Changes

Summary

Fixes for boundary triangle orientation with refine (details)
Split trapped edges with refine. Check for all 0 element in distance function. Other small fixes. (details)
Forgot to update refineParam::checkInputs (details)
Updates to refine interface and print requested complexity with MOESS (details)
Use log_eucliean edge length with refine (details)
Try to fix suitesparse metis dilemma. Add more g++ and clang++ copmiler versions. (details)
gnu 11 fixes (details)
Remove -lc++ from clang flags (details)
Add missing include (details)
Upgrade ccache (details)
Fix SANSparallel MMA optimization (details)
Cleanup for last commit (details)
Update ccache path (details)
Compile fixes for clang-10 (details)
Relax tolerance (details)
More compile fixes (details)
Warning fixes (details)
Lots of compile warnings and other fixes (details)
Use default functions in MatrixSymS. Increase execution times for coverage. Warning fixes. (details)
Fix typo (details)
Relax toleranes. Upgrade to AFLR 10.17.5. (details)
Use appropriate architecture for AFLR (details)
Update AFLR3 and use TRANSP_INT_BL for Body Force boundaries (details)
Fix warnings (details)
Update finding and checking AFLR (details)
Relax execution time (details)
Intel is just different... (details)
Relax more tolerances and fix indentations (details)
More intel relaxation (details)
Use system lcov and relax intel tolerance (details)
Use xHost instead of xhost so ccache works with Intel (details)

Commit 0384d47f37496fefbeecf56b7c0037cfd7ed272d by galbramc Fixes for boundary triangle orientation with refine
The file was modified	src/Meshing/refine/MesherInterface_refine.cpp
The file was modified	src/Meshing/refine/refine_grid.cpp
The file was modified	src/Meshing/refine/MesherInterface_refine.h
Commit d0722de24558694e7808f98c88f947ffc66af832 by galbramc Split trapped edges with refine. Check for all 0 element in distance function. Other small fixes.
The file was modified	src/Meshing/refine/MesherInterface_refine.cpp
The file was modified	test/unit/Meshing/EPIC/WriteSolution_PX_btest.cpp
The file was modified	src/Field/Partition/LagrangeElementGroup.cpp
The file was modified	src/Field/DistanceFunction/DistanceFunction.cpp
The file was modified	test/unit/Meshing/AFLR/AFLR3_btest.cpp
Commit 173be378e6d81fd89f677d75baf875bf71408938 by galbramc Forgot to update refineParam::checkInputs
The file was modified	src/Meshing/refine/MesherInterface_refineParams.cpp
Commit b871a29a925dfcad67f9cf04b7f00b7cc9854d2a by galbramc Updates to refine interface and print requested complexity with MOESS
The file was modified	src/Meshing/refine/XField_refine.cpp
The file was modified	src/Adaptation/MOESS/NodalMetrics/NodalMetrics_impl.h
The file was modified	src/Adaptation/MOESS/NLOPT/MOESS_SANS_Optimizer_NLOPT/MOESS_SANS_Optimizer_NLOPT_impl.h
The file was modified	src/Adaptation/MOESS/NLOPT/MOESS_PX_Optimizer_NLOPT/MOESS_PX_Optimizer_NLOPT_impl.h
The file was modified	src/Adaptation/MOESS/NodalMetrics.h
The file was modified	src/Meshing/refine/MesherInterface_refine.cpp
The file was modified	src/Field/DistanceFunction/DistanceFunction.cpp
Commit 14b1266ea75972abfe984a67cbd8fe07f005b33c by galbramc Use log_eucliean edge length with refine
The file was modified	src/Meshing/refine/refine_ptr.h
Commit 57f2b83d7cbaf327ab4eae3dfead24d36f340fc3 by galbramc Try to fix suitesparse metis dilemma. Add more g++ and clang++ copmiler versions.
The file was modified	CMakeInclude/Checks/CheckSUITESPARSE.cmake
The file was modified	CMakeInclude/Finds/FindSUITESPARSE.cmake
The file was modified	CMakeInclude/Compiler.cmake
Commit c2998d7baa671c51a5f3f8b33dc8398b439dc042 by galbramc gnu 11 fixes
The file was modified	src/Discretization/HDG/IntegrandFunctor_HDG_PTC.h
The file was modified	src/Discretization/LIP_HACK/IntegrandBoundaryFrameTrace_Galerkin.h
The file was modified	src/Discretization/LIP_HACK/IntegrandBoundaryTrace_Galerkin_WakeCut_LIP_SRA.h
The file was modified	src/Discretization/VMSDBR2/IntegrandTrace_VMSD_BR2.h
The file was modified	test/sandbox/Solve4D_L2Project_toy.cpp
The file was modified	test/unit/Discretization/Galerkin/JacobianCell_Galerkin_CR_btest.cpp
The file was modified	src/Discretization/HDG/JacobianInteriorTrace_HDG.h
The file was modified	src/Discretization/LIP_HACK/IntegrandFunctor_Galerkin_WakeCut_sansLG.h
The file was modified	src/LinearAlgebra/DenseLinAlg/StaticSize/MatrixS_Mul.h
The file was modified	src/Discretization/LIP_HACK/IntegrandFunctor_Galerkin_WakeCut_LIP.h
The file was modified	src/Discretization/Galerkin/IntegrandInteriorTrace_SIP_Galerkin.h
The file was modified	src/Discretization/DG/IntegrandInteriorTrace_DGBR2.h
The file was modified	src/LinearAlgebra/DenseLinAlg/DynamicSize/MatrixD.h
Commit 91fdcc77723fd44f56783a12ea88016f6a1ba713 by galbramc Remove -lc++ from clang flags
The file was modified	CMakeInclude/CompilerFlags.cmake
Commit 919355da4f8d3f59cb47c160fc0d388cbcd8a705 by galbramc Add missing include
The file was modified	src/Field/NormalField/NormalField_Volume.cpp
Commit bf3917fef5e6f95a40c25ed84ebac4f0b1449fbb by galbramc Upgrade ccache
The file was modified	scripts/jenkins/jenkins_env.sh
Commit 2a6a60718a4e3cb8b6d391caff7d7a4113d27618 by galbramc Fix SANSparallel MMA optimization
The file was modified	src/Adaptation/MOESS/MMA/MOESS_SANS_Optimizer_MMA.h
The file was modified	src/Adaptation/MOESS/ReferenceElementCost.h
The file was modified	src/Adaptation/MOESS/MOESS_SANS_Optimizer_Base/MOESS_SANS_Optimizer_Base_impl.h
The file was modified	src/Adaptation/MOESS/MMA/MOESS_SANS_Optimizer_MMA/MOESS_SANS_Optimizer_MMA_impl.h
The file was modified	src/Adaptation/MOESS/NLOPT/MOESS_SANS_Optimizer_NLOPT/MOESS_SANS_Optimizer_NLOPT_impl.h
The file was modified	src/Adaptation/MOESS/NLOPT/MOESS_PX_Optimizer_NLOPT/MOESS_PX_Optimizer_NLOPT_impl.h
The file was modified	test/unit/Adaptation/MOESS/MMA/MOESS_SANS_Optimizer_MMA_btest.cpp
The file was modified	src/LinearAlgebra/DenseLinAlg/StaticSize/MatrixS_Mul.h
Commit 5b05a6de25ca0111eb0b12e15cd2f4f405737754 by galbramc Cleanup for last commit
The file was modified	src/Adaptation/MOESS/MMA/MOESS_SANS_Optimizer_MMA/MOESS_SANS_Optimizer_MMA_impl.h
Commit 57311883dc2893273cdaf25d63bfa4e0ce8f07d8 by galbramc Update ccache path
The file was modified	scripts/jenkins/jenkins_env.sh
Commit 3e4fbab2b1424d239670c6df41fefa0589f20305 by galbramc Compile fixes for clang-10
The file was modified	src/PanelMethod/PiecewiseConstSourcePanel_FlatPlate3D.h
The file was modified	src/LinearAlgebra/SparseLinAlg/PETSc/PETScSolver_CRS_double.cpp
Commit 786a750a6dae3b447cc0bf4f27467474752ecce2 by galbramc Relax tolerance
The file was modified	test/unit/Adaptation/MOESS/MMA/MOESS_SANS_Optimizer_MMA_btest.cpp
Commit 3426ec6f52f7b6d79ff8f83f7e90ff96c98a18f9 by galbramc More compile fixes
The file was modified	src/LinearAlgebra/SparseLinAlg/PETSc/PETScSolver_impl.h
The file was modified	src/Quadrature/Quadrature_Simplex_StroudConical.cpp
Commit 46542a6d85871ef06ee2a8cf7c7732b50c857155 by galbramc Warning fixes
The file was modified	test/unit/pde/NS/PDENavierStokes2D_btest.cpp
The file was modified	test/unit/pde/NS/PDERANSSA3D_btest.cpp
The file was modified	test/unit/pde/NS/PDENavierStokes3D_btest.cpp
The file was modified	test/unit/pde/NS/PDEEulermitAVDiffusion3D_btest.cpp
The file was modified	test/unit/pde/NS/BCRANSSA3D_mitState_btest.cpp
The file was modified	test/unit/pde/NS/PDERANSSA2D_btest.cpp
The file was modified	src/Meshing/avro/XField_avro.h
The file was modified	src/Meshing/avro/XField_avro_impl.h
Commit a4ccbd8a6e2903ce26485134777ebed79e7b265e by galbramc Lots of compile warnings and other fixes
The file was modified	src/Field/XFieldVolume_Instantiate_3D.cpp
The file was modified	CMakeInclude/CompilerFlags.cmake
The file was modified	scripts/jenkins/SANS_Weekly.sh
The file was modified	test/system/CodeConsistency/PDEmitAVSensor3D_Consistency_RANSSA_btest.cpp
The file was modified	test/system/CodeConsistency/PDEmitAVSensor3D_Consistency_btest.cpp
The file was modified	scripts/jenkins/SANS_Nightly.sh
The file was modified	src/Field/XFieldArea_Instantiate_2D.cpp
The file was modified	test/sandbox/Adapt2D_VMSDBR2_NavierStokes_Blottner_Mach20_AV_HTC_toy.cpp
The file was modified	test/unit/pde/ArtificialViscosity/PDEmitAVSensor3D_btest.cpp
The file was modified	src/Field/XFieldLine_Instantiate_1D.cpp
The file was modified	test/unit/SolutionTrek/Continuation/PseudoTime_btest.cpp
The file was modified	scripts/jenkins/SANS_Commit.sh
The file was modified	test/unit/SolutionTrek/Continuation/ImplicitResidualSmoothing_btest.cpp
Commit 50efe80a17876b34e5cb5802300e7fdb1ad08fa3 by galbramc Use default functions in MatrixSymS. Increase execution times for coverage. Warning fixes.
The file was modified	test/unit/Discretization/VMSDBR2/AlgebraicEquationSet_VMSDBR2_Triangle_SA_btest.cpp
The file was modified	test/unit/UnitGrids/XField2D_GilesPierceNozzle_HACK_btest.cpp
The file was modified	test/unit/Discretization/Block/CMakeLists.txt
The file was modified	test/unit/Discretization/GloballyConstrained/CMakeLists.txt
The file was modified	test/unit/Discretization/Galerkin/CMakeLists.txt
The file was modified	src/pde/TCNE/TCNEChemistryModels.h
The file was modified	test/unit/LinearAlgebra/DenseLinAlg/MatrixSymS_InverseLDLT_btest.cpp
The file was modified	src/LinearAlgebra/DenseLinAlg/StaticSize/MatrixSymS.h
The file was modified	test/unit/Discretization/VMSDBR2/AlgebraicEquationSet_VMSDBR2_Triangle_AD_btest.cpp
Commit d189b68e188ffc943b7973810fb336052a19215c by galbramc Fix typo
The file was modified	test/unit/Discretization/GloballyConstrained/CMakeLists.txt
Commit 7d743ee0e87675068986efd00f28a60c4ff643eb by galbramc Relax toleranes. Upgrade to AFLR 10.17.5.
The file was modified	scripts/jenkins/jenkins_env.sh
The file was modified	src/Meshing/EGTess/EGTessModel_aflr4.cpp
The file was modified	CMakeInclude/CompilerFlags.cmake
The file was modified	test/unit/LinearAlgebra/DenseLinAlg/MatrixSymS_InverseLDLT_btest.cpp
Commit a583fa587eb08512210ef26b88cd444e20746b7f by galbramc Use appropriate architecture for AFLR
The file was modified	CMakeInclude/Finds/FindAFLR.cmake
Commit 38b070e79b11f3d01dc3dd16e2fadfd93cbc72c1 by galbramc Update AFLR3 and use TRANSP_INT_BL for Body Force boundaries
The file was modified	src/Meshing/AFLR/AFLR3.cpp
The file was modified	src/UserInterfaces/BodyForceSolver_impl.h
Commit bc31e454145a0f578ba099347214bf718770111a by galbramc Fix warnings
The file was modified	test/unit/pde/AnalyticFunction/ScalarFunction3D_btest.cpp
The file was modified	test/unit/pde/PorousMedia/PermeabilityModel2D_btest.cpp
The file was modified	test/unit/pde/ShallowWater/ShallowWaterSolution2D_btest.cpp
The file was modified	test/unit/pde/AnalyticFunction/ScalarFunction2D_btest.cpp
The file was modified	test/unit/pde/AdvectionDiffusion/BCAdvectionDiffusion2D_btest.cpp
Commit 7609782460b4bb4ff99ed25f15ba25a4c2462f7c by galbramc Update finding and checking AFLR
The file was modified	CMakeInclude/Checks/aflr_test.cxx
The file was modified	CMakeInclude/Finds/FindAFLR.cmake
Commit 5785e4330b5c0f7ac3df3bf776968254bd20ed9f by galbramc Relax execution time
The file was modified	test/unit/Discretization/VMSDBR2/CMakeLists.txt
Commit ae581790dd33cc9297b75ee01ca0c043c0581a3e by galbramc Intel is just different...
The file was modified	test/unit/Adaptation/MOESS/MMA/MOESS_SANS_Optimizer_MMA_btest.cpp
Commit e72d27806141d6f0cbb1bd0d5b247743ce1f35b5 by galbramc Relax more tolerances and fix indentations
The file was modified	test/unit/Field/Element/ElementSpacetime_Pentatope_btest.cpp
The file was modified	test/unit/Discretization/HDG/IntegrandInteriorTrace_HDG_NS_btest.cpp
The file was modified	test/unit/Discretization/Block/CMakeLists.txt
Commit a5df871b3e442a7363447f3c3740b4e9cddda828 by galbramc More intel relaxation
The file was modified	test/unit/Field/Element/ElementSpacetime_Pentatope_btest.cpp
Commit ec03449aaac6e4ffe331d93334d127bf6d683f72 by galbramc Use system lcov and relax intel tolerance
The file was modified	scripts/jenkins/jenkins_env.sh
The file was modified	test/system/Asymptotic/ErrorEstimateOrder_2D_CG_Nodal_Triangle_AD_btest.cpp
Commit 0e4f3e1692205d0f65c4c8c917f59e29f524beb1 by galbramc Use xHost instead of xhost so ccache works with Intel
The file was modified	CMakeInclude/CompilerFlags.cmake