Chemistry Interfaces for Krome, Uclchem, and KromeSph - #1282
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elkogerville wants to merge 143 commits into
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elkogerville wants to merge 143 commits into
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…it, and fixing download statements
elkogerville
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area: community_code
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This PR adds
Uclchem,Krome, andKromeSphas a community code in AMUSE.This PR also adds the new
ChemicalEvolutionInterfaceand other chemical evolution interfaces insrc/amuse/community/interfaces/chem.pyUclchem is a gas-grain chemical code for astrochemical modelling.
Implementation Notes
• Krome and Uclchem were rewritten to have near identical interfaces for similar user experiences
• Created new methods for chemistry specific operations:
•
get_abundances_by_name-> method that takes a list of species names as input and returns the corresponding abundances for that particle•
get_abundance-> method that takes in a species index and returns the abundance for that specific species•
set_abundance-> corresponding method that sets the abundance of a species for a particle•
set_abundances-> vectorized method that can set the entire abundance array of a particle from a numpy array• Added u.habing to
units.pyUclchem Notes:
• The interface is completely written in Python.
• The Uclchem version is pinned to the latest release
v4.0.0• Uses the new
ChemicalEvolutionInterfaceKrome Notes:
• Krome was already implemented in AMUSE but this PR refactors the interfaces to use
ChemicalEvolutionInterface• All fortran files were rewritten in modern fortran syntax for future maintainability.
KromeSph Notes:
• KromeSph is an alternate compilation of Krome more suitable for coupled hydrodynamical simulations with Krome.
• Temperature and number density particle attributes were replaced with internal energy and density for more seamless coupling with hydro codes via channels.
• Additional chemistry interface mixins in
src/amuse/community/interfaces/chem.pywere created to support this interfaceCloses issue #1261