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CLAUDE.md
LICENSE
README.md
mkdocs.yml
pyproject.toml
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.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/config.yml
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data/README.md
data/test/density_2d_lookup.dat
data/test/eos_test.dat
data/test/liquidus_1d_lookup.dat
data/test/solidus_1d_lookup.dat
docs/getting_started.md
docs/index.md
docs/proteus-framework.md
docs/Community/CODE_OF_CONDUCT.md
docs/Community/CONTRIBUTING.md
docs/Community/contact.md
docs/Explanations/code_architecture.md
docs/Explanations/core_bc.md
docs/Explanations/cvode_jax.md
docs/Explanations/energy_diagnostics.md
docs/Explanations/energy_equation.md
docs/Explanations/eos_sanity_checks.md
docs/Explanations/heat_transport.md
docs/Explanations/jax_jacobian_factory.md
docs/Explanations/mixing_length.md
docs/Explanations/model.md
docs/Explanations/phase_transitions.md
docs/Explanations/phi_step_cap_rationale.md
docs/Explanations/pressure_eos.md
docs/Explanations/proteus_coupling.md
docs/Explanations/spider_comparison.md
docs/Explanations/testing.md
docs/Explanations/two_phase_flow.md
docs/Explanations/verification.md
docs/How-to/build_tests.md
docs/How-to/configuration.md
docs/How-to/installation.md
docs/How-to/netcdf.md
docs/How-to/phi-step-cap.md
docs/How-to/proteus_coupling.md
docs/How-to/solver-method-tuning.md
docs/How-to/usage-paths.md
docs/How-to/usage.md
docs/How-to/utbl-parameterisation.md
docs/Reference/cli.md
docs/Reference/data.md
docs/Reference/publications.md
docs/Reference/api/aragog.config.md
docs/Reference/api/aragog.eos.md
docs/Reference/api/aragog.jax.md
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docs/Reference/api/aragog.output.md
docs/Reference/api/aragog.solver.md
docs/Reference/api/index.md
docs/Tutorials/build_test.md
docs/Tutorials/firstrun.md
docs/assets/PROTEUS_black_on_white_logo_only.png
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docs/figures/vv/fig_07_mass_coord_jacobian.pdf
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docs/javascripts/external-links.js
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fwl_aragog.egg-info/PKG-INFO
fwl_aragog.egg-info/SOURCES.txt
fwl_aragog.egg-info/dependency_links.txt
fwl_aragog.egg-info/entry_points.txt
fwl_aragog.egg-info/requires.txt
fwl_aragog.egg-info/top_level.txt
src/aragog/__init__.py
src/aragog/cli.py
src/aragog/parser.py
src/aragog/utilities.py
src/aragog/cfg/__init__.py
src/aragog/cfg/abe_liquid.cfg
src/aragog/cfg/abe_mixed.cfg
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src/aragog/config/energy.py
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src/aragog/config/phases.py
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src/aragog/eos/entropy.py
src/aragog/eos/entropy_phase.py
src/aragog/jax/__init__.py
src/aragog/jax/eos.py
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tests/test_jax_mesh_gravity_fallback.py
tests/test_jax_module_branches.py
tests/test_jax_no_phi_vol_source.py
tests/test_jax_radio_per_step.py
tests/test_jax_utbl_cardano.py
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tests/test_misc_edge_branches.py
tests/test_parser.py
tests/test_parser_toml_dispatch.py
tests/test_permeability_constants.py
tests/test_phi_step_cap.py
tests/test_phi_step_cap_armed_smoke.py
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tools/verification/run_bc_verification.py
tools/verification/run_ic_heating_verification.py
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