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00a289e
test file
elkogerville Nov 13, 2025
4b98191
remove test file
elkogerville Nov 13, 2025
53becee
created amuse_uclchem directory in amuse/src
elkogerville Nov 13, 2025
2aeb166
added uclchem to src/amuse/community and added DS_Store to gitignore
elkogerville Nov 13, 2025
24542e9
added uclchem src to amuse/sec/amuse_uclchem/src
elkogerville Nov 13, 2025
5af1567
cleaned up Uclchem in amuse/community
elkogerville Apr 9, 2026
563a429
uclchem support
elkogerville Apr 10, 2026
ce346af
fixed uclchem amuse_deps
elkogerville Apr 10, 2026
b719d88
started working on UCLChem Makefile
elkogerville Apr 10, 2026
f67774b
uclchem interface.f90
elkogerville Apr 10, 2026
2c01779
uclchem interface.py
elkogerville Apr 10, 2026
35f0e42
rm amuse_helpers.f90
elkogerville Apr 10, 2026
a56fbb9
fixed amuse UCLCHEM Makefile to properly download and compile the cod…
elkogerville Apr 16, 2026
5985f15
fixed uclchem deps
elkogerville Apr 16, 2026
341095a
fixed bugs in UCLCHEM Makefile compiling uclchem without downloading …
elkogerville Apr 17, 2026
02e2efc
fixed typo in amuse_uclchem/__init__.py
elkogerville Apr 17, 2026
ed8ab65
fixed uclchem test imports
elkogerville Apr 17, 2026
111fcc8
def UclchemImplementation to replace interface.cc
elkogerville Apr 17, 2026
ea59285
uclchem pyproject.toml changes
elkogerville Apr 17, 2026
efc2c9c
cleanup uclchem forwarding interface.py
elkogerville Apr 17, 2026
7ee863b
made uclchem a build dependency in Makefile
elkogerville Apr 29, 2026
adfb4ab
fixed import statement in interface.py uclchem
elkogerville Apr 29, 2026
c3a1571
added missing configure script for uclchem
elkogerville Apr 29, 2026
9ed7b1e
fixed shared folder not simlinking properly uclchem
elkogerville Apr 29, 2026
cf496f7
added LiteratureReferencesMixIn to UclchemInterface
elkogerville Apr 29, 2026
948de38
cleaned up uclchem toml
elkogerville Apr 29, 2026
85e2808
added MODEL_MAP to uclchemImplementation
elkogerville Apr 29, 2026
982299d
working new_particle uclchem
elkogerville Apr 30, 2026
126d327
def get_state set_state and helper function _is_valid_particle_index
elkogerville Apr 30, 2026
3596e0a
def UclchemInterface and Uclchem methods, parameters, particle sets
elkogerville Apr 30, 2026
8e30a3b
def TestUclchem test add_particle
elkogerville Apr 30, 2026
5392b7f
def set/get_number_density uclchem
elkogerville Apr 30, 2026
2d9a04f
set/get_number_density uclchem legacy interface
elkogerville Apr 30, 2026
2861794
test_uclchem TestUclchemInterface def test_getters_and_setters
elkogerville Apr 30, 2026
8078856
def get/set_temperature uclchem
elkogerville Apr 30, 2026
490b10d
uclchem tests
elkogerville Apr 30, 2026
613c93c
uclchem interface.py cleanup and more setters / getters
elkogerville May 3, 2026
8ed7842
def delete particle uclchem
elkogerville May 3, 2026
f32b0ef
updated uclchem tests
elkogerville May 3, 2026
04be0a8
docstrings for UclchemImplementation
elkogerville May 4, 2026
99a56e6
docstrings for uclchem implementation
elkogerville May 4, 2026
99a606c
def evolve_model UclchemImplementation
elkogerville May 4, 2026
f77cd8b
UclchemImplementation docs, added units to evolve model and property …
elkogerville May 4, 2026
c12e3ce
cleanup uclchem interface.py
elkogerville May 6, 2026
383e2e1
def get_abundance, get_abundance_name, get_abundance_index
elkogerville May 6, 2026
92f61a8
uclchemimplementation clean up __init__
elkogerville May 8, 2026
f4e65c4
commit_params now validates chemical model, commit_particles initiali…
elkogerville May 8, 2026
acbb321
chemical model now validated with _validate_chemical_model, get_time …
elkogerville May 8, 2026
0e45d42
refactored evolve_model to use physics and abundance arrays directly …
elkogerville May 8, 2026
e8152a8
uclchem docs and cleanup
elkogerville May 8, 2026
a3bbd8c
uclchem implementation docs
elkogerville May 8, 2026
4d7a97d
added docs to evolve_model and check that input time is in future
elkogerville May 8, 2026
d6d7fd4
def set_abundance
elkogerville May 8, 2026
ff6b925
add zeta and radfield to particle attributes sent to uclchem
elkogerville May 8, 2026
d60f0c0
uclchem interface.py cleanup
elkogerville May 8, 2026
6aa19f2
finished test_getters_and_setters
elkogerville May 8, 2026
a0408e7
fixed bug in Uclchem Makefile causing Uclchem to be redownloaded ever…
elkogerville May 11, 2026
ecb6f4e
fixed zeta bug in uclchem interface, now correctly normalizes ionrate…
elkogerville May 11, 2026
eb0862b
added docs to uclchem implementation __init__
elkogerville May 12, 2026
d7f0a4f
def test_get_abundances uclchem
elkogerville May 12, 2026
fb83d63
def Uclchem.get_abundances to query a list of abundances of a particle"
elkogerville May 12, 2026
0104f58
cleaned up uclchem tests
elkogerville May 19, 2026
e90cb97
renamed self.particles to self.uclchem_particles to distinguish the l…
elkogerville May 19, 2026
4067ba2
added better docstrings for amuse.rfi.python_code.ValueHolder in Uclc…
elkogerville May 19, 2026
a4482b1
def get_number_of_particles uclchem
elkogerville May 19, 2026
f261dc3
def get_firstlast_abundance uclchem interface, def gridded_getter/set…
elkogerville May 27, 2026
5585bc2
clean up uclchem interface
elkogerville May 27, 2026
8c11ab9
update abundance attribute to abundances
elkogerville Jun 22, 2026
bdadf04
fixed index managment in uclchem with _get_particle_index_by_id
elkogerville Jun 22, 2026
26d9597
fixed adding and removing particle tests
elkogerville Jun 22, 2026
9a6de28
fixed typo in VectorAttribute
elkogerville Jun 30, 2026
8c63ead
fix imports uclchem
elkogerville Aug 23, 2026
ec3fa67
rm unused interface.f90 uclchem
elkogerville Sep 14, 2026
399343c
fix pinned version Uclchem
elkogerville Sep 14, 2026
59b1fb3
cleanup uclchem interface
elkogerville Sep 14, 2026
23f2649
rename _get_particle_index_by_id to _id_to_storage_index
elkogerville Sep 14, 2026
b33b44b
cleanup uclchem interface
elkogerville Sep 14, 2026
fa893ea
cleanup uclchem interface
elkogerville Sep 14, 2026
2aaaa05
add chem.py to amuse interfaces
elkogerville Sep 14, 2026
f753e08
fix uclchem tests
elkogerville Sep 14, 2026
5f1d5c1
updated uclchem packages
elkogerville Sep 14, 2026
2f03281
rename abundance_index parameter to species_index
elkogerville Sep 14, 2026
f52b509
modernized krome interface.f90
elkogerville Sep 14, 2026
c5dd1bf
cleanup krome interface.py
elkogerville Sep 14, 2026
c088ac1
remove un-needed code in interface.py krome
elkogerville Sep 14, 2026
48b5dc7
fixed Krome tests
elkogerville Sep 14, 2026
a7ad9a7
modernize amuse_helpers.f90 krome
elkogerville Sep 14, 2026
4022b35
clean up
elkogerville Sep 14, 2026
62f6255
fix uclchem tests
elkogerville Sep 14, 2026
59b2de6
fix import shims krome
elkogerville Sep 14, 2026
96f2811
cleanup config.mk.in uclchem
elkogerville Sep 15, 2026
1ef985c
add more particle getters and setters to chem interface
elkogerville Sep 15, 2026
f9ec310
clean up chem.py
elkogerville Sep 15, 2026
f2e4d65
add setters and getters to krome
elkogerville Sep 15, 2026
1d0eb78
clean up krome interface.py
elkogerville Sep 15, 2026
379ffbf
cleanup interface.f90 krome
elkogerville Sep 15, 2026
792fd7e
add test for KromeInterface setters and getters
elkogerville Sep 15, 2026
ce42dbe
remove redundant setters and getters uclchem interface.py
elkogerville Sep 15, 2026
f6eee02
cleanup
elkogerville Sep 15, 2026
e333b57
register habing in units.py
elkogerville Sep 15, 2026
650aad0
clean up uclchem parameters
elkogerville Sep 15, 2026
bc3c705
finish renaming abundance_index to species_index
elkogerville Sep 15, 2026
7f31128
fix uclchem tests broken import
elkogerville Sep 15, 2026
c21d050
test_delete_particles krome
elkogerville Sep 16, 2026
ea8f78a
class ChemTemperatureNumberDensityInterface mixin to split chem inter…
elkogerville Sep 16, 2026
4856e50
rename to ChemNumberDensityTemperatureInterface, and propagate in cod…
elkogerville Sep 16, 2026
a96e408
cleaned up chem.py docs
elkogerville Sep 16, 2026
ce32154
class ChemDensityInternalEnergyInterface mixin for density and intern…
elkogerville Sep 16, 2026
7707070
cleanup krome interface
elkogerville Sep 16, 2026
0275125
test that deleting particles in krome correctly deletes the abundances
elkogerville Sep 16, 2026
e621aa6
cleanup uclchem docs
elkogerville Sep 16, 2026
1328f10
test that deleting particles in uclchem correctly deletes the abundances
elkogerville Sep 16, 2026
08167c8
cleanup krome docs
elkogerville Sep 16, 2026
2b3aacc
import shim for kromesph
elkogerville Sep 16, 2026
0181461
kromesph makefile
elkogerville Sep 16, 2026
b5e19ba
kromesph interface.f90
elkogerville Sep 16, 2026
c5b1f43
kromesph interface.py
elkogerville Sep 16, 2026
4211e55
krome sph __init__
elkogerville Sep 16, 2026
11f3e2c
kromesph packages/
elkogerville Sep 16, 2026
6ffb783
kromesph shared/
elkogerville Sep 16, 2026
2034696
test_kromesph.py
elkogerville Sep 16, 2026
addb1ee
kromesph inner Makefile
elkogerville Sep 16, 2026
abdb6ae
kromesph amusehelpers
elkogerville Sep 16, 2026
164fe8f
kromesph hash.f90
elkogerville Sep 16, 2026
4191292
krome_constants_amuse.f90 kromesph
elkogerville Sep 16, 2026
a690bdd
fix krome tests
elkogerville Sep 16, 2026
03a46fe
cleanup uclchem tests
elkogerville Sep 16, 2026
11f0b85
added missing ionrate setters and getters in kromesph interface.f90
elkogerville Sep 16, 2026
7626f2c
two new mixins for chemistry evolution
elkogerville Sep 16, 2026
ba6bed2
propagate mixin for kromesph
elkogerville Sep 16, 2026
9943a24
propagate mixin for uclchem
elkogerville Sep 16, 2026
b818a48
Update .gitignore
elkogerville Sep 16, 2026
601b56e
fix whitespace issue
elkogerville Sep 16, 2026
0e284fc
cleanup krome tests
elkogerville Sep 16, 2026
291f2b3
fix kromesph worker name
elkogerville Sep 16, 2026
2085146
add missing setters and getters in kromesph
elkogerville Sep 16, 2026
359d4ee
fix some kromesph tests
elkogerville Sep 16, 2026
7fcaa4e
fix more kromesph tests
elkogerville Sep 16, 2026
8e72959
fix kromesph tests and interface
elkogerville Sep 16, 2026
61ac9b5
fix more kromesph tests
elkogerville Sep 16, 2026
59f0edb
fixed particle sets in krome, uclchem, and kromesph
elkogerville Sep 16, 2026
bd05329
new test kromesph
elkogerville Sep 16, 2026
7624518
uclchem particle set definition
elkogerville Sep 16, 2026
ddbec75
fix indexing of krome.species
elkogerville Sep 17, 2026
1b120f2
add more Krome tests
elkogerville Sep 17, 2026
ec3ceb5
fix krome __init__
elkogerville Sep 17, 2026
8d832a3
add more kromesph tests
elkogerville Sep 17, 2026
7a0a0d8
fix mu unit conversion bug in kromesph amuse_helpers.f90
elkogerville Sep 17, 2026
bf14494
fix kromesph tests
elkogerville Sep 17, 2026
48f65e7
fix kromesph tests
elkogerville Sep 17, 2026
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1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -455,3 +455,4 @@ packages/dist

# standard directory for a virtualenv
env/

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