Rearranging core library

prisms-center · Dec 16, 2024 · 051c885 · 051c885
1 parent c03da3f
commit 051c885
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Showing 169 changed files with 209 additions and 3,427 deletions.
diff --git a/.clang-tidy b/.clang-tidy
@@ -9,20 +9,15 @@ Checks: >
   cppcoreguidelines-*,
   -cppcoreguidelines-avoid-const-or-ref-data-members,
   -cppcoreguidelines-non-private-member-variables-in-classes,
-  -cppcoreguidelines-avoid-magic-numbers,
   hicpp-*,
   misc-*,
   -misc-non-private-member-variables-in-classes,
-  -misc-include-cleaner,
   modernize-*,
   -modernize-use-trailing-return-type,
   mpi-*,
   performance-*,
   readability-*,
   -readability-else-after-return,
-  -readability-static-accessed-through-instance,
-  -readability-avoid-const-params-in-decls,
-  -readability-magic-numbers,
   -readability-identifier-length,
 
 WarningsAsErrors: '*'
diff --git a/applications/CHAC_anisotropy/customPDE.h b/applications/CHAC_anisotropy/customPDE.h
@@ -1,4 +1,4 @@
-#include "matrixFreePDE.h"
+#include <core/matrixFreePDE.h>
 
 using namespace dealii;
 
@@ -29,7 +29,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] Vector<double>    &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;
 

diff --git a/applications/CHAC_anisotropyRegularized/customPDE.h b/applications/CHAC_anisotropyRegularized/customPDE.h
@@ -1,4 +1,4 @@
-#include "matrixFreePDE.h"
+#include <core/matrixFreePDE.h>
 
 using namespace dealii;
 
@@ -29,7 +29,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] Vector<double>    &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;
 

diff --git a/applications/CHAC_performance_test/customPDE.h b/applications/CHAC_performance_test/customPDE.h
@@ -1,4 +1,4 @@
-#include "matrixFreePDE.h"
+#include <core/matrixFreePDE.h>
 
 using namespace dealii;
 
@@ -29,7 +29,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] Vector<double>    &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;
 

diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/customPDE.h b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/customPDE.h
@@ -1,4 +1,4 @@
-#include "matrixFreePDE.h"
+#include <core/matrixFreePDE.h>
 
 using namespace dealii;
 
@@ -29,7 +29,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] Vector<double>    &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;
 

diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1b/customPDE.h b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1b/customPDE.h
@@ -1,4 +1,4 @@
-#include "matrixFreePDE.h"
+#include <core/matrixFreePDE.h>
 
 using namespace dealii;
 
@@ -29,7 +29,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] Vector<double>    &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;
 

diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/customPDE.h b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/customPDE.h
@@ -1,6 +1,6 @@
 #include <deal.II/base/exceptions.h>
 
-#include "matrixFreePDE.h"
+#include <core/matrixFreePDE.h>
 
 using namespace dealii;
 
@@ -31,7 +31,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] Vector<double>    &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;
 

diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark2a/customPDE.h b/applications/CHiMaD_benchmarks/CHiMaD_benchmark2a/customPDE.h
@@ -1,4 +1,4 @@
-#include "matrixFreePDE.h"
+#include <core/matrixFreePDE.h>
 
 using namespace dealii;
 
@@ -29,7 +29,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] Vector<double>    &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;
 

diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark3a/customPDE.h b/applications/CHiMaD_benchmarks/CHiMaD_benchmark3a/customPDE.h
@@ -1,4 +1,4 @@
-#include "matrixFreePDE.h"
+#include <core/matrixFreePDE.h>
 
 using namespace dealii;
 
@@ -29,7 +29,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] Vector<double>    &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;
 

diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark6a/customPDE.h b/applications/CHiMaD_benchmarks/CHiMaD_benchmark6a/customPDE.h
@@ -1,4 +1,4 @@
-#include "matrixFreePDE.h"
+#include <core/matrixFreePDE.h>
 
 using namespace dealii;
 
@@ -29,7 +29,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] Vector<double>    &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;
 

diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/customPDE.h b/applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/customPDE.h
@@ -1,7 +1,7 @@
 #include <deal.II/base/tensor.h>
 #include <deal.II/grid/manifold.h>
 
-#include "matrixFreePDE.h"
+#include <core/matrixFreePDE.h>
 
 using namespace dealii;
 
@@ -32,7 +32,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] Vector<double>    &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;
 

diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark7a/customPDE.h b/applications/CHiMaD_benchmarks/CHiMaD_benchmark7a/customPDE.h
@@ -1,4 +1,4 @@
-#include "matrixFreePDE.h"
+#include <core/matrixFreePDE.h>
 
 using namespace dealii;
 
@@ -29,7 +29,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] Vector<double>    &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;
 

diff --git a/applications/MgNd_precipitate_single_Bppp/customPDE.h b/applications/MgNd_precipitate_single_Bppp/customPDE.h
@@ -1,4 +1,4 @@
-#include "matrixFreePDE.h"
+#include <core/matrixFreePDE.h>
 
 using namespace dealii;
 
@@ -41,7 +41,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] Vector<double>    &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;
 

diff --git a/applications/allenCahn/customPDE.h b/applications/allenCahn/customPDE.h
@@ -1,4 +1,4 @@
-#include "matrixFreePDE.h"
+#include <core/matrixFreePDE.h>
 
 using namespace dealii;
 
@@ -29,7 +29,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] Vector<double>    &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;
 

diff --git a/applications/allenCahn_conserved/customPDE.h b/applications/allenCahn_conserved/customPDE.h
@@ -1,4 +1,4 @@
-#include "matrixFreePDE.h"
+#include <core/matrixFreePDE.h>
 
 using namespace dealii;
 
@@ -29,7 +29,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] Vector<double>    &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;
 

diff --git a/applications/alloySolidification/customPDE.h b/applications/alloySolidification/customPDE.h
@@ -1,4 +1,4 @@
-#include "matrixFreePDE.h"
+#include <core/matrixFreePDE.h>
 
 using namespace dealii;
 
@@ -29,7 +29,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] Vector<double>    &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;
 

diff --git a/applications/alloySolidification_uniform/customPDE.h b/applications/alloySolidification_uniform/customPDE.h
@@ -1,4 +1,4 @@
-#include "matrixFreePDE.h"
+#include <core/matrixFreePDE.h>
 
 using namespace dealii;
 
@@ -29,7 +29,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] Vector<double>    &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;
 

diff --git a/applications/anisotropyFacet/customPDE.h b/applications/anisotropyFacet/customPDE.h
@@ -1,4 +1,4 @@
-#include "matrixFreePDE.h"
+#include <core/matrixFreePDE.h>
 
 using namespace dealii;
 
@@ -29,7 +29,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] Vector<double>    &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;
 

diff --git a/applications/cahnHilliard/customPDE.h b/applications/cahnHilliard/customPDE.h
@@ -1,4 +1,4 @@
-#include "matrixFreePDE.h"
+#include <core/matrixFreePDE.h>
 
 using namespace dealii;
 
@@ -29,7 +29,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] Vector<double>    &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;
 

diff --git a/applications/corrosion/customPDE.h b/applications/corrosion/customPDE.h
@@ -1,4 +1,4 @@
-#include "matrixFreePDE.h"
+#include <core/matrixFreePDE.h>
 
 using namespace dealii;
 
@@ -29,7 +29,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] Vector<double>    &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;
 

diff --git a/applications/corrosion_microgalvanic/customPDE.h b/applications/corrosion_microgalvanic/customPDE.h
@@ -1,6 +1,5 @@
-#include "matrixFreePDE.h"
-
 #include <cmath>
+#include <core/matrixFreePDE.h>
 #include <iostream>
 using namespace std;
 
@@ -31,7 +30,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] dealii::Vector<double> &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;
 

diff --git a/applications/coupledCahnHilliardAllenCahn/customPDE.h b/applications/coupledCahnHilliardAllenCahn/customPDE.h
@@ -1,4 +1,4 @@
-#include "matrixFreePDE.h"
+#include <core/matrixFreePDE.h>
 
 using namespace dealii;
 
@@ -29,7 +29,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] Vector<double>    &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;
 

diff --git a/applications/dendriticSolidification/customPDE.h b/applications/dendriticSolidification/customPDE.h
@@ -1,4 +1,4 @@
-#include "matrixFreePDE.h"
+#include <core/matrixFreePDE.h>
 
 using namespace dealii;
 
@@ -29,7 +29,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] Vector<double>    &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;
 

diff --git a/applications/eshelbyInclusion/customPDE.h b/applications/eshelbyInclusion/customPDE.h
@@ -1,4 +1,4 @@
-#include "matrixFreePDE.h"
+#include <core/matrixFreePDE.h>
 
 using namespace dealii;
 
@@ -29,7 +29,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] Vector<double>    &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;
 

diff --git a/applications/fickianDiffusion/customPDE.h b/applications/fickianDiffusion/customPDE.h
@@ -1,4 +1,4 @@
-#include "matrixFreePDE.h"
+#include <core/matrixFreePDE.h>
 
 using namespace dealii;
 
@@ -29,7 +29,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
                             [[maybe_unused]] Vector<double>    &vector_BC) override;
 
 private:
-#include "typeDefs.h"
+#include <core/typeDefs.h>
 
   const userInputParameters<dim> userInputs;