Fix spelling (Exawind#912)

.codespell-ignore-words

@@ -0,0 +1,9 @@
+blocs
+inout
+dout
+pres
+degress
+vell
+nd
+fo
+ue

.codespellrc

@@ -0,0 +1,3 @@
+[codespell]
+skip = .git,*.ipynb,*.bib,*.ps,*.patch,spack-build-*,*/build,*/submods,plt*,chk*,__pycache__,.ccls,.ccls-cache,*.pdf,DU21_A17.txt,inspect_abl_io.html
+ignore-words = .codespell-ignore-words

.github/workflows/ci.yml

@@ -149,6 +149,7 @@ jobs:
                ccache-${{github.workflow}}-${{github.job}}-git-
       - name: Prepare CUDA environment
         run: |
+          ${{github.workspace}}/submods/amrex/.github/workflows/dependencies/ubuntu_free_disk_space.sh
           sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub
           echo "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64 /" | sudo tee /etc/apt/sources.list.d/cuda.list
           sudo apt-get update
@@ -204,12 +205,13 @@ jobs:
                ccache-${{github.workflow}}-${{github.job}}-git-
       - name: Prepare HIP environment
         run: |
+          ${{github.workspace}}/submods/amrex/.github/workflows/dependencies/ubuntu_free_disk_space.sh
           wget -q -O - https://repo.radeon.com/rocm/rocm.gpg.key | sudo apt-key add -
           echo 'deb [arch=amd64] https://repo.radeon.com/rocm/apt/5.6.1/ ubuntu main' | sudo tee /etc/apt/sources.list.d/rocm.list
           echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$PATH' | sudo tee -a /etc/profile.d/rocm.sh
           sudo apt-get update
           sudo apt-get install -y \
-              build-essential rocm-dev roctracer-dev rocprofiler-dev rocrand-dev rocprim-dev rocm-libs
+              build-essential rocm-dev rocrand-dev rocprim-dev
       - name: Configure and build
         run: |
           source /etc/profile.d/rocm.sh
@@ -266,6 +268,7 @@ jobs:
       - name: Prepare SyCL environment
         run: |
           export DEBIAN_FRONTEND=noninteractive
+          ${{github.workspace}}/submods/amrex/.github/workflows/dependencies/ubuntu_free_disk_space.sh
           sudo wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
           sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
           echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
@@ -409,6 +412,25 @@ jobs:
         uses: github/codeql-action/upload-sarif@v2
         with:
           sarif_file: sarif-results/cpp.sarif
+  Lint-codespell:
+    needs: Formatting
+    runs-on: ubuntu-latest
+    steps:
+      - name: Clone
+        uses: actions/checkout@v3
+        with:
+          submodules: false
+      - name: Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+      - name: Dependencies
+        run: |
+          # Install Python packages
+          python -m pip install --upgrade pip
+          pip install codespell
+      - name: Run codespell
+        run: codespell
 #  Docker:
 #    needs: Formatting
 #    runs-on: ubuntu-latest

amr-wind/boundary_conditions/BCInterface.H

@@ -10,7 +10,7 @@
 
 /**
  *  \defgroup field_bc Boundary conditions management
- *  Boundary conditions managment
+ *  Boundary conditions management
  *
  *  This group documents the boundary condition management interface within
  *  AMR-Wind. Boundary conditions are registered on a Field instance and are

amr-wind/core/FieldRepo.H

@@ -131,7 +131,7 @@ public:
     /** Create a new field instance
      *
      *  @param name Unique identifier for this field
-     *  @param ncomp Number of components in this field (defalt: 1)
+     *  @param ncomp Number of components in this field (default: 1)
      *  @param ngrow Number of ghost cells/nodes for this field (default: 1)
      *  @param nstates Number of time states for this field (default: 1)
      *  @param floc Field location (default: cell-centered)
@@ -267,7 +267,7 @@ public:
      *
      *  Integer fields are used for masks and iblanking with overset meshes
      *
-     *  \param name [in] Unique indentifier for the field
+     *  \param name [in] Unique identifier for the field
      */
     IntField& declare_int_field(
         const std::string& name,

amr-wind/core/MLMGOptions.cpp

@@ -96,7 +96,7 @@ void MLMGOptions::operator()(amrex::MLMG& mlmg)
         else if (hypre_interface == "semi_structured")
             mlmg.setHypreInterface(amrex::Hypre::Interface::semi_structed);
         else if (hypre_interface == "structured")
-            mlmg.setHypreInterface(amrex::Hypre::Interface::structed);
+            mlmg.setHypreInterface(amrex::Hypre::Interface::structured);
         else
             amrex::Abort(
                 "Invalid hypre interface. Valid options: ij semi_structured "

amr-wind/core/SimTime.H

@@ -185,7 +185,7 @@ private:
     //! Initial starting time index for generating checkpoint files
     int m_chkpt_start_index{0};
 
-    //! Initial starting time index for generating ouput files
+    //! Initial starting time index for generating output files
     int m_plt_start_index{0};
 
     //! Initial starting time index for regriding

amr-wind/equation_systems/PDE.H

@@ -30,7 +30,7 @@ public:
     using SchemeType = Scheme;
 
     //! Unique identifier used to register and create this instance on-demand
-    //! through the factor iterface
+    //! through the factor interface
     static std::string identifier()
     {
         return PDE::pde_name() + "-" + Scheme::scheme_name();

amr-wind/equation_systems/PDEBase.H

@@ -43,7 +43,7 @@ namespace pde {
  *  terms, the diffusion term, and the convective term. A PDE may declare
  *  additional fields that are not stored in this object, but can be queried
  *  using the FieldRepo instance. For example, the incompressible Navier-Stokes
- *  (ICNS) always declars density and pressure in addition to the velocity
+ *  (ICNS) always declares density and pressure in addition to the velocity
  *  fields.
  *
  */
@@ -59,7 +59,7 @@ public:
     //! Perform initialization actions for a PDE after the mesh is generated
     virtual void initialize() = 0;
 
-    //! Preform updates specific to PDE after a regrid is performed
+    //! Perform updates specific to PDE after a regrid is performed
     virtual void post_regrid_actions() = 0;
 
     //! Compute the source (forcing) terms for this PDE

amr-wind/equation_systems/icns/source_terms/ABLMeanBoussinesq.H

@@ -7,7 +7,7 @@
 
 namespace amr_wind::pde::icns {
 
-/** Boussinesq bouyancy source term
+/** Boussinesq buoyancy source term
  *  \ingroup icns_src we_abl
  *
  *  \f[

amr-wind/equation_systems/icns/source_terms/BoussinesqBuoyancy.H

@@ -6,7 +6,7 @@
 
 namespace amr_wind::pde::icns {
 
-/** Boussinesq bouyancy source term
+/** Boussinesq buoyancy source term
  *  \ingroup icns_src we_abl
  *
  *  \f[

amr-wind/immersed_boundary/bluff_body/bluff_body_ops.H

@@ -13,7 +13,7 @@ namespace amr_wind::ib {
 namespace bluff_body {
 
 /** Parse common data for modeling non-blade bluff bodies via an immersed
- * bounary
+ * boundary
  */
 void read_inputs(
     BluffBodyBaseData& /*wdata*/,

amr-wind/incflo.cpp

@@ -213,7 +213,7 @@ bool incflo::regrid_and_update()
         m_sim.post_manager().post_regrid_actions();
     }
 
-    // update cell counts if unitialized or if a regrid happened
+    // update cell counts if uninitialized or if a regrid happened
     if (m_cell_count == -1 || m_time.do_regrid()) {
         m_cell_count = 0;
         for (int i = 0; i <= finest_level; i++) {

amr-wind/ocean_waves/relaxation_zones/stokes_waves_K.H

@@ -127,7 +127,7 @@ AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE void stokes_coefficients(
 
     if (StokesOrder > 5 || StokesOrder < 2) {
         amrex::Abort(
-            "invalid stokes order speficied. It should be between 2,3,4 or 5 ");
+            "invalid stokes order specified. It should be between 2,3,4 or 5 ");
     }
 }
 

amr-wind/physics/ChannelFlow.H

@@ -83,7 +83,7 @@ private:
 
     WallFunction m_wall_func;
 
-    //! Wall normal directon - Default y direction
+    //! Wall normal direction - Default y direction
     int m_norm_dir{1};
 
     //! initial density value

amr-wind/physics/SyntheticTurbulence.cpp

@@ -171,7 +171,7 @@ void load_turb_plane_data(
     auto wvel = ncf.var("wvel");
 
     if ((ir - il) == 1) {
-        // two consequtive planes load them in one shot
+        // two consecutive planes load them in one shot
         uvel.get(&turb_grid.uvel[0], start, count);
         vvel.get(&turb_grid.vvel[0], start, count);
         wvel.get(&turb_grid.wvel[0], start, count);
@@ -458,7 +458,7 @@ SyntheticTurbulence::SyntheticTurbulence(const CFDSim& sim)
     // vector)
     m_turb_grid.tr_mat = vs::zrot(270.0 - wind_direction);
 
-    amrex::Print() << "Synthethic turbulence forcing initialized \n"
+    amrex::Print() << "Synthetic turbulence forcing initialized \n"
                    << "  Turbulence file = " << m_turb_filename << "\n"
                    << "  Box lengths = [" << m_turb_grid.box_len[0] << ", "
                    << m_turb_grid.box_len[1] << ", " << m_turb_grid.box_len[2]

amr-wind/physics/multiphase/MultiPhase.H

@@ -6,7 +6,7 @@
 
 /** Multiphase physics
  *
- * This class implemnts the necessary code to simulate multiphase
+ * This class implements the necessary code to simulate multiphase
  * (air-water interaction) problems with AMR-Wind. It reads the
  * namespace `MultiPhase' from the input file to determine how the
  * initial conditions are generated.

amr-wind/physics/multiphase/MultiPhase.cpp

@@ -29,7 +29,7 @@ MultiPhase::MultiPhase(CFDSim& sim)
         m_interface_capturing_method = amr_wind::InterfaceCapturingMethod::VOF;
         auto& vof_eqn = sim.pde_manager().register_transport_pde("VOF");
         m_vof = &(vof_eqn.fields().field);
-        // Create levelset as a auxilliary field only !
+        // Create levelset as a auxiliary field only !
         m_levelset = &(m_sim.repo().get_field("levelset"));
         const amrex::Real levelset_default = 0.0;
         BCScalar bc_ls(*m_levelset);
@@ -47,7 +47,7 @@ MultiPhase::MultiPhase(CFDSim& sim)
         m_interface_capturing_method = amr_wind::InterfaceCapturingMethod::VOF;
         auto& vof_eqn = sim.pde_manager().register_transport_pde("VOF");
         m_vof = &(vof_eqn.fields().field);
-        // Create levelset as a auxilliary field only !
+        // Create levelset as a auxiliary field only !
         m_levelset = &(m_sim.repo().get_field("levelset"));
         const amrex::Real levelset_default = 0.0;
         BCScalar bc_ls(*m_levelset);

amr-wind/utilities/sampling/DTUSpinnerSampler.H

@@ -12,7 +12,7 @@ namespace amr_wind::sampling {
  *  Defines probes along a line defined by a time history from `m_azimuth_table`
  *  and `m_elevation_table` with a length of `m_length`. This determines the
  * `start` and `end` points at every time-step and divides the line into equal
- * segements as determined by `num_points`. The length of each segment is given
+ * segments as determined by `num_points`. The length of each segment is given
  * by \f[ m_length / (num_points - 1) \f]
  */
 class DTUSpinnerSampler : public LidarSampler

amr-wind/utilities/sampling/DTUSpinnerSampler.cpp

@@ -80,7 +80,7 @@ void DTUSpinnerSampler::sampling_locations(SampleLocType& locs) const
 
         int offset = k * AMREX_SPACEDIM;
 
-        // Loop per spacial dimension
+        // Loop per spatial dimension
         for (int d = 0; d < AMREX_SPACEDIM; ++d) {
             dx[d] = (m_end[d + offset] - m_start[d + offset]) / ndiv;
         }

amr-wind/utilities/sampling/Enstrophy.H

@@ -9,7 +9,7 @@ namespace amr_wind::enstrophy {
 /** enstrophy object
  *  \ingroup Enstrophy
  *
- *  A concrete impelementation of the post-processing interface that deals with
+ *  A concrete implementation of the post-processing interface that deals with
  *  the total enstrophy
  *
  */

amr-wind/utilities/sampling/FieldNorms.H

@@ -9,7 +9,7 @@ namespace amr_wind::field_norms {
 /** field norm object
  *  \ingroup Field Norm
  *
- *  A concrete impelementation of the post-processing interface that deals with
+ *  A concrete implementation of the post-processing interface that deals with
  *  norms of fields. FIXME: need to update this
  *
  */

amr-wind/utilities/sampling/KineticEnergy.H

@@ -9,7 +9,7 @@ namespace amr_wind::kinetic_energy {
 /** kinetic energy object
  *  \ingroup Kinetic Energy
  *
- *  A concrete impelementation of the post-processing interface that deals with
+ *  A concrete implementation of the post-processing interface that deals with
  *  integrating total kinetic energy
  *
  */

amr-wind/utilities/sampling/LidarSampler.H

@@ -12,7 +12,7 @@ namespace amr_wind::sampling {
  *  Defines probes along a line defined by a time history from `m_azimuth_table`
  *  and `m_elevation_table` with a length of `m_length`. This determines the
  * `start` and `end` points at every time-step and divides the line into equal
- * segements as determined by `num_points`. The length of each segment is given
+ * segments as determined by `num_points`. The length of each segment is given
  * by \f[ m_length / (num_points - 1) \f]
  */
 class LidarSampler : public LineSampler

amr-wind/utilities/sampling/LineSampler.H

@@ -9,7 +9,7 @@ namespace amr_wind::sampling {
  *  \ingroup sampling
  *
  *  Defines probes along a line defined by `start` and `end` coordinates and
- *  divides it into equal segements as determined by `num_points`. The length of
+ *  divides it into equal segments as determined by `num_points`. The length of
  *  each segment is given by \f[ (end - start) / (num_points - 1) \f]
  */
 class LineSampler : public SamplerBase::Register<LineSampler>

amr-wind/utilities/sampling/Sampling.H

@@ -26,10 +26,10 @@ namespace amr_wind::sampling {
 /** Collection of data sampling objects
  *  \ingroup sampling
  *
- *  A concrete impelementation of the post-processing interface that deals with
+ *  A concrete implementation of the post-processing interface that deals with
  *  data probes. Multiple instances of sampling entities (e.g., point cloud or
  *  probes, line, or plane samplers) can be registered. Internally, the data
- *  probles are represented as amr_wind::sampling::SamplingContainer for
+ *  problems are represented as amr_wind::sampling::SamplingContainer for
  *  tracking their position within the CFD mesh and updating the fields of
  *  interest.
  *

amr-wind/utilities/sampling/WaveEnergy.H

@@ -12,7 +12,7 @@ namespace amr_wind::wave_energy {
  *  A concrete implementation of the post-processing interface that deals with
  *  integrating total wave energy. This routine calculates the kinetic energy
  *  (KE) and potential energy (PE) according to the following definitions. It
- *  caclulates the correct potential energy offset, assuming an equilibrium
+ *  calculates the correct potential energy offset, assuming an equilibrium
  *  water level of 0 unless specified otherwise by an input parameter. It also
  *  assumes the traditional coordinate system, where interface height/depth is
  *  in z.

amr-wind/wind_energy/actuator/ActuatorContainer.cpp

@@ -298,7 +298,7 @@ void ActuatorContainer::populate_field_buffers()
 
 /** Helper method for ActuatorContainer::sample_fields
  *
- *  Performs a trilinear interpolation of the velocity/desnity field to particle
+ *  Performs a trilinear interpolation of the velocity/density field to particle
  *  locations. It also updates the particle locations such that the next
  *  Redistribute call restores the particles back to their original MPI rank
  *  where they were created.

amr-wind/wind_energy/actuator/actuator_types.H

@@ -90,7 +90,7 @@ struct ActGrid
     //! Velocity vector at the sampled locations
     VecList vel;
 
-    //! Density at the smapled locations
+    //! Density at the sampled locations
     RealList density;
 
     /** Helper method to resize the data arrays defined on the grid

amr-wind/wind_energy/actuator/actuator_utils.H

@@ -75,7 +75,7 @@ gaussian1d(const amrex::Real& dist, const amrex::Real& eps)
 
 /** Compute distance between two points
  *
- * @param origin Origin for the cylindrical coodinate system
+ * @param origin Origin for the cylindrical coordinate system
  * @param normal Normal  relative to origin (defines cylinder orientation)
  * @param point1 location of the first point in Cartesian coordinates
  * @param point2 location of second point in Cartesian coordinates

amr-wind/wind_energy/actuator/disk/disk_spreading.H

@@ -224,7 +224,7 @@ public:
             } else if (key == "LinearBasis") {
                 m_function = &SpreadingFunction::linear_basis_spreading;
             } else {
-                amrex::Abort("Invalide spreading type");
+                amrex::Abort("Invalid spreading type");
             }
         } else {
             m_function = &SpreadingFunction::linear_basis_in_theta;

docs/doxygen/main_page.md

@@ -1,7 +1,7 @@
 # AMR-Wind API documentation {#mainpage}
 
 [AMR-Wind](https://github.com/exawind/amr-wind) is a massively parallel,
-block-structured adaptive-mesh, incompressible flow sover for wind turbine and
+block-structured adaptive-mesh, incompressible flow solver for wind turbine and
 wind farm simulations. The codebase is a wind-focused fork of
 [incflo](https://github.com/AMReX-Codes/incflo). The solver is built on top of
 the [AMReX library](https://amrex-codes.github.io/amrex). AMReX library provides
@@ -56,7 +56,7 @@ is organized in subdirectories described below:
 - `docs` -- User manual (Sphinx-based) and Doxygen files
 - `submods` -- Third-party libraries and dependencies
 - `test` -- Regression tests and associated infrastructure
-- `tools` -- Miscellanous post-processing scripts and other utilities
+- `tools` -- Miscellaneous post-processing scripts and other utilities
 
 When developing new features, we strongly recommend creating a unit-test and
 develop features incrementally and testing as you add capabilities. Unit-tests

docs/sphinx/developer/coding_guidelines.rst

@@ -22,13 +22,13 @@ team.
    <https://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines>`_ for best
    practices when coding in C++.
 
-**Write code targeting heterogenous architectures**
+**Write code targeting heterogeneous architectures**
 
    All code must be written in a way such that it can run on GPUs without
    errors. Please consult the `GPU section
    <https://amrex-codes.github.io/amrex/docs_html/GPU_Chapter.html>`_ in AMReX
    documentation to learn the correct data structures and looping paradigms to
-   use when targeting heterogenous architectures.
+   use when targeting heterogeneous architectures.
 
 **Unit and regression tests**