Merge branch 'development'

.github/workflows/c-linter.yml

@@ -0,0 +1,37 @@
+name: cpp-linter
+
+on: [pull_request]
+jobs:
+  cpp-linter:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Get submodules 
+        run: git submodule update --init
+
+      - name: Run cpp linter
+        uses: AMReX-Astro/cpp-linter-action@master
+        with: 
+          build_path: 'Exec/science/flame_wave'
+          make_options: '-j 2 USE_OMP=FALSE USE_MPI=FALSE USE_CUDA=FALSE DEBUG=TRUE'
+          ignore_files: 'amrex|Microphysics'
+          header_filter: 'Castro'
+
+      - name: Archive clang tidy report
+        uses: actions/upload-artifact@v1
+        with:
+          name: clang-tidy-report
+          path: clang-tidy-report.txt
+
+    #   - name: Archive clang format report
+    #     uses: actions/upload-artifact@v1
+    #     with:
+    #       name: clang-format-report
+    #       path: clang-format-report.txt
+
+      - name: Archive cppcheck report
+        uses: actions/upload-artifact@v1
+        with:
+          name: cppcheck-report
+          path: cppcheck-report.txt

.github/workflows/gh-pages.yml

@@ -0,0 +1,61 @@
+name: github pages
+
+on:
+  push:
+    branches:
+      - master
+      - development
+
+jobs:
+  deploy:
+    runs-on: ubuntu-18.04
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install pandoc and doxygen 
+        run: |
+          sudo apt install pandoc doxygen
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.8'
+
+      - name: Upgrade pip
+        run: |
+          # install pip=>20.1 to use "pip cache dir"
+          python3 -m pip install --upgrade pip
+
+      - name: Get pip cache dir
+        id: pip-cache
+        run: echo "::set-output name=dir::$(pip cache dir)"
+
+      - name: Cache dependencies
+        uses: actions/cache@v1
+        with:
+          path: ${{ steps.pip-cache.outputs.dir }}
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install dependencies
+        run: python3 -m pip install -r ./requirements.txt
+
+      - name: Build docs
+        if: ${{ endsWith(github.ref, 'master') }}
+        env:
+          GITHUB_BRANCH: 'master'
+        run: ./deploy_docs_action.sh
+
+      - name: Build docs 
+        if: ${{ endsWith(github.ref, 'development') }}
+        env:
+          GITHUB_BRANCH: 'development'
+        run: ./deploy_docs_action.sh
+
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./out
+          keep_files: true

.github/workflows/slack-notify.yml

@@ -0,0 +1,33 @@
+on: 
+  pull_request:
+    types: synchronize
+name: Slack Notification 
+jobs:
+  slackNotification:
+    name: Slack Notification
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        ref: ${{ github.event.pull_request.head.sha }} 
+
+    - name : GITHUB CONTEXT
+      env: 
+        GITHUB_CONTEXT: ${{ toJson(github) }} 
+      run: echo "$GITHUB_CONTEXT"
+
+    - name: Get commit message
+      run: |
+        MSG=$(git log --format=%B -n 1)
+        echo "::set-env name=COMMIT_MSG::$MSG" 
+
+    - name: Slack Notification 
+      uses: AMReX-Astro/slack-action@master
+      with:
+        slack_webhook: ${{ secrets.SLACK_WEBHOOK }}
+        slack_channel: castro
+        message: ${{ env.COMMIT_MSG }}
+        pr_link: ${{ github.event.pull_request.head.repo.html_url }}
+        author_avatar: ${{ github.event.pull_request.user.avatar_url }}
+        commit_sha: ${{ github.event.pull_request.head.sha }}
+        before_sha: ${{ github.event.before }}

.travis.yml

@@ -2,31 +2,6 @@ dist: bionic
 
 matrix:
   include:
-    - name: "deploy docs"
-      if: branch = development OR branch = master
-      language: python
-      python:
-        - "3.7-dev"
-      before_install:
-        - export PATH=$(echo $PATH | tr ':' "\n" | sed '/\/opt\/python/d' | tr "\n" ":" | sed "s|::|:|g")
-      addons:
-        apt:
-            packages:
-            - g++
-            - gfortran
-            - libgmp-dev
-            - libmpfr-dev
-            - pandoc
-            - doxygen
-      install:
-        - pip install -r requirements.txt
-      before_script:
-        - export AMREX_HOME=~/amrex
-      script:
-        - ls -l
-        - pwd
-        - ./deploy_docs.sh
-
     - name: "clang static analysis"
       if: type = pull_request OR type = api OR type = cron
       language: cpp

CHANGES.md

@@ -1,3 +1,23 @@
+# 20.06
+
+   * The parameter castro.density_reset_method has been removed. A density
+     reset now unconditionally sets the density to small_dens, the temperature
+     to small_temp, and zeros out the velocities. (#989)
+
+   * A constrained-transport corner transport upwind MHD solver has been
+     added.  This can be used by compiling with USE_MPI = TRUE.  Presently
+     it only works for a single level (no AMR).  (#307)
+
+   * A burning timestep limiter dtnuc_T has been added which restricts the
+     burning from updating the temperature by more than the factor
+     dtnuc_T * T / dT/dt. (#972)
+
+   * The reaction weights metric implemented in version 20.05 (#863) has been
+     added to the simplified SDC reactions driver. (#930)
+
+   * When using the simplified SDC integration scheme, we now save new-time
+     Reactions_Type data to plotfiles. (#929)
+
 # 20.05
 
    * The parameter use_custom_knapsack_weights and its associated

Docs/Makefile

@@ -17,6 +17,7 @@ help:
 clean:
 	rm -rf build doxy_files source/class source/file source/namespace source/preprocessed_files
 	rm -f source/classlist.rst source/filelist.rst source/namespacelist.rst
+	rm -f source/yt_example.rst
 	rm -rf source/preprocessed_files
 	rm -rf source/*_files.rst
 
@@ -28,6 +29,7 @@ ifneq ($(NO_DOXYGEN),TRUE)
 	breathe-apidoc --o source doxy_files/xml -g class,file
 	python3 make_api.py
 endif
+	jupyter nbconvert --to rst source/yt_example.ipynb
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 # Catch-all target: route all unknown targets to Sphinx using the new
@@ -39,4 +41,5 @@ ifneq ($(NO_DOXYGEN),TRUE)
 	breathe-apidoc --o source doxy_files/xml -g class,file
 endif
 	python3 make_api.py
+	jupyter nbconvert --to rst source/yt_example.ipynb
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

Docs/source/FlowChart.rst

@@ -196,9 +196,13 @@ of each step.
 
    -  Free any memory allocated for the level advance.
 
+
+.. _sec:strangctu:
+
 CTU w/ Strang-split Reactions Flowchart
 ---------------------------------------
 
+
 This described the flow using the CTU + Strang-split reactions,
 including gravity, rotation, and diffusion.  This integration is
 selected via ``castro.time_integration_method = 0``.

Docs/source/Hydrodynamics.rst

@@ -107,7 +107,7 @@ several main data structures that hold the state.
    are “gas” only and those with the “tot” subscript are “gas + radiation”.
 
    .. _table:primlist:
-   .. table:: The integer variable keys for accessing the primitive state vector.
+   .. table:: Primitive State Vector Integer Keys
 
       +-----------------------+------------------------+-----------------------+
       | **variable**          | **quantity**           | **note**              |

Docs/source/Introduction.rst

@@ -2,7 +2,7 @@
 Introduction to Castro
 **********************
 
-Castro is a adaptive mesh, radiation hydrodynamics code that is
+Castro is a adaptive mesh, radiation/MHD hydrodynamics code that is
 designed to model astrophysical reacting flows on massively parallel
 computers.
 
@@ -12,12 +12,15 @@ Castro's major capabilities:
     hydrodynamics; 4th order hydro for uniform grids.
     (see :ref:`ch:hydro`)
 
-  * generalized retry mechanism for recovering from physical
-    violations over a timestep (see :ref:`ch:retry`)
+  * 3-dimension constrained transport ideal MHD (single level only currently)
+    (see :ref:`ch:mhd`)
 
   * multigroup flux-limited diffusion radiation hydrodynamics
     (see :ref:`ch:radiation`)
 
+  * generalized retry mechanism for recovering from physical
+    violations over a timestep (see :ref:`ch:retry`)
+
   * adaptive mesh refinement with subcycling; jumps of 2x and 4x
     between levels (see :ref:`ch:amr`)
 

Docs/source/Preface.rst

@@ -38,9 +38,17 @@ Improvements to the gravity solver and rotation were described in:
   * *Double White Dwarf Mergers on Adaptive Meshes I. Methodology and
     Code
     Verification*, M. P. Katz, M. Zingale, A. C. Calder, F. D. Swesty,
-    A. S. Almgren, W. Zhang 2016, ApJ, 819, 94.
+    A. S. Almgren, & W. Zhang, 2016, ApJ, 819, 94.
     http://dx.doi.org/10.3847/0004-637X/819/2/94
 
+The 4th order reactive hydrodynamics spectral deferred corrections solver
+was described in:
+
+  * *Improved Coupling of Hydrodynamics and Nuclear Reactions via Spectral Deferred Corrections*
+    M. Zingale, M. P. Katz, J. B. Bell, M. L. Minion, A. J. Nonaka, & W. Zhang,
+    2019, ApJ, 886, 105.
+    https://ui.adsabs.harvard.edu/link_gateway/2019ApJ...886..105Z/doi:10.3847/1538-4357/ab4e1d
+
 The development of AMReX library is led by the
 Center for Computational Sciences and Engineering / Lawrence Berkeley
 National Laboratory. Castro development is done collaboratively,

Docs/source/_static/theme_overrides.css

@@ -14,6 +14,10 @@ code.docutils.literal.notranslate {
    font-size: 95%;
 }
 
+div#example-notebook div.highlight-default div.highlight {
+    background-color: inherit;
+}
+
 /* override table width restrictions */
 @media screen and (min-width: 767px) {
 

Docs/source/build_system.rst

@@ -223,16 +223,18 @@ This is the current build system process.
 
 * ``set_variables.py`` is called
 
-  .. index:: set_variables.py, _variables, state_indices.F90, state_indices.H
+  .. index:: set_variables.py, _variables, state_indices_nd.F90, state_indices.H
 
   * This processes the Castro ``_variables`` file and writes
-    ``state_indices.F90`` and ``state_indices.H`` into the
+    ``state_indices_nd.F90`` and ``state_indices.H`` into the
     ``tmp_build_dir/castro_sources/`` directory.
 
     These are used to define the size of the various state arrays and
     the integer keys to index each state variable.
 
-  * The hook for this is in ``Make.Castro`` in the build rule for ``state_indices.F90``
+  * The hook for this is in ``Make.auto_source`` in the build rule for ``state_indices_nd.F90``
+
+  * You can test this portion of the build system by doing ``make test_variables``
 
 * (for ``general_null networks``), ``actual_network.F90`` is created
 

Docs/source/conf.py

@@ -56,7 +56,8 @@ def get_version():
               'sphinx.ext.autosummary',
               'numpydoc',
               'sphinx.ext.githubpages',
-              'breathe']
+              'breathe',
+              'IPython.sphinxext.ipython_console_highlighting']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -99,7 +100,7 @@ def get_version():
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = []
+exclude_patterns = ['**.ipynb_checkpoints']
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'

Docs/source/creating_a_problem.rst

@@ -169,10 +169,13 @@ Here, we compute the coordinates of the zone center, ``x``, ``y``, and ``z``
 from the zone indices, ``i``, ``j``, and ``k``.
 
 
+.. _create:bcs:
 
 Boundary conditions
 -------------------
 
+.. index:: boundary conditions
+
 Standard boundary conditions, including outflow (zero-gradient), periodic,
 and symmetry (reflect) are handled by AMReX directly.  Castro has a special
 hydrostatic boundary condition that can be used for the lower boundary.  It
@@ -189,13 +192,36 @@ hydrostatic boundary condition here, we set::
    castro.hse_interp_temp = 1
    castro.hse_reflect_vels = 1
 
-The first parameter tells Castro to use the HSE boundary condition.  The next two
-control how the temperature and velocity are treated.
-
-A different special boundary condition, ``"interp"`` is available at
+The first parameter tells Castro to use the HSE boundary condition.
+In filling the ghost cells, hydrostatic equilibrum will be integrated
+from the last interior zone into the boundary.  We need one more
+equation for this integration, so we either interpolate the density or
+temperature into the ghost cells, depending on the value of
+``castro.hse_interp_temp``.  Finally, ``castro.hse_reflect_vels``
+determines how we treat the velocity.  The default is to give is a
+zero gradient, but in tests we've found that reflecting the velocity
+while integrating the HSE profile can be better.  For modeling a
+plane-parallel hydrostatic atmosphere, using the hydrostatic boundary
+conditions instead of a simple symmetry boundary is essential when
+using the standard CTU PPM solver.
+
+A different special boundary condition, based on outflow, is available at
 the upper boundary.  This works together with the ``model_parser``
 module to fill the ghost cells at the upper boundary with the initial
-model data.
+model data.  You set this as::
+
+   castro.hi_bc = 2 2
+
+   castro.fill_ambient_bc = 1
+   castro.ambient_fill_dir = 1
+   castro.ambient_outflow_vel = 1
+
+where ``ambient_fill_dir`` is the 0-based direction to fill using an
+ambient state defined by the problem setup.  In this example, we will
+override the outflow (2) boundary condition in the y-direction.  That
+problem setup needs to fill the ``ambient_state(:)`` array defined in
+``ambient_module``.  An example of using this boundary is in the
+``flame_wave`` problem.
 
 The implementations of these boundary conditions is found in
 ``Castro/Source/problems/bc_ext_fill_nd.F90``.