paddle 1.1.1__tar.gz → 1.1.4__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- paddle-1.1.4/.bumpversion.cfg +12 -0
- paddle-1.1.4/.github/workflows/bump-and-tag.yaml +78 -0
- paddle-1.1.4/.github/workflows/cd.yml +55 -0
- paddle-1.1.4/.github/workflows/ci.yml +60 -0
- paddle-1.1.4/.gitignore +207 -0
- paddle-1.1.4/.pre-commit-config.yaml +17 -0
- paddle-1.1.4/LICENSE +21 -0
- {paddle-1.1.1 → paddle-1.1.4}/PKG-INFO +8 -13
- paddle-1.1.4/README.md +2 -0
- {paddle-1.1.1 → paddle-1.1.4}/pyproject.toml +9 -6
- {paddle-1.1.1 → paddle-1.1.4}/src/paddle/__init__.py +2 -5
- {paddle-1.1.1 → paddle-1.1.4}/src/paddle/crm.py +14 -14
- {paddle-1.1.1 → paddle-1.1.4}/src/paddle/evolve_kinetics.py +6 -4
- {paddle-1.1.1 → paddle-1.1.4}/src/paddle/find_init_params.py +14 -12
- {paddle-1.1.1 → paddle-1.1.4}/src/paddle/setup_profile.py +39 -37
- {paddle-1.1.1 → paddle-1.1.4}/src/paddle/write_profile.py +10 -8
- {paddle-1.1.1/src/paddle → paddle-1.1.4/tests}/data/saturn1d.yaml +1 -1
- {paddle-1.1.1 → paddle-1.1.4}/tests/test_saturn_adiabat.py +25 -21
- paddle-1.1.1/.gitignore +0 -14
- paddle-1.1.1/README.md +0 -8
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[bumpversion]
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current_version = 1.1.4
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commit = True
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tag = True
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[bumpversion:file:src/paddle/__init__.py]
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search = __version__ = "{current_version}"
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replace = __version__ = "{new_version}"
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[bumpversion:file:pyproject.toml]
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search = version = "{current_version}"
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replace = version = "{new_version}"
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name: Bump Version and Tag
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on:
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pull_request:
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types: [closed]
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branches: [main]
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env:
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PYTHON_VERSION: "3.11"
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jobs:
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bump-version:
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runs-on: ubuntu-latest
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permissions:
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contents: write
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pull-requests: write
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: ${{ env.PYTHON_VERSION }}
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- name: Configure Git
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run: |
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git config user.name "github-actions[bot]"
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git config user.email "github-actions[bot]@users.noreply.github.com"
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- name: Bump version and push tag
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id: bump_version
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uses: jasonamyers/github-bumpversion-action@v1.0.5
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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- name: Push changes
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uses: ad-m/github-push-action@master
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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branch: ${{ github.ref }}
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tags: true
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- name: Generate Release Notes
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uses: octokit/request-action@v2.x
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id: get_release_notes
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with:
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route: POST /repos/${{ github.repository }}/releases/generate-notes
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tag_name: v${{ steps.bump_version.outputs.new_ver }}
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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- name: Create GitHub release
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id: create_release
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uses: actions/create-release@v1.1.4
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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with:
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tag_name: v${{ steps.bump_version.outputs.new_ver }}
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release_name: Release v${{ steps.bump_version.outputs.new_ver }}
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draft: false
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prerelease: false
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body: ${{ fromJson(steps.get_release_notes.outputs.data).body }}
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- name: Post comment on PR with release notes
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uses: actions/github-script@v7
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with:
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script: |
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const notes = `${{ fromJson(steps.get_release_notes.outputs.data).body }}`;
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github.rest.issues.createComment({
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issue_number: context.payload.pull_request.number,
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owner: context.repo.owner,
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repo: context.repo.repo,
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body: `🎉 Released v${{ steps.bump_version.outputs.new_ver }}!\n\n${notes}`
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})
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name: Deploy to PyPI
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on:
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push:
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branches: [main]
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tags: [v*]
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jobs:
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build:
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name: Build distribution artifacts
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runs-on: ubuntu-latest
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Setup Host Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.11"
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cache: pip
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- name: Install build backend
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run: |
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python -m pip install --upgrade pip
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pip install build
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- name: Build sdist and wheel
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run: python -m build
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- name: Upload artifacts
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uses: actions/upload-artifact@v4
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with:
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name: dist
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path: dist/*
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publish-pypi:
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name: Publish to PyPI
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needs: build
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runs-on: ubuntu-latest
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permissions:
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id-token: write
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contents: read
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steps:
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- name: Download wheels
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uses: actions/download-artifact@v4
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with:
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name: dist
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path: dist
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- name: Publish to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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user: __token__
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password: ${{ secrets.PYPI_API_TOKEN }}
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verbose: true
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name: Continuous Integration
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on:
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pull_request:
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branches: [main]
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push:
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branches: [main]
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tags: [v*]
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env:
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PYTHON_VERSION: "3.11"
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BUILD_TYPE: Release
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jobs:
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pre-commit:
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runs-on: ubuntu-latest
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steps:
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- name: Check out code
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: ${{ env.PYTHON_VERSION }}
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- name: Install style checkers
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run: pip install --user cpplint cppcheck clang-format==20.1.4
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- name: Cache pre-commit
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uses: actions/cache@v3
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with:
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path: ~/.cache/pre-commit
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key: ${{ runner.os }}-pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
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restore-keys: |
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${{ runner.os }}-pre-commit-
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- name: Run pre-commit
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uses: pre-commit/action@v3.0.1
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build-and-test:
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needs: pre-commit
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: true
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matrix:
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os: [ubuntu-latest, macOS-latest]
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steps:
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- name: Check out code
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: ${{ env.PYTHON_VERSION }}
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cache: "pip"
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- name: Install Python dependencies
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run: |
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pip install numpy pytest 'pyharp>=1.7.1' 'torch==2.7.1'
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paddle-1.1.4/.gitignore
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[codz]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py.cover
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.hypothesis/
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.pytest_cache/
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cover/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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instance/
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.webassets-cache
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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target/
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# Jupyter Notebook
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profile_default/
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ipython_config.py
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# pyenv
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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# UV
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# commonly ignored for libraries.
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# poetry
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# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
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# commonly ignored for libraries.
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#poetry.lock
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#poetry.toml
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# pdm
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# pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
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# https://pdm-project.org/en/latest/usage/project/#working-with-version-control
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#pdm.lock
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# pixi
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#pixi.lock
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.pixi
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.envrc
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# pytype static type analyzer
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.pytype/
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cython_debug/
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# PyCharm
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# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
|
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# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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# and can be added to the global gitignore or merged into this file. For a more nuclear
|
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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#.idea/
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# Abstra
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# Abstra is an AI-powered process automation framework.
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# Ignore directories containing user credentials, local state, and settings.
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# Learn more at https://abstra.io/docs
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.abstra/
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# Visual Studio Code
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# Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
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# that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
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# and can be added to the global gitignore or merged into this file. However, if you prefer,
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# you could uncomment the following to ignore the entire vscode folder
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# .vscode/
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# Ruff stuff:
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.ruff_cache/
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# PyPI configuration file
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.pypirc
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# Cursor
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# Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
|
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# exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
|
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|
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# refer to https://docs.cursor.com/context/ignore-files
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.cursorignore
|
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+
.cursorindexingignore
|
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+
|
|
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|
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# Marimo
|
|
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|
+
marimo/_static/
|
|
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|
+
marimo/_lsp/
|
|
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|
+
__marimo__/
|
|
@@ -0,0 +1,17 @@
|
|
|
1
|
+
repos:
|
|
2
|
+
- repo: https://github.com/pre-commit/pre-commit-hooks
|
|
3
|
+
rev: v4.0.1
|
|
4
|
+
hooks:
|
|
5
|
+
- id: requirements-txt-fixer
|
|
6
|
+
- id: trailing-whitespace
|
|
7
|
+
exclude: ^(data|patches)/.*$
|
|
8
|
+
- id: end-of-file-fixer
|
|
9
|
+
exclude: ^(data|patches)/.*$
|
|
10
|
+
- id: check-yaml
|
|
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|
+
exclude: ^data/
|
|
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|
+
|
|
13
|
+
- repo: https://github.com/psf/black
|
|
14
|
+
rev: 24.10.0 # Use the latest stable version
|
|
15
|
+
hooks:
|
|
16
|
+
- id: black
|
|
17
|
+
args: [--line-length=88]
|
paddle-1.1.4/LICENSE
ADDED
|
@@ -0,0 +1,21 @@
|
|
|
1
|
+
MIT License
|
|
2
|
+
|
|
3
|
+
Copyright (c) 2025 Elijah Mullens
|
|
4
|
+
|
|
5
|
+
Permission is hereby granted, free of charge, to any person obtaining a copy
|
|
6
|
+
of this software and associated documentation files (the "Software"), to deal
|
|
7
|
+
in the Software without restriction, including without limitation the rights
|
|
8
|
+
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
|
9
|
+
copies of the Software, and to permit persons to whom the Software is
|
|
10
|
+
furnished to do so, subject to the following conditions:
|
|
11
|
+
|
|
12
|
+
The above copyright notice and this permission notice shall be included in all
|
|
13
|
+
copies or substantial portions of the Software.
|
|
14
|
+
|
|
15
|
+
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
|
16
|
+
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
|
17
|
+
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
|
18
|
+
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
|
19
|
+
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
|
20
|
+
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
|
|
21
|
+
SOFTWARE.
|
|
@@ -1,11 +1,12 @@
|
|
|
1
1
|
Metadata-Version: 2.4
|
|
2
2
|
Name: paddle
|
|
3
|
-
Version: 1.1.
|
|
4
|
-
Summary:
|
|
5
|
-
Project-URL: Homepage, https://github.com/
|
|
6
|
-
Project-URL: Repository, https://github.com/
|
|
7
|
-
Project-URL: Issues, https://github.com/
|
|
8
|
-
Author-email: Cheng Li <chengcli@umich.edu>
|
|
3
|
+
Version: 1.1.4
|
|
4
|
+
Summary: Python Atmospheric Dynamics: Discovery and Learning about Exoplanets. An open-source, user-friendly python frontend of canoe
|
|
5
|
+
Project-URL: Homepage, https://github.com/elijah-mullens/paddle
|
|
6
|
+
Project-URL: Repository, https://github.com/elijah-mullens/paddle
|
|
7
|
+
Project-URL: Issues, https://github.com/elijah-mullens/paddle/issues
|
|
8
|
+
Author-email: Elijah Mullens <eem85@cornell.edu>, Cheng Li <chengcli@umich.edu>
|
|
9
|
+
License-File: LICENSE
|
|
9
10
|
Classifier: Development Status :: 3 - Alpha
|
|
10
11
|
Classifier: Intended Audience :: Developers
|
|
11
12
|
Classifier: Intended Audience :: Science/Research
|
|
@@ -29,10 +30,4 @@ Requires-Dist: pytest>=7; extra == 'dev'
|
|
|
29
30
|
Description-Content-Type: text/markdown
|
|
30
31
|
|
|
31
32
|
# paddle
|
|
32
|
-
|
|
33
|
-
A minimal, utility subroutines for canoe
|
|
34
|
-
|
|
35
|
-
## Install
|
|
36
|
-
|
|
37
|
-
```bash
|
|
38
|
-
pip install paddle
|
|
33
|
+
Python Atmospheric Dynamics: Discovering and Learning about Exoplanets. An open-source, user-friendly python version of canoe.
|
paddle-1.1.4/README.md
ADDED
|
@@ -4,11 +4,14 @@ build-backend = "hatchling.build"
|
|
|
4
4
|
|
|
5
5
|
[project]
|
|
6
6
|
name = "paddle"
|
|
7
|
-
version = "1.1.
|
|
8
|
-
description = "
|
|
7
|
+
version = "1.1.4"
|
|
8
|
+
description = "Python Atmospheric Dynamics: Discovery and Learning about Exoplanets. An open-source, user-friendly python frontend of canoe"
|
|
9
9
|
readme = "README.md"
|
|
10
10
|
requires-python = ">=3.9"
|
|
11
|
-
authors = [
|
|
11
|
+
authors = [
|
|
12
|
+
{ name = "Elijah Mullens", email = "eem85@cornell.edu" },
|
|
13
|
+
{ name = "Cheng Li", email = "chengcli@umich.edu" },
|
|
14
|
+
]
|
|
12
15
|
keywords = []
|
|
13
16
|
classifiers = [
|
|
14
17
|
"Development Status :: 3 - Alpha",
|
|
@@ -39,9 +42,9 @@ dev = [
|
|
|
39
42
|
]
|
|
40
43
|
|
|
41
44
|
[project.urls]
|
|
42
|
-
Homepage = "https://github.com/
|
|
43
|
-
Repository = "https://github.com/
|
|
44
|
-
Issues = "https://github.com/
|
|
45
|
+
Homepage = "https://github.com/elijah-mullens/paddle"
|
|
46
|
+
Repository = "https://github.com/elijah-mullens/paddle"
|
|
47
|
+
Issues = "https://github.com/elijah-mullens/paddle/issues"
|
|
45
48
|
|
|
46
49
|
[project.scripts]
|
|
47
50
|
paddle = "paddle.__main__:main"
|
|
@@ -3,8 +3,5 @@ from .write_profile import write_profile
|
|
|
3
3
|
from .find_init_params import find_init_params
|
|
4
4
|
from .evolve_kinetics import evolve_kinetics
|
|
5
5
|
|
|
6
|
-
__all__ = ["setup_profile",
|
|
7
|
-
|
|
8
|
-
"find_init_params",
|
|
9
|
-
"evolve_kinetics"]
|
|
10
|
-
__version__ = "1.1.1"
|
|
6
|
+
__all__ = ["setup_profile", "write_profile", "find_init_params", "evolve_kinetics"]
|
|
7
|
+
__version__ = "1.1.4"
|
|
@@ -4,20 +4,20 @@ import time
|
|
|
4
4
|
import kintera
|
|
5
5
|
import numpy as np
|
|
6
6
|
from snapy import (
|
|
7
|
-
|
|
8
|
-
|
|
9
|
-
|
|
10
|
-
|
|
11
|
-
|
|
12
|
-
|
|
7
|
+
index,
|
|
8
|
+
MeshBlockOptions,
|
|
9
|
+
MeshBlock,
|
|
10
|
+
OutputOptions,
|
|
11
|
+
NetcdfOutput,
|
|
12
|
+
)
|
|
13
13
|
from kintera import (
|
|
14
|
-
|
|
15
|
-
|
|
16
|
-
|
|
17
|
-
|
|
18
|
-
|
|
14
|
+
ThermoOptions,
|
|
15
|
+
ThermoX,
|
|
16
|
+
KineticsOptions,
|
|
17
|
+
Kinetics,
|
|
18
|
+
)
|
|
19
19
|
|
|
20
|
-
if __name__ ==
|
|
20
|
+
if __name__ == "__main__":
|
|
21
21
|
# input file
|
|
22
22
|
infile = "earth.yaml"
|
|
23
23
|
device = "cpu"
|
|
@@ -46,7 +46,7 @@ if __name__ == '__main__':
|
|
|
46
46
|
|
|
47
47
|
# set up initial condition
|
|
48
48
|
w = setup_initial_condition(block, thermo_x)
|
|
49
|
-
print("w = ", w[:,0,0
|
|
49
|
+
print("w = ", w[:, 0, 0, :])
|
|
50
50
|
|
|
51
51
|
# integration
|
|
52
52
|
current_time = 0.0
|
|
@@ -70,7 +70,7 @@ if __name__ == '__main__':
|
|
|
70
70
|
block.forward(dt, stage)
|
|
71
71
|
|
|
72
72
|
# evolve kinetics
|
|
73
|
-
u[index.icy:] += evolve_kinetics(block, kinet, thermo_x)
|
|
73
|
+
u[index.icy :] += evolve_kinetics(block, kinet, thermo_x)
|
|
74
74
|
|
|
75
75
|
current_time += dt
|
|
76
76
|
count += 1
|
|
@@ -2,12 +2,14 @@ import torch
|
|
|
2
2
|
import snapy
|
|
3
3
|
import kintera
|
|
4
4
|
|
|
5
|
+
|
|
5
6
|
def evolve_kinetics(
|
|
6
7
|
hydro_w: torch.Tensor,
|
|
7
|
-
block: snapy.MeshBlock,
|
|
8
|
-
kinet: kintera.Kinetics,
|
|
8
|
+
block: snapy.MeshBlock,
|
|
9
|
+
kinet: kintera.Kinetics,
|
|
9
10
|
thermo_x: kintera.ThermoX,
|
|
10
|
-
dt
|
|
11
|
+
dt,
|
|
12
|
+
) -> torch.Tensor:
|
|
11
13
|
"""
|
|
12
14
|
Evolve the chemical kinetics for one time step using implicit method.
|
|
13
15
|
|
|
@@ -26,7 +28,7 @@ def evolve_kinetics(
|
|
|
26
28
|
|
|
27
29
|
temp = eos.compute("W->T", (hydro_w,))
|
|
28
30
|
pres = hydro_w[snapy.index.ipr]
|
|
29
|
-
xfrac = thermo_y.compute("Y->X", (hydro_w[snapy.index.icy:],))
|
|
31
|
+
xfrac = thermo_y.compute("Y->X", (hydro_w[snapy.index.icy :],))
|
|
30
32
|
conc = thermo_x.compute("TPX->V", (temp, pres, xfrac))
|
|
31
33
|
cp_vol = thermo_x.compute("TV->cp", (temp, conc))
|
|
32
34
|
|
|
@@ -4,16 +4,18 @@ import numpy as np
|
|
|
4
4
|
|
|
5
5
|
from .setup_profile import setup_profile
|
|
6
6
|
|
|
7
|
+
|
|
7
8
|
def find_init_params(
|
|
8
|
-
|
|
9
|
-
|
|
10
|
-
|
|
11
|
-
|
|
12
|
-
|
|
13
|
-
|
|
14
|
-
|
|
15
|
-
|
|
16
|
-
|
|
9
|
+
block: snapy.MeshBlock,
|
|
10
|
+
param: dict[str, float],
|
|
11
|
+
*,
|
|
12
|
+
target_T: float = 300.0,
|
|
13
|
+
target_P: float = 1.0e5,
|
|
14
|
+
method: str = "moist-adiabat",
|
|
15
|
+
max_iter: int = 50,
|
|
16
|
+
ftol: float = 1.0e-2,
|
|
17
|
+
verbose: bool = True,
|
|
18
|
+
):
|
|
17
19
|
"""Find initial parameters that yield desired T and P
|
|
18
20
|
|
|
19
21
|
Args:
|
|
@@ -44,14 +46,15 @@ def find_init_params(
|
|
|
44
46
|
temp = eos.compute("W->T", (w,)).squeeze()
|
|
45
47
|
|
|
46
48
|
# calculate 1D pressure
|
|
47
|
-
pres = w[snapy.index.ipr
|
|
49
|
+
pres = w[snapy.index.ipr, ...].squeeze()
|
|
48
50
|
|
|
49
51
|
# temperature function
|
|
50
52
|
t_func = interp1d(
|
|
51
53
|
pres.log().cpu().numpy(),
|
|
52
54
|
temp.log().cpu().numpy(),
|
|
53
55
|
kind="linear",
|
|
54
|
-
fill_value="extrapolate"
|
|
56
|
+
fill_value="extrapolate",
|
|
57
|
+
)
|
|
55
58
|
|
|
56
59
|
temp1 = np.exp(t_func(np.log(target_P)))
|
|
57
60
|
if verbose:
|
|
@@ -69,4 +72,3 @@ def find_init_params(
|
|
|
69
72
|
count += 1
|
|
70
73
|
|
|
71
74
|
raise RuntimeError("Failed to converge within the maximum number of iterations.")
|
|
72
|
-
|
|
@@ -4,18 +4,19 @@ import torch
|
|
|
4
4
|
import snapy
|
|
5
5
|
import kintera
|
|
6
6
|
|
|
7
|
+
|
|
7
8
|
def integrate_neutral(
|
|
8
|
-
|
|
9
|
-
|
|
10
|
-
|
|
11
|
-
|
|
12
|
-
|
|
13
|
-
|
|
14
|
-
|
|
15
|
-
|
|
9
|
+
thermo_x: kintera.ThermoX,
|
|
10
|
+
temp: torch.Tensor,
|
|
11
|
+
pres: torch.Tensor,
|
|
12
|
+
xfrac: torch.Tensor,
|
|
13
|
+
grav: float,
|
|
14
|
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dz: float,
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max_iter: int = 100,
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+
) -> Tuple[torch.Tensor, torch.Tensor, torch.Tensor]:
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"""
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A neutral density profile assumes no cloud and:
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-
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+
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(1) dP/dz = -rho*g
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(2) d(rho)/dz = ...
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@@ -68,15 +69,16 @@ def integrate_neutral(
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return temp2, pres2, xfrac2
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+
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def integrate_dry_adiabat(
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-
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-
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-
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-
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-
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-
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-
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-
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+
thermo_x: kintera.ThermoX,
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temp: torch.Tensor,
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pres: torch.Tensor,
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xfrac: torch.Tensor,
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grav: float,
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dz: float,
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max_iter: int = 100,
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+
) -> Tuple[torch.Tensor, torch.Tensor, torch.Tensor]:
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"""
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A dry adiabatic profile assumes no cloud and:
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@@ -84,12 +86,12 @@ def integrate_dry_adiabat(
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(2) dP/dz = -rho*g
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In discretized form:
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-
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+
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cp_bar = 0.5 * (cp(T_old) + cp(T_new))
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T_new = T_old - g/bar * dz
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rho_bar = 0.5 * (rho_old + rho_new)
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P_new = P_old - rho_bar * g * dz
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-
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+
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"""
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conc1 = thermo_x.compute("TPX->V", [temp, pres, xfrac])
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cp1 = thermo_x.compute("TV->cp", [temp, conc1]) / conc1.sum(-1)
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@@ -136,11 +138,10 @@ def integrate_dry_adiabat(
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return temp2, pres2, xfrac2
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+
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def setup_profile(
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-
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-
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-
method: str = "moist-adiabat"
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-
) -> torch.Tensor:
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+
block: snapy.MeshBlock, param: dict[str, float] = {}, method: str = "moist-adiabat"
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+
) -> torch.Tensor:
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"""
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Set up an adiabatic initial condition for the mesh block.
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147
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@@ -175,16 +176,16 @@ def setup_profile(
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"moist-adiabat",
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"isothermal",
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"pseudo-adiabat",
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-
"neutral"
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+
"neutral",
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]
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|
if method not in valid_methods:
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raise ValueError(f"Invalid method '{method}'. Choose from {valid_methods}.")
|
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184
|
-
Ts = param.get("Ts", 300.)
|
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|
-
Ps = param.get("Ps", 1.
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+
Ts = param.get("Ts", 300.0)
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+
Ps = param.get("Ps", 1.0e5)
|
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186
187
|
grav = param.get("grav", 9.8)
|
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187
|
-
Tmin = param.get("Tmin", 0.)
|
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+
Tmin = param.get("Tmin", 0.0)
|
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189
|
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189
190
|
# get handles to modules
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191
|
coord = block.module("hydro.coord")
|
|
@@ -204,8 +205,7 @@ def setup_profile(
|
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204
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|
ny = len(thermo_y.options.species()) - 1
|
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205
206
|
nvar = 5 + ny
|
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206
207
|
|
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207
|
-
w = torch.zeros((nvar, nc3, nc2, nc1),
|
|
208
|
-
dtype=x1v.dtype, device=x1v.device)
|
|
208
|
+
w = torch.zeros((nvar, nc3, nc2, nc1), dtype=x1v.dtype, device=x1v.device)
|
|
209
209
|
|
|
210
210
|
temp = Ts * torch.ones((nc3, nc2), dtype=w.dtype, device=w.device)
|
|
211
211
|
pres = Ps * torch.ones((nc3, nc2), dtype=w.dtype, device=w.device)
|
|
@@ -216,7 +216,7 @@ def setup_profile(
|
|
|
216
216
|
xfrac[..., index] = param.get(f"x{name}", 0.0)
|
|
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217
|
|
|
218
218
|
# dry air mole fraction
|
|
219
|
-
xfrac[..., 0] = 1. - xfrac[..., 1:].sum(dim=-1)
|
|
219
|
+
xfrac[..., 0] = 1.0 - xfrac[..., 1:].sum(dim=-1)
|
|
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220
|
|
|
221
221
|
# start and end indices for the vertical direction
|
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|
# excluding ghost cells
|
|
@@ -227,7 +227,7 @@ def setup_profile(
|
|
|
227
227
|
dz = coord.buffer("dx1f")[ifirst]
|
|
228
228
|
|
|
229
229
|
# half a grid to cell center
|
|
230
|
-
thermo_x.extrapolate_ad(temp, pres, xfrac, grav, dz / 2.)
|
|
230
|
+
thermo_x.extrapolate_ad(temp, pres, xfrac, grav, dz / 2.0)
|
|
231
231
|
|
|
232
232
|
# adiabatic extrapolation
|
|
233
233
|
if method == "isothermal":
|
|
@@ -245,17 +245,19 @@ def setup_profile(
|
|
|
245
245
|
xfrac /= xfrac.sum(dim=-1, keepdim=True)
|
|
246
246
|
conc = thermo_x.compute("TPX->V", [temp, pres, xfrac])
|
|
247
247
|
|
|
248
|
-
w[snapy.index.ipr, ..., i] = pres
|
|
248
|
+
w[snapy.index.ipr, ..., i] = pres
|
|
249
249
|
w[snapy.index.idn, ..., i] = thermo_x.compute("V->D", [conc])
|
|
250
|
-
w[snapy.index.icy:, ...,i] = thermo_x.compute("X->Y", [xfrac])
|
|
250
|
+
w[snapy.index.icy :, ..., i] = thermo_x.compute("X->Y", [xfrac])
|
|
251
251
|
|
|
252
252
|
dz = coord.buffer("dx1f")[i]
|
|
253
253
|
if method.split("-")[0] == "dry":
|
|
254
|
-
temp, pres, xfrac = integrate_dry_adiabat(
|
|
254
|
+
temp, pres, xfrac = integrate_dry_adiabat(
|
|
255
|
+
thermo_x, temp, pres, xfrac, grav, dz
|
|
256
|
+
)
|
|
255
257
|
elif method.split("-")[0] == "neutral":
|
|
256
|
-
temp, pres, xfrac = integrate_neutral(thermo_x, temp, pres, xfrac, grav, dz)
|
|
258
|
+
temp, pres, xfrac = integrate_neutral(thermo_x, temp, pres, xfrac, grav, dz)
|
|
257
259
|
else:
|
|
258
|
-
thermo_x.extrapolate_ad(temp, pres, xfrac, grav, dz)
|
|
260
|
+
thermo_x.extrapolate_ad(temp, pres, xfrac, grav, dz)
|
|
259
261
|
|
|
260
262
|
if torch.any(temp < Tmin):
|
|
261
263
|
i_isothermal = i + 1
|
|
@@ -276,5 +278,5 @@ def setup_profile(
|
|
|
276
278
|
conc = thermo_x.compute("TPX->V", [temp, pres, xfrac])
|
|
277
279
|
w[snapy.index.ipr, ..., i] = pres
|
|
278
280
|
w[snapy.index.idn, ..., i] = thermo_x.compute("V->D", [conc])
|
|
279
|
-
w[snapy.index.icy:, ..., i] = thermo_x.compute("X->Y", [xfrac])
|
|
281
|
+
w[snapy.index.icy :, ..., i] = thermo_x.compute("X->Y", [xfrac])
|
|
280
282
|
return w
|
|
@@ -7,11 +7,12 @@ import torch
|
|
|
7
7
|
import kintera
|
|
8
8
|
import snapy
|
|
9
9
|
|
|
10
|
+
|
|
10
11
|
def write_profile(
|
|
11
12
|
filename: str,
|
|
12
13
|
hydro_w: torch.Tensor,
|
|
13
14
|
block: snapy.MeshBlock,
|
|
14
|
-
ref_pressure: float = 1.
|
|
15
|
+
ref_pressure: float = 1.0e5,
|
|
15
16
|
comment: Optional[str] = None,
|
|
16
17
|
) -> None:
|
|
17
18
|
"""
|
|
@@ -46,27 +47,28 @@ def write_profile(
|
|
|
46
47
|
raise ValueError("hydro_w must have shape (N, 1, 1, L).")
|
|
47
48
|
|
|
48
49
|
# calculate a height grid
|
|
49
|
-
pres = hydro_w[snapy.index.ipr
|
|
50
|
+
pres = hydro_w[snapy.index.ipr, ...].squeeze() / 1.0e5 # Pa -> bar
|
|
50
51
|
zlev_func = interp1d(
|
|
51
52
|
pres.log().cpu().numpy(),
|
|
52
53
|
coord.buffer("x1v").cpu().numpy(),
|
|
53
54
|
kind="linear",
|
|
54
|
-
fill_value="extrapolate"
|
|
55
|
-
|
|
56
|
-
|
|
55
|
+
fill_value="extrapolate",
|
|
56
|
+
)
|
|
57
|
+
zref = zlev_func(np.log(ref_pressure / 1.0e5))
|
|
58
|
+
zlev = (coord.buffer("x1v") - zref) / 1.0e3 # m -> km
|
|
57
59
|
|
|
58
60
|
# calculate temperature
|
|
59
61
|
temp = eos.compute("W->T", (hydro_w,)).squeeze()
|
|
60
62
|
|
|
61
63
|
# calculate mole fractions
|
|
62
|
-
xfrac = thermo_y.compute("Y->X", (hydro_w[snapy.index.icy
|
|
64
|
+
xfrac = thermo_y.compute("Y->X", (hydro_w[snapy.index.icy :, ...],)).squeeze()
|
|
63
65
|
|
|
64
66
|
# calculate heat capacity
|
|
65
|
-
conc = thermo_x.compute("TPX->V", (temp, pres * 1.
|
|
67
|
+
conc = thermo_x.compute("TPX->V", (temp, pres * 1.0e5, xfrac))
|
|
66
68
|
cpx = thermo_x.compute("TV->cp", (temp, conc)) / conc.sum(-1)
|
|
67
69
|
|
|
68
70
|
# calculate entropy
|
|
69
|
-
ens = thermo_x.compute("TPV->S", (temp, pres * 1.
|
|
71
|
+
ens = thermo_x.compute("TPV->S", (temp, pres * 1.0e5, conc)) / conc.sum(-1)
|
|
70
72
|
|
|
71
73
|
with open(filename, "w") as f:
|
|
72
74
|
# write comments
|
|
@@ -1,45 +1,48 @@
|
|
|
1
1
|
from importlib import resources
|
|
2
2
|
from paddle import (
|
|
3
|
-
|
|
4
|
-
|
|
5
|
-
|
|
6
|
-
|
|
3
|
+
setup_profile,
|
|
4
|
+
write_profile,
|
|
5
|
+
find_init_params,
|
|
6
|
+
)
|
|
7
7
|
from snapy import (
|
|
8
|
-
|
|
9
|
-
|
|
10
|
-
|
|
8
|
+
MeshBlockOptions,
|
|
9
|
+
MeshBlock,
|
|
10
|
+
)
|
|
11
11
|
from kintera import ThermoX
|
|
12
12
|
|
|
13
|
+
|
|
13
14
|
def setup_saturn_profile():
|
|
14
|
-
path = resources.files("paddle") / "data" / "saturn1d.yaml"
|
|
15
|
+
# path = resources.files("paddle") / "data" / "saturn1d.yaml"
|
|
16
|
+
path = "data" / "saturn1d.yaml"
|
|
15
17
|
print(f"Reading input file: {path}")
|
|
16
18
|
|
|
17
19
|
op_block = MeshBlockOptions.from_yaml(str(path))
|
|
18
20
|
block = MeshBlock(op_block)
|
|
19
21
|
|
|
20
22
|
param = {
|
|
21
|
-
"Ts": 600
|
|
22
|
-
"Ps": 100.
|
|
23
|
-
"Tmin": 85
|
|
23
|
+
"Ts": 600.0,
|
|
24
|
+
"Ps": 100.0e5,
|
|
25
|
+
"Tmin": 85.0,
|
|
24
26
|
"xH2O": 8.91e-3,
|
|
25
27
|
"xNH3": 3.52e-4,
|
|
26
28
|
"xH2S": 8.08e-5,
|
|
27
29
|
"grav": 10.44,
|
|
28
30
|
}
|
|
29
31
|
|
|
30
|
-
#method = "pseudo-adiabat"
|
|
31
|
-
#method = "moist-adiabat"
|
|
32
|
+
# method = "pseudo-adiabat"
|
|
33
|
+
# method = "moist-adiabat"
|
|
32
34
|
method = "dry-adiabat"
|
|
33
35
|
|
|
34
36
|
param = find_init_params(
|
|
35
|
-
|
|
36
|
-
|
|
37
|
-
|
|
38
|
-
|
|
39
|
-
|
|
40
|
-
|
|
41
|
-
|
|
42
|
-
|
|
37
|
+
block,
|
|
38
|
+
param,
|
|
39
|
+
target_T=134.0,
|
|
40
|
+
target_P=1.0e5,
|
|
41
|
+
method=method,
|
|
42
|
+
max_iter=50,
|
|
43
|
+
ftol=1.0e-2,
|
|
44
|
+
verbose=True,
|
|
45
|
+
)
|
|
43
46
|
|
|
44
47
|
w = setup_profile(block, param, method=method)
|
|
45
48
|
|
|
@@ -50,5 +53,6 @@ def setup_saturn_profile():
|
|
|
50
53
|
write_profile("saturn_profile.txt", w, block)
|
|
51
54
|
return w
|
|
52
55
|
|
|
56
|
+
|
|
53
57
|
if __name__ == "__main__":
|
|
54
58
|
w = setup_saturn_profile()
|
paddle-1.1.1/.gitignore
DELETED