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Merge branch 'development' into plot_max_level
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zingale authored Nov 3, 2022
2 parents 274a06d + b27642d commit 1615357
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16 changes: 8 additions & 8 deletions .github/workflows/c-linter.yml
Original file line number Diff line number Diff line change
Expand Up @@ -5,16 +5,16 @@ jobs:
cpp-linter:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
with:
fetch-depth: 0

- name: Get submodules
- name: Get submodules
run: |
git submodule update --init
cd external/Microphysics
git fetch; git checkout development
cd ../amrex
cd ../amrex
git fetch; git checkout development
cd ../..
Expand All @@ -23,11 +23,11 @@ jobs:
sudo apt-get update -y -qq
sudo apt-get -qq -y install curl clang-tidy cmake jq clang cppcheck clang-format bear g++>=9.3.0 gfortran>=9.3.0
- name: Get cpp linter repo
- name: Get cpp linter repo
run: |
cd external
cd external
git clone https://github.com/AMReX-Astro/cpp-linter-action.git
cd ..
cd ..
- name: Check header includes
run: |
Expand All @@ -37,9 +37,9 @@ jobs:
- name: Run cpp linter
run: python3 external/cpp-linter-action/run_on_changed_files.py ${{ github.event.pull_request.base.sha }} ${{ github.event.pull_request.head.sha }} -header-filter=Castro -ignore-files="amrex|Microphysics" -run-linter

- name: Archive clang tidy report
uses: actions/upload-artifact@v1
uses: actions/upload-artifact@v3
with:
name: clang-tidy-report
path: clang-tidy-report.txt
6 changes: 3 additions & 3 deletions .github/workflows/create_release.yml
Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,8 @@ on:
push:
# Sequence of patterns matched against refs/tags
tags:
- '[0-9][0-9].[0-9][0-9]'
- '[0-9][0-9].[0-9][0-9]'

name: Create Release

jobs:
Expand All @@ -12,7 +12,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout code
uses: actions/checkout@v2
uses: actions/checkout@v3

- name: Get the version
id: get_version
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44 changes: 44 additions & 0 deletions .github/workflows/docs-test.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
name: docs build

on:
push:
branches:
- development
- main
pull_request:
branches:
- development

jobs:
docs:
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v3
with:
fetch-depth: 0
- name: Install pandoc and doxygen
run: |
sudo apt install pandoc doxygen
- 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 -r ./requirements.txt

- name: Build docs
run: |
cd Docs/
make SPHINXOPTS=-v NO_DOXYGEN=TRUE html
44 changes: 44 additions & 0 deletions .github/workflows/flame_wave-compare.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
name: flame_wave

on: [pull_request]
jobs:
flame_wave-2d:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
with:
fetch-depth: 0

- name: Get submodules
run: |
git submodule update --init
cd external/Microphysics
git fetch; git checkout development
cd ../amrex
git fetch; git checkout development
cd ../..
- name: Install dependencies
run: |
sudo apt-get update -y -qq
sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0
- name: Compile flame_wave
run: |
cd Exec/science/flame_wave
make DEBUG=TRUE USE_MPI=FALSE -j 4
- name: Run flame_wave
run: |
cd Exec/science/flame_wave
./Castro2d.gnu.DEBUG.ex inputs_2d.testsuite max_step=2 castro.sum_interval=1 amr.plot_files_output=0 amr.checkpoint_files_output=0
- name: Check grid_diag.out
run: |
cd Exec/science/flame_wave
diff grid_diag.out ci-benchmarks/grid_diag.out
- name: Check species_diag.out
run: |
cd Exec/science/flame_wave
diff species_diag.out ci-benchmarks/species_diag.out
7 changes: 4 additions & 3 deletions .github/workflows/gh-pages.yml
Original file line number Diff line number Diff line change
Expand Up @@ -14,12 +14,13 @@ jobs:

- name: Install pandoc and doxygen
run: |
sudo apt update
sudo apt install pandoc doxygen
- name: Setup Python
uses: actions/setup-python@v3
uses: actions/setup-python@v4
with:
python-version: '3.9'
python-version: '3.10'

- name: Upgrade pip
run: |
Expand All @@ -31,7 +32,7 @@ jobs:
run: echo "::set-output name=dir::$(pip cache dir)"

- name: Cache dependencies
uses: actions/cache@v1
uses: actions/cache@v3
with:
path: ${{ steps.pip-cache.outputs.dir }}
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
Expand Down
14 changes: 7 additions & 7 deletions .github/workflows/gpu_action.yml
Original file line number Diff line number Diff line change
Expand Up @@ -5,23 +5,23 @@ jobs:
gpu-compilation:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
with:
fetch-depth: 0

- name: Get submodules
- name: Get submodules
run: |
git submodule update --init
cd external/Microphysics
git fetch; git checkout development
cd ../amrex
cd ../amrex
git fetch; git checkout development
cd ../..
- name: Install dependencies
run: |
sudo apt-get update -y -qq
sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0 gfortran>=9.3.0
sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0
- name: Install CUDA
# from https://developer.nvidia.com/cuda-downloads?target_os=Linux&target_arch=x86_64&Distribution=Ubuntu&target_version=20.04&target_type=deb_network
Expand All @@ -33,11 +33,11 @@ jobs:
sudo apt-get update
sudo apt-get -y install cuda
- name: Get cpp linter repo
- name: Get cpp linter repo
run: |
cd external
cd external
git clone https://github.com/AMReX-Astro/cpp-linter-action.git
cd ..
cd ..
- name: Check header includes
run: |
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/sedov-compare.yml
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ jobs:
- name: Install dependencies
run: |
sudo apt-get update -y -qq
sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0 gfortran>=9.3.0
sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0
- name: Compile Sedov
run: |
Expand Down
18 changes: 18 additions & 0 deletions CHANGES.md
Original file line number Diff line number Diff line change
@@ -1,3 +1,21 @@
# 22.11

* We now output the location where the timestep is set (#2273)

# 22.09

* Added an option `castro.allow_non_unit_aspect_zones` to permit
Castro to be run with dx != dy != dz. This support is experimental.

# 22.08

* fixed an issue with restart when using Poisson gravity (#2253)

* the source term corrector can now be used with simplified-SDC
(#2252)

* derefinement can now be specified via AMRErrorTag (#2238)

# 22.06

* castro.stopping_criterion_field and castro.stopping_criterion_value have
Expand Down
23 changes: 22 additions & 1 deletion Docs/source/AMR.rst
Original file line number Diff line number Diff line change
Expand Up @@ -67,14 +67,35 @@ describing when to tag. These are:
* ``field_name`` : name of the string defining the field in the code

If a refinement indicator is added, either
``value_greater``, ``value_less``, or ``gradient`` must be provided.
``value_greater``, ``value_less``, ``gradient`` or ``relative_gradient`` must be provided.

.. note::

Zones adjacent to a physical boundary cannot be tagged for refinement when
using the Poisson gravity solver. If your tagging criteria are met in these
zones, they will be ignored.

Sometimes, we wish to force the code to derefine based on a critera,
even if other indicators tagged a zone for refinement. This is
accomplished by created another refinement indicator and setting the
``derefine`` field to ``1``. For example, to derefine any zone where
the density is less than ``1.e4``, we could do:

::

amr.refine.dencutoff.derefine = 1
amr.refine.dencutoff.field_name = density
amr.refine.dencutoff.value_less = 1.e4

where ``dencutoff`` is lised under ``amr.refinement_indicators``.

.. note::

Any derefinement indicators should appear after those that tag for
refinement in the ``amr.refinement_indicators`` list, so it is
applied after all the refinement tagging is done.


.. index:: problem_tagging.H

We provide also the ability for the user to define their own tagging criteria.
Expand Down
10 changes: 4 additions & 6 deletions Exec/Make.Castro
Original file line number Diff line number Diff line change
Expand Up @@ -113,6 +113,10 @@ ifeq ($(USE_CUDA),TRUE)
CUDA_VERBOSE = FALSE
endif

AMREX_NO_PROBINIT := TRUE

include $(AMREX_HOME)/Tools/GNUMake/Make.defs

ifeq ($(USE_GPU),TRUE)
# We don't currently support host-side OpenMP being enabled
# when using GPUs. Throw an error to prevent this case.
Expand All @@ -121,10 +125,6 @@ ifeq ($(USE_GPU),TRUE)
endif
endif

AMREX_NO_PROBINIT := TRUE

include $(AMREX_HOME)/Tools/GNUMake/Make.defs

CASTRO_AUTO_SOURCE_DIR := $(TmpBuildDir)/castro_sources/$(optionsSuffix).EXE


Expand Down Expand Up @@ -195,8 +195,6 @@ ifeq ($(USE_REACT), TRUE)
# we only implement this for C++ reactions
endif

USE_CXX_REACTIONS = TRUE
DEFINES += -DCXX_REACTIONS
endif

ifeq ($(USE_REACT_SPARSE_JACOBIAN), TRUE)
Expand Down
427 changes: 427 additions & 0 deletions Exec/hydro_tests/acoustic_pulse/analysis/acoustic_aspect_test.ipynb

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