diff --git a/.codespell-ignore-words b/.codespell-ignore-words new file mode 100644 index 000000000..f24c3a56b --- /dev/null +++ b/.codespell-ignore-words @@ -0,0 +1,4 @@ +Blocs +inout +ptd +recuse diff --git a/.codespellrc b/.codespellrc new file mode 100644 index 000000000..5f01f69fd --- /dev/null +++ b/.codespellrc @@ -0,0 +1,3 @@ +[codespell] +skip = .git,*.ipynb,*.bib,*.ps,*.patch,*~,CHANGES,*/tmp_build_dir +ignore-words = .codespell-ignore-words diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml new file mode 100644 index 000000000..bec24c5c7 --- /dev/null +++ b/.github/workflows/codespell.yml @@ -0,0 +1,23 @@ +name: codespell + +on: [push, pull_request] + +concurrency: + group: ${{ github.ref }}-${{ github.head_ref }}-codespell + cancel-in-progress: true + +jobs: + codespell: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + + - name: Install codespell + run: | + sudo apt-get update + sudo apt-get install -y --no-install-recommends python3-pip + pip3 install --user codespell + + - name: Run codespell + run: codespell diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index 766fd930f..e76e4d8d9 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -5,7 +5,7 @@ We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender -identity and expression, level of experience, education, socio-economic status, +identity and expression, level of experience, education, socioeconomic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation. diff --git a/Docs/sphinx_documentation/source/EB.rst b/Docs/sphinx_documentation/source/EB.rst index 73fed8b59..d2255daf3 100644 --- a/Docs/sphinx_documentation/source/EB.rst +++ b/Docs/sphinx_documentation/source/EB.rst @@ -21,7 +21,7 @@ incflo provides several options of embedded boundary geometries. The inputs para determines which geometry is selected by :cpp:`incflo::MakeEBGeometry()` within :cpp:`incflo/src/embedded_boundaries`. The procedure to create your own EB geometry is described in the AMReX documentation on :ref:`amrex:sec:EB:ebinit`. As discussed in the AMReX documentation, note that when constructing the EB, we must specify a -maxium coarsening level (``max_crse_level``): +maximum coarsening level (``max_crse_level``): .. highlight:: c++ diff --git a/Docs/sphinx_documentation/source/GettingStarted.rst b/Docs/sphinx_documentation/source/GettingStarted.rst index 863aee58c..15867edc4 100644 --- a/Docs/sphinx_documentation/source/GettingStarted.rst +++ b/Docs/sphinx_documentation/source/GettingStarted.rst @@ -370,4 +370,4 @@ files are used for restarting the code. For more information see the AMReX Docum Visualizing the Results ======================= -Options for visualizing the data are discussed in the AMReX Documenation on :ref:`amrex:Chap:Visualization`. +Options for visualizing the data are discussed in the AMReX Documentation on :ref:`amrex:Chap:Visualization`. diff --git a/Docs/sphinx_documentation/source/InputsProblemDefinition.rst b/Docs/sphinx_documentation/source/InputsProblemDefinition.rst index 477c99cf8..4434800e4 100644 --- a/Docs/sphinx_documentation/source/InputsProblemDefinition.rst +++ b/Docs/sphinx_documentation/source/InputsProblemDefinition.rst @@ -65,10 +65,9 @@ Setting basic boundary conditions can be specified by inputs preceded by "xlo", The implementation requires that there is EB separating the inflow and outflow regions, and only currently treats constant viscosity (i.e. requires the inputs file contains ``incflo.use_tensor_solve = false``). It does allow for non-constant scalar diffusivity. To create a new problem setup with mixed BCs, one must additionally - specify the Dirchlet and Neumann areas in ``prob/prob_bc.cpp`` In this file there are functions to set the needed BC info for the diffusion solver, the MAC projection, and with the same function, the nodal projection and advection. Comments in the code provide a detailed explaination for each instance. For addditional details on mixed BCs, also see AMReX-Hydro's documentation (:ref:`bcs`). + specify the Dirchlet and Neumann areas in ``prob/prob_bc.cpp`` In this file there are functions to set the needed BC info for the diffusion solver, the MAC projection, and with the same function, the nodal projection and advection. Comments in the code provide a detailed explanation for each instance. For additional details on mixed BCs, also see AMReX-Hydro's documentation (:ref:`bcs`). .. To create a new setup: initial conditions go in prob/prob_init_fluid.cpp inflow boundary conditions are set in prob/prob_bc.H -- the BCType for mixed bc is set at foextrap here to allow the outflow to get appropriately filled, which would already have happened before reaching these functions. - diff --git a/src/boundary_conditions/incflo_set_bcs.cpp b/src/boundary_conditions/incflo_set_bcs.cpp index 6d930080c..efe172595 100644 --- a/src/boundary_conditions/incflo_set_bcs.cpp +++ b/src/boundary_conditions/incflo_set_bcs.cpp @@ -156,7 +156,7 @@ incflo::make_robinBC_MFs(int lev, MultiFab* state) Array4 const& f_arr = robin_f.array(mfi); if (state) { - // state has filled boundry, so can use its ghost cells for the BC values + // state has filled boundary, so can use its ghost cells for the BC values Array4 const& bcv = state->const_array(mfi); // Diffusion, solving for velocity, density, tracer // diff --git a/src/convection/incflo_compute_advection_term.cpp b/src/convection/incflo_compute_advection_term.cpp index 30a4c8f8d..c1f178865 100644 --- a/src/convection/incflo_compute_advection_term.cpp +++ b/src/convection/incflo_compute_advection_term.cpp @@ -224,7 +224,7 @@ incflo::compute_convective_term (Vector const& conv_u, { // // BDS needs umac on physical boundaries. - // Godunov handles physical boundaries interally, but needs periodic ghosts filled. + // Godunov handles physical boundaries internally, but needs periodic ghosts filled. // MOL doesn't need any umac ghost cells, so it doesn't get here. // Real fake_time = 0.; diff --git a/src/particles/ParticleData.H b/src/particles/ParticleData.H index fcf60e69f..a95bb00b5 100644 --- a/src/particles/ParticleData.H +++ b/src/particles/ParticleData.H @@ -210,7 +210,7 @@ class ParticleData return m_namelist_unalloc; } - /*! queries if containe has species of a certain name */ + /*! queries if container has species of a certain name */ inline bool contains ( const std::string& a_name ) const { BL_PROFILE("ParticleData::contains()"); @@ -238,4 +238,3 @@ class ParticleData #endif #endif - diff --git a/src/prob/prob_init_fluid.cpp b/src/prob/prob_init_fluid.cpp index e776b3c87..08634fa7c 100644 --- a/src/prob/prob_init_fluid.cpp +++ b/src/prob/prob_init_fluid.cpp @@ -858,7 +858,7 @@ void incflo::init_periodic_tracer (Box const& vbx, Box const& /*gbx*/, tracer(i,j,k,1) = A *(std::sin(C*(y+z) - Real(0.00042)) + Real(1.0)) * std::exp(x); }); } else { - Abort("Unknow periodic tracer probtype"); + Abort("Unknown periodic tracer probtype"); } } diff --git a/src/setup/init.cpp b/src/setup/init.cpp index 5ca9f2310..a7ded2b4c 100644 --- a/src/setup/init.cpp +++ b/src/setup/init.cpp @@ -82,7 +82,7 @@ void incflo::ReadParameters () m_redistribution_type != "StateRedist") amrex::Abort("redistribution type must be NoRedist, FluxRedist, or StateRedist"); - if (m_advection_type == "Godunov" && m_godunov_ppm) amrex::Abort("Cant use PPM with EBGodunov"); + if (m_advection_type == "Godunov" && m_godunov_ppm) amrex::Abort("Can't use PPM with EBGodunov"); pp.query("write_geom_chk", m_write_geom_chk); #endif diff --git a/test_2d/benchmark.rotated_planes_y b/test_2d/benchmark.rotated_planes_y index bea99287e..f38389f3e 100644 --- a/test_2d/benchmark.rotated_planes_y +++ b/test_2d/benchmark.rotated_planes_y @@ -85,7 +85,7 @@ cylinder.center = 0.0 0.0 0.0 incflo.probtype = 6 # Note that with this prob_type, ic_u is used to mean the velocity -# along the direction of the cylinder, irregardless of the direction +# along the direction of the cylinder, regardless of the direction # of the cylinder incflo.ic_u = -0.5 # incflo.ic_v = 0.8660254038 # diff --git a/test_bds_2d/inputs.circ_traceradvect b/test_bds_2d/inputs.circ_traceradvect index 885bf919c..d2531d7c7 100644 --- a/test_bds_2d/inputs.circ_traceradvect +++ b/test_bds_2d/inputs.circ_traceradvect @@ -1,4 +1,4 @@ -amrex.fpe_trap_invalid=1 # hav a trap to catch a bug +amrex.fpe_trap_invalid=1 # have a trap to catch a bug incflo.probtype = 14 #¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨# # SIMULATION STOP # diff --git a/test_bds_2d/inputs.gaussian_traceradvect b/test_bds_2d/inputs.gaussian_traceradvect index bdd0e2af9..1e1ab63c3 100644 --- a/test_bds_2d/inputs.gaussian_traceradvect +++ b/test_bds_2d/inputs.gaussian_traceradvect @@ -1,4 +1,4 @@ -amrex.fpe_trap_invalid=1 # hav a trap to catch a bug +amrex.fpe_trap_invalid=1 # have a trap to catch a bug incflo.probtype = 15 #¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨# # SIMULATION STOP # diff --git a/test_bds_3d/inputs.circ_traceradvect b/test_bds_3d/inputs.circ_traceradvect index 0b68d0e33..ea60992f8 100644 --- a/test_bds_3d/inputs.circ_traceradvect +++ b/test_bds_3d/inputs.circ_traceradvect @@ -1,4 +1,4 @@ -amrex.fpe_trap_invalid=1 # hav a trap to catch a bug +amrex.fpe_trap_invalid=1 # have a trap to catch a bug incflo.probtype = 14 #¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨# # SIMULATION STOP # diff --git a/test_bds_3d/inputs.gaussian_traceradvect b/test_bds_3d/inputs.gaussian_traceradvect index a1b322789..0fbf34ce4 100644 --- a/test_bds_3d/inputs.gaussian_traceradvect +++ b/test_bds_3d/inputs.gaussian_traceradvect @@ -1,4 +1,4 @@ -amrex.fpe_trap_invalid=1 # hav a trap to catch a bug +amrex.fpe_trap_invalid=1 # have a trap to catch a bug incflo.probtype = 15 #¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨# # SIMULATION STOP #