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UCLCHEM v3.4.0 #77

Merged
merged 34 commits into from
Oct 14, 2024
Merged

UCLCHEM v3.4.0 #77

merged 34 commits into from
Oct 14, 2024

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GijsVermarien
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@GijsVermarien GijsVermarien commented Oct 14, 2024 •
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We release UCLCHEM 3.4.0 with some additions to both user experience, technical improvements and new features:

  • The biggest addition is a new mode where you can run UCLCHEM solely in memory, not requiring you to save and load the csv files that we relied on for long. A tutorial on how to do this, can be found in notebooks/2a_modelling_objects_on_disk.py
  • We implement a new postprocessing mode, similar to what the NEATH paper does (https://fpriestley.github.io/neath/). This also allows for running much more flexible models.
  • We now check whether the user specified branching ratios correctly, this means that if the total for reactions is larger than 1.0, we divide by the total. We also do it for three way split reactions, since often people write 0.33, resulting in 1% not being accounted for.
  • We move to the RATE22 database as the default one, some species are renamed (https://umistdatabase.uk/)
  • The tutorial notebooks have been moved to the notebooks directory and were revised a bit.
  • radfield is now always a column in the output csv files, removing the need for two extra lines at the top of each uclchem csv file.
  • A small chemistry network is added, this runs quickly and can be used for toy problems and code testing.

Small changes:

  • The standard uv yield is now 0.03
  • The magnetic field is now a parameter that can be passed for shock models
  • The analysis scripts work once again in the gas phase, the grains still have some issues (see: Incorrect production and destruction in analysis.py #37)
  • We improved test coverage
  • We now have precommit configured to improve code quality

Marcus-Keil and others added 30 commits January 17, 2023 11:04
@Marcus-Keil
Adding feature to return array in python
7d61f98
@GijsVermarien
Merge remote-tracking branch 'origin/main' into HEAD
b3d01e5
@Marcus-Keil
Added return array functionality
44f80b5
@GijsVermarien
Merge pull request #35 from uclchem/main
b87bd9d 
Upstream to develop
@Marcus-Keil
Changes to test_uclchem and wrap.f90 to prevent segfault
8037e88
@GijsVermarien
Increased molecule character limit to 32
58849b5
@GijsVermarien
Added correct optional arguments to the test script
573d744
@GijsVermarien
Merge branch 'features/return_array' of github.com:uclchem/uclchem in…
7b04829 
…to HEAD
@GijsVermarien
Refactor of return_array
c7822fd 
Changed some keywords to be more in line with numpy
Added a check to raise errors when io / memory mode a mixed
Fixed a bug caused by running old io and then in memory
@GijsVermarien
Merge pull request #34 from uclchem/features/return_array
a7107a5 
Features/return array
@GijsVermarien
Merge remote-tracking branch 'origin/main' into develop
efe33f3
@katarzynadutkowska @GijsVermarien
Magnetic parameter bm0 added as a new default parameter
0da1f69
@GijsVermarien
Add specname_out to cshock
c4378e9
@psharda
add axex labels and show grid (#48)
8a7cd10
@GijsVermarien
Move to UMIST22 (#56)
27ccfbb 
* Update the Python requirement (#54)

* Update the Python requirement

The newest type hints make the code incompatible with Python <= 3.8, so adjust the requirement accordingly.

* Also update the requirement in pyproject.

* Add pytest as a requirement

* Add UCLCHEM compiled with UMIST22 as its database

* Add the option to comment UMIST

* Change the reference files to be the ones generated with UMIST22

* Add UMIST22 as the default reaction database

* Move umist12 to a legacy folder
@GijsVermarien @fpriestley
Features/postprocessing (#59)
82db119 
This is a large rewrite that combines the return_array feature with postprocessing to allow for running arbitrary temperature,density (and column density) profiles.

* Update Makefile

* Update main.f90

* Update chemistry.f90

* Update wrap.f90

* Added CLI config files and docs

* Added graceful out of bound checking for return arrays

* Working example of postprocessing code with return array

* Add postprocessing example script

* Fix clean_array and self-consistent makerates

- Fixed clean_array to work with the new more efficient time array allocation
- update makerates to be self-consistent by writing the correct parameters to both f90 and py

* Small fixes to smooth out all tests

- Finally added HSIO as a species
- made the option usecoldens explicit so as not to rely on present statements (they don't work nicely with f2py)
- fixed small startabunds mode error
- restored makefile to work and removed debug
- added error code for running out of array points
- function to retrieve species
- fixed test

* Restored pyproject to use git-versioning

* Move get_f2py_signature to debug.py

* Move analysis.py to use MAX_SPECIES

* Comment out debug line in sputtering

* Remove headers from example files

* Moved ODE conservation to test suite

* Changed the test to more useful in pytest

* Fixed get_odes boundary check

* Fixed path for test_run_stages

* Add paths to loading as well

* Add correct paths

* Removed print statements we no longer need

---------

Co-authored-by: fpriestley <[email protected]>
@GijsVermarien
Merge remote-tracking branch 'origin/main' into develop
a2abdca
@GijsVermarien
Merge pull request #63 from uclchem/fix/upstream_build_2409
e75bb7d 
Fix/upstream build 2409
@GijsVermarien
Update defaultparameters.f90
0ffef5d
@GijsVermarien
Fix constant writing on the python side
37c42a3
@GijsVermarien
Self consistent constants for develop branch
32d7268
@GijsVermarien
Add n_species to test script
10b7e60
@GijsVermarien
Merge pull request #64 from uclchem/fix/lower_uv_yield
1131628 
Update defaultparameters.f90
@GijsVermarien
Merge pull request #65 from uclchem/fix/makerates_constants
8a39ee0 
Fix/makerates constants
@GijsVermarien
Add network branching ratio checks
160b00f
@GijsVermarien
Fixed bug where reactions after sorting got labeled wrong
87bcf1a
@GijsVermarien
Move branching ratios and fix adding reactions
c250891 
If reactions were added after the Network class was instanstiated
before, they would get a wrong index and override the internal
reaction dict in the wrong place. Now we take the max + 1 instead
of the last element, which ensure this cannot happen again.
@GijsVermarien
Merge pull request #69 from uclchem/features/branching_ratio_checks
a2b3b1d 
Features/branching ratio checks
@GijsVermarien
Remove H2 diss from UMIST and add better duplicate checking (#71)
db99bdb 
* Remove H2 diss from UMIST and simplify the checks some

* Added a source tag to reactions and improve duplication check

* Add small chemistry network for better unit tests

* Disable NH2+H2CO from our custom reactions in favour of UMIT22

* Add better check for duplicate important reactions
@GijsVermarien
Isolate the changes to analysis.py (#73)
f603a21
@GijsVermarien
Fix the timepoints for jshock
2ce1c39
@GijsVermarien
Fix/rad and dusttemp in csv (#75)
d3f6b8f 
* Fix the timepoints for jshock

* Add writing of radfield and dusttemp to file
@GijsVermarien
Features/updated notebooks (#76)
9ebda25 
* Move timepoints to the models API

Users can now change the number of timepoints in realtime

* Added new notebooks with timepoint support and small fixes

* Update notebooks.yml

* Update workflow and add precommit

* Modernize the nbstripout

* Precommit and format notebooks

* Try another kernel name

* Another attempt at getting the notebooks testing to work

* Fix small things in notebooks

* Update notebooks.yml
@GijsVermarien
Small last additions to makerates
347b4f5
@GijsVermarien GijsVermarien changed the title Develop UCLCHEM v3.4.0 Oct 14, 2024
@GijsVermarien GijsVermarien merged commit ddbe587 into main Oct 14, 2024
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4 participants
@GijsVermarien @Marcus-Keil @katarzynadutkowska @psharda