CI: Add codespell (#165)

.codespell-ignore-words

@@ -0,0 +1,7 @@
+Blocs
+checkin
+inout
+Lond
+pres
+ptd
+recuse

.codespellrc

@@ -0,0 +1,3 @@
+[codespell]
+skip = .git,*.ipynb,*.nb,*.bib,*.ps,*.patch,*~,CHANGES,*/tmp_build_dir,Cell_D_*
+ignore-words = .codespell-ignore-words

.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

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.
 

Docs/sphinx_documentation/source/AlgorithmOptions.rst

@@ -1,15 +1,15 @@
 
 .. _Chap:AlgorithmOptions:
 
-Algortihm Options
+Algorithm Options
 =================
 
 .. _sec:conserv:
 
 Conservative vs. Non-conservative
 ---------------------------------
 
-The following must be preceeded by "ns."
+The following must be preceded by "ns."
 
 +-------------------------+------------------------------------------------------------------------------+-------------+--------------+
 | | Description | Type | Default |
@@ -37,7 +37,7 @@ IAMR has the option to use a Method of Lines (MOL) or Godunov scheme to compute
 
 
 For problems without embedded boundaries, there are additional options when using the Godunov method. The following must
-be preceeded by "godunov."
+be preceded by "godunov."
 
 +-------------------------+-------------------------------------------------------------------------+-------------+--------------+
 | | Description | Type | Default |
@@ -51,7 +51,7 @@ be preceeded by "godunov."
 Diffusion
 ---------
 
-The following must be preceeded by "ns."
+The following must be preceded by "ns."
 
 +-------------------------+-----------------------------------------------------------------------+-------------+--------------+
 | | Description | Type | Default |

Docs/sphinx_documentation/source/Contributing.rst

@@ -119,10 +119,10 @@ Now you are free to play with your fork (for additional information, you can vis
 Making code changes
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-We do `not` reccomend making any changes within the ``development`` branch. Doing so
+We do `not` recommend making any changes within the ``development`` branch. Doing so
 will make your local ``development`` branch diverge from the matching branch in the
 main IAMR repository.
-Instead, we reccomend creating a new branch based on the ``development`` branch.
+Instead, we recommend creating a new branch based on the ``development`` branch.
 To proceed, make sure you are on the ``development`` branch within the IAMR directory.
 Then create branch ``<branch_name>`` (the branch name should reflect the piece
 of code you want to add, like ``high_order_interpolation``) with

Docs/sphinx_documentation/source/Debugging.rst

@@ -17,7 +17,7 @@ Diffusion and viscosity can be turned off by setting ``ns.vel_visc_coef = 0`` an
 ``ns.scal_diff_coefs = 0``.
 
 Sometimes, restarting from a checkpoint file can reduce the amount of time spent waiting for
-the code to fail durning the debugging process.
+the code to fail during the debugging process.
 
 If the problem only happens with multilevel runs, ``amr.subcycling_mode = None`` will turn
 time subcycling off and advance the whole system at the same dt.

Docs/sphinx_documentation/source/Getting_Started.rst

@@ -161,7 +161,7 @@ If you would like to display the data in another format, please let us know
 and we will point you to whatever we have that can help.
 
 Here we provide instructions on downloading
-and using Amrvis. For more infomation on visualization, including using other software
+and using Amrvis. For more information on visualization, including using other software
 for visualization, please see the :ref:`Visualization` Section.
 
 

Docs/sphinx_documentation/source/ProblemSetup.rst

@@ -5,7 +5,7 @@ Problem Setup
 
 To setup a new problem you must specify:
 
-#. intial conditions
+#. initial conditions
 
 #. resolution
 
@@ -237,7 +237,7 @@ As an example,
  xlo.tracer = 0.
  xlo.temp = 1.
 
-sets the boundary condtion type at the low x face to be an inflow with
+sets the boundary condition type at the low x face to be an inflow with
 xlo.type = “mass_inflow”.
 Then xlo.velocity = 1. 0. 0. sets the inflow velocity,
 xlo.density = 1. sets the inflow density,
@@ -263,7 +263,7 @@ zhi.velocity = 1. 0. 0. sets the wall at the high z face to be moving in the
 x-direction.
 Note that IAMR allows walls to move tangentially, but not in the normal direction.
 
-Users can create more complex Dirichlet boundary condtions by writing
+Users can create more complex Dirichlet boundary conditions by writing
 their own fill function in ``NS_bcfill.H``, then using that function to create
 an ``amrex::StateDescriptor::BndryFunc`` object and specifying which variables
 will use it in ``NS_setup.cpp``. More information on boundary conditions is in
@@ -274,7 +274,7 @@ Tagging criteria for creating AMR Levels
 
 If ``amr.max_level`` is greater than zero, then user specified tagging criteria are
 used to define regions for higher levels of refinement.
-For infomation on tagging see :ref:`sec:tagging`
+For information on tagging see :ref:`sec:tagging`
 
 
 .. _sec:EB-basics:

Docs/sphinx_documentation/source/RunningProblems.rst

@@ -187,7 +187,7 @@ The following inputs must be preceded by "amr." and control checkpoint/restart.
 | check_per | Frequency of checkpoint output by (approximate) simulation time; | Real | -1.0 |
 | | if -1 then no checkpoints will be written. (See note below) | | |
 +-------------------------+-----------------------------------------------------------------------+-------------+-----------+
-| checkpoint_files_output | Should we write checkpoint files? (Takes precident over check_int | Int | 1 |
+| checkpoint_files_output | Should we write checkpoint files? (Takes precedent over check_int | Int | 1 |
 | | and check_per) | | |
 +-------------------------+-----------------------------------------------------------------------+-------------+-----------+
 | check_file | Prefix to use for checkpoint output | String | chk |
@@ -279,7 +279,7 @@ This file has the same format as the ASCII input file:
 Log Files
 ~~~~~~~~~~~~~~~~
 
-The following inputs must be preceeded by "amr."
+The following inputs must be preceded by "amr."
 
 +-------------------------+-----------------------------------------------------------------------+-------------+-----------+
 | | Description | Type | Default |
@@ -565,7 +565,7 @@ Initializing the Calculation
 
 These options determine how we initialize the data for the calculation. The data initialization process
 ensures that the initial state is consistent with the constraint, and if applicable, the various AMR levels
-are consistent with eachother.
+are consistent with each other.
 
 The following inputs must be preceded by "ns."
 
@@ -584,7 +584,7 @@ The following inputs must be preceded by "ns."
 Checking Conservation
 ---------------------
 
-IAMR has the option to sum up the total mass (and a few other quantites) at a user-defined interval.
+IAMR has the option to sum up the total mass (and a few other quantities) at a user-defined interval.
 
 +-------------------------+-----------------------------------------------------------------------+-------------+--------------+
 | | Description | Type | Default |
@@ -605,4 +605,3 @@ for example.
 
 Note that by default the tracer not conservative. To conservatively advect the tracer,
 that option must be set in the inputs (see :ref:`sec:conserv`).
-

Docs/sphinx_documentation/source/SetupAndRunning.rst

@@ -20,10 +20,10 @@ infrastructure to read in the inputs parameters.
 (See AMReX's documentation on ``ParmParse`` here: :ref:`sec:basics:parmparse`.)
 
 .. tip::
- Before making any code changes, we highly reccomend creating a new git branch.
+ Before making any code changes, we highly recommend creating a new git branch.
 
 Extra points if the new branch's name reflects the changes, e.g. ``couette_flow``.
-We do `not` reccomend making any changes within the ``development`` branch because
+We do `not` recommend making any changes within the ``development`` branch because
 doing so will make your local ``development`` branch diverge from the matching branch
 in the main IAMR repository. This can lead to difficulties pulling in updates and bug-fixes
 from the main IAMR repo.

Docs/sphinx_documentation/source/Software.rst

@@ -170,7 +170,7 @@ how the interpolation is to be done, in both space and time. Importantly,
 the interpolation also requires that coarse data be well-defined over
 a time interval that brackets the time instant for which we are evaluating
 the grow cell value – this places requirements on how the time-integration
-of the various AMR levels are sequenced relative to eachother.
+of the various AMR levels are sequenced relative to each other.
 In AMReX, the field data associated with the system state, as well as the metadata
 associated with inter-level transfers, is bundled (encapsulated) in
 a class called “StateData”. The metadata
@@ -198,7 +198,7 @@ the user supplies data to fill grow cells.
 
 IAMR provides the ability to specify constant Dirichlet BCs
 in the inputs file (see section :ref:`sec:dirichlet`).
-Users can create more complex Dirichlet boundary condtions by writing
+Users can create more complex Dirichlet boundary conditions by writing
 their own fill function in ``NS_bcfill.H``, then using that function to create
 an ``amrex::StateDescriptor::BndryFunc`` object and specifying which variables
 will use it in ``NS_setup.cpp``.
@@ -369,7 +369,7 @@ the discussion of tiling in AMReX's documentation, :ref:`amrex:sec:basics:mfiter
 AMReX’s Non-Tiling Approach
 ---------------------------
 
-At the highest abstraction level, we have MultiFab (mulitple
+At the highest abstraction level, we have MultiFab (multiple
 FArrayBoxes). A MultiFab contains an array of Boxes (a Box contains integers specifying the index space it
 covers), including Boxes owned by other processors for the
 purpose of communication, an array of MPI ranks specifying which MPI
@@ -433,11 +433,11 @@ Note that the code is almost identical to the one with the non-tiling approach.
 Some comments:
 
 - The iterator now takes an extra argument to turn on tiling
- (set to true). There is another interface fo MFIter
+ (set to true). There is another interface of MFIter
  that can take an IntVect that explicitly gives the tile size
  in each coordinate direction.
 
- If we don’t explictly specify the tile size at the loop, then the
+ If we don’t explicitly specify the tile size at the loop, then the
  runtime parameter :cpp:`fabarray.mfiter_tile_size` can be used to set it
  globally.
 
@@ -701,9 +701,9 @@ Explicitly defined tagging functions
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Explicitly defined error estimation functions can be used either instead of or in addition to
-dynmaically generated funtions. These functions can be added to NavierStokes::errorEst() in
+dynamically generated functions. These functions can be added to NavierStokes::errorEst() in
 NS_error.cpp. Any dynamically generated error functions will operate first.
-Please note that while CLEARing a tagged cell is possible, it is not reccomended as it
+Please note that while CLEARing a tagged cell is possible, it is not recommended as it
 may not have the desired effect.
 
 
@@ -744,7 +744,7 @@ the MultiFab was written to disk.
 
 Think of the number :math:`N` as the number of independent I/O pathways in
 your underlying parallel filesystem. Of course a “real” parallel
-filesytem should be able to handle any reasonable value of :math:`N`. The
+filesystem should be able to handle any reasonable value of :math:`N`. The
 value -1 forces :math:`N` to the number of CPUs on which you’re
 running, which means that each CPU writes to a unique file, which can
 create a very large number of files, which can lead to inode issues.

Docs/sphinx_documentation/source/Tutorials.rst

@@ -76,7 +76,7 @@ Non-EB:
 * **Hotspot**: A hot bubble rising in closed box. Evolves a temperature field and uses
  a low Mach number constraint in place of incompressible. AMR refinement criteria is
  based on the temperature, but only 2D uses AMR by default. The 3D setup features an
- open top (outflow BC) and demonstates how to allow refinement at the outflow (which
+ open top (outflow BC) and demonstrates how to allow refinement at the outflow (which
  is turned off in IAMR by default).
 
 
@@ -136,12 +136,10 @@ Non-EB:
 * **HIT**: Homogeneous isentropic forced turbulence with constant density.
  This demonstrates defining a new forcing function by using a local edited
  version of ``NS_getForce.cpp``. IAMR's make system is automatically configured
- to select any local versions of files and ignore the corresponding verions in
+ to select any local versions of files and ignore the corresponding versions in
  ``IAMR/Source``. This problem is 3D only.
 
 
 * **Particles**: Particles in a double shear layer. Uses 2 levels of refinement
  and fixed grids. With fixed grids, a grid file (called ``fixed_grids_ml`` here) is
  used to define the grids for levels >= 1.
-
-

Docs/sphinx_documentation/source/Visualization.rst

@@ -210,7 +210,7 @@ the domain:
 :math:`>>>` value, location = pf.h.find\_max(‘density’)
 
 The list goes on. A full list of methods and attributes associated
-with the heirarchy object (and most any yt object or function) can be
+with the hierarchy object (and most any yt object or function) can be
 accessed by the help function:
 
 :math:`>>>` help(pf.h)
@@ -247,7 +247,7 @@ available units. We can access the data within the container:
 
 When the creation of objects is time-consuming, it can be convenient
 to save objects so they can be used in another session. To save an
-object as part of the .yt file affiliated with the heirarchy:
+object as part of the .yt file affiliated with the hierarchy:
 
 :math:`>>>` pf.h.save\_object(my\_data\_container, ‘sphere\_to\_analyze\_later’)
 

Exec/eb_run2d/regtest.2d.bubble

@@ -128,9 +128,9 @@ ns.redistribution_type = FluxRedist
 prob.probtype = 2
 prob.blob_center = 0.0 1.5 
 prob.blob_radius = 0.2
-# Background density is 1. Density is incresed by a factor of density_ic inside
+# Background density is 1. Density is increased by a factor of density_ic inside
 # the bubble
 prob.density_ic = 2.0
 
 #mag_vort is stepping out of bounds
-#amr.derive_plot_vars = mag_vort diveru avg_pressure
+#amr.derive_plot_vars = mag_vort diveru avg_pressure

Exec/run2d/regtest.2d.hotspot_rz

@@ -127,7 +127,7 @@ prob.probtype = 6
 prob.blob_center = 0.0 0.01 
 prob.blob_radius = 0.003
 prob.interface_width = 0.00000006
-# Background density is 1. Density is incresed by a factor of density_ic inside
+# Background density is 1. Density is increased by a factor of density_ic inside
 # the bubble
 prob.density_ic = 1.229
 # Can also set up a flow, defaults to zero

RELEASE_NOTES

@@ -2,8 +2,8 @@
 Release version 17.09 (September, 2017)
 
 11/3/17
-Release version 17.11 (Novermber, 2017)
-Small changes to documentation and code commments.
+Release version 17.11 (November, 2017)
+Small changes to documentation and code comments.
 Added a test problem with an input tracer being forced into the domain with an inflow jet.
 
 12/1/17 
@@ -71,7 +71,7 @@ Minor compiler settings fixes
 6/3/19
 Bug fix in filling u_mac ghost cells
 Fix create_umac_grown for periodic cases
-Misc code cleanup; extra arguments, extraenous calls, compiler quieting
+Misc code cleanup; extra arguments, extraneous calls, compiler quieting
 Parallel reduction cleanup
 Various changes to be consistent with AMReX interfaces
 
@@ -156,7 +156,7 @@ Minor tiling fixes
 
 12/2/20
 Creation from Embiggen of a tool to extrapolate coarse checkpoint file to a finest mesh
-Add a "stop_interval" parameter to allow the simulation to stop at a specfic additional time interval after the physical time of a restart checkpoint file
+Add a "stop_interval" parameter to allow the simulation to stop at a specific additional time interval after the physical time of a restart checkpoint file
 Remove Dpdt_Type and code related to Pressure temporal-centeredness at a Point (vs. Interval)
 Test case updates
 
@@ -176,7 +176,7 @@ Many small updates to several parts of the code, including:
 4/1/21
 Cleanup unused options, problems, and inputs files
 Fixes to ref_ratio=4 ghost cell bugs
-Port some initializtion kernels to C++
+Port some initialization kernels to C++
 Port some derived functions to C++
 Port boundary filling functions to C++
 Ghost cell filling bugs
@@ -214,7 +214,7 @@ Various EB and advection updates and fixes
 
 9/1/21
 Diffusion changes - use new multicomponent MLMG solver
-In the temperature solve, let ns.temp_cond_coef represent (lamba/c_p)
+In the temperature solve, let ns.temp_cond_coef represent (lambda/c_p)
 Hydrodynamic algorithm updates
 Updates to create_umac_grown
 Embedded boundary compile updates
@@ -225,7 +225,7 @@ Moved slope routines to AMReX-Hydro
 Documentation reorganization
 Misc. AMR fixes
 Misc. cleanup (re-org, quiet compiler warnings, remove unused code)
-Misc. compiler fixes and general updates to test and bechmark problems
+Misc. compiler fixes and general updates to test and benchmark problems
 
 11/2/21
 Various GPU fixes
@@ -290,4 +290,4 @@ Fix bug in multilevel velocity sync. Misc code cleanup.
 
 12/1/22
 Allow BDS for velocity advection (but still not in computing MAC velocities). Note this changes behavior for advection_scheme=BDS option, which before only used BDS for scalars and used Godunov for velocity.
-Fix norm calculation in Tutorials/TaylorGreen/benchmarks. Minor clean up.
+Fix norm calculation in Tutorials/TaylorGreen/benchmarks. Minor clean up.