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Molecular CR model implementation #31

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@holm10 holm10 commented May 23, 2023

Implementation of collisional-radiative model for hydrogen molecules, including molecular particle and energy rates.

  • Molecular CRM model is controlled by switch bbb.ismolcrm
  • Model only active is ishymol
  • Model only reads CR rate files when ismolcrm > 0 -> not necessary for backwards-compatibility
  • Switch defaults to 0, using old molecular model when ishymol
  • bbb.ishymol is a float, scaling linearly between the models
  • CR model fully activated when ismolcrm=1, old model completely deactivated
  • Model adds a dimensions to dissociation-related arrays, as molecular dissociation produces less than 2 atoms (depending on the local quasi steady-state equilibrium)
  • Corresponding arrays for molecular particle and energy transfer into ions and atoms have been added
  • Internal routine engbal has been updated to reflect these changes

To do:

  • Resolve albedo-like recycling of atoms into atoms -> albedo-like recycling of atoms to atoms & molecules given factor
  • Simplify control of recycled atomic/molecular fraction
  • Provide (minimal) working example of simulation using the molecular CRM

@holm10 holm10 changed the title Molecular CRM model implementation Molecular CR model implementation May 24, 2023
@holm10 holm10 self-assigned this Feb 9, 2024
Updates UEDGE to V8.1.0.0
Update run_testsuite.yml to correspond to master tests
- Adds pyproject.toml for building w/ PIP
- Modifies build to use Forthon compatible w/ numpy >2.0
- Hardens tests and wheel builds
- Removes Py3.7 builds (EOL)
- fniycbo options via isfniycbozero
  - Makes fniycbo-switch index-dependent
  - Fixes switch for double-null geometries
- Hardens checkver to allow code execution without connection to PyPi
- Implemements build and install using pyproject.toml
- Updates Workflows to ensure compatibility of Forhton with numpy>2.0
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