From 4fe9cdcbc469603f4f39de9dbe87cfa0ea08b2df Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ezequiel=20P=C3=A1ssaro?= Date: Tue, 21 Mar 2023 13:51:44 -0300 Subject: [PATCH] Ci/update refdata ga (#41) * Adding rate matrix index (#2132) * adding NlteIndexHelper class * adding nlte_ionization_species to io/schemas/plasma.yml * adding nlte_excitation_species to io/schemas/plasma.yml * added nlte_ionization_species in assemble_plasma * fixed the issue with getting nlte_ionization_species from config * fixed transforming string from config to tuple for nlte ionization species * ran black * attempt of writing tests 1 * ran black * test attempt 2 * black on test_hdf_plasma * experimenting with revert * attempt 3 * reverted tardis/plasma/tests/test_complete_plasmas.py * reverted tardis/plasma/tests/test_hdf_plasma.py * adding cofig for nlte * adding fixture for tardis_cofig_verysimple_nlte * added test_plasma_nlte_section_config * ran black * fixed the issue with the test, ran it locally * ran black on necessary files * updated description in schemas * switching from nlte_ionization to be used from self * ran black * changed nlte_properties_new to nlte_solver_properties * adding nlte_rate_equation_matrix.py * reverting to previous commit * Restructuring NumbaModel (#2136) * Added NumbaRadial1DGeometry * Added to_numba function * Fixed incorrect naming of numba spec * Updated docstring * Updated to_numba docstring * Updated docstring * Updated numba model to contain only time explosion * updated docstring formatting error * Moved geometry to new geometry sub package * Updated all functions where numba model was used * Updated to specify units * converting time_explosion to seconds specifically * Added numba geometry fixture * Updated tests to work with numba geometry * Updated formatting * Fixed issue with geometry initialization * Fixed formatting * Add missing cell to download atom data (#2146) * Possible fix for prerelease workflow (#2127) * Possible fix for prerelease workflow * Fix double @ symbol * Changed to v2 * Pin setuptools_scm to v6 (#2147) * Pin setuptools_scm to v6 * Fix typo * Adding nlte_rate_equation_solver.py (#2140) * added nlte_rate_equation_matrix * adding the rate_equation_matrix * moved rate_matrix into a class NLTERateEquationSolver * fixed a bug in rate_matrix_index, added an example for checking if rate matrix works properly * changed the initial electron density for now * added tests, fixed a small bug * added some doctrings * fixed a typo * added some doctrings * added some doctrings part 2 * added some docstrings part 3 * removed unnecessary import * Update tardis/plasma/properties/nlte_rate_equation_solver.py Co-authored-by: Christian Vogl * changed how atomic number is created from rate_matrix_index * changed call of a function * got rid of unnecessary if statement in set_nlte_ion_rate * renamed last_row to charge_conservation_row * switched 0, 1 to atomic_number and ion_number to make it more readable * swtihed from rates to coefficients * changed the matrix set up to only keep necessary row for nlte_ion * ran black * fixing some doctrings * swtiched from using numbers to index names * switched the return statement to NotImplementedError * changed groupby from 0, 1 to atomic number, ion number * fixed an issue in the test * ran black Co-authored-by: Christian Vogl * Set specific qgrid feedstock version (#2152) * Pre-release 2022.11.17 (#2155) Automated changes for pre-release 2022.11.17 * Post-release 2022.11.17 (#2156) Automated changes for post-release 2022.11.17 * Pre-release 2022.11.20 (#2160) Automated changes for pre-release 2022.11.20 * Fix relativistic packet initialization (#2159) * Fix setting of full relativity flag * Add relativistic packet source Co-authored-by: Stuart Sim * Fix relativistic vpackets on inner boundary Co-authored-by: Stuart Sim * Fixing typos for nlte ion (#2154) * fixing typos on rate_matrix * changed the np arange to use 0 instead of 0.0 * NLTE jacobian matrix (#2158) * added jacobian matrix and deriv block functions * added doctrings * ran black * switched from df to array * added an initial test * ran black * reorganized the tests * added doctrings * added todo comments for future work * ran black * Kilonova missing zeta (#2150) * solved KN ZetaData issue * KN missing Zeta fixed * mailmap changed * Pre-release 2022.12.11 (#2172) Automated changes for pre-release 2022.12.11 * Post-release 2022.12.12 (#2173) Automated changes for post-release 2022.12.12 * Add missing __init__.py files to transport and geometry subpackages (#2170) * Add missing __init__.py files to transport subpackage * Add missing __init__.py file to geometry subpackage * Pre-release 2022.12.25 (#2180) Automated changes for pre-release 2022.12.25 * Post-release 2022.12.26 (#2182) Automated changes for post-release 2022.12.26 * Pre-release 2023.01.08 (#2186) Automated changes for pre-release 2023.01.08 * Post-release 2023.01.11 (#2188) Automated changes for post-release 2023.01.11 * Downloading nlte_atom_data in ref data (#2187) adding nlte_atom_data to be downloaded * Adding nlte solver (#2171) * adding solver part in the calculate method * adding the objective function * added the solution vector method * final touches for the solver * tests, attempt 1 * ran black * fixed the issue with tests * ran black * added missing doctrings in the nlte_rate_equation_solver.py * added doctrings to tests * changed the test to explicitly calculate the lte solution ion number densities. * ran black * added the atom data file to download_reference_data.sh * fixed download_reference_data.sh * Revert "added the atom data file to download_reference_data.sh" This reverts commit 58ce29e116bf6bee4d12facc95682a2af940e050. * got rid of index i, kept only shell * switched DataFrame to pandas.DataFrame in the docstrings * docstring bug fix * got rid of the deepcopy of nlte atomic data file * changed the number of shells to 5 * Update tardis/io/tests/data/tardis_configv1_nlte.yml Co-authored-by: Christian Vogl * Update tardis/plasma/properties/nlte_rate_equation_solver.py Co-authored-by: Christian Vogl * Update tardis/io/tests/data/tardis_configv1_nlte.yml Co-authored-by: Christian Vogl * Update tardis/io/tests/data/tardis_configv1_nlte.yml Co-authored-by: Christian Vogl * ran black * Update tardis/plasma/properties/nlte_rate_equation_solver.py Co-authored-by: Christian Vogl * Update tardis/plasma/tests/test_nlte_solver.py Co-authored-by: Christian Vogl * restructured a summary in a docstring for the solution_vector_block * ran black * added the test for w=0 case * Update tardis/plasma/properties/nlte_rate_equation_solver.py Co-authored-by: Christian Vogl * Update tardis/plasma/properties/nlte_rate_equation_solver.py Co-authored-by: Christian Vogl * Update tardis/plasma/tests/test_nlte_solver.py Co-authored-by: Christian Vogl * fixed an issue in a docsting * fixed an issue in a docsting * removed a TODO comment Co-authored-by: Christian Vogl * Rename T variables to temperature (#2185) * fixes #1600 * fixes #1600 * Update tardis/montecarlo/packet_source.py Co-authored-by: Atharva Arya <55894364+atharva-2001@users.noreply.github.com> * fixes codestyle * improve codestyle * rename the function * Update packet_source.py * improve codequality * add commit * Update packet_source.py Co-authored-by: Atharva Arya <55894364+atharva-2001@users.noreply.github.com> * Fixing test_store_runner_to_hdf (#2198) * checking if the object has the attribute decode * fixed another decode issue * Reading nlte_excitation_species from config (#2195) * implementing nlte_excitation * ran black * fixed a typo * got rid of unnecessary lines * rewrote tests * made a change on assigning the config values to plasma properties * fixed the tests * Update tardis/io/tests/test_config_reader.py Co-authored-by: Christian Vogl --------- Co-authored-by: Christian Vogl * Fix config reader tests (#2200) Fix config tests * Pre-release 2023.02.05 (#2205) Automated changes for pre-release 2023.02.05 * Post-release 2023.02.06 (#2206) Automated changes for post-release 2023.02.06 * Add version tag to simulation objects (#2190) * Add test for versioning info * Add version string to simulation objects * Add name to mailmap * Add another alias to mailmap * Pre-release 2023.02.12 (#2208) Automated changes for pre-release 2023.02.12 * Post-release 2023.02.16 (#2210) Automated changes for post-release 2023.02.16 * Pre-release 2023.02.19 (#2211) Automated changes for pre-release 2023.02.19 * Cache LFS objects in the tests workflow (#2194) * Cache LFS objects (actions/checkout#165) * Delete steps to see file size Delete commented step which used to download LFS objects using the bash script * Add lfs:false flag * Add my username to .mailmap * Cache hit and allow pytest to run all tests * Do git lfs checkout if the cache key is found * Post-release 2023.02.20 (#2213) Automated changes for post-release 2023.02.20 * Correct the description of 'no_of_packets' in Monte Carlo Configuration (#2214) * Correct the description of 'no_of_packets' in Monte Carlo Configuration * Added a simple description * Pre-release 2023.02.26 (#2222) Automated changes for pre-release 2023.02.26 * Post-release 2023.02.27 (#2223) Automated changes for post-release 2023.02.27 * Add docstrings to subpackages (#2204) * add docstring to subpackage grid * Add docstrings to subpackages * Change comments to docstrings * add docstrings to subpackages * rename gui/__init__.py * Reformat using black * add contributor infos to mailmap file * add extended summary to docstrings * Add extended summary to plasma/properties * Update tardis/io/parsers/__init__.py Co-authored-by: Sona Chitchyan --------- Co-authored-by: kim Co-authored-by: Sona Chitchyan * Docs Fix: Download Atom Data in rpacket_tracking.ipynb (#2236) Download atom data from the function * Fix for automerge (#2242) Use gh CLI to approve pull requests; use new token * Fix for release dates (#2243) * MonteCarlo packet progress bar completes to 100% (#2237) * Refresh packet progress bar after every iteration * Udpdated .mailmap * Reformatted with black * Fix team reviewers on workflows (#2246) * Pre-release 2023.03.20 (#2247) Automated changes for pre-release 2023.03.20 * Post-release 2023.03.20 (#2248) Automated changes for post-release 2023.03.20 * Create new workflow * Patch for arepo tests * Restore deleted parameter * Black format; Add missing skip reason * Fix typo in comment * Add more comments * Create slash command dispatcher * Changes to dispatcher * Black format --------- Co-authored-by: Sona Chitchyan Co-authored-by: Satwik Kambham Co-authored-by: Andrew Co-authored-by: Christian Vogl Co-authored-by: tardis-bot <60989672+tardis-bot@users.noreply.github.com> Co-authored-by: Stuart Sim Co-authored-by: gleck97 <86471143+gleck97@users.noreply.github.com> Co-authored-by: ABHISHEK PATIDAR <95904102+1e9abhi1e10@users.noreply.github.com> Co-authored-by: Atharva Arya <55894364+atharva-2001@users.noreply.github.com> Co-authored-by: Kim <44905449+kimsina@users.noreply.github.com> Co-authored-by: Abhishek Patidar <1e9abhi1e10@gmail.com> Co-authored-by: Le Truong <43793681+PommesFrittes@users.noreply.github.com> Co-authored-by: kim Co-authored-by: Shreyas Singh <125031481+shreyas3156@users.noreply.github.com> --- .ci-helpers/download_reference_data.sh | 4 +- .ci-helpers/get_next_version.py | 7 +- .github/workflows/dispatcher.yml | 20 + .github/workflows/post-release.yml | 22 +- .github/workflows/pre-release.yml | 22 +- .github/workflows/release.yml | 2 +- .github/workflows/tests.yml | 29 +- .github/workflows/update-refdata.yml | 90 + .mailmap | 16 + .zenodo.json | 90 +- CHANGELOG.md | 122 +- CITATION.cff | 83 +- README.rst | 57 +- conda-linux-64.lock | 407 +- conda-lock.yml | 7120 +++++++++-------- conda-osx-64.lock | 393 +- docs/io/output/rpacket_tracking.ipynb | 13 +- .../montecarlo_packet_visualization.ipynb | 11 + docs/resources/credits.rst | 57 +- tardis/analysis.py | 4 +- tardis/analysis/opacities.py | 6 +- tardis/base.py | 4 +- tardis/conftest.py | 23 + tardis/grid/__init__.py | 6 + tardis/gui/__init.py__ | 0 tardis/gui/__init__.py | 9 + tardis/io/__init__.py | 4 + tardis/io/atom_data/__init__.py | 4 + tardis/io/logger/__init__.py | 3 + tardis/io/parsers/__init__.py | 9 + tardis/io/schemas/montecarlo.yml | 2 +- tardis/io/schemas/plasma.yml | 8 + tardis/io/tests/data/tardis_configv1_nlte.yml | 70 + tardis/io/tests/test_arepo_parser.py | 2 + tardis/io/tests/test_config_reader.py | 152 +- tardis/io/tests/test_model_reader.py | 28 +- tardis/model/__init__.py | 8 + tardis/model/base.py | 32 +- tardis/model/geometry/__init__.py | 10 + tardis/model/geometry/radial1d.py | 76 + tardis/montecarlo/__init__.py | 9 + tardis/montecarlo/base.py | 29 +- .../montecarlo/montecarlo_numba/__init__.py | 4 + tardis/montecarlo/montecarlo_numba/base.py | 23 +- .../montecarlo_numba/formal_integral.py | 60 +- .../montecarlo_numba/formal_integral_cuda.py | 27 +- .../montecarlo_numba/interaction.py | 4 +- .../montecarlo_numba/numba_interface.py | 15 +- .../montecarlo_numba/single_packet_loop.py | 30 +- .../montecarlo_numba/tests/conftest.py | 10 +- .../tests/test_cuda_formal_integral.py | 50 +- .../tests/test_numba_formal_integral.py | 48 +- .../montecarlo_numba/tests/test_packet.py | 15 +- .../tests/test_single_packet_loop.py | 5 +- .../montecarlo_numba/tests/test_vpacket.py | 32 +- tardis/montecarlo/montecarlo_numba/vpacket.py | 57 +- tardis/montecarlo/packet_source.py | 98 +- tardis/plasma/__init__.py | 4 + tardis/plasma/properties/__init__.py | 9 + tardis/plasma/properties/atomic.py | 2 +- .../plasma/properties/continuum_processes.py | 4 +- .../properties/nlte_rate_equation_solver.py | 701 ++ tardis/plasma/properties/plasma_input.py | 12 + .../plasma/properties/property_collections.py | 5 + tardis/plasma/properties/rate_matrix_index.py | 65 + .../properties/transition_probabilities.py | 4 +- tardis/plasma/properties/util/__init__.py | 4 +- tardis/plasma/standard_plasmas.py | 40 + tardis/plasma/tests/test_nlte_solver.py | 318 + tardis/scripts/__init__.py | 3 + tardis/simulation/__init__.py | 4 + tardis/simulation/base.py | 4 + tardis/simulation/tests/test_simulation.py | 6 + tardis/stats/__init__.py | 4 +- tardis/tests/fixtures/atom_data.py | 51 + tardis/transport/__init__.py | 3 + tardis/transport/geometry/__init__.py | 3 + tardis/transport/r_packet_transport.py | 21 +- tardis/util/__init__.py | 4 +- tardis/util/base.py | 16 +- tardis_env3.yml | 4 +- 81 files changed, 6759 insertions(+), 4073 deletions(-) create mode 100644 .github/workflows/dispatcher.yml create mode 100644 .github/workflows/update-refdata.yml delete mode 100644 tardis/gui/__init.py__ create mode 100644 tardis/gui/__init__.py create mode 100644 tardis/io/tests/data/tardis_configv1_nlte.yml create mode 100644 tardis/model/geometry/__init__.py create mode 100644 tardis/model/geometry/radial1d.py create mode 100644 tardis/plasma/properties/nlte_rate_equation_solver.py create mode 100644 tardis/plasma/properties/rate_matrix_index.py create mode 100644 tardis/plasma/tests/test_nlte_solver.py create mode 100644 tardis/transport/__init__.py create mode 100644 tardis/transport/geometry/__init__.py diff --git a/.ci-helpers/download_reference_data.sh b/.ci-helpers/download_reference_data.sh index d1167f0bedd..28c37ecb783 100644 --- a/.ci-helpers/download_reference_data.sh +++ b/.ci-helpers/download_reference_data.sh @@ -12,10 +12,12 @@ FILES=('atom_data/kurucz_cd23_chianti_H_He.h5' 'sdec_ref.h5' 'unit_test_data.h5' 'arepo_data/arepo_snapshot.hdf5' - 'arepo_data/arepo_snapshot.json') + 'arepo_data/arepo_snapshot.json' + 'nlte_atom_data/TestNLTE_He_Ti.h5') mkdir -p $REF_PATH/atom_data mkdir -p $REF_PATH/arepo_data +mkdir -p $REF_PATH/nlte_atom_data for FILE in "${FILES[@]}" do diff --git a/.ci-helpers/get_next_version.py b/.ci-helpers/get_next_version.py index 497ac2107ce..0be3077414e 100644 --- a/.ci-helpers/get_next_version.py +++ b/.ci-helpers/get_next_version.py @@ -14,8 +14,11 @@ iso_date = date(*release).isoformat() iso_date = iso_date.replace("-",".") -version = f"{iso_date}.{str(build)}" -version = version.rstrip(".0") if version.endswith(".0") else version +if build > 0: + version = f"{iso_date}.{str(build)}" + +else: + version = iso_date print(version) diff --git a/.github/workflows/dispatcher.yml b/.github/workflows/dispatcher.yml new file mode 100644 index 00000000000..ddb455b6487 --- /dev/null +++ b/.github/workflows/dispatcher.yml @@ -0,0 +1,20 @@ +name: slash-command +on: + issue_comment: + types: [created] + +jobs: + dispatch: + runs-on: ubuntu-latest + steps: + - name: Slash Command Dispatcher + uses: peter-evans/slash-command-dispatch@v3 + with: + token: ${{ secrets.BOT_TOKEN }} + commands: | + update-refdata + repository: tardis-sn/tardis + issue-type: pull-request + permission: triage + allow-edits: true + reaction_token: ${{ secrets.BOT_TOKEN }} diff --git a/.github/workflows/post-release.yml b/.github/workflows/post-release.yml index 9bf1e60bb19..5216453b00e 100644 --- a/.github/workflows/post-release.yml +++ b/.github/workflows/post-release.yml @@ -124,23 +124,29 @@ jobs: > The `post_release` workflow waits for a webhook and then updates the citation files. If the file is not modified by this pull request, please check the latest release on [Zenodo's website](https://zenodo.org/record/592480), close this pull request, and [manually run the workflow](https://docs.github.com/en/actions/managing-workflow-runs/manually-running-a-workflow). > > This pull request should be auto-merged. - labels: build-docs - reviewers: wkerzendorf, andrewfullard, epassaro + labels: automated, build-docs + team-reviewers: tardis-infrastructure id: create-pr - name: Wait for pull request run: sleep 30 - - name: Approve pull request - uses: juliangruber/approve-pull-request-action@v1 - with: - github-token: ${{ secrets.PR_APPROVAL_TOKEN }} - number: ${{ steps.create-pr.outputs.pull-request-number }} + - name: Approve pull request (I) + run: gh pr review ${{ steps.create-pr.outputs.pull-request-number }} --approve + env: + GITHUB_TOKEN: ${{ secrets.INFRASTRUCTURE_COORDINATOR_TOKEN }} + if: steps.create-pr.outputs.pull-request-operation == 'created' + + - name: Approve pull request (II) + run: gh pr review ${{ steps.create-pr.outputs.pull-request-number }} --approve + env: + GITHUB_TOKEN: ${{ secrets.CORE_COORDINATOR_TOKEN }} if: steps.create-pr.outputs.pull-request-operation == 'created' - name: Enable automerge uses: peter-evans/enable-pull-request-automerge@v2 with: - token: ${{ secrets.BOT_TOKEN }} + token: ${{ secrets.INFRASTRUCTURE_COORDINATOR_TOKEN }} pull-request-number: ${{ steps.create-pr.outputs.pull-request-number }} merge-method: squash + if: steps.create-pr.outputs.pull-request-operation == 'created' diff --git a/.github/workflows/pre-release.yml b/.github/workflows/pre-release.yml index c9baa76dde0..b79a2eed2b3 100644 --- a/.github/workflows/pre-release.yml +++ b/.github/workflows/pre-release.yml @@ -134,23 +134,29 @@ jobs: > ``` > > Once all the checks pass, you can safely merge this pull request manually. - labels: build-docs - reviewers: wkerzendorf, andrewfullard, epassaro + labels: automated, build-docs + team-reviewers: tardis-infrastructure id: create-pr - name: Wait for pull request run: sleep 30 - - name: Approve pull request - uses: juliangruber/approve-pull-request-action@v1 - with: - github-token: ${{ secrets.PR_APPROVAL_TOKEN }} - number: ${{ steps.create-pr.outputs.pull-request-number }} + - name: Approve pull request (I) + run: gh pr review ${{ steps.create-pr.outputs.pull-request-number }} --approve + env: + GITHUB_TOKEN: ${{ secrets.INFRASTRUCTURE_COORDINATOR_TOKEN }} + if: steps.create-pr.outputs.pull-request-operation == 'created' + + - name: Approve pull request (II) + run: gh pr review ${{ steps.create-pr.outputs.pull-request-number }} --approve + env: + GITHUB_TOKEN: ${{ secrets.CORE_COORDINATOR_TOKEN }} if: steps.create-pr.outputs.pull-request-operation == 'created' - name: Enable automerge uses: peter-evans/enable-pull-request-automerge@v2 with: - token: ${{ secrets.BOT_TOKEN }} + token: ${{ secrets.INFRASTRUCTURE_COORDINATOR_TOKEN }} pull-request-number: ${{ steps.create-pr.outputs.pull-request-number }} merge-method: squash + if: steps.create-pr.outputs.pull-request-operation == 'created' diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index c515ebb50e0..c02b21fcbc1 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -28,7 +28,7 @@ jobs: python-version: '3.x' - name: Install setuptools_scm - run: pip install setuptools_scm + run: pip install 'setuptools_scm<7' - name: Show current version run: python .ci-helpers/get_current_version.py diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index d9c3c9e2cab..bf5810b368a 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -47,8 +47,33 @@ jobs: steps: - uses: actions/checkout@v2 - - name: Download reference data - run: bash .ci-helpers/download_reference_data.sh + - name: Clone tardis-sn/tardis-refdata + uses: actions/checkout@v2 + with: + repository: tardis-sn/tardis-refdata + path: tardis-refdata + lfs: false + + - name: Create LFS file list + run: git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id + working-directory: tardis-refdata + + - name: Restore LFS cache + uses: actions/cache@v2 + id: lfs-cache + with: + path: tardis-refdata/.git/lfs + key: ${{ runner.os }}-lfs-${{ hashFiles('tardis-refdata/.lfs-assets-id') }}-v1 + + - name: Git LFS Pull + run: git lfs pull + working-directory: tardis-refdata + if: steps.lfs-cache.outputs.cache-hit != 'true' + + - name: Git LFS Checkout + run: git lfs checkout + working-directory: tardis-refdata + if: steps.lfs-cache.outputs.cache-hit == 'true' - name: Setup environment uses: conda-incubator/setup-miniconda@v2 diff --git a/.github/workflows/update-refdata.yml b/.github/workflows/update-refdata.yml new file mode 100644 index 00000000000..cc36cd2a6b3 --- /dev/null +++ b/.github/workflows/update-refdata.yml @@ -0,0 +1,90 @@ +# For more information about TARDIS pipelines, please refer to: +# +# https://tardis-sn.github.io/tardis/development/continuous_integration.html + +name: update-refdata + +on: + repository_dispatch: + types: [update-refdata-command] + +env: + PYTEST_FLAGS: --tardis-refdata=${{ github.workspace }}/tardis-refdata --generate-reference + CACHE_NUMBER: 0 # increase to reset cache manually + +concurrency: + group: ${{ github.workflow }}-${{ github.head_ref || github.ref }} + cancel-in-progress: true + +defaults: + run: + shell: bash -l {0} + +jobs: + build: + if: github.event_name == 'workflow_dispatch' || + (github.event_name == 'pull_request' && + contains(github.event.pull_request.labels.*.name, 'update-refdata')) + + runs-on: ubuntu-latest + steps: + + - uses: actions/checkout@v2 +# if: github.event_name != 'pull_request_target' +# +# - name: Checkout pull/${{ github.event.number }} +# uses: actions/checkout@v2 +# with: +# ref: ${{ github.event.pull_request.head.sha }} +# if: github.event_name == 'pull_request_target' + + - uses: actions/checkout@v2 + with: + repository: tardis-sn/tardis-refdata + path: tardis-refdata + lfs: false + + - name: Create LFS file list + run: git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id + working-directory: tardis-refdata + + - name: Restore LFS cache + uses: actions/cache@v2 + id: lfs-cache + with: + path: tardis-refdata/.git/lfs + key: ${{ runner.os }}-lfs-${{ hashFiles('tardis-refdata/.lfs-assets-id') }}-v${{ env.CACHE_NUMBER }} + + - name: Pull LFS objects + run: git lfs pull + working-directory: tardis-refdata + if: steps.lfs-cache.outputs.cache-hit != 'true' + + - name: Checkout LFS repository + run: git lfs checkout + working-directory: tardis-refdata + if: steps.lfs-cache.outputs.cache-hit == 'true' + + - name: Setup environment + uses: conda-incubator/setup-miniconda@v2 + with: + miniforge-variant: Mambaforge + miniforge-version: latest + activate-environment: tardis + use-mamba: true + + - uses: actions/cache@v2 + with: + path: /usr/share/miniconda3/envs/tardis + key: conda-linux-64-${{ hashFiles('conda-linux-64.lock') }}-v${{ env.CACHE_NUMBER }} + id: cache-conda + + - name: Update environment + run: mamba update -n tardis --file conda-linux-64.lock + if: steps.cache-conda.outputs.cache-hit != 'true' + + - name: Install package + run: pip install -e . + + - name: Generate new reference data + run: pytest tardis ${{ env.PYTEST_FLAGS }} diff --git a/.mailmap b/.mailmap index e06791f37dd..e533677002e 100644 --- a/.mailmap +++ b/.mailmap @@ -1,3 +1,4 @@ +Abhishek Patidar <1e9abhi1e10@gmail.com> Adam Suban-Loewen Alexander Holas @@ -32,6 +33,7 @@ Arjun Savel Arjun Savel <35353555+arjunsavel@users.noreply.gi Atharva Arya Atharva Arya Atharva Arya +Atharva Arya atharva-2001 Atharva Arya Atharva Arya <55894364+atharva-2001@users.noreply.github.com> Atharwa Kharkar @@ -70,6 +72,9 @@ Frederik Beaujean Frederik Beaujean Gaurav Gautam gautam1168 +Gerrit Leck +Gerrit Leck Gerrit Leck + Isaac Smith Isaac Smith Isaac Smith <71480393+smithis7@users.noreply.github.com> Isaac Smith smithis7 <71480393+smithis7@users.noreply.github.com> @@ -108,6 +113,9 @@ Kevin Cawley KevinCawley <72036796+KevinCawley@users.noreply. Kevin Yap +Kim Lingemann kimsina +Kim Lingemann kim + Laud Bentil Laud Bentil Laud Bentil @@ -161,6 +169,9 @@ Sampark Sharma Shilpi Prasad Shilpi Prasad Shilpi <72646134+shilpiprd@users.noreply.github.com> +Shreyas Singh +Shreyas Singh shreyas3156 + Satwik Kambham Satwik Kambham code-explorer @@ -219,3 +230,8 @@ Youssef Eweis Youssef Eweis Rohith Varma Buddaraju rohithvarma3000 Rohith Varma Buddaraju Rohith + +Le Truong + +Kim Lingemann kimsina +Kim Lingemann kim diff --git a/.zenodo.json b/.zenodo.json index a6244335f42..1c7d2a4e4e3 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -31,7 +31,8 @@ }, { "name": "Camacho, Yssa", - "orcid": "0000-0002-9830-3880" + "orcid": "0000-0002-9830-3880", + "affiliation": "Rutgers The State University of New Jersey" }, { "name": "Jan\u010dauskas, Vytautas", @@ -99,10 +100,10 @@ "affiliation": "Michigan State University" }, { - "name": "Cawley, Kevin" + "name": "Smith, Isaac" }, { - "name": "Smith, Isaac" + "name": "Cawley, Kevin" }, { "name": "Singhal, Jaladh", @@ -111,6 +112,9 @@ { "name": "Arya, Atharva" }, + { + "name": "O'Brien, Jack" + }, { "name": "Barbosa, Talytha" }, @@ -120,9 +124,6 @@ { "name": "Yu, Jenny" }, - { - "name": "O'Brien, Jack" - }, { "name": "Patel, Maryam" }, @@ -133,6 +134,9 @@ "name": "Gillanders, James", "orcid": "0000-0002-8094-6108" }, + { + "name": "Chitchyan, Sona" + }, { "name": "Savel, Arjun" }, @@ -156,29 +160,29 @@ "name": "Alam, Arib" }, { - "name": "Magee, Mark" + "name": "Bartnik, Matthew" }, { - "name": "Bartnik, Matthew" + "name": "Magee, Mark" }, { - "name": "Shields, Joshua" + "name": "Varma Buddaraju, Rohith" }, { - "name": "Chitchyan, Sona" + "name": "Kambham, Satwik" }, { - "name": "Livneh, Ran" + "name": "Shields, Joshua" }, { - "name": "Rajagopalan, Srinath" + "name": "Livneh, Ran" }, { "name": "Mishra, Sashank", "orcid": "0000-0001-8302-1584" }, { - "name": "Floers, Andreas" + "name": "Rajagopalan, Srinath" }, { "name": "Reichenbach, John" @@ -187,13 +191,19 @@ "name": "Jain, Rinkle" }, { - "name": "Singh, Sourav" + "name": "Floers, Andreas" }, { "name": "Brar, Antreev" }, { - "name": "Sofiatti, Caroline" + "name": "Singh, Sourav" + }, + { + "name": "Holas, Alexander" + }, + { + "name": "Bhakar, Jayant" }, { "name": "Kowalski, Nathan" @@ -202,11 +212,20 @@ "name": "Selsing, Jonatan" }, { - "name": "Varma Buddaraju, Rohith" + "name": "Kumar, Aman" + }, + { + "name": "Sofiatti, Caroline" }, { "name": "Talegaonkar, Chinmay" }, + { + "name": "Singh, Shreyas" + }, + { + "name": "Singh Rathore, Parikshit" + }, { "name": "Prasad, Shilpi" }, @@ -216,14 +235,11 @@ { "name": "Sharma, Sampark" }, - { - "name": "Singh Rathore, Parikshit" - }, { "name": "Patel, Pratik" }, { - "name": "Martinez, Laureano" + "name": "Yap, Kevin" }, { "name": "Patra, Nilesh" @@ -232,49 +248,55 @@ "name": "Sarafina, Nance" }, { - "name": "Yap, Kevin" + "name": "Zaheer, Musabbiha" }, { - "name": "Zaheer, Musabbiha" + "name": "Sandler, Morgan" }, { - "name": "Gupta, Suyash" + "name": "Truong, Le" }, { - "name": "Dasgupta, Debajyoti" + "name": "Gupta, Suyash" }, { "name": "Nayak U, Ashwin" }, { - "name": "Kolliboyina, Chaitanya" + "name": "Lemoine, Thom" }, { - "name": "Volodin, Dmitry" + "name": "Wahi, Ujjwal" }, { - "name": "Sandler, Morgan" + "name": "Aggarwal, Yash" }, { - "name": "Kumar, Atul" + "name": "Gupta, Harshul" }, { - "name": "Kharkar, Atharwa" + "name": "Volodin, Dmitry" }, { - "name": "Holas, Alexander" + "name": "PATIDAR, ABHISHEK" }, { - "name": "kumar, aman" + "name": "Dasgupta, Debajyoti" }, { - "name": "Lemoine, Thom" + "name": "Patidar, Abhishek" }, { - "name": "Wahi, Ujjwal" + "name": "Kharkar, Atharwa" }, { - "name": "Aggarwal, Yash" + "name": "Kumar, Atul" + }, + { + "name": "Kolliboyina, Chaitanya" + }, + { + "name": "Martinez, Laureano" } ] } \ No newline at end of file diff --git a/CHANGELOG.md b/CHANGELOG.md index 5dfeeaa4291..751054e4003 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,109 @@ ## Change Log +### release-2023.03.20 (2023/03/20 16:39 +00:00) +- [#2247](https://github.com/tardis-sn/tardis/pull/2247) Pre-release 2023.03.20 (#2247) (@tardis-bot) +- [#2246](https://github.com/tardis-sn/tardis/pull/2246) Fix team reviewers on workflows (#2246) (@epassaro) +- [#2237](https://github.com/tardis-sn/tardis/pull/2237) MonteCarlo packet progress bar completes to 100% (#2237) (@shreyas3156) +- [#2243](https://github.com/tardis-sn/tardis/pull/2243) Fix for release dates (#2243) (@epassaro) +- [#2242](https://github.com/tardis-sn/tardis/pull/2242) Fix for automerge (#2242) (@epassaro) +- [#2236](https://github.com/tardis-sn/tardis/pull/2236) Docs Fix: Download Atom Data in rpacket_tracking.ipynb (#2236) (@atharva-2001) +- [#2204](https://github.com/tardis-sn/tardis/pull/2204) Add docstrings to subpackages (#2204) (@PommesFrittes) +- [#2223](https://github.com/tardis-sn/tardis/pull/2223) Post-release 2023.02.27 (#2223) (@tardis-bot) + +### release-2023.02.27 (2023/02/27 13:53 +00:00) +- [#2222](https://github.com/tardis-sn/tardis/pull/2222) Pre-release 2023.02.26 (#2222) (@tardis-bot) +- [#2214](https://github.com/tardis-sn/tardis/pull/2214) Correct the description of 'no_of_packets' in Monte Carlo Configuration (#2214) (@1e9abhi1e10) +- [#2213](https://github.com/tardis-sn/tardis/pull/2213) Post-release 2023.02.20 (#2213) (@tardis-bot) +- [#2194](https://github.com/tardis-sn/tardis/pull/2194) Cache LFS objects in the tests workflow (#2194) (@atharva-2001) + +### release-2023.02.2 (2023/02/20 15:04 +00:00) +- [#2211](https://github.com/tardis-sn/tardis/pull/2211) Pre-release 2023.02.19 (#2211) (@tardis-bot) +- [#2210](https://github.com/tardis-sn/tardis/pull/2210) Post-release 2023.02.16 (#2210) (@tardis-bot) + +### release-2023.02.16 (2023/02/16 14:18 +00:00) +- [#2208](https://github.com/tardis-sn/tardis/pull/2208) Pre-release 2023.02.12 (#2208) (@tardis-bot) +- [#2190](https://github.com/tardis-sn/tardis/pull/2190) Add version tag to simulation objects (#2190) (@kimsina) +- [#2206](https://github.com/tardis-sn/tardis/pull/2206) Post-release 2023.02.06 (#2206) (@tardis-bot) + +### release-2023.02.06 (2023/02/06 15:00 +00:00) +- [#2205](https://github.com/tardis-sn/tardis/pull/2205) Pre-release 2023.02.05 (#2205) (@tardis-bot) +- [#2200](https://github.com/tardis-sn/tardis/pull/2200) Fix config reader tests (#2200) (@chvogl) +- [#2195](https://github.com/tardis-sn/tardis/pull/2195) Reading nlte_excitation_species from config (#2195) (@sonachitchyan) +- [#2198](https://github.com/tardis-sn/tardis/pull/2198) Fixing test_store_runner_to_hdf (#2198) (@sonachitchyan) +- [#2185](https://github.com/tardis-sn/tardis/pull/2185) Rename T variables to temperature (#2185) (@1e9abhi1e10) +- [#2171](https://github.com/tardis-sn/tardis/pull/2171) Adding nlte solver (#2171) (@sonachitchyan) +- [#2187](https://github.com/tardis-sn/tardis/pull/2187) Downloading nlte_atom_data in ref data (#2187) (@sonachitchyan) +- [#2188](https://github.com/tardis-sn/tardis/pull/2188) Post-release 2023.01.11 (#2188) (@tardis-bot) + +### release-2023.01.11 (2023/01/11 16:25 +00:00) +- [#2186](https://github.com/tardis-sn/tardis/pull/2186) Pre-release 2023.01.08 (#2186) (@tardis-bot) +- [#2182](https://github.com/tardis-sn/tardis/pull/2182) Post-release 2022.12.26 (#2182) (@tardis-bot) + +### release-2022.12.26 (2022/12/26 14:51 +00:00) +- [#2180](https://github.com/tardis-sn/tardis/pull/2180) Pre-release 2022.12.25 (#2180) (@tardis-bot) +- [#2170](https://github.com/tardis-sn/tardis/pull/2170) Add missing __init__.py files to transport and geometry subpackages (#2170) (@epassaro) +- [#2173](https://github.com/tardis-sn/tardis/pull/2173) Post-release 2022.12.12 (#2173) (@tardis-bot) + +### release-2022.12.12 (2022/12/12 15:02 +00:00) +- [#2172](https://github.com/tardis-sn/tardis/pull/2172) Pre-release 2022.12.11 (#2172) (@tardis-bot) +- [#2150](https://github.com/tardis-sn/tardis/pull/2150) Kilonova missing zeta (#2150) (@gleck97) +- [#2158](https://github.com/tardis-sn/tardis/pull/2158) NLTE jacobian matrix (#2158) (@sonachitchyan) +- [#2154](https://github.com/tardis-sn/tardis/pull/2154) Fixing typos for nlte ion (#2154) (@sonachitchyan) +- [#2159](https://github.com/tardis-sn/tardis/pull/2159) Fix relativistic packet initialization (#2159) (@chvogl) + +### release-2022.11.21 (2022/11/21 15:15 +00:00) +- [#2160](https://github.com/tardis-sn/tardis/pull/2160) Pre-release 2022.11.20 (#2160) (@tardis-bot) +- [#2156](https://github.com/tardis-sn/tardis/pull/2156) Post-release 2022.11.17 (#2156) (@tardis-bot) + +### release-2022.11.17 (2022/11/17 18:45 +00:00) +- [#2155](https://github.com/tardis-sn/tardis/pull/2155) Pre-release 2022.11.17 (#2155) (@tardis-bot) +- [#2152](https://github.com/tardis-sn/tardis/pull/2152) Set specific qgrid feedstock version (#2152) (@andrewfullard) +- [#2140](https://github.com/tardis-sn/tardis/pull/2140) Adding nlte_rate_equation_solver.py (#2140) (@sonachitchyan) +- [#2147](https://github.com/tardis-sn/tardis/pull/2147) Pin setuptools_scm to v6 (#2147) (@epassaro) +- [#2127](https://github.com/tardis-sn/tardis/pull/2127) Possible fix for prerelease workflow (#2127) (@andrewfullard) +- [#2146](https://github.com/tardis-sn/tardis/pull/2146) Add missing cell to download atom data (#2146) (@epassaro) +- [#2136](https://github.com/tardis-sn/tardis/pull/2136) Restructuring NumbaModel (#2136) (@code-explorer) +- [#2132](https://github.com/tardis-sn/tardis/pull/2132) Adding rate matrix index (#2132) (@sonachitchyan) +- [#2130](https://github.com/tardis-sn/tardis/pull/2130) moved helium nlte to a seperate file `helium_nlte.py` (#2130) (@sonachitchyan) +- [#2124](https://github.com/tardis-sn/tardis/pull/2124) Cleaning model state (#2124) (@code-explorer) +- [#2096](https://github.com/tardis-sn/tardis/pull/2096) Small bug fix for He NLTE. (#2096) (@aoife-boyle) +- [#1923](https://github.com/tardis-sn/tardis/pull/1923) Fixing latex_label Parameter within write_to_tex function (#1923) (@bartnikm) +- [#2095](https://github.com/tardis-sn/tardis/pull/2095) Removing outdated documentation and creating developer tools section (#2095) (@smithis7) +- [#2099](https://github.com/tardis-sn/tardis/pull/2099) Arbitrary isotope decay handling and positronium (#2099) (@andrewfullard) +- [#2118](https://github.com/tardis-sn/tardis/pull/2118) Integrating experimental model state (#2118) (@code-explorer) +- [#2120](https://github.com/tardis-sn/tardis/pull/2120) Update arepo docs notebook to be pre-run (#2120) (@AlexHls) +- [#2115](https://github.com/tardis-sn/tardis/pull/2115) added docs for montecarlo packet visualization (#2115) (@jayantbhakar) +- [#2117](https://github.com/tardis-sn/tardis/pull/2117) Runs cells in arepo notebook to avoid downloading files (#2117) (@andrewfullard) +- [#2103](https://github.com/tardis-sn/tardis/pull/2103) New geometry class (#2103) (@code-explorer) +- [#2111](https://github.com/tardis-sn/tardis/pull/2111) New TARDIS flowchart and cleaning up physics walkthrough (#2111) (@smithis7) +- [#2098](https://github.com/tardis-sn/tardis/pull/2098) New Composition Class (#2098) (@code-explorer) +- [#2108](https://github.com/tardis-sn/tardis/pull/2108) Rework Estimators and Convergence Docs (#2108) (@smithis7) +- [#2105](https://github.com/tardis-sn/tardis/pull/2105) Documentation for Features In-Progress (#2105) (@smithis7) +- [#2107](https://github.com/tardis-sn/tardis/pull/2107) Added positronium notes (#2107) (@andrewfullard) +- [#2091](https://github.com/tardis-sn/tardis/pull/2091) Added interaction type in rpacket_tracker (#2091) (@jayantbhakar) +- [#2110](https://github.com/tardis-sn/tardis/pull/2110) removed scatter function from interaction.py (#2110) (@sonachitchyan) +- [#2106](https://github.com/tardis-sn/tardis/pull/2106) Resturcture ABCs import from collections module (#2106) (@rohithvarma3000) +- [#2093](https://github.com/tardis-sn/tardis/pull/2093) Fixing Docs Warnings (#2093) (@smithis7) +- [#2073](https://github.com/tardis-sn/tardis/pull/2073) rpacket_tracker returns dataframe (#2073) (@jayantbhakar) +- [#2104](https://github.com/tardis-sn/tardis/pull/2104) Re-produced PR 1826 (#2104) (@andrewfullard) +- [#2097](https://github.com/tardis-sn/tardis/pull/2097) Creating new docs building instructions (#2097) (@smithis7) +- [#2088](https://github.com/tardis-sn/tardis/pull/2088) Arepo docs fix (#2088) (@AlexHls) +- [#1941](https://github.com/tardis-sn/tardis/pull/1941) Improved arepo parser (#1941) (@AlexHls) +- [#2026](https://github.com/tardis-sn/tardis/pull/2026) Adding physics introduction to documentation (#2026) (@smithis7) +- [#2084](https://github.com/tardis-sn/tardis/pull/2084) Fix broken links in workflow files and goverance md (#2084) (@rohithvarma3000) +- [#2083](https://github.com/tardis-sn/tardis/pull/2083) Moved `trace_packet` to tardis tansport (#2083) (@Rodot-) +- [#2082](https://github.com/tardis-sn/tardis/pull/2082) Added documetation on how to compare environment before update (#2082) (@jaladh-singhal) +- [#2076](https://github.com/tardis-sn/tardis/pull/2076) Modified Function Name in Config validator according to PEP8 (#2076) (@rohithvarma3000) +- [#2062](https://github.com/tardis-sn/tardis/pull/2062) Remove yaml_load_config_file (#2062) (@aman1971) +- [#2052](https://github.com/tardis-sn/tardis/pull/2052) Created a smart HDF Reader which can re-produce simulation object (#2052) (@code-explorer) +- [#2070](https://github.com/tardis-sn/tardis/pull/2070) Pre-release 2022.06.26 (#2070) (@tardis-bot) +- [#2069](https://github.com/tardis-sn/tardis/pull/2069) Wait for pull request creation (#2069) (@epassaro) +- [#2067](https://github.com/tardis-sn/tardis/pull/2067) Begin geometry subfolder (#2067) (@nolanbrown01) +- [#2050](https://github.com/tardis-sn/tardis/pull/2050) Update Jsonschema package to V4 (#2050) (@rohithvarma3000) +- [#2065](https://github.com/tardis-sn/tardis/pull/2065) Continuing geometry restructure (#2065) (@nolanbrown01) +- [#2063](https://github.com/tardis-sn/tardis/pull/2063) Initial geometry restructure (#2063) (@nolanbrown01) +- [#2061](https://github.com/tardis-sn/tardis/pull/2061) Post-release 2022.06.19 (#2061) (@tardis-bot) + ### release-2022.06.19 (2022/06/19 02:25 +00:00) - [#2060](https://github.com/tardis-sn/tardis/pull/2060) Pre-release 2022.06.19 (#2060) (@tardis-bot) - [#2036](https://github.com/tardis-sn/tardis/pull/2036) Restructure code to remove the single_packet_seed field (#2036) (@rohithvarma3000) @@ -212,8 +316,6 @@ - [#1738](https://github.com/tardis-sn/tardis/pull/1738) TARDIS Grid (#1738) (@marxwillia) - [#1755](https://github.com/tardis-sn/tardis/pull/1755) changing note format (#1755) (@smithis7) - [#1740](https://github.com/tardis-sn/tardis/pull/1740) Renamed `montecarlo_logger.py` to `montecarlo_tracking.py` (#1740) (@DhruvSondhi) - -### release-2021.7.25.0 (2021/07/23 16:16 +00:00) - [#1697](https://github.com/tardis-sn/tardis/pull/1697) Interact Button in Documentation (#1697) (@smithis7) - [#1636](https://github.com/tardis-sn/tardis/pull/1636) Adding Convergence Plots (#1636) (@atharva-2001) - [#1723](https://github.com/tardis-sn/tardis/pull/1723) Edit docstring in `run_tardis` (#1723) (@atharva-2001) @@ -224,36 +326,24 @@ - [#1737](https://github.com/tardis-sn/tardis/pull/1737) Add Jaladh to mailmap (#1737) (@jaladh-singhal) - [#1739](https://github.com/tardis-sn/tardis/pull/1739) Fixed IPython Displaying the Plasma Stratification (Table) even when the Logger is turned Off (#1739) (@DhruvSondhi) - [#1742](https://github.com/tardis-sn/tardis/pull/1742) Reduce damping_constant under t_inner for tardis_example.yml (#1742) (@atharva-2001) - -### release-2021.7.18.0 (2021/07/16 14:41 +00:00) - [#1665](https://github.com/tardis-sn/tardis/pull/1665) Demonstrating the `nelements` and the `species_list` functionality in the SDEC plot notebook (@atharva-2001) - [#1727](https://github.com/tardis-sn/tardis/pull/1727) Fixing Quickstart Metadata (#1727) (@smithis7) - [#1726](https://github.com/tardis-sn/tardis/pull/1726) display "latest" in doc version (#1726) (@epassaro) - [#1716](https://github.com/tardis-sn/tardis/pull/1716) Small fixes to docs (#1716) (@smithis7) - [#1722](https://github.com/tardis-sn/tardis/pull/1722) Added missing import for IonNumberDensityHeNLTE (#1722) (@DhruvSondhi) - [#1714](https://github.com/tardis-sn/tardis/pull/1714) Removed Formatting from exisiting log messages (#1714) (@DhruvSondhi) - -### release-2021.7.14.0 (2021/07/14 15:39 +00:00) - [#1707](https://github.com/tardis-sn/tardis/pull/1707) Open in VSCode badge (#1707) (@wkerzendorf) - [#1713](https://github.com/tardis-sn/tardis/pull/1713) fix package data for conda-forge package (#1713) (@epassaro) - [#1711](https://github.com/tardis-sn/tardis/pull/1711) Changed the xlim and the ylabel in the quickstart notebook plot (#1711) (@Rodot-) - -### release-2021.7.12.0 (2021/07/12 20:05 +00:00) - [#1686](https://github.com/tardis-sn/tardis/pull/1686) fix pip install (#1686) (@epassaro) - [#1701](https://github.com/tardis-sn/tardis/pull/1701) Adding Logging Support for Caught Exceptions (#1701) (@DhruvSondhi) - [#1684](https://github.com/tardis-sn/tardis/pull/1684) Moved Simulation & Montecarlo Logging Frameworks to `tardis/io/logger` folder (#1684) (@DhruvSondhi) - [#1691](https://github.com/tardis-sn/tardis/pull/1691) Create profiling documentation directory (#1691) (@KevinCawley) - -### release-2021.7.11.0 (2021/07/09 17:07 +00:00) - [#1680](https://github.com/tardis-sn/tardis/pull/1680) Added docstring-coverage badge (#1680) (@epassaro) - [#1696](https://github.com/tardis-sn/tardis/pull/1696) Adding mu and r to virtual packet logging (#1696) (@smithis7) - [#1695](https://github.com/tardis-sn/tardis/pull/1695) Enabling spectrum plotting in the frequency domain (#1695) (@smithis7) - -### release-2021.7.5 (2021/07/05 14:32 +00:00) - [#1688](https://github.com/tardis-sn/tardis/pull/1688) final changes for release pipeline (#1688) (@epassaro) - [#1683](https://github.com/tardis-sn/tardis/pull/1683) prepare release pipeline for CalVer (#1683) (@epassaro) - -### release-2021.07.01 (2021/07/01 23:05 +00:00) - [#1674](https://github.com/tardis-sn/tardis/pull/1674) APE 17 migration (#1674) (@epassaro) - [#1658](https://github.com/tardis-sn/tardis/pull/1658) add refdata repo selection in template (#1658) (@epassaro) - [#1682](https://github.com/tardis-sn/tardis/pull/1682) Opacities script with proper credit (#1682) (@andrewfullard) @@ -585,8 +675,6 @@ - [#1032](https://github.com/tardis-sn/tardis/pull/1032) Add Mark Magee to .mailmap (#1032) (@epassaro) - [#1025](https://github.com/tardis-sn/tardis/pull/1025) Add `compilers` to environment YAML file (#1025) (@epassaro) - [#1026](https://github.com/tardis-sn/tardis/pull/1026) Minor changes (#1026) (@epassaro) - -### 3.0.dev3396 (2020/02/07 15:00 +00:00) - [#1027](https://github.com/tardis-sn/tardis/pull/1027) Added Mark Magee (#1027) (@MarkMageeAstro) - [#1024](https://github.com/tardis-sn/tardis/pull/1024) Add epassaro orcid (#1024) (@epassaro) - [#1022](https://github.com/tardis-sn/tardis/pull/1022) added Alice's orcid (#1022) (@harpolea) @@ -596,8 +684,6 @@ - [#1018](https://github.com/tardis-sn/tardis/pull/1018) Updated .mailmap (#1018) (@epassaro) - [#1010](https://github.com/tardis-sn/tardis/pull/1010) Pipeline for comparing reference data (#1010) (@epassaro) - [#1016](https://github.com/tardis-sn/tardis/pull/1016) Removed GH Action for release versions (#1016) (@epassaro) - -### 3.0.dev3388 (2020/01/25 22:36 +00:00) - [#1013](https://github.com/tardis-sn/tardis/pull/1013) Fixed typo (#1013) (@epassaro) - [#1006](https://github.com/tardis-sn/tardis/pull/1006) Trying to get the right version number for automatic release (#1006) (@epassaro) - [#1008](https://github.com/tardis-sn/tardis/pull/1008) Improvements for the update_reference section [docs] (#1008) (@epassaro) diff --git a/CITATION.cff b/CITATION.cff index 044abb1c1f0..61aa14bdc62 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -3,8 +3,8 @@ cff-version: 1.0.3 message: If you use this software, please cite it using these metadata. # FIXME title as repository name might not be the best name, please make human readable -title: 'tardis-sn/tardis: TARDIS v2022.06.19' -doi: 10.5281/zenodo.6662839 +title: 'tardis-sn/tardis: TARDIS v2023.03.20' +doi: 10.5281/zenodo.7753535 # FIXME splitting of full names is error prone, please check if given/family name are correct authors: - given-names: Wolfgang @@ -32,6 +32,7 @@ authors: orcid: https://orcid.org/0000-0003-2024-2819 - given-names: Yssa family-names: Camacho + affiliation: Rutgers The State University of New Jersey orcid: https://orcid.org/0000-0002-9830-3880 - given-names: Vytautas family-names: Jančauskas @@ -81,23 +82,23 @@ authors: family-names: Fullard affiliation: Michigan State University orcid: https://orcid.org/0000-0001-7343-1678 -- given-names: Kevin - family-names: Cawley - given-names: Isaac family-names: Smith +- given-names: Kevin + family-names: Cawley - given-names: Jaladh family-names: Singhal orcid: https://orcid.org/0000-0002-8310-0829 - given-names: Atharva family-names: Arya +- given-names: Jack + family-names: O'Brien - given-names: Talytha family-names: Barbosa - given-names: Dhruv family-names: Sondhi - given-names: Jenny family-names: Yu -- given-names: Jack - family-names: O'Brien - given-names: Maryam family-names: Patel - given-names: Kaushik @@ -105,12 +106,14 @@ authors: - given-names: James family-names: Gillanders orcid: https://orcid.org/0000-0002-8094-6108 +- given-names: Sona + family-names: Chitchyan - given-names: Arjun family-names: Savel -- given-names: Youssef - family-names: Eweis - given-names: Martin family-names: Reinecke +- given-names: Youssef + family-names: Eweis - given-names: Tomas family-names: Bylund - given-names: Laud @@ -124,43 +127,53 @@ authors: family-names: Bartnik - given-names: Mark family-names: Magee +- given-names: Rohith + family-names: Varma Buddaraju +- given-names: Satwik + family-names: Kambham - given-names: Joshua family-names: Shields - given-names: Ran family-names: Livneh -- given-names: Sona - family-names: Chitchyan -- given-names: Srinath - family-names: Rajagopalan - given-names: Sashank family-names: Mishra orcid: https://orcid.org/0000-0001-8302-1584 -- given-names: Andreas - family-names: Floers +- given-names: Srinath + family-names: Rajagopalan - given-names: John family-names: Reichenbach - given-names: Rinkle family-names: Jain +- given-names: Andreas + family-names: Floers - given-names: Antreev family-names: Brar - given-names: Sourav family-names: Singh -- given-names: Caroline - family-names: Sofiatti +- given-names: Alexander + family-names: Holas +- given-names: Jayant + family-names: Bhakar - given-names: Nathan family-names: Kowalski -- given-names: Chinmay - family-names: Talegaonkar - given-names: Jonatan family-names: Selsing +- given-names: Aman + family-names: Kumar +- given-names: Caroline + family-names: Sofiatti +- given-names: Chinmay + family-names: Talegaonkar +- given-names: Shreyas + family-names: Singh - given-names: Parikshit family-names: Singh Rathore - given-names: Shilpi family-names: Prasad - given-names: Shashank family-names: Venkat -- given-names: Rohith - family-names: Varma Buddaraju +- given-names: Sampark + family-names: Sharma - given-names: Pratik family-names: Patel - given-names: Kevin @@ -173,35 +186,37 @@ authors: family-names: Zaheer - given-names: Morgan family-names: Sandler -- given-names: Thom - family-names: Lemoine +- given-names: Le + family-names: Truong - given-names: Suyash family-names: Gupta - given-names: Ashwin family-names: Nayak U +- given-names: Thom + family-names: Lemoine - given-names: Ujjwal family-names: Wahi - given-names: Yash family-names: Aggarwal -- given-names: aman - family-names: kumar -- given-names: Sampark - family-names: Sharma +- given-names: Harshul + family-names: Gupta - given-names: Dmitry family-names: Volodin -- given-names: Laureano - family-names: Martinez +- given-names: ABHISHEK + family-names: PATIDAR - given-names: Debajyoti family-names: Dasgupta -- given-names: Alexander - family-names: Holas +- given-names: Abhishek + family-names: Patidar - given-names: Atharwa family-names: Kharkar -- given-names: Chaitanya - family-names: Kolliboyina - given-names: Atul family-names: Kumar -version: release-2022.06.19 -date-released: 2022-06-19 +- given-names: Chaitanya + family-names: Kolliboyina +- given-names: Laureano + family-names: Martinez +version: release-2023.03.20 +date-released: 2023-03-20 repository-code: https://github.com/tardis-sn/tardis license: other-open diff --git a/README.rst b/README.rst index d807f6bd6b6..5acbd3dd72e 100644 --- a/README.rst +++ b/README.rst @@ -110,14 +110,14 @@ The following BibTeX entries are needed for the references: adsnote = {Provided by the SAO/NASA Astrophysics Data System} } -.. |CITATION| replace:: kerzendorf_wolfgang_2022_6662839 +.. |CITATION| replace:: kerzendorf_wolfgang_2023_7753535 -.. |DOI_BADGE| image:: https://img.shields.io/badge/DOI-10.5281/zenodo.6662839-blue - :target: https://doi.org/10.5281/zenodo.6662839 +.. |DOI_BADGE| image:: https://img.shields.io/badge/DOI-10.5281/zenodo.7753535-blue + :target: https://doi.org/10.5281/zenodo.7753535 .. code-block:: bibtex - @software{kerzendorf_wolfgang_2022_6662839, + @software{kerzendorf_wolfgang_2023_7753535, author = {Kerzendorf, Wolfgang and Sim, Stuart and Vogl, Christian and @@ -142,71 +142,78 @@ The following BibTeX entries are needed for the references: Barna, Barnabás and Gautam, Gaurav and Fullard, Andrew and - Cawley, Kevin and Smith, Isaac and + Cawley, Kevin and Singhal, Jaladh and Arya, Atharva and + O'Brien, Jack and Barbosa, Talytha and Sondhi, Dhruv and Yu, Jenny and - O'Brien, Jack and Patel, Maryam and Varanasi, Kaushik and Gillanders, James and + Chitchyan, Sona and Savel, Arjun and - Eweis, Youssef and Reinecke, Martin and + Eweis, Youssef and Bylund, Tomas and Bentil, Laud and Eguren, Jordi and Alam, Arib and Bartnik, Matthew and Magee, Mark and + Varma Buddaraju, Rohith and + Kambham, Satwik and Shields, Joshua and Livneh, Ran and - Chitchyan, Sona and - Rajagopalan, Srinath and Mishra, Sashank and - Floers, Andreas and + Rajagopalan, Srinath and Reichenbach, John and Jain, Rinkle and + Floers, Andreas and Brar, Antreev and Singh, Sourav and - Sofiatti, Caroline and + Holas, Alexander and + Bhakar, Jayant and Kowalski, Nathan and - Talegaonkar, Chinmay and Selsing, Jonatan and + Kumar, Aman and + Sofiatti, Caroline and + Talegaonkar, Chinmay and + Singh, Shreyas and Singh Rathore, Parikshit and Prasad, Shilpi and Venkat, Shashank and - Varma Buddaraju, Rohith and + Sharma, Sampark and Patel, Pratik and Yap, Kevin and Patra, Nilesh and Sarafina, Nance and Zaheer, Musabbiha and Sandler, Morgan and - Lemoine, Thom and + Truong, Le and Gupta, Suyash and Nayak U, Ashwin and + Lemoine, Thom and Wahi, Ujjwal and Aggarwal, Yash and - kumar, aman and - Sharma, Sampark and + Gupta, Harshul and Volodin, Dmitry and - Martinez, Laureano and + PATIDAR, ABHISHEK and Dasgupta, Debajyoti and - Holas, Alexander and + Patidar, Abhishek and Kharkar, Atharwa and + Kumar, Atul and Kolliboyina, Chaitanya and - Kumar, Atul}, - title = {tardis-sn/tardis: TARDIS v2022.06.19}, - month = jun, - year = 2022, + Martinez, Laureano}, + title = {tardis-sn/tardis: TARDIS v2023.03.20}, + month = mar, + year = 2023, publisher = {Zenodo}, - version = {release-2022.06.19}, - doi = {10.5281/zenodo.6662839}, - url = {https://doi.org/10.5281/zenodo.6662839} + version = {release-2023.03.20}, + doi = 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79d1805fb03..dab42fbe73d 100644 --- a/conda-lock.yml +++ b/conda-lock.yml @@ -15,8 +15,8 @@ metadata: - url: conda-forge used_env_vars: [] content_hash: - linux-64: 4206c5101b01be252b909c680dbe1de7159edd0259f8ec0a8491008ceaa3d2c8 - osx-64: 4530a4a40fa93e6820e8fbec748f5ba36a639a646c469ce156e977fd109847d3 + linux-64: fa30d7960ef38249093acccd4fe826d982cfa3cf8134bed3984c7d5f3458ce88 + osx-64: a526dae1720b6e8b1881c6c214cf02b7514c9c757d4bfa5fb8fa273eacd219da platforms: - linux-64 - osx-64 @@ -37,14 +37,14 @@ package: - category: main dependencies: {} hash: - md5: c320890f77fd1d617fa876e0982002c2 - sha256: e2aa0004ae9907f8c150d4cb3d00f8146b812f7f6906142c5258cca3eb2c7abf + md5: ff9f73d45c4a07d6f424495288a26080 + sha256: 8f6c81b0637771ae0ea73dc03a6d30bec3326ba3927f2a7b91931aa2d59b1789 manager: conda name: ca-certificates optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.6.15-ha878542_0.tar.bz2 - version: 2022.6.15 + url: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda + version: 2022.12.7 - category: main dependencies: {} hash: @@ -92,47 +92,47 @@ package: - category: main dependencies: {} hash: - md5: 4915c8a17ab5f4477a3c281d76008182 - sha256: 9bcca76702bdeb72f2305d55a165c5b91c6fcd33ae0391c701a952b7a04a18ac + md5: bed72a66ece736ba7e7898a721738613 + sha256: 68301bfc55216fa37403011f25202313b010fcb378adab000e042042175fbfe3 manager: conda name: git-lfs optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/git-lfs-3.2.0-ha770c72_0.tar.bz2 - version: 3.2.0 + url: https://conda.anaconda.org/conda-forge/linux-64/git-lfs-3.3.0-ha770c72_0.conda + version: 3.3.0 - category: main dependencies: {} hash: - md5: bd4f2e711b39af170e7ff15163fe87ee - sha256: ad7985a9ff622880cf87c42db1ffe2dfb040d8175c1bb352fc8f3705c7e0962f + md5: 7aca3059a1729aa76c597603f10b0dd3 + sha256: f6cc89d887555912d6c61b295d398cff9ec982a3417d38025c45d5dd9b9e79cd manager: conda name: ld_impl_linux-64 optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.36.1-hea4e1c9_2.tar.bz2 - version: 2.36.1 + url: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda + version: '2.40' - category: main dependencies: {} hash: - md5: b02605b875559ff99f04351fd5040760 - sha256: 4d20cbd5dbe47e0dacd298d5cc0745ae19dcd5cd7cfaf937387adc876ee481c7 + md5: 164b4b1acaedc47ee7e658ae6b308ca3 + sha256: 03ea784edd12037dc3a7a0078ff3f9c3383feabb34d5ba910bb2fd7a21a2d961 manager: conda name: libgfortran5 optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-12.1.0-hdcd56e2_16.tar.bz2 - version: 12.1.0 + url: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-12.2.0-h337968e_19.tar.bz2 + version: 12.2.0 - category: main dependencies: {} hash: - md5: 6f5ba041a41eb102a1027d9e68731be7 - sha256: 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'2.18' + url: https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.8-3_cp38.conda + version: '3.8' - category: main dependencies: font-ttf-dejavu-sans-mono: '' @@ -172,28 +172,28 @@ package: version: '1' - category: main dependencies: - libgfortran5: 12.1.0 hdcd56e2_16 + libgfortran5: 12.2.0 h337968e_19 hash: - md5: 6bf15e29a20f614b18ae89368260d0a2 - sha256: 8b9ebde578c74c9e2d93cbe6940a09ee4d0ca4080a0f385bdcd10be536f07abb + md5: cd7a806282c16e1f2d39a7e80d3a3e0d + sha256: c7d061f323e80fbc09564179073d8af303bf69b953b0caddcf79b47e352c746f manager: conda name: libgfortran-ng optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-12.1.0-h69a702a_16.tar.bz2 - version: 12.1.0 + url: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-12.2.0-h69a702a_19.tar.bz2 + version: 12.2.0 - category: main dependencies: _libgcc_mutex: 0.1 conda_forge hash: - md5: f013cf7749536ce43d82afbffdf499ab - sha256: 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- version: 12.1.0 + url: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-12.2.0-h65d4601_19.tar.bz2 + version: 12.2.0 - category: main dependencies: libgcc-ng: '>=9.3.0' @@ -258,17 +258,17 @@ package: version: 1.18.1 - category: main dependencies: - libgcc-ng: '>=10.3.0' - libstdcxx-ng: '>=10.3.0' + libgcc-ng: '>=12' + libstdcxx-ng: '>=12' hash: - md5: e1b07832504eeba765d648389cc387a9 - sha256: 0db0e8690f8f7f4543d81e612947962b61518c61036bf7bdb53146f64dfca852 + md5: c4fbad8d4bddeb3c085f18cbf97fbfad + sha256: b44db0b92ae926b3fbbcd57c179fceb64fa11a9f9d09082e03be58b74dcad832 manager: conda name: expat optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/expat-2.4.8-h27087fc_0.tar.bz2 - version: 2.4.8 + url: https://conda.anaconda.org/conda-forge/linux-64/expat-2.5.0-h27087fc_0.tar.bz2 + version: 2.5.0 - category: main dependencies: libgcc-ng: '>=7.5.0' @@ -283,15 +283,27 @@ package: version: 1.0.10 - category: main dependencies: - libgcc-ng: '>=7.5.0' + libgcc-ng: '>=12' + hash: + md5: 14947d8770185e5153fdd04d4673ed37 + sha256: 4fcfedc44e4c9a053f0416f9fc6ab6ed50644fca3a761126dbd00d09db1f546a + manager: conda + name: gettext + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/gettext-0.21.1-h27087fc_0.tar.bz2 + version: 0.21.1 +- category: main + dependencies: + libgcc-ng: '>=12' hash: - md5: 626e68ae9cc5912d6adb79d318cf962d - sha256: 6ecacdbdf5cd9d2b46211b15a2f7db428ea5edd0cae9be89ccd837fc7b35643f + md5: 96f3b11872ef6fad973eac856cd2624f + sha256: 41ec165704ccce2faa0437f4f53c03c06261a2cc9ff7614828e51427d9261f4b manager: conda name: giflib optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/giflib-5.2.1-h36c2ea0_2.tar.bz2 + url: https://conda.anaconda.org/conda-forge/linux-64/giflib-5.2.1-h0b41bf4_3.conda version: 5.2.1 - category: main dependencies: @@ -334,15 +346,15 @@ package: version: '70.1' - category: main dependencies: - libgcc-ng: '>=10.3.0' + libgcc-ng: '>=12' hash: - md5: 4828c7f7208321cfbede4880463f4930 - sha256: 38880f346654488b5dfc1b01cd5e00c94e8cb43ac71a5610c491a0540ec11c7a + md5: c7a069243e1fbe9a556ed2ec030e6407 + sha256: 8f73194d09c9ea4a7e2b3562766b8d72125cc147b62c7cf83393e3a3bbfd581b manager: conda name: jpeg optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/jpeg-9e-h166bdaf_1.tar.bz2 + url: https://conda.anaconda.org/conda-forge/linux-64/jpeg-9e-h0b41bf4_3.conda version: 9e - category: main dependencies: @@ -358,41 +370,41 @@ package: version: 1.6.1 - category: main dependencies: - libgcc-ng: '>=9.4.0' - libstdcxx-ng: '>=9.4.0' + libgcc-ng: '>=12' + libstdcxx-ng: '>=12' hash: - md5: 7fcefde484980d23f0ec24c11e314d2e - sha256: 4f08723bfa7cdcbaccb4f73bbb2399327177c27d270f15d4561dbbb320d1eefc + md5: 76bbff344f0134279f225174e9064c8f + sha256: cb55f36dcd898203927133280ae1dc643368af041a48bcf7c026acb7c47b0c12 manager: conda name: lerc optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/lerc-3.0-h9c3ff4c_0.tar.bz2 - version: '3.0' + url: https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2 + version: 4.0.0 - category: main dependencies: - libgcc-ng: '>=10.3.0' + libgcc-ng: '>=12' hash: - md5: f82dc1c78bcf73583f2656433ce2933c - sha256: a9f1d1bcf4aa12b7e0930d054ee039402c3bd176b764a322b63d0d9ac5e619c8 + md5: 9194c9bf9428035a05352d031462eae4 + sha256: ddc961a36d498aaafd5b71078836ad5dd247cc6ba7924157f3801a2f09b77b14 manager: conda name: libbrotlicommon optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/libbrotlicommon-1.0.9-h166bdaf_7.tar.bz2 + url: https://conda.anaconda.org/conda-forge/linux-64/libbrotlicommon-1.0.9-h166bdaf_8.tar.bz2 version: 1.0.9 - category: main dependencies: libgcc-ng: '>=12' hash: - md5: d56e3db8fa642fb383f18f5be35eeef2 - sha256: 5927cd3350c5c91e50c6ce3cd54557e35a26445f366ae6080cfc2dd5bdda8d8c + md5: 5cc781fd91968b11a8a7fdbee0982676 + sha256: f9983a8ea03531f2c14bce76c870ca325c0fddf0c4e872bff1f78bc52624179c manager: conda name: libdeflate optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.12-h166bdaf_0.tar.bz2 - version: '1.12' + url: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.17-h0b41bf4_0.conda + version: '1.17' - category: main dependencies: libgcc-ng: '>=7.5.0' @@ -419,16 +431,28 @@ package: version: 3.4.2 - category: main dependencies: - libgcc-ng: '>=7.5.0' + libgcc-ng: '>=10.3.0' hash: - md5: 5c0f338a513a2943c659ae619fca9211 - sha256: 1ba9d434e982536abbbcd63505276270cb3a62844a0f1b6e52962e70be078abe + md5: b62b52da46c39ee2bc3c162ac7f1804d + sha256: 6a81ebac9f1aacdf2b4f945c87ad62b972f0f69c8e0981d68e111739e6720fd7 manager: conda name: libiconv optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.16-h516909a_0.tar.bz2 - version: '1.16' + url: https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-h166bdaf_0.tar.bz2 + version: '1.17' +- category: main + dependencies: + libgcc-ng: '>=12' + hash: + md5: b4f717df2d377410b462328bf0e8fb7d + sha256: 0d8b666ca4deabf948a76654df0fa1277145bed1c9e8a58e18a649c22c5f1c3e + manager: conda + name: libjpeg-turbo + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-2.1.4-h166bdaf_0.tar.bz2 + version: 2.1.4 - category: main dependencies: libgcc-ng: '>=9.4.0' @@ -443,18 +467,18 @@ package: version: 2.0.0 - category: main dependencies: - libgcc-ng: '>=10.3.0' + libgcc-ng: '>=12' libgfortran-ng: '' - libgfortran5: '>=10.3.0' + libgfortran5: '>=10.4.0' hash: - md5: 9b6d0781953c9e353faee494336cc229 - sha256: 2e840f4165a62dd826d16e0d51b3928bed46ca33fe943addd52c84f55ccc9551 + md5: 8c5963a49b6035c40646a763293fbb35 + sha256: 018372af663987265cb3ca8f37ac8c22b5f39219f65a0c162b056a30af11bba0 manager: conda name: libopenblas optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.20-pthreads_h78a6416_0.tar.bz2 - version: 0.3.20 + url: https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.21-pthreads_h78a6416_3.tar.bz2 + version: 0.3.21 - category: main dependencies: libgcc-ng: '>=7.5.0' @@ -469,16 +493,16 @@ package: version: 1.0.18 - category: main dependencies: - libgcc-ng: '>=9.4.0' + libgcc-ng: '>=12' hash: - md5: 16e143a1ed4b4fd169536373957f6fee - sha256: eadbb80c922dce355c0f8f7fc560f20f61263245799d076a1d5251d147d0d250 + md5: f204c8ba400ec475452737094fb81d52 + sha256: 345b3b580ef91557a82425ea3f432a70a8748c040deb14570b9f4dca4af3e3d1 manager: conda name: libtool optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/libtool-2.4.6-h9c3ff4c_1008.tar.bz2 - version: 2.4.6 + url: https://conda.anaconda.org/conda-forge/linux-64/libtool-2.4.7-h27087fc_0.conda + version: 2.4.7 - category: main dependencies: libgcc-ng: '>=9.3.0' @@ -493,41 +517,41 @@ package: version: 2.32.1 - category: main dependencies: - libgcc-ng: '>=9.4.0' + libgcc-ng: '>=12' hash: - md5: 46cf26ecc8775a0aab300ea1821aaa3c - sha256: 549a977d44c7f40e4a94e421d4e332a2d5ba2d79b4038302eb3352a21e0b2b94 + md5: ac2ccf7323d21f2994e4d1f5da664f37 + sha256: 221f2e138dd264b7394b88f08884d93825d38800a51415059e813c02467abfd1 manager: conda name: libwebp-base optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.2.2-h7f98852_1.tar.bz2 - version: 1.2.2 + url: https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.2.4-h166bdaf_0.tar.bz2 + version: 1.2.4 - category: main dependencies: libgcc-ng: '>=12' hash: - md5: 58eaff4f91891978af3625e7bbf958af - sha256: 6282bc3ac5689b277ef66b7d9b18b4afa449995bfa3883be9863dbc88dacfcd5 + md5: f3f9de449d32ca9b9c66a22863c96f41 + sha256: 22f3663bcf294d349327e60e464a51cd59664a71b8ed70c28a9f512d10bc77dd manager: conda name: libzlib optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.12-h166bdaf_1.tar.bz2 - version: 1.2.12 + url: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h166bdaf_4.tar.bz2 + version: 1.2.13 - category: main dependencies: - libgcc-ng: '>=9.3.0' - libstdcxx-ng: '>=9.3.0' + libgcc-ng: '>=12' + libstdcxx-ng: '>=12' hash: - md5: fbe97e8fa6f275d7c76a09e795adc3e6 - sha256: 56313fe4e602319682d4ea05c0ed3c5c45fc79884a5896f2cb7436b15d6987f9 + md5: 318b08df404f9c9be5712aaa5a6f0bb0 + sha256: 1b4c105a887f9b2041219d57036f72c4739ab9e9fe5a1486f094e58c76b31f5f manager: conda name: lz4-c optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.9.3-h9c3ff4c_1.tar.bz2 - version: 1.9.3 + url: https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.9.4-hcb278e6_0.conda + version: 1.9.4 - category: main dependencies: libgcc-ng: '>=7.5.0' @@ -557,14 +581,14 @@ package: ca-certificates: '' libgcc-ng: '>=12' hash: - md5: 995e819f901ee0c4411e4f50d9b31a82 - sha256: 52d8934ac8e2437207ec82e5f7f3b7dd6d8a0e5d19dae242037f0e27b3b94077 + md5: 2d833be81a21128e317325a01326d36f + sha256: d378afcec34b86fef4da3ebd622b3e614cb3f71e54b6a5a10adb1d23745ecc72 manager: conda name: openssl optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/openssl-1.1.1p-h166bdaf_0.tar.bz2 - version: 1.1.1p + url: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.0-h0b41bf4_0.conda + version: 3.1.0 - category: main dependencies: libgcc-ng: '>=9.3.0' @@ -604,17 +628,17 @@ package: version: '0.4' - category: main dependencies: - libgcc-ng: '>=10.3.0' - libstdcxx-ng: '>=10.3.0' + libgcc-ng: '>=12' + libstdcxx-ng: '>=12' hash: - md5: 418adb239781d9690afc6b1a05514c37 - sha256: 7e324caf1922a94e4c3432854624d25ef1fa361866981584725863c840fde5d2 + md5: e6d228cd0bb74a51dd18f5bfce0b4115 + sha256: 02219f2382b4fe39250627dade087a4412d811936a5a445636b7260477164eac manager: conda name: snappy optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/snappy-1.1.9-hbd366e4_1.tar.bz2 - version: 1.1.9 + url: https://conda.anaconda.org/conda-forge/linux-64/snappy-1.1.10-h9fff704_0.conda + version: 1.1.10 - category: main dependencies: libgcc-ng: '>=9.3.0' @@ -677,15 +701,15 @@ package: version: 0.11.1 - category: main dependencies: - libgcc-ng: '>=9.3.0' + libgcc-ng: '>=12' hash: - md5: 1e15f6ad85a7d743a2ac68dae6c82b98 - sha256: d45c4d1c8372c546711eb3863c76d899d03a67c3edb3b5c2c46c9492814cbe03 + md5: bce9f945da8ad2ae9b1d7165a64d0f87 + sha256: b8dda3b560e8a7830fe23be1c58cc41f407b2e20ae2f3b6901eb5842ba62b743 manager: conda name: xorg-xextproto optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/xorg-xextproto-7.3.0-h7f98852_1002.tar.bz2 + url: https://conda.anaconda.org/conda-forge/linux-64/xorg-xextproto-7.3.0-h0b41bf4_1003.conda version: 7.3.0 - category: main dependencies: @@ -701,16 +725,16 @@ package: version: 7.0.31 - category: main dependencies: - libgcc-ng: '>=7.5.0' + libgcc-ng: '>=12' hash: - md5: 33f601066901f3e1a85af3522a8113f9 - sha256: 1e2823cb2a526bc3a7031ad5dbfb992891f9ff9740d1c17cb6dbb8ebdfd33b27 + md5: 2161070d867d1b1204ea749c8eec4ef0 + sha256: 03a6d28ded42af8a347345f82f3eebdd6807a08526d47899a42d62d319609162 manager: conda name: xz optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.5-h516909a_1.tar.bz2 - version: 5.2.5 + url: https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2 + version: 5.2.6 - category: main dependencies: libgcc-ng: '>=9.4.0' @@ -725,54 +749,41 @@ package: version: 0.2.5 - category: main dependencies: - libffi: '>=3.4.2,<3.5.0a0' - libgcc-ng: '>=9.4.0' - hash: - md5: af49250eca8e139378f8ff0ae9e57251 - sha256: 1bb53c99b4943d210c881aad9158fb0235b348498bad1a7076d1f2bef6671922 - manager: conda - name: gettext - optional: false - platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/gettext-0.19.8.1-h73d1719_1008.tar.bz2 - version: 0.19.8.1 -- category: main - dependencies: - libopenblas: '>=0.3.20,<1.0a0' + libopenblas: '>=0.3.21,<1.0a0' hash: - md5: 04eb983975a1be3e57d6d667414cd774 - sha256: fad1fafee244f0632b887bc958f48b7ee2aa7949cf647ed641df8bdaa81d5070 + md5: d9b7a8639171f6c6fa0a983edabcfe2b + sha256: 4e4c60d3fe0b95ffb25911dace509e3532979f5deef4364141c533c5ca82dd39 manager: conda name: libblas optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-15_linux64_openblas.tar.bz2 + url: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-16_linux64_openblas.tar.bz2 version: 3.9.0 - category: main dependencies: - libbrotlicommon: 1.0.9 h166bdaf_7 - libgcc-ng: '>=10.3.0' + libbrotlicommon: 1.0.9 h166bdaf_8 + libgcc-ng: '>=12' hash: - md5: 37a460703214d0d1b421e2a47eb5e6d0 - sha256: 71044774a475423a2033c4999907ba0b3558649f8fe7d404caba15f8b58780ee + md5: 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https://conda.anaconda.org/conda-forge/linux-64/libbrotlienc-1.0.9-h166bdaf_8.tar.bz2 version: 1.0.9 - category: main dependencies: @@ -787,6 +798,32 @@ package: platform: linux-64 url: https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2 version: 3.1.20191231 +- category: main + dependencies: + libgcc-ng: '>=12' + libzlib: '>=1.2.13,<1.3.0a0' + hash: + md5: e1c890aebdebbfbf87e2c917187b4416 + sha256: a32b36d34e4f2490b99bddbc77d01a674d304f667f0e62c89e02c961addef462 + manager: conda + name: libpng + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.39-h753d276_0.conda + version: 1.6.39 +- category: main + dependencies: + libgcc-ng: '>=12' + libzlib: '>=1.2.13,<1.3.0a0' + hash: + md5: 2e5f9a37d487e1019fd4d8113adb2f9f + sha256: 6008a0b914bd1a3510a3dba38eada93aa0349ebca3a21e5fa276833c8205bf49 + manager: conda + name: libsqlite + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.40.0-h753d276_0.tar.bz2 + version: 3.40.0 - category: main dependencies: libgcc-ng: '>=9.4.0' @@ -802,19 +839,61 @@ package: platform: linux-64 url: https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.13-h7f98852_1004.tar.bz2 version: '1.13' +- category: main + dependencies: + icu: '>=70.1,<71.0a0' + libgcc-ng: '>=12' + libiconv: '>=1.17,<2.0a0' + libzlib: '>=1.2.13,<1.3.0a0' + xz: '>=5.2.6,<6.0a0' + hash: + md5: 29474f139e5017090f218ef6b3753efd + sha256: fe7a739103454593d4a83d33223443700031140ac1b1e726d653a8db98960790 + manager: conda + name: libxml2 + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.10.3-hca2bb57_3.conda + version: 2.10.3 - category: main dependencies: gmp: '>=6.2.1,<7.0a0' - libgcc-ng: '>=7.5.0' + libgcc-ng: '>=12' hash: - md5: ea9ebeddb066da8fad4a815e61b139be - sha256: d2d71ac6ed3b32f06b7db2691e0a1760016ce13fb0c50a9de6ed1ccc33e35ff3 + md5: 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+ libgcc-ng: '>=12' + libstdcxx-ng: '>=12' + libzlib: '>=1.2.13,<1.3.0a0' hash: - md5: 3db63b53bb194dbaa7dc3d8833e98da2 - sha256: 8ac9d80e4eefbb59f1470f921a7dd4c8a7398bc4d9251d1ba1be7bb1bbb05fe5 + md5: 6b63daed8feeca47be78f323e793d555 + sha256: fbe49a8c8df83c2eccb37c5863ad98baeb29796ec96f2c503783d7b89bf80c98 manager: conda name: zstd optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.2-h8a70e8d_1.tar.bz2 + url: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.2-h3eb15da_6.conda version: 1.5.2 - category: main dependencies: - libgcc-ng: '>=10.3.0' - libstdcxx-ng: '>=10.3.0' - libzlib: '>=1.2.11,<1.3.0a0' + libgcc-ng: '>=12' + libstdcxx-ng: '>=12' + libzlib: '>=1.2.13,<1.3.0a0' lz4-c: '>=1.9.3,<1.10.0a0' snappy: '>=1.1.9,<2.0a0' zstd: '>=1.5.2,<1.6.0a0' hash: - md5: 37baca23e60af4130cfc03e8ab9f8e22 - sha256: 3635408361a0d168c289d0e32927b1e1c1e4e563439b4ce7153e787201c6a4e0 + md5: bcf0664a2dbbbb86cbd4c1e6ff10ddd6 + sha256: 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https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.0.9-h166bdaf_8.tar.bz2 version: 1.0.9 +- category: main + dependencies: + libgcc-ng: '>=12' + libpng: '>=1.6.39,<1.7.0a0' + libzlib: '>=1.2.13,<1.3.0a0' + hash: + md5: e1232042de76d24539a436d37597eb06 + sha256: 1eb913727b54e9aa63c6d9a1177db4e2894cee97c5f26910a2b61899d5ac904f + manager: conda + name: freetype + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-hca18f0e_1.conda + version: 2.12.1 +- category: main + dependencies: + libgcc-ng: '>=9.3.0' + libgfortran-ng: '' + libgfortran5: '>=9.3.0' + libstdcxx-ng: '>=9.3.0' + zlib: '>=1.2.11,<1.3.0a0' + hash: + md5: ad631c2272b0226cebc56f1a552ff96c + sha256: d438edab677890c3f43c069d4257aa38d17eca61676c9c04b3c5feb441eff21c + manager: conda + name: hdf5 + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/hdf5-1.10.5-nompi_h5b725eb_1114.tar.bz2 + version: 1.10.5 - category: main 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'>=1.2.11,<1.3.0a0' @@ -4549,28 +4893,57 @@ package: version: 4.3.4 - category: main dependencies: - libzlib: 1.2.12 hfe4f2af_1 + libzlib: 1.2.13 hfd90126_4 hash: - md5: 12fdf8350ef315e7ad48693346067405 - sha256: 23cb7d8939f8447e745708a5487f2415b32455fc7111ae7ed88081dc6c3dc5bd + md5: be90e6223c74ea253080abae19b3bdb1 + sha256: 9db69bb5fc3e19093b550e25d1158cdf82f4f8eddc1f80f8d7d9de33eb8535a4 manager: conda name: zlib optional: false platform: osx-64 - url: https://conda.anaconda.org/conda-forge/osx-64/zlib-1.2.12-hfe4f2af_1.tar.bz2 - version: 1.2.12 + url: https://conda.anaconda.org/conda-forge/osx-64/zlib-1.2.13-hfd90126_4.tar.bz2 + version: 1.2.13 +- category: main + dependencies: + libcxx: '>=14.0.6' + libzlib: '>=1.2.13,<1.3.0a0' + hash: + md5: 40a188783d3c425bdccc9ae9104acbb8 + sha256: f845dafb0b488703ce81e25b6f27ed909ee9061b730c172e6b084fcf7156231f + manager: conda + name: zstd + optional: false + platform: osx-64 + url: 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platform: osx-64 - url: https://conda.anaconda.org/conda-forge/osx-64/brotli-bin-1.0.9-h5eb16cf_7.tar.bz2 + url: https://conda.anaconda.org/conda-forge/osx-64/brotli-bin-1.0.9-hb7f2c08_8.tar.bz2 version: 1.0.9 - category: main dependencies: @@ -4584,6 +4957,19 @@ package: platform: osx-64 url: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2 version: '1' +- category: main + dependencies: + libpng: '>=1.6.39,<1.7.0a0' + libzlib: '>=1.2.13,<1.3.0a0' + hash: + md5: 852224ea3e8991a8342228eab274840e + sha256: 0aea2b93d0da8bf022501857de93f2fc0e362fabcd83c4579be8d8f5bc3e17cb + manager: conda + name: freetype + optional: false + platform: osx-64 + url: https://conda.anaconda.org/conda-forge/osx-64/freetype-2.12.1-h3f81eb7_1.conda + version: 2.12.1 - category: main dependencies: libcxx: '>=12.0.1' @@ -4602,31 +4988,31 @@ package: dependencies: libgfortran5: '' hash: - md5: 60f48cef2d50674e0428c5579b6c3f66 - sha256: 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+https://conda.anaconda.org/conda-forge/noarch/ipywidgets-7.7.3-pyhd8ed1ab_0.conda#a3a25d9f92c2eca9ef37d833eee0b82b +https://conda.anaconda.org/conda-forge/noarch/qgrid-1.3.1-pyhd8ed1ab_4.tar.bz2#fff68c7404813a1eb2678425f00e9917 diff --git a/docs/io/output/rpacket_tracking.ipynb b/docs/io/output/rpacket_tracking.ipynb index 168727da619..16f64f0ca93 100644 --- a/docs/io/output/rpacket_tracking.ipynb +++ b/docs/io/output/rpacket_tracking.ipynb @@ -150,7 +150,18 @@ "metadata": {}, "outputs": [], "source": [ - "from tardis import run_tardis" + "from tardis import run_tardis\n", + "from tardis.io.atom_data.util import download_atom_data" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7d8471c3", + "metadata": {}, + "outputs": [], + "source": [ + "download_atom_data('kurucz_cd23_chianti_H_He')" ] }, { diff --git a/docs/io/visualization/montecarlo_packet_visualization.ipynb b/docs/io/visualization/montecarlo_packet_visualization.ipynb index ebd21756299..62b80f30871 100644 --- a/docs/io/visualization/montecarlo_packet_visualization.ipynb +++ b/docs/io/visualization/montecarlo_packet_visualization.ipynb @@ -23,6 +23,7 @@ "source": [ "from tardis import run_tardis\n", "from tardis.io.config_reader import Configuration\n", + "from tardis.io.atom_data.util import download_atom_data\n", "import plotly.express as px\n", "import plotly.graph_objects as go\n", "import math\n", @@ -31,6 +32,16 @@ "import random" ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Download atom data\n", + "download_atom_data('kurucz_cd23_chianti_H_He')" + ] + }, { "cell_type": "code", "execution_count": null, diff --git a/docs/resources/credits.rst b/docs/resources/credits.rst index 09d31041d10..6f621117cb5 100644 --- a/docs/resources/credits.rst +++ b/docs/resources/credits.rst @@ -74,14 +74,14 @@ The following BibTeX entries are needed for the references: adsnote = {Provided by the SAO/NASA Astrophysics Data System} } -.. |CITATION| replace:: kerzendorf_wolfgang_2022_6662839 +.. |CITATION| replace:: kerzendorf_wolfgang_2023_7753535 -.. |DOI_BADGE| image:: https://img.shields.io/badge/DOI-10.5281/zenodo.6662839-blue - :target: https://doi.org/10.5281/zenodo.6662839 +.. |DOI_BADGE| image:: https://img.shields.io/badge/DOI-10.5281/zenodo.7753535-blue + :target: https://doi.org/10.5281/zenodo.7753535 .. code-block:: bibtex - @software{kerzendorf_wolfgang_2022_6662839, + @software{kerzendorf_wolfgang_2023_7753535, author = {Kerzendorf, Wolfgang and Sim, Stuart and Vogl, Christian and @@ -106,70 +106,77 @@ The following BibTeX entries are needed for the references: Barna, Barnabás and Gautam, Gaurav and Fullard, Andrew and - Cawley, Kevin and Smith, Isaac and + Cawley, Kevin and Singhal, Jaladh and Arya, Atharva and + O'Brien, Jack and Barbosa, Talytha and Sondhi, Dhruv and Yu, Jenny and - O'Brien, Jack and Patel, Maryam and Varanasi, Kaushik and Gillanders, James and + Chitchyan, Sona and Savel, Arjun and - Eweis, Youssef and Reinecke, Martin and + Eweis, Youssef and Bylund, Tomas and Bentil, Laud and Eguren, Jordi and Alam, Arib and Bartnik, Matthew and Magee, Mark and + Varma Buddaraju, Rohith and + Kambham, Satwik and Shields, Joshua and Livneh, Ran and - Chitchyan, Sona and - Rajagopalan, Srinath and Mishra, Sashank and - Floers, Andreas and + Rajagopalan, Srinath and Reichenbach, John and Jain, Rinkle and + Floers, Andreas and Brar, Antreev and Singh, Sourav and - Sofiatti, Caroline and + Holas, Alexander and + Bhakar, Jayant and Kowalski, Nathan and - Talegaonkar, Chinmay and Selsing, Jonatan and + Kumar, Aman and + Sofiatti, Caroline and + Talegaonkar, Chinmay and + Singh, Shreyas and Singh Rathore, Parikshit and Prasad, Shilpi and Venkat, Shashank and - Varma Buddaraju, Rohith and + Sharma, Sampark and Patel, Pratik and Yap, Kevin and Patra, Nilesh and Sarafina, Nance and Zaheer, Musabbiha and Sandler, Morgan and - Lemoine, Thom and + Truong, Le and Gupta, Suyash and Nayak U, Ashwin and + Lemoine, Thom and Wahi, Ujjwal and Aggarwal, Yash and - kumar, aman and - Sharma, Sampark and + Gupta, Harshul and Volodin, Dmitry and - Martinez, Laureano and + PATIDAR, ABHISHEK and Dasgupta, Debajyoti and - Holas, Alexander and + Patidar, Abhishek and Kharkar, Atharwa and + Kumar, Atul and Kolliboyina, Chaitanya and - Kumar, Atul}, - title = {tardis-sn/tardis: TARDIS v2022.06.19}, - month = jun, - year = 2022, + Martinez, Laureano}, + title = {tardis-sn/tardis: TARDIS v2023.03.20}, + month = mar, + year = 2023, publisher = {Zenodo}, - version = {release-2022.06.19}, - doi = {10.5281/zenodo.6662839}, - url = {https://doi.org/10.5281/zenodo.6662839} + version = {release-2023.03.20}, + doi = {10.5281/zenodo.7753535}, + url = {https://doi.org/10.5281/zenodo.7753535} } diff --git a/tardis/analysis.py b/tardis/analysis.py index c2f469ed8b7..b6aad9fced4 100644 --- a/tardis/analysis.py +++ b/tardis/analysis.py @@ -1,4 +1,6 @@ -# codes to for analyse the model. +""" +Code to analyse the model. +""" import re import os diff --git a/tardis/analysis/opacities.py b/tardis/analysis/opacities.py index a0ae8b0e196..315c669e40b 100644 --- a/tardis/analysis/opacities.py +++ b/tardis/analysis/opacities.py @@ -372,13 +372,13 @@ def _calc_planck_mean_opacity(self): for i in range(self.nshells): delta_nu = self.nu_bins[1:] - self.nu_bins[:-1] - T = self.mdl.plasma.t_rad[i] - bb_nu = Blackbody(T) + temperature = self.mdl.plasma.t_rad[i] + bb_nu = Blackbody(temperature) tmp = ( bb_nu(self.nu_bins[:-1]) * delta_nu * self.kappa_tot[:, 0] ).sum() - tmp /= (bb_nu(self.nu_bins[:-1], T) * delta_nu).sum() + tmp /= (bb_nu(self.nu_bins[:-1], temperature) * delta_nu).sum() kappa_planck_mean[i] = tmp diff --git a/tardis/base.py b/tardis/base.py index fd9b5457f3d..3f429bdfbba 100644 --- a/tardis/base.py +++ b/tardis/base.py @@ -1,4 +1,6 @@ -# Functions that are important for the general usage of TARDIS. +""" +Functions that are important for the general usage of TARDIS. +""" import logging diff --git a/tardis/conftest.py b/tardis/conftest.py index 6ce70d42595..997d1c17bd4 100644 --- a/tardis/conftest.py +++ b/tardis/conftest.py @@ -51,6 +51,14 @@ def pytest_configure(config): packagename = os.path.basename(os.path.dirname(__file__)) TESTED_VERSIONS[packagename] = __version__ + # Create a marker to ignore the `--generate-reference` flag. A use case for this + # marker is when there is data in the reference data repository that can't be + # generated by TARDIS, like the Arepo snapshots. + config.addinivalue_line( + "markers", + "ignore_generate: mark test to not generate new reference data", + ) + # Uncomment the last two lines in this block to treat all DeprecationWarnings as # exceptions. For Astropy v2.0 or later, there are 2 additional keywords, @@ -99,6 +107,14 @@ def pytest_addoption(parser): help="Run integration tests with less packets.", ) +# Required by the `ignore_generate` marker +def pytest_collection_modifyitems(config, items): + if config.getoption("--generate-reference"): + skip_generate = pytest.mark.skip(reason="Skip generate reference data") + for item in items: + if "ignore_generate" in item.keywords: + item.add_marker(skip_generate) + # ------------------------------------------------------------------------- # project specific fixtures @@ -145,6 +161,13 @@ def tardis_config_verysimple(): ) +@pytest.fixture(scope="function") +def tardis_config_verysimple_nlte(): + return yaml_load_file( + "tardis/io/tests/data/tardis_configv1_nlte.yml", YAMLLoader + ) + + ### # HDF Fixtures ### diff --git a/tardis/grid/__init__.py b/tardis/grid/__init__.py index eb8bb8410b2..1b5b3213ca9 100644 --- a/tardis/grid/__init__.py +++ b/tardis/grid/__init__.py @@ -1 +1,7 @@ +""" +Storing a grid of TARDIS parameters that +facilitates running large numbers of +simulations easily. +""" + from tardis.grid.base import * diff --git a/tardis/gui/__init.py__ b/tardis/gui/__init.py__ deleted file mode 100644 index e69de29bb2d..00000000000 diff --git a/tardis/gui/__init__.py b/tardis/gui/__init__.py new file mode 100644 index 00000000000..a22e23fccfd --- /dev/null +++ b/tardis/gui/__init__.py @@ -0,0 +1,9 @@ +""" +Creation of the basic framework for the TARDIS GUI. + +The data that should be displayed in the GUI is put into +respective data structures (either a tree or a table), such +that they can be used in the widgets. These widgets are +used to form the building blocks of the basic framework for +the GUI. +""" diff --git a/tardis/io/__init__.py b/tardis/io/__init__.py index ca4d671e64b..c1d44a57897 100644 --- a/tardis/io/__init__.py +++ b/tardis/io/__init__.py @@ -1,3 +1,7 @@ +""" +A collection of subpackages and submodules to handle input and output data. +""" + # readin model_data from tardis.io.model_reader import ( read_simple_ascii_density, diff --git a/tardis/io/atom_data/__init__.py b/tardis/io/atom_data/__init__.py index 5fd5f11b1ce..39d2bbdfef1 100644 --- a/tardis/io/atom_data/__init__.py +++ b/tardis/io/atom_data/__init__.py @@ -1,2 +1,6 @@ +""" +Getting and handling the atomic data. +""" + from tardis.io.atom_data.base import AtomData from tardis.io.atom_data.atom_web_download import download_atom_data diff --git a/tardis/io/logger/__init__.py b/tardis/io/logger/__init__.py index e69de29bb2d..78bc5622358 100644 --- a/tardis/io/logger/__init__.py +++ b/tardis/io/logger/__init__.py @@ -0,0 +1,3 @@ +""" +Managing the logging output. +""" diff --git a/tardis/io/parsers/__init__.py b/tardis/io/parsers/__init__.py index ef3825cde24..2ae18fa4d7b 100644 --- a/tardis/io/parsers/__init__.py +++ b/tardis/io/parsers/__init__.py @@ -1,3 +1,12 @@ +""" +A collection of parsers to read data of different formats. + +Accepted data formats are Arepo snapshots, the Blondin toy-model +format, CSVY files and STELLA files. These are parsed into +either CSV files, YAML files or Pandas DataFrames, which are +data formats interpretable by TARDIS. +""" + from tardis.io.parsers.blondin_toymodel import ( read_blondin_toymodel, convert_blondin_toymodel, diff --git a/tardis/io/schemas/montecarlo.yml b/tardis/io/schemas/montecarlo.yml index 430fbf8db67..f3664e253eb 100644 --- a/tardis/io/schemas/montecarlo.yml +++ b/tardis/io/schemas/montecarlo.yml @@ -17,7 +17,7 @@ properties: no_of_packets: type: number multipleOf: 1.0 - description: Seed for the random number generator + description: The number of packets used in each iteration. iterations: type: number multipleOf: 1.0 diff --git a/tardis/io/schemas/plasma.yml b/tardis/io/schemas/plasma.yml index 63d30da7173..9d39845db9d 100644 --- a/tardis/io/schemas/plasma.yml +++ b/tardis/io/schemas/plasma.yml @@ -111,6 +111,14 @@ properties: type: number default: 0.9 description: Value used for estimating the electron temperature from radiation temperature. + nlte_ionization_species: + type: array + default: [] + description: List of species treated with nlte ionization. In the format ["H I", "He II"] etc. + nlte_excitation_species: + type: array + default: [] + description: List of species treated with nlte excitation. In the format ["H I", "He II"] etc. required: - ionization - excitation diff --git a/tardis/io/tests/data/tardis_configv1_nlte.yml b/tardis/io/tests/data/tardis_configv1_nlte.yml new file mode 100644 index 00000000000..ee3c640e4f5 --- /dev/null +++ b/tardis/io/tests/data/tardis_configv1_nlte.yml @@ -0,0 +1,70 @@ +tardis_config_version: v1.0 + +supernova: + luminosity_requested: 9.05 log_lsun + time_explosion: 16 day + +atom_data: TestNLTE_Ti.h5 + +model: + structure: + type: specific + velocity: + start: 6395 km/s + stop: 12500 km/s + num: 5 + density: + type : power_law + time_0: 16.0 day + rho_0: 1.948e-14 g/cm^3 + v_0: 8000 km/s + exponent: -10 + + abundances: + type: uniform + H: 0.9 + He: 0.099 + Ti: 1e-3 + +plasma: + disable_electron_scattering: no + ionization: lte + excitation: lte + radiative_rates_type: dilute-blackbody + line_interaction_type: macroatom + initial_t_inner: 12000 K + link_t_rad_t_electron: 1.0 + nlte_ionization_species: [H I, He II, Ti II] + + continuum_interaction: + species: + - H I + - Ti II + - He II + + enable_adiabatic_cooling: True + + + +montecarlo: + seed: 23111963 + no_of_packets: 100000 + iterations: 1 + nthreads: 1 + + last_no_of_packets: 1000 + no_of_virtual_packets: 0 + + convergence_strategy: + type: damped + damping_constant: 0.5 + threshold: 0.05 + fraction: 0.8 + hold_iterations: 3 + +spectrum: + start: 250 angstrom + stop: 10000 angstrom + num: 10000 + method: integrated + compute: Automatic diff --git a/tardis/io/tests/test_arepo_parser.py b/tardis/io/tests/test_arepo_parser.py index 5d65afdea90..663e9c263ea 100644 --- a/tardis/io/tests/test_arepo_parser.py +++ b/tardis/io/tests/test_arepo_parser.py @@ -114,9 +114,11 @@ def get_full_reference_data(): return data +@pytest.mark.ignore_generate def test_cone_profile(get_cone_csvy_model, get_cone_reference_data): assert get_cone_csvy_model == get_cone_reference_data +@pytest.mark.ignore_generate def test_full_profile(get_full_csvy_model, get_full_reference_data): assert get_full_csvy_model == get_full_reference_data diff --git a/tardis/io/tests/test_config_reader.py b/tardis/io/tests/test_config_reader.py index 36462eb289a..d69221e1420 100644 --- a/tardis/io/tests/test_config_reader.py +++ b/tardis/io/tests/test_config_reader.py @@ -7,7 +7,10 @@ from jsonschema.exceptions import ValidationError from tardis.io import config_reader +from astropy.units import Quantity from tardis.io.config_reader import Configuration +from tardis.plasma.exceptions import PlasmaConfigError +from tardis.plasma.standard_plasmas import assemble_plasma def data_path(filename): @@ -97,17 +100,15 @@ def test_model_section_config(tardis_config_verysimple): tardis_config_verysimple["model"]["structure"]["velocity"][ "start" - ] = "2.0e4 km/s" + ] = Quantity("2.0e4 km/s") tardis_config_verysimple["model"]["structure"]["velocity"][ "stop" - ] = "1.1e4 km/s" - with pytest.raises(ValueError) as ve: - if ( - conf.model.structure.velocity.start - < conf.model.structure.velocity.stop - ): - raise ValueError("Stop Value must be greater than Start Value") - assert ve.type is ValueError + ] = Quantity("1.1e4 km/s") + + with pytest.raises(ValueError): + conf = Configuration.from_config_dict( + tardis_config_verysimple, validate=True, config_dirname="test" + ) def test_supernova_section_config(tardis_config_verysimple): @@ -126,33 +127,29 @@ def test_supernova_section_config(tardis_config_verysimple): ------ Assertion based on validation for specified values """ - conf = Configuration.from_config_dict( - tardis_config_verysimple, validate=True, config_dirname="test" + tardis_config_verysimple["supernova"]["time_explosion"] = Quantity( + "-10 day" ) - tardis_config_verysimple["supernova"]["time_explosion"] = "-10 day" + with pytest.raises(ValueError): + conf = Configuration.from_config_dict( + tardis_config_verysimple, validate=True, config_dirname="test" + ) + + tardis_config_verysimple["supernova"]["time_explosion"] = Quantity("10 day") tardis_config_verysimple["supernova"][ "luminosity_wavelength_start" - ] = "15 angstrom" + ] = Quantity("15 angstrom") tardis_config_verysimple["supernova"][ "luminosity_wavelength_end" - ] = "0 angstrom" - with pytest.raises(ValueError) as ve: - if conf.supernova.time_explosion.value > 0: - raise ValueError("Time of Explosion cannot be negative") - assert ve.type is ValueError - - with pytest.raises(ValueError) as ve: - if ( - conf.supernova.luminosity_wavelength_start.value - < conf.supernova.luminosity_wavelength_end.value - ): - raise ValueError( - "End Limit must be greater than Start Limit for Luminosity" - ) - assert ve.type is ValueError - - -def test_plasma_section_config(tardis_config_verysimple): + ] = Quantity("0 angstrom") + with pytest.raises(ValueError): + conf = Configuration.from_config_dict( + tardis_config_verysimple, validate=True, config_dirname="test" + ) + + +@pytest.mark.parametrize("key", ["initial_t_inner", "initial_t_rad"]) +def test_plasma_section_config(key, tardis_config_verysimple): """ Configuration Validation Test for Plasma Section of the Tardis Config YAML File @@ -168,17 +165,73 @@ def test_plasma_section_config(tardis_config_verysimple): ------ Assertion based on validation for specified values """ - conf = Configuration.from_config_dict( - tardis_config_verysimple, validate=True, config_dirname="test" - ) - tardis_config_verysimple["plasma"]["initial_t_inner"] = "-100 K" - tardis_config_verysimple["plasma"]["initial_t_rad"] = "-100 K" - with pytest.raises(ValueError) as ve: - if (conf.plasma.initial_t_inner.value >= -1) and ( - conf.plasma.initial_t_rad.value >= -1 - ): - raise ValueError("Initial Temperatures are Invalid") - assert ve.type is ValueError + tardis_config_verysimple["plasma"][key] = Quantity("-100 K") + with pytest.raises(ValueError): + conf = Configuration.from_config_dict( + tardis_config_verysimple, validate=True, config_dirname="test" + ) + + +def test_plasma_nlte_section_config( + tardis_config_verysimple_nlte, + nlte_raw_model, + nlte_atom_data, +): + """ + Configuration Validation Test for Plasma Section of the Tardis Config YAML File. + + Validates: + nlte_ionization_species: should be included in continuum_interaction + + Parameter + --------- + `tardis_config_verysimple_nlte` : YAML File + `nlte_raw_model` : A simple model + `nlte_atom_data` : An example atomic dataset + + Result + ------ + Assertion based on validation for specified values + """ + tardis_config_verysimple_nlte["plasma"]["continuum_interaction"][ + "species" + ] = [ + "He I", + ] + tardis_config_verysimple_nlte["plasma"]["nlte_ionization_species"] = ["H I"] + config = Configuration.from_config_dict(tardis_config_verysimple_nlte) + with pytest.raises(PlasmaConfigError) as ve: + assemble_plasma(config, nlte_raw_model, nlte_atom_data) + + +def test_plasma_nlte_exc_section_config( + tardis_config_verysimple_nlte, nlte_raw_model, nlte_atom_data +): + """ + Configuration Validation Test for Plasma Section of the Tardis Config YAML File. + + Validates: + nlte_excitation_species: should be included in continuum_interaction + + Parameter + --------- + `tardis_config_verysimple_nlte` : YAML File + `nlte_raw_model` : A simple model + `nlte_atom_data` : An example atomic dataset + + Result + ------ + Assertion based on validation for specified values + """ + tardis_config_verysimple_nlte["plasma"]["continuum_interaction"][ + "species" + ] = [ + "He I", + ] + tardis_config_verysimple_nlte["plasma"]["nlte_excitation_species"] = ["H I"] + config = Configuration.from_config_dict(tardis_config_verysimple_nlte) + with pytest.raises(PlasmaConfigError): + plasma = assemble_plasma(config, nlte_raw_model, nlte_atom_data) def test_spectrum_section_config(tardis_config_verysimple): @@ -196,12 +249,9 @@ def test_spectrum_section_config(tardis_config_verysimple): ------ Assertion based on validation for specified values """ - conf = Configuration.from_config_dict( - tardis_config_verysimple, validate=True, config_dirname="test" - ) - tardis_config_verysimple["spectrum"]["start"] = "2500 angstrom" - tardis_config_verysimple["spectrum"]["stop"] = "500 angstrom" - with pytest.raises(ValueError) as ve: - if not conf.spectrum.stop.value < conf.spectrum.start.value: - raise ValueError("Start Value must be less than Stop Value") - assert ve.type is ValueError + tardis_config_verysimple["spectrum"]["start"] = Quantity("2500 angstrom") + tardis_config_verysimple["spectrum"]["stop"] = Quantity("500 angstrom") + with pytest.raises(ValueError): + conf = Configuration.from_config_dict( + tardis_config_verysimple, validate=True, config_dirname="test" + ) diff --git a/tardis/io/tests/test_model_reader.py b/tardis/io/tests/test_model_reader.py index 5b3a401d9d3..e6f3b394c01 100644 --- a/tardis/io/tests/test_model_reader.py +++ b/tardis/io/tests/test_model_reader.py @@ -341,10 +341,16 @@ def test_store_runner_to_hdf(simulation_verysimple, tmp_path): f["runner/last_line_interaction_shell_id"], runner_data["last_line_interaction_shell_id"], ) - assert ( - f["runner/line_interaction_type"][()].decode("utf-8") - == runner_data["line_interaction_type"] - ) + if hasattr(f["runner/line_interaction_type"][()], "decode"): + assert ( + f["runner/line_interaction_type"][()].decode("utf-8") + == runner_data["line_interaction_type"] + ) + else: + assert np.array_equal( + f["runner/line_interaction_type"][()], + runner_data["line_interaction_type"], + ) assert np.array_equal( f["runner/nu_bar_estimator"], runner_data["nu_bar_estimator"] ) @@ -362,10 +368,16 @@ def test_store_runner_to_hdf(simulation_verysimple, tmp_path): f["runner/spectrum_frequency_cgs"], runner_data["spectrum_frequency"].value, ) - assert ( - f["runner/spectrum_method"][()].decode("utf-8") - == runner_data["spectrum_method"] - ) + if hasattr(f["runner/spectrum_method"][()], "decode"): + assert ( + f["runner/spectrum_method"][()].decode("utf-8") + == runner_data["spectrum_method"] + ) + else: + assert np.array_equal( + f["runner/spectrum_method"][()], + runner_data["spectrum_method"], + ) assert np.array_equal( f["runner/stim_recomb_cooling_estimator"], runner_data["stim_recomb_cooling_estimator"], diff --git a/tardis/model/__init__.py b/tardis/model/__init__.py index 66f102eba18..3399f042e29 100644 --- a/tardis/model/__init__.py +++ b/tardis/model/__init__.py @@ -1 +1,9 @@ +""" +Holding information about the TARDIS model. + +This includes information about the shell structure, +density, abundance, temperatures and dilution +factor of the model used in the simulation. +""" + from tardis.model.base import * diff --git a/tardis/model/base.py b/tardis/model/base.py index af0a62e8257..77bbbb78ed2 100644 --- a/tardis/model/base.py +++ b/tardis/model/base.py @@ -6,6 +6,7 @@ from tardis import constants import radioactivedecay as rd from radioactivedecay.utils import Z_DICT +from tardis.model.geometry.radial1d import Radial1DGeometry from tardis.util.base import quantity_linspace, is_valid_nuclide_or_elem from tardis.io.parsers.csvy import load_csvy @@ -24,35 +25,6 @@ logger = logging.getLogger(__name__) -class Radial1DGeometry: - """ - Holds information about model geometry for radial 1D models. - - Parameters - ---------- - r_inner : astropy.units.quantity.Quantity - r_outer : astropy.units.quantity.Quantity - v_inner : astropy.units.quantity.Quantity - v_outer : astropy.units.quantity.Quantity - - Attributes - ---------- - volume : astropy.units.quantity.Quantity - Volume in each shell - """ - - def __init__(self, r_inner, r_outer, v_inner, v_outer): - self.r_inner = r_inner - self.r_outer = r_outer - self.v_inner = v_inner - self.v_outer = v_outer - - @property - def volume(self): - """Volume in shell computed from r_outer and r_inner""" - return (4.0 / 3) * np.pi * (self.r_outer**3 - self.r_inner**3) - - class Composition: """ Holds information about model composition @@ -113,7 +85,7 @@ class ModelState: Parameters ---------- composition : tardis.model.Composition - geometry : tardis.model.Radial1DGeometry + geometry : tardis.model.geometry.radial1d.Radial1DGeometry time_explosion : astropy.units.quantity.Quantity Attributes diff --git a/tardis/model/geometry/__init__.py b/tardis/model/geometry/__init__.py new file mode 100644 index 00000000000..44b4461913d --- /dev/null +++ b/tardis/model/geometry/__init__.py @@ -0,0 +1,10 @@ +""" +Holding information about model geometry for radial 1D models. + +The information stored about the model are the following attributes: +r_inner : The radius of the inner shell boundaries +r_outer : The radius of the outer shell boundaries +v_inner : The velocity of the inner boundaries of each shell +v_outer : The velocity of the outer boundaries of each shell +volume : Volume of each shell computed from r_outer and r_inner +""" diff --git a/tardis/model/geometry/radial1d.py b/tardis/model/geometry/radial1d.py new file mode 100644 index 00000000000..db0a064884a --- /dev/null +++ b/tardis/model/geometry/radial1d.py @@ -0,0 +1,76 @@ +from numba import float64 +from numba.experimental import jitclass +import numpy as np +from astropy import units as u + + +class Radial1DGeometry: + """ + Holds information about model geometry for radial 1D models. + + Parameters + ---------- + r_inner : astropy.units.quantity.Quantity + r_outer : astropy.units.quantity.Quantity + v_inner : astropy.units.quantity.Quantity + v_outer : astropy.units.quantity.Quantity + + Attributes + ---------- + volume : astropy.units.quantity.Quantity + Volume in each shell + """ + + def __init__(self, r_inner, r_outer, v_inner, v_outer): + self.r_inner = r_inner + self.r_outer = r_outer + self.v_inner = v_inner + self.v_outer = v_outer + + @property + def volume(self): + """Volume in shell computed from r_outer and r_inner""" + return (4.0 / 3) * np.pi * (self.r_outer**3 - self.r_inner**3) + + def to_numba(self): + """ + Returns a new NumbaRadial1DGeometry object + + Returns + ------- + NumbaRadial1DGeometry + Numba version of Radial1DGeometry with properties in cgs units + """ + return NumbaRadial1DGeometry( + self.r_inner.to(u.cm).value, + self.r_outer.to(u.cm).value, + self.v_inner.to(u.cm / u.s).value, + self.v_outer.to(u.cm / u.s).value, + ) + + +numba_geometry_spec = [ + ("r_inner", float64[:]), + ("r_outer", float64[:]), + ("v_inner", float64[:]), + ("v_outer", float64[:]), +] + + +@jitclass(numba_geometry_spec) +class NumbaRadial1DGeometry(object): + def __init__(self, r_inner, r_outer, v_inner, v_outer): + """ + Radial 1D Geometry for the Numba mode + + Parameters + ---------- + r_inner : numpy.ndarray + r_outer : numpy.ndarray + v_inner : numpy.ndarray + v_outer : numpy.ndarray + """ + self.r_inner = r_inner + self.r_outer = r_outer + self.v_inner = v_inner + self.v_outer = v_outer diff --git a/tardis/montecarlo/__init__.py b/tardis/montecarlo/__init__.py index 222ee95b0b8..eeb3ef212bd 100644 --- a/tardis/montecarlo/__init__.py +++ b/tardis/montecarlo/__init__.py @@ -1 +1,10 @@ +""" +Faciliating the MonteCarlo iterations. + +During a simulation run, a number of MonteCarlo iterations specified +in the configuration are run using the numba compiler. +Most of the iterations are used to calculate the steady-state plasma +properties and with the last iteration, the spectrum is determined. +""" + from tardis.montecarlo.base import * diff --git a/tardis/montecarlo/base.py b/tardis/montecarlo/base.py index 91f6819538d..c04c81ad4a6 100644 --- a/tardis/montecarlo/base.py +++ b/tardis/montecarlo/base.py @@ -106,7 +106,12 @@ def __init__( self.seed = seed if packet_source is None: - self.packet_source = source.BlackBodySimpleSource(seed) + if not enable_full_relativity: + self.packet_source = source.BlackBodySimpleSource(seed) + else: + self.packet_source = source.BlackBodySimpleSourceRelativistic( + seed + ) else: self.packet_source = packet_source # inject different packets @@ -202,7 +207,9 @@ def _initialize_geometry_arrays(self, model): self.v_inner_cgs = model.v_inner.to("cm/s").value self.v_outer_cgs = model.v_outer.to("cm/s").value - def _initialize_packets(self, T, no_of_packets, iteration, radius): + def _initialize_packets( + self, temperature, no_of_packets, iteration, radius, time_explosion + ): # the iteration is added each time to preserve randomness # across different simulations with the same temperature, # for example. We seed the random module instead of the numpy module @@ -211,9 +218,15 @@ def _initialize_packets(self, T, no_of_packets, iteration, radius): seed = self.seed + iteration rng = np.random.default_rng(seed=seed) seeds = rng.choice(MAX_SEED_VAL, no_of_packets, replace=True) - radii, nus, mus, energies = self.packet_source.create_packets( - T, no_of_packets, rng, radius - ) + if not self.enable_full_relativity: + radii, nus, mus, energies = self.packet_source.create_packets( + temperature, no_of_packets, rng, radius + ) + else: + radii, nus, mus, energies = self.packet_source.create_packets( + temperature, no_of_packets, rng, radius, time_explosion + ) + mc_config_module.packet_seeds = seeds self.input_r = radii self.input_nu = nus @@ -344,7 +357,11 @@ def run( self._initialize_geometry_arrays(model) self._initialize_packets( - model.t_inner.value, no_of_packets, iteration, model.r_inner[0] + model.t_inner.value, + no_of_packets, + iteration, + model.r_inner[0], + model.time_explosion, ) configuration_initialize(self, no_of_virtual_packets) diff --git a/tardis/montecarlo/montecarlo_numba/__init__.py b/tardis/montecarlo/montecarlo_numba/__init__.py index d73c539a7a9..a4eb6dc3c3a 100644 --- a/tardis/montecarlo/montecarlo_numba/__init__.py +++ b/tardis/montecarlo/montecarlo_numba/__init__.py @@ -1,3 +1,7 @@ +""" +Implements the main loop of the MonteCarlo routine. +""" + from llvmlite import binding binding.set_option("tmp", "-non-global-value-max-name-size=2048") diff --git a/tardis/montecarlo/montecarlo_numba/base.py b/tardis/montecarlo/montecarlo_numba/base.py index 6dd4af64b94..d2812911732 100644 --- a/tardis/montecarlo/montecarlo_numba/base.py +++ b/tardis/montecarlo/montecarlo_numba/base.py @@ -29,7 +29,11 @@ ) from tardis.montecarlo.montecarlo_numba import njit_dict from numba.typed import List -from tardis.util.base import update_iterations_pbar, update_packet_pbar +from tardis.util.base import ( + update_iterations_pbar, + update_packet_pbar, + refresh_packet_pbar, +) def montecarlo_radial1d( @@ -49,13 +53,9 @@ def montecarlo_radial1d( runner._output_nu, runner._output_energy, ) - + numba_radial_1d_geometry = model.model_state.geometry.to_numba() numba_model = NumbaModel( - runner.r_inner_cgs, - runner.r_outer_cgs, - runner.v_inner_cgs, - runner.v_outer_cgs, - model.time_explosion.to("s").value, + model.model_state.time_explosion.to("s").value, ) numba_plasma = numba_plasma_initialize(plasma, runner.line_interaction_type) estimators = Estimators( @@ -89,6 +89,7 @@ def montecarlo_radial1d( rpacket_trackers, ) = montecarlo_main_loop( packet_collection, + numba_radial_1d_geometry, numba_model, numba_plasma, estimators, @@ -131,6 +132,7 @@ def montecarlo_radial1d( virt_packet_last_line_interaction_out_id ).ravel() update_iterations_pbar(1) + refresh_packet_pbar() # Condition for Checking if RPacket Tracking is enabled if montecarlo_configuration.RPACKET_TRACKING: runner.rpacket_tracker = rpacket_trackers @@ -139,6 +141,7 @@ def montecarlo_radial1d( @njit(**njit_dict) def montecarlo_main_loop( packet_collection, + numba_radial_1d_geometry, numba_model, numba_plasma, estimators, @@ -158,8 +161,9 @@ def montecarlo_main_loop( Parameters ---------- packet_collection : PacketCollection + numba_radial_1d_geometry : NumbaRadial1DGeometry numba_model : NumbaModel - numba_plasma : NumbaPlasma + numba_plasma : NumbaPlasma estimators : NumbaEstimators spectrum_frequency : astropy.units.Quantity frequency binspas @@ -247,7 +251,7 @@ def montecarlo_main_loop( seed = packet_seeds[i] np.random.seed(seed) r_packet = RPacket( - numba_model.r_inner[0], + numba_radial_1d_geometry.r_inner[0], packet_collection.packets_input_mu[i], packet_collection.packets_input_nu[i], packet_collection.packets_input_energy[i], @@ -260,6 +264,7 @@ def montecarlo_main_loop( loop = single_packet_loop( r_packet, + numba_radial_1d_geometry, numba_model, numba_plasma, estimators, diff --git a/tardis/montecarlo/montecarlo_numba/formal_integral.py b/tardis/montecarlo/montecarlo_numba/formal_integral.py index 85d18018029..bd08b09f1f1 100644 --- a/tardis/montecarlo/montecarlo_numba/formal_integral.py +++ b/tardis/montecarlo/montecarlo_numba/formal_integral.py @@ -36,6 +36,7 @@ class IntegrationError(Exception): @njit(**njit_dict) def numba_formal_integral( + geometry, model, plasma, iT, @@ -66,8 +67,8 @@ def numba_formal_integral( # global read-only values size_line, size_shell = tau_sobolev.shape size_tau = size_line * size_shell - R_ph = model.r_inner[0] # make sure these are cgs - R_max = model.r_outer[size_shell - 1] + R_ph = geometry.r_inner[0] # make sure these are cgs + R_max = geometry.r_outer[size_shell - 1] pp = np.zeros(N, dtype=np.float64) # check exp_tau = np.zeros(size_tau, dtype=np.float64) exp_tau = np.exp(-tau_sobolev.T.ravel()) # maybe make this 2D? @@ -108,7 +109,9 @@ def numba_formal_integral( p = pp[p_idx] # initialize z intersections for p values - size_z = populate_z(model, p, z, shell_id) # check returns + size_z = populate_z( + geometry, model, p, z, shell_id + ) # check returns # initialize I_nu if p <= R_ph: I_nu[p_idx] = intensity_black_body(nu * z[0], iT) @@ -220,8 +223,8 @@ class NumbaFormalIntegrator(object): with numba. """ - def __init__(self, model, plasma, points=1000): - + def __init__(self, geometry, model, plasma, points=1000): + self.geometry = geometry self.model = model self.plasma = plasma self.points = points @@ -242,6 +245,7 @@ def formal_integral( Simple wrapper for the numba implementation of the formal integral """ return numba_formal_integral( + self.geometry, self.model, self.plasma, iT, @@ -291,23 +295,33 @@ def __init__(self, model, plasma, runner, points=1000): def generate_numba_objects(self): """instantiate the numba interface objects needed for computing the formal integral""" - self.numba_model = NumbaModel( + from tardis.model.geometry.radial1d import NumbaRadial1DGeometry + + self.numba_radial_1d_geometry = NumbaRadial1DGeometry( self.runner.r_inner_i, self.runner.r_outer_i, self.runner.r_inner_i / self.model.time_explosion.to("s").value, self.runner.r_outer_i / self.model.time_explosion.to("s").value, - self.model.time_explosion.to("s").value, + ) + self.numba_model = NumbaModel( + self.model.time_explosion.cgs.value, ) self.numba_plasma = numba_plasma_initialize( self.original_plasma, self.runner.line_interaction_type ) if self.runner.use_gpu: self.integrator = CudaFormalIntegrator( - self.numba_model, self.numba_plasma, self.points + self.numba_radial_1d_geometry, + self.numba_model, + self.numba_plasma, + self.points, ) else: self.integrator = NumbaFormalIntegrator( - self.numba_model, self.numba_plasma, self.points + self.numba_radial_1d_geometry, + self.numba_model, + self.numba_plasma, + self.points, ) def check(self, raises=True): @@ -602,7 +616,7 @@ def formal_integral(self, nu, N): @njit(**njit_dict_no_parallel) -def populate_z(model, p, oz, oshell_id): +def populate_z(geometry, model, p, oz, oshell_id): """Calculate p line intersections This function calculates the intersection points of the p-line with @@ -615,13 +629,13 @@ def populate_z(model, p, oz, oshell_id): :oshell_id: (int64) will be set with the corresponding shell_ids """ # abbreviations - r = model.r_outer - N = len(model.r_inner) # check + r = geometry.r_outer + N = len(geometry.r_inner) # check inv_t = 1 / model.time_explosion z = 0 offset = N - if p <= model.r_inner[0]: + if p <= geometry.r_inner[0]: # intersect the photosphere for i in range(N): oz[i] = 1 - calculate_z(r[i], p, inv_t) @@ -729,12 +743,24 @@ def trapezoid_integration(array, h): @njit(**njit_dict_no_parallel) -def intensity_black_body(nu, T): - """Get the black body intensity at frequency nu - and temperature T""" +def intensity_black_body(nu, temperature): + """ + Calculate the blackbody intensity. + + Parameters + ---------- + nu : float64 + frequency + temperature : float64 + Temperature + + Returns + ------- + float64 + """ if nu == 0: return np.nan # to avoid ZeroDivisionError - beta_rad = 1 / (KB_CGS * T) + beta_rad = 1 / (KB_CGS * temperature) coefficient = 2 * H_CGS * C_INV * C_INV return coefficient * nu * nu * nu / (np.exp(H_CGS * nu * beta_rad) - 1) diff --git a/tardis/montecarlo/montecarlo_numba/formal_integral_cuda.py b/tardis/montecarlo/montecarlo_numba/formal_integral_cuda.py index 13a1a47ebaa..007c26031e5 100644 --- a/tardis/montecarlo/montecarlo_numba/formal_integral_cuda.py +++ b/tardis/montecarlo/montecarlo_numba/formal_integral_cuda.py @@ -41,11 +41,11 @@ def cuda_formal_integral( Parameters ---------- r_inner : array(float64, 1d, C) - self.model.r_inner + self.geometry.r_inner r_outer : array(float64, 1d, C) - self.model.r_outer + self.geometry.r_outer time_explosion: float64 - self.model.time_explosion + self.geometry.time_explosion line_list_nu : array(float64, 1d, A) self.plasma.line_list_nu iT : np.float64 @@ -216,8 +216,8 @@ class CudaFormalIntegrator(object): with CUDA. """ - def __init__(self, model, plasma, points=1000): - + def __init__(self, geometry, model, plasma, points=1000): + self.geometry = geometry self.model = model self.plasma = plasma self.points = points @@ -246,7 +246,7 @@ def formal_integral( exp_tau = np.zeros(size_tau, dtype=np.float64) # array(float64, 1d, C) exp_tau = np.exp(-tau_sobolev.T.ravel()) # array(float64, 1d, C) pp[::] = calculate_p_values( - self.model.r_outer[size_shell - 1], N + self.geometry.r_outer[size_shell - 1], N ) # array(float64, 1d, C) I_nu = np.zeros( @@ -262,8 +262,8 @@ def formal_integral( blocks_per_grid = (inu_size // THREADS_PER_BLOCK) + 1 cuda_formal_integral[blocks_per_grid, THREADS_PER_BLOCK]( - self.model.r_inner, - self.model.r_outer, + self.geometry.r_inner, + self.geometry.r_outer, self.model.time_explosion, self.plasma.line_list_nu, iT.value, @@ -475,15 +475,16 @@ def trapezoid_integration_cuda(arr, dx): @cuda.jit(device=True) -def intensity_black_body_cuda(nu, T): +def intensity_black_body_cuda(nu, temperature): """ - Get the black body intensity at frequency nu - and temperature T + Calculate the blackbody intensity. Parameters ---------- nu : float64 - T : float64 + frequency + temperature : float64 + Temperature Returns ------- @@ -491,7 +492,7 @@ def intensity_black_body_cuda(nu, T): """ if nu == 0: return np.nan # to avoid ZeroDivisionError - beta_rad = 1 / (KB_CGS * T) + beta_rad = 1 / (KB_CGS * temperature) coefficient = 2 * H_CGS * C_INV * C_INV return coefficient * nu * nu * nu / (math.exp(H_CGS * nu * beta_rad) - 1) diff --git a/tardis/montecarlo/montecarlo_numba/interaction.py b/tardis/montecarlo/montecarlo_numba/interaction.py index c57f82bfd72..d56464556c8 100644 --- a/tardis/montecarlo/montecarlo_numba/interaction.py +++ b/tardis/montecarlo/montecarlo_numba/interaction.py @@ -116,9 +116,9 @@ def sample_nu_free_free(numba_plasma, shell): Frequency of the free-free emission process """ - T = numba_plasma.t_electrons[shell] + temperature = numba_plasma.t_electrons[shell] zrand = np.random.random() - return -K_B * T / H * np.log(zrand) + return -K_B * temperature / H * np.log(zrand) @njit(**njit_dict_no_parallel) diff --git a/tardis/montecarlo/montecarlo_numba/numba_interface.py b/tardis/montecarlo/montecarlo_numba/numba_interface.py index 455fb4419ce..051a177d0a5 100644 --- a/tardis/montecarlo/montecarlo_numba/numba_interface.py +++ b/tardis/montecarlo/montecarlo_numba/numba_interface.py @@ -13,33 +13,22 @@ C_SPEED_OF_LIGHT = const.c.to("cm/s").value + numba_model_spec = [ - ("r_inner", float64[:]), - ("r_outer", float64[:]), ("time_explosion", float64), - ("v_inner", float64[:]), - ("v_outer", float64[:]), ] @jitclass(numba_model_spec) class NumbaModel(object): - def __init__(self, r_inner, r_outer, v_inner, v_outer, time_explosion): + def __init__(self, time_explosion): """ Model for the Numba mode Parameters ---------- - r_inner : numpy.ndarray - r_outer : numpy.ndarray - v_inner : numpy.ndarray - v_outer : numpy.ndarray time_explosion : float """ - self.r_inner = r_inner - self.r_outer = r_outer - self.v_inner = v_inner - self.v_outer = v_outer self.time_explosion = time_explosion diff --git a/tardis/montecarlo/montecarlo_numba/single_packet_loop.py b/tardis/montecarlo/montecarlo_numba/single_packet_loop.py index 6e237a7c371..24c398d9f66 100644 --- a/tardis/montecarlo/montecarlo_numba/single_packet_loop.py +++ b/tardis/montecarlo/montecarlo_numba/single_packet_loop.py @@ -40,6 +40,7 @@ @njit def single_packet_loop( r_packet, + numba_radial_1d_geometry, numba_model, numba_plasma, estimators, @@ -50,6 +51,7 @@ def single_packet_loop( Parameters ---------- r_packet : tardis.montecarlo.montecarlo_numba.r_packet.RPacket + numba_radial_1d_geometry : tardis.montecarlo.montecarlo_numba.numba_interface.NumbaRadial1DGeometry numba_model : tardis.montecarlo.montecarlo_numba.numba_interface.NumbaModel numba_plasma : tardis.montecarlo.montecarlo_numba.numba_interface.NumbaPlasma estimators : tardis.montecarlo.montecarlo_numba.numba_interface.Estimators @@ -71,7 +73,11 @@ def single_packet_loop( r_packet.initialize_line_id(numba_plasma, numba_model) trace_vpacket_volley( - r_packet, vpacket_collection, numba_model, numba_plasma + r_packet, + vpacket_collection, + numba_radial_1d_geometry, + numba_model, + numba_plasma, ) if montecarlo_configuration.RPACKET_TRACKING: @@ -102,6 +108,7 @@ def single_packet_loop( escat_prob = chi_e / chi_continuum # probability of e-scatter distance, interaction_type, delta_shell = trace_packet( r_packet, + numba_radial_1d_geometry, numba_model, numba_plasma, estimators, @@ -124,6 +131,7 @@ def single_packet_loop( chi_continuum = chi_e distance, interaction_type, delta_shell = trace_packet( r_packet, + numba_radial_1d_geometry, numba_model, numba_plasma, estimators, @@ -138,7 +146,7 @@ def single_packet_loop( r_packet, distance, numba_model.time_explosion, estimators ) move_packet_across_shell_boundary( - r_packet, delta_shell, len(numba_model.r_inner) + r_packet, delta_shell, len(numba_radial_1d_geometry.r_inner) ) elif interaction_type == InteractionType.LINE: @@ -153,7 +161,11 @@ def single_packet_loop( numba_plasma, ) trace_vpacket_volley( - r_packet, vpacket_collection, numba_model, numba_plasma + r_packet, + vpacket_collection, + numba_radial_1d_geometry, + numba_model, + numba_plasma, ) elif interaction_type == InteractionType.ESCATTERING: @@ -165,7 +177,11 @@ def single_packet_loop( thomson_scatter(r_packet, numba_model.time_explosion) trace_vpacket_volley( - r_packet, vpacket_collection, numba_model, numba_plasma + r_packet, + vpacket_collection, + numba_radial_1d_geometry, + numba_model, + numba_plasma, ) elif ( montecarlo_configuration.CONTINUUM_PROCESSES_ENABLED @@ -186,7 +202,11 @@ def single_packet_loop( ) trace_vpacket_volley( - r_packet, vpacket_collection, numba_model, numba_plasma + r_packet, + vpacket_collection, + numba_radial_1d_geometry, + numba_model, + numba_plasma, ) else: pass diff --git a/tardis/montecarlo/montecarlo_numba/tests/conftest.py b/tardis/montecarlo/montecarlo_numba/tests/conftest.py index 91d1ae63cfd..bd61cb80ff1 100644 --- a/tardis/montecarlo/montecarlo_numba/tests/conftest.py +++ b/tardis/montecarlo/montecarlo_numba/tests/conftest.py @@ -45,15 +45,15 @@ def verysimple_numba_plasma(nb_simulation_verysimple): ) +@pytest.fixture(scope="package") +def verysimple_numba_radial_1d_geometry(nb_simulation_verysimple): + return nb_simulation_verysimple.model.model_state.geometry.to_numba() + + @pytest.fixture(scope="package") def verysimple_numba_model(nb_simulation_verysimple): - runner = nb_simulation_verysimple.runner model = nb_simulation_verysimple.model return NumbaModel( - runner.r_inner_cgs, - runner.r_outer_cgs, - runner.v_inner_cgs, - runner.v_outer_cgs, model.time_explosion.to("s").value, ) diff --git a/tardis/montecarlo/montecarlo_numba/tests/test_cuda_formal_integral.py b/tardis/montecarlo/montecarlo_numba/tests/test_cuda_formal_integral.py index 9eaa077c22b..264ba7a1414 100644 --- a/tardis/montecarlo/montecarlo_numba/tests/test_cuda_formal_integral.py +++ b/tardis/montecarlo/montecarlo_numba/tests/test_cuda_formal_integral.py @@ -12,6 +12,7 @@ import tardis.montecarlo.montecarlo_numba.formal_integral_cuda as formal_integral_cuda import tardis.montecarlo.montecarlo_numba.formal_integral as formal_integral_numba +from tardis.model.geometry.radial1d import NumbaRadial1DGeometry from tardis.montecarlo.montecarlo_numba.numba_interface import NumbaModel @@ -31,14 +32,14 @@ not GPUs_available, reason="No GPU is available to test CUDA function" ) @pytest.mark.parametrize( - ["nu", "T"], + ["nu", "temperature"], [ (1e14, 1e4), (0, 1), (1, 1), ], ) -def test_intensity_black_body_cuda(nu, T): +def test_intensity_black_body_cuda(nu, temperature): """ Initializes the test of the cuda version against the numba implementation of the @@ -46,21 +47,21 @@ def test_intensity_black_body_cuda(nu, T): is done as both results have 15 digits of precision. """ actual = np.zeros(3) - black_body_caller[1, 3](nu, T, actual) + black_body_caller[1, 3](nu, temperature, actual) - expected = formal_integral_numba.intensity_black_body(nu, T) + expected = formal_integral_numba.intensity_black_body(nu, temperature) ntest.assert_allclose(actual, expected, rtol=1e-14) @cuda.jit -def black_body_caller(nu, T, actual): +def black_body_caller(nu, temperature, actual): """ This calls the CUDA function and fills out the array """ x = cuda.grid(1) - actual[x] = formal_integral_cuda.intensity_black_body_cuda(nu, T) + actual[x] = formal_integral_cuda.intensity_black_body_cuda(nu, temperature) @pytest.mark.skipif( @@ -112,16 +113,26 @@ def trapezoid_integration_caller(data, h, actual): @pytest.fixture(scope="function", params=TESTDATA_model) -def formal_integral_model(request): +def formal_integral_geometry(request): """ This gets the Numba model to be used in later tests """ r = request.param["r"] - model = NumbaModel( + geometry = NumbaRadial1DGeometry( r[:-1], r[1:], r[:-1] * c.c.cgs.value, r[1:] * c.c.cgs.value, + ) + return geometry + + +@pytest.fixture(scope="function") +def formal_integral_model(): + """ + This gets the Numba model to be used in later tests + """ + model = NumbaModel( 1 / c.c.cgs.value, ) return model @@ -131,7 +142,9 @@ def formal_integral_model(request): not GPUs_available, reason="No GPU is available to test CUDA function" ) @pytest.mark.parametrize(["p", "p_loc"], [(0.0, 0), (0.5, 1), (1.0, 2)]) -def test_calculate_z_cuda(formal_integral_model, p, p_loc): +def test_calculate_z_cuda( + formal_integral_geometry, formal_integral_model, p, p_loc +): """ Initializes the test of the cuda version against the numba implementation of the @@ -140,8 +153,8 @@ def test_calculate_z_cuda(formal_integral_model, p, p_loc): """ actual = np.zeros(3) inv_t = 1.0 / formal_integral_model.time_explosion - size = len(formal_integral_model.r_outer) - r_outer = formal_integral_model.r_outer + size = len(formal_integral_geometry.r_outer) + r_outer = formal_integral_geometry.r_outer for r in r_outer: calculate_z_caller[1, 3](r, p, inv_t, actual) expected = formal_integral_numba.calculate_z(r, p, inv_t) @@ -166,26 +179,30 @@ def calculate_z_caller(r, p, inv_t, actual): ["p", "p_loc"], [(1e-5, 0), (1e-3, 1), (0.1, 2), (0.5, 3), (0.99, 4), (1, 5)], ) -def test_populate_z(formal_integral_model, p, p_loc): +def test_populate_z(formal_integral_geometry, formal_integral_model, p, p_loc): """ Initializes the test of the cuda version against the numba implementation of the populate_z """ - size = len(formal_integral_model.r_inner) + size = len(formal_integral_geometry.r_inner) oz = np.zeros(size * 2) expected_oz = np.zeros(size * 2) oshell_id = np.zeros_like(oz, dtype=np.int64) expected_oshell_id = np.zeros_like(oz, dtype=np.int64) expected = formal_integral_numba.populate_z( - formal_integral_model, p, expected_oz, expected_oshell_id + formal_integral_geometry, + formal_integral_model, + p, + expected_oz, + expected_oshell_id, ) actual = np.zeros(6) populate_z_caller[1, 6]( - formal_integral_model.r_inner, - formal_integral_model.r_outer, + formal_integral_geometry.r_inner, + formal_integral_geometry.r_outer, formal_integral_model.time_explosion, p, oz, @@ -361,6 +378,7 @@ def test_full_formal_integral( # This is to force the for formal_integrator_numba to use the numba version # as it is automatically set to the CUDA version when there is a GPU available formal_integrator_numba.integrator = NumbaFormalIntegrator( + formal_integrator_numba.numba_radial_1d_geometry, formal_integrator_numba.numba_model, formal_integrator_numba.numba_plasma, formal_integrator_numba.points, diff --git a/tardis/montecarlo/montecarlo_numba/tests/test_numba_formal_integral.py b/tardis/montecarlo/montecarlo_numba/tests/test_numba_formal_integral.py index 2a83aa0e550..2c49ed8a8ab 100644 --- a/tardis/montecarlo/montecarlo_numba/tests/test_numba_formal_integral.py +++ b/tardis/montecarlo/montecarlo_numba/tests/test_numba_formal_integral.py @@ -8,21 +8,22 @@ from tardis.util.base import intensity_black_body import tardis.montecarlo.montecarlo_numba.formal_integral as formal_integral from tardis.montecarlo.montecarlo_numba.numba_interface import NumbaModel +from tardis.model.geometry.radial1d import NumbaRadial1DGeometry @pytest.mark.parametrize( - ["nu", "T"], + ["nu", "temperature"], [ (1e14, 1e4), (0, 1), (1, 1), ], ) -def test_intensity_black_body(nu, T): +def test_intensity_black_body(nu, temperature): func = formal_integral.intensity_black_body - actual = func(nu, T) + actual = func(nu, temperature) print(actual, type(actual)) - expected = intensity_black_body(nu, T) + expected = intensity_black_body(nu, temperature) ntest.assert_almost_equal(actual, expected) @@ -55,25 +56,32 @@ def calculate_z(r, p): @pytest.fixture(scope="function", params=TESTDATA) -def formal_integral_model(request): +def formal_integral_geometry(request): r = request.param["r"] - model = NumbaModel( + geometry = NumbaRadial1DGeometry( r[:-1], r[1:], r[:-1] * c.c.cgs.value, r[1:] * c.c.cgs.value, + ) + return geometry + + +@pytest.fixture(scope="function") +def formal_integral_model(): + model = NumbaModel( 1 / c.c.cgs.value, ) return model @pytest.mark.parametrize("p", [0.0, 0.5, 1.0]) -def test_calculate_z(formal_integral_model, p): +def test_calculate_z(formal_integral_geometry, formal_integral_model, p): func = formal_integral.calculate_z inv_t = 1.0 / formal_integral_model.time_explosion - size = len(formal_integral_model.r_outer) - r_outer = formal_integral_model.r_outer + size = len(formal_integral_geometry.r_outer) + r_outer = formal_integral_geometry.r_outer for r in r_outer: actual = func(r, p, inv_t) @@ -85,7 +93,9 @@ def test_calculate_z(formal_integral_model, p): @pytest.mark.parametrize("p", [0, 0.5, 1]) -def test_populate_z_photosphere(formal_integral_model, p): +def test_populate_z_photosphere( + formal_integral_geometry, formal_integral_model, p +): """ Test the case where p < r[0] That means we 'hit' all shells from inside to outside. @@ -94,15 +104,15 @@ def test_populate_z_photosphere(formal_integral_model, p): formal_integral_model, None, None ) func = formal_integral.populate_z - size = len(formal_integral_model.r_outer) - r_inner = formal_integral_model.r_inner - r_outer = formal_integral_model.r_outer + size = len(formal_integral_geometry.r_outer) + r_inner = formal_integral_geometry.r_inner + r_outer = formal_integral_geometry.r_outer p = r_inner[0] * p oz = np.zeros_like(r_inner) oshell_id = np.zeros_like(oz, dtype=np.int64) - N = func(formal_integral_model, p, oz, oshell_id) + N = func(formal_integral_geometry, formal_integral_model, p, oz, oshell_id) assert N == size ntest.assert_allclose(oshell_id, np.arange(0, size, 1)) @@ -111,7 +121,7 @@ def test_populate_z_photosphere(formal_integral_model, p): @pytest.mark.parametrize("p", [1e-5, 0.5, 0.99, 1]) -def test_populate_z_shells(formal_integral_model, p): +def test_populate_z_shells(formal_integral_geometry, formal_integral_model, p): """ Test the case where p > r[0] """ @@ -120,9 +130,9 @@ def test_populate_z_shells(formal_integral_model, p): ) func = formal_integral.populate_z - size = len(formal_integral_model.r_inner) - r_inner = formal_integral_model.r_inner - r_outer = formal_integral_model.r_outer + size = len(formal_integral_geometry.r_inner) + r_inner = formal_integral_geometry.r_inner + r_outer = formal_integral_geometry.r_outer p = r_inner[0] + (r_outer[-1] - r_inner[0]) * p idx = np.searchsorted(r_outer, p, side="right") @@ -148,7 +158,7 @@ def test_populate_z_shells(formal_integral_model, p): r_outer[np.arange(idx, size, 1)], p ) - N = func(formal_integral_model, p, oz, oshell_id) + N = func(formal_integral_geometry, formal_integral_model, p, oz, oshell_id) assert N == expected_N diff --git a/tardis/montecarlo/montecarlo_numba/tests/test_packet.py b/tardis/montecarlo/montecarlo_numba/tests/test_packet.py index eb23e3c35da..2d8dba261e3 100644 --- a/tardis/montecarlo/montecarlo_numba/tests/test_packet.py +++ b/tardis/montecarlo/montecarlo_numba/tests/test_packet.py @@ -10,6 +10,7 @@ import tardis.montecarlo.montecarlo_numba.utils as utils import tardis.montecarlo.montecarlo_numba.numba_interface as numba_interface +from tardis.model.geometry.radial1d import NumbaRadial1DGeometry from tardis import constants as const import tardis.montecarlo.montecarlo_numba.numba_config as numba_config @@ -25,12 +26,18 @@ @pytest.fixture(scope="function") -def model(): - return numba_interface.NumbaModel( +def geometry(): + return NumbaRadial1DGeometry( r_inner=np.array([6.912e14, 8.64e14], dtype=np.float64), r_outer=np.array([8.64e14, 1.0368e15], dtype=np.float64), v_inner=np.array([-1, -1], dtype=np.float64), v_outer=np.array([-1, -1], dtype=np.float64), + ) + + +@pytest.fixture(scope="function") +def model(): + return numba_interface.NumbaModel( time_explosion=5.2e7, ) @@ -62,12 +69,12 @@ def estimators(): ({"mu": -0.3, "r": 7.5e14}, {"d_boundary": 709376919351035.9}), ], ) -def test_calculate_distance_boundary(packet_params, expected_params, model): +def test_calculate_distance_boundary(packet_params, expected_params, geometry): mu = packet_params["mu"] r = packet_params["r"] d_boundary = calculate_distances.calculate_distance_boundary( - r, mu, model.r_inner[0], model.r_outer[0] + r, mu, geometry.r_inner[0], geometry.r_outer[0] ) # Accuracy to within 0.1cm diff --git a/tardis/montecarlo/montecarlo_numba/tests/test_single_packet_loop.py b/tardis/montecarlo/montecarlo_numba/tests/test_single_packet_loop.py index 58f4e03d304..9eccd5a9313 100644 --- a/tardis/montecarlo/montecarlo_numba/tests/test_single_packet_loop.py +++ b/tardis/montecarlo/montecarlo_numba/tests/test_single_packet_loop.py @@ -11,12 +11,14 @@ @pytest.mark.xfail(reason="Need to fix estimator differences across runs") # TODO set RNG consistently def test_verysimple_single_packet_loop( + verysimple_numba_radial_1d_geometry, verysimple_numba_model, verysimple_numba_plasma, verysimple_estimators, verysimple_vpacket_collection, verysimple_packet_collection, ): + numba_radial_1d_geometry = verysimple_numba_radial_1d_geometry packet_collection = verysimple_packet_collection vpacket_collection = verysimple_vpacket_collection numba_model = verysimple_numba_model @@ -25,7 +27,7 @@ def test_verysimple_single_packet_loop( i = 0 r_packet = RPacket( - verysimple_numba_model.r_inner[0], + numba_radial_1d_geometry.r_inner[0], packet_collection.packets_input_mu[i], packet_collection.packets_input_nu[i], packet_collection.packets_input_energy[i], @@ -33,6 +35,7 @@ def test_verysimple_single_packet_loop( ) single_packet_loop( r_packet, + numba_radial_1d_geometry, numba_model, numba_plasma, numba_estimators, diff --git a/tardis/montecarlo/montecarlo_numba/tests/test_vpacket.py b/tardis/montecarlo/montecarlo_numba/tests/test_vpacket.py index 9c70cfb7189..493e60648b0 100644 --- a/tardis/montecarlo/montecarlo_numba/tests/test_vpacket.py +++ b/tardis/montecarlo/montecarlo_numba/tests/test_vpacket.py @@ -44,7 +44,10 @@ def v_packet_initialize_line_id(v_packet, numba_plasma, numba_model): def test_trace_vpacket_within_shell( - v_packet, verysimple_numba_model, verysimple_numba_plasma + v_packet, + verysimple_numba_radial_1d_geometry, + verysimple_numba_model, + verysimple_numba_plasma, ): # Give the vpacket a reasonable line ID v_packet_initialize_line_id( @@ -56,7 +59,10 @@ def test_trace_vpacket_within_shell( distance_boundary, delta_shell, ) = vpacket.trace_vpacket_within_shell( - v_packet, verysimple_numba_model, verysimple_numba_plasma + v_packet, + verysimple_numba_radial_1d_geometry, + verysimple_numba_model, + verysimple_numba_plasma, ) npt.assert_almost_equal(tau_trace_combined, 8164850.891288479) @@ -65,7 +71,10 @@ def test_trace_vpacket_within_shell( def test_trace_vpacket( - v_packet, verysimple_numba_model, verysimple_numba_plasma + v_packet, + verysimple_numba_radial_1d_geometry, + verysimple_numba_model, + verysimple_numba_plasma, ): # Set seed because of RNG in trace_vpacket np.random.seed(1) @@ -76,7 +85,10 @@ def test_trace_vpacket( ) tau_trace_combined = vpacket.trace_vpacket( - v_packet, verysimple_numba_model, verysimple_numba_plasma + v_packet, + verysimple_numba_radial_1d_geometry, + verysimple_numba_model, + verysimple_numba_plasma, ) npt.assert_almost_equal(tau_trace_combined, 8164850.891288479) @@ -94,6 +106,7 @@ def test_trace_vpacket_volley( packet, verysimple_packet_collection, verysimple_3vpacket_collection, + verysimple_numba_radial_1d_geometry, verysimple_numba_model, verysimple_numba_plasma, ): @@ -105,6 +118,7 @@ def test_trace_vpacket_volley( vpacket.trace_vpacket_volley( packet, verysimple_3vpacket_collection, + verysimple_numba_radial_1d_geometry, verysimple_numba_model, verysimple_numba_plasma, ) @@ -124,8 +138,14 @@ def broken_packet(): def test_trace_bad_vpacket( - broken_packet, verysimple_numba_model, verysimple_numba_plasma + broken_packet, + verysimple_numba_radial_1d_geometry, + verysimple_numba_model, + verysimple_numba_plasma, ): vpacket.trace_vpacket( - broken_packet, verysimple_numba_model, verysimple_numba_plasma + broken_packet, + verysimple_numba_radial_1d_geometry, + verysimple_numba_model, + verysimple_numba_plasma, ) diff --git a/tardis/montecarlo/montecarlo_numba/vpacket.py b/tardis/montecarlo/montecarlo_numba/vpacket.py index af4c4c9f763..fb99a0f4ffc 100644 --- a/tardis/montecarlo/montecarlo_numba/vpacket.py +++ b/tardis/montecarlo/montecarlo_numba/vpacket.py @@ -28,7 +28,10 @@ angle_aberration_CMF_to_LF, ) -from tardis.montecarlo.montecarlo_numba.numba_config import SIGMA_THOMSON +from tardis.montecarlo.montecarlo_numba.numba_config import ( + SIGMA_THOMSON, + C_SPEED_OF_LIGHT, +) vpacket_spec = [ ("r", float64), @@ -65,12 +68,14 @@ def __init__( @njit(**njit_dict_no_parallel) -def trace_vpacket_within_shell(v_packet, numba_model, numba_plasma): +def trace_vpacket_within_shell( + v_packet, numba_radial_1d_geometry, numba_model, numba_plasma +): """ Trace VPacket within one shell (relatively simple operation) """ - r_inner = numba_model.r_inner[v_packet.current_shell_id] - r_outer = numba_model.r_outer[v_packet.current_shell_id] + r_inner = numba_radial_1d_geometry.r_inner[v_packet.current_shell_id] + r_outer = numba_radial_1d_geometry.r_outer[v_packet.current_shell_id] distance_boundary, delta_shell = calculate_distance_boundary( v_packet.r, v_packet.mu, r_inner, r_outer @@ -133,7 +138,9 @@ def trace_vpacket_within_shell(v_packet, numba_model, numba_plasma): @njit(**njit_dict_no_parallel) -def trace_vpacket(v_packet, numba_model, numba_plasma): +def trace_vpacket( + v_packet, numba_radial_1d_geometry, numba_model, numba_plasma +): """ Trace single vpacket. Parameters @@ -153,11 +160,13 @@ def trace_vpacket(v_packet, numba_model, numba_plasma): tau_trace_combined_shell, distance_boundary, delta_shell, - ) = trace_vpacket_within_shell(v_packet, numba_model, numba_plasma) + ) = trace_vpacket_within_shell( + v_packet, numba_radial_1d_geometry, numba_model, numba_plasma + ) tau_trace_combined += tau_trace_combined_shell move_packet_across_shell_boundary( - v_packet, delta_shell, len(numba_model.r_inner) + v_packet, delta_shell, len(numba_radial_1d_geometry.r_inner) ) if tau_trace_combined > montecarlo_configuration.tau_russian: @@ -189,7 +198,11 @@ def trace_vpacket(v_packet, numba_model, numba_plasma): @njit(**njit_dict_no_parallel) def trace_vpacket_volley( - r_packet, vpacket_collection, numba_model, numba_plasma + r_packet, + vpacket_collection, + numba_radial_1d_geometry, + numba_model, + numba_plasma, ): """ Shoot a volley of vpackets (the vpacket collection specifies how many) @@ -201,6 +214,8 @@ def trace_vpacket_volley( [description] vpacket_collection : [type] [description] + numba_radial_1d_geometry : [type] + [description] numba_model : [type] [description] numba_plasma : [type] @@ -218,8 +233,10 @@ def trace_vpacket_volley( return ### TODO theoretical check for r_packet nu within vpackets bins - is done somewhere else I think - if r_packet.r > numba_model.r_inner[0]: # not on inner_boundary - r_inner_over_r = numba_model.r_inner[0] / r_packet.r + if ( + r_packet.r > numba_radial_1d_geometry.r_inner[0] + ): # not on inner_boundary + r_inner_over_r = numba_radial_1d_geometry.r_inner[0] / r_packet.r mu_min = -math.sqrt(1 - r_inner_over_r * r_inner_over_r) v_packet_on_inner_boundary = False if montecarlo_configuration.full_relativity: @@ -230,6 +247,11 @@ def trace_vpacket_volley( v_packet_on_inner_boundary = True mu_min = 0.0 + if montecarlo_configuration.full_relativity: + inv_c = 1 / C_SPEED_OF_LIGHT + inv_t = 1 / numba_model.time_explosion + beta_inner = numba_radial_1d_geometry.r_inner[0] * inv_t * inv_c + mu_bin = (1.0 - mu_min) / no_of_vpackets r_packet_doppler_factor = get_doppler_factor( r_packet.r, r_packet.mu, numba_model.time_explosion @@ -238,7 +260,16 @@ def trace_vpacket_volley( v_packet_mu = mu_min + i * mu_bin + np.random.random() * mu_bin if v_packet_on_inner_boundary: # The weights are described in K&S 2014 - weight = 2 * v_packet_mu / no_of_vpackets + if not montecarlo_configuration.full_relativity: + weight = 2 * v_packet_mu / no_of_vpackets + else: + weight = ( + 2 + * (v_packet_mu + beta_inner) + / (2 * beta_inner + 1) + / no_of_vpackets + ) + else: weight = (1 - mu_min) / (2 * no_of_vpackets) @@ -272,7 +303,9 @@ def trace_vpacket_volley( i, ) - tau_vpacket = trace_vpacket(v_packet, numba_model, numba_plasma) + tau_vpacket = trace_vpacket( + v_packet, numba_radial_1d_geometry, numba_model, numba_plasma + ) v_packet.energy *= math.exp(-tau_vpacket) diff --git a/tardis/montecarlo/packet_source.py b/tardis/montecarlo/packet_source.py index 78bcc275b8c..3a42679586e 100644 --- a/tardis/montecarlo/packet_source.py +++ b/tardis/montecarlo/packet_source.py @@ -53,7 +53,9 @@ def create_uniform_packet_energies(no_of_packets, rng): return np.ones(no_of_packets) / no_of_packets @staticmethod - def create_blackbody_packet_nus(T, no_of_packets, rng, l_samples=1000): + def create_blackbody_packet_nus( + temperature, no_of_packets, rng, l_samples=1000 + ): """ Create packet :math:`\\nu` distributed using the algorithm described in Bjorkman & Wood 2001 (page 4) which references @@ -61,27 +63,21 @@ def create_blackbody_packet_nus(T, no_of_packets, rng, l_samples=1000): First, generate a uniform random number, :math:`\\xi_0 \\in [0, 1]` and determine the minimum value of :math:`l, l_{\\rm min}`, that satisfies the condition - .. math:: \\sum_{i=1}^{l} i^{-4} \\ge {{\\pi^4}\\over{90}} m_0 \\;. - Next obtain four additional uniform random numbers (in the range 0 to 1) :math:`\\xi_1, \\xi_2, \\xi_3, {\\rm and } \\xi_4`. Finally, the packet frequency is given by - .. math:: x = -\\ln{(\\xi_1\\xi_2\\xi_3\\xi_4)}/l_{\\rm min}\\;. - where :math:`x=h\\nu/kT` - Parameters ---------- - T : float - temperature + temperature : float + Absolute Temperature. no_of_packets : int l_samples : int number of l_samples needed in the algorithm - Returns ------- array of frequencies: numpy.ndarray @@ -100,7 +96,7 @@ def create_blackbody_packet_nus(T, no_of_packets, rng, l_samples=1000): xis_prod = np.prod(xis[1:], 0) x = ne.evaluate("-log(xis_prod)/l") - return x * (const.k_B.cgs.value * T) / const.h.cgs.value + return x * (const.k_B.cgs.value * temperature) / const.h.cgs.value class BlackBodySimpleSource(BasePacketSource): @@ -109,13 +105,12 @@ class BlackBodySimpleSource(BasePacketSource): part. """ - def create_packets(self, T, no_of_packets, rng, radius): + def create_packets(self, temperature, no_of_packets, rng, radius): """Generate black-body packet properties as arrays Parameters ---------- - T : float64 - Temperature + temperature : float64 no_of_packets : int Number of packets rng : numpy random number generator @@ -134,8 +129,83 @@ def create_packets(self, T, no_of_packets, rng, radius): Packet energies """ radii = np.ones(no_of_packets) * radius - nus = self.create_blackbody_packet_nus(T, no_of_packets, rng) + nus = self.create_blackbody_packet_nus(temperature, no_of_packets, rng) mus = self.create_zero_limb_darkening_packet_mus(no_of_packets, rng) energies = self.create_uniform_packet_energies(no_of_packets, rng) return radii, nus, mus, energies + + +class BlackBodySimpleSourceRelativistic(BlackBodySimpleSource): + def create_packets( + self, temperature, no_of_packets, rng, radius, time_explosion + ): + """Generate relativistic black-body packet properties as arrays + + Parameters + ---------- + temperature : float64 + Absolute Temperature + no_of_packets : int + Number of packets + rng : numpy random number generator + radius : float64 + Initial packet radius + time_explosion: float64 + Time elapsed since explosion + + Returns + ------- + array + Packet radii + array + Packet frequencies + array + Packet directions + array + Packet energies + """ + self.beta = ((radius / time_explosion) / const.c).to("") + return super().create_packets(temperature, no_of_packets, rng, radius) + + def create_zero_limb_darkening_packet_mus(self, no_of_packets, rng): + """ + Create zero-limb-darkening packet :math:`\mu^\prime` distributed + according to :math:`\\mu^\\prime=2 \\frac{\\mu^\\prime + \\beta}{2 \\beta + 1}`. + The complicated distribution is due to the fact that the inner boundary + on which the packets are initialized is not comoving with the material. + + Parameters + ---------- + no_of_packets : int + number of packets to be created + """ + z = rng.random(no_of_packets) + beta = self.beta + return -beta + np.sqrt(beta**2 + 2 * beta * z + z) + + def create_uniform_packet_energies(self, no_of_packets, rng): + """ + Uniformly distribute energy in arbitrary units where the ensemble of + packets has energy of 1 multiplied by relativistic correction factors. + + Parameters + ---------- + no_of_packets : int + number of packets + + Returns + ------- + energies for packets : numpy.ndarray + """ + beta = self.beta + gamma = 1.0 / np.sqrt(1 - beta**2) + static_inner_boundary2cmf_factor = (2 * beta + 1) / (1 - beta**2) + energies = np.ones(no_of_packets) / no_of_packets + # In principle, the factor gamma should be applied to the time of + # simulation to account for time dilation between the lab and comoving + # frame. However, all relevant quantities (luminosities, estimators, ...) + # are calculated as ratios of packet energies and the time of simulation. + # Thus, we can absorb the factor gamma in the packet energies, which is + # more convenient. + return energies * static_inner_boundary2cmf_factor / gamma diff --git a/tardis/plasma/__init__.py b/tardis/plasma/__init__.py index 67591ed64b5..ec0d4cd7358 100644 --- a/tardis/plasma/__init__.py +++ b/tardis/plasma/__init__.py @@ -1 +1,5 @@ +""" +Dealing with plasma properties and calculations related to it. +""" + from tardis.plasma.base import BasePlasma diff --git a/tardis/plasma/properties/__init__.py b/tardis/plasma/properties/__init__.py index 1ffcfba81aa..8ec73b81bcb 100644 --- a/tardis/plasma/properties/__init__.py +++ b/tardis/plasma/properties/__init__.py @@ -1,3 +1,10 @@ +""" +Store and calculate the properties of the plasma. + +Each plasma object has an array of properties which are then used to calculate plasma parameter values. +Every property has a calculate function that returns the values of its outputs. +""" + from tardis.plasma.properties.atomic import * from tardis.plasma.properties.general import * from tardis.plasma.properties.ion_population import * @@ -10,3 +17,5 @@ from tardis.plasma.properties.continuum_processes import * from tardis.plasma.properties.transition_probabilities import * from tardis.plasma.properties.helium_nlte import * +from tardis.plasma.properties.rate_matrix_index import * +from tardis.plasma.properties.nlte_rate_equation_solver import * diff --git a/tardis/plasma/properties/atomic.py b/tardis/plasma/properties/atomic.py index d073c70030b..236edb01ecc 100644 --- a/tardis/plasma/properties/atomic.py +++ b/tardis/plasma/properties/atomic.py @@ -632,7 +632,7 @@ def _filter_atomic_property(self, zeta_data, selected_atoms): zeta_data_check = counter(zeta_data.atomic_number.values) keys = np.array(list(zeta_data_check.keys())) values = np.array(zeta_data_check.values()) - if np.alltrue(keys + 1 == values): + if np.alltrue(keys + 1 == values) and keys: return zeta_data else: # raise IncompleteAtomicData('zeta data') diff --git a/tardis/plasma/properties/continuum_processes.py b/tardis/plasma/properties/continuum_processes.py index 640568e3764..48f003a0d00 100644 --- a/tardis/plasma/properties/continuum_processes.py +++ b/tardis/plasma/properties/continuum_processes.py @@ -990,9 +990,9 @@ def calculate(self, t_electrons): @njit(error_model="numpy", fastmath=True) def nu_ff(shell): - T = t_electrons[shell] + temperature = t_electrons[shell] zrand = np.random.random() - return -K_B * T / H * np.log(zrand) + return -K_B * temperature / H * np.log(zrand) return nu_ff diff --git a/tardis/plasma/properties/nlte_rate_equation_solver.py b/tardis/plasma/properties/nlte_rate_equation_solver.py new file mode 100644 index 00000000000..b1d82a94d7f --- /dev/null +++ b/tardis/plasma/properties/nlte_rate_equation_solver.py @@ -0,0 +1,701 @@ +import pandas as pd +import numpy as np +from scipy.optimize import root + +from tardis.plasma.properties.base import ProcessingPlasmaProperty + +__all__ = [ + "NLTERateEquationSolver", +] + + +class NLTERateEquationSolver(ProcessingPlasmaProperty): + outputs = ("ion_number_density_nlte", "electron_densities_nlte") + + def calculate( + self, + gamma, + alpha_sp, + alpha_stim, + coll_ion_coeff, + coll_recomb_coeff, + partition_function, + levels, + level_boltzmann_factor, + phi, + rate_matrix_index, + number_density, + ): + """Calculates ion number densities and electron densities using NLTE ionization. + + Parameters + ---------- + gamma : pandas.DataFrame + The rate coefficient for radiative ionization. + alpha_sp : pandas.DataFrame + The rate coefficient for spontaneous recombination. + alpha_stim : pandas.DataFrame + The rate coefficient for stimulated recombination. + coll_ion_coeff : pandas.DataFrame + The rate coefficient for collisional ionization in the Seaton + approximation. + coll_recomb_coeff : pandas.DataFrame + The rate coefficient for collisional recombination. + partition_function : pandas.DataFrame + General partition function. Indexed by atomic number, ion number. + levels : MultiIndex + (atomic_number, ion_number, level_number) + Index of filtered atomic data. + level_boltzmann_factor : pandas.DataFrame + General Boltzmann factor. + phi : pandas.DataFrame + Saha Factors. + rate_matrix_index : MultiIndex + (atomic_number, ion_number, treatment type) + If ion is treated in LTE or nebular ionization, 3rd index is "lte_ion", + if treated in NLTE ionization, 3rd index is "nlte_ion". + number_density : pandas.DataFrame + Number density in each shell for each species. + + Returns + ------- + ion_number_densities_nlte : pandas.DataFrame + Number density with NLTE ionization treatment. + electron_densities_nlte : Series + Electron density with NLTE ionization treatment. + """ + + ( + total_photo_ion_coefficients, + total_rad_recomb_coefficients, + total_coll_ion_coefficients, + total_coll_recomb_coefficients, + ) = self.prepare_ion_recomb_coefficients_nlte_ion( + gamma, + alpha_sp, + alpha_stim, + coll_ion_coeff, + coll_recomb_coeff, + partition_function, + levels, + level_boltzmann_factor, + ) + + initial_electron_densities = number_density.sum(axis=0) + atomic_numbers = ( + rate_matrix_index.get_level_values("atomic_number") + .unique() + .drop("n_e") + ) # dropping the n_e index, as rate_matrix_index's first index is (atomic_numbers, "n_e") + + index = rate_matrix_index.droplevel("level_number").drop("n_e") + ion_number_density_nlte = pd.DataFrame( + 0.0, index=index, columns=phi.columns + ) + electron_densities_nlte = pd.Series(0.0, index=phi.columns) + + for shell in phi.columns: + solution_vector = self.prepare_solution_vector( + number_density[shell] + ) + first_guess = self.prepare_first_guess( + atomic_numbers, + number_density[shell], + initial_electron_densities[shell], + ) + solution = root( + self.population_objective_function, + first_guess, + args=( + atomic_numbers, + phi[shell], + solution_vector, + rate_matrix_index, + total_photo_ion_coefficients[shell], + total_rad_recomb_coefficients[shell], + total_coll_ion_coefficients[shell], + total_coll_recomb_coefficients[shell], + ), + jac=True, + ) + assert solution.success + ion_number_density_nlte[shell] = solution.x[:-1] + electron_densities_nlte[shell] = solution.x[-1] + # TODO: change the jacobian and rate matrix to use shell id and get coefficients from the attribute of the class. + return ion_number_density_nlte, electron_densities_nlte + + @staticmethod + def calculate_rate_matrix( + atomic_numbers, + phi_shell, + electron_density, + rate_matrix_index, + total_photo_ion_coefficients, + total_rad_recomb_coefficients, + total_coll_ion_coefficients, + total_coll_recomb_coefficients, + ): + """ + + Parameters + ---------- + phi_shell : pandas.DataFrame + Saha Factors in the current shell + electron_density : float + Guess for electron density in the current shell + rate_matrix_index : pandas.MultiIndex + Index used for constructing the rate matrix + total_photo_ion_coefficients : pandas.DataFrame + Photo ionization coefficients + total_rad_recomb_coefficients : pandas.DataFrame + Radiative recombination coefficients (should get multiplied by electron density) + total_coll_ion_coefficients : pandas.DataFrame + Collisional ionization coefficients (should get multiplied by electron density) + total_coll_recomb_coefficients : pandas.DataFrame + Collisional recombination coefficients (should get multiplied by electron density^2) + + Returns + ------- + pandas.DataFrame + Rate matrix used for NLTE solver. + """ + rate_matrix = pd.DataFrame( + 0.0, columns=rate_matrix_index, index=rate_matrix_index + ) + total_rad_recomb_coefficients = ( + total_rad_recomb_coefficients * electron_density + ) + total_coll_ion_coefficients = ( + total_coll_ion_coefficients * electron_density + ) + total_coll_recomb_coefficients = ( + total_coll_recomb_coefficients * electron_density**2 + ) + for atomic_number in atomic_numbers: + ion_numbers = rate_matrix.loc[atomic_number].index.get_level_values( + "ion_number" + ) + phi_block = phi_shell.loc[atomic_number] + rate_matrix_block = NLTERateEquationSolver.lte_rate_matrix_block( + phi_block, electron_density + ) + + nlte_ion_numbers = ion_numbers[ + rate_matrix.loc[atomic_number].index.get_level_values( + "level_number" + ) + == "nlte_ion" + ] + # >>> lte_ion_numbers is for future use in NLTE excitation treatment + lte_ion_numbers = ion_numbers[ + rate_matrix.loc[atomic_number].index.get_level_values( + "level_number" + ) + == "lte_ion" + ] + # <<< + for ion_number in nlte_ion_numbers: + rate_matrix_block = NLTERateEquationSolver.set_nlte_ion_rate( + rate_matrix_block, + atomic_number, + ion_number, + total_rad_recomb_coefficients.loc[(atomic_number,)], + total_photo_ion_coefficients.loc[(atomic_number,)], + total_coll_ion_coefficients.loc[(atomic_number,)], + total_coll_recomb_coefficients.loc[(atomic_number,)], + ) + rate_matrix.loc[ + (atomic_number, slice(None)), (atomic_number) + ] = rate_matrix_block + + charge_conservation_row = ( + NLTERateEquationSolver.prepare_charge_conservation_row( + atomic_numbers + ) + ) + rate_matrix.loc[("n_e", slice(None))] = charge_conservation_row + return rate_matrix + + @staticmethod + def set_nlte_ion_rate( + rate_matrix_block, + atomic_number, + ion_number, + total_rad_recomb_coefficients, + total_photo_ion_coefficients, + total_coll_ion_coefficients, + total_coll_recomb_coefficients, + ): + """Calculates the row for the species treated in NLTE ionization + + Parameters + ---------- + rate_matrix_block : numpy.array + The diagonal block corresponding to current atomic number. + atomic_number : int + Current atomic number + ion_number : int + Current ion number + total_rad_recomb_coefficients : pandas.DataFrame + Rad. recomb. coefficients for current atomic number + total_photo_ion_coefficients : pandas.DataFrame + Photo ionization coefficients for current atomic number + total_coll_ion_coefficients : pandas.DataFrame + Collisional ionization coefficients for current atomic number + total_coll_recomb_coefficients : pandas.DataFrame + Collisional recombination coefficients for current atomic number + + Returns + ------- + numpy.array + Rate matrix block with a changed row for NLTE ionization treatment + """ + ion_coefficients = ( + total_photo_ion_coefficients + total_coll_ion_coefficients + ) + recomb_coefficients = ( + total_rad_recomb_coefficients + total_coll_recomb_coefficients + ) + if atomic_number != ion_number: + ion_coeff_matrix_ion_row = NLTERateEquationSolver.ion_matrix( + ion_coefficients, atomic_number, ion_number + ) + recomb_coeff_matrix_ion_row = NLTERateEquationSolver.recomb_matrix( + recomb_coefficients, atomic_number, ion_number + ) + rate_matrix_block[ion_number, :] = ( + ion_coeff_matrix_ion_row + recomb_coeff_matrix_ion_row + ) + return rate_matrix_block + + @staticmethod + def lte_rate_matrix_block(phi_block, electron_density): + """Creates the generic LTE block for rate matrix. + + Parameters + ---------- + phi_block : pandas.DataFrame + Saha Factors for current atomic number + electron_density : float + Current guess for electron density + + Returns + ------- + numpy.array + LTE block for rate matrix + """ + lte_rate_vector_block = -1.0 * np.hstack([*phi_block.values, -1.0]) + lte_rate_matrix_block = np.diag(lte_rate_vector_block) + n_e_initial = np.ones(len(phi_block)) * electron_density + n_e_matrix = np.diag(n_e_initial, 1) + lte_rate_matrix_block += n_e_matrix + lte_rate_matrix_block[-1, :] = 1.0 + return lte_rate_matrix_block + + @staticmethod + def prepare_phi(phi): + """ + Makes sure that phi does not have any 0 entries. + """ + phi[phi == 0.0] = 1.0e-10 * phi[phi > 0.0].min().min() + return phi + + @staticmethod + def recomb_matrix(recomb_coefficients, atomic_number, ion_number): + """Constructs a recombination rate matrix from the recombination rates. + + Parameters + ---------- + recomb_coefficients : pandas.DataFrame + Recombination coefficients. + atomic_number : int64 + Current atomic number. Used for the dimension of a square matrix. + ion_number : int64 + Current ion number. Used for returning the correct row. + + Returns + ------- + numpy.ndarray + """ + offdiag = np.zeros(atomic_number) + index = recomb_coefficients.index + for i in index: + offdiag[i] = recomb_coefficients.loc[i] + diag = np.hstack([np.zeros(1), -offdiag]) + return (np.diag(diag) + np.diag(offdiag, k=1))[ion_number, :] + + @staticmethod + def ion_matrix(ion_coefficients, atomic_number, ion_number): + """Constructs an ionization rate matrix from the ionization rates. + + Parameters + ---------- + ion_coefficients : pandas.DataFrame + Recombination coefficients. + atomic_number : int64 + Current atomic number. Used for the dimension of a square matrix. + ion_number : int64 + Current ion number. Used for returning the correct row. + + Returns + ------- + numpy.ndarray + """ + offdiag = np.zeros(atomic_number) + index = ion_coefficients.index + for i in index: + offdiag[i] = ion_coefficients.loc[i] + diag = np.hstack([-offdiag, np.zeros(1)]) + return (np.diag(diag) + np.diag(offdiag, k=-1))[ion_number, :] + + @staticmethod + def prepare_charge_conservation_row(atomic_numbers): + """Prepares the last row of the rate_matrix. This row corresponds to the charge + density equation.""" + charge_conservation_row = [] + for atomic_number in atomic_numbers: + charge_conservation_row.append(np.arange(0, atomic_number + 1)) + charge_conservation_row = np.hstack([*charge_conservation_row, -1]) + # TODO needs to be modified for use in nlte_excitation + return charge_conservation_row + + @staticmethod + def prepare_ion_recomb_coefficients_nlte_ion( + gamma, + alpha_sp, + alpha_stim, + coll_ion_coeff, + coll_recomb_coeff, + partition_function, + levels, + level_boltzmann_factor, + ): + """ + Prepares the ionization and recombination coefficients by grouping them for + ion numbers. + + Parameters + ---------- + gamma : pandas.DataFrame + The rate coefficient for radiative ionization. + alpha_sp : pandas.DataFrame + The rate coefficient for spontaneous recombination. + alpha_stim : pandas.DataFrame + The rate coefficient for stimulated recombination. + coll_ion_coeff : pandas.DataFrame + The rate coefficient for collisional ionization in the Seaton + approximation. + coll_recomb_coeff : pandas.DataFrame + The rate coefficient for collisional recombination. + partition_function : pandas.DataFrame + General partition function. Indexed by atomic number, ion number. + levels : MultiIndex + (atomic_number, ion_number, level_number) + Index of filtered atomic data. + level_boltzmann_factor : pandas.DataFrame + General Boltzmann factor. + Returns + ------- + total_photo_ion_coefficients + Photoionization coefficients grouped by atomic number and ion number. + total_rad_recomb_coefficients + Radiative recombination coefficients grouped by atomic number and ion number. + total_coll_ion_coefficients + Collisional ionization coefficients grouped by atomic number and ion number. + total_coll_recomb_coefficients + Collisional recombination coefficients grouped by atomic number and ion number. + """ + indexer = pd.Series( + np.arange(partition_function.shape[0]), + index=partition_function.index, + ) + _ion2level_idx = indexer.loc[levels.droplevel("level_number")].values + partition_function_broadcast = partition_function.values[_ion2level_idx] + level_population_fraction = pd.DataFrame( + level_boltzmann_factor.values / partition_function_broadcast, + index=levels, + ) + total_photo_ion_coefficients = ( + (level_population_fraction.loc[gamma.index] * gamma) + .groupby(level=("atomic_number", "ion_number")) + .sum() + ) + total_rad_recomb_coefficients = ( + (alpha_sp + alpha_stim) + .groupby(level=["atomic_number", "ion_number"]) + .sum() + ) + total_coll_ion_coefficients = ( + ( + level_population_fraction.loc[coll_ion_coeff.index] + * coll_ion_coeff + ) + .groupby(level=("atomic_number", "ion_number")) + .sum() + ) + total_coll_recomb_coefficients = ( + (coll_recomb_coeff) + .groupby(level=("atomic_number", "ion_number")) + .sum() + ) + return ( + total_photo_ion_coefficients, + total_rad_recomb_coefficients, + total_coll_ion_coefficients, + total_coll_recomb_coefficients, + ) + + @staticmethod + def jacobian_matrix( + atomic_numbers, + populations, + rate_matrix, + rate_matrix_index, + total_rad_recomb_coefficients, + total_coll_ion_coefficients, + total_coll_recomb_coefficients, + ): + """Creates the jacobian matrix used for NLTE ionization solver + + Parameters + ---------- + populations : numpy.array + Ion populations, electron density + rate_matrix : pandas.DataFrame + Rate matrix used for NLTE solver. + rate_matrix_index : MultiIndex + (atomic_number, ion_number, treatment type) + If ion is treated in LTE or nebular ionization, 3rd index is "lte_ion", + if treated in NLTE ionization, 3rd index is "nlte_ion". + total_rad_recomb_coefficients : pandas.DataFrame + Radiative recombination coefficients grouped by atomic number and ion number. + total_coll_ion_coefficients : pandas.DataFrame + Collisional ionization coefficients(should get multiplied by electron density). + total_coll_recomb_coefficients : pandas.DataFrame + Collisional recombination coefficients(should get multiplied by electron density). + + Returns + ------- + numpy.array + Jacobian matrix used for NLTE ionization solver + """ + # TODO: for future use, can be vectorized. + index = 0 + jacobian_matrix = rate_matrix.copy().values + jacobian_matrix[:-1, -1] = populations[1:] + for atomic_number in atomic_numbers: + for i in range(index, index + atomic_number): + if rate_matrix_index[i][2] == "nlte_ion": + jacobian_matrix[ + i, -1 + ] = NLTERateEquationSolver.deriv_matrix_block( + atomic_number, + total_rad_recomb_coefficients.loc[(atomic_number,)], + total_coll_ion_coefficients.loc[(atomic_number,)], + total_coll_recomb_coefficients.loc[(atomic_number,)], + populations[index : index + atomic_number + 1], + populations[-1], + )[ + i - index + ] + index += atomic_number + 1 + jacobian_matrix[index - 1, -1] = 0 # number conservation row + return jacobian_matrix + + @staticmethod + def deriv_matrix_block( + atomic_number, + total_rad_recomb_coefficients, + total_coll_ion_coefficients, + total_coll_recomb_coefficients, + current_ion_number_densities, + current_electron_density, + ): + """Calculates the dot product of the derivative of rate matrix and ion number densities+electron density column. + + Parameters + ---------- + atomic_number : int64 + Current atomic number + total_rad_recomb_coefficients : pandas.DataFrame + Radiative recombination coefficients grouped by atomic number and ion number. + total_coll_ion_coefficients : pandas.DataFrame + Collisional ionization coefficients. + total_coll_recomb_coefficients : pandas.DataFrame + Collisional recombination coefficients. + current_ion_number_densities : numpy.array + Current ion number densities for the current atomic number. + current_electron_density : float64 + Current electron density + + Returns + ------- + numpy.array + Returns the part of the last column of the jacobian matrix, corresponding to atomic number. + """ + ion_numbers = np.arange(0, atomic_number) + radiative_rate_coeff_matrix = NLTERateEquationSolver.recomb_matrix( + total_rad_recomb_coefficients, atomic_number, ion_numbers + ) + coll_recomb_matrix = ( + NLTERateEquationSolver.recomb_matrix( + total_coll_recomb_coefficients, atomic_number, ion_numbers + ) + * current_electron_density + * 2 + ) + coll_ion_coeff_matrix = NLTERateEquationSolver.ion_matrix( + total_coll_ion_coefficients, atomic_number, ion_numbers + ) + deriv_matrix = ( + radiative_rate_coeff_matrix + + coll_ion_coeff_matrix + + coll_recomb_matrix + ) + return np.dot(deriv_matrix, current_ion_number_densities) + + def prepare_first_guess( + self, atomic_numbers, number_density, electron_density + ): + """Constructs a first guess for ion number densities and electron density, where all species are singly ionized. + + Parameters + ---------- + atomic_numbers : numpy.array + All atomic numbers present in the plasma. + number_density : pandas.DataFrame + Number density of present species. + electron_density : float + Current value of electron density. + + Returns + ------- + numpy.array + Guess for ion number densities and electron density. + """ + # TODO needs to be changed for excitation + array_size = (number_density.index.values + 1).sum() + 1 + first_guess = np.zeros(array_size) + index = 1 + for atomic_number in atomic_numbers: + first_guess[index] = number_density.loc[atomic_number] + index += atomic_number + 1 + first_guess[-1] = electron_density + return first_guess + + def population_objective_function( + self, + populations, + atomic_numbers, + phi, + solution_vector, + rate_matrix_index, + total_photo_ion_coefficients, + total_rad_recomb_coefficients, + total_coll_ion_coefficients, + total_coll_recomb_coefficients, + ): + """Main set of equations for the NLTE ionization solver. + + To solve the statistical equilibrium equations, we need to find the root + of the objective function A*x - B, where x are the populations, + A is the matrix of rates, and B is the solution vector. + + Parameters + ---------- + populations : numpy.array + Current values of ion number densities and electron density. + atomic_numbers : numpy.array + All atomic numbers present in the plasma. + phi : pandas.DataFrame + Saha Factors of the current shell. + solution_vector : numpy.array + Solution vector for the set of equations. + rate_matrix_index : pandas.MultiIndex + (atomic_number, ion_number, treatment type) + If ion is treated in LTE or nebular ionization, 3rd index is "lte_ion", + if treated in NLTE ionization, 3rd index is "nlte_ion". + total_photo_ion_coefficients : pandas.DataFrame + Photo ion. coefficients for current atomic number + total_rad_recomb_coefficients : pandas.DataFrame + Radiative recombination coefficients for current atomic number + total_coll_ion_coefficients : pandas.DataFrame + Collisional ionization coefficients for current atomic number + total_coll_recomb_coefficients : pandas.DataFrame + Coll. recomb. coefficients for current atomic number + Returns + ------- + (numpy.array, numpy.array) + Returns the objective function and jacobian of the rate matrix in a tuple. + """ + electron_density = populations[-1] + rate_matrix = self.calculate_rate_matrix( + atomic_numbers, + phi, + electron_density, + rate_matrix_index, + total_photo_ion_coefficients, + total_rad_recomb_coefficients, + total_coll_ion_coefficients, + total_coll_recomb_coefficients, + ) + jacobian_matrix = self.jacobian_matrix( + atomic_numbers, + populations, + rate_matrix, + rate_matrix_index, + total_rad_recomb_coefficients, + total_coll_ion_coefficients, + total_coll_recomb_coefficients, + ) + return ( + np.dot(rate_matrix.values, populations) - solution_vector, + jacobian_matrix, + ) + + def solution_vector_block(self, atomic_number, number_density): + """Block of the solution vector for the current atomic number. + + Block for the solution vector has the form (0, 0, ..., 0, number_density). + Length is equal to atomic_number+1. + + Parameters + ---------- + atomic_number : int + Current atomic number. + number_density : float + Number density of the current atomic number. + + Returns + ------- + numpy.array + Block of the solution vector corresponding to the current atomic number. + """ + solution_vector = np.zeros(atomic_number + 1) + solution_vector[-1] = number_density + return solution_vector + + def prepare_solution_vector(self, number_density): + """Constructs the solution vector for the NLTE ionization solver set of equations by combining + all solution verctor blocks. + + Parameters + ---------- + number_density : pandas.DataFrame + Number densities of all present species. + + Returns + ------- + numpy.array + Solution vector for the NLTE ionization solver. + """ + atomic_numbers = number_density.index + solution_array = [] + for atomic_number in atomic_numbers: + solution_array.append( + self.solution_vector_block( + atomic_number, number_density.loc[atomic_number] + ) + ) + solution_vector = np.hstack(solution_array + [0]) + return solution_vector diff --git a/tardis/plasma/properties/plasma_input.py b/tardis/plasma/properties/plasma_input.py index 12ff405e09e..2d7b67ca4d6 100644 --- a/tardis/plasma/properties/plasma_input.py +++ b/tardis/plasma/properties/plasma_input.py @@ -15,6 +15,8 @@ "TInner", "Volume", "ContinuumInteractionSpecies", + "NLTEIonizationSpecies", + "NLTEExcitationSpecies", ] @@ -148,3 +150,13 @@ class ContinuumInteractionSpecies(Input): """ outputs = ("continuum_interaction_species",) + + +class NLTEIonizationSpecies(Input): + + outputs = ("nlte_ionization_species",) + + +class NLTEExcitationSpecies(Input): + + outputs = ("nlte_excitation_species",) diff --git a/tardis/plasma/properties/property_collections.py b/tardis/plasma/properties/property_collections.py index a7cbcffa5b3..9716bda572b 100644 --- a/tardis/plasma/properties/property_collections.py +++ b/tardis/plasma/properties/property_collections.py @@ -16,6 +16,8 @@ class PlasmaPropertyCollection(list): LinkTRadTElectron, HeliumTreatment, ContinuumInteractionSpecies, + NLTEIonizationSpecies, + NLTEExcitationSpecies, ] ) basic_properties = PlasmaPropertyCollection( @@ -57,6 +59,9 @@ class PlasmaPropertyCollection(list): BetaSobolev, ] ) +nlte_solver_properties = PlasmaPropertyCollection( + [NLTEIndexHelper, NLTERateEquationSolver] +) helium_nlte_properties = PlasmaPropertyCollection( [ HeliumNLTE, diff --git a/tardis/plasma/properties/rate_matrix_index.py b/tardis/plasma/properties/rate_matrix_index.py new file mode 100644 index 00000000000..ab16121b57f --- /dev/null +++ b/tardis/plasma/properties/rate_matrix_index.py @@ -0,0 +1,65 @@ +import pandas as pd +from tardis.plasma.properties.base import ProcessingPlasmaProperty + +__all__ = [ + "NLTEIndexHelper", +] + + +class NLTEIndexHelper(ProcessingPlasmaProperty): + outputs = ("rate_matrix_index",) + + def __init__( + self, + plasma_parent, + nlte_ionization_species=0, + nlte_excitation_species=0, + ): + super().__init__(plasma_parent) + self.nlte_ionization_species = nlte_ionization_species + self.nlte_excitation_species = nlte_excitation_species + + def calculate( + self, levels, nlte_ionization_species, nlte_excitation_species + ): + """Generates rate_matrix_index using levels and changing the last index(level) to + "lte_ion" if that ion_number is treated in LTE or nebular, "nlte_ion" for NLTE ionization and + keeps the levels for the rest. + + Parameters + ---------- + levels : MultiIndex + (Atomic number, Ion number, Level) + nlte_ionization_species : list + List of tuples for (atomic number, ion number) which are treated in NLTE ionization. + + Returns + ------- + MultiIndex + """ + nlte_excitation_species = [] # not yet implemented + rate_matrix_index = pd.MultiIndex.from_tuples( + list( + self.calculate_rate_matrix_index( + levels, + nlte_ionization_species, + nlte_excitation_species, + ) + ), + names=levels.names, + ).drop_duplicates() + return rate_matrix_index + + def calculate_rate_matrix_index( + self, levels, nlte_ionization_species, nlte_excitation_species=[] + ): + for level in levels: + if level[:2] in nlte_ionization_species: + yield (*level[:2], "nlte_ion") + elif (level[:2] not in nlte_ionization_species) and ( + level[:2] not in nlte_excitation_species + ): + yield (*level[:2], "lte_ion") + else: + yield level + yield ("n_e", "n_e", "n_e") diff --git a/tardis/plasma/properties/transition_probabilities.py b/tardis/plasma/properties/transition_probabilities.py index fa0c386c375..9def7e650df 100644 --- a/tardis/plasma/properties/transition_probabilities.py +++ b/tardis/plasma/properties/transition_probabilities.py @@ -357,7 +357,9 @@ def calculate( deactivation_channel_probs = p_deactivation.copy() deactivation_channel_probs = pd.concat( [ - level_idxs2transition_idx.loc[deactivation_channel_probs.index], + level_idxs2transition_idx.reindex( + deactivation_channel_probs.index + ), deactivation_channel_probs, ], axis=1, diff --git a/tardis/plasma/properties/util/__init__.py b/tardis/plasma/properties/util/__init__.py index 8b137891791..9aec5b1c60a 100644 --- a/tardis/plasma/properties/util/__init__.py +++ b/tardis/plasma/properties/util/__init__.py @@ -1 +1,3 @@ - +""" +Calculating transition probabilities for macro_atom interactions. +""" diff --git a/tardis/plasma/standard_plasmas.py b/tardis/plasma/standard_plasmas.py index 696918402a3..4961d0c6dd6 100644 --- a/tardis/plasma/standard_plasmas.py +++ b/tardis/plasma/standard_plasmas.py @@ -5,6 +5,7 @@ import pandas as pd from tardis.io.atom_data import AtomData +from tardis.plasma.properties.rate_matrix_index import NLTEIndexHelper from tardis.util.base import species_string_to_tuple from tardis.plasma import BasePlasma from tardis.plasma.properties.base import TransitionProbabilitiesProperty @@ -28,6 +29,7 @@ adiabatic_cooling_properties, two_photon_properties, isotope_properties, + nlte_solver_properties, ) from tardis.plasma.exceptions import PlasmaConfigError @@ -123,6 +125,15 @@ def assemble_plasma(config, model, atom_data=None): "in the configuration." ) + nlte_ionization_species = [ + species_string_to_tuple(s) + for s in config.plasma.nlte_ionization_species + ] + nlte_excitation_species = [ + species_string_to_tuple(s) + for s in config.plasma.nlte_excitation_species + ] + kwargs = dict( t_rad=model.t_radiative, abundance=model.abundance, @@ -132,6 +143,8 @@ def assemble_plasma(config, model, atom_data=None): w=model.dilution_factor, link_t_rad_t_electron=config.plasma.link_t_rad_t_electron, continuum_interaction_species=continuum_interaction_species, + nlte_ionization_species=nlte_ionization_species, + nlte_excitation_species=nlte_excitation_species, ) plasma_modules = basic_inputs + basic_properties @@ -167,6 +180,33 @@ def assemble_plasma(config, model, atom_data=None): property_kwargs[MarkovChainTransProbsCollector] = { "inputs": transition_probabilities_outputs } + if ( + config.plasma.nlte_ionization_species + or config.plasma.nlte_excitation_species + ): + if config.plasma.nlte_ionization_species: + nlte_ionization_species = config.plasma.nlte_ionization_species + for species in nlte_ionization_species: + if not ( + species in config.plasma.continuum_interaction.species + ): + raise PlasmaConfigError( + f"NLTE ionization species {species} not in continuum species." + ) + if config.plasma.nlte_excitation_species: + nlte_excitation_species = config.plasma.nlte_excitation_species + for species in nlte_excitation_species: + if not ( + species in config.plasma.continuum_interaction.species + ): + raise PlasmaConfigError( + f"NLTE excitation species {species} not in continuum species." + ) + property_kwargs[NLTEIndexHelper] = { + "nlte_ionization_species": config.plasma.nlte_ionization_species, + "nlte_excitation_species": config.plasma.nlte_excitation_species, + } + plasma_modules += nlte_solver_properties kwargs.update( gamma_estimator=None, diff --git a/tardis/plasma/tests/test_nlte_solver.py b/tardis/plasma/tests/test_nlte_solver.py new file mode 100644 index 00000000000..7062a1d01cb --- /dev/null +++ b/tardis/plasma/tests/test_nlte_solver.py @@ -0,0 +1,318 @@ +import os + +import pytest +import numpy as np +import pandas as pd +from copy import deepcopy +from numpy.testing import assert_allclose, assert_almost_equal +from tardis.io.config_reader import Configuration +from tardis.model.base import Radial1DModel +from tardis.plasma.properties import NLTERateEquationSolver +from tardis.io.atom_data.base import AtomData +from tardis.plasma.properties.ion_population import IonNumberDensity +from tardis.plasma.standard_plasmas import assemble_plasma + + +@pytest.fixture +def simple_index_nlte_ion(): + """Simple fixture for nlte_ion treatment for H I and He II. + + Returns + ------- + MultiIndex + MultiIndex for HI and HeII. + """ + return pd.MultiIndex.from_tuples( + [(1, 0), (2, 1)], names=("atomic_number", "ion_number") + ) + + +@pytest.fixture +def simple_index_lte_ion(): + """Simple fixture for lte_ion treatment for H II and He I and He III. + + Returns + ------- + MultiIndex + MultiIndex for H II and He I and He III. + """ + return pd.MultiIndex.from_tuples( + [(1, 1), (2, 1), (2, 2)], names=("atomic_number", "ion_number") + ) + + +@pytest.fixture +def simple_rate_matrix_index(): + """Simple rate_matrix_index for NTLE ionization treatment of H I and He II. + + Returns + ------- + MultiIndex + (atomic_number, ion_number, treatment) + """ + return pd.MultiIndex.from_tuples( + [ + (1, 0, "nlte_ion"), + (1, 1, "lte_ion"), + (2, 0, "lte_ion"), + (2, 1, "nlte_ion"), + (2, 2, "lte_ion"), + ("n_e", "n_e", "n_e"), + ], + names=("atomic_number", "ion_number", "level_number"), + ) + + +@pytest.fixture +def simple_total_photo_ion_coefficients(simple_index_nlte_ion): + """Simple coefficients for photoionization of H I and He II. + + Returns + ------- + DataFrame + Photoionization coefficients for H I and He II. + """ + simple_photo_ion_coefficients = [0.03464792, 0.68099508] + return pd.DataFrame( + simple_photo_ion_coefficients, index=simple_index_nlte_ion + ) + + +@pytest.fixture +def simple_total_rad_recomb_coefficients(simple_index_nlte_ion): + """Simple coefficients for radiative recombination of H I and He II. + + Returns + ------- + DataFrame + Radiative recombination coefficients for H I and He II. + """ + simple_rad_recomb_coefficients = [0.43303813, 0.66140309] + return pd.DataFrame( + simple_rad_recomb_coefficients, index=simple_index_nlte_ion + ) + + +@pytest.fixture +def simple_total_col_ion_coefficients(simple_index_nlte_ion): + """Simple coefficients for collisional ionization of H I and He II. + + Returns + ------- + DataFrame + Collisional ionization coefficients for H I and He II. + """ + simple_col_ion_coefficients = [0.19351674, 0.69214007] + return pd.DataFrame( + simple_col_ion_coefficients, index=simple_index_nlte_ion + ) + + +@pytest.fixture +def simple_total_col_recomb_coefficients(simple_index_nlte_ion): + """Simple coefficients for collisional recombination of H I and He II. + + Returns + ------- + DataFrame + Collisional recombination coefficients for H I and He II. + """ + simple_col_recomb_coefficients = [0.06402515, 0.29785023] + return pd.DataFrame( + simple_col_recomb_coefficients, index=simple_index_nlte_ion + ) + + +@pytest.fixture +def simple_phi(simple_index_lte_ion): + """Simple Saha factors for H II, He I and He III.""" + simple_phi = [0.18936306, 0.15726292, 0.79851244] + return pd.DataFrame(simple_phi, index=simple_index_lte_ion) + + +@pytest.fixture +def simple_electron_density(): + """Simple electron density.""" + return 0.2219604493076 + + +def test_rate_matrix( + simple_phi, + simple_electron_density, + simple_rate_matrix_index, + simple_total_photo_ion_coefficients, + simple_total_rad_recomb_coefficients, + simple_total_col_ion_coefficients, + simple_total_col_recomb_coefficients, +): + """ + Using a simple case of nlte_ion for HI and HeII, checks if the calculate_rate_matrix generates the correct data. + """ + atomic_numbers = [1, 2] + actual_rate_matrix = NLTERateEquationSolver.calculate_rate_matrix( + atomic_numbers, + simple_phi, + simple_electron_density, + simple_rate_matrix_index, + simple_total_photo_ion_coefficients, + simple_total_rad_recomb_coefficients, + simple_total_col_ion_coefficients, + simple_total_col_recomb_coefficients, + ) + desired_rate_matrix = [ + [-0.077601, 0.099272, 0.000000, 0.000000, 0.000000, 0.0], + [1.000000, 1.000000, 0.000000, 0.000000, 0.000000, 0.0], + [0.000000, 0.000000, -0.157263, 0.221960, 0.000000, 0.0], + [0.000000, 0.000000, 0.000000, -0.834623, 0.161479, 0.0], + [0.000000, 0.000000, 1.000000, 1.000000, 1.000000, 0.0], + [0.000000, 1.000000, 0.000000, 1.000000, 2.000000, -1.0], + ] + + assert_almost_equal( + desired_rate_matrix, np.array(actual_rate_matrix), decimal=6 + ) + + +def test_jacobian_matrix( + simple_phi, + simple_electron_density, + simple_rate_matrix_index, + simple_total_photo_ion_coefficients, + simple_total_rad_recomb_coefficients, + simple_total_col_ion_coefficients, + simple_total_col_recomb_coefficients, +): + """ + Using a simple case of nlte_ion for HI and HeII, + checks if the jacobian_matrix generates the correct data. + """ + atomic_numbers = [1, 2] + + initial_guess = [ + 0.7192433675307516, + 0.8101666197902874, + 0.7171853313284426, + 0.040220760173800496, + 0.2878574499274399, + simple_electron_density, + ] + simple_rate_matrix = NLTERateEquationSolver.calculate_rate_matrix( + atomic_numbers, + simple_phi, + simple_electron_density, + simple_rate_matrix_index, + simple_total_photo_ion_coefficients, + simple_total_rad_recomb_coefficients, + simple_total_col_ion_coefficients, + simple_total_col_recomb_coefficients, + ) + + actual_jacobian_matrix = NLTERateEquationSolver.jacobian_matrix( + atomic_numbers, + initial_guess, + simple_rate_matrix, + simple_rate_matrix_index, + simple_total_rad_recomb_coefficients, + simple_total_col_ion_coefficients, + simple_total_col_recomb_coefficients, + ) + + desired_jacobian_matrix = [ + [-0.07760098, 0.09927163, 0.0, 0.0, 0.0, 0.23467404], + [1.0, 1.0, 0.0, 0.0, 0.0, 0.0], + [0.0, 0.0, -0.15726292, 0.22196045, 0.0, 0.04022076], + [0.0, 0.0, 0.0, -0.8346228, 0.16147935, 0.20061248], + [0.0, 0.0, 1.0, 1.0, 1.0, 0.0], + [0.0, 1.0, 0.0, 1.0, 2.0, -1.0], + ] + assert_almost_equal(actual_jacobian_matrix, desired_jacobian_matrix) + + +@pytest.fixture +def nlte_raw_plasma_w1( + tardis_model_config_nlte, nlte_raw_model, nlte_atom_data +): + """ + Plasma assembled with dilution factors set to 1.0. + """ + new_w = np.ones_like(nlte_raw_model.dilution_factor) + nlte_raw_model.dilution_factor = new_w + plasma = assemble_plasma( + tardis_model_config_nlte, nlte_raw_model, nlte_atom_data + ) + return plasma + + +@pytest.fixture +def nlte_raw_plasma_w0( + tardis_model_config_nlte, nlte_raw_model, nlte_atom_data +): + """ + Plasma assembled with dilution factors set to 0.0. + """ + new_w = np.zeros_like(nlte_raw_model.dilution_factor) + nlte_raw_model.dilution_factor = new_w + plasma = assemble_plasma( + tardis_model_config_nlte, nlte_raw_model, nlte_atom_data + ) + return plasma + + +def test_critical_case_w1(nlte_raw_plasma_w1): + """Check that the LTE and NLTE solution agree for w=1.0.""" + ion_number_density_nlte = nlte_raw_plasma_w1.ion_number_density_nlte.values + ion_number_density_nlte[ion_number_density_nlte < 1e-10] = 0.0 + + ind = IonNumberDensity(nlte_raw_plasma_w1) + ion_number_density_lte = ind.calculate( + nlte_raw_plasma_w1.thermal_phi_lte, + nlte_raw_plasma_w1.partition_function, + nlte_raw_plasma_w1.number_density, + )[0] + + ion_number_density_lte = ion_number_density_lte.values + ion_number_density_lte[ + ion_number_density_lte < 1e-10 + ] = 0.0 # getting rid of small numbers. + assert_allclose( + ion_number_density_lte, + ion_number_density_nlte, + rtol=1e-2, + ) + + +def test_critical_case_w0(nlte_raw_plasma_w0): + """Check that the LTE and NLTE solution agree for w=0.0.""" + nlte_solver = NLTERateEquationSolver(nlte_raw_plasma_w0) + ion_number_density_nlte = nlte_solver.calculate( + nlte_raw_plasma_w0.gamma, + 0.0, # to test collisions only, we set the radiative recombination rate to 0 + nlte_raw_plasma_w0.alpha_stim, + nlte_raw_plasma_w0.coll_ion_coeff, + nlte_raw_plasma_w0.coll_recomb_coeff, + nlte_raw_plasma_w0.partition_function, + nlte_raw_plasma_w0.levels, + nlte_raw_plasma_w0.level_boltzmann_factor, + nlte_raw_plasma_w0.phi, + nlte_raw_plasma_w0.rate_matrix_index, + nlte_raw_plasma_w0.number_density, + )[0] + ion_number_density_nlte = ion_number_density_nlte.values + ion_number_density_nlte[ion_number_density_nlte < 1e-10] = 0.0 + + ind = IonNumberDensity(nlte_raw_plasma_w0) + ion_number_density_lte = ind.calculate( + nlte_raw_plasma_w0.thermal_phi_lte, + nlte_raw_plasma_w0.partition_function, + nlte_raw_plasma_w0.number_density, + )[0] + + ion_number_density_lte = ion_number_density_lte.values + ion_number_density_lte[ + ion_number_density_lte < 1e-10 + ] = 0.0 # getting rid of small numbers. + assert_allclose( + ion_number_density_lte, + ion_number_density_nlte, + rtol=1e-2, + ) diff --git a/tardis/scripts/__init__.py b/tardis/scripts/__init__.py index e69de29bb2d..63fb31fbbbd 100644 --- a/tardis/scripts/__init__.py +++ b/tardis/scripts/__init__.py @@ -0,0 +1,3 @@ +""" +Translate cmfgen format to a format TARDIS can use. +""" diff --git a/tardis/simulation/__init__.py b/tardis/simulation/__init__.py index 8c88a5ab087..101ac28d6f7 100644 --- a/tardis/simulation/__init__.py +++ b/tardis/simulation/__init__.py @@ -1 +1,5 @@ +""" +Handling simulation runs. +""" + from tardis.simulation.base import Simulation diff --git a/tardis/simulation/base.py b/tardis/simulation/base.py index e47b12916c6..18d7f63ad47 100644 --- a/tardis/simulation/base.py +++ b/tardis/simulation/base.py @@ -2,6 +2,7 @@ import logging import numpy as np import pandas as pd +import tardis from astropy import units as u from tardis import constants as const from collections import OrderedDict @@ -106,6 +107,8 @@ class Simulation(PlasmaStateStorerMixin, HDFWriterMixin): convergence_plots_kwargs: dict nthreads : int The number of threads to run montecarlo with + version: str + The TARDIS version in use when instantiating the simulation object .. note:: TARDIS must be built with OpenMP support in order for ``nthreads`` to have effect. @@ -157,6 +160,7 @@ def __init__( self.luminosity_requested = luminosity_requested self.nthreads = nthreads self.show_progress_bars = show_progress_bars + self.version = tardis.__version__ if convergence_strategy.type in ("damped"): self.convergence_strategy = convergence_strategy diff --git a/tardis/simulation/tests/test_simulation.py b/tardis/simulation/tests/test_simulation.py index 88f3daff827..f877a176d39 100644 --- a/tardis/simulation/tests/test_simulation.py +++ b/tardis/simulation/tests/test_simulation.py @@ -11,6 +11,7 @@ import pandas as pd import pandas.util.testing as pdt import astropy.units as u +import tardis @pytest.fixture(scope="module") @@ -156,3 +157,8 @@ def test_plasma_state_storer_reshape( # assert_quantity_allclose( # t_rad, simulation_compare_data['test1/t_rad'] * u.Unit('K'), atol=0.0 * u.Unit('K')) + + +def test_version_tag(simulation_without_loop): + simulation = simulation_without_loop + assert simulation.version == tardis.__version__ diff --git a/tardis/stats/__init__.py b/tardis/stats/__init__.py index 8b137891791..b174821c479 100644 --- a/tardis/stats/__init__.py +++ b/tardis/stats/__init__.py @@ -1 +1,3 @@ - +""" +Providing Poisson statistics that govern the MonteCarlo processes. +""" diff --git a/tardis/tests/fixtures/atom_data.py b/tardis/tests/fixtures/atom_data.py index 520ede4b980..a1cdd8456d6 100644 --- a/tardis/tests/fixtures/atom_data.py +++ b/tardis/tests/fixtures/atom_data.py @@ -4,6 +4,8 @@ import pytest from tardis.io.atom_data.base import AtomData +from tardis.io.config_reader import Configuration +from tardis.model.base import Radial1DModel DEFAULT_ATOM_DATA_UUID = "864f1753714343c41f99cb065710cace" @@ -40,3 +42,52 @@ def atomic_dataset(atomic_data_fname): def kurucz_atomic_data(atomic_dataset): atomic_data = deepcopy(atomic_dataset) return atomic_data + + +@pytest.fixture # (scope="session") +def nlte_atomic_data_fname(tardis_ref_path): + """ + File name for the atomic data file used in NTLE ionization solver tests. + """ + atomic_data_fname = os.path.join( + tardis_ref_path, "nlte_atom_data", "TestNLTE_He_Ti.h5" + ) + + atom_data_missing_str = ( + f"{atomic_data_fname} atomic datafiles " f"does not seem to exist" + ) + + if not os.path.exists(atomic_data_fname): + pytest.exit(atom_data_missing_str) + + return atomic_data_fname + + +@pytest.fixture # (scope="session") +def nlte_atomic_dataset(nlte_atomic_data_fname): + """ + Atomic dataset used for NLTE ionization solver tests. + """ + nlte_atomic_data = AtomData.from_hdf(nlte_atomic_data_fname) + return nlte_atomic_data + + +@pytest.fixture # (scope="session") +def nlte_atom_data(nlte_atomic_dataset): + + atomic_data = deepcopy(nlte_atomic_dataset) + return atomic_data + + +data_path = os.path.join("tardis", "io", "tests", "data") + + +@pytest.fixture # (scope="session") +def tardis_model_config_nlte(): + filename = "tardis_configv1_nlte.yml" + return Configuration.from_yaml(os.path.join(data_path, filename)) + + +@pytest.fixture # (scope="session") +def nlte_raw_model(tardis_model_config_nlte): + return Radial1DModel.from_config(tardis_model_config_nlte) diff --git a/tardis/transport/__init__.py b/tardis/transport/__init__.py new file mode 100644 index 00000000000..41612a06e1d --- /dev/null +++ b/tardis/transport/__init__.py @@ -0,0 +1,3 @@ +""" +Handling the packet propagation. +""" diff --git a/tardis/transport/geometry/__init__.py b/tardis/transport/geometry/__init__.py new file mode 100644 index 00000000000..d585337f711 --- /dev/null +++ b/tardis/transport/geometry/__init__.py @@ -0,0 +1,3 @@ +""" +Calculating distances. +""" diff --git a/tardis/transport/r_packet_transport.py b/tardis/transport/r_packet_transport.py index 9a889935538..7f81de251d5 100644 --- a/tardis/transport/r_packet_transport.py +++ b/tardis/transport/r_packet_transport.py @@ -15,9 +15,7 @@ from tardis.transport.frame_transformations import ( get_doppler_factor, ) -from tardis.montecarlo.montecarlo_numba.numba_config import ( - ENABLE_FULL_RELATIVITY, -) +import tardis.montecarlo.montecarlo_numba.numba_config as nc from tardis.montecarlo.montecarlo_numba.opacities import calculate_tau_electron from tardis.montecarlo.montecarlo_numba.r_packet import ( InteractionType, @@ -27,7 +25,13 @@ @njit(**njit_dict_no_parallel) def trace_packet( - r_packet, numba_model, numba_plasma, estimators, chi_continuum, escat_prob + r_packet, + numba_radial_1d_geometry, + numba_model, + numba_plasma, + estimators, + chi_continuum, + escat_prob, ): """ Traces the RPacket through the ejecta and stops when an interaction happens (heart of the calculation) @@ -35,6 +39,7 @@ def trace_packet( Parameters ---------- r_packet : tardis.montecarlo.montecarlo_numba.r_packet.RPacket + numba_radial_1d_geometry : tardis.montecarlo.montecarlo_numba.numba_interface.NumbaRadial1DGeometry numba_model : tardis.montecarlo.montecarlo_numba.numba_interface.NumbaModel numba_plasma : tardis.montecarlo.montecarlo_numba.numba_interface.NumbaPlasma estimators : tardis.montecarlo.montecarlo_numba.numba_interface.Estimators @@ -43,8 +48,8 @@ def trace_packet( ------- """ - r_inner = numba_model.r_inner[r_packet.current_shell_id] - r_outer = numba_model.r_outer[r_packet.current_shell_id] + r_inner = numba_radial_1d_geometry.r_inner[r_packet.current_shell_id] + r_outer = numba_radial_1d_geometry.r_outer[r_packet.current_shell_id] ( distance_boundary, @@ -204,8 +209,8 @@ def move_r_packet(r_packet, distance, time_explosion, numba_estimator): comov_nu = r_packet.nu * doppler_factor comov_energy = r_packet.energy * doppler_factor - # Account for length contraction and angle aberration - if ENABLE_FULL_RELATIVITY: + # Account for length contraction + if nc.ENABLE_FULL_RELATIVITY: distance *= doppler_factor set_estimators( diff --git a/tardis/util/__init__.py b/tardis/util/__init__.py index 6dd4694b3ef..e1b28566f74 100644 --- a/tardis/util/__init__.py +++ b/tardis/util/__init__.py @@ -1 +1,3 @@ -# Utilities for TARDIS +""" +Utilities for TARDIS. +""" diff --git a/tardis/util/base.py b/tardis/util/base.py index cd2a3f326ac..8a690fb2df4 100644 --- a/tardis/util/base.py +++ b/tardis/util/base.py @@ -285,19 +285,19 @@ def create_synpp_yaml(radial1d_mdl, fname, shell_no=0, lines_db=None): yaml.dump(yaml_reference, stream=f, explicit_start=True) -def intensity_black_body(nu, T): +def intensity_black_body(nu, temperature): """ Calculate the intensity of a black-body according to the following formula .. math:: - I(\\nu, T) = \\frac{2h\\nu^3}{c^2}\\frac{1} + I(\\nu, temperature) = \\frac{2h\\nu^3}{c^2}\\frac{1} {e^{h\\nu \\beta_\\textrm{rad}} - 1} Parameters ---------- nu : float Frequency of light - T : float + temperature : float Temperature in kelvin Returns @@ -305,7 +305,7 @@ def intensity_black_body(nu, T): Intensity : float Returns the intensity of the black body """ - beta_rad = 1 / (k_B_cgs * T) + beta_rad = 1 / (k_B_cgs * temperature) coefficient = 2 * h_cgs / c_cgs**2 intensity = ne.evaluate( "coefficient * nu**3 / " "(exp(h_cgs * nu * beta_rad) -1 )" @@ -699,6 +699,14 @@ def update_packet_pbar(i, current_iteration, no_of_packets, total_iterations): packet_pbar.update(i) +def refresh_packet_pbar(): + """ + Refresh packet progress bar after each iteration. + + """ + packet_pbar.refresh() + + def update_iterations_pbar(i): """ Update progress bar for each iteration. diff --git a/tardis_env3.yml b/tardis_env3.yml index db14dd9876c..f4c7344e0c4 100644 --- a/tardis_env3.yml +++ b/tardis_env3.yml @@ -10,7 +10,7 @@ dependencies: - python=3.8 - setuptools - - setuptools_scm + - setuptools_scm<7 - pip - numpy=1.19 - scipy=1.5 @@ -38,7 +38,7 @@ dependencies: - matplotlib-base - ipywidgets - plotly - - qgrid + - qgrid=1.3.1=pyhd8ed1ab_4 # qgrid-feedstock/issues/18 # --- Packages not required for conda-forge recipe ---