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In gamma ray code : Changed times to np.geomspace #2415

Merged
merged 2 commits into from
Sep 21, 2023
Merged

In gamma ray code : Changed times to np.geomspace #2415

merged 2 commits into from
Sep 21, 2023

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@Knights-Templars Knights-Templars self-assigned this Sep 20, 2023
wkerzendorf
wkerzendorf reviewed Sep 20, 2023
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tardis/energy_input/gamma_ray_transport.py
times = np.zeros(time_steps + 1)

# log time steps
for i in range(time_steps + 1):
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this looks like a good choice (example comment)

@andrewfullard
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I think this is a great change, but I would like to see a before/after comparison of the time steps to make sure this does the same thing as my old code.

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I think this is a great change, but I would like to see a before/after comparison of the time steps to make sure this does the same thing as my old code.

Thanks @andrewfullard. I have tested with np.isclose and is numericaally the same.

wkerzendorf
wkerzendorf reviewed Sep 20, 2023
View reviewed changes
tardis/energy_input/gamma_ray_transport.py
+ (np.log(time_end) - np.log(time_start)) / time_steps * i
)
times[i] = np.exp(times[i])
times = np.geomspace(time_start, time_end, time_steps + 1)
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Suggested change
times = np.geomspace(time_start, time_end, time_steps + 1)
times = np.logspace(time_start, time_end, time_steps + 1, base=np.e)

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I think that's better (example comment)

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codecov bot commented Sep 20, 2023

Codecov Report

Merging #2415 (d00a2c3) into master (7312e0b) will increase coverage by 0.01%.
Report is 1 commits behind head on master.
The diff coverage is 0.00%.

❗ Current head d00a2c3 differs from pull request most recent head f90be16. Consider uploading reports for the commit f90be16 to get more accurate results

@@            Coverage Diff             @@
##           master    #2415      +/-   ##
==========================================
+ Coverage   66.90%   66.92%   +0.01%     
==========================================
  Files         153      153              
  Lines       13596    13593       -3     
==========================================
  Hits         9097     9097              
+ Misses       4499     4496       -3
Files Changed Coverage Δ
tardis/energy_input/gamma_ray_transport.py 0.00% <0.00%> (ø)

... and 1 file with indirect coverage changes

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

@wkerzendorf wkerzendorf merged commit ff5a120 into tardis-sn:master Sep 21, 2023
8 checks passed
atharva-2001 added a commit to atharva-2001/tardis that referenced this pull request Nov 28, 2023
@atharva-2001 @tardis-bot
@wkerzendorf @Knights-Templars @AlexHls @jvshields @chvogl @andrewfullard
Benchmarks oct 23 fix (#37)
41f83c3 
* Allow Simulation Tests to Run Independently  (tardis-sn#2407)

* Modify test_packet_source.py so that sim and tardis/tests can run

* remove BasePacketSource

* format

* Add docstrings

* Pre-release 2023.09.17 (tardis-sn#2411)

Automated changes for pre-release 2023.09.17

* upgrading env in 2022 (tardis-sn#2410)

* fix several bugs related to upgrade

* fix the get function in pandas

* fixed several incompatibilities for new libraries

* fixed up the changes in pandas testing and other reindexing issues

* fix other bugs with new environment

* blackify tardis

* updated the conda-lock file

* add lock files

* update cache number

* fix simulation tests

* remove units for testing

* blackify

* Update tardis/visualization/tools/tests/test_sdec_plot.py

good catch

Co-authored-by: Atharva Arya <[email protected]>

* add assert

* reset caches

---------

Co-authored-by: Atharva Arya <[email protected]>

* In gamma ray code : Changed times to np.geomspace (tardis-sn#2415)

* Changed times to np.geomspace

* Added myself to mailmap

* rename RadialModel1D to SimulationState (tardis-sn#2417)

* rename RadialModel1D to SimulationState

* black files

* rename simulation_state2 (tardis-sn#2421)

* fixup of many files to make them pass the tests

* change model for typo

* Ignore tests in docstr coverage (tardis-sn#2424)

ignore tests in docstr coverage

* Disabled formal integral for continuum interaction (tardis-sn#2426)

Disabled formal integral

Co-authored-by: Alexander Holas <alexander.holas@h-its>

* add linelist exposure to atom data and reader, built on current (tardis-sn#2428)

* add linelist exposure to atom data and reader, built on current

* add josh to mailmap

* Modified how setup input energy takes isotope name. Earlier it was ga… (tardis-sn#2425)

Modified how setup input energy takes isotope name. Earlier it was gamma_ray_lines.Isotope

* Added a function to calculate shell masses (tardis-sn#2434)

* Added a function to calculate shell masses

* Added a function to calculate shell masses

* changed shell masses with the new function

* Fix duplicate entries in continuum line list (tardis-sn#2443)

* Workaround list access

* Formatting

* Added error if duplicate

* Remove duplicates

* Fix typo, add comment

* Remove bandaid fix

* Cleanup

* More cleanup

* Fix numba parallel issues (tardis-sn#2447)

* Enabled parallel

* Fix the mistake

* Update docs

* Change glob patterns in `setup.cfg`  (tardis-sn#2441)

* Fix package_data in setup.cfg, mainly io and viz

* more folders

* Test pip installation

* Remove test step

* Fix more folders

* restructure of geometry (tardis-sn#2422)

* restructure of geometry

* add radial1d boundary logic

* black format

* several fixes

* fix epsilon

* add testing of boundaries

* change the r_inner_active

* first integration with `from_config` working

* hunting down density indexing bug

* all model tests (without csvy) pass

* more fixes

* fix of model to simulation_state

* fix inner boundary packet error

* fix some leftovers

* final fix for csvy

* blackify

* restructure to readers and remove some leftover code

* further cleanup

* first start of the restructure

* add comment about removing quantitiness

* add velocity check

* add new abundance functions

* remove default units

* Add FAQ section to documentation (tardis-sn#2450)

* Add faq

* Added Overview

* Fix typo

* Remove lock file creation from pre release workflow (tardis-sn#2432)

* Install latest version of mamba

* Unpin conda lock installatiion

* Split lockfilee creation to separate workflow

* change docs installation- put a warning for conda forge installation and comment out install from package

* fix

* delete create lockfiles

* download llock file

* Pre-release 2023.10.20 (tardis-sn#2452)

Automated changes for pre-release 2023.10.20

* Add verbose assert to NLTE rate equation (tardis-sn#2457)

* add verbose assert

* formatting

* Fix bug in relativistic packet source (tardis-sn#2453)

* Fix bug in relativistic packet source

* Add initial test for BlackBodySimpleSourceRelativistic

* Remove incorrect docstring

* Update tardis/montecarlo/tests/test_packet_source.py

Co-authored-by: Wolfgang Kerzendorf <[email protected]>

* Update tardis/montecarlo/tests/test_packet_source.py

Co-authored-by: Wolfgang Kerzendorf <[email protected]>

* Rename all occurences of blackbodysimplesourcerelativistic

* Do not hardcore blackbody_simplesource_relativistic.beta

---------

Co-authored-by: Wolfgang Kerzendorf <[email protected]>

* Enable nlte ionization as plasma component (tardis-sn#2458)

* Rename nlte ion and electron

* Enable NLTE

* Fix typo

* Add docs

* Fix transitionprob dtype

* dtype conversion

* dtype for sparse matrix

* Typing in numba

* Fix test variable name

* Add missing electron density case

* Fix typo

* Update docstr-cov.yml to fix failing action (tardis-sn#2462)

* Update docstr-cov.yml to fix failing action

* Explicitly install setuptools

* NLTE Ionization solver polish (tardis-sn#2461)

* assertion for first guess

* Add checks to decay

* Fix greater equal

* Fix deprecated series index

* Pre-release 2023.11.05 (tardis-sn#2466)

Automated changes for pre-release 2023.11.05

* Tests Plasma Using Syrupy (tardis-sn#2413)

* Add syrupy classes to conftest

* Add syrupy to env file

* Another folder for syrupy data

* Save as npy instead of txt

* Use syrupy fixtures

* Different assertion functions for pandas dataframes and series

* Zeta data fix

* Blackify

* Blackify conftest

* test_hdf_plasmas using syrupy

* Install syrupy with conda

* Remove additional line adding syrupy as a plugin

* Set update snapshots config option when generate reference is selected

* Remove old refdata code from test plasmas complete

* Create plasma conftest file

* Text based snapshot fixture with custom location

* Snapshot path

* tardis regressions my fork

* Refactor test_hdf_plasmas.py

* Format using black

* test nlte excitation using syrupy

* nlte solver

* plasma continuum

* test tardis model density config

* Lock files

* Increase cache no

* format using black

* cleanup- sort dependencies, delete comments

* Documentation to run these tests

* remove commented out fixtures which are not used anywhere

* docs code render fix

* tests final cleanup

* renaming files, yet to deal with ambr snapshot extension and curly brackets

* renaming snapshots

* Add comments

* Add astropy import guard (tardis-sn#2470)

* Add astropy import guard

* mailmap

* Reading in decay radiation data in atom data (tardis-sn#2471)

* Reading in decay radiation data in atom data

* Added docstring

* Fixes the checksum

* Pre-release 2023.11.26 (tardis-sn#2477)

Automated changes for pre-release 2023.11.26

* Update plasma configuration documentation (tardis-sn#2459)

* update plasma docs

* Update mailmap

* Fix typo

* Add ruff rules and docs (tardis-sn#2478)

* Add ruff rules and docs

* Update pyproject.toml

Co-authored-by: Wolfgang Kerzendorf <[email protected]>

* rebuild docs

---------

Co-authored-by: Wolfgang Kerzendorf <[email protected]>

* Decay energy chain (tardis-sn#2448)

* Added a function to calculate shell masses

* Added a function to calculate shell masses

* changed shell masses with the new function

* Changed mass fraction to masses in to_inventories()

* Co-authored-by: Wolfgang Kerzendorf <[email protected]>

* Added a function to calculate total decays

* Added a function to calculate energies from gamma rays and positrons.

* added a function to calculate average energies of gamma rays and positrons

* Added a fucntion to calculate each decay chain energies

* Added dictionaries to handle multiple isotopes

* Changed value to values

* added tests for gamma_ray_transport

* Added tests for calculating activity

* Added test for activity

* Added tests for two isotope

* Changed Ni_isotope_mass

* Added pytest paramterize

* Added test for calculating shell masses

* Ran test for checking activity of parent nuclide with analytical solution.

* The function test_activity matches with the radioactivedecay output upto 14 decimal places. The Avogadro's number used in radioactivedecay is not from astropy.

* Added tests for checking if iso_dict is returning the right key.

* Added test for inventories dictionary.

* Added a test to check if the calculate_average_energy function passes the right list ahead.

* Added new function for testing energy budget from each decay chain.

* Added a new function for energy per mass

* Reading in decay radiation data in atom data

* Add

* Added tests for gamma ray transport.

* Added tests for all functions for gamma_ray_transport. Added docstrings.

* Changing decay energy chain

* Added a function to get taus

* Added tests for multiple isotopes

* Fixes the test calculate shell masses with hand calculated values

* Use Mamba instead of conda

* Run asv for last 5 commits

* Add pull request trigger temporarily

* Reset

---------

Co-authored-by: tardis-bot <[email protected]>
Co-authored-by: Wolfgang Kerzendorf <[email protected]>
Co-authored-by: Anirban <[email protected]>
Co-authored-by: Alexander Holas <[email protected]>
Co-authored-by: Alexander Holas <alexander.holas@h-its>
Co-authored-by: Joshua Shields <[email protected]>
Co-authored-by: Anirban <[email protected]>
Co-authored-by: Christian Vogl <[email protected]>
Co-authored-by: Andrew <[email protected]>
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