Changes

Implemented mitLG symmetry wall BC for four-equation IBL3

by shunz

edit	`src/pde/IBL/BCIBL3D.h`
edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_toy.cpp`
edit	`src/Discretization/Galerkin/IntegrandBoundaryTrace_Dirichlet_mitLG_Galerkin_manifold.h`
edit	`src/pde/IBL/BCIBL3D.cpp`

allowed for some tolerance in finding boundary trace elements

by shunz

edit	`src/Field/FindElementFromX.cpp`

Reparametrized flat plate grid',s S-duct geometry

by shunz

edit	`test/sandbox/Solve3D_VMSDBR2_NavierStokes_Sduct_toy.cpp`
edit	`test/unit/UnitGrids/XField3D_FlatPlate_X1.h`
edit	`test/unit/UnitGrids/XField3D_FlatPlate_X1.cpp`

added z margin in BL sampling so that points are in the computational domain even for coarse grids. , Make flat plate grid spacing uniform in x on the plate

by shunz

edit	`src/Field/FindElementFromX.cpp`
edit	`test/sandbox/Solve3D_VMSDBR2_NavierStokes_Sduct_toy.cpp`
edit	`test/unit/UnitGrids/XField3D_FlatPlate_X1.cpp`

changed default to more BL sampling stations

by shunz

edit	`test/sandbox/Solve3D_VMSDBR2_NavierStokes_Sduct_toy.cpp`

Make screen output more concise for BL sampling

by shunz

edit	`src/Field/FindElementFromX.cpp`

Added , local basis vector e1 and e2 for IBL3 mitLG BC

by shunz

edit	`src/Discretization/Galerkin/IntegrandBoundaryTrace_Dirichlet_mitLG_Galerkin_manifold.h`
edit	`src/pde/NDConvert/BCNDConvertSpace3D.h`
edit	`src/pde/IBL/BCIBL3D.h`

minor refactoring of screen printout

by shunz

edit	`test/unit/UnitGrids/XField3D_Box_Hex_X1.cpp`

Turned on gradient calculation for mitLG BC for IBL3/manifold

by shunz

edit	`src/Discretization/Galerkin/IntegrandBoundaryTrace_Dirichlet_mitLG_Galerkin_manifold.h`

changed half expanding nozzle to sin shape (without kink)

by shunz

edit	`test/unit/UnitGrids/XField3D_Box_Hex_X1.cpp`

minor cleanup

by shunz

edit	`src/pde/IBL/BCIBL3D.h`

renamed IBL3D slip-wall BC type

by shunz

edit	`test/sandbox/Solve3D_Coupled_FP_IBL3_duct_toy.cpp`
edit	`test/sandbox/Solve3D_Coupled3x3_IBLFourEqn_FlatPlate_torpedo_agrid45_toy.cpp`
edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_toy.cpp`
edit	`test/unit/Discretization/Block/AlgebraicEquationSet_Block4x4_FP_Auxv_Auxi_IBL3_Quad_btest.cpp`
edit	`src/pde/IBL/BCIBL3D.h`
edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_ring_toy.cpp`

Some more renaming of slip wall BC mitLG for IBL3

by shunz

edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_toy.cpp`
edit	`src/pde/IBL/BCIBL3D.h`
edit	`src/pde/IBL/BCIBL3D.cpp`

Make 3-eq IBL3 variable data a templated class

by shunz

edit	`src/pde/IBL/IBLVarDataType3D.h`
edit	`test/unit/Discretization/Block/AlgebraicEquationSet_Block3x3_Auxv_Auxi_IBL_Quad_btest.cpp`
edit	`src/pde/IBL/VarInterpret3D.h`
edit	`test/sandbox/Solve3D_Uncoupled_IBL_FlatPlate_Blasius_toy.cpp`
edit	`test/unit/Discretization/Block/AlgebraicEquationSet_Block3x3_Auxv_Auxi_IBL_Triangle_btest.cpp`
edit	`test/unit/pde/IBL/PDEIBL3D_btest.cpp`
edit	`test/system/AnalyticSolve/AnalyticSolve3D_IBL3D_StagnationFlow_LamiBL_Triangle_btest.cpp`

More refactoring due to VarDataIBL3D being templated now. Also minor cleanup

by shunz

edit	`src/pde/IBL/BCIBL3D.h`
edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_ring_toy.cpp`
edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_toy.cpp`

Added slip-wall mitState BC for 3-eq IBL3D. , Refactored PDEIBL for 3-eq formulation to keep up with 4-eq formulation

by shunz

edit	`test/unit/UnitGrids/XField3D_Box_Hex_X1.h`
edit	`src/pde/IBL/BCIBL3D.cpp`
edit	`src/pde/IBL/PDEIBLFourEqn3D.h`
edit	`test/unit/UnitGrids/XField3D_Box_Hex_X1.cpp`
edit	`src/pde/IBL/BCIBL3D.h`
edit	`src/pde/IBL/PDEIBL3D.h`
edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_ring_toy.cpp`

Added instantiations for 3-eq IBL3

by shunz

edit	`src/pde/IBL/BCIBL3D.h`
edit	`src/LinearAlgebra/SparseLinAlg/PETSc/PETScSolver_MatrixBlock_4x4_Instantiate.cpp`
edit	`src/NonLinearSolver/NewtonSolver_MatrixBlock_4x4_Instantiate.cpp`
edit	`src/LinearAlgebra/SparseLinAlg/Direct/UMFPACK/UMFPACKSolver_MatrixBlock_4x4_Instantiate.cpp`
edit	`src/LinearAlgebra/SparseLinAlg/ScalarMatrix_CRS_int.cpp`
edit	`src/LinearAlgebra/SparseLinAlg/Krylov/FGMRES_MatrixBlock_4x4_Instantiate.cpp`
edit	`src/NonLinearSolver/LineUpdate/HalvingSearchLineUpdate_MatrixBlock_4x4_Instantiate.cpp`
edit	`src/LinearAlgebra/SparseLinAlg/Direct/MKL_PARDISO/MKL_PARDISOSolver_MatrixBlock_4x4_Instantiate.cpp`

Add mitLG slip-wall BC for 3-eq IBL3D

by shunz

edit	`src/pde/IBL/BCIBL3D.cpp`
edit	`src/pde/IBL/BCIBL3D.h`

Added KE equation normalized by qe^2 for 3-eqn IBL3D

by shunz

edit	`src/pde/IBL/PDEIBL3D.h`

minor refactoring of a sandbox case

by shunz

edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_toy.cpp`

Refactored 3-eq IBL to use J &, E as momentum and kinetic energy fluxes instead of P &, K

by shunz

edit	`src/LinearAlgebra/DenseLinAlg/StaticSize/MatMul/MatrixS_MatMul_Native_Surreal_Instantiate.cpp`
edit	`src/pde/IBL/PDEIBL3D.h`

Added a sandbox case of 3-eq IBL3 in duct

by shunz

add	`test/sandbox/Solve3D_3eqn_IBL3_duct_toy.cpp`
edit	`src/pde/IBL/PDEIBL3D.h`

minor cleanup

by shunz

edit	`test/sandbox/Solve3D_3eqn_IBL3_duct_toy.cpp`

added explicit instantiation

by shunz

edit	`src/LinearAlgebra/DenseLinAlg/StaticSize/MatMul/MatrixS_MatMul_Native_Surreal_Instantiate.cpp`

Added an elbow-shaped hex box grid

by shunz

edit	`test/unit/UnitGrids/XField3D_Box_Hex_X1.cpp`
edit	`test/unit/UnitGrids/XField3D_Box_Hex_X1.h`

Added macro to switch kinetic energy flux definition (K vs E) in 3-eqn IBL3D

by shunz

edit	`src/pde/IBL/PDEIBL3D.h`

minor cleanup of a sandbox case

by shunz

Added macro to switch momentum flux definition (P vs J) in 3-eqn IBL3D

by shunz

edit	`src/pde/IBL/PDEIBL3D.h`

fix a recently introduced bug in source term when using P momentum flux in 3-eqn IBL3

by shunz

edit	`src/pde/IBL/PDEIBL3D.h`

cleanup of 3-eqn IBL3 BC

by shunz

edit	`src/pde/IBL/BCIBL3D.cpp`
edit	`src/pde/IBL/BCIBL3D.h`

Enabled constant wall transpiration in linearized incompressible potential (LIP) BC

by shunz

edit	`test/sandbox/Solve3D_3eqn_IBL3_duct_toy.cpp`
edit	`src/pde/FullPotential/BCLinearizedIncompressiblePotential3D.h`
edit	`src/pde/FullPotential/BCLinearizedIncompressiblePotential3D.cpp`

Refactored a sandbox case: uncoupled 3-eqn IBL3 with prescribed qe

by shunz

edit	`test/sandbox/Solve3D_Uncoupled_IBLThreeEqn_FlatPlate_toy.cpp`
edit	`test/sandbox/Solve3D_3eqn_IBL3_duct_toy.cpp`

Turned on PTC for a sandbox case

by shunz

edit	`test/sandbox/Solve3D_Uncoupled_IBLThreeEqn_FlatPlate_toy.cpp`

Examined 3-eqn IBL3 (Nishida closure) characteristics without source terms

by shunz

edit	`test/sandbox/Solve3D_Uncoupled_IBLThreeEqn_FlatPlate_toy.cpp`

Sandbox case refactoring: LIP in/out flow BC, solution &, quadrature order. , BC 3-eqn IBL3 cleanup and addition of mitLG Dirichlet BC

by shunz

edit	`test/sandbox/Solve3D_3eqn_IBL3_duct_toy.cpp`
edit	`src/pde/IBL/BCIBL3D.h`
edit	`src/pde/IBL/BCIBL3D.cpp`

Cleanup of IBL3 BC

by shunz

edit	`src/pde/IBL/BCIBL3D.cpp`
edit	`src/pde/IBL/BCIBL3D.h`

Refactored closure models: 2D closures are now uniquely contained in a single file, avoiding copy-pasting code in multiple spots

by shunz

delete	`src/pde/IBL/SecondaryVar2D.h`
edit	`src/pde/IBL/ClosureFourEqn3D_Lami.h`
edit	`src/pde/IBL/ThicknessesCoefficients2D_CorrelationClosure_impl.h`
edit	`src/pde/IBL/CMakeLists.txt`
edit	`src/pde/IBL/PDEIBLSplitAmpLag2D.h`
edit	`test/unit/pde/IBL/PDEIBL2D_btest.cpp`
edit	`src/pde/IBL/PDEIBLUniField.h`
edit	`test/unit/pde/IBL/ThicknessesCoefficients2D_CorrelationClosure_btest.cpp`
edit	`test/unit/pde/IBL/ThicknessesCoefficients2D_ProfileClosure_btest.cpp`
edit	`src/pde/IBL/PDEIBLFourEqn3D.h`
delete	`src/pde/IBL/SecondaryVar2D_impl.h`
edit	`src/pde/IBL/ThicknessesCoefficients3D.h`
edit	`src/pde/IBL/ClosureRelations3D_Nishida.h`
edit	`src/pde/IBL/IBLMiscClosures.h`
edit	`src/pde/IBL/ClosureFourEqn3D_Turb_Regularized.h`
edit	`src/pde/IBL/PDEIBL2D.h`
edit	`src/pde/IBL/PDEIBL3D.h`
edit	`src/pde/IBL/ThicknessesCoefficients3D_CorrelationClosure_impl.h`
edit	`src/pde/IBL/ThicknessesCoefficients2D.h`
edit	`src/pde/IBL/ThicknessesCoefficients2D_ProfileClosure_impl.h`
edit	`src/pde/IBL/ThicknessesCoefficients3D_CorrelationClosureFourEqn_impl.h`
edit	`src/pde/IBL/ClosureRelations3D_NeuralNet.h`
edit	`src/pde/IBL/ClosureRelationsFourEqn3D_CurveFit_lowDissipation.h`
delete	`src/pde/IBL/SecondaryVar2D.cpp`
edit	`src/pde/IBL/ClosureFourEqn3D_Turb_NeuralNet.h`
delete	`test/unit/pde/IBL/SecondaryVar2D_btest.cpp`

fixed lingering typos

by shunz

edit	`src/pde/IBL/PDEIBL3D.h`

Refactoring to keep up with 3-eqn IBL3 PDE',s gas model change

by shunz

edit	`test/unit/Discretization/Block/AlgebraicEquationSet_Block3x3_Auxv_Auxi_IBL_Quad_btest.cpp`
edit	`test/system/AnalyticSolve/AnalyticSolve3D_IBL3D_StagnationFlow_LamiBL_Triangle_btest.cpp`
edit	`test/unit/Discretization/Block/AlgebraicEquationSet_Block3x3_Auxv_Auxi_IBL_Triangle_btest.cpp`

Changed default 3-eqn IBL3 closure to Nishida. , Updated pyrite files for associated 2D stagnation flow case

by shunz

edit	`test/system/IO/AnalyticSolve/IBL3D_StagnationFlow_LamiBL_Triangle_nelem1d2_p4_Test.txt`
edit	`test/system/IO/AnalyticSolve/IBL3D_StagnationFlow_LamiBL_Triangle_nelem1d1_p2_Test.txt`
edit	`src/pde/IBL/FluidModels.h`
edit	`test/system/IO/AnalyticSolve/IBL3D_StagnationFlow_LamiBL_Triangle_nelem1d2_p1_Test.txt`
edit	`test/system/IO/AnalyticSolve/IBL3D_StagnationFlow_LamiBL_Triangle_nelem1d2_p3_Test.txt`
edit	`test/system/IO/AnalyticSolve/IBL3D_StagnationFlow_LamiBL_Triangle_nelem1d1_p4_Test.txt`
edit	`src/pde/IBL/ThicknessesCoefficients3D_CorrelationClosure_impl.h`
edit	`test/system/IO/AnalyticSolve/IBL3D_StagnationFlow_LamiBL_Triangle_nelem1d1_p0_Test.txt`
edit	`test/system/IO/AnalyticSolve/IBL3D_StagnationFlow_LamiBL_Triangle_nelem1d2_p2_Test.txt`
edit	`test/system/AnalyticSolve/AnalyticSolve3D_IBL3D_StagnationFlow_LamiBL_Triangle_btest.cpp`
edit	`test/system/IO/AnalyticSolve/IBL3D_StagnationFlow_LamiBL_Triangle_nelem1d1_p3_Test.txt`
edit	`test/system/IO/AnalyticSolve/IBL3D_StagnationFlow_LamiBL_Triangle_nelem1d1_p1_Test.txt`
edit	`test/system/IO/AnalyticSolve/IBL3D_StagnationFlow_LamiBL_Triangle_nelem1d2_p0_Test.txt`

Had to turn on dummy turb 3-eqn IBL3 closure due to lami-turb blending

by shunz

edit	`src/pde/IBL/ThicknessesCoefficients3D_CorrelationClosure_impl.h`
edit	`src/pde/IBL/PDEIBL3D.h`

Updated 3-eqn IBL3 BC vector to include Falkner-Skan inflow mitLG

by shunz

edit	`src/pde/IBL/BCIBL3D.h`

Minor refactoring of sandbox cases

by shunz

edit	`test/sandbox/Solve3D_3eqn_IBL3_duct_toy.cpp`
edit	`test/sandbox/Solve3D_Uncoupled_IBLThreeEqn_FlatPlate_toy.cpp`

minor refactoring of sandbox cases

by shunz

edit	`test/sandbox/Solve3D_Coupled3x3_IBLFourEqn_FlatPlate_torpedo_agrid45_toy.cpp`
edit	`test/sandbox/Solve3D_Uncoupled_IBLThreeEqn_FlatPlate_toy.cpp`
edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_toy.cpp`

Add screen printout for numerical flux type and separated macro toggles for turning on/off amp and lag equations in 3-eqn IBL3 PDE

by shunz

edit	`src/pde/IBL/PDEIBL3D.h`

minor refactoring of sandbox case

by shunz

edit	`test/sandbox/Solve3D_Uncoupled_IBLThreeEqn_FlatPlate_toy.cpp`

fix warning on style

by shunz

edit	`src/pde/IBL/PDEIBL3D.h`

Refactored 3-eqn IBL3D to allow for runtime options for Lax-Friedrichs flux variants: based on qe or qn

by shunz

edit	`test/sandbox/Solve3D_Uncoupled_IBLThreeEqn_FlatPlate_toy.cpp`
edit	`test/sandbox/Solve3D_3eqn_IBL3_duct_toy.cpp`
edit	`src/pde/IBL/PDEIBL3D.h`

Changed 3-eqn IBL3 slip-wall BC to adaptively switch between no-crossflow and BCNone depending interior characteristic direction

by shunz

edit	`test/sandbox/Solve3D_3eqn_IBL3_duct_toy.cpp`
edit	`src/pde/IBL/BCIBL3D.h`

mucked with a sandbox case for uncoupled 3-eqn IBL3

by shunz

edit	`test/sandbox/Solve3D_Uncoupled_IBLThreeEqn_FlatPlate_toy.cpp`

minor cleanup while playing with 3-eqn IBL3D on the duct case

by shunz

edit	`src/pde/IBL/ThicknessesCoefficients3D_CorrelationClosure_impl.h`
edit	`src/pde/IBL/PDEIBL3D.h`
edit	`test/sandbox/Solve3D_3eqn_IBL3_duct_toy.cpp`
edit	`test/unit/UnitGrids/XField3D_Box_Hex_X1.cpp`

typo fix. the issue didn',t cause any trouble though

by shunz

edit	`test/sandbox/Solve3D_3eqn_IBL3_duct_toy.cpp`

Added a sandbox case of 3-eqn IBL3 for duct ring BL. Also cleaned up other similar cases

by shunz

add	`test/sandbox/Solve3D_3eqn_IBL3_duct_ring_toy.cpp`
edit	`src/pde/IBL/BCIBL3D.h`
edit	`test/sandbox/Solve3D_3eqn_IBL3_duct_toy.cpp`
edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_toy.cpp`
edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_ring_toy.cpp`
edit	`test/sandbox/Solve3D_Coupled3x3_IBLFourEqn_FlatPlate_torpedo_agrid45_toy.cpp`

fixed a harmless typo

by shunz

edit	`src/Discretization/Galerkin/IntegrandInteriorTrace_Galerkin_manifold.h`

Added some runtime checks for 3D manifold related trace normal and surface basis vectors

by shunz

edit	`src/Field/Element/ElementXField_LocalAxesManager.h`
edit	`src/Field/Element/TraceUnitNormal.h`
edit	`src/pde/IBL/PDEIBL3D.h`

mucked with mitLG slip-sidewall BC for 4-eqn IBL3 -->, decided not to use for now

by shunz

edit	`src/pde/IBL/BCIBL3D.h`

Refactored assertions for e0_X in 3D manifold cell integrand specialized for IBL3

by shunz

edit	`src/Discretization/Galerkin/IntegrandCell_Galerkin_manifold_IBL3D.h`

mucked with 3-eqn IBL3 on duct ring case with corner fairing

by shunz

edit	`test/sandbox/Solve3D_3eqn_IBL3_duct_ring_toy.cpp`
edit	`test/unit/UnitGrids/XField3D_Box_Hex_X1.cpp`

Separated IBL3D BC stuff for 3-eqn and 4-eqn

by shunz

edit	`src/pde/IBL/BCIBL3D.h`
edit	`test/system/AnalyticSolve/AnalyticSolve3D_IBLFourEqn_StagnationFlow_LamiBL_Triangle_btest.cpp`
edit	`test/unit/Discretization/Block/AlgebraicEquationSet_Block4x4_FP_Auxv_Auxi_IBL3_Quad_btest.cpp`
edit	`test/unit/Discretization/Block/AlgebraicEquationSet_Block3x3_Auxv_Auxi_IBLFourEqn_Quad_btest.cpp`
edit	`src/pde/IBL/BCIBL3D.cpp`
edit	`test/sandbox/Solve3D_Uncoupled_IBLFourEqn_FlatPlate_Blasius_toy.cpp`
edit	`test/sandbox/Solve3D_Uncoupled_IBLFourEqn_FlatPlate_StagnationRadial_toy.cpp`
add	`src/pde/IBL/BCIBLFourEqn3D.h`
edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_ring_toy.cpp`
edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_toy.cpp`
edit	`test/sandbox/Solve3D_Coupled3x3_IBLFourEqn_FlatPlate_torpedo_agrid45_toy.cpp`
add	`src/pde/IBL/BCIBLFourEqn3D.cpp`
edit	`src/pde/IBL/CMakeLists.txt`
edit	`test/sandbox/Solve3D_Coupled_FP_IBL3_duct_toy.cpp`

Typo fix in 3-eqn IBL3 PDE',s source (not used). , Cleanup &, renaming. , Refactored 4-eqn IBL3 slipwall BC to be adaptive based crossflow characteristics

by shunz

edit	`test/unit/Discretization/Block/AlgebraicEquationSet_Block4x4_FP_Auxv_Auxi_IBL3_Quad_btest.cpp`
edit	`test/sandbox/Solve3D_Coupled_FP_IBL3_duct_toy.cpp`
edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_toy.cpp`
edit	`src/pde/IBL/PDEIBL3D.h`
edit	`src/pde/IBL/BCIBL3D.h`
edit	`test/sandbox/Solve3D_Coupled3x3_IBLFourEqn_FlatPlate_torpedo_agrid45_toy.cpp`
edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_ring_toy.cpp`
edit	`src/pde/IBL/BCIBLFourEqn3D.h`

Refactored 4-eqn IBL3 PDE to keep up-to-date with 3-eqn formulation

by shunz

edit	`src/pde/IBL/PDEIBLFourEqn3D.h`
edit	`src/pde/IBL/PDEIBL3D.h`

cleaned up 4-eqn IBL3 BC vectors

by shunz

edit	`test/sandbox/Solve3D_Uncoupled_IBLFourEqn_FlatPlate_Blasius_toy.cpp`
edit	`src/pde/IBL/BCIBLFourEqn3D.cpp`
edit	`src/pde/IBL/BCIBLFourEqn3D.h`
edit	`test/sandbox/Solve3D_Coupled3x3_IBLFourEqn_FlatPlate_torpedo_agrid45_toy.cpp`
edit	`test/sandbox/Solve3D_Coupled_FP_IBL3_duct_toy.cpp`
edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_ring_toy.cpp`
edit	`test/unit/Discretization/Block/AlgebraicEquationSet_Block4x4_FP_Auxv_Auxi_IBL3_Quad_btest.cpp`
edit	`test/unit/Discretization/Block/AlgebraicEquationSet_Block3x3_Auxv_Auxi_IBLFourEqn_Quad_btest.cpp`

Refactored NS Sduct case to sample at grid nodes so that sidewall points can be covered

by shunz

edit	`test/sandbox/Solve3D_VMSDBR2_NavierStokes_Sduct_toy.cpp`

More refactoring to sample BL at grid vertex stations

by shunz

edit	`test/sandbox/Solve3D_VMSDBR2_NavierStokes_Sduct_toy.cpp`

refactored 4-eqn IBL3 S-duct sandbox case to keep up with 3-eqn IBL3

by shunz

edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_toy.cpp`

refactored 3-eq IBL3 case to compare with DBL3 on wing-body setup

by shunz

edit	`test/sandbox/Solve3D_Uncoupled_IBLThreeEqn_FlatPlate_toy.cpp`

added mitLG full-state inflow BC for 4-eqn IBL3

by shunz

edit	`src/pde/IBL/BCIBLFourEqn3D.cpp`
edit	`src/pde/IBL/BCIBLFourEqn3D.h`

Added an uncoupled 4-eq IBL3 flat plate BL sandbox case with manufactured qe. , Minor edits to 3-eq IBL3 BC/PDE

by shunz

edit	`src/pde/IBL/BCIBL3D.h`
edit	`src/pde/IBL/PDEIBL3D.h`
add	`test/sandbox/Solve3D_Uncoupled_IBLFourEqn_FlatPlate_toy.cpp`

Changed default slip-sidewall BC back to zero-crossflow (from the previous adaptive formulation). , Compared 3-eq and 4-eq IBL3 on a case with crossover cp distribution

by shunz

edit	`test/sandbox/Solve3D_Uncoupled_IBLThreeEqn_FlatPlate_toy.cpp`
edit	`src/pde/IBL/BCIBLFourEqn3D.h`
edit	`src/pde/IBL/BCIBL3D.h`
edit	`test/sandbox/Solve3D_Uncoupled_IBLFourEqn_FlatPlate_toy.cpp`

minor tweaking to sandbox cases

by shunz

edit	`test/sandbox/Solve3D_3eqn_IBL3_duct_ring_toy.cpp`
edit	`test/sandbox/Solve3D_3eqn_IBL3_duct_toy.cpp`

Removed redundant parameter in mitLG BC class

by shunz

edit	`src/pde/IBL/BCIBLFourEqn3D.h`
edit	`src/pde/IBL/BCIBLFourEqn3D.cpp`

torpedo case cleanup

by shunz

edit	`test/sandbox/Solve3D_Coupled3x3_IBLFourEqn_FlatPlate_torpedo_agrid45_toy.cpp`

tweaked quadrature order for auxi and auxv equations in torpedo case. minor cleanup

by shunz

edit	`test/sandbox/Solve3D_Coupled3x3_IBLFourEqn_FlatPlate_torpedo_agrid45_toy.cpp`

bugfix in G variable initialization in torpedo case

by shunz

edit	`test/sandbox/Solve3D_Coupled3x3_IBLFourEqn_FlatPlate_torpedo_agrid45_toy.cpp`

separated PDE instantiation cpp files for 3-eqn and 4-eqn IBL3

by shunz

edit	`src/pde/IBL/PDEIBL3D.cpp`
edit	`src/pde/IBL/CMakeLists.txt`
add	`src/pde/IBL/PDEIBLFourEqn3D.cpp`

make lag equation G=0 when turned off

by shunz

edit	`src/pde/IBL/PDEIBLFourEqn3D.h`

minor cleanup of sandbox case

by shunz

edit	`test/sandbox/Solve3D_Coupled3x3_IBLFourEqn_FlatPlate_torpedo_agrid45_toy.cpp`

added a crude restart capability for torpedo case by saving/reading DOF file

by shunz

edit	`test/sandbox/Solve3D_Coupled3x3_IBLFourEqn_FlatPlate_torpedo_agrid45_toy.cpp`

Added sphere/doublet option for flat plate panel method. , Refactored torpedo/sphere case I/O so that saved floating point numbers don',t go below limit (s.t. they cannot be represented when read in and would cause errors). Other minor refactoring

by shunz

edit	`src/PanelMethod/PiecewiseConstSourcePanel_FlatPlate3D.h`
edit	`test/sandbox/Solve3D_Uncoupled_IBLFourEqn_FlatPlate_toy.cpp`
edit	`test/sandbox/Solve3D_Coupled3x3_IBLFourEqn_FlatPlate_torpedo_agrid45_toy.cpp`

ran 3D IBL3 free transition case with sphere/doublet

by shunz

edit	`test/sandbox/Solve3D_Coupled3x3_IBLFourEqn_FlatPlate_torpedo_agrid45_toy.cpp`

minor tweak to 4-eqn IBL3 pde. Only keep ntcrit growth source term for now.

by shunz

edit	`src/pde/IBL/PDEIBLFourEqn3D.h`

minor tweak to torpedo sandbox case

by shunz

edit	`test/sandbox/Solve3D_Coupled3x3_IBLFourEqn_FlatPlate_torpedo_agrid45_toy.cpp`

Added an macro option to turn of amplification equation for 4-eq IBL3 (i.e. nt = 0)

by shunz

edit	`src/pde/IBL/PDEIBLFourEqn3D.h`

refactored torpedo case restart capability

by shunz

edit	`test/sandbox/Solve3D_Coupled3x3_IBLFourEqn_FlatPlate_torpedo_agrid45_toy.cpp`

added crude restart capability for S-duct case for IBL3 (copied from torpedo). minor cleanup

by shunz

edit	`src/pde/IBL/BCIBLFourEqn3D.h`
edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_toy.cpp`

relaxed floating-point comparison tolerance a little bit

by shunz

edit	`src/pde/IBL/PDEIBLFourEqn3D.h`

refactoring duct ring sandbox case for 4-eqn IBL3

by shunz

edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_ring_toy.cpp`

minor cleanup

by shunz

edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_ring_toy.cpp`
edit	`test/sandbox/Solve3D_3eqn_IBL3_duct_ring_toy.cpp`

added comments to the duct ring grid

by shunz

edit	`test/unit/UnitGrids/XField3D_BoxBoundaries_Quad_X1.cpp`

Added a constant full state inflow BC for 4-eqn IBL3

by shunz

edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_ring_toy.cpp`
edit	`src/pde/IBL/BCIBLFourEqn3D.cpp`
edit	`src/pde/IBL/BCIBLFourEqn3D.h`
edit	`src/pde/IBL/PDEIBLFourEqn3D.h`

added printout for examing duct ring surface grid

by shunz

edit	`test/unit/UnitGrids/XField3D_BoxBoundaries_Quad_X1_btest.cpp`

mucking with turbulent S-duct flow case

by shunz

edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_toy.cpp`

Make duct and duct ring cases the same for 4-eqn IBL3

by shunz

edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_ring_toy.cpp`
edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_toy.cpp`

tweaked IBL3 output

by shunz

edit	`src/pde/IBL/ElementProjectionOutputIBL3D.h`

added safety check in Qauxv 3D projection

by shunz

edit	`src/pde/IBL/IntegrandCell_ProjectToQauxv3D.h`

minor cleanup

by shunz

edit	`src/pde/IBL/ClosureFourEqn3D_Turb_Regularized.h`

fixed a bug in 4-eqn IBL3 upwinding (i.e. R trace normal vector y-component). , Used L value by mistake and problematic only when nrmL != nrmR, e.g. in corner.

by shunz

edit	`src/pde/IBL/PDEIBLFourEqn3D.h`

added commented-out print statements for debugging

by shunz

edit	`src/pde/NDConvert/PDENDConvertSpace3D.h`

changed default dissipation relation correction to 1

by shunz

edit	`src/pde/IBL/ClosureFourEqn3D_Turb_NeuralNet.h`
edit	`src/pde/IBL/ClosureFourEqn3D_Turb_Regularized.h`

changed default 3D qauxi project to use no upwinding

by shunz

edit	`src/pde/IBL/ProjectToQauxi3D.h`

examined effect of discontinuous velocity field for 4-eqn IBL3

by shunz

edit	`test/sandbox/Solve3D_Uncoupled_IBLFourEqn_FlatPlate_toy.cpp`

refactored calculation of profile basis {q1,q2,nrm_bl} to allow for different formulations

by shunz

edit	`src/pde/IBL/IntegrandCell_ProjectToQauxv3D.h`
edit	`src/pde/IBL/BCIBLFourEqn3D.h`
edit	`src/pde/IBL/QauxvInterpret3D.h`
edit	`test/unit/pde/IBL/ProjectToQauxi3D_btest.cpp`
edit	`src/pde/IBL/BCIBL3D.h`
edit	`test/unit/pde/IBL/PDEIBLFourEqn3D_btest.cpp`
edit	`src/pde/IBL/ElementProjectionOutputIBL3D.h`
edit	`src/pde/IBL/PDEIBLFourEqn3D.h`
edit	`src/pde/IBL/ProjectToQauxi3D.h`
edit	`test/unit/pde/IBL/AlgebraicEquationSet_ProjectToQauxv_3D_btest.cpp`
edit	`src/pde/IBL/PDEIBL3D.h`

mucked with different BL profile normal vector definition in sandbox case

by shunz

edit	`test/sandbox/Solve3D_Coupled_LIP_IBL3_duct_ring_toy.cpp`

Refactored 3D sheet quad grid for IBL3. (simplified grid contruction using XFieldLagrange. allowing for more general curved manifold grid)

by shunz

edit	`test/unit/UnitGrids/XField3D_Sheet_Quad_X1.cpp`
edit	`test/unit/UnitGrids/XField3D_Sheet_Quad_X1_btest.cpp`
edit	`test/unit/UnitGrids/XField3D_Sheet_Quad_X1.h`
edit	`test/unit/UnitGrids/XField3D_BoxBoundary_Quad_X1.cpp`
edit	`test/unit/UnitGrids/XField3D_BoxBoundaries_Quad_X1.cpp`

replaced a few least-used IBL3 output

by shunz

edit	`src/pde/IBL/ElementProjectionOutputIBL3D.h`

added an option for arc fairing for duct hex grid

by shunz

edit	`test/unit/UnitGrids/XField3D_Box_Hex_X1.cpp`

generalize fairing from arc of circle to ellipse

by shunz

edit	`test/unit/UnitGrids/XField3D_Box_Hex_X1.cpp`

added corner fairing option to S-duct hex grid

by shunz

edit	`test/unit/UnitGrids/XField3D_Box_Hex_X1.cpp`

Set no fairing for duct wall surface grid

by shunz

edit	`test/unit/UnitGrids/XField3D_Box_Hex_X1.cpp`

tried a case of uncoupled IBL on arc surface

by shunz

edit	`test/sandbox/Solve3D_Uncoupled_IBLFourEqn_FlatPlate_toy.cpp`

fixed outdated stuff due to updates of Axisymmetric API and Field directory reorg

by shunz

edit	`test/sandbox/Solve3D_Uncoupled_IBLFourEqn_FlatPlate_toy.cpp`
edit	`src/Discretization/Galerkin/IntegrandBoundaryTrace_Dirichlet_mitLG_Galerkin_manifold.h`
edit	`test/unit/UnitGrids/XField3D_Box_Hex_X1.cpp`
edit	`test/unit/UnitGrids/XField3D_Sheet_Quad_X1.cpp`

fixed too-narrow assertion. updated use of interior trace group indexing

by shunz

edit	`src/PanelMethod/PiecewiseConstSourcePanel_FlatPlate3D.h`
edit	`test/sandbox/Solve3D_Coupled3x3_IBLFourEqn_FlatPlate_torpedo_agrid45_toy.cpp`

file IO updates in test case

by shunz

edit	`test/system/CodeConsistency/Solve2D_Coupled4x4_IBLSplitAmpLag_CorrelationClosure_CapturedTransition_PTC_btest.cpp`

Played with a case with step/sigmoid function of inlet BC to show qe-based alpha is not too dissipative

by shunz

edit	`src/pde/IBL/BCIBLFourEqn3D.h`
edit	`test/sandbox/Solve3D_Uncoupled_IBLFourEqn_FlatPlate_toy.cpp`

played with 2D IBL cases to compare heuristic and corrected LF fluxes in PhD thesis

by shunz

edit	`src/pde/IBL/PDEIBLSplitAmpLag2D.h`
edit	`test/sandbox/Solve2D_Coupled4x4_IBL_fx67k170_single_run_toy.cpp`

Add legacy VTK and Exodus metric files

by galbramc

edit	`test/unit/Meshing/CMakeLists.txt`
add	`CMakeInclude/Builds/BuildSEACAS.cmake`
edit	`src/MPI/continuousElementMap.h`
edit	`src/Topology/ElementTopology.h`
add	`CMakeInclude/Checks/seacas_test.cxx`
edit	`src/Field/output/output_VTK.h`
add	`src/Meshing/Exodus/CMakeLists.txt`
add	`src/Meshing/VTK/WriteMeshMetric_lVTK.cpp`
edit	`src/Meshing/gmsh/WriteMesh_gmsh.cpp`
add	`CMakeInclude/Finds/FindSEACAS.cmake`
edit	`src/Field/XField/Partition/XField_Lagrange_impl.h`
add	`test/unit/Meshing/Exodus/CMakeLists.txt`
edit	`src/Field/output/output_VTK_LIP.cpp`
add	`src/Meshing/Exodus/ReadMetric_Exodus.cpp`
add	`src/Meshing/VTK/CMakeLists.txt`
add	`test/unit/Meshing/VTK/WriteMeshMetric_lVTK_btest.cpp`
edit	`CMakeInclude/MakeSummaryFile.cmake`
add	`src/Meshing/Exodus/WriteMeshMetric_Exodus.cpp`
edit	`src/Meshing/EGADS/transform.cpp`
add	`src/Meshing/Exodus/EXStatus.h`
add	`src/Meshing/Exodus/XField_Exodus.cpp`
edit	`CMakeInclude/Dependencies.cmake`
add	`test/unit/Meshing/Exodus/WriteMeshMetric_Exodus_btest.cpp`
add	`CMakeInclude/Checks/CheckSEACAS.cmake`
edit	`src/Meshing/ugrid/WriteMesh_ugrid.cpp`
add	`test/unit/Meshing/VTK/CMakeLists.txt`
add	`src/Meshing/Exodus/EXtoSANS.h`
add	`src/Meshing/Exodus/WriteMeshMetric_Exodus.h`
add	`src/Meshing/VTK/WriteMeshMetric_lVTK.h`
edit	`src/Field/XField/Partition/XField_Lagrange_Distribute_impl.h`
add	`src/Meshing/Exodus/EXtoSANS.cpp`
add	`src/Meshing/Exodus/ReadMetric_Exodus.h`
add	`src/Meshing/Exodus/XField_Exodus.h`
edit	`src/Meshing/CMakeLists.txt`
edit	`src/Field/XField/Partition/XField_Lagrange.h`
edit	`CMakeLists.txt`

VTK fixes

by galbramc

edit	`src/Meshing/VTK/WriteMeshMetric_lVTK.cpp`
edit	`test/unit/Meshing/VTK/WriteMeshMetric_lVTK_btest.cpp`

Fixed Body Force solver sensitvity

by galbramc

edit	`src/Topology/ElementTopology.h`
edit	`src/UserInterfaces/BodyForceSolver_impl.h`

Warning fixes

by galbramc

edit	`src/Field/XField/Partition/XField_Lagrange_Distribute_impl.h`

fixed vera errors: long line

by shunz

edit	`src/PanelMethod/PiecewiseConstSourcePanel_FlatPlate3D.h`

fixed vera errors: long line

by shunz

edit	`src/pde/IBL/PDEIBL3D.h`

updated include paths

by shunz

edit	`test/sandbox/Solve3D_3eqn_IBL3_duct_toy.cpp`
edit	`test/sandbox/Solve3D_3eqn_IBL3_duct_ring_toy.cpp`

updated include paths

by shunz

edit	`test/sandbox/Solve3D_Uncoupled_IBLThreeEqn_FlatPlate_toy.cpp`
edit	`src/pde/IBL/AlgebraicEquationSet_ProjectToQauxv_3D.h`

removed outdated sandbox case

by shunz

delete test/sandbox/Solve3D_Uncoupled_IBL_FlatPlate_Blasius_toy.cpp

updated usage of 3D quad sheet grid',s interior trace group count

by shunz

edit	`test/unit/Discretization/Block/AlgebraicEquationSet_Block3x3_Auxv_Auxi_IBLFourEqn_Quad_btest.cpp`
edit	`test/system/AnalyticSolve/AnalyticSolve3D_IBL3D_StagnationFlow_LamiBL_Triangle_btest.cpp`
edit	`test/system/AnalyticSolve/AnalyticSolve3D_IBLFourEqn_StagnationFlow_LamiBL_Triangle_btest.cpp`
edit	`test/sandbox/Solve3D_Uncoupled_IBLFourEqn_FlatPlate_Blasius_toy.cpp`
edit	`test/sandbox/Solve3D_Uncoupled_IBLFourEqn_FlatPlate_StagnationRadial_toy.cpp`
edit	`test/unit/Discretization/Block/AlgebraicEquationSet_Block3x3_Auxv_Auxi_IBL_Quad_btest.cpp`
edit	`test/unit/Discretization/Block/AlgebraicEquationSet_Block3x3_Auxv_Auxi_IBL_Triangle_btest.cpp`

updated pyrite files. relaxed pyrite tolerance. fixed IO file/path names

by shunz

edit	`test/system/IO/AnalyticSolve/IBLFourEqn3D_StagnationFlow_LamiBL_Triangle_nelem1d1_p2_Test.txt`
edit	`test/system/AnalyticSolve/AnalyticSolve3D_IBL3D_StagnationFlow_LamiBL_Triangle_btest.cpp`
edit	`test/system/IO/AnalyticSolve/IBLFourEqn3D_StagnationFlow_LamiBL_Triangle_nelem1d2_p2_Test.txt`
edit	`test/system/IO/AnalyticSolve/IBLFourEqn3D_StagnationFlow_LamiBL_Triangle_nelem1d1_p1_Test.txt`
edit	`test/system/CodeConsistency/Solve2D_Coupled4x4_IBLSplitAmpLag_CorrelationClosure_CapturedTransition_PTC_btest.cpp`
edit	`test/system/IO/AnalyticSolve/IBLFourEqn3D_StagnationFlow_LamiBL_Triangle_nelem1d1_p0_Test.txt`
edit	`test/system/IO/AnalyticSolve/IBLFourEqn3D_StagnationFlow_LamiBL_Triangle_nelem1d1_p3_Test.txt`
edit	`test/system/IO/AnalyticSolve/IBLFourEqn3D_StagnationFlow_LamiBL_Triangle_nelem1d1_p4_Test.txt`
edit	`test/system/IO/AnalyticSolve/IBLFourEqn3D_StagnationFlow_LamiBL_Triangle_nelem1d2_p0_Test.txt`
edit	`test/system/IO/AnalyticSolve/IBLFourEqn3D_StagnationFlow_LamiBL_Triangle_nelem1d2_p1_Test.txt`
edit	`test/system/IO/AnalyticSolve/IBLFourEqn3D_StagnationFlow_LamiBL_Triangle_nelem1d2_p3_Test.txt`
edit	`test/system/IO/AnalyticSolve/IBLFourEqn3D_StagnationFlow_LamiBL_Triangle_nelem1d2_p4_Test.txt`

turned off file output

by shunz

edit	`test/system/CodeConsistency/Solve2D_Coupled4x4_IBLSplitAmpLag_CorrelationClosure_CapturedTransition_PTC_btest.cpp`

relaxed tolerance for intel

by shunz

edit	`test/unit/pde/IBL/ProjectToQauxi3D_btest.cpp`

relaxed tolerance again for intel

by shunz

edit	`test/system/AnalyticSolve/AnalyticSolve3D_IBLFourEqn_StagnationFlow_LamiBL_Triangle_btest.cpp`

Remove depricated sprintf

by galbramc

edit	`src/Meshing/refine/XField_refine.cpp`
edit	`src/Meshing/EGTess/EGTessModel_aflr4.cpp`
edit	`src/Meshing/Exodus/WriteMeshMetric_Exodus.cpp`
edit	`src/Meshing/AFLR/AFLR2.cpp`
edit	`src/tools/BackTraceException.cpp`

Add cirumfirential body force

by galbramc

edit	`src/Field/output_Tecplot/output_Tecplot_RotorSource.cpp`

Use system valgrind

by galbramc

edit	`scripts/jenkins/jenkins_env.sh`

Fix warning

by galbramc

edit	`test/unit/Python/Parameters_btest.cpp`

Derivative calculation fixes for asymmetric body forces

by galbramc

edit	`src/UserInterfaces/BodyForceSolver_impl.h`
edit	`src/Meshing/EGADS/RotorSource/Rotor.cpp`
edit	`src/Meshing/EGADS/RotorSource/Rotor.h`
edit	`test/unit/Field/NormalField_btest.cpp`

Suppress sanitizer odr violations. Add the ability for ugrid reader to

by galbramc

edit	`src/Meshing/ugrid/XFieldArea_ugrid.cpp`
edit	`src/UserInterfaces/BodyForceSolver_impl.h`
edit	`src/Meshing/EPIC/XField_PX.cpp`
edit	`src/Meshing/ugrid/CMakeLists.txt`
edit	`src/Meshing/ugrid/XField_ugrid.h`
edit	`src/UserInterfaces/BodyForceSolver.h`
edit	`src/Meshing/ugrid/XFieldVolume_ugrid.cpp`
edit	`src/UserInterfaces/PythonUI/PySANS_BodyForce.cpp`
add	`src/Meshing/ugrid/mapbc.h`
edit	`test/unit/Meshing/ugrid/XField_ugrid_btest.cpp`
add	`src/Meshing/ugrid/mapbc.cpp`
edit	`scripts/jenkins/jenkins_env.sh`

CMake file fix

by galbramc

edit	`src/Meshing/VTK/CMakeLists.txt`

Forgot to update files. Some cppcheck fixes.

by galbramc

edit	`src/Meshing/ugrid/mapbc.h`
edit	`src/Meshing/ugrid/mapbc.cpp`
edit	`scripts/cppcheck/suppressions.txt`
edit	`src/Meshing/ugrid/XField_ugrid.h`
edit	`src/Meshing/ugrid/XFieldArea_ugrid.cpp`
edit	`src/Meshing/ugrid/XFieldVolume_ugrid.cpp`
edit	`test/unit/Python/Parameters_btest.cpp`

Update 2D SA_R to latest deffinition on TMR

by galbramc

edit	`test/unit/pde/NS/PDERANSSA2D_btest.cpp`
edit	`src/pde/NS/PDERANSSA2D.h`

Fix abs with fabs

by galbramc

edit	`src/pde/NS/PDERANSSA2D.h`

SANS_refine/builddir=release_clang,buildnode=reynolds #125

Duration: 17 min

Compiler Errors

/jenkins/workspace/SANS_refine/builddir/release_clang/buildnode/reynolds/src/Meshing/refine/MultiScale_metric.cpp:93:7: error: no matching function for call to 'ref_metric_lp'

SANS_refine/builddir=release_gnu10,buildnode=reynolds #125

Duration: 22 min

/jenkins/workspace/SANS_refine/builddir/release_gnu10/buildnode/reynolds/src/Meshing/refine/MultiScale_metric.cpp:93:54: error: cannot convert &lsquo,REF_DBL*&rsquo, {aka &lsquo,double*&rsquo,} to &lsquo,REF_RECON_RECONSTRUCTION&rsquo, {aka &lsquo,REF_RECON_RECONSTRUCTIONS&rsquo,}

SANS_refine/builddir=release_gnu11,buildnode=reynolds #125

Duration: 22 min

Compiler Errors

/jenkins/workspace/SANS_refine/builddir/release_gnu11/buildnode/reynolds/src/Meshing/refine/MultiScale_metric.cpp:93:54: error: cannot convert &lsquo,REF_DBL*&rsquo, {aka &lsquo,double*&rsquo,} to &lsquo,REF_RECON_RECONSTRUCTION&rsquo, {aka &lsquo,REF_RECON_RECONSTRUCTIONS&rsquo,}

SANS_refine/builddir=release_gnu9,buildnode=reynolds #125

Duration: 20 min

Compiler Errors

/jenkins/workspace/SANS_refine/builddir/release_gnu9/buildnode/reynolds/src/Meshing/refine/MultiScale_metric.cpp:93:54: error: cannot convert &lsquo,REF_DBL*&rsquo, {aka &lsquo,double*&rsquo,} to &lsquo,REF_RECON_RECONSTRUCTION&rsquo, {aka &lsquo,REF_RECON_RECONSTRUCTIONS&rsquo,}

SANS_refine/builddir=release_intel,buildnode=reynolds #125

Duration: 32 min

Compiler Errors

/jenkins/workspace/SANS_refine/builddir/release_intel/buildnode/reynolds/src/Meshing/refine/MultiScale_metric.cpp(93): error: argument of type ",REF_DBL={double} *", is incompatible with parameter of type ",REF_RECON_RECONSTRUCTION={REF_RECON_RECONSTRUCTIONS}",

	BUILD FAILURE
Build URL	https://acdl.mit.edu/csi/job/SANS_refine/125/
Project:	SANS_refine
Date of build:	Fri, 18 Nov 2022 04:19:40 -0500
Build duration:	33 min and counting
Build cause:	Started by upstream project "SANS_refine_poll" build number 95
Built on:	reynolds