From: Artem Zhmurov <zhmurov@gmail.com>
Date: Mon, 26 Apr 2021 07:24:27 +0000 (+0000)
Subject: Clang-11 fixes for applied forces
X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=f86919ebfba5ee507799f918c709a66576cedf03;p=alexxy%2Fgromacs.git

Clang-11 fixes for applied forces
---

diff --git a/src/gromacs/applied_forces/awh/awh.cpp b/src/gromacs/applied_forces/awh/awh.cpp
index 6f2a8db5ea..de3ebea891 100644
--- a/src/gromacs/applied_forces/awh/awh.cpp
+++ b/src/gromacs/applied_forces/awh/awh.cpp
@@ -116,14 +116,10 @@ struct BiasCoupledToSystem
  */
 static bool anyDimUsesPull(const AwhBiasParams& awhBiasParams)
 {
-    for (const auto& awhDimParam : awhBiasParams.dimParams())
-    {
-        if (awhDimParam.coordinateProvider() == AwhCoordinateProviderType::Pull)
-        {
-            return true;
-        }
-    }
-    return false;
+    return std::any_of(
+            awhBiasParams.dimParams().begin(), awhBiasParams.dimParams().end(), [](const auto& awhDimParam) {
+                return awhDimParam.coordinateProvider() == AwhCoordinateProviderType::Pull;
+            });
 }
 
 /*! \brief Checks whether any dimension uses pulling as a coordinate provider.
@@ -133,14 +129,9 @@ static bool anyDimUsesPull(const AwhBiasParams& awhBiasParams)
  */
 static bool anyDimUsesPull(const AwhParams& awhParams)
 {
-    for (const auto& awhBiasParam : awhParams.awhBiasParams())
-    {
-        if (anyDimUsesPull(awhBiasParam))
-        {
-            return true;
-        }
-    }
-    return false;
+    return std::any_of(awhParams.awhBiasParams().begin(),
+                       awhParams.awhBiasParams().end(),
+                       [](const auto& awhBiasParam) { return anyDimUsesPull(awhBiasParam); });
 }
 
 /*! \brief Checks whether any dimension uses pulling as a coordinate provider.
@@ -150,14 +141,9 @@ static bool anyDimUsesPull(const AwhParams& awhParams)
  */
 static bool anyDimUsesPull(const ArrayRef<BiasCoupledToSystem> biasCoupledToSystem)
 {
-    for (const auto& biasCts : biasCoupledToSystem)
-    {
-        if (!biasCts.pullCoordIndex_.empty())
-        {
-            return true;
-        }
-    }
-    return false;
+    return std::any_of(biasCoupledToSystem.begin(), biasCoupledToSystem.end(), [](const auto& biasCts) {
+        return !biasCts.pullCoordIndex_.empty();
+    });
 }
 
 BiasCoupledToSystem::BiasCoupledToSystem(Bias bias, const std::vector<int>& pullCoordIndex) :
@@ -506,7 +492,7 @@ void Awh::writeToEnergyFrame(int64_t step, t_enxframe* frame) const
 
     /* Get the total number of energy subblocks that AWH needs */
     int numSubblocks = 0;
-    for (auto& biasCoupledToSystem : biasCoupledToSystem_)
+    for (const auto& biasCoupledToSystem : biasCoupledToSystem_)
     {
         numSubblocks += biasCoupledToSystem.bias_.numEnergySubblocksToWrite();
     }
@@ -524,7 +510,7 @@ void Awh::writeToEnergyFrame(int64_t step, t_enxframe* frame) const
 
     /* Transfer AWH data blocks to energy sub blocks */
     int energySubblockCount = 0;
-    for (auto& biasCoupledToSystem : biasCoupledToSystem_)
+    for (const auto& biasCoupledToSystem : biasCoupledToSystem_)
     {
         energySubblockCount += biasCoupledToSystem.bias_.writeToEnergySubblocks(
                 &(awhEnergyBlock->sub[energySubblockCount]));
@@ -554,14 +540,9 @@ bool Awh::needForeignEnergyDifferences(const int64_t step) const
     /* Check whether the bias(es) that has/have a FEP lambda dimension should sample coordinates
      * this step. Since the biases may have different sampleCoordStep it is necessary to check
      * this combination. */
-    for (const auto& biasCts : biasCoupledToSystem_)
-    {
-        if (biasCts.bias_.hasFepLambdaDimension() && biasCts.bias_.isSampleCoordStep(step))
-        {
-            return true;
-        }
-    }
-    return false;
+    return std::any_of(biasCoupledToSystem_.begin(), biasCoupledToSystem_.end(), [step](const auto& biasCts) {
+        return biasCts.bias_.hasFepLambdaDimension() && biasCts.bias_.isSampleCoordStep(step);
+    });
 }
 
 std::unique_ptr<Awh> prepareAwhModule(FILE*                 fplog,
diff --git a/src/gromacs/applied_forces/awh/awh.h b/src/gromacs/applied_forces/awh/awh.h
index 7529537394..d44f295eb2 100644
--- a/src/gromacs/applied_forces/awh/awh.h
+++ b/src/gromacs/applied_forces/awh/awh.h
@@ -275,7 +275,6 @@ private:
      */
     bool isOutputStep(int64_t step) const;
 
-private:
     std::vector<BiasCoupledToSystem> biasCoupledToSystem_; /**< AWH biases and definitions of their coupling to the system. */
     const int64_t    seed_;   /**< Random seed for MC jumping with umbrella type bias potential. */
     const int        nstout_; /**< Interval in steps for writing to energy file. */
diff --git a/src/gromacs/applied_forces/awh/biasstate.cpp b/src/gromacs/applied_forces/awh/biasstate.cpp
index 636f724c8c..55442b10fd 100644
--- a/src/gromacs/applied_forces/awh/biasstate.cpp
+++ b/src/gromacs/applied_forces/awh/biasstate.cpp
@@ -314,7 +314,7 @@ void BiasState::calcConvolvedPmf(ArrayRef<const DimParams> dimParams,
     {
         double           freeEnergyWeights = 0;
         const GridPoint& point             = grid.point(m);
-        for (auto& neighbor : point.neighbor)
+        for (const auto& neighbor : point.neighbor)
         {
             /* Do not convolve the bias along a lambda axis - only use the pmf from the current point */
             if (!pointsHaveDifferentLambda(grid, m, neighbor))
@@ -411,7 +411,7 @@ int BiasState::warnForHistogramAnomalies(const BiasGrid& grid, int biasIndex, do
     /* Sum up the histograms and get their normalization */
     double sumVisits  = 0;
     double sumWeights = 0;
-    for (auto& pointState : points_)
+    for (const auto& pointState : points_)
     {
         if (pointState.inTargetRegion())
         {
@@ -677,7 +677,7 @@ void BiasState::doSkippedUpdatesInNeighborhood(const BiasParams& params, const B
 
     /* For each neighbor point of the center point, refresh its state by adding the results of all past, skipped updates. */
     const std::vector<int>& neighbors = grid.point(coordState_.gridpointIndex()).neighbor;
-    for (auto& neighbor : neighbors)
+    for (const auto& neighbor : neighbors)
     {
         bool didUpdate = points_[neighbor].performPreviouslySkippedUpdates(
                 params, histogramSize_.numUpdates(), weightHistScaling, logPmfsumScaling);
diff --git a/src/gromacs/applied_forces/awh/biaswriter.h b/src/gromacs/applied_forces/awh/biaswriter.h
index 420a26ff63..20451d9215 100644
--- a/src/gromacs/applied_forces/awh/biaswriter.h
+++ b/src/gromacs/applied_forces/awh/biaswriter.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -193,7 +193,6 @@ private:
      */
     void prepareBiasOutput(const Bias& bias);
 
-private:
     std::vector<AwhEnergyBlock>       block_; /**< The data blocks */
     std::map<AwhOutputEntryType, int> outputTypeToBlock_; /**< Start block index for each variable, -1 when variable should not be written */
 };
diff --git a/src/gromacs/applied_forces/awh/correlationgrid.h b/src/gromacs/applied_forces/awh/correlationgrid.h
index a1c4338d03..eaaed1c22b 100644
--- a/src/gromacs/applied_forces/awh/correlationgrid.h
+++ b/src/gromacs/applied_forces/awh/correlationgrid.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -150,7 +150,6 @@ public:
      */
     int getNumBlocks() const;
 
-public:
     const double             dtSample;           /**< Time in between samples. */
     const BlockLengthMeasure blockLengthMeasure; /**< The measure for the block length. */
 private:
diff --git a/src/gromacs/applied_forces/awh/histogramsize.cpp b/src/gromacs/applied_forces/awh/histogramsize.cpp
index 15d1ace4ba..c42e913f79 100644
--- a/src/gromacs/applied_forces/awh/histogramsize.cpp
+++ b/src/gromacs/applied_forces/awh/histogramsize.cpp
@@ -155,7 +155,7 @@ bool histogramIsEquilibrated(ArrayRef<const PointState> pointStates)
     /* Get the total weight of the total weight histogram; needed for normalization. */
     double totalWeight     = 0;
     int    numTargetPoints = 0;
-    for (auto& pointState : pointStates)
+    for (const auto& pointState : pointStates)
     {
         if (!pointState.inTargetRegion())
         {
@@ -177,7 +177,7 @@ bool histogramIsEquilibrated(ArrayRef<const PointState> pointStates)
     /* Sum up weight of points that do or don't pass the check. */
     double equilibratedWeight    = 0;
     double notEquilibratedWeight = 0;
-    for (auto& pointState : pointStates)
+    for (const auto& pointState : pointStates)
     {
         double targetWeight  = pointState.target();
         double sampledWeight = pointState.weightSumTot() * inverseTotalWeight;
diff --git a/src/gromacs/applied_forces/awh/tests/.clang-tidy b/src/gromacs/applied_forces/awh/tests/.clang-tidy
new file mode 100644
index 0000000000..0adf51e3ee
--- /dev/null
+++ b/src/gromacs/applied_forces/awh/tests/.clang-tidy
@@ -0,0 +1,91 @@
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+#         -cppcoreguidelines-non-private-member-variables-in-classes,
+#         -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+#         -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+#         -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+#         -cppcoreguidelines-avoid-magic-numbers,
+#         -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+#         -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+#         -cppcoreguidelines-narrowing-conversions,
+#         -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+#         -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+#         -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+#         -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+#         -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks:  clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+         bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+         -readability-inconsistent-declaration-parameter-name,
+         -readability-function-size,-readability-else-after-return,
+         modernize-use-nullptr,modernize-use-emplace,
+         modernize-make-unique,modernize-make-shared,
+         modernize-avoid-bind,
+         modernize-use-override,
+         modernize-redundant-void-arg,modernize-use-bool-literals,
+         cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+         -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+         -cppcoreguidelines-avoid-goto,
+         google-*,-google-build-using-namespace,-google-explicit-constructor,
+         -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+         -cppcoreguidelines-non-private-member-variables-in-classes,
+         -misc-non-private-member-variables-in-classes,
+         -readability-isolate-declaration,
+         -cppcoreguidelines-avoid-c-arrays,
+         -cppcoreguidelines-avoid-magic-numbers,
+         -readability-magic-numbers,
+         -cppcoreguidelines-macro-usage,
+         -cppcoreguidelines-narrowing-conversions,
+         -bugprone-narrowing-conversions,
+         -google-readability-avoid-underscore-in-googletest-name,
+         -cppcoreguidelines-init-variables,
+         -misc-no-recursion,
+         -cppcoreguidelines-avoid-non-const-global-variables,
+         -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+  - key:           cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+    value:         1
+  - key:           modernize-make-unique.IncludeStyle
+    value:         google
+  - key:           modernize-make-shared.IncludeStyle
+    value:         google
+  - key:           readability-implicit-bool-conversion.AllowIntegerConditions
+    value:         1
+  - key:           readability-implicit-bool-conversion.AllowPointerConditions
+    value:         1
+  - key:           bugprone-dangling-handle.HandleClasses
+    value:         std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+  - key:           performance-unnecessary-copy-initialization.AllowedTypes
+    value:         shared_ptr
+  - key:           performance-unnecessary-value-param.AllowedTypes
+    value:         shared_ptr
diff --git a/src/gromacs/applied_forces/awh/tests/bias.cpp b/src/gromacs/applied_forces/awh/tests/bias.cpp
index e1015c5b6d..880ae18f90 100644
--- a/src/gromacs/applied_forces/awh/tests/bias.cpp
+++ b/src/gromacs/applied_forces/awh/tests/bias.cpp
@@ -188,7 +188,7 @@ TEST_P(BiasTest, ForcesBiasPmf)
     }
 
     std::vector<double> pointBias, logPmfsum;
-    for (auto& point : bias.state().points())
+    for (const auto& point : bias.state().points())
     {
         pointBias.push_back(point.bias());
         logPmfsum.push_back(point.logPmfSum());
diff --git a/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp b/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp
index 787b88f960..5e1e016185 100644
--- a/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp
+++ b/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp
@@ -200,7 +200,7 @@ TEST_P(BiasFepLambdaStateTest, ForcesBiasPmf)
     }
 
     std::vector<double> pointBias, logPmfsum;
-    for (auto& point : bias.state().points())
+    for (const auto& point : bias.state().points())
     {
         pointBias.push_back(point.bias());
         logPmfsum.push_back(point.logPmfSum());
diff --git a/src/gromacs/applied_forces/awh/tests/biasgrid.cpp b/src/gromacs/applied_forces/awh/tests/biasgrid.cpp
index d008eac9ec..3d4d2565bc 100644
--- a/src/gromacs/applied_forces/awh/tests/biasgrid.cpp
+++ b/src/gromacs/applied_forces/awh/tests/biasgrid.cpp
@@ -149,7 +149,7 @@ TEST(biasGridTest, neighborhood)
             haveCorrectNumNeighbors = false;
         }
 
-        for (auto& j : point.neighbor)
+        for (const auto& j : point.neighbor)
         {
             if (j >= 0 && j < numPoints)
             {
@@ -187,7 +187,7 @@ TEST(biasGridTest, neighborhood)
         }
 
         /* Clear the marked points in the checking grid */
-        for (auto& neighbor : point.neighbor)
+        for (const auto& neighbor : point.neighbor)
         {
             if (neighbor >= 0 && neighbor < numPoints)
             {
diff --git a/src/gromacs/applied_forces/densityfitting/densityfitting.cpp b/src/gromacs/applied_forces/densityfitting/densityfitting.cpp
index af6af7678a..b5d10ea80d 100644
--- a/src/gromacs/applied_forces/densityfitting/densityfitting.cpp
+++ b/src/gromacs/applied_forces/densityfitting/densityfitting.cpp
@@ -198,7 +198,7 @@ public:
     void setSimulationTimeStep(double timeStep) { simulationTimeStep_ = timeStep; }
 
     //! Return the simulation time step
-    double simulationTimeStep() { return simulationTimeStep_; }
+    double simulationTimeStep() const { return simulationTimeStep_; }
 
 private:
     //! The reference density to fit to
diff --git a/src/gromacs/applied_forces/densityfitting/densityfittingparameters.h b/src/gromacs/applied_forces/densityfitting/densityfittingparameters.h
index 0e123ef5bc..f6dc43ae95 100644
--- a/src/gromacs/applied_forces/densityfitting/densityfittingparameters.h
+++ b/src/gromacs/applied_forces/densityfitting/densityfittingparameters.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -83,9 +83,9 @@ struct DensityFittingParameters
     //! The time constant for the adaptive force scaling in ps
     real adaptiveForceScalingTimeConstant_ = 4;
     //! Translation of the structure, so that the coordinates that are fitted are x+translation
-    std::string translationString_ = "";
+    std::string translationString_;
     //! Linear transformation of the structure, so that the coordinates that are fitted are Matrix * x
-    std::string transformationMatrixString_ = "";
+    std::string transformationMatrixString_;
 };
 
 /*!\brief Check if two structs holding density fitting parameters are equal.
diff --git a/src/gromacs/applied_forces/densityfitting/tests/.clang-tidy b/src/gromacs/applied_forces/densityfitting/tests/.clang-tidy
new file mode 100644
index 0000000000..0adf51e3ee
--- /dev/null
+++ b/src/gromacs/applied_forces/densityfitting/tests/.clang-tidy
@@ -0,0 +1,91 @@
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+#         -cppcoreguidelines-non-private-member-variables-in-classes,
+#         -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+#         -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+#         -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+#         -cppcoreguidelines-avoid-magic-numbers,
+#         -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+#         -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+#         -cppcoreguidelines-narrowing-conversions,
+#         -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+#         -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+#         -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+#         -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+#         -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks:  clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+         bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+         -readability-inconsistent-declaration-parameter-name,
+         -readability-function-size,-readability-else-after-return,
+         modernize-use-nullptr,modernize-use-emplace,
+         modernize-make-unique,modernize-make-shared,
+         modernize-avoid-bind,
+         modernize-use-override,
+         modernize-redundant-void-arg,modernize-use-bool-literals,
+         cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+         -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+         -cppcoreguidelines-avoid-goto,
+         google-*,-google-build-using-namespace,-google-explicit-constructor,
+         -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+         -cppcoreguidelines-non-private-member-variables-in-classes,
+         -misc-non-private-member-variables-in-classes,
+         -readability-isolate-declaration,
+         -cppcoreguidelines-avoid-c-arrays,
+         -cppcoreguidelines-avoid-magic-numbers,
+         -readability-magic-numbers,
+         -cppcoreguidelines-macro-usage,
+         -cppcoreguidelines-narrowing-conversions,
+         -bugprone-narrowing-conversions,
+         -google-readability-avoid-underscore-in-googletest-name,
+         -cppcoreguidelines-init-variables,
+         -misc-no-recursion,
+         -cppcoreguidelines-avoid-non-const-global-variables,
+         -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+  - key:           cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+    value:         1
+  - key:           modernize-make-unique.IncludeStyle
+    value:         google
+  - key:           modernize-make-shared.IncludeStyle
+    value:         google
+  - key:           readability-implicit-bool-conversion.AllowIntegerConditions
+    value:         1
+  - key:           readability-implicit-bool-conversion.AllowPointerConditions
+    value:         1
+  - key:           bugprone-dangling-handle.HandleClasses
+    value:         std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+  - key:           performance-unnecessary-copy-initialization.AllowedTypes
+    value:         shared_ptr
+  - key:           performance-unnecessary-value-param.AllowedTypes
+    value:         shared_ptr
diff --git a/src/gromacs/applied_forces/tests/.clang-tidy b/src/gromacs/applied_forces/tests/.clang-tidy
new file mode 100644
index 0000000000..0adf51e3ee
--- /dev/null
+++ b/src/gromacs/applied_forces/tests/.clang-tidy
@@ -0,0 +1,91 @@
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+#         -cppcoreguidelines-non-private-member-variables-in-classes,
+#         -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+#         -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+#         -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+#         -cppcoreguidelines-avoid-magic-numbers,
+#         -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+#         -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+#         -cppcoreguidelines-narrowing-conversions,
+#         -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+#         -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+#         -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+#         -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+#         -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks:  clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+         bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+         -readability-inconsistent-declaration-parameter-name,
+         -readability-function-size,-readability-else-after-return,
+         modernize-use-nullptr,modernize-use-emplace,
+         modernize-make-unique,modernize-make-shared,
+         modernize-avoid-bind,
+         modernize-use-override,
+         modernize-redundant-void-arg,modernize-use-bool-literals,
+         cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+         -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+         -cppcoreguidelines-avoid-goto,
+         google-*,-google-build-using-namespace,-google-explicit-constructor,
+         -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+         -cppcoreguidelines-non-private-member-variables-in-classes,
+         -misc-non-private-member-variables-in-classes,
+         -readability-isolate-declaration,
+         -cppcoreguidelines-avoid-c-arrays,
+         -cppcoreguidelines-avoid-magic-numbers,
+         -readability-magic-numbers,
+         -cppcoreguidelines-macro-usage,
+         -cppcoreguidelines-narrowing-conversions,
+         -bugprone-narrowing-conversions,
+         -google-readability-avoid-underscore-in-googletest-name,
+         -cppcoreguidelines-init-variables,
+         -misc-no-recursion,
+         -cppcoreguidelines-avoid-non-const-global-variables,
+         -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+  - key:           cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+    value:         1
+  - key:           modernize-make-unique.IncludeStyle
+    value:         google
+  - key:           modernize-make-shared.IncludeStyle
+    value:         google
+  - key:           readability-implicit-bool-conversion.AllowIntegerConditions
+    value:         1
+  - key:           readability-implicit-bool-conversion.AllowPointerConditions
+    value:         1
+  - key:           bugprone-dangling-handle.HandleClasses
+    value:         std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+  - key:           performance-unnecessary-copy-initialization.AllowedTypes
+    value:         shared_ptr
+  - key:           performance-unnecessary-value-param.AllowedTypes
+    value:         shared_ptr