Clangd cleanup

.clang-tidy

@@ -3,6 +3,9 @@
 # altera-struct-pack-align: does not affect the code for non FPGA targets -- gets interesting for OpenCL kernels
 # boost-use-ranges: we do not want to use boost at all, to not increase our dependencies even more!!!
 # bugprone-suspicious-include: flags more or less only false positives
+# fuchsia-default-arguments-calls: there is a second check that disallows default arguments in function definitions, which is more important to us than this check (this for example triggers for simple std::vector constructors)
+# fuchsia-overloaded-operator: we actually WANT to overload operators, so this check is not useful for us
+# fuchsia-trailing-return: we actually WANT to use trailing return types, very useful for template functions, so this check is not useful for us
 
 # Checks to be absolutely enabled:
 # cert-env33-c: ::system is not available on all platforms, and we do not want to use it anyway
@@ -14,6 +17,9 @@
 # cppcoreguidelines-pro-type-union-access: should be possible to avoid this warning for Vector3D, but needs a rework of the code base
 # cppcoreguidelines-pro-type-member-init: needs a rework of the code base, but should be possible to fix it for all classes
 # cppcoreguidelines-owning-memory: needs a rework of the code base, but should be possible to fix it for all classes
+# fuchsia-statically-constructed-objects: needs a rework of the global const maps like atomMassMap, atomNumberMap, hubbardDerivMap3ob, etc. to avoid this warning
+# fuchsia-virtual-inheritance: needs a huge rework of the engine code base, but should be possible to fix it for all classes
+# fuchsia-multiple-inheritance: needs a huge rework of the engine code base, but should be possible to fix it for all classes
 ---
 Checks:          
   '
@@ -26,6 +32,7 @@ Checks:
   concurrency*,
   cppcoreguidelines*,
   darwin*,
+  fuchsia*,
   -cppcoreguidelines-owning-memory,
   -cppcoreguidelines-pro-type-member-init,
   -cppcoreguidelines-pro-type-union-access,
@@ -35,9 +42,16 @@ Checks:
   -bugprone-easily-swappable-parameters,
   -cert-env33-c,
   -cert-err58-cpp,
+  -fuchsia-statically-constructed-objects,
+  -fuchsia-virtual-inheritance,
+  -fuchsia-multiple-inheritance,
   -altera-struct-pack-align,
   -altera-unroll-loops,
-  -bugprone-suspicious-include
+  -boost-use-ranges,
+  -bugprone-suspicious-include,
+  -fuchsia-default-arguments-calls,
+  -fuchsia-overloaded-operator,
+  -fuchsia-trailing-return,
   '
 WarningsAsErrors: ''
 HeaderFileExtensions:
@@ -91,14 +105,6 @@ CheckOptions:
 ...
 
 ### TO BE INCLUDED IN THE FUTURE
-  # fuchsia-default-arguments-calls,
-  # fuchsia-default-arguments-declarations,
-  # fuchsia-header-anon-namespaces,
-  # fuchsia-multiple-inheritance,
-  # fuchsia-overloaded-operator,
-  # fuchsia-statically-constructed-objects,
-  # fuchsia-trailing-return,
-  # fuchsia-virtual-inheritance,
   # google-build-explicit-make-pair,
   # google-build-namespaces,
   # google-build-using-namespace,

apps/capabilities.cpp

@@ -62,7 +62,7 @@ namespace
         cli::JsonWriter       &json,
         const std::string_view name,
         const std::string_view type,
-        const std::string_view unit = ""
+        const std::string_view unit
     )
     {
         json.beginObject(name);
@@ -71,6 +71,15 @@ namespace
             json.value("unit", unit);
     }
 
+    void beginParameter(
+        cli::JsonWriter       &json,
+        const std::string_view name,
+        const std::string_view type
+    )
+    {
+        beginParameter(json, name, type, "");
+    }
+
     void writeBuildCapabilities(cli::JsonWriter &json)
     {
         json.beginObject("build");

apps/validation.cpp

@@ -423,6 +423,11 @@ namespace
     }
 }   // namespace
 
+cli::ValidationResult cli::validateInputFile(std::string_view inputFile)
+{
+    return validateInputFile(inputFile, ValidationScope::INSTALLED);
+}
+
 cli::ValidationResult cli::validateInputFile(
     const std::string_view inputFile,
     const ValidationScope  scope

apps/validation.hpp

@@ -58,7 +58,11 @@ namespace cli
 
     [[nodiscard]] ValidationResult validateInputFile(
         std::string_view inputFile,
-        ValidationScope  scope = ValidationScope::INSTALLED
+        ValidationScope  scope
+    );
+
+    [[nodiscard]] ValidationResult validateInputFile(
+        std::string_view inputFile
     );
 
     void writeValidationJson(

benchmarks/.clang-tidy

@@ -1,3 +1,7 @@
 InheritParentConfig: true
-Checks: >
-  -cppcoreguidelines-avoid-magic-numbers
+Checks:
+  '
+  -cppcoreguidelines-avoid-magic-numbers,
+  -fuchsia-statically-constructed-objects,
+  -cert-err58-cpp
+  '

benchmarks/src/box/benchmarkBox.cpp

@@ -157,7 +157,6 @@ namespace
         }
     }
 
-    // NOLINTBEGIN(cert-err58-cpp)
     BENCHMARK(BM_OrthorhombicShiftVector);
     BENCHMARK(BM_TriclinicShiftVector);
     BENCHMARK(BM_OrthorhombicWrapPosition);
@@ -166,6 +165,5 @@ namespace
     BENCHMARK(BM_TriclinicToOrthoSpace);
     BENCHMARK(BM_TriclinicToSimSpace);
     BENCHMARK(BM_TriclinicTensorRoundTrip);
-    // NOLINTEND(cert-err58-cpp)
 
 }   // namespace

benchmarks/src/math/benchmarkLinearAlgebra.cpp

@@ -184,7 +184,6 @@ namespace
         }
     }
 
-    // NOLINTBEGIN(cert-err58-cpp)
     BENCHMARK(BM_VectorArithmetic);
     BENCHMARK(BM_DotProduct);
     BENCHMARK(BM_CrossProduct);
@@ -195,5 +194,4 @@ namespace
     BENCHMARK(BM_MatrixProduct);
     BENCHMARK(BM_MatrixTranspose);
     BENCHMARK(BM_MatrixDeterminant);
-    // NOLINTEND(cert-err58-cpp)
 }   // namespace

benchmarks/src/potential/benchmarkPairPotentials.cpp

@@ -101,7 +101,6 @@ namespace
         runCoulombBenchmark(state, potential);
     }
 
-    // NOLINTBEGIN(cert-err58-cpp)
     BENCHMARK(BM_LennardJones)
         ->ArgName("distance_milliangstrom")
         ->Arg(1500)
@@ -132,5 +131,4 @@ namespace
         ->Arg(1500)
         ->Arg(3000)
         ->Arg(6000);
-    // NOLINTEND(cert-err58-cpp)
 }   // namespace

benchmarks/src/simulationBox/benchmarkKinetics.cpp

@@ -99,7 +99,6 @@ namespace
         setItemsProcessed(state, simBox);
     }
 
-    // NOLINTBEGIN(cert-err58-cpp)
     BENCHMARK(BM_Temperature)
         ->ArgName("cells_per_side")
         ->Arg(5)
@@ -116,5 +115,4 @@ namespace
         ->Arg(5)
         ->Arg(8)
         ->Arg(12);
-    // NOLINTEND(cert-err58-cpp)
 }   // namespace

changes/developer/internal.clangd.md

@@ -1,2 +1,3 @@
 - fix a lot of more small clang-tidy warnings (larger one will be handled in separate PRs)
 - address all cppcoreguidline clang-tidy checks and all darwin checks
+- add most important fuchsia clang-tidy warnings (especially no default arguments)

include/QM/external/externalQMRunner.hpp

@@ -51,9 +51,9 @@ namespace QM
     class ExternalQMRunner : public QMRunner
     {
        protected:
-        std::string                     _scriptPath  = SCRIPT_PATH_;
-        const static inline std::string _singularity = SINGULARITY_;
-        const static inline std::string _staticBuild = STATIC_BUILD_;
+        std::string            _scriptPath  = SCRIPT_PATH_;
+        constexpr static auto *_singularity = SINGULARITY_;
+        constexpr static auto *_staticBuild = STATIC_BUILD_;
 
         [[nodiscard]] std::string resolveScriptPath(
             std::string_view script
@@ -91,8 +91,8 @@ namespace QM
          *******************************/
 
         [[nodiscard]] const std::string &getScriptPath() const;
-        [[nodiscard]] const std::string &getSingularity() const;
-        [[nodiscard]] const std::string &getStaticBuild() const;
+        [[nodiscard]] std::string        getSingularity() const;
+        [[nodiscard]] std::string        getStaticBuild() const;
 
         void setScriptPath(const std::string_view &scriptPath);
     };

include/config/atomMassMap.hpp

@@ -85,4 +85,4 @@ namespace constants
 
 }   // namespace constants
 
-#endif   // _ATOM_MASS_MAP_HPP_
+#endif   // _ATOM_MASS_MAP_HPP_

include/config/atomNumberMap.hpp

@@ -70,4 +70,4 @@ namespace constants
 
 }   // namespace constants
 
-#endif   // _ATOM_NUMBER_MAP_HPP_
+#endif   // _ATOM_NUMBER_MAP_HPP_

include/exceptions/exceptions.hpp

@@ -81,8 +81,9 @@ namespace customException
        public:
         explicit CustomException(
             const std::string_view message,
-            std::optional<size_t>  lineNumber = std::nullopt
+            std::optional<size_t>  lineNumber
         );
+        explicit CustomException(const std::string_view message);
 
         void colorfulOutput(const Color::Code, const std::string_view) const;
         void setLineNumber(const size_t lineNumber) noexcept;

include/input/inputFileParser/QMInputParser.hpp

@@ -42,10 +42,8 @@ namespace input
         bool _resolveBuiltInSlakosPath;
 
        public:
-        explicit QMInputParser(
-            engine::Engine &,
-            bool resolveBuiltInSlakosPath = true
-        );
+        explicit QMInputParser(engine::Engine &, bool resolveBuiltInSlakosPath);
+        explicit QMInputParser(engine::Engine &);
 
         void parseQMMethod(const std::vector<std::string> &, const size_t);
         void parseQMScript(const std::vector<std::string> &, const size_t);

include/input/inputFileParser/filesInputParser.hpp

@@ -42,10 +42,8 @@ namespace input
         bool _validateFilePaths;
 
        public:
-        explicit FilesInputParser(
-            engine::Engine &,
-            bool validateFilePaths = true
-        );
+        explicit FilesInputParser(engine::Engine &, bool validateFilePaths);
+        explicit FilesInputParser(engine::Engine &);
 
         void parseIntraNonBondedFile(
             const std::vector<std::string> &,

include/input/inputFileReader.hpp

@@ -76,9 +76,10 @@ namespace input
         explicit InputFileReader(
             const std::string_view &,
             engine::Engine &,
-            bool validateFilePaths        = true,
-            bool resolveBuiltInSlakosPath = true
+            bool validateFilePaths,
+            bool resolveBuiltInSlakosPath
         );
+        explicit InputFileReader(const std::string_view &, engine::Engine &);
 
         void read();
         void addKeywords();

include/settings/qmSettings.hpp

@@ -180,8 +180,9 @@ namespace settings
         static void setSlakosType(const std::string_view &slakos);
         static void setSlakosType(
             const SlakosType slakos,
-            bool             resolveBuiltInPath = true
+            bool             resolveBuiltInPath
         );
+        static void setSlakosType(const SlakosType slakos);
         static void setSlakosPath(const std::string_view &path);
 
         static void setUseDispersionCorrection(const bool use);

src/QM/external/externalQMRunner.cpp

@@ -279,22 +279,16 @@ const std::string &ExternalQMRunner::getScriptPath() const
 /**
  * @brief getter for the singularity path
  *
- * @return const std::string&
+ * @return std::string
  */
-const std::string &ExternalQMRunner::getSingularity() const
-{
-    return _singularity;
-}
+std::string ExternalQMRunner::getSingularity() const { return _singularity; }
 
 /**
  * @brief getter for the static build path
  *
- * @return const std::string&
+ * @return std::string
  */
-const std::string &ExternalQMRunner::getStaticBuild() const
-{
-    return _staticBuild;
-}
+std::string ExternalQMRunner::getStaticBuild() const { return _staticBuild; }
 
 /**
  * @brief setter for the script path

src/exceptions/exceptions.cpp

@@ -39,6 +39,16 @@ CustomException::CustomException(
 {
 }
 
+/**
+ * @brief Construct a new Custom Exception:: Custom Exception object
+ *
+ * @param message
+ */
+CustomException::CustomException(const std::string_view message)
+    : CustomException(message, std::nullopt)
+{
+}
+
 /**
  * @brief Adds a source line if the exception has no line yet.
  *

src/input/inputFileParser/QMInputParser.cpp

@@ -44,6 +44,20 @@ using namespace engine;
 using namespace references;
 using namespace constants;
 
+/**
+ * @brief Construct a new QMInputParser:: QMInputParser object
+ *
+ * @details following keywords are added to the _keywordFuncMap,
+ * _keywordRequiredMap and _keywordCountMap: 1) qm_prog <string> 2) qm_script
+ * <string>
+ *
+ * @param engine
+ */
+QMInputParser::QMInputParser(engine::Engine &engine)
+    : QMInputParser(engine, true)
+{
+}
+
 /**
  * @brief Construct a new QMInputParser:: QMInputParser object
  *

src/input/inputFileParser/filesInputParser.cpp

@@ -37,6 +37,24 @@ using namespace customException;
 using namespace settings;
 using namespace utilities;
 
+/**
+ * @brief Construct a new Input File Parser Non Coulomb Type:: Input File Parser
+ * Non Coulomb Type object
+ *
+ * @details following keywords are added to the _keywordFuncMap,
+ * _keywordRequiredMap and _keywordCountMap: 1) intra-nonBonded_file <string> 2)
+ * topology_file <string> 3) parameter_file <string> 4) start_file <string>
+ * (required) 5) rpmd_start_file <string> 6) moldescriptor_file <string>
+ * 7) guff_path <string> (deprecated) 8) guff_file <string>
+ * 9) mshake_file <string> 10) dftb_file <string> 11) turbomole_file <string>
+ *
+ * @param engine
+ */
+FilesInputParser::FilesInputParser(Engine &engine)
+    : FilesInputParser(engine, true)
+{
+}
+
 /**
  * @brief Construct a new Input File Parser Non Coulomb Type:: Input File Parser
  * Non Coulomb Type object

src/input/inputFileReader.cpp

@@ -59,6 +59,24 @@ using namespace utilities;
 using namespace customException;
 using std::make_unique;
 
+/**
+ * @brief Construct a new Input File Reader:: Input File Reader object
+ *
+ * @details adds all parsers to the _parsers vector and calls addKeywords() to
+ * add all keywords to the _keywordFuncMap, _keywordRequiredMap and
+ * _keywordCountMap
+ *
+ * @param fileName
+ * @param engine
+ */
+InputFileReader::InputFileReader(
+    const std::string_view &fileName,
+    engine::Engine         &engine
+)
+    : InputFileReader(fileName, engine, true, true)
+{
+}
+
 /**
  * @brief Construct a new Input File Reader:: Input File Reader object
  *