Adding nlte_rate_equation_solver.py #2140
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## master #2140 +/- ##
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+ Coverage 61.66% 61.87% +0.21%
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Files 77 78 +1
Lines 8697 8782 +85
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- Misses 3334 3348 +14
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Co-authored-by: Christian Vogl <[email protected]>
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andrewfullard
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| ) | ||
| atomic_numbers = ( | ||
| rate_matrix_index.get_level_values(0).unique().drop("n_e") | ||
| ) # dropping the n_e index |
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rate_matrix_index's 1st index is atomic number and "n_e" added in the end for constructing the rate_matrix in the right shape. That's why I'm getting rid of the last index and dropping repeated values(as each atomic number has multiple corresponding rows)
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can you put this in the comments
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sonachitchyan
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Nov 16, 2022
| Saha Factors. | ||
| rate_matrix_index : MultiIndex | ||
| (atomic_number, ion_number, level/treatment type) | ||
| If ion is treated in LTE ionization, 3rd index is "lte_ion", |
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| If ion is treated in LTE ionization, 3rd index is "lte_ion", | |
| If ion is treated in LTE or nebular ionization, 3rd index is "lte_ion", |
| phi : DataFrame | ||
| Saha Factors. | ||
| rate_matrix_index : MultiIndex | ||
| (atomic_number, ion_number, level/treatment type) |
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I guess for now you could remove the level/ since we are only doing NLTE ionization (and the levels part is also not explained in the rest of the docstring).
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| Returns | ||
| ------- | ||
| ion_number_densities_nlte: DataFrame |
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| ion_number_densities_nlte: DataFrame | |
| ion_number_densities_nlte : DataFrame |
| ------- | ||
| ion_number_densities_nlte: DataFrame | ||
| Number density with NLTE ionization treatment. | ||
| electron_densities_nlte: Series |
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| electron_densities_nlte: Series | |
| electron_densities_nlte : Series |
| ion_number_densities_nlte: DataFrame | ||
| Number density with NLTE ionization treatment. | ||
| electron_densities_nlte: Series | ||
| Electron density with NLTE ionizaion treatment. |
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| Electron density with NLTE ionizaion treatment. | |
| Electron density with NLTE ionization treatment. |
| ------- | ||
| total_photo_ion_coefficients: | ||
| Photoinization coefficients grouped by atomic number and ion number. | ||
| total_rad_recomb_coefficients: |
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| total_rad_recomb_coefficients: | |
| total_rad_recomb_coefficients |
| Photoinization 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: |
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| total_coll_ion_coefficients: | |
| total_coll_ion_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: |
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| total_coll_recomb_coefficients: | |
| total_coll_recomb_coefficients |
| Returns | ||
| ------- | ||
| total_photo_ion_coefficients: | ||
| Photoinization coefficients grouped by atomic number and ion number. |
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| Photoinization coefficients grouped by atomic number and ion number. | |
| Photoionization coefficients grouped by atomic number and ion number. |
| @@ -14,24 +14,41 @@ def __init__(self, plasma_parent, nlte_ionization_species=0): | |||
| self.nlte_ionization_species = nlte_ionization_species | |||
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| def calculate(self, levels, nlte_ionization_species): | |||
| """Generates rate_matrix_index using levels and changing the last index(level) to | |||
| "lte_ion" if that ion_number is treated in LTE, "nlte_ion" for NLTE ionizatin and | |||
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| "lte_ion" if that ion_number is treated in LTE, "nlte_ion" for NLTE ionizatin and | |
| "lte_ion" if that ion_number is treated in LTE or nebular, "nlte_ion" for NLTE ionization and |
This was referenced Nov 16, 2022
epassaro
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Mar 21, 2023
* Adding rate matrix index (tardis-sn#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 (tardis-sn#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 (tardis-sn#2146) * Possible fix for prerelease workflow (tardis-sn#2127) * Possible fix for prerelease workflow * Fix double @ symbol * Changed to v2 * Pin setuptools_scm to v6 (tardis-sn#2147) * Pin setuptools_scm to v6 * Fix typo * Adding nlte_rate_equation_solver.py (tardis-sn#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 <[email protected]> * 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 <[email protected]> * Set specific qgrid feedstock version (tardis-sn#2152) * Pre-release 2022.11.17 (tardis-sn#2155) Automated changes for pre-release 2022.11.17 * Post-release 2022.11.17 (tardis-sn#2156) Automated changes for post-release 2022.11.17 * Pre-release 2022.11.20 (tardis-sn#2160) Automated changes for pre-release 2022.11.20 * Fix relativistic packet initialization (tardis-sn#2159) * Fix setting of full relativity flag * Add relativistic packet source Co-authored-by: Stuart Sim <[email protected]> * Fix relativistic vpackets on inner boundary Co-authored-by: Stuart Sim <[email protected]> * Fixing typos for nlte ion (tardis-sn#2154) * fixing typos on rate_matrix * changed the np arange to use 0 instead of 0.0 * NLTE jacobian matrix (tardis-sn#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 (tardis-sn#2150) * solved KN ZetaData issue * KN missing Zeta fixed * mailmap changed * Pre-release 2022.12.11 (tardis-sn#2172) Automated changes for pre-release 2022.12.11 * Post-release 2022.12.12 (tardis-sn#2173) Automated changes for post-release 2022.12.12 * Add missing __init__.py files to transport and geometry subpackages (tardis-sn#2170) * Add missing __init__.py files to transport subpackage * Add missing __init__.py file to geometry subpackage * Pre-release 2022.12.25 (tardis-sn#2180) Automated changes for pre-release 2022.12.25 * Post-release 2022.12.26 (tardis-sn#2182) Automated changes for post-release 2022.12.26 * Pre-release 2023.01.08 (tardis-sn#2186) Automated changes for pre-release 2023.01.08 * Post-release 2023.01.11 (tardis-sn#2188) Automated changes for post-release 2023.01.11 * Downloading nlte_atom_data in ref data (tardis-sn#2187) adding nlte_atom_data to be downloaded * Adding nlte solver (tardis-sn#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 58ce29e. * 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 <[email protected]> * Update tardis/plasma/properties/nlte_rate_equation_solver.py Co-authored-by: Christian Vogl <[email protected]> * Update tardis/io/tests/data/tardis_configv1_nlte.yml Co-authored-by: Christian Vogl <[email protected]> * Update tardis/io/tests/data/tardis_configv1_nlte.yml Co-authored-by: Christian Vogl <[email protected]> * ran black * Update tardis/plasma/properties/nlte_rate_equation_solver.py Co-authored-by: Christian Vogl <[email protected]> * Update tardis/plasma/tests/test_nlte_solver.py Co-authored-by: Christian Vogl <[email protected]> * 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 <[email protected]> * Update tardis/plasma/properties/nlte_rate_equation_solver.py Co-authored-by: Christian Vogl <[email protected]> * Update tardis/plasma/tests/test_nlte_solver.py Co-authored-by: Christian Vogl <[email protected]> * fixed an issue in a docsting * fixed an issue in a docsting * removed a TODO comment Co-authored-by: Christian Vogl <[email protected]> * Rename T variables to temperature (tardis-sn#2185) * fixes tardis-sn#1600 * fixes tardis-sn#1600 * Update tardis/montecarlo/packet_source.py Co-authored-by: Atharva Arya <[email protected]> * fixes codestyle * improve codestyle * rename the function * Update packet_source.py * improve codequality * add commit * Update packet_source.py Co-authored-by: Atharva Arya <[email protected]> * Fixing test_store_runner_to_hdf (tardis-sn#2198) * checking if the object has the attribute decode * fixed another decode issue * Reading nlte_excitation_species from config (tardis-sn#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 <[email protected]> --------- Co-authored-by: Christian Vogl <[email protected]> * Fix config reader tests (tardis-sn#2200) Fix config tests * Pre-release 2023.02.05 (tardis-sn#2205) Automated changes for pre-release 2023.02.05 * Post-release 2023.02.06 (tardis-sn#2206) Automated changes for post-release 2023.02.06 * Add version tag to simulation objects (tardis-sn#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 (tardis-sn#2208) Automated changes for pre-release 2023.02.12 * Post-release 2023.02.16 (tardis-sn#2210) Automated changes for post-release 2023.02.16 * Pre-release 2023.02.19 (tardis-sn#2211) Automated changes for pre-release 2023.02.19 * Cache LFS objects in the tests workflow (tardis-sn#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 (tardis-sn#2213) Automated changes for post-release 2023.02.20 * Correct the description of 'no_of_packets' in Monte Carlo Configuration (tardis-sn#2214) * Correct the description of 'no_of_packets' in Monte Carlo Configuration * Added a simple description * Pre-release 2023.02.26 (tardis-sn#2222) Automated changes for pre-release 2023.02.26 * Post-release 2023.02.27 (tardis-sn#2223) Automated changes for post-release 2023.02.27 * Add docstrings to subpackages (tardis-sn#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 <[email protected]> --------- Co-authored-by: kim <[email protected]> Co-authored-by: Sona Chitchyan <[email protected]> * Docs Fix: Download Atom Data in rpacket_tracking.ipynb (tardis-sn#2236) Download atom data from the function * Fix for automerge (tardis-sn#2242) Use gh CLI to approve pull requests; use new token * Fix for release dates (tardis-sn#2243) * MonteCarlo packet progress bar completes to 100% (tardis-sn#2237) * Refresh packet progress bar after every iteration * Udpdated .mailmap * Reformatted with black * Fix team reviewers on workflows (tardis-sn#2246) * Pre-release 2023.03.20 (tardis-sn#2247) Automated changes for pre-release 2023.03.20 * Post-release 2023.03.20 (tardis-sn#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 <[email protected]> Co-authored-by: Satwik Kambham <[email protected]> Co-authored-by: Andrew <[email protected]> Co-authored-by: Christian Vogl <[email protected]> Co-authored-by: tardis-bot <[email protected]> Co-authored-by: Stuart Sim <[email protected]> Co-authored-by: gleck97 <[email protected]> Co-authored-by: ABHISHEK PATIDAR <[email protected]> Co-authored-by: Atharva Arya <[email protected]> Co-authored-by: Kim <[email protected]> Co-authored-by: Abhishek Patidar <[email protected]> Co-authored-by: Le Truong <[email protected]> Co-authored-by: kim <[email protected]> Co-authored-by: Shreyas Singh <[email protected]>
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📝 Description
This PR creates the rate matrix which will be further used in NLTE Solver implementation. The matrix is a block diagonal, constructed from blocks corresponding to each species and treating some of the ion numbers in NLTE ionization.
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