add codespell (#399)

.codespell-ignore-words

@@ -0,0 +1,18 @@
+blocs
+bloc
+inout
+pres
+bion
+tye
+delt
+thi
+daa
+numer
+clen
+coul
+dum
+crate
+vie
+fromm
+nd
+hsi

.codespellrc

@@ -0,0 +1,5 @@
+[codespell]
+skip = .git,*.ipynb,*.bib,*.ps,*~,periodic_table.list,track-enucdot-profile
+ignore-words = .codespell-ignore-words
+
+

.github/workflows/codespell.yml

@@ -0,0 +1,39 @@
+name: codespell
+
+on:
+  push:
+    branches:
+      - development
+      - main
+  pull_request:
+    branches:
+      - development
+
+jobs:
+  codespell:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Cache pip
+        uses: actions/cache@v3
+        with:
+          # this path is specific to Ubuntu
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install dependencies
+        run: pip install codespell
+
+      - name: Run codespell
+        run: |
+          codespell
+

CITATION

@@ -1,6 +1,6 @@
 MAESTROeX derives from MAESTRO.  When citing the code, please cite the
-two primary alrogithm papers below as well as any of the MAESTRO papers appropriate
-to the discussion.
+two primary algorithm papers below as well as any of the MAESTRO
+papers appropriate to the discussion.
 
    @ARTICLE{2019ApJ...887..212F,
           author = {{Fan}, Duoming and {Nonaka}, Andrew and {Almgren}, Ann S. and

Exec/science/README

@@ -19,7 +19,7 @@ flame/
 
 sub_chandra/
 
-   Surpise! We're modelling convection.  This time in 3D spherical
+   Surprise! We're modelling convection.  This time in 3D spherical
    in the helium shell on the surface of a sub-Chandrasekhar mass
    carbon/oxygen white dwarf.  Such systems can potentially yield
    a variety of explosive outcomes.  This setup is the basis for

Exec/science/code_comp/MaestroBaseState.cpp

@@ -99,7 +99,7 @@ void Maestro::InitBaseState(BaseState<Real>& rho0, BaseState<Real>& rhoh0,
 
         // do HSE using RK2
 
-        // out intergration starts at y - h
+        // out integration starts at y - h
         Real h = r == 0 ? base_geom.dr(n) * 0.5 : base_geom.dr(n);
 
         auto k = dUdy(y - h, U_old);

Exec/science/rotating_star/ModelParser.cpp

@@ -33,7 +33,7 @@ void ModelParser::ReadFile(const std::string& model_file_name) {
         varnames_stored[i] = maestro::trim(line.substr(ipos));
     }
 
-    // alocate storage for the model data
+    // allocate storage for the model data
     model_state.resize(npts_model);
     for (auto i = 0; i < npts_model; ++i) {
         model_state[i].resize(nvars_model);

Exec/science/urca/analysis/fad_excess.f90

@@ -68,7 +68,7 @@ program fad_excess
 
   plot_name(1) = "adiabatic excess"
 
-  ! parse the arguements
+  ! parse the arguments
   narg = command_argument_count()
 
   farg = 1

Exec/science/urca/analysis/fconv_radial.f90

@@ -86,7 +86,7 @@ program fconv_radial
   component_names(2) = "adiabatic gradient"
   component_names(3) = "ledoux gradient"
 
-  ! parse the arguements
+  ! parse the arguments
   narg = command_argument_count()
 
   farg = 1

Exec/science/urca/analysis/fneutrinos.f90

@@ -108,7 +108,7 @@ program fneutrinos
   dx = plotfile_get_dx(pf, 1)
 
   ! get the index bounds for the finest level.
-  ! Note, lo and hi are ZERO-based indicies
+  ! Note, lo and hi are ZERO-based indices
   flo = lwb(plotfile_get_pd_box(pf, pf%flevel))
   fhi = upb(plotfile_get_pd_box(pf, pf%flevel))
 

Exec/science/urca/analysis/probin.f90

@@ -3,7 +3,7 @@
 ! This file is automatically generated by write_probin.py at
 ! compile-time.
 !
-! To add a runtime parameter, do so by editting the appropriate _parameters
+! To add a runtime parameter, do so by editing the appropriate _parameters
 ! file.
 
 ! This module stores the runtime parameters.  The probin_init() routine is

Exec/science/urca/analysis/scripts/slice-convgrad

@@ -1,8 +1,9 @@
 #!/usr/bin/env python
+import argparse
+
+import numpy as np
 import yt
 from yt import derived_field
-import numpy as np
-import argparse
 
 parser = argparse.ArgumentParser()
 parser.add_argument('infile', type=str, help='Name of input plotfile.')
@@ -15,7 +16,7 @@ parser.add_argument('-sign', '--sign', action='store_true', help='If supplied, p
 parser.add_argument('-fmin', '--field_min', type=float, help='Minimum scale for colorbar.')
 parser.add_argument('-fmax', '--field_max', type=float, help='Maximum scale for colorbar.')
 parser.add_argument('-log', '--logscale', action='store_true', help='If supplied, use a log scale for the field.')
-parser.add_argument('-symlog', '--symlog', action='store_true', help='If supplied, use symlog scaling, which is linear near zero, to accomodate positive and negative values.')
+parser.add_argument('-symlog', '--symlog', action='store_true', help='If supplied, use symlog scaling, which is linear near zero, to accommodate positive and negative values.')
 parser.add_argument('-linthresh', '--linthresh', type=float, help='Linear threshold for symlog scaling. (Default is 0.1)')
 parser.add_argument('-dc', '--drawcells', action='store_true', help='If supplied, draw the cell edges.')
 parser.add_argument('-dg', '--drawgrids', action='store_true', help='If supplied, draw the grids.')

Exec/science/urca/analysis/scripts/slice-enucdot

@@ -1,15 +1,16 @@
 #!/usr/bin/env python
+import argparse
+
+import numpy as np
 import yt
 from yt import derived_field
-import numpy as np
-import argparse
 
 parser = argparse.ArgumentParser()
 parser.add_argument('infile', type=str, help='Name of input plotfile.')
 parser.add_argument('-w', '--width', type=float,
                     help='Width of slice (cm). Default is domain width.')
 parser.add_argument('-axis', '--axis', type=str, default='x', help='Axis along which to slice. Should be "x", "y", or "z".')
-parser.add_argument('-symlog', '--symlog', action='store_true', help='If supplied, use symlog scaling, which is linear near zero, to accomodate positive and negative values of Hnuc.')
+parser.add_argument('-symlog', '--symlog', action='store_true', help='If supplied, use symlog scaling, which is linear near zero, to accommodate positive and negative values of Hnuc.')
 parser.add_argument('-logmax', '--logmax', type=float,
                     help='Log of the +/- maximum Hnuc value.')
 parser.add_argument('-rho', '--rhocontours', type=float, nargs='+', help='Draws contours for the densities provided (g/cm^3).')

Exec/science/urca/analysis/scripts/slice-field

@@ -4,11 +4,12 @@ Use yt to slice a boxlib plotfile supplied through the domain center.
 
 Donald E. Willcox
 """
-import yt
-from yt import derived_field
-import numpy as np
 import argparse
+
+import numpy as np
+import yt
 from UrcaAnalysis.yt_extensions import UrcaShellFields
+from yt import derived_field
 
 parser = argparse.ArgumentParser()
 parser.add_argument('infile', type=str, help='Name of input plotfile.')
@@ -19,7 +20,7 @@ parser.add_argument('-axis', '--axis', type=str, default='x',
 parser.add_argument('-w', '--width', type=float,
                     help='Width of slice (cm). Default is domain width.')
 parser.add_argument('-log', '--logscale', action='store_true', help='If supplied, use a log scale for the field.')
-parser.add_argument('-symlog', '--symlog', type=float, help='If supplied, use symlog scaling, which is linear near zero, to accomodate positive and negative values of the field. Pass the value of the field at which to linearize the colorbar.')
+parser.add_argument('-symlog', '--symlog', type=float, help='If supplied, use symlog scaling, which is linear near zero, to accommodate positive and negative values of the field. Pass the value of the field at which to linearize the colorbar.')
 parser.add_argument('-rho', '--rhocontours', type=float, nargs='+', help='Draws contours for the densities provided (g/cm^3).')
 parser.add_argument('-rhocolors', '--rhocolors', type=str, nargs='+', default='cyan', help='Color(s) of density contours.')
 parser.add_argument('-ctr', '--center', type=float, nargs='+', help='Centers the plot on the coordinates provided (x, y, z).')

Exec/science/urca/analysis/scripts/streamlines

@@ -1,11 +1,10 @@
 #!/usr/bin/env python
-import yt
-import numpy as np
 import matplotlib.pylab as pl
-
-from yt.visualization.api import Streamlines
-from yt.units import cm
+import numpy as np
+import yt
 from mpl_toolkits.mplot3d import Axes3D
+from yt.units import cm
+from yt.visualization.api import Streamlines
 
 # Load the dataset
 ds = yt.load('wd_512_rhoc4-5_plt64636')
@@ -24,7 +23,7 @@ pos = pos_dx
 streamlines = Streamlines(ds, pos, ('boxlib', 'x_vel'), ('boxlib', 'y_vel'), ('boxlib', 'z_vel'), get_magnitude=True, volume=ds.all_data())
 streamlines.integrate_through_volume()
 
-# Create a 3D plot, trace the streamlines throught the 3D volume of the plot
+# Create a 3D plot, trace the streamlines through the 3D volume of the plot
 fig=pl.figure()
 ax = Axes3D(fig)
 for stream in streamlines.streamlines:

Exec/test_problems/double_bubble/MaestroInitData.cpp

@@ -3,7 +3,7 @@
 using namespace amrex;
 using namespace problem_rp;
 
-// prototype for pertubation function to be called on the
+// prototype for perturbation function to be called on the
 // device (if USE_CUDA=TRUE)
 AMREX_GPU_DEVICE
 void Perturb(const Real p0, const Real* s0, Real* perturbations,

Exec/test_problems/reacting_bubble/MaestroInitData.cpp

@@ -5,7 +5,7 @@
 using namespace amrex;
 using namespace problem_rp;
 
-// prototype for pertubation function to be called on the
+// prototype for perturbation function to be called on the
 // device (if USE_CUDA=TRUE)
 AMREX_GPU_DEVICE
 void Perturb(const Real p0_init, const Real* s0, Real* perturbations,

Exec/test_problems/rt/MaestroInitData.cpp

@@ -3,7 +3,7 @@
 using namespace amrex;
 using namespace problem_rp;
 
-// prototype for pertubation function to be called on the
+// prototype for perturbation function to be called on the
 // device (if USE_CUDA=TRUE)
 AMREX_GPU_DEVICE
 void Perturb(const Real p0, const Real* s0, Real* scal_pert, Real* vel_pert,

Exec/unit_tests/test_basestate/README

@@ -42,7 +42,7 @@ plane-parallel test problem:
 ------------------------------------------------------------------------------
 analytical CNO cycle test problem:
 
-  make sure to change the nework in GNUmakefile to H_core_null
+  make sure to change the network in GNUmakefile to H_core_null
 
 
 ------------------------------------------------------------------------------

Exec/unit_tests/test_diffusion/MaestroInit.cpp

@@ -124,7 +124,7 @@ void Maestro::MakeNewLevelFromScratch(int lev, Real time, const BoxArray& ba,
             const auto x = prob_lo[0] + (Real(i) + 0.5) * dx[0] - center_p[0];
             const auto y = prob_lo[1] + (Real(j) + 0.5) * dx[1] - center_p[1];
 
-            // apply the guassian enthalpy pulse at constant density
+            // apply the Gaussian enthalpy pulse at constant density
             const auto dist2 = x * x + y * y;
 
             const auto h_zone =

Exec/unit_tests/test_react/scripts/fsnapshot.f90

@@ -183,7 +183,7 @@ subroutine fplotfile_get_comps(pltfile, comps_sz, comps)
   !characters.
 
   !Perhaps there is a more elegant solution, but I've just resized the array to
-  !accomodate all of the characters and it works as a rudimentary work-around if
+  !accommodate all of the characters and it works as a rudimentary work-around if
   !one is really determined to have a string returned.
 
 !f2py intent(in) :: pltfile
@@ -340,7 +340,7 @@ subroutine fplotfile_get_data_3d(pltfile, component, mydata, nx, ny, nz, ierr)
 
 
   ! get the index bounds and dx for the coarse level.  Note, lo and
-  ! hi are ZERO based indicies
+  ! hi are ZERO based indices
   lo = lwb(plotfile_get_pd_box(pf, 1))
   hi = upb(plotfile_get_pd_box(pf, 1))
 

README.md

@@ -29,7 +29,7 @@ http://amrex-astro.github.io/MAESTROeX/
   required, as is Python (>= 3.6) and standard tools available in any
   Unix-like environments (e.g., Perl and `sed`).
 
-  For GPU computing, CUDA 10 or later is requred.
+  For GPU computing, CUDA 10 or later is required.
 
 - To stay up-to-date with MAESTROeX, you will want to periodically
   pull changes from the repository by typing `git pull`.
@@ -43,7 +43,7 @@ http://amrex-astro.github.io/MAESTROeX/
   git clone --recursive https://github.com/AMReX-Astro/MAESTROeX.git
   ```
 
-  To add the submodules to an exisiting clone, from the top-level
+  To add the submodules to an existing clone, from the top-level
   MAESTROeX directory, do:
 
   ```

Source/MaestroMakew0.cpp

@@ -948,7 +948,7 @@ void Maestro::Tridiag(const BaseStateArray<Real>& a,
     auto gam = gam_s.array();
 
     if (b(0) == 0) {
-        Abort("tridiag: CANT HAVE B(0) = 0.0");
+        Abort("tridiag: CAN NOT HAVE B(0) = 0.0");
     }
 
     Real bet = b(0);

Source/MaestroNodalProj.cpp

@@ -388,7 +388,7 @@ void Maestro::NodalProj(int proj_type, Vector<MultiFab>& rhcc,
     } else if (proj_type == pressure_iters_comp) {
         // Vproj = Vproj - sig*grad(phi)
         // we do this manually instead of using mlndlap.updateVelocity() because
-        // for alt_energy_fix we neet beta0*grad(phi)
+        // for alt_energy_fix we need beta0*grad(phi)
         for (int lev = 0; lev <= finest_level; ++lev) {
             for (int dir = 0; dir < AMREX_SPACEDIM; ++dir) {
                 MultiFab::Multiply(gphi[lev], sig[lev], 0, dir, 1, 0);
@@ -404,7 +404,7 @@ void Maestro::NodalProj(int proj_type, Vector<MultiFab>& rhcc,
     } else if (proj_type == regular_timestep_comp) {
         // Vproj = Vproj - sig*grad(phi)
         // we do this manually instead of using mlndlap.updateVelocity() because
-        // for alt_energy_fix we neet beta0*grad(phi)
+        // for alt_energy_fix we need beta0*grad(phi)
         for (int lev = 0; lev <= finest_level; ++lev) {
             for (int dir = 0; dir < AMREX_SPACEDIM; ++dir) {
                 MultiFab::Multiply(gphi[lev], sig[lev], 0, dir, 1, 0);

Util/diagnostics/README.md

@@ -17,13 +17,13 @@ be output:
 Additional arguments depend on the problem:
 
 - **1d**: no additional arguments are required
-- **2d cylindrical**: extra arguents `--xctr x` and `--yctr y` giving the coordinates
+- **2d cylindrical**: extra arguments `--xctr x` and `--yctr y` giving the coordinates
 of the domain center (x,y) can be provided (both default to 0.0)
 - **2d spherical**: the argument `--sphr` *must* be provided to indicate a spherical
 problem, and the `--yctr y` argument can be provided to give the y coordinate of
 the domain center (defaults to 0.0)
-- **3d cylindrical**: extra arguents `--xctr x` and `--yctr y` giving the coordinates
+- **3d cylindrical**: extra arguments `--xctr x` and `--yctr y` giving the coordinates
 of the domain center (x,y) can be provided (both default to 0.0)
 - **3d spherical**: the argument `--sphr` *must* be provided to indicate a spherical
-problem, and extra arguents `--xctr x`, `--yctr y` and `--zctr z` giving the coordinates
+problem, and extra arguments `--xctr x`, `--yctr y` and `--zctr z` giving the coordinates
 of the domain center (x,y,z) can be provided (all default to 0.0)

Util/model_parser/ModelParser.cpp

@@ -33,7 +33,7 @@ void ModelParser::ReadFile(const std::string& model_file_name) {
         varnames_stored[i] = maestro::trim(line.substr(ipos));
     }
 
-    // alocate storage for the model data
+    // allocate storage for the model data
     model_state.resize(npts_model);
     for (auto i = 0; i < npts_model; ++i) {
         model_state[i].resize(nvars_model);
@@ -204,4 +204,4 @@ Real ModelParser::Interpolate(const Real r, const int ivar,
     }
 
     return interpolate;
-}
+}

paper/paper.md

@@ -68,7 +68,7 @@ of density and pressure stratification.
 The code leverages the new AMReX software framework [@AMReX] for block-structured
 adaptive mesh refinement (AMR) applications, allowing for scalability
 to large fractions of leadership-class machines.
-Our approach to parallization uses a hybrid MPI/OpenMP approach, with increasing GPU support.
+Our approach to parallelization uses a hybrid MPI/OpenMP approach, with increasing GPU support.
 Microphysics are provided by the Starkiller-Astro libraries [@starkiller].
 The code contains documentation through sphinx, a large suite of test problems, and
 nightly regression tests on a number of architectures.

sphinx_docs/source/Godunov.rst

@@ -892,7 +892,7 @@ Then upwind based on :math:`v_{\ib-\half\eb_y}^{1D}`:
    u_{R,\ib-\half\eb_y}^{y|z}, & v_{\ib-\half\eb_y}^{1D} < 0.
    \end{cases}
 
-We use an analogous procedure to compute five more intemediate states,
+We use an analogous procedure to compute five more intermediate states,
 :math:`u_{\ib-\half\eb_z}^{z|y}, v_{\ib-\half\eb_x}^{x|z},
 v_{\ib-\half\eb_z}^{z|x}, w_{\ib-\half\eb_x}^{x|y}`, and
 :math:`w_{\ib-\half\eb_y}^{y|x}`. Then we do a full-dimensional