Merge branch 'development'

.gitignore

@@ -43,6 +43,7 @@ AMReX_buildInfo.cpp
 
 # These files are created at build time
 Exec/**/extern.F90
+Exec/**/extern_parameters.*
 Exec/**/prob_params_auto.F90
 Exec/**/actual_network.F90
 Exec/**/helm_table.dat
@@ -57,14 +58,14 @@ Exec/**/set_godunov.H
 
 Backtrace.*
 
-sphinx_docs/build
-sphinx_docs/doxy_files
-sphinx_docs/class
-sphinx_docs/classlist.rst
-sphinx_docs/source/file/
-sphinx_docs/source/filelist.rst
-sphinx_docs/source/namespace/
-sphinx_docs/source/namespacelist.rst
-sphinx_docs/source/runtime_parameters.rst
-sphinx_docs/source/*_files.rst
-sphinx_docs/source/preprocessed_files
+Docs/build
+Docs/doxy_files
+Docs/class
+Docs/classlist.rst
+Docs/source/file/
+Docs/source/filelist.rst
+Docs/source/namespace/
+Docs/source/namespacelist.rst
+Docs/source/runtime_parameters.rst
+Docs/source/*_files.rst
+Docs/source/preprocessed_files

.travis.yml

@@ -3,14 +3,12 @@ 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")
-      #  - pwd
-      #  - cd ~/; git clone https://github.com/amrex-codes/amrex
-      #  - cd ~/; git clone https://github.com/amrex-codes/regression_testing
       addons:
         apt:
             packages:
@@ -27,15 +25,7 @@ matrix:
       script:
         - ls -l
         - pwd
-      # after_success:
         - ./deploy_docs.sh
-      # deploy:
-      #   provider: pages
-      #   skip-cleanup: true
-      #   github-token: $GITHUB_TOKEN
-      #   keep-history: true
-      #   on:
-      #     branch: master
 
     - name: "clang static analysis"
       if: type = pull_request OR type = api OR type = cron
@@ -45,12 +35,8 @@ matrix:
       before_install:
         - cd ~/; git clone https://github.com/amrex-codes/amrex
         - cd ~/amrex; git checkout development
-        # - find . -type f -regex ".*\(\.f90\|\.F90\|\.cpp\|\.H\)" -exec bash -c 'echo "#endif" >> "{}"' \;
-        # - find . -type f -regex ".*\(\.f90\|\.F90\|\.cpp\|\.H\)" -exec bash -c 'sed -i "1s/^/#ifndef __clang_analyzer__\n/" {}' \;
         - cd ~/; git clone https://github.com/starkiller-astro/Microphysics.git
         - cd ~/Microphysics; git checkout development
-        # - find . -type f -regex ".*\(\.f90\|\.F90\|\.cpp\|\.H\)" -exec bash -c 'echo "#endif" >> "{}"' \;
-        # - find . -type f -regex ".*\(\.f90\|\.F90\|\.cpp\|\.H\)" -exec bash -c 'sed -i "1s/^/#ifndef __clang_analyzer__\n/" {}' \;
         - cd $TRAVIS_BUILD_DIR
       addons:
         apt:

CHANGES.md

@@ -1,3 +1,26 @@
+# 20.04
+
+   * The parameter castro.allow_small_energy has been removed. The
+     code behavior is now similar to what it would have been with
+     allow_small_energy == 0 (the internal energy can never be
+     smaller than that allowed by small_temp). (#817)
+
+   * All boundary fill interfaces other than hypfill and denfill have
+     been removed. So, we no longer support overriding the boundary
+     conditions for data other than State_Type. Radiation still has
+     its own set of custom boundary conditions that can be accessed
+     through the inputs file, as described in the docs. (#815)
+
+   * The conversion of the CTU hydrodynamics code to C++ continues.
+     The Riemann solvers were converted to C++ (#801) and the
+     hybrid momentum routines (#805), the PLM reconstruction (#814),
+     the conversion of primitive to conserved variables (#804)
+
+   * We've changed how the backup for retries is done.  Presently if
+     use_retry is enabled we make a pre-emptive copy of the StateData
+     right at the beginning of the timestep.  Now we only backup when
+     we detect that a retry is needed (#812)
+
 # 20.03
 
    * We now depend on the fundamental constants from Microphysics

Docs/add_doxy_headers.py

@@ -412,6 +412,4 @@ def process_fortran_file(filename):
     if filename[-2:] == ".H":
         process_header_file(filename)
     elif filename[-4:] == ".cpp":
-        process_cpp_file(filename)
-    elif filename[-4:].lower() == ".f90":
-        process_fortran_file(filename)
+        process_cpp_file(filename)

Docs/make_api.py

@@ -163,19 +163,6 @@ def fortran_apidoc(filename, filepath):
 
                         subdir_output_data += """file/{}
    """.format(rst_name)
-                    elif f[-4:] == ".F90" or f[-4:] == ".f90":
-
-                        # NOTE: I've had to declare some exceptions here as
-                        # for some reason sphinx does not like these files
-                        if subdir == 'problems' and (f[-6:-4] == '1d' or f[-6:-4] == '2d' or f[-6:-4] == '3d'):
-                            continue
-
-                        if f not in ['HABEC_1D.F90', 'HABEC_2D.F90', 'HABEC_3D.F90', 'RAD_1D.F90', 'RAD_2D.F90', 'RAD_3D.F90']:
-
-                            fortran_apidoc(f, os.path.join(rootdir, subdir))
-
-                            subdir_output_data += """file/{}
-   """.format(f[:-4] + "_f")
 
                 subdir_file.write(subdir_output_data)
 

Docs/preprocess_files.py

@@ -104,19 +104,6 @@ def remove_device_routines(filename, filepath):
 
 if __name__ == "__main__":
 
-    excl_files = ['HABEC_1D.F90', 'HABEC_2D.F90', 'HABEC_3D.F90', 'RAD_1D.F90', 'RAD_2D.F90', 'RAD_3D.F90', 'bc_fill_3d.F90',
-                  'problem_tagging_3d.f90',
-                  'bc_ext_fill_3d.F90',
-                  'Prob_1d.f90',
-                  'Prob_3d.f90',
-                  'bc_ext_fill_1d.F90',
-                  'bc_fill_1d.F90',
-                  'bc_ext_fill_2d.F90',
-                  'problem_tagging_1d.f90',
-                  'bc_fill_2d.F90',
-                  'Prob_2d.f90',
-                  'problem_tagging_2d.f90']
-
     # make the output directory if it does not exist
     if not os.path.exists(outdir):
         os.makedirs(outdir)
@@ -129,7 +116,7 @@ def remove_device_routines(filename, filepath):
         # loop over files in subdirectories and run strip_directives on all
         # C++ header files and Fortran files
         for f in sorted(os.listdir(os.path.join(rootdir, subdir))):
-            if ((f[-2:] == ".H" and f[-4:] != "_F.H") or f[-4:] == ".F90" or f[-4:] == ".f90") and f not in excl_files:
+            if (f[-2:] == ".H" and f[-4:] != "_F.H"):
                 strip_directives(f, os.path.join(rootdir, subdir), outdir)
                 delete_lines(f, outdir)
                 remove_device_routines(f, outdir)

Docs/source/Hydrodynamics.rst

@@ -640,14 +640,8 @@ We compute the primtive variables from the conserved variables.
 
 -  :math:`p,T`: use the EOS.
 
-   First, if castro.allow_negative_energy is 0 (it defaults to
-   1) and :math:`e < 0`, we do the following:
-
-   #. Use the EOS to set :math:`e = e(\rho,T_{\rm small},X_k)`.
-
-   #. If :math:`e < 0`, abort the program with an error message.
-
-   Now, use the EOS to compute :math:`p,T = p,T(\rho,e,X_k)`.
+   First, we use the EOS to ensure :math:`e` is no smaller than :math:`e(\rho,T_{\rm small},X_k)`.
+   Then we use the EOS to compute :math:`p,T = p,T(\rho,e,X_k)`.
 
 We also compute the flattening coefficient, :math:`\chi\in[0,1]`, used in
 the edge state prediction to further limit slopes near strong shocks.
@@ -1151,11 +1145,6 @@ Density Resets
 
 Need to document density_reset_method
 
-Energy
-------
-
-Need to document allow_negative_energy and allow_small_energy
-
 .. _app:hydro:flux_limiting:
 
 Flux Limiting

Docs/source/_static/theme_overrides.css

@@ -28,3 +28,19 @@ code.docutils.literal.notranslate {
    }
 }
 
+.wy-side-nav-search>div.branch{
+    font-weight:normal;
+    color:rgba(255,255,255,0.3);
+    font-size:100%;
+    display:inline-block;
+    padding:4px 6px;
+    margin-top:.8em;
+    margin-bottom:.5em;
+}
+
+.wy-side-nav-search>div.branch>a{
+    /* margin-top:-.4045em;
+    margin-bottom:.809em; */
+    color:#fcfcfc;
+    font-weight:bold;
+}

Docs/source/_templates/dev_layout.html

@@ -0,0 +1,11 @@
+{% extends "!layout.html" %}
+  {% block footer %} {{ super() }}
+{% endblock %}
+
+
+{% block sidebartitle %}
+{{ super() }}
+    <div class="branch">
+        Branch: <a href="{{ pathto('../', 1) }}{{ pagename }}{{file_suffix}}">master</a> | <a href="{{ pathto('', 1) }}{{ pagename }}{{file_suffix}}">development</a>
+    </div>
+{% endblock %}

Docs/source/_templates/layout.html

@@ -0,0 +1,11 @@
+{% extends "!layout.html" %}
+  {% block footer %} {{ super() }}
+{% endblock %}
+
+
+{% block sidebartitle %}
+{{ super() }}
+    <div class="branch">
+        Branch: <a href="{{ pathto('', 1) }}{{ pagename }}{{file_suffix}}">master</a> | <a href="{{ pathto('', 1) }}dev/{{ pagename }}{{file_suffix}}">development</a>
+    </div>
+{% endblock %}

Docs/source/conf.py

@@ -56,9 +56,7 @@ def get_version():
               'sphinx.ext.autosummary',
               'numpydoc',
               'sphinx.ext.githubpages',
-              'breathe',
-              'sphinxfortran.fortran_domain',
-              'sphinxfortran.fortran_autodoc']
+              'breathe']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -77,7 +75,7 @@ def get_version():
 
 # General information about the project.
 project = 'Castro'
-copyright = '2018, Castro development tem'
+copyright = '2018-2020, Castro development tem'
 author = 'Castro development team'
 
 html_logo = "castro_logo_hot_200.png"
@@ -234,10 +232,4 @@ def get_version():
 
 breathe_doxygen_config_options = {'EXTRACT_ALL': 'YES',
                                   'SHOW_USED_FILES': 'YES', 'RECURSIVE': 'YES'
-                                  }
-
-# -- Options for sphinx-fortran -----------------------------------------
-
-fortran_src = [os.path.abspath('preprocessed_files')]
-
-fortran_ext = ['f90', 'F90']
+                                  }

Docs/source/development.rst

@@ -191,3 +191,16 @@ accompanied by a Castro change, it is best practice to ensure that
 the PRs in both Microphysics and Castro have been approved, then
 merge the Microphysics PR, then add the update to the Microphysics
 submodule to the Castro PR, then merge. A similar process applies for AMReX.
+
+
+Continuous Integration
+======================
+
+We use Travis CI to run integration tests on the code and to build and deploy the documentation. The current status of these tests on the development branch can be found here:
+
+.. image:: https://travis-ci.com/AMReX-Astro/Castro.svg?branch=development
+   :target: https://travis-ci.com/AMReX-Astro/Castro
+
+Currently, travis runs the `clang static analyzer <https://clang-analyzer.llvm.org/>`_, which finds potential bugs in the code. It also runs a script to convert any tabs in the code into spaces. Both of these are run on pull requests to the Castro GitHub repo, and are run weekly on the development branch. 
+
+The travis build settings can be found in the ``.travis.yml`` file.

Docs/source/radiation.rst

@@ -366,40 +366,15 @@ See Krumholz et al. 2007 for some discussion on this.
 Boundary Conditions
 -------------------
 
-Castro needs to know about the boundary conditions for both
-the hydrodynamics and radiation portions of the evolution.
-
-Hydrodynamics Evolution
-~~~~~~~~~~~~~~~~~~~~~~~
-
-For the hydrodynamics portion of the solve, the boundary conditions
-for the normal hydrodynamic state values will be set by the problem’s
-hypfill routine (which typically just calls filcc to handle
-the usual hydrodynamics boundary types: outflow, symmetry, etc.).
-
-A corresponding radfill routine needs to be written to fill the
-ghost cells for the radiation energy density during the hydrodynamics
-evolution. Again, this usually will just default to calling
-filcc.
-
-Note: if any of the hydrodynamic boundary conditions types are set
-to Inflow, then you will need to ensure that the radfill
-routine explicitly handles the boundary condition implementation
-for the radiation energy density in that case—the filcc
-routine will not do a hydrodynamic Inflow boundary.
-
-Radiation Evolution
-~~~~~~~~~~~~~~~~~~~
-
-The following parameters are for radiation boundary in the diffusion
+The following parameters are for the radiation boundary in the diffusion
 equation. They do not affect hydrodynamic boundaries.
 
 -  radiation.lo_bc
 
    This sets the action to take at the lower edge of the domain in
    each coordinate direction. Possible values are:
 
-   -  101 *Dirchlet*:
+   -  101 *Dirichlet*:
 
       Specify the radiation energy density on the boundary.
       For gray radiation, this could be :math:`E_r = a T^4`.

Exec/Make.Castro

@@ -8,6 +8,11 @@ BLAS_LIBRARY ?= -lopenblas
 
 TOP := $(CASTRO_HOME)
 
+# Allow a problem setup to define a root location.
+# Otherwise, assume we're building in the current directory.
+
+PROBLEM_DIR ?= ./
+
 # Microphysics is a git submodule of Castro. By default
 # we assume it is in the external/ directory.
 # The user may override this with their own installation
@@ -132,6 +137,7 @@ endif
 
 USE_MLMG = FALSE
 
+
 #------------------------------------------------------------------------------
 # Castro directories
 #------------------------------------------------------------------------------
@@ -292,6 +298,8 @@ Bpack	+= $(foreach dir, $(Pdirs), $(AMREX_HOME)/Src/$(dir)/Make.package)
 # directory
 NETWORK_OUTPUT_PATH = $(CASTRO_AUTO_SOURCE_DIR)
 
+USE_CXX_EOS := TRUE
+
 include $(MICROPHYSICS_HOME)/Make.Microphysics_extern
 
 Bpack += $(foreach dir, $(EXTERN_CORE), $(dir)/Make.package)

Exec/Make.auto_source

@@ -45,7 +45,7 @@ ifeq ($(USE_PROB_PARAMS), TRUE)
 endif
 
 PROB_PARAMS_TEMPLATE := $(TOP)/Util/scripts/prob_params.template
-PROB_PARAMETERS := ./_prob_params
+PROB_PARAMETERS := $(PROBLEM_DIR)/_prob_params
 
 $(CASTRO_AUTO_SOURCE_DIR)/prob_params_auto.F90: $(PROB_PARAMETERS) $(PROB_PARAMS_TEMPLATE)
 	@if [ ! -d $(CASTRO_AUTO_SOURCE_DIR) ]; then mkdir -p $(CASTRO_AUTO_SOURCE_DIR); fi