Automatic Linting for Fortran/C/C++ (#151)

* C/CPP Linting with Clang tool * More linting work * Further linting with Fortran. * Some formatting for examples. * Force check examples to fail * Fix check examples flag.
william-dawson · May 27, 2020 · 9fb50d7 · 9fb50d7
1 parent 422aead
commit 9fb50d7
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diff --git a/Examples/ComplexMatrix/main.f90 b/Examples/ComplexMatrix/main.f90
@@ -41,9 +41,9 @@ PROGRAM ComplexMatrix
 
   !! Process The Input
   !! Process the input parameters.
-  DO counter=1,command_argument_count(),2
-     CALL get_command_argument(counter,argument)
-     CALL get_command_argument(counter+1,argument_value)
+  DO counter=1,COMMAND_ARGUMENT_COUNT(),2
+     CALL GET_COMMAND_ARGUMENT(counter,argument)
+     CALL GET_COMMAND_ARGUMENT(counter+1,argument_value)
      SELECT CASE(argument)
      CASE('--input_file')
         input_file = argument_value
@@ -66,12 +66,12 @@ PROGRAM ComplexMatrix
 
   CALL WriteHeader("Command Line Parameters")
   CALL EnterSubLog
-  CALL WriteElement(key="input_file", value=input_file)
-  CALL WriteElement(key="exponential_file", value=exponential_file)
-  CALL WriteElement(key="process_rows", value=process_rows)
-  CALL WriteElement(key="process_columns", value=process_columns)
-  CALL WriteElement(key="process_slices", value=process_slices)
-  CALL WriteElement(key="threshold", value=threshold)
+  CALL WriteElement(key="input_file", VALUE=input_file)
+  CALL WriteElement(key="exponential_file", VALUE=exponential_file)
+  CALL WriteElement(key="process_rows", VALUE=process_rows)
+  CALL WriteElement(key="process_columns", VALUE=process_columns)
+  CALL WriteElement(key="process_slices", VALUE=process_slices)
+  CALL WriteElement(key="threshold", VALUE=threshold)
   CALL ExitSubLog
 
   !! Construct The Hermitian Matrix

diff --git a/Examples/GraphTheory/main.f90 b/Examples/GraphTheory/main.f90
@@ -47,9 +47,9 @@ PROGRAM GraphTheory
   CALL MPI_Comm_size(MPI_COMM_WORLD, total_processors, ierr)
 
   !! Process the input parameters.
-  DO counter=1,command_argument_count(),2
-     CALL get_command_argument(counter,argument)
-     CALL get_command_argument(counter+1,argument_value)
+  DO counter=1,COMMAND_ARGUMENT_COUNT(),2
+     CALL GET_COMMAND_ARGUMENT(counter,argument)
+     CALL GET_COMMAND_ARGUMENT(counter+1,argument_value)
      SELECT CASE(argument)
      CASE('--output_file')
         output_file = argument_value

diff --git a/Examples/HydrogenAtom/main.f90 b/Examples/HydrogenAtom/main.f90
@@ -51,9 +51,9 @@ PROGRAM HydrogenAtom
   CALL MPI_Comm_size(MPI_COMM_WORLD, total_processors, ierr)
 
   !! Process the input parameters.
-  DO counter=1,command_argument_count(),2
-     CALL get_command_argument(counter,argument)
-     CALL get_command_argument(counter+1,argument_value)
+  DO counter=1,COMMAND_ARGUMENT_COUNT(),2
+     CALL GET_COMMAND_ARGUMENT(counter,argument)
+     CALL GET_COMMAND_ARGUMENT(counter+1,argument_value)
      SELECT CASE(argument)
      CASE('--convergence_threshold')
         READ(argument_value,*) convergence_threshold

diff --git a/Examples/MatrixMaps/main.f90 b/Examples/MatrixMaps/main.f90
@@ -26,9 +26,9 @@ PROGRAM MatrixMapsProgram
   CALL MPI_Comm_rank(MPI_COMM_WORLD,rank, ierr)
 
   !! Process the input parameters.
-  DO counter=1,command_argument_count(),2
-     CALL get_command_argument(counter,argument)
-     CALL get_command_argument(counter+1,argument_value)
+  DO counter=1,COMMAND_ARGUMENT_COUNT(),2
+     CALL GET_COMMAND_ARGUMENT(counter,argument)
+     CALL GET_COMMAND_ARGUMENT(counter+1,argument_value)
      SELECT CASE(argument)
      CASE('--input_matrix')
         input_matrix = argument_value
@@ -45,9 +45,9 @@ PROGRAM MatrixMapsProgram
   !! Print out parameters.
   CALL WriteHeader("Command Line Parameters")
   CALL EnterSubLog
-  CALL WriteElement(key="input_matrix", value=input_matrix)
-  CALL WriteElement(key="output_matrix", value=output_matrix)
-  CALL WriteElement(key="process_slices", value=process_slices)
+  CALL WriteElement(key="input_matrix", VALUE=input_matrix)
+  CALL WriteElement(key="output_matrix", VALUE=output_matrix)
+  CALL WriteElement(key="process_slices", VALUE=process_slices)
   CALL ExitSubLog
 
   !! Read in the matrices from file.

diff --git a/Examples/OverlapMatrix/main.f90 b/Examples/OverlapMatrix/main.f90
@@ -47,9 +47,9 @@ PROGRAM OverlapExample
   CALL MPI_Comm_rank(MPI_COMM_WORLD,rank, ierr)
 
   !! Process the input parameters.
-  DO counter=1,command_argument_count(),2
-     CALL get_command_argument(counter,argument)
-     CALL get_command_argument(counter+1,argument_value)
+  DO counter=1,COMMAND_ARGUMENT_COUNT(),2
+     CALL GET_COMMAND_ARGUMENT(counter,argument)
+     CALL GET_COMMAND_ARGUMENT(counter+1,argument_value)
      SELECT CASE(argument)
      CASE('--basis_functions')
         READ(argument_value,*) basis_functions

diff --git a/Examples/PremadeMatrix/main.f90 b/Examples/PremadeMatrix/main.f90
@@ -41,9 +41,9 @@ PROGRAM PremadeMatrixProgram
   CALL MPI_Comm_rank(MPI_COMM_WORLD,rank, ierr)
 
   !! Process the input parameters.
-  DO counter=1,command_argument_count(),2
-     CALL get_command_argument(counter,argument)
-     CALL get_command_argument(counter+1,argument_value)
+  DO counter=1,COMMAND_ARGUMENT_COUNT(),2
+     CALL GET_COMMAND_ARGUMENT(counter,argument)
+     CALL GET_COMMAND_ARGUMENT(counter+1,argument_value)
      SELECT CASE(argument)
      CASE('--hamiltonian')
         hamiltonian_file = argument_value
@@ -74,16 +74,16 @@ PROGRAM PremadeMatrixProgram
 
   CALL WriteHeader("Command Line Parameters")
   CALL EnterSubLog
-  CALL WriteElement(key="hamiltonian", value=hamiltonian_file)
-  CALL WriteElement(key="overlap", value=overlap_file)
-  CALL WriteElement(key="density", value=density_file_out)
-  CALL WriteElement(key="process_rows", value=process_rows)
-  CALL WriteElement(key="process_columns", value=process_columns)
-  CALL WriteElement(key="process_slices", value=process_slices)
-  CALL WriteElement(key="number_of_electrons", value=number_of_electrons)
-  CALL WriteElement(key="threshold", value=threshold)
-  CALL WriteElement(key="converge_overlap", value=converge_overlap)
-  CALL WriteElement(key="converge_density", value=converge_density)
+  CALL WriteElement(key="hamiltonian", VALUE=hamiltonian_file)
+  CALL WriteElement(key="overlap", VALUE=overlap_file)
+  CALL WriteElement(key="density", VALUE=density_file_out)
+  CALL WriteElement(key="process_rows", VALUE=process_rows)
+  CALL WriteElement(key="process_columns", VALUE=process_columns)
+  CALL WriteElement(key="process_slices", VALUE=process_slices)
+  CALL WriteElement(key="number_of_electrons", VALUE=number_of_electrons)
+  CALL WriteElement(key="threshold", VALUE=threshold)
+  CALL WriteElement(key="converge_overlap", VALUE=converge_overlap)
+  CALL WriteElement(key="converge_density", VALUE=converge_density)
   CALL ExitSubLog
 
   !! Read in the matrices from file.

diff --git a/Source/C/DensityMatrixSolvers_c.h b/Source/C/DensityMatrixSolvers_c.h
@@ -18,9 +18,8 @@ void HPCP_wrp(const int *ih_Hamiltonian, const int *ih_InverseSquareRoot,
               const double *chemical_potential_out,
               const int *ih_solver_parameters);
 void ScaleAndFold_wrp(const int *ih_Hamiltonian,
-                      const int *ih_InverseSquareRoot,
-                      const int *nel, int *ih_Density,
-                      const double *homo, const double *lumo,
+                      const int *ih_InverseSquareRoot, const int *nel,
+                      int *ih_Density, const double *homo, const double *lumo,
                       const double *energy_value_out,
                       const int *ih_solver_parameters);
 void EnergyDensityMatrix_wrp(const int *ih_Hamiltonian, const int *ih_Density,

diff --git a/Source/C/EigenBounds_c.h b/Source/C/EigenBounds_c.h
@@ -5,6 +5,6 @@ void GershgorinBounds_wrp(const int *ih_Hamiltonian, double *max_value,
                           double *min_value);
 void PowerBounds_wrp(const int *ih_Hamiltonian, double *max_value,
                      const int *ih_solver_parameters);
-void DistributedEigenDecomposition_wrp(const int *ih_this, int* ih_eigenvectors,
+void DistributedEigenDecomposition_wrp(const int *ih_this, int *ih_eigenvectors,
                                        const int *ih_solver_parameters);
 #endif
diff --git a/Source/C/PSMatrix_c.h b/Source/C/PSMatrix_c.h
@@ -44,8 +44,8 @@ void GetMatrixSlice_wrp(const int *ih_this, int *ih_submatrix, int *start_row,
 void TransposeMatrix_ps_wrp(const int *ih_matA, int *ih_transmat);
 void ConjugateMatrix_ps_wrp(int *ih_matA);
 void ConjugateMatrix_ps_wrp(int *ih_matA);
-void ResizeMatrix_ps_wrp(int *ih_this, const int* new_size);
-void GetMatrixProcessGrid_ps_wrp(const int* ih_this, int* ih_grid);
+void ResizeMatrix_ps_wrp(int *ih_this, const int *new_size);
+void GetMatrixProcessGrid_ps_wrp(const int *ih_this, int *ih_grid);
 
 void DotMatrix_psr_wrp(const int *ih_matA, const int *ih_matB, double *product);
 void DotMatrix_psc_wrp(const int *ih_matA, const int *ih_matB,

diff --git a/Source/CPlusPlus/MatrixConversion.cc b/Source/CPlusPlus/MatrixConversion.cc
@@ -10,8 +10,8 @@ extern "C" {
 ////////////////////////////////////////////////////////////////////////////////
 namespace NTPoly {
 //////////////////////////////////////////////////////////////////////////////
-void MatrixConversion::SnapMatrixToSparsityPattern(Matrix_ps& mata,
-	                                               const Matrix_ps& matb) {
+void MatrixConversion::SnapMatrixToSparsityPattern(Matrix_ps &mata,
+                                                   const Matrix_ps &matb) {
   SnapMatrixToSparsityPattern_wrp(mata.ih_this, matb.ih_this);
 }
 } // namespace NTPoly
diff --git a/Source/CPlusPlus/MatrixConversion.h b/Source/CPlusPlus/MatrixConversion.h
@@ -11,12 +11,12 @@ class MatrixConversion {
   //! Some codes use a fixed sparsity pattern for a matrix instead of filtering
   //! small values. Using this routine, the matrix is filled to have the same
   //! pattern as the second matrix argument. Zeros of the sparsity pattern are
-  //! left in, whereas values outside the sparsity are removed. This can 
+  //! left in, whereas values outside the sparsity are removed. This can
   //! faciliate conversion between formats.
   //! \param mata the matrix to modify.
   //! \param matb the matrix which defines the sparsity pattern.
-  static void SnapMatrixToSparsityPattern(Matrix_ps& mata, 
-                                          const Matrix_ps& matb);
+  static void SnapMatrixToSparsityPattern(Matrix_ps &mata,
+                                          const Matrix_ps &matb);
 };
 } // namespace NTPoly
 #endif
diff --git a/Source/CPlusPlus/PSMatrix.cc b/Source/CPlusPlus/PSMatrix.cc
@@ -1,5 +1,5 @@
-#include "PMatrixMemoryPool.h"
 #include "PSMatrix.h"
+#include "PMatrixMemoryPool.h"
 #include "Permutation.h"
 #include "ProcessGrid.h"
 #include "TripletList.h"

diff --git a/Source/CPlusPlus/SMatrix.cc b/Source/CPlusPlus/SMatrix.cc
@@ -1,5 +1,5 @@
-#include "MatrixMemoryPool.h"
 #include "SMatrix.h"
+#include "MatrixMemoryPool.h"
 #include "TripletList.h"
 using std::complex;
 using std::string;

diff --git a/Source/CPlusPlus/SolverBase.cc b/Source/CPlusPlus/SolverBase.cc
@@ -1,5 +1,5 @@
-#include "PSMatrix.h"
 #include "SolverBase.h"
+#include "PSMatrix.h"
 #include "SolverParameters.h"
 
 ////////////////////////////////////////////////////////////////////////////////

diff --git a/Source/CPlusPlus/SolverParameters.cc b/Source/CPlusPlus/SolverParameters.cc
@@ -1,5 +1,5 @@
-#include "Permutation.h"
 #include "SolverParameters.h"
+#include "Permutation.h"
 
 ////////////////////////////////////////////////////////////////////////////////
 extern "C" {

diff --git a/Source/CPlusPlus/TripletList.cc b/Source/CPlusPlus/TripletList.cc
@@ -1,5 +1,5 @@
-#include "Triplet.h"
 #include "TripletList.h"
+#include "Triplet.h"
 
 #include <complex>
 

diff --git a/Source/Fortran/ChebyshevSolversModule.F90 b/Source/Fortran/ChebyshevSolversModule.F90
@@ -32,19 +32,19 @@ MODULE ChebyshevSolversModule
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   INTERFACE ConstructPolynomial
      MODULE PROCEDURE ConstructPolynomial_cheby
-  END INTERFACE
+  END INTERFACE ConstructPolynomial
   INTERFACE DestructPolynomial
      MODULE PROCEDURE DestructPolynomial_cheby
-  END INTERFACE
+  END INTERFACE DestructPolynomial
   INTERFACE SetCoefficient
      MODULE PROCEDURE SetCoefficient_cheby
-  END INTERFACE
+  END INTERFACE SetCoefficient
   INTERFACE Compute
      MODULE PROCEDURE Compute_cheby
-  END INTERFACE
+  END INTERFACE Compute
   INTERFACE FactorizedCompute
      MODULE PROCEDURE FactorizedCompute_cheby
-  END INTERFACE
+  END INTERFACE FactorizedCompute
 CONTAINS!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   !> Construct a Chebyshev polynomial object.
   PURE SUBROUTINE ConstructPolynomial_cheby(this, degree)
@@ -114,8 +114,8 @@ SUBROUTINE Compute_cheby(InputMat, OutputMat, poly, solver_parameters_in)
     IF (solver_parameters%be_verbose) THEN
        CALL WriteHeader("Chebyshev Solver")
        CALL EnterSubLog
-       CALL WriteElement(key="Method", value="Standard")
-       CALL WriteElement(key="Degree", value=degree-1)
+       CALL WriteElement(key="Method", VALUE="Standard")
+       CALL WriteElement(key="Degree", VALUE=degree-1)
        CALL PrintParameters(solver_parameters)
     END IF
 
@@ -225,8 +225,8 @@ SUBROUTINE FactorizedCompute_cheby(InputMat, OutputMat, poly, &
     IF (solver_parameters%be_verbose) THEN
        CALL WriteHeader("Chebyshev Solver")
        CALL EnterSubLog
-       CALL WriteElement(key="Method", value="Recursive")
-       CALL WriteElement(key="Degree", value=degree-1)
+       CALL WriteElement(key="Method", VALUE="Recursive")
+       CALL WriteElement(key="Degree", VALUE=degree-1)
        CALL PrintParameters(solver_parameters)
     END IF