├── DEV_commands ├── compile_cython_modules_win.txt ├── profiling_win.txt └── sphix_run_win.txt ├── DEV_profiling ├── 00_FoamReader │ ├── profile_after.txt │ ├── profile_before.txt │ ├── profile_cell.txt │ ├── profile_face.txt │ ├── profile_poly_area_cy.txt │ ├── profile_poly_area_py.txt │ ├── profile_quad_area_v_v_cy.txt │ └── profile_quad_area_v_v_py.txt ├── 01_SimpleSolver │ ├── bottlenecks.ods │ ├── profile_2DChannelFlow_after.txt │ ├── profile_2DChannelFlow_before.txt │ ├── profile_calcf_cellgrad_updcellgrad_after.txt │ ├── profile_calcf_cellgrad_updcellgrad_before.txt │ ├── profile_expl_divergence_init_after.txt │ ├── profile_expl_divergence_init_before.txt │ ├── profile_impl_laplace_init_after.txt │ ├── profile_impl_laplace_init_before.txt │ ├── profile_update_bcs_after.txt │ └── profile_update_bcs_before.txt ├── 02_squareCylinder │ ├── VolumeField_update_boundary_values.log │ ├── VolumeField_update_boundary_values.log2 │ ├── calculated_fields_GaussFaceGradient_init.log │ ├── calculated_fields_GaussFaceGradient_init.log2 │ ├── imlaplace_init_10.log │ ├── imlaplace_init_10_win.log │ ├── squareCylinder.log │ ├── squareCylinder.log2 │ ├── squareCylinder.xml │ ├── squareCylinder_10.log │ ├── squareCylinder_10.log2 │ ├── squareCylinder_10.xls │ ├── squareCylinder_imlaplace_init_win.log │ ├── squareCylinder_imlaplace_init_win.log2 │ ├── squareCylinder_imlaplace_init_win.xls │ ├── squareCylinder_imlaplace_init_win_cont.log │ ├── squareCylinder_imlaplace_init_win_cont.log2 │ ├── squareCylinder_imlaplace_init_win_cont.log3 │ └── squareCylinder_line_profile_10.log └── 03_linear_solvers │ ├── cython.txt │ ├── cython.txt~ │ ├── cython2.txt │ └── gsnumpy_gscython_gsdense.txt ├── DEV_references ├── Bosch_Rodi.pdf ├── Fractional_Step_method_Kim_Moin.pdf ├── IMEX_methods_Ascher_Ruuth_Wetton_1995.pdf ├── Issa_1984.pdf ├── Lid_Driven_Cavity_JAJCEVIC_1 (3).pdf ├── MArthur_Murthy_1998.pdf ├── Rhie_Chow_1983.pdf ├── flow_past_a_square_cylinder │ └── Breuer_1999.pdf ├── jmssp.2010.265.270.pdf ├── lecture_notes11.pdf └── short-math-guide.pdf ├── DEV_resources ├── Ascher1995.pdf ├── Fractional_Step_method_Kim_Moin.pdf ├── LATEX_ShortSymbInd.pdf ├── MSH_file_format.odt ├── MSH_node_ordering.odt ├── VTK_file-formats.pdf └── painless-conjugate-gradient.pdf ├── DEV_todos ├── FINDINGS.txt ├── TODO_CHECKED.txt └── TODO_CHECKED.txt~ ├── LICENSE ├── README.md ├── _FIELD_FILES └── .placeholder ├── _MESH ├── 2dChannel │ ├── blockMeshDict │ ├── boundary │ ├── faces │ ├── neighbour │ ├── owner │ └── points ├── 2dChannel_2x │ ├── blockMeshDict │ ├── boundary │ ├── faces │ ├── neighbour │ ├── owner │ └── points ├── 2dChannel_wide │ ├── blockMeshDict │ ├── boundary │ ├── faces │ ├── neighbour │ ├── owner │ └── points ├── 45degflow │ ├── boundary │ ├── faces │ ├── neighbour │ ├── owner │ └── points ├── 6sidedBlock │ ├── boundary │ ├── faces │ ├── neighbour │ ├── owner │ └── points ├── OF_mesh │ ├── boundary.msh │ ├── cells.msh │ ├── defaultFaces_0.vtk │ └── pyCFD_mesh_0.vtk ├── SmithHutton1 │ ├── constant │ │ ├── polyMesh │ │ │ ├── blockMeshDict │ │ │ ├── boundary │ │ │ ├── faces │ │ │ ├── neighbour │ │ │ ├── owner │ │ │ └── points │ │ └── transportProperties │ └── empty.foam ├── boundary ├── cavity │ ├── boundary │ ├── faces │ ├── neighbour │ ├── owner │ └── points ├── elbow │ ├── boundary │ ├── faces │ ├── neighbour │ ├── owner │ └── points ├── elbow_0p001 │ └── constant │ │ └── polyMesh │ │ ├── boundary │ │ ├── faces │ │ ├── neighbour │ │ ├── owner │ │ └── points ├── faces ├── hex2_mesh │ ├── boundary.msh │ └── cells.msh ├── inclinedBlock │ ├── boundary │ ├── faces │ ├── neighbour │ ├── owner │ └── points ├── inclinedBlock20x20 │ ├── boundary │ ├── faces │ ├── neighbour │ ├── owner │ └── points ├── neighbour ├── owner ├── points ├── smithhutton │ ├── boundary │ ├── faces │ ├── neighbour │ ├── owner │ └── points └── tetra_mesh │ ├── boundary.msh │ ├── cells.msh │ └── cells.vtk ├── _OUTPUT └── .placeholder ├── channelNonDim.py ├── pyCFD_VTK_tools ├── __init__.py └── vtkTools.py ├── pyCFD_calculation ├── __init__.py ├── _time_loop.py └── time_loop.py ├── pyCFD_config ├── __init__.py └── config.py ├── pyCFD_doc ├── Makefile ├── README ├── _images │ ├── ANIM_P.gif │ ├── ANIM_P.png │ ├── ANIM_U.gif │ ├── ANIM_U.png │ ├── ANIM_U_VEC.gif │ ├── ANIM_U_VEC.png │ ├── HRS_U_C_D.pdf │ ├── HRS_U_C_D.png │ ├── colbar_ANIM_P.png │ ├── colbar_ANIM_U.png │ ├── domain_H.png │ ├── front.png │ ├── incl_diff_bcs2.png │ ├── incl_diff_phi.png │ ├── incl_diff_phi_non_orto.png │ ├── incl_diff_res.png │ ├── non_orto.png │ ├── sh_bcs.png │ ├── sh_bcs2.png │ ├── sh_diff.png │ ├── sh_diff_bcs2.png │ ├── sh_diff_interp.png │ ├── sh_diff_res.png │ ├── sh_minmod.png │ ├── sh_phi_distr.png │ ├── sh_res.png │ ├── sh_stoic.png │ ├── sh_uds.png │ ├── sh_velo.png │ ├── sqcyl_cd.png │ ├── sqcyl_cd_zoom.png │ ├── sqcyl_div.png │ ├── sqcyl_ind_vort.png │ ├── sqcyl_mass.png │ ├── sqcyl_mesh.png │ ├── sqcyl_mesh2.png │ ├── sqcyl_residuals.png │ ├── svg │ │ ├── HRS_U_C_D.svg │ │ ├── domain_H.svg │ │ ├── incl_diff_bcs.svg │ │ ├── non_orto.svg │ │ ├── sh_bcs.svg │ │ ├── sh_diff_bcs.svg │ │ ├── sqcyl_ind_vort.svg │ │ ├── sqcyl_mesh.svg │ │ ├── unpdate_grad_weights.svg │ │ └── unpdate_linear_weights.svg │ ├── update_grad_weights.png │ └── update_linear_weights.png ├── conf.py ├── cont_codeintroduction.rst ├── cont_inclined_diff_script.rst ├── cont_introduction.rst ├── cont_nondim.rst ├── cont_simple.rst ├── cont_smith_hutton_diff_script.rst ├── cont_smith_hutton_script.rst ├── cont_solution.rst ├── cont_square_cylinder_script.rst ├── cont_testoperators.rst ├── index.rst ├── make_printable.sh ├── make_printable.vim_script ├── modules.rst ├── pyCFD_VTK_tools.rst ├── pyCFD_calculation.rst ├── pyCFD_config.rst ├── pyCFD_fields.rst ├── pyCFD_general.cython_boost_linux2.rst ├── pyCFD_general.rst ├── pyCFD_geometric_tools.cython_boost_linux2.rst ├── pyCFD_geometric_tools.rst ├── pyCFD_linear_solvers.cython_boost_linux2.rst ├── pyCFD_linear_solvers.rst ├── pyCFD_mesh.rst ├── pyCFD_monitors.rst ├── pyCFD_operators.rst ├── pyCFD_output.rst └── pyCFD_test_functions.rst ├── pyCFD_doc_PDF ├── Makefile ├── _build │ ├── doctrees │ │ ├── environment.pickle │ │ ├── modules.doctree │ │ ├── printable.doctree │ │ ├── pyCFD_VTK_tools.doctree │ │ ├── pyCFD_calculation.doctree │ │ ├── pyCFD_config.doctree │ │ ├── pyCFD_fields.doctree │ │ ├── pyCFD_general.cython_boost_linux2.doctree │ │ ├── pyCFD_general.doctree │ │ ├── pyCFD_geometric_tools.cython_boost_linux2.doctree │ │ ├── pyCFD_geometric_tools.doctree │ │ ├── pyCFD_linear_solvers.cython_boost_linux2.doctree │ │ ├── pyCFD_linear_solvers.doctree │ │ ├── pyCFD_mesh.doctree │ │ ├── pyCFD_monitors.doctree │ │ ├── pyCFD_operators.doctree │ │ ├── pyCFD_output.doctree │ │ └── pyCFD_test_functions.doctree │ └── latex │ │ └── printable.pdf ├── _images ├── conf.py └── modules.rst ├── pyCFD_fields ├── __init__.py ├── calculated_fields.py ├── fields.py └── initialization.py ├── pyCFD_general ├── __init__.py └── cython_boost_linux2 │ ├── __init__.py │ ├── __init__.pyc │ ├── build │ └── temp.linux-x86_64-2.7 │ │ └── cy_general.o │ ├── compile_cython_modules.sh │ ├── cy_general.c │ ├── cy_general.pyx │ ├── cy_general.so │ ├── setup.py │ └── setup.pyc ├── pyCFD_geometric_tools ├── __init__.py ├── cython_boost_linux2 │ ├── __init__.py │ ├── __init__.pyc │ ├── build │ │ └── temp.linux-x86_64-2.7 │ │ │ └── cy_geometric_tools.o │ ├── compile_cython_modules.sh │ ├── cy_geometric_tools.c │ ├── cy_geometric_tools.html │ ├── cy_geometric_tools.pyx │ ├── cy_geometric_tools.so │ ├── setup.py │ └── setup.pyc ├── cython_boost_win32 │ ├── __init__.py │ ├── __init__.pyc │ ├── build │ │ └── temp.win32-2.7 │ │ │ └── Release │ │ │ ├── cy_geometric_tools.def │ │ │ └── cy_geometric_tools.o │ ├── compile_cython_modules.sh │ ├── cy_geometric_tools.c │ ├── cy_geometric_tools.pyd │ ├── cy_geometric_tools.pyx │ └── setup.py └── geomTools.py ├── pyCFD_linear_solvers ├── __init__.py ├── compile_cython_modules.sh ├── cython_boost_linux2 │ ├── __init__.py │ ├── __init__.pyc │ ├── build │ │ └── temp.linux-x86_64-2.7 │ │ │ └── cy_linear_solvers.o │ ├── compile_cython_modules_win.txt │ ├── cy_linear_solvers.c │ ├── cy_linear_solvers.pyx │ ├── cy_linear_solvers.so │ └── setup.py ├── cython_boost_win32 │ ├── __init__.py │ ├── __init__.pyc │ ├── build │ │ └── temp.win32-2.7 │ │ │ └── Release │ │ │ ├── cy_linear_solvers.def │ │ │ └── cy_linear_solvers.o │ ├── cy_linear_solvers.c │ ├── cy_linear_solvers.pyd │ ├── cy_linear_solvers.pyx │ └── setup.py └── linear_solvers.py ├── pyCFD_mesh ├── __init__.py ├── cell.py ├── face.py ├── generic_mesh.py ├── mesh.py ├── mesh_object.py ├── patch.py ├── readers.py ├── sub_mesh.py └── vertex.py ├── pyCFD_monitors ├── __init__.py └── monitors.py ├── pyCFD_operators ├── __init__.py ├── cython_boost_linux2 │ ├── __init__.py │ ├── __init__.pyc │ ├── build │ │ └── temp.linux-x86_64-2.7 │ │ │ ├── cy_geometric_tools.o │ │ │ └── cy_operators.o │ ├── compile_cython_modules.sh │ ├── cy_operators.c │ ├── cy_operators.pyx │ ├── cy_operators.so │ └── setup.py ├── cython_boost_win32 │ ├── __init__.py │ ├── __init__.pyc │ ├── build │ │ └── temp.win32-2.7 │ │ │ └── Release │ │ │ ├── cy_operators.def │ │ │ └── cy_operators.o │ ├── compile_cython_modules.sh │ ├── cy_operators.c │ ├── cy_operators.pyd │ ├── cy_operators.pyx │ └── setup.py ├── explicit_operators.py ├── generic_equation.py ├── generic_operator.py ├── implicit_operators.py └── vector_operations.py ├── pyCFD_output ├── __init__.py ├── output.py └── output_other.py ├── pyCFD_test_functions ├── __init__.py └── testFunctions.py ├── test2DCavity.gnuplot ├── test2DCavity.py ├── test2DChannelFlow.gnuplot ├── test2DChannelFlow.py ├── test2DChannelFlow.py.lprof ├── test2DChannelFlowIMEX.py ├── testConvection_45degFlow.py ├── testConvection_SmithHutton.py ├── testDiffusion_6sidedBlock.py ├── testDiffusion_SmithHutton.py ├── testDiffusion_inclinedBlock.py ├── testGradient.py ├── 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