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CF Merger #3: Compositional Flow models #1236
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bf2f146
ENH: Added total energy balance and Fouriers Law for compositional flow.
vlipovac 6b6047e
ENH: Added component mass balance class to compositional flow.
vlipovac 143245d
Merge 'develop' into composite-flow
vlipovac 7b006fe
WIP: Work on solutionstrategy for compositional flow.
vlipovac 451bb79
WIP: Added some methods to SolutionStrategy for compositional flow.
vlipovac 89e7883
MOD: Refactoring compositional mixins and adding Flash mixin.
vlipovac 4f26e49
MOD: Refactoring compositional flow model to include secondary expres…
vlipovac 2305192
MOD: Refactoring mass balances to fractional flow simulation and non-…
vlipovac 5726191
MOD: Refactoring composite package s.t. variables and proparties are …
vlipovac 0422197
FIX: Access to refactored mixture density in compositinal balance equ…
vlipovac acf3c0c
MOD: Refactoring composite mixins to fit general structure.
vlipovac 1fe84be
MOD: CF model now has a separate mixin dealing with mobility terms.
vlipovac 9570af3
MOD: Access to weights in advective flux and removal of some inconsis…
vlipovac c74c902
MOD: Re-worked representation of phase properties as instances of Sec…
vlipovac edaef33
MOD: Adding boundary and initial equilibrium to CF model set-up.
vlipovac 14f5605
MOD: Reworking SecondaryExpression class to account for time index, i…
vlipovac a6fc3e0
MOD: Enhancing solution strategy on CF framework, renaming some quant…
vlipovac 6e6b95c
MOD: Solution of CF linear system uses Schur complement to eliminate …
vlipovac 7258bae
Merge 'develop' into composite-flow
vlipovac 93f0217
MOD: Adding option to store derivatives in time and iterate sense for…
vlipovac 3d22cbe
FIX: Various fixes in CF framework.
vlipovac f5872cc
FIX: Time step and iterate indexation in secondary expressions.
vlipovac a296017
FIX: Data access in secondary operators, definition of primary vars a…
vlipovac e459e72
BREAKING: Several modifications in CF framework which need to be tested.
vlipovac 83e8ba0
MOD: Changing several aspects of CF framework to accomodate constitut…
vlipovac 498825c
MOD: Splitting some functionality of the CF framework into hierarchic…
vlipovac 3ac5ffc
MOD: Splitting of functionality for CF models with and without LE.
vlipovac 713a7ea
MOD: Fixing BC mixins for CF and CFLE after functionality split.
vlipovac 4de16e2
WIP: Debugging CFLE.
vlipovac e8f04d6
FIX: non-linear permeability tensor for pressure and interface equati…
vlipovac 4ad0a73
DEV: Reduced system is now an option
OmarDuran cb89370
Multi phase component flow (#1146)
OmarDuran 48c60d8
WIP: Brine system with constant states in space and time
OmarDuran e22ab9c
MAINT: Simplifying DriesnerBrineOBL.py
OmarDuran 49f098f
STY: black on geothermal example
OmarDuran f339ee0
Merge branch 'develop' into composite-flow
OmarDuran 0b11f96
MAINT: Fix inconsistency while discretize nonlinear operators
OmarDuran 78ef8a0
MOD: partial fractions are now constant 1 if only one component in ph…
vlipovac 5322389
MOD: Partial fractions (not extended) are constant 1 if only 1 compon…
vlipovac 2f05b41
MOD: Constitutively eliminated variables include BC update
vlipovac c19b9f0
BUG: incorrect flux
OmarDuran 41ffa40
BUG: incorrect overall flux
OmarDuran b933a26
FIX: Access to bc type for advective flux upwinding
vlipovac a687bb6
FIX: fluid state calculation of density derivative now avoids divisio…
vlipovac 87282b2
MAINT: ongoing work
OmarDuran 9f26a87
Merge branch 'composite-flow' of https://github.com/pmgbergen/porepy …
OmarDuran f06a4ee
BUG: incorrect outlet boundary fluxes
OmarDuran 987cb31
MAINT: simple setting
OmarDuran e2d17ba
MIN: Changes in Soereide script
vlipovac 9ba1d15
FIX: Usage of BC operators in upwinding in advective fluxes.
vlipovac 410b43d
BUG: energy residuals are not close to zero with pure diffusion
OmarDuran a8e8773
MAINT: Units conversion in BOL are implicit
OmarDuran 4eeeaf1
WIP: Falling back to tracer setting
OmarDuran 7fd2db1
WIP: Still nonlinear setting
OmarDuran c199420
WIP: Tracer setting similar to Driesner
OmarDuran f866523
MAINT: Correct inlet BCs for transport with fractured media
OmarDuran 3b3f71b
FIX: Model set-up for correlations and tracer
vlipovac 56fd920
WIP: Ongoing work with complex geometry
OmarDuran 48b3a3e
MAINT: Fetching inlet and outlet via sphere membership query
OmarDuran 3b9b196
MAINT: Example Geometries tested on tracer-like setting.
OmarDuran 0f604d2
MAINT: Fix a typo in initial pressure method.
OmarDuran 1608274
MAINT: Isenthalpic flow process on Benchmark2DC3 + DriesnerOBL
OmarDuran ae9afa1
MAINT: Black
OmarDuran 0438e89
MAINT: isort
OmarDuran 6b4bc38
MAINT: Default setting
OmarDuran cd62168
MAINT: Simple Petsc support
OmarDuran 149bc94
DEV: Adding a tracer like setting
OmarDuran 2a372e5
MAINT: Variables order agrees with assembled equations.
OmarDuran a8f1947
WIP: Ongoing work with linear trace
OmarDuran 4460c1c
MAINT: Adding extra dependencies
OmarDuran c2ed00c
Numba modifications to eliminate import overhead (#1148)
vlipovac f196984
WIP: Depuration CFLE model
vlipovac 8299698
MAINT: rename to secondary_variables_names
OmarDuran 1ffd8ae
MAINT: set it is an unordered collection
OmarDuran 13da937
FIX: Parsing only value of AD operator functions. MOD: Logging in com…
vlipovac 6dfa769
MIN: Logging in pr eos.
vlipovac daadc40
MAINt: Incorrect jacobian in linear descriptions
OmarDuran 15ba363
Merge branch 'develop' into composite_flow_tests
OmarDuran 4103d92
Merge branch 'develop' into composite-flow
OmarDuran c5a1494
Merge branch 'composite-flow' into composite_flow_tests
OmarDuran 9e50b5d
MAINT: after_nonlinear_convergence has void signature
OmarDuran df35043
Merge branch 'composite-flow' into composite_flow_tests
OmarDuran ede8f64
Merge branch 'composite-flow' of github.com:pmgbergen/porepy into com…
vlipovac 3c132ef
TEST: Adding tests for computation of Peng-Robinson EoS.
vlipovac f2ee267
TEST: Added Taylor expansion test for PR EOS.
vlipovac 25dac93
MOD: Changing argument order in PR compressibility factor and optimiz…
vlipovac 6de21fb
MIN: Removing custom scripts folder from branch
vlipovac 3d10555
MIN: NO JIT flag in tests for PR EOS.
vlipovac 208cae9
Merge branch 'composite-flow' into composite_flow_tests
OmarDuran a51213e
MAINT: Minor refactor on compositional_flow
OmarDuran dbc997f
MIN: Refactor Soereide model
vlipovac b8238a4
MOD+FIX: Compiled computation of compressibility factor in PR and NPI…
vlipovac b04c264
Merge branch 'develop' into composite-flow
vlipovac 89b9d47
MIN: assimilate with develop
vlipovac ae3429f
MOD: Purging code merged in PR #1 b36ad26
vlipovac 913d3cb
FIX: Minor fixes in CFLE after merger
vlipovac e445eb4
Merge branch 'composite-flow' into composite_flow_tests
OmarDuran 7b7ca07
FIX: numba pT flash
vlipovac 7c7bc27
MOD: Refactoring numba computations and PhaseStates.
vlipovac 9b68f80
FIX: numba ph uniflash
vlipovac 70c49c3
FIX: I don't know what is fixed, but CFLE works now.
vlipovac 971b702
MIN: fixes in logging
vlipovac 23c16dd
MOD: replacing semismooth min by pp.ad.maximum
vlipovac 9738d8c
MOD: Removing cancelation of Fourier flux.
vlipovac e8dd588
Composite fix numba (#1177)
vlipovac c1ac9aa
Merge branch 'composite-flow' into composite_flow_tests
OmarDuran 9a95a9f
BUG: now is parsing derivatives
OmarDuran 9aae417
WIP: Some simulations with TD correlations
OmarDuran aa975bc
WIP: Improved setting
OmarDuran 8b0a5c7
Merge branch 'composite-flow' into composite_flow_tests
OmarDuran bf6ca95
Fine simulation set-up.
vlipovac 4ddcae8
MAINT: Add 26 predicates for Taylor expansion
OmarDuran ebf3fd4
STY: black on geometrical predicates and VTK interpolator
OmarDuran acd5d16
min changes in CFLE set-up
vlipovac 45e2456
Merge branch 'composite-flow' of github.com:pmgbergen/porepy into com…
vlipovac 33f6c7c
Merge branch 'composite_fix_numba' into composite-flow
vlipovac 679cca1
General face-lift for compositional subpackage
vlipovac 9a66bb4
STY: isort, black, flake8, mypy
vlipovac 5dbed84
Merge branch 'develop' into composite-flow
vlipovac 0af0621
TEST: Adding tests for mixture set-up and mixin.
vlipovac 52ccb85
WIP: Partial setting
OmarDuran d5cd6fd
Merge branch 'develop' into composite_flow_tests
OmarDuran 910a1d6
Merge branch 'develop' into composite-flow
OmarDuran 53b8e55
Merge branch 'composite-flow' into composite_flow_tests
OmarDuran b24186a
MAINT: update signature
OmarDuran 937f326
WIP: Ongoing with physical depuration with a tracer like setting
OmarDuran 012252f
WIP: ongoing work on comparing FV with a pure mixed approach
OmarDuran eb681e7
WIP: Refining flash strategy to domains
vlipovac 0c7c2fd
WIP: incorrect flux
OmarDuran cfceec2
WIP: Testing set-up for Soereide model
vlipovac 2b5d0bc
Merge branch 'composite-flow' of github.com:pmgbergen/porepy into com…
vlipovac ca75f46
FIX: Adapt 1-phase linear tracer to new DOF choice (no partial fracti…
vlipovac 5ab13d3
Merge branch 'develop' into composite-flow
OmarDuran 828ea6a
MOD: Clean-up in CF model, switching to 1 mobility discretization.
vlipovac e7fca30
ENH: Adding option to define fractional flow BC in CF model.
vlipovac 9bf09b2
MOD: naming for fractional flow bc DATA
vlipovac 23b7bb7
MOD: Adding compatibility to use DarcyFluxAd
vlipovac 7bc51a0
FIX: Advective weights in fractional flow BC setting only when called…
vlipovac 0147cf0
FIX: Adding reference porosity required for AdTpfa
vlipovac b876007
WIP: partial refactor on TDriesner flow
OmarDuran 2a2c4c0
WIP: mayor refactor
OmarDuran 027b973
WIP: Driesner setting is again running
OmarDuran 77a827c
WIP: Tracer like model is operational
OmarDuran 295616d
STY: clean up subfolders and examples with two-components and two-phases
OmarDuran 2df5954
WIP: ongoing work with refactor Driesner flow
OmarDuran d65bffd
WIP: Ongoing work with a stable simulation with correlations
OmarDuran dba4687
WIP: internal conversion to Kelvin
OmarDuran c1fb777
MAINT: deafult setting
OmarDuran fe7077e
MAINT: remove assertion for global mass conservation
OmarDuran fb00305
Merge branch 'develop' into composite-flow
vlipovac a5529dc
Synch surrogate factory with branch develop
vlipovac 2ece758
DOC: minor improvement in documentation for Driesner flow example
OmarDuran 58237b8
MAINT: Removing useless file and minor documentation
OmarDuran 156e319
DOC: minor improvement in documentation for tracer flow example
OmarDuran 095f707
MAINT: rename file to tracer_flow
OmarDuran 72336cd
MAINT: Delet obsolete script
OmarDuran ba7291c
Add constitutive modeling for pure water single phase flow with dries…
99a4932
Add geometry for 1D problem
b9ea82c
MAINT: VTK files with PHZ spec for expanded pressure range
OmarDuran a29f1d7
MAINT: VTK files with PTZ specs
OmarDuran b423cd2
Merge branch 'composite-flow' into composite-flow-PTZ-PHZ
OmarDuran 335df87
MAINT: Adding an extra ptz sampler
OmarDuran 70f71f4
WIP: Adding translation to VTKSampler
OmarDuran 5d0eeb7
WIP: Ready to test PTZ sampler
OmarDuran e992204
Update geothermal_flow.py
OmarDuran 21c7ad1
WIP: working on Isothermal IC specs.
OmarDuran d2b89e0
WIP: step to correct fields
OmarDuran 91f70dc
WIP: Simulation is almost ok with Fig. 4. P. Weis. 2014
OmarDuran f377001
MAINT: Minor correction in VTKSampler
OmarDuran d841bd2
DOC: improving documentation of geothermal_flow.py
OmarDuran b4e7024
MAINT: user spec fields with constant extension.
OmarDuran bb0ccef
MAINT: expanded range for vtks
OmarDuran 0d33987
MAINT: Adding mutual exclusion state for VTK sampler
OmarDuran bb3653f
WIP: Better control on memory for VTKSampler
OmarDuran ae9faeb
MOD: Adapting compositional subpackage and models to changes in merge…
vlipovac 6c15065
Merge branch 'develop' into composite-flow
vlipovac c263f6b
MOD: Adapt solutionstrategyCF to recent changes in from develop.
vlipovac 89aa41e
Merge branch 'composite-flow' of github.com:pmgbergen/porepy into com…
vlipovac 5eca010
MOD: Updating examples/geothermal_flow/ to latest changes
vlipovac 7a988ad
STY: mypy for compositional_flow.py
vlipovac 6c16acf
Reducing content according to merging plan.
vlipovac ccb2bfe
MOD: Remove artifacts
vlipovac c26347e
DOC: Update documentation in CF model.
vlipovac fe8f11f
FIX: Tests adapted to CF update.
vlipovac 5707340
MIN: isort black flake8 on compositional/__init__.py
vlipovac dc5bfa3
MIN: Fix typing of _combine_boundary_operators in MassBalanceEquation
vlipovac fe0e3cf
STY: Appease mypy
vlipovac 422ba0c
Merge branch 'develop' into cf_merger_3
vlipovac b864ed7
MIN: Sync with develop
vlipovac 7d7dd60
MIN: Update compositional_flow.py to latest changes in develop
vlipovac fb4ad0a
MIN: Sync with develop
vlipovac de3a76c
MIN: Sync with develop
vlipovac 537f186
MIN: Adding checks whether SurrogateFactory is used for phase propert…
vlipovac b24a201
MOD: Adapting examples/geothermal_flow to recent changes and making t…
vlipovac 84fee82
MIN: Fixing inline doc
vlipovac c6556aa
Merge branch 'develop' into cf_merger_3
vlipovac 6f4d173
ENH/MOD: Introducing InitialConditionsMixin and refactoring code to b…
vlipovac c9f0f01
Merge branch 'develop' into cf_merger_3
vlipovac cfaf9d6
MIN: removing merging artifact
vlipovac c8b6db7
MOD: Adding functionality of MobilityCF to FluidMobility
vlipovac 46be460
Testing whether mypy for 3.12 will be satisfied.
vlipovac d987158
MIN: fix in error message.
vlipovac 7319016
FIX: mypy issue.
vlipovac 33f2ee0
MOD: Generalizing the notion of mobility.
vlipovac 9b2c703
MOD: Introducing consistent naming for advection weights in various b…
vlipovac 579c4ed
DOC: improving documentation of new classes.
vlipovac aab4006
DOC: Improve docs in compositional_flow
vlipovac 60b212a
TUT: Finishing tutorial on tracer flow.
vlipovac c7ea4f3
MIN: Spellchecking tracer flow tutorial.
vlipovac 63da8c1
Purge files which will not be merged yet.
vlipovac d65fbc5
MOD: Switching base model BC classes to new intermediate class for BC…
vlipovac 9f05724
Merge branch 'develop' into cf_merger_3
vlipovac ef0deb8
FIX: tracer tutorial.
vlipovac 53880e5
MOD: Unifying TwoVariable- and basic energy equation.
vlipovac 3070363
MOD: Merging functionality of BC primary vars into base BC mixin.
vlipovac 49d6d41
Merge branch 'develop' into cf_merger_3
vlipovac 9c8c212
MOD: Unifying total mass balance with component mass balance and the …
vlipovac 9dcad9a
TEST: Adding linear tracer test.
vlipovac 1d83579
TEST: Adding test for 3-phase tracer using full CF framework.
vlipovac f0b49c4
MIN: Clean-up in some docs.
vlipovac 332cc8e
MIN: Clean-up in some docs.
vlipovac e11e5b6
Merge branch 'develop' into cf_merger_3
keileg 37f752b
MAINT: Minor clean-up of top-level __init__
keileg 207e7f8
DOC: Cleanup docs in compositional_mixins
keileg ee4f669
DOC: Minor updates to documentations.
keileg 5ca8289
MAINT: documentation and various updates of CF flow
keileg 7e04e30
MAINT: Minor changes related to compositional flow PR
keileg 88b7c99
DOC: Cosmetic changes
IvarStefansson 59b0db7
MIN: Fixing issues introduced by review.
vlipovac 5f808f5
MOD: Changes from review.
vlipovac bdefd21
MIN: CF module docs.
vlipovac 7fd3eb8
Merge branch 'develop' into cf_merger_3
vlipovac 09f3723
MIN: Spelling in docs.
vlipovac 6443ebf
DOC: Minor changes of documentation
keileg ef56eb3
MOD: Diffusive total mass balance overrides only flux methods now.
vlipovac 54f9e48
MOD: Removing compound-tracer transport equations from basic CF module.
vlipovac f356c5d
MOD: Splitting SolutionStrategyCF into parts. Renaming CF classes to …
vlipovac 4b553a3
MOD: Renaming various mobilities with mass terms.
vlipovac 976d760
MOD: Moving inquiries about elimination of ref phase and component to…
vlipovac 833a370
TUT: Tracer tutorial does not duplicate code anymore.
vlipovac 16121cb
TEST: Linear tracer test does not duplicate code anymore.
vlipovac 277810c
Merge branch 'cf_merger_3' of github.com:pmgbergen/porepy into cf_mer…
vlipovac 88cad54
Update src/porepy/models/initial_condition.py
vlipovac 87c8e58
STY: flake8 after GH commit.
vlipovac b6a0d85
MIN: Adding safe-super ignore for mypy in implementations of actual m…
vlipovac 45b0475
MOD: Initial conditions mixins cover now all variables in base models.
vlipovac 039b9ee
MOD: Renaming partial models in compositional flow module to *Template.
vlipovac 0488ba0
TESTS: Adding exact solution accounting for numerical solution to lin…
vlipovac 2392b26
Merge branch 'develop' into cf_merger_3
vlipovac 1489a27
FIX: Issue introduced by merger with develop
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Two comments:
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I don't feel I know the impact/usage of this, so I'm not sure my opinion is very well founded. Would an option to include only a subset to top-level and in files using compositional extensively simply import compositional explicitly?
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Reverted this change to import only the Variables and fluid mixin classes.
Changed the usage of the other function imported by the star-import to
import porepy.compositional as compositional
compositional.function()
throughout porepy.
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I guess the reason for keeping the variables and fluidmixin is that these will show up in all models, since all models in a sense are compositional? If correct, please add a short comment to this effect, so that I don't get confused about what is so special about these classes whenever I look at this line.
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All models have the fluid mixin, that is correct. But only truly multiphase multicomponent models require the
CompositionalVariables
. Do you want only theFluidMixin
included on the top level?