Update add smoothed transport #861
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1) separate individual aspects of BCs (adiabatic, slip, etc.) into their own component classes 2) use *_plus for values that will be used in conjunction with *_minus values in numerical flux functions, and *_bc for values that will be used to compute flux directly
… and use it in SymmetryBoundary
… construction in BCs
Co-authored-by: tulioricci <[email protected]>
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Apr 10, 2023
* Fix up boundary treatments per Mengaldo * fix? * Update boundary.py file * Update initializers.py file * Update misc.rst and test_bc.py * Update pulse-mpi.py * Fixes after checking the test and examples * Flake8 boundary.py * Remove line that was making the test fail * Remove missing class from docs thingy * Add missing boundary class in module doc * Update mirgecom/initializers.py Removing excessive piece of code Co-authored-by: Mike Campbell <[email protected]> * Flake8 initializers.py * Bring the None check to __init__ in LinearOutBC * Add ortho axis util * Docstyle * Add state option to initializers.py * switch install.sh to Open MPI * more details * Including 3D slip wall BC * Fixing flake8 in boundary.py * Update outflow --> pressureoutflow * put in adiabatic slip * small changes to pass docs * Add rot mat util, test * Update calls to rotmat * Fix up axes getter call with new API * Update docs for new boundary routine. * Update boundary.py fix bug in tensor multiplication * update adiabatic slip to specify a flux instead of using numerical flux function * Add smoothness to see how production behaves * Of course it wouldn't work * Use custom production branch * Fix doc err * Add Tulios fix for creating smoothness field. * Undo production env customization * Add fluid API test for limiting * Clean up some lingering linting ish * Dropping pre-computing viscosity because it is only useful for PowerLaw, but not for other transport models * Some minor tweaks * Remove janky density-based indicator option. * disable mypy for imported packages without type stubs * add CI job * fix mypy errors * fix CI * install * fix ctypes * install types * install explicitly * Use productions version of these files. * Apply suggestions from code review Co-authored-by: Mike Campbell <[email protected]> * empty commit to trigger CI * empty commit to bump CI * flake8 example * Push to kick CI. * Update for upstream API changes * Fix up doc issues? * Clean up remaining doc ish. * Add mod pyrometheus to requirements * Pressure and temperature were inverted * Try override for mixture averaged diffusivity routine. * Spell num_species corretly. * Spell make_array properly. * Disable override func * Remove override function for pyro.get_species_mass_diffusivities_mixavg * Add option to turn off inviscid terms in CNS operator. * Deflake8 * partial update * tweak mengaldo BC code 1) separate individual aspects of BCs (adiabatic, slip, etc.) into their own component classes 2) use *_plus for values that will be used in conjunction with *_minus values in numerical flux functions, and *_bc for values that will be used to compute flux directly * use grad_temperature_bc instead of grad_temperature_plus * changing smoothness to smoothness_mu, preparing for additional smoothness variables * remove duplicated inviscid/viscous flux methods * first stab at adding beta and kappa smoothness * make inviscid/viscous flux internal variables * change grad_momentum_bc to grad_velocity_bc in _SlipBoundaryComponent and use it in SymmetryBoundary * deprecate SymmetryBoundary * add comment about energy for inviscid * only use _ldg_bnd_flux_for_grad in mengaldo BCs * rename state_plus to state_plus_inviscid and explain why * don't pass callbacks to base class constructor unless they're expected to be used * add FIXME * add some docstrings * simplify cv_plus/cv_bc construction by using cv.replace * add replace_fluid_state function and use it to further simplify state construction in BCs * tweak some docstrings * add note * updating transport class to use new smoothness * restore SymmetryBoundary docstring to avoid unused reference error in doc build * Reset CI * Deawkwardize doc wording. * updates to new transport class * Deflake8 * Make clear that lewis must be an array * cleaning up and fixing examples * Try to fix doc err. * Partial update * Refactor Mengaldo: Isothermal, and Adiabatic for clarity * Update doublemach to provide its own boundary. This AV is deprecated, preparing for removal * Matts changes update 1. * Add Matts replace fluid state helper * Use smoothness consistent * Switch to mengaldo bcs * Update doc with boundary interface change. * Undo test changes * Random cleanup * Remove duplicate func. * Update docs * Add another Poinsot ref, fix doc err? * Extricate AV-specific junk from fluid boundaries. * Extricate AV from fluid boundaries. * Use production MANIFEST.in, try to fix gmsh ish with doublemach. * Try to fix Porter gmsh issue. * Update per final review comments * Update outdated comment * Remove old doc entry * Update add smoothed transport (#861) * Add option to turn off inviscid terms in CNS operator. * Deflake8 * partial update * tweak mengaldo BC code 1) separate individual aspects of BCs (adiabatic, slip, etc.) into their own component classes 2) use *_plus for values that will be used in conjunction with *_minus values in numerical flux functions, and *_bc for values that will be used to compute flux directly * use grad_temperature_bc instead of grad_temperature_plus * remove duplicated inviscid/viscous flux methods * make inviscid/viscous flux internal variables * change grad_momentum_bc to grad_velocity_bc in _SlipBoundaryComponent and use it in SymmetryBoundary * deprecate SymmetryBoundary * add comment about energy for inviscid * only use _ldg_bnd_flux_for_grad in mengaldo BCs * rename state_plus to state_plus_inviscid and explain why * don't pass callbacks to base class constructor unless they're expected to be used * add FIXME * add some docstrings * simplify cv_plus/cv_bc construction by using cv.replace * add replace_fluid_state function and use it to further simplify state construction in BCs * tweak some docstrings * add note * restore SymmetryBoundary docstring to avoid unused reference error in doc build * Reset CI * Deawkwardize doc wording. * Make clear that lewis must be an array * Add option to turn off inviscid terms in CNS operator. (#856) Co-authored-by: tulioricci <[email protected]> * Try to fix doc err. * Adding variable spec. diff to PowerLawTransp (#772) Co-authored-by: Mike Campbell <[email protected]> Co-authored-by: Matthias Diener <[email protected]> * Partial update * Refactor Mengaldo: Isothermal, and Adiabatic for clarity * Update doublemach to provide its own boundary. This AV is deprecated, preparing for removal * Matts changes update 1. * Add Matts replace fluid state helper * Use smoothness consistent * Switch to mengaldo bcs * Update doc with boundary interface change. * Undo test changes * Random cleanup * Remove duplicate func. * Update docs * Add another Poinsot ref, fix doc err? * Extricate AV-specific junk from fluid boundaries. * Extricate AV from fluid boundaries. * Use production MANIFEST.in, try to fix gmsh ish with doublemach. * Update lingering bcs * Update per final review comments * Update outdated comment --------- Co-authored-by: Matthew Smith <[email protected]> Co-authored-by: tulioricci <[email protected]> Co-authored-by: Tulio <[email protected]> Co-authored-by: Matthias Diener <[email protected]> * Merge upstream changes * Use zeros_like, not 0* * Zero smoothness * Modify MxTransp to handle single species case (#870) Check for singular case * Remove volume_viscosity from interface --------- Co-authored-by: Mike Campbell <[email protected]> Co-authored-by: Matthias Diener <[email protected]> Co-authored-by: Mike Anderson <[email protected]> Co-authored-by: anderson2981 <[email protected]> Co-authored-by: Matthew Smith <[email protected]>
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Update to latest production chain
cc: @anderson2981
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