/threefry.cpp index 6552fec98a..7afd82665c 100644 --- a/src/gromacs/random/tests/threefry.cpp +++ b/src/gromacs/random/tests/threefry.cpp @@ -244,6 +244,6 @@ TEST_F(ThreeFry2x64Test, ExhaustInternalCounter) EXPECT_THROW_GMX(rngA(), gmx::InternalError); } -} // namespace anonymous +} // namespace -} // namespace gmx +} // namespace gmx diff --git a/src/gromacs/random/tests/uniformintdistribution.cpp b/src/gromacs/random/tests/uniformintdistribution.cpp index b7cd01ef61..b718ada683 100644 --- a/src/gromacs/random/tests/uniformintdistribution.cpp +++ b/src/gromacs/random/tests/uniformintdistribution.cpp @@ -122,6 +122,6 @@ TEST(UniformIntDistributionTest, AltParam) } -} // namespace anonymous +} // namespace -} // namespace gmx +} // namespace gmx diff --git a/src/gromacs/random/tests/uniformrealdistribution.cpp b/src/gromacs/random/tests/uniformrealdistribution.cpp index 599d89ebea..0214912b00 100644 --- a/src/gromacs/random/tests/uniformrealdistribution.cpp +++ b/src/gromacs/random/tests/uniformrealdistribution.cpp @@ -145,6 +145,6 @@ TEST(UniformRealDistributionTest, AltParam) EXPECT_REAL_EQ_TOL(valA, valB, gmx::test::ulpTolerance(0)); } -} // namespace anonymous +} // namespace -} // namespace gmx +} // namespace gmx diff --git a/src/gromacs/random/threefry.h b/src/gromacs/random/threefry.h index 5c1d428485..44e9a38d8c 100644 --- a/src/gromacs/random/threefry.h +++ b/src/gromacs/random/threefry.h @@ -278,7 +278,7 @@ highBitCounter } } }; -} +} // namespace internal /*! \brief General implementation class for ThreeFry counter-based random engines. * diff --git a/src/gromacs/selection/selectionenums.h b/src/gromacs/selection/selectionenums.h index 1492715dfe..34d4b28dde 100644 --- a/src/gromacs/selection/selectionenums.h +++ b/src/gromacs/selection/selectionenums.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2010,2012,2013,2014,2015,2016, by the GROMACS development team, led by + * Copyright (c) 2010,2012,2013,2014,2015,2016,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -133,6 +133,6 @@ struct SelectionTopologyProperties bool needsMasses; }; -} +} // namespace gmx #endif diff --git a/src/gromacs/simd/simd.h b/src/gromacs/simd/simd.h index 3c1c54b79a..51bb2da4bd 100644 --- a/src/gromacs/simd/simd.h +++ b/src/gromacs/simd/simd.h @@ -97,7 +97,7 @@ struct SimdDoubleTag {}; struct SimdFInt32Tag {}; /*! \libinternal \brief Tag type to select to load SimdDInt32 with simdLoad(U) */ struct SimdDInt32Tag {}; -} +} // namespace gmx /*! \name SIMD predefined macros to describe high-level capabilities * diff --git a/src/gromacs/simd/support.cpp b/src/gromacs/simd/support.cpp index 9525a054bd..d7b5839251 100644 --- a/src/gromacs/simd/support.cpp +++ b/src/gromacs/simd/support.cpp @@ -310,4 +310,4 @@ simdCheck(gmx::SimdType wanted, /*! \endcond */ -} +} // namespace gmx diff --git a/src/gromacs/simd/tests/base.cpp b/src/gromacs/simd/tests/base.cpp index bc16427175..d7d13c0ad5 100644 --- a/src/gromacs/simd/tests/base.cpp +++ b/src/gromacs/simd/tests/base.cpp @@ -127,5 +127,5 @@ SimdBaseTest::compareVectorRealUlp(const char * refExpr, const char * tstExpr, /*! \} */ /*! \endcond */ -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/simd/tests/base.h b/src/gromacs/simd/tests/base.h index 2f85847a59..1718763e3f 100644 --- a/src/gromacs/simd/tests/base.h +++ b/src/gromacs/simd/tests/base.h @@ -192,7 +192,7 @@ class SimdBaseTest : public ::testing::Test std::pair range_; //!< Range for math function tests. }; -} // namespace -} // namespace +} // namespace test +} // namespace gmx #endif // GMX_SIMD_TESTS_BASE_H diff --git a/src/gromacs/simd/tests/scalar.cpp b/src/gromacs/simd/tests/scalar.cpp index 2b3f9f9e6a..9ae28508eb 100644 --- a/src/gromacs/simd/tests/scalar.cpp +++ b/src/gromacs/simd/tests/scalar.cpp @@ -333,6 +333,6 @@ TEST(SimdScalarTest, cvtIB2B) /*! \} */ /*! \endcond internal */ -} // namespace anonymous -} // namespace test -} // namespace gmx +} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/simd/tests/scalar_math.cpp b/src/gromacs/simd/tests/scalar_math.cpp index df297937b3..8ce6a3d519 100644 --- a/src/gromacs/simd/tests/scalar_math.cpp +++ b/src/gromacs/simd/tests/scalar_math.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by + * Copyright (c) 2014,2015,2016,2017,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -408,6 +408,6 @@ TEST(SimdScalarMathTest, pmePotentialCorrectionSingleAccuracy) /*! \} */ /*! \endcond internal */ -} // namespace anonymous -} // namespace test -} // namespace gmx +} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/simd/tests/scalar_util.cpp b/src/gromacs/simd/tests/scalar_util.cpp index 76e64c78a8..a234d48fdb 100644 --- a/src/gromacs/simd/tests/scalar_util.cpp +++ b/src/gromacs/simd/tests/scalar_util.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by + * Copyright (c) 2014,2015,2016,2017,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -220,6 +220,6 @@ TEST(SimdScalarUtilTest, reduceIncr4ReturnSum) /*! \} */ /*! \endcond internal */ -} // namespace anonymous -} // namespace test -} // namespace gmx +} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/simd/tests/simd.cpp b/src/gromacs/simd/tests/simd.cpp index 8655f64dcd..77a91e7900 100644 --- a/src/gromacs/simd/tests/simd.cpp +++ b/src/gromacs/simd/tests/simd.cpp @@ -267,7 +267,7 @@ SimdTest::compareSimdEq(const char * refExpr, const char * tstExpr, /*! \} */ /*! \endcond */ -} // namespace -} // namespace +} // namespace test +} // namespace gmx #endif // GMX_SIMD diff --git a/src/gromacs/simd/tests/simd.h b/src/gromacs/simd/tests/simd.h index 60fb2ba2e8..8c0ecbd96b 100644 --- a/src/gromacs/simd/tests/simd.h +++ b/src/gromacs/simd/tests/simd.h @@ -305,8 +305,8 @@ SimdInt32 setSimdIntFrom1I(int value); /*! \} */ /*! \endcond */ -} // namespace -} // namespace +} // namespace test +} // namespace gmx #endif // GMX_SIMD diff --git a/src/gromacs/simd/tests/simd4.cpp b/src/gromacs/simd/tests/simd4.cpp index 86858d67b8..fa98e14828 100644 --- a/src/gromacs/simd/tests/simd4.cpp +++ b/src/gromacs/simd/tests/simd4.cpp @@ -146,7 +146,7 @@ Simd4Test::compareSimd4RealEq(const char * refExpr, const char * tstExpr, /*! \} */ /*! \endcond */ -} // namespace -} // namespace +} // namespace test +} // namespace gmx #endif // GMX_SIMD diff --git a/src/gromacs/simd/tests/simd4.h b/src/gromacs/simd/tests/simd4.h index b7971035dd..bee86fd969 100644 --- a/src/gromacs/simd/tests/simd4.h +++ b/src/gromacs/simd/tests/simd4.h @@ -181,8 +181,8 @@ Simd4Real setSimd4RealFrom1R(real value); /*! \} */ /*! \endcond */ -} // namespace -} // namespace +} // namespace test +} // namespace gmx #endif // GMX_SIMD diff --git a/src/gromacs/simd/tests/simd4_floatingpoint.cpp b/src/gromacs/simd/tests/simd4_floatingpoint.cpp index 451dadd7dc..007b25e0fa 100644 --- a/src/gromacs/simd/tests/simd4_floatingpoint.cpp +++ b/src/gromacs/simd/tests/simd4_floatingpoint.cpp @@ -354,7 +354,7 @@ TEST_F(Simd4FloatingpointTest, transpose) /*! \endcond */ } // namespace -} // namespace -} // namespace +} // namespace test +} // namespace gmx #endif // GMX_SIMD diff --git a/src/gromacs/simd/tests/simd4_math.cpp b/src/gromacs/simd/tests/simd4_math.cpp index 989eca2800..5ae601e32a 100644 --- a/src/gromacs/simd/tests/simd4_math.cpp +++ b/src/gromacs/simd/tests/simd4_math.cpp @@ -223,7 +223,7 @@ TEST_F(Simd4MathTest, invsqrtSingleaccuracy) /*! \} */ /*! \endcond */ -} // namespace -} // namespace +} // namespace test +} // namespace gmx #endif // GMX_SIMD diff --git a/src/gromacs/simd/tests/simd4_vector_operations.cpp b/src/gromacs/simd/tests/simd4_vector_operations.cpp index 97ae2d2d1f..60653ecbc0 100644 --- a/src/gromacs/simd/tests/simd4_vector_operations.cpp +++ b/src/gromacs/simd/tests/simd4_vector_operations.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by + * Copyright (c) 2014,2015,2017,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -79,7 +79,7 @@ TEST_F(Simd4VectorOperationsTest, norm2) /*! \endcond */ } // namespace -} // namespace -} // namespace +} // namespace test +} // namespace gmx #endif // GMX_SIMD diff --git a/src/gromacs/simd/tests/simd_floatingpoint.cpp b/src/gromacs/simd/tests/simd_floatingpoint.cpp index 825df83b6f..d92cabf994 100644 --- a/src/gromacs/simd/tests/simd_floatingpoint.cpp +++ b/src/gromacs/simd/tests/simd_floatingpoint.cpp @@ -526,7 +526,7 @@ TEST_F(SimdFloatingpointTest, cvtDouble2Float) /*! \endcond */ } // namespace -} // namespace -} // namespace +} // namespace test +} // namespace gmx #endif // GMX_SIMD diff --git a/src/gromacs/simd/tests/simd_floatingpoint_util.cpp b/src/gromacs/simd/tests/simd_floatingpoint_util.cpp index a957201707..72912172a3 100644 --- a/src/gromacs/simd/tests/simd_floatingpoint_util.cpp +++ b/src/gromacs/simd/tests/simd_floatingpoint_util.cpp @@ -991,6 +991,6 @@ TEST_F(SimdFloatingpointUtilTest, loadU4NOffset) /*! \} */ /*! \endcond */ -} // namespace -} // namespace -} // namespace +} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/simd/tests/simd_integer.cpp b/src/gromacs/simd/tests/simd_integer.cpp index b2a99ecd78..0f1e06496a 100644 --- a/src/gromacs/simd/tests/simd_integer.cpp +++ b/src/gromacs/simd/tests/simd_integer.cpp @@ -314,7 +314,7 @@ TEST_F(SimdIntegerTest, cvtIB2B) /*! \endcond */ } // namespace -} // namespace -} // namespace +} // namespace test +} // namespace gmx #endif // GMX_SIMD diff --git a/src/gromacs/simd/tests/simd_math.cpp b/src/gromacs/simd/tests/simd_math.cpp index a62d893a9a..8fa8733a66 100644 --- a/src/gromacs/simd/tests/simd_math.cpp +++ b/src/gromacs/simd/tests/simd_math.cpp @@ -986,7 +986,7 @@ TEST_F(SimdMathTest, pmePotentialCorrectionSingleAccuracy) /*! \} */ /*! \endcond */ -} // namespace -} // namespace +} // namespace test +} // namespace gmx #endif // GMX_SIMD diff --git a/src/gromacs/simd/tests/simd_vector_operations.cpp b/src/gromacs/simd/tests/simd_vector_operations.cpp index 147493db01..9229e32922 100644 --- a/src/gromacs/simd/tests/simd_vector_operations.cpp +++ b/src/gromacs/simd/tests/simd_vector_operations.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by + * Copyright (c) 2014,2015,2017,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -125,7 +125,7 @@ TEST_F(SimdVectorOperationsTest, cprod) /*! \endcond */ } // namespace -} // namespace -} // namespace +} // namespace test +} // namespace gmx #endif // GMX_SIMD diff --git a/src/gromacs/tables/cubicsplinetable.cpp b/src/gromacs/tables/cubicsplinetable.cpp index da94daf08c..e49007e506 100644 --- a/src/gromacs/tables/cubicsplinetable.cpp +++ b/src/gromacs/tables/cubicsplinetable.cpp @@ -298,7 +298,7 @@ fillSingleCubicSplineTableData(ArrayRef function, } -} // namespace anonymous +} // namespace diff --git a/src/gromacs/tables/quadraticsplinetable.cpp b/src/gromacs/tables/quadraticsplinetable.cpp index de4487ad98..979c146704 100644 --- a/src/gromacs/tables/quadraticsplinetable.cpp +++ b/src/gromacs/tables/quadraticsplinetable.cpp @@ -261,7 +261,7 @@ fillDdfzTableData(const std::vector &functionTableData, } } -} // namespace anonymous +} // namespace diff --git a/src/gromacs/tables/tableinput.h b/src/gromacs/tables/tableinput.h index 8f8725c53c..a866b8816f 100644 --- a/src/gromacs/tables/tableinput.h +++ b/src/gromacs/tables/tableinput.h @@ -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) 2016,2017,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -58,6 +58,7 @@ namespace gmx struct AnalyticalSplineTableInput { + //NOLINTNEXTLINE(google-runtime-member-string-references) const std::string &desc; //!< \libinternal Brief description of function std::function function; //!< \libinternal Analytical form of function std::function derivative; //!< \libinternal Analytical derivative @@ -68,6 +69,7 @@ AnalyticalSplineTableInput struct NumericalSplineTableInput { + //NOLINTNEXTLINE(google-runtime-member-string-references) const std::string &desc; //!< \libinternal Brief description of function ArrayRef function; //!< \libinternal Vector with function values ArrayRef derivative; //!< \libinternal Vector with derivative values diff --git a/src/gromacs/taskassignment/decidegpuusage.cpp b/src/gromacs/taskassignment/decidegpuusage.cpp index 94e7274552..4e7691bc63 100644 --- a/src/gromacs/taskassignment/decidegpuusage.cpp +++ b/src/gromacs/taskassignment/decidegpuusage.cpp @@ -408,4 +408,4 @@ bool decideWhetherToUseGpusForPme(const bool useGpuForNonbonded, return false; } -} // namespace +} // namespace gmx diff --git a/src/gromacs/taskassignment/decidegpuusage.h b/src/gromacs/taskassignment/decidegpuusage.h index 694024202b..0730d52b9a 100644 --- a/src/gromacs/taskassignment/decidegpuusage.h +++ b/src/gromacs/taskassignment/decidegpuusage.h @@ -186,6 +186,6 @@ bool decideWhetherToUseGpusForPme(bool useGpuForNonbonded, int numPmeRanksPerSimulation, bool gpusWereDetected); -} +} // namespace gmx #endif diff --git a/src/gromacs/taskassignment/findallgputasks.cpp b/src/gromacs/taskassignment/findallgputasks.cpp index ea19040a7c..10716733ff 100644 --- a/src/gromacs/taskassignment/findallgputasks.cpp +++ b/src/gromacs/taskassignment/findallgputasks.cpp @@ -219,4 +219,4 @@ findAllGpuTasksOnThisNode(ArrayRef gpuTasksOnThisRank, return gpuTasksOnRanksOfThisNode; } -} // namespace +} // namespace gmx diff --git a/src/gromacs/taskassignment/findallgputasks.h b/src/gromacs/taskassignment/findallgputasks.h index 6c84f8b6d6..090c1c800b 100644 --- a/src/gromacs/taskassignment/findallgputasks.h +++ b/src/gromacs/taskassignment/findallgputasks.h @@ -60,6 +60,6 @@ GpuTasksOnRanks findAllGpuTasksOnThisNode(ArrayRef gpuTasksOnThisRank, const PhysicalNodeCommunicator &physicalNodeComm); -} // namespace +} // namespace gmx #endif diff --git a/src/gromacs/taskassignment/reportgpuusage.cpp b/src/gromacs/taskassignment/reportgpuusage.cpp index e3daa7ea41..e1cb200375 100644 --- a/src/gromacs/taskassignment/reportgpuusage.cpp +++ b/src/gromacs/taskassignment/reportgpuusage.cpp @@ -139,4 +139,4 @@ reportGpuUsage(const MDLogger &mdlog, GMX_LOG(mdlog.warning).appendText(output); } -} // namespace +} // namespace gmx diff --git a/src/gromacs/taskassignment/reportgpuusage.h b/src/gromacs/taskassignment/reportgpuusage.h index 8fba70b560..400cdeb165 100644 --- a/src/gromacs/taskassignment/reportgpuusage.h +++ b/src/gromacs/taskassignment/reportgpuusage.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2017, by the GROMACS development team, led by + * Copyright (c) 2017,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -78,6 +78,6 @@ reportGpuUsage(const MDLogger &mdlog, bool bPrintHostName); -} // namespace +} // namespace gmx #endif diff --git a/src/gromacs/taskassignment/resourcedivision.cpp b/src/gromacs/taskassignment/resourcedivision.cpp index ab1436759a..ad7a544e49 100644 --- a/src/gromacs/taskassignment/resourcedivision.cpp +++ b/src/gromacs/taskassignment/resourcedivision.cpp @@ -946,4 +946,4 @@ void checkHardwareOversubscription(int numThreadsOnT } } -} // namespace +} // namespace gmx diff --git a/src/gromacs/taskassignment/resourcedivision.h b/src/gromacs/taskassignment/resourcedivision.h index 5fcc64e6e4..5ff290eabc 100644 --- a/src/gromacs/taskassignment/resourcedivision.h +++ b/src/gromacs/taskassignment/resourcedivision.h @@ -130,6 +130,6 @@ void checkHardwareOversubscription(int numThreadsOnT const PhysicalNodeCommunicator &comm, const MDLogger &mdlog); -} // namespace +} // namespace gmx #endif diff --git a/src/gromacs/taskassignment/taskassignment.cpp b/src/gromacs/taskassignment/taskassignment.cpp index 5749d437e3..136587e3cb 100644 --- a/src/gromacs/taskassignment/taskassignment.cpp +++ b/src/gromacs/taskassignment/taskassignment.cpp @@ -325,4 +325,4 @@ runTaskAssignment(const std::vector &gpuIdsToUse, // would require communication. } -} // namespace +} // namespace gmx diff --git a/src/gromacs/taskassignment/taskassignment.h b/src/gromacs/taskassignment/taskassignment.h index c6217a8b03..7c8250a564 100644 --- a/src/gromacs/taskassignment/taskassignment.h +++ b/src/gromacs/taskassignment/taskassignment.h @@ -131,6 +131,6 @@ bool hasTaskType(const GpuTaskMapping &mapping) return mapping.task_ == TaskType; } -} // namespace +} // namespace gmx #endif diff --git a/src/gromacs/taskassignment/tests/usergpuids.cpp b/src/gromacs/taskassignment/tests/usergpuids.cpp index c4756770dd..066336746c 100644 --- a/src/gromacs/taskassignment/tests/usergpuids.cpp +++ b/src/gromacs/taskassignment/tests/usergpuids.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2017, by the GROMACS development team, led by + * Copyright (c) 2017,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -138,5 +138,5 @@ TEST(GpuIdStringHandlingTest, InvalidInputsThrow) } } // namespace -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/taskassignment/usergpuids.cpp b/src/gromacs/taskassignment/usergpuids.cpp index e3e06e0677..78ed11a45a 100644 --- a/src/gromacs/taskassignment/usergpuids.cpp +++ b/src/gromacs/taskassignment/usergpuids.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2017, by the GROMACS development team, led by + * Copyright (c) 2017,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -157,4 +157,4 @@ void checkUserGpuIds(const gmx_gpu_info_t &gpu_info, } } -} // namespace +} // namespace gmx diff --git a/src/gromacs/taskassignment/usergpuids.h b/src/gromacs/taskassignment/usergpuids.h index 006e6b283e..fa362bd730 100644 --- a/src/gromacs/taskassignment/usergpuids.h +++ b/src/gromacs/taskassignment/usergpuids.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2017, by the GROMACS development team, led by + * Copyright (c) 2017,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -135,6 +135,6 @@ void checkUserGpuIds(const gmx_gpu_info_t &gpu_info, const std::vector &compatibleGpus, const std::vector &gpuIds); -} // namespace +} // namespace gmx #endif diff --git a/src/gromacs/topology/block.h b/src/gromacs/topology/block.h index e07003a90b..10d30e192a 100644 --- a/src/gromacs/topology/block.h +++ b/src/gromacs/topology/block.h @@ -184,7 +184,7 @@ class RangePartitioning std::vector index_ = { 0 }; /**< The list of block begin/end indices */ }; -} // nsamespace gmx +} // namespace gmx /* Deprecated, C-style version of RangePartitioning */ typedef struct t_block diff --git a/src/gromacs/trajectory/energyframe.cpp b/src/gromacs/trajectory/energyframe.cpp index ba76ee0a81..3ef6c4f70e 100644 --- a/src/gromacs/trajectory/energyframe.cpp +++ b/src/gromacs/trajectory/energyframe.cpp @@ -98,4 +98,4 @@ EnergyFrame::MapConstIterator EnergyFrame::find(const std::string &key) const return values_.find(key); } -} // namespace +} // namespace gmx diff --git a/src/gromacs/trajectory/energyframe.h b/src/gromacs/trajectory/energyframe.h index c83453fbb0..0819a8eccf 100644 --- a/src/gromacs/trajectory/energyframe.h +++ b/src/gromacs/trajectory/energyframe.h @@ -112,6 +112,6 @@ class EnergyFrame double time_; }; -} // namespace +} // namespace gmx #endif diff --git a/src/gromacs/trajectoryanalysis/modules/angle.h b/src/gromacs/trajectoryanalysis/modules/angle.h index 24b81c7356..6b40390679 100644 --- a/src/gromacs/trajectoryanalysis/modules/angle.h +++ b/src/gromacs/trajectoryanalysis/modules/angle.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by + * Copyright (c) 2011,2012,2013,2014,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -60,6 +60,6 @@ class AngleInfo } // namespace analysismodules -} // namespace gmxana +} // namespace gmx #endif diff --git a/src/gromacs/trajectoryanalysis/tests/clustsize.cpp b/src/gromacs/trajectoryanalysis/tests/clustsize.cpp index 72ed81be66..eda82a7635 100644 --- a/src/gromacs/trajectoryanalysis/tests/clustsize.cpp +++ b/src/gromacs/trajectoryanalysis/tests/clustsize.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2017, by the GROMACS development team, led by + * Copyright (c) 2017,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -151,6 +151,6 @@ TEST_F(ClustsizeTest, MolCSize) } // namespace -} // namespace +} // namespace test -} // namespace +} // namespace gmx diff --git a/src/gromacs/trajectoryanalysis/tests/test_selection.cpp b/src/gromacs/trajectoryanalysis/tests/test_selection.cpp index 0812235611..51e748ef3c 100644 --- a/src/gromacs/trajectoryanalysis/tests/test_selection.cpp +++ b/src/gromacs/trajectoryanalysis/tests/test_selection.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2010,2011,2012,2013,2014,2015,2017, by the GROMACS development team, led by + * Copyright (c) 2010,2011,2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -180,7 +180,7 @@ SelectionTester::writeOutput() { } -} +} // namespace gmx /*! \internal \brief * The main function for the selection testing tool. diff --git a/src/gromacs/utility/coolstuff.cpp b/src/gromacs/utility/coolstuff.cpp index 343482a115..90a90ff480 100644 --- a/src/gromacs/utility/coolstuff.cpp +++ b/src/gromacs/utility/coolstuff.cpp @@ -827,4 +827,4 @@ std::string getCoolQuote() } } -} // namespace +} // namespace gmx diff --git a/src/gromacs/utility/niceheader.cpp b/src/gromacs/utility/niceheader.cpp index d1ce03149c..64b0713d5c 100644 --- a/src/gromacs/utility/niceheader.cpp +++ b/src/gromacs/utility/niceheader.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2017, by the GROMACS development team, led by + * Copyright (c) 2017,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -72,4 +72,4 @@ void niceHeader(TextWriter *writer, const char *fn, char commentChar) writer->writeLine(formatString("%c", commentChar)); } -} // namespace +} // namespace gmx diff --git a/src/gromacs/utility/niceheader.h b/src/gromacs/utility/niceheader.h index fb72ca82ca..e93e0de928 100644 --- a/src/gromacs/utility/niceheader.h +++ b/src/gromacs/utility/niceheader.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2017, by the GROMACS development team, led by + * Copyright (c) 2017,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -57,6 +57,6 @@ class TextWriter; * \throws std::bad_alloc if out of memory. */ void niceHeader(TextWriter *writer, const char *fn, char commentChar); -} // namespace +} // namespace gmx #endif diff --git a/src/gromacs/utility/physicalnodecommunicator.cpp b/src/gromacs/utility/physicalnodecommunicator.cpp index 6c912add49..703f5d5643 100644 --- a/src/gromacs/utility/physicalnodecommunicator.cpp +++ b/src/gromacs/utility/physicalnodecommunicator.cpp @@ -124,4 +124,4 @@ void PhysicalNodeCommunicator::barrier() const #endif } -} // namespace +} // namespace gmx diff --git a/src/gromacs/utility/physicalnodecommunicator.h b/src/gromacs/utility/physicalnodecommunicator.h index f6d74055e8..a85d987750 100644 --- a/src/gromacs/utility/physicalnodecommunicator.h +++ b/src/gromacs/utility/physicalnodecommunicator.h @@ -84,6 +84,6 @@ class PhysicalNodeCommunicator void barrier() const; }; -} // namespace +} // namespace gmx #endif diff --git a/src/gromacs/utility/tests/alignedallocator-impl.h b/src/gromacs/utility/tests/alignedallocator-impl.h index 1982c1a874..aa77d1f29d 100644 --- a/src/gromacs/utility/tests/alignedallocator-impl.h +++ b/src/gromacs/utility/tests/alignedallocator-impl.h @@ -123,7 +123,7 @@ TYPED_TEST(AllocatorTest, VectorAllocatesAndReservesWithAlignment) //NOLINT(misc } } -} // namespace -} // namespace +} // namespace test +} // namespace gmx #endif diff --git a/src/gromacs/utility/tests/alignedallocator.cpp b/src/gromacs/utility/tests/alignedallocator.cpp index 11a695336f..e188dcb8d0 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, by the GROMACS development team, led by + * Copyright (c) 2015,2017,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and 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 @@ using AllocatorTypesToTest = ::testing::Types, TYPED_TEST_CASE(AllocatorTest, AllocatorTypesToTest); -} // namespace -} // namespace +} // namespace test +} // namespace gmx // Includes tests common to all allocation policies. #include "gromacs/utility/tests/alignedallocator-impl.h" @@ -84,5 +84,5 @@ TYPED_TEST(AllocatorTest, StatelessAllocatorUsesNoMemory) sizeof(std::vector)); } -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/utility/tests/arrayref.cpp b/src/gromacs/utility/tests/arrayref.cpp index 99153f5b5d..47dddfb5a7 100644 --- a/src/gromacs/utility/tests/arrayref.cpp +++ b/src/gromacs/utility/tests/arrayref.cpp @@ -268,4 +268,4 @@ TEST(DISABLED_ArrayRefTest, GenericTests) } // namespace -} // namespace +} // namespace gmx diff --git a/src/gromacs/utility/tests/gmxregex.cpp b/src/gromacs/utility/tests/gmxregex.cpp index 697bf13eb6..95d6495474 100644 --- a/src/gromacs/utility/tests/gmxregex.cpp +++ b/src/gromacs/utility/tests/gmxregex.cpp @@ -118,5 +118,5 @@ TEST(RegexBasicTest, MatchesForCharacterClassesWorkWhenSupported) } } // namespace -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/utility/tests/mutex.cpp b/src/gromacs/utility/tests/mutex.cpp index 2cc6990c15..cc3b890134 100644 --- a/src/gromacs/utility/tests/mutex.cpp +++ b/src/gromacs/utility/tests/mutex.cpp @@ -240,5 +240,5 @@ TEST(MutexTaskTest, MutualExclusionWorksWithTryLockOnSameThread) } } // namespace -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp b/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp index 5260a4b516..b88421aca7 100644 --- a/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp +++ b/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp @@ -61,4 +61,4 @@ TEST(PhysicalNodeCommunicatorTest, CanCallBarrier) } } // namespace -} // namespace +} // namespace gmx diff --git a/src/gromacs/utility/tests/physicalnodecommunicator.cpp b/src/gromacs/utility/tests/physicalnodecommunicator.cpp index 86ed2ebc2e..275a176165 100644 --- a/src/gromacs/utility/tests/physicalnodecommunicator.cpp +++ b/src/gromacs/utility/tests/physicalnodecommunicator.cpp @@ -59,4 +59,4 @@ TEST(PhysicalNodeCommunicatorTest, CanCallBarrier) } } // namespace -} // namespace +} // namespace gmx diff --git a/src/gromacs/utility/tests/stringutil.cpp b/src/gromacs/utility/tests/stringutil.cpp index 621544f642..0fea8f8fd9 100644 --- a/src/gromacs/utility/tests/stringutil.cpp +++ b/src/gromacs/utility/tests/stringutil.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2012,2014,2015,2016,2017, by the GROMACS development team, led by + * Copyright (c) 2012,2014,2015,2016,2017,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -432,5 +432,5 @@ TEST_F(TextLineWrapperTest, WrapsCorrectlyWithExtraWhitespace) } } // namespace -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/utility/tests/textreader.cpp b/src/gromacs/utility/tests/textreader.cpp index aa1b3e8b5f..5f24ff6633 100644 --- a/src/gromacs/utility/tests/textreader.cpp +++ b/src/gromacs/utility/tests/textreader.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2017, by the GROMACS development team, led by + * Copyright (c) 2017,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -276,5 +276,5 @@ INSTANTIATE_TEST_CASE_P(ParsesLinesDifferently, TextReaderTest, )); } // namespace -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/gromacs/utility/tests/typetraits.cpp b/src/gromacs/utility/tests/typetraits.cpp index d6c8abd187..31e6cfcbef 100644 --- a/src/gromacs/utility/tests/typetraits.cpp +++ b/src/gromacs/utility/tests/typetraits.cpp @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2017, by the GROMACS development team, led by + * Copyright (c) 2017,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -50,4 +50,4 @@ TEST(TypeTraitsTest, IsIntegralConstant) EXPECT_TRUE((isIntegralConstant, long>::value)); } } -} +} // namespace gmx diff --git a/src/programs/mdrun/mdrun.cpp b/src/programs/mdrun/mdrun.cpp index 1d56da89b9..ae214d59a5 100644 --- a/src/programs/mdrun/mdrun.cpp +++ b/src/programs/mdrun/mdrun.cpp @@ -525,4 +525,4 @@ int Mdrunner::mainFunction(int argc, char *argv[]) return rc; } -} // namespace +} // namespace gmx diff --git a/src/programs/mdrun/tests/energycomparison.cpp b/src/programs/mdrun/tests/energycomparison.cpp index 2fe371aa6d..babe81bf93 100644 --- a/src/programs/mdrun/tests/energycomparison.cpp +++ b/src/programs/mdrun/tests/energycomparison.cpp @@ -75,5 +75,5 @@ void compareEnergyFrames(const EnergyFrame &reference, } } -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/programs/mdrun/tests/energycomparison.h b/src/programs/mdrun/tests/energycomparison.h index a8522cc92c..b6e0aa51ef 100644 --- a/src/programs/mdrun/tests/energycomparison.h +++ b/src/programs/mdrun/tests/energycomparison.h @@ -68,7 +68,7 @@ void compareEnergyFrames(const EnergyFrame &reference, const EnergyFrame &test, const EnergyTolerances &tolerances); -} // namespace -} // namespace +} // namespace test +} // namespace gmx #endif diff --git a/src/programs/mdrun/tests/energyreader.cpp b/src/programs/mdrun/tests/energyreader.cpp index 91a742424f..eb4d9d72a8 100644 --- a/src/programs/mdrun/tests/energyreader.cpp +++ b/src/programs/mdrun/tests/energyreader.cpp @@ -194,5 +194,5 @@ EnergyFrameReader::frame() return EnergyFrame(*enxframeGuard_.get(), indicesOfEnergyFields_); } -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/programs/mdrun/tests/energyreader.h b/src/programs/mdrun/tests/energyreader.h index 7a25900554..1191852c06 100644 --- a/src/programs/mdrun/tests/energyreader.h +++ b/src/programs/mdrun/tests/energyreader.h @@ -154,7 +154,7 @@ class EnergyFrameReader GMX_DISALLOW_COPY_AND_ASSIGN(EnergyFrameReader); }; -} // namespace -} // namespace +} // namespace test +} // namespace gmx #endif diff --git a/src/programs/mdrun/tests/initialconstraints.cpp b/src/programs/mdrun/tests/initialconstraints.cpp index 9b3e4c1afe..d76d6cd187 100644 --- a/src/programs/mdrun/tests/initialconstraints.cpp +++ b/src/programs/mdrun/tests/initialconstraints.cpp @@ -128,6 +128,6 @@ const EnergyIntegratorType c_integratorsToTest [] = {"md", "md-vv", "md-vv-avek" INSTANTIATE_TEST_CASE_P(Checking, InitialConstraintsTest, ::testing::ValuesIn(c_integratorsToTest)); -} -} -} +} // namespace +} // namespace test +} // namespace gmx diff --git a/src/programs/mdrun/tests/moduletest.cpp b/src/programs/mdrun/tests/moduletest.cpp index aeed2e7cf3..e0aa9973cc 100644 --- a/src/programs/mdrun/tests/moduletest.cpp +++ b/src/programs/mdrun/tests/moduletest.cpp @@ -89,7 +89,7 @@ GMX_TEST_OPTIONS(MdrunTestOptions, options) } //! \endcond -} +} // namespace SimulationRunner::SimulationRunner(TestFileManager *fileManager) : mdpOutputFileName_(fileManager->getTemporaryFilePath("output.mdp")), diff --git a/src/programs/mdrun/tests/multisim.cpp b/src/programs/mdrun/tests/multisim.cpp index 386474de9d..315e9b97d2 100644 --- a/src/programs/mdrun/tests/multisim.cpp +++ b/src/programs/mdrun/tests/multisim.cpp @@ -115,5 +115,5 @@ TEST_F(MultiSimTerminationTest, WritesCheckpointAfterMaxhTerminationAndThenResta runMaxhTest(); } -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/programs/mdrun/tests/multisimtest.cpp b/src/programs/mdrun/tests/multisimtest.cpp index add40e2a6d..1ffedbddc1 100644 --- a/src/programs/mdrun/tests/multisimtest.cpp +++ b/src/programs/mdrun/tests/multisimtest.cpp @@ -169,5 +169,5 @@ void MultiSimTest::runMaxhTest() helper.runSecondMdrun(); } -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/programs/mdrun/tests/multisimtest.h b/src/programs/mdrun/tests/multisimtest.h index 5633f834db..96d7f7ea21 100644 --- a/src/programs/mdrun/tests/multisimtest.h +++ b/src/programs/mdrun/tests/multisimtest.h @@ -107,7 +107,7 @@ class MultiSimTest : public ::testing::Test, TestFileManager fileManager_; }; -} // namespace -} // namespace +} // namespace test +} // namespace gmx #endif diff --git a/src/programs/mdrun/tests/pmetest.cpp b/src/programs/mdrun/tests/pmetest.cpp index 287ebe9d2e..4a97813c5e 100644 --- a/src/programs/mdrun/tests/pmetest.cpp +++ b/src/programs/mdrun/tests/pmetest.cpp @@ -249,6 +249,6 @@ TEST_F(PmeTest, ScalesTheBox) runTest(runModes); } -} -} -} +} // namespace +} // namespace test +} // namespace gmx diff --git a/src/programs/mdrun/tests/replicaexchange.cpp b/src/programs/mdrun/tests/replicaexchange.cpp index 370bc7bf95..14a72b00e4 100644 --- a/src/programs/mdrun/tests/replicaexchange.cpp +++ b/src/programs/mdrun/tests/replicaexchange.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) 2013,2014,2015,2016,2018, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -86,5 +86,5 @@ TEST_F(ReplicaExchangeTerminationTest, WritesCheckpointAfterMaxhTerminationAndTh runMaxhTest(); } -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp b/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp index 794b342666..3bd8ec8e75 100644 --- a/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp +++ b/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp @@ -204,6 +204,6 @@ TEST_F(BondedInteractionsTest, TabulatedDihedralWorks) checkMdrun(); } -} // namespace +} // namespace test -} // namespace +} // namespace gmx diff --git a/src/programs/mdrun/tests/termination.cpp b/src/programs/mdrun/tests/termination.cpp index bce57464a1..3b289ef53e 100644 --- a/src/programs/mdrun/tests/termination.cpp +++ b/src/programs/mdrun/tests/termination.cpp @@ -94,5 +94,5 @@ TEST_F(MdrunTerminationTest, CheckpointRestartWorksWithNoAppend) helper.runSecondMdrunWithNoAppend(); } -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/programs/mdrun/tests/terminationhelper.cpp b/src/programs/mdrun/tests/terminationhelper.cpp index 34c6225437..8f2dbc4257 100644 --- a/src/programs/mdrun/tests/terminationhelper.cpp +++ b/src/programs/mdrun/tests/terminationhelper.cpp @@ -93,5 +93,5 @@ void TerminationHelper::runSecondMdrunWithNoAppend() ASSERT_EQ(0, runner_->callMdrun(secondPart)); } -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/programs/mdrun/tests/terminationhelper.h b/src/programs/mdrun/tests/terminationhelper.h index e9c1a8e130..5acde75894 100644 --- a/src/programs/mdrun/tests/terminationhelper.h +++ b/src/programs/mdrun/tests/terminationhelper.h @@ -93,7 +93,7 @@ class TerminationHelper SimulationRunner *runner_; }; -} // namespace -} // namespace +} // namespace test +} // namespace gmx #endif diff --git a/src/programs/mdrun/tests/tpitest.cpp b/src/programs/mdrun/tests/tpitest.cpp index db16d0c93b..e3dc3115f9 100644 --- a/src/programs/mdrun/tests/tpitest.cpp +++ b/src/programs/mdrun/tests/tpitest.cpp @@ -141,6 +141,6 @@ TEST_P(TpiTest, ReproducesOutput) INSTANTIATE_TEST_CASE_P(Simple, TpiTest, ::testing::Values(1993, 2994)); -} -} -} +} // namespace +} // namespace test +} // namespace gmx diff --git a/src/programs/mdrun/tests/trajectorycomparison.cpp b/src/programs/mdrun/tests/trajectorycomparison.cpp index e6905b2067..b11433b05d 100644 --- a/src/programs/mdrun/tests/trajectorycomparison.cpp +++ b/src/programs/mdrun/tests/trajectorycomparison.cpp @@ -209,5 +209,5 @@ void compareTrajectoryFrames(const TrajectoryFrame &reference, compareForces(reference, test, matchSettings, tolerances.forces); } -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/programs/mdrun/tests/trajectorycomparison.h b/src/programs/mdrun/tests/trajectorycomparison.h index cfa018ccc8..be416d5c6d 100644 --- a/src/programs/mdrun/tests/trajectorycomparison.h +++ b/src/programs/mdrun/tests/trajectorycomparison.h @@ -106,7 +106,7 @@ void compareTrajectoryFrames(const TrajectoryFrame &reference, const TrajectoryFrameMatchSettings &matchSettings, const TrajectoryTolerances &tolerances); -} // namespace -} // namespace +} // namespace test +} // namespace gmx #endif diff --git a/src/programs/mdrun/tests/trajectoryreader.cpp b/src/programs/mdrun/tests/trajectoryreader.cpp index cf43cf89ee..cf282fdf40 100644 --- a/src/programs/mdrun/tests/trajectoryreader.cpp +++ b/src/programs/mdrun/tests/trajectoryreader.cpp @@ -156,5 +156,5 @@ TrajectoryFrameReader::frame() return TrajectoryFrame(*trxframeGuard_.get()); } -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/programs/mdrun/tests/trajectoryreader.h b/src/programs/mdrun/tests/trajectoryreader.h index 9de1f9e47e..d5fbdac103 100644 --- a/src/programs/mdrun/tests/trajectoryreader.h +++ b/src/programs/mdrun/tests/trajectoryreader.h @@ -136,7 +136,7 @@ class TrajectoryFrameReader //! Convenience smart pointer typedef typedef std::unique_ptr TrajectoryFrameReaderPtr; -} // namespace -} // namespace +} // namespace test +} // namespace gmx #endif diff --git a/src/testutils/testasserts.cpp b/src/testutils/testasserts.cpp index c7990838d4..f68d401ffe 100644 --- a/src/testutils/testasserts.cpp +++ b/src/testutils/testasserts.cpp @@ -79,7 +79,7 @@ GMX_TEST_OPTIONS(ExceptionOptions, options) "exceptions")); } //! \endcond -} +} // namespace namespace internal { diff --git a/src/testutils/testasserts.h b/src/testutils/testasserts.h index 8e6b2e4d97..2267c3ed97 100644 --- a/src/testutils/testasserts.h +++ b/src/testutils/testasserts.h @@ -79,7 +79,7 @@ namespace internal */ void processExpectedException(const std::exception &ex); //! \endcond -} +} // namespace internal //! \libinternal \addtogroup module_testutils //! \{ diff --git a/src/testutils/testmatchers.cpp b/src/testutils/testmatchers.cpp index 67a79975d5..2644274c22 100644 --- a/src/testutils/testmatchers.cpp +++ b/src/testutils/testmatchers.cpp @@ -172,5 +172,5 @@ RVecEq(const FloatingPointTolerance &tolerance) return testing::MakeMatcher(new RVecMatcher(tolerance)); } -} // namespace -} // namespace +} // namespace test +} // namespace gmx diff --git a/src/testutils/testmatchers.h b/src/testutils/testmatchers.h index c78d3e960c..0394d2b914 100644 --- a/src/testutils/testmatchers.h +++ b/src/testutils/testmatchers.h @@ -102,7 +102,7 @@ RealEq(const FloatingPointTolerance &tolerance); testing::Matcher < std::tuple < RVec, RVec>> RVecEq(const FloatingPointTolerance &tolerance); -} // namespace -} // namespace +} // namespace test +} // namespace gmx #endif -- 2.22.0