UCLCHEM v3.4.0

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 and dustTemp are 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: #37)
• We improved test coverage
• We now have precommit configured to improve code quality

What's Changed

• Upstream to develop by @GijsVermarien in #35
• Features/return array by @Marcus-Keil in #34
• Magnetic parameter bm0 added as a new default parameter by @katarzynadutkowska in #52
• Add specname_out to cshock by @GijsVermarien in #53
• Update pyproject.toml by @GijsVermarien in #55
• Add axes labels and show grid by @psharda in #48
• Move to UMIST22 by @GijsVermarien in #56
• Features/postprocessing by @GijsVermarien in #59
• Add smaller than 2 dependencies by @GijsVermarien in #60
• Constrain dependencies further by @GijsVermarien in #61
• Fix/upstream build 2409 by @GijsVermarien in #63
• Update defaultparameters.f90 by @GijsVermarien in #64
• Fix/makerates constants by @GijsVermarien in #65
• Added read the docs config file by @GijsVermarien in #66
• Update .readthedocs.yaml by @GijsVermarien in #67
• We cannot have fortran here... :( by @GijsVermarien in #68
• Features/branching ratio checks by @GijsVermarien in #69
• Remove H2 diss from UMIST and add better duplicate checking by @GijsVermarien in #71
• Isolate the changes to analysis.py by @GijsVermarien in #73
• Fix/jshock points by @GijsVermarien in #74
• Fix/rad and dusttemp in csv by @GijsVermarien in #75
• Features/updated notebooks by @GijsVermarien in #76
• Small last additions to makerates by @GijsVermarien in #78
• UCLCHEM v3.4.0 by @GijsVermarien in #77

New Contributors

• @katarzynadutkowska made their first contribution in #52
• @psharda made their first contribution in #48

Full Changelog: v3.3.3...v3.4.0

v3.3.3 Updated Python requirement

Move to Python >=3.9 and added pytest as a dependency.

Pytest fixes, Path fix and faster pip install

See #47.

Note to ourselves: we should automate the process of uclchem.github.io whenever a new release is created.

Fixed Makerates compare scripts

Updated the compare scripts to newest makerates (#44)

Updated the scripts to compare the species, reactions and networks with the newest version of Makerates (>3.2.0)

v3.3.0 New installer

We move to a new installer, since numpy distutils was going to be deprecated soon. The big change is that we now need to use editable install pip install -e . instead of pip install . to install the package.

Full Changelog: v3.2.1...v.3.3.0

What's Changed

• Features/new installer by @GijsVermarien in #40
• Fixed v.3.3.0 -> v3.3.0 typo

Full Changelog: v3.2.1...v3.3.0

v3.2.1

New minor release has the production and destruction in analysis removed from printing as the function is reimplemented.

What's Changed

• Remove writing of production and destruction by @GijsVermarien in #36

Full Changelog: v3.2.0...v3.2.1

v3.2.0

UCLCHEM 3.2 consists of refactoring Makerates and moving it into the Python source.

• Moved makerates code into the python source
  This allows one to interact with the Network, Reaction and Species code directly.
• The repr and str methods that are added to the Species, Reactions and Network are better suited for manipulation with Python
  Replaced print statements in Makerates with the logging module
• Refactored the inner working of makerates
• Everything is now more object oriented with getter and setter methods for many parameters. This allows for adding many checks.
  Added parser to accept verbosity and settings path for Makerates.py
  Now one can specify which configuration file to use by specifying the path to it. The default stays user_settings.yaml
• Two reactions are added to be consistent with the freezeouts.
  HEH+ and H3+ were freezing out to #HEH and #H3 which was not correct per se, so two reactions are added to make them freeze out to more sensible constituents:

H3+,FREEZE,,#H,#H,#H,,1,1,0,,,
HEH+,FREEZE,,#H,#HE,,,1,1,0,,,

What's Changed

• Update README.md by @GijsVermarien in #26
• Added citation information by @GijsVermarien in #31
• Features/improve makerates by @GijsVermarien in #32
• UCLCHEM V3.2.0 by @GijsVermarien in #33

New Contributors

• @GijsVermarien made their first contribution in #26

Full Changelog: v3.1.0...v3.2.0

v3.1.0

V3.1

Version 3.1 implements excited species which are grain surface species put into excited states by cosmic rays. We've also fixed any bugs the UCLCHEM team found when using v3.0. The result is a stable, well tested release which we recommend all users move to for their next chemical modelling project.

What's Changed

Excited Species

• New treatment for excited species on the grains.

Bug Fixes

• Fixed F2PY bug for analysis.py

More details:

• #wrap (Jon) by @rossodonoghue92 in #23
• #Shocks by @jonholdship in #24

Full Changelog: v3.0.0...v3.1.0

UCLCHEM v3.0

UCLCHEM is now Python first. The underlying code is still written in Fortran but the code is pip installable and intended to be used entirely via the python module.

Overview of Changes

• All physics modules can be accessed from a single install, as different python functions
• (Optional) Improved CRIR treatment following Padovani et al. 2018.
• (Optional) improved CR dissociation of H2 following Padovani et al. 2018b.
• Minor bug fixes and big performance boosts - code runs in as little as half the time
• The docs have been updated to include detailed tutorials on code use, lists of all parameters, explanation of the Python API and science background
• Makerates now produces networks in with much less input from the user and automatically moves the files to the src folder. You just need to pip install afterwards

V2.0.3 HITs paper release

Stability improvements, abs/rel tol picked by grid search.