Merge branch 'main' of github.com:amrex-astro/MAESTROeX

.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
+

CHANGES.md

@@ -1,4 +1,14 @@
-# 23.08
+# 24.01
+
+  * Fixed a race condition on GPUs (#402)
+
+# 23.10
+
+  * a new option, `basestate_use_pres_model` was added (#398)
+    this allows us to use (rho, p) from the initial model instead of
+    (rho, T) to establish the thermodynamics.
+
+# 23.09
 
   * remove the SDC code paths.  This is no longer supported by
     Microphysics and is not being tested.
@@ -7,7 +17,7 @@
 
   * the test_diffusion unit test was cleaned up and now gives the
     expected convergence (#336, #381)
-    
+
 # 23.05
 
   * MAESTROeX now monitors the burn_t success flag and aborts if there

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/flame/_parameters

@@ -24,7 +24,7 @@ smooth_len_frac         real                 0.025
 XC12_ref_threshold      real                 1.d-3
 
 # do the burning only once for each vertical coordinate
-do_average_burn         logical              .false.
+do_average_burn         integer              0
 
 # acceptable relative error for a cell compared to the average
 # at that vertical coord if do_average_burn = T (should be smaller

Exec/science/fully_convective_star/_parameters

@@ -1,10 +1,10 @@
 @namespace: problem
 
-velpert_amplitude         real 1.e5
-velpert_radius            real 2.e7
-velpert_scale             real 1.e7
-velpert_steep             real 1.e5
-tag_density_1             real 1.0
-tag_density_2             real 0.1
-tag_density_3             real 0.05
-use_analytic_heating      logical .false.
+velpert_amplitude         real      1.e5
+velpert_radius            real      2.e7
+velpert_scale             real      1.e7
+velpert_steep             real      1.e5
+tag_density_1             real      1.0
+tag_density_2             real      0.1
+tag_density_3             real      0.05
+use_analytic_heating      integer   0

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/rotating_star/_parameters

@@ -1,12 +1,12 @@
 @namespace: problem
 
-velpert_amplitude         real 1.e5
-velpert_radius            real 2.e7
-velpert_scale             real 1.e7
-velpert_steep             real 1.e5
-tag_density_1             real 5.e7
-tag_density_2             real 1.e8
-tag_density_3             real 1.e8
-particle_temp_cutoff      real 6.e8
-particle_tpert_threshold  real 2.e7
-use_analytic_heating      logical .false.
+velpert_amplitude         real      1.e5
+velpert_radius            real      2.e7
+velpert_scale             real      1.e7
+velpert_steep             real      1.e5
+tag_density_1             real      5.e7
+tag_density_2             real      1.e8
+tag_density_3             real      1.e8
+particle_temp_cutoff      real      6.e8
+particle_tpert_threshold  real      2.e7
+use_analytic_heating      integer   0

Exec/science/toy_convect/_parameters

@@ -1,7 +1,7 @@
 @namespace: problem
 
 # Velocity field initialization
-apply_vel_field                     logical            .false.
+apply_vel_field                     integer            0
 
 # Initial velocity field vortex scale
 velpert_scale                       real               1.0d2

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/science/xrb_layered/_parameters

@@ -15,7 +15,7 @@ xrb_pert_type                       integer            1
 xrb_pert_height                     real               -1.0d0
 
 # Turn on (.true.) or off (.false.) sponging at the bottom of the domain.
-xrb_use_bottom_sponge               logical            .false.
+xrb_use_bottom_sponge               integer            0
 
 # minimum value to use for the sponge
 sponge_min                          real               0.01d0
@@ -25,7 +25,7 @@ sponge_min                          real               0.01d0
 diag_define_layer                real               0.1
 
 # Velocity field initialization
-apply_vel_field                     logical            .false.
+apply_vel_field                     integer            0
 
 # Initial velocity field vortex scale (2-d); thickness of velocity layer (3-d)
 velpert_scale                       real               1.0d2
@@ -43,7 +43,7 @@ velpert_steep                       real               12.d0
 num_vortices                        integer            1
 
 # look at the deltap diagnostic
-do_deltap_diag                      logical            .false.
+do_deltap_diag                      integer            0
 
 # minimum value to use for species in tag_boxes
 tag_minval                          real               1.0d-4
@@ -56,7 +56,7 @@ tag_maxval                          real               0.99d0
 tag_xfac                           real                1.d-16
 
 # density tagging
-do_dens_tagging                    logical             .false.
+do_dens_tagging                    integer             0
 
 lo_dens_tag                        real                5.4d5
 hi_dens_tag                        real                1.75d6

Exec/science/xrb_mixed/_parameters

@@ -15,7 +15,7 @@ xrb_pert_type                       integer            1
 xrb_pert_height                     real               -1.0d0
 
 # Turn on (.true.) or off (.false.) sponging at the bottom of the domain.
-xrb_use_bottom_sponge               logical            .false.
+xrb_use_bottom_sponge               integer            0
 
 # minimum value to use for the sponge
 sponge_min                          real               0.01d0
@@ -25,7 +25,7 @@ sponge_min                          real               0.01d0
 diag_define_layer                real               0.1
 
 # Velocity field initialization
-apply_vel_field                     logical            .false.
+apply_vel_field                     integer            0
 
 # Initial velocity field vortex scale (2-d); thickness of velocity layer (3-d)
 velpert_scale                       real               1.0d2
@@ -43,7 +43,7 @@ velpert_steep                       real               12.d0
 num_vortices                        integer            1
 
 # look at the deltap diagnostic
-do_deltap_diag                      logical            .false.
+do_deltap_diag                      integer            0
 
 # minimum value to use for species in tag_boxes
 tag_minval                          real               1.0d-4
@@ -56,7 +56,7 @@ tag_maxval                          real               0.99d0
 tag_xfac                           real                1.d-16
 
 # density tagging
-do_dens_tagging                    logical             .false.
+do_dens_tagging                    integer             0
 
 lo_dens_tag                        real                5.4d5
 hi_dens_tag                        real                1.75d6

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,