Added explicit statements

cppcheck warnings

src/analysis/AnalysisBase.h

@@ -56,7 +56,7 @@ protected:
   AnalysisBase* my_input_data;
 public:
   static void registerKeywords( Keywords& keys );
-  AnalysisBase(const ActionOptions&);
+  explicit AnalysisBase(const ActionOptions&);
 /// These are required because we inherit from both ActionAtomistic and ActionWithArguments
   void lockRequests();
   void unlockRequests();

src/analysis/EuclideanDissimilarityMatrix.cpp

@@ -44,7 +44,7 @@ private:
   Matrix<double> dissimilarities;
 public:
   static void registerKeywords( Keywords& keys );
-  EuclideanDissimilarityMatrix( const ActionOptions& ao );
+  explicit EuclideanDissimilarityMatrix( const ActionOptions& ao );
 /// Do the analysis
   void performAnalysis();
 /// This ensures that classes that use this data know that dissimilarities were set

src/analysis/FarthestPointSampling.cpp

@@ -40,7 +40,7 @@ private:
   unsigned seed;
 public:
   static void registerKeywords( Keywords& keys );
-  FarthestPointSampling( const ActionOptions& ao );
+  explicit FarthestPointSampling( const ActionOptions& ao );
   void selectLandmarks();
 };
 

src/analysis/LandmarkSelectionBase.h

@@ -45,7 +45,7 @@ protected:
   void voronoiAnalysis( const std::vector<unsigned>& myindices, std::vector<double>& lweights, std::vector<unsigned>& assignments ) const ;
 public:
   static void registerKeywords( Keywords& keys );
-  LandmarkSelectionBase( const ActionOptions& ao );
+  explicit LandmarkSelectionBase( const ActionOptions& ao );
 /// Return the number of data points
   unsigned getNumberOfDataPoints() const ;
 /// Return the index of the data point in the base class

src/analysis/LandmarkStaged.cpp

@@ -43,7 +43,7 @@ private:
   double gamma;
 public:
   static void registerKeywords( Keywords& keys );
-  LandmarkStaged( const ActionOptions& ao );
+  explicit LandmarkStaged( const ActionOptions& ao );
   void selectLandmarks();
 };
 

src/analysis/OutputColvarFile.cpp

@@ -52,7 +52,7 @@ private:
   std::vector<std::string> req_vals;
 public:
   static void registerKeywords( Keywords& keys );
-  OutputColvarFile( const ActionOptions& );
+  explicit OutputColvarFile( const ActionOptions& );
   void performTask( const unsigned&, const unsigned&, MultiValue& ) const { plumed_error(); }
   void performAnalysis();
 };

src/analysis/PrintDissimilarityMatrix.cpp

@@ -42,7 +42,7 @@ private:
   std::string fname;
 public:
   static void registerKeywords( Keywords& keys );
-  PrintDissimilarityMatrix( const ActionOptions& ao );
+  explicit PrintDissimilarityMatrix( const ActionOptions& ao );
   void performAnalysis();
   void performTask( const unsigned&, const unsigned&, MultiValue& ) const { plumed_error(); }
 };

src/analysis/ReadDissimilarityMatrix.cpp

@@ -51,7 +51,7 @@ private:
   std::vector<double> weights;
 public:
   static void registerKeywords( Keywords& keys );
-  ReadDissimilarityMatrix( const ActionOptions& ao );
+  explicit ReadDissimilarityMatrix( const ActionOptions& ao );
   unsigned getNumberOfDataPoints() const ;
 // Return the index of the data point in the base class
   unsigned getDataPointIndexInBase( const unsigned& idata ) const ;

src/analysis/ReselectLandmarks.cpp

@@ -42,7 +42,7 @@ private:
   LandmarkSelectionBase* mylandmarks;
 public:
   static void registerKeywords( Keywords& keys );
-  ReselectLandmarks( const ActionOptions& ao );
+  explicit ReselectLandmarks( const ActionOptions& ao );
   void selectLandmarks();
 };
 

src/analysis/SelectRandomFrames.cpp

@@ -40,7 +40,7 @@ private:
   unsigned seed;
 public:
   static void registerKeywords( Keywords& keys );
-  SelectRandomFrames( const ActionOptions& ao );
+  explicit SelectRandomFrames( const ActionOptions& ao );
   void selectLandmarks();
 };
 

src/analysis/WhamHistogram.cpp

@@ -37,7 +37,7 @@ This can be used to output the a histogram using the weighted histogram techniqu
 class WhamHistogram : public ActionShortcut {
 public:
   static void registerKeywords( Keywords& keys );
-  WhamHistogram( const ActionOptions& );
+  explicit WhamHistogram( const ActionOptions& );
 };
 
 PLUMED_REGISTER_ACTION(WhamHistogram,"WHAM_HISTOGRAM")

src/analysis/WhamWeights.cpp

@@ -37,7 +37,7 @@ This can be used to output the data that has been stored in an Analysis object.
 class WhamWeights : public ActionShortcut {
 public:
   static void registerKeywords( Keywords& keys );
-  WhamWeights( const ActionOptions& );
+  explicit WhamWeights( const ActionOptions& );
 };
 
 PLUMED_REGISTER_ACTION(WhamWeights,"WHAM_WEIGHTS")

src/dimred/DimensionalityReductionBase.h

@@ -43,7 +43,7 @@ protected:
   DimensionalityReductionBase* dimredbase;
 public:
   static void registerKeywords( Keywords& keys );
-  DimensionalityReductionBase( const ActionOptions& );
+  explicit DimensionalityReductionBase( const ActionOptions& );
 /// Get the ith data point (this returns the projection)
   virtual void getProjection( const unsigned& idata, std::vector<double>& point, double& weight );
 /// Actually perform the analysis

src/dimred/OutputPCAProjections.cpp

@@ -50,7 +50,7 @@ private:
   std::string filename;
 public:
   static void registerKeywords( Keywords& keys );
-  OutputPCAProjection( const ActionOptions& );
+  explicit OutputPCAProjection( const ActionOptions& );
   void performTask( const unsigned&, const unsigned&, MultiValue& ) const { plumed_error(); }
   void performAnalysis();
 };

src/dimred/ProjectNonLandmarkPoints.cpp

@@ -53,7 +53,7 @@ private:
   void generateProjection( const unsigned& idat, std::vector<double>& point );
 public:
   static void registerKeywords( Keywords& keys );
-  ProjectNonLandmarkPoints( const ActionOptions& ao );
+  explicit ProjectNonLandmarkPoints( const ActionOptions& ao );
 /// Get a reference configuration (this returns the projection)
   analysis::DataCollectionObject& getStoredData( const unsigned& idat, const bool& calcdist );
 /// Overwrite getArguments so we get arguments from underlying class

src/dimred/SketchMap.cpp

@@ -37,7 +37,7 @@ This can be used to output the data that has been stored in an Analysis object.
 class SketchMap : public ActionShortcut {
 public:
   static void registerKeywords( Keywords& keys );
-  SketchMap( const ActionOptions& );
+  explicit SketchMap( const ActionOptions& );
 };
 
 PLUMED_REGISTER_ACTION(SketchMap,"SKETCH_MAP")

src/dimred/SketchMapBase.h

@@ -49,7 +49,7 @@ protected:
   double mixparam;
 public:
   static void registerKeywords( Keywords& keys );
-  SketchMapBase( const ActionOptions& );
+  explicit SketchMapBase( const ActionOptions& );
 /// This starts the process of calculating the projections
   void calculateProjections( const Matrix<double>&, Matrix<double>& );
 /// This finishes the process of calculating the prjections

src/dimred/SketchMapConjGrad.cpp

@@ -40,7 +40,7 @@ private:
   double cgtol;
 public:
   static void registerKeywords( Keywords& keys );
-  SketchMapConjGrad( const ActionOptions& ao );
+  explicit SketchMapConjGrad( const ActionOptions& ao );
   void minimise( Matrix<double>& );
 };
 

src/dimred/SketchMapPointwise.cpp

@@ -43,7 +43,7 @@ private:
   std::vector<unsigned> npoints, nfgrid;
 public:
   static void registerKeywords( Keywords& keys );
-  SketchMapPointwise( const ActionOptions& ao );
+  explicit SketchMapPointwise( const ActionOptions& ao );
   void minimise( Matrix<double>& );
 };
 

src/dimred/SketchMapRead.cpp

@@ -53,7 +53,7 @@ private:
   std::vector<std::unique_ptr<ReferenceConfiguration> > myframes;
 public:
   static void registerKeywords( Keywords& keys );
-  SketchMapRead( const ActionOptions& ao );
+  explicit SketchMapRead( const ActionOptions& ao );
   void minimise( Matrix<double>& );
   analysis::DataCollectionObject& getStoredData( const unsigned& idata, const bool& calcdist );
   unsigned getNumberOfDataPoints() const ;