Chemistry Interfaces for Krome, Uclchem, and KromeSph - #1282

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elkogerville wants to merge 150 commits into

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elkogerville:chemistry

Commits on Nov 13, 2025

Commits on Apr 9, 2026

cleaned up Uclchem in amuse/community
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5af1567

Commits on Apr 10, 2026

uclchem support
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fixed uclchem amuse_deps
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started working on UCLChem Makefile
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uclchem interface.f90
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uclchem interface.py
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rm amuse_helpers.f90
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35f0e42

Commits on Apr 16, 2026

fixed amuse UCLCHEM Makefile to properly download and compile the code from github
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a56fbb9
fixed uclchem deps
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5985f15

Commits on Apr 17, 2026

fixed bugs in UCLCHEM Makefile compiling uclchem without downloading it, and fixing download statements
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341095a
fixed typo in amuse_uclchem/__init__.py
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fixed uclchem test imports
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def UclchemImplementation to replace interface.cc
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uclchem pyproject.toml changes
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cleanup uclchem forwarding interface.py
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Commits on Apr 29, 2026

made uclchem a build dependency in Makefile
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fixed import statement in interface.py uclchem
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adfb4ab
added missing configure script for uclchem
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c3a1571
fixed shared folder not simlinking properly uclchem
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9ed7b1e
added LiteratureReferencesMixIn to UclchemInterface
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cf496f7
cleaned up uclchem toml
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added MODEL_MAP to uclchemImplementation
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Commits on Apr 30, 2026

working new_particle uclchem
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def get_state set_state and helper function _is_valid_particle_index
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def UclchemInterface and Uclchem methods, parameters, particle sets
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def TestUclchem test add_particle
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def set/get_number_density uclchem
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set/get_number_density uclchem legacy interface
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test_uclchem TestUclchemInterface def test_getters_and_setters
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def get/set_temperature uclchem
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uclchem tests
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Commits on May 3, 2026

uclchem interface.py cleanup and more setters / getters
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def delete particle uclchem
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updated uclchem tests
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Commits on May 4, 2026

Commits on May 6, 2026

cleanup uclchem interface.py
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def get_abundance, get_abundance_name, get_abundance_index
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383e2e1

Commits on May 8, 2026

uclchemimplementation clean up __init__
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commit_params now validates chemical model, commit_particles initializes the abundance array
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chemical model now validated with _validate_chemical_model, get_time docs
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refactored evolve_model to use physics and abundance arrays directly instead of relying on previous model
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uclchem docs and cleanup
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uclchem implementation docs
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added docs to evolve_model and check that input time is in future
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def set_abundance
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add zeta and radfield to particle attributes sent to uclchem
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ff6b925
uclchem interface.py cleanup
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d60f0c0
finished test_getters_and_setters
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Commits on May 11, 2026

Commits on May 12, 2026

added docs to uclchem implementation __init__
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def test_get_abundances uclchem
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def Uclchem.get_abundances to query a list of abundances of a particle"
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Commits on May 27, 2026

Commits on Jun 22, 2026

update abundance attribute to abundances
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fixed index managment in uclchem with _get_particle_index_by_id
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bdadf04
fixed adding and removing particle tests
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26d9597

Commits on Jun 30, 2026

fixed typo in VectorAttribute
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9a6de28

Commits on Aug 23, 2026

fix imports uclchem
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8c63ead

Commits on Sep 14, 2026

rm unused interface.f90 uclchem
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ec3fa67
fix pinned version Uclchem
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cleanup uclchem interface
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rename _get_particle_index_by_id to _id_to_storage_index
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cleanup uclchem interface
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b33b44b
cleanup uclchem interface
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fa893ea
add chem.py to amuse interfaces
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2aaaa05
fix uclchem tests
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f753e08
updated uclchem packages
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rename abundance_index parameter to species_index
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modernized krome interface.f90
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cleanup krome interface.py
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c5dd1bf
remove un-needed code in interface.py krome
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fixed Krome tests
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48b5dc7
modernize amuse_helpers.f90 krome
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clean up
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fix uclchem tests
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fix import shims krome
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Commits on Sep 15, 2026

cleanup config.mk.in uclchem
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add more particle getters and setters to chem interface
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clean up chem.py
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add setters and getters to krome
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clean up krome interface.py
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cleanup interface.f90 krome
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add test for KromeInterface setters and getters
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remove redundant setters and getters uclchem interface.py
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cleanup
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register habing in units.py
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clean up uclchem parameters
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finish renaming abundance_index to species_index
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fix uclchem tests broken import
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Commits on Sep 16, 2026

test_delete_particles krome
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class ChemTemperatureNumberDensityInterface mixin to split chem interface btwn number density/temp and density/internal energy
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rename to ChemNumberDensityTemperatureInterface, and propagate in codebase
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cleaned up chem.py docs
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class ChemDensityInternalEnergyInterface mixin for density and internal energy setters and getters in chemistry codes
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cleanup krome interface
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test that deleting particles in krome correctly deletes the abundances
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cleanup uclchem docs
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test that deleting particles in uclchem correctly deletes the abundances
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cleanup krome docs
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import shim for kromesph
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kromesph makefile
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kromesph interface.f90
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kromesph interface.py
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krome sph __init__
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kromesph packages/
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kromesph shared/
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test_kromesph.py
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kromesph inner Makefile
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kromesph amusehelpers
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kromesph hash.f90
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krome_constants_amuse.f90 kromesph
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fix krome tests
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a690bdd
cleanup uclchem tests
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03a46fe
added missing ionrate setters and getters in kromesph interface.f90
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two new mixins for chemistry evolution
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7626f2c
propagate mixin for kromesph
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ba6bed2
propagate mixin for uclchem
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9943a24
Update .gitignore
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b818a48
fix whitespace issue
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601b56e
cleanup krome tests
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0e284fc
fix kromesph worker name
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291f2b3
add missing setters and getters in kromesph
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fix some kromesph tests
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359d4ee
fix more kromesph tests
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7fcaa4e
fix kromesph tests and interface
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8e72959
fix more kromesph tests
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61ac9b5
fixed particle sets in krome, uclchem, and kromesph
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new test kromesph
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uclchem particle set definition
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Commits on Sep 17, 2026

fix indexing of krome.species
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add more Krome tests
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fix krome __init__
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ec3ceb5
add more kromesph tests
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fix mu unit conversion bug in kromesph amuse_helpers.f90
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fix kromesph tests
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fix kromesph tests
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