From 09a1a4cb08a282cb927719e16eba989a5623c1ae Mon Sep 17 00:00:00 2001
From: anderson2981 <41346365+anderson2981@users.noreply.github.com>
Date: Thu, 9 Nov 2023 16:11:29 -0600
Subject: [PATCH 1/2] Add av diff (#978)
* modify transport
* add support for av=3, diffusivity
* busy work
* stuff
* removed density from artificial diffusivity
---------
Co-authored-by: Mike Campbell <mtcampbe@illinois.edu>
---
examples/ablation-workshop.py | 4 +-
mirgecom/eos.py | 10 +++
mirgecom/gas_model.py | 44 +++++++++++-
mirgecom/transport.py | 132 ++++++++++++++++++++++++++++++++++
4 files changed, 188 insertions(+), 2 deletions(-)
diff --git a/examples/ablation-workshop.py b/examples/ablation-workshop.py
index bce9a1361..6668745a3 100644
--- a/examples/ablation-workshop.py
+++ b/examples/ablation-workshop.py
@@ -488,7 +488,8 @@ def get_species_source_terms(self, cv: ConservedVars, temperature: DOFArray):
raise NotImplementedError
def dependent_vars(self, cv: ConservedVars, temperature_seed=None,
- smoothness_mu=None, smoothness_kappa=None, smoothness_beta=None):
+ smoothness_mu=None, smoothness_kappa=None,
+ smoothness_d=None, smoothness_beta=None):
raise NotImplementedError
@@ -755,6 +756,7 @@ def make_state(cv, temperature_seed, material_densities):
smoothness_mu=zeros,
smoothness_kappa=zeros,
smoothness_beta=zeros,
+ smoothness_d=zeros,
species_enthalpies=cv.species_mass, # empty array
)
diff --git a/mirgecom/eos.py b/mirgecom/eos.py
index 149e19687..d7de23cee 100644
--- a/mirgecom/eos.py
+++ b/mirgecom/eos.py
@@ -77,6 +77,7 @@ class GasDependentVars:
.. attribute:: smoothness_mu
.. attribute:: smoothness_kappa
.. attribute:: smoothness_beta
+ .. attribute:: smoothness_d
"""
temperature: DOFArray
@@ -84,6 +85,7 @@ class GasDependentVars:
speed_of_sound: DOFArray
smoothness_mu: DOFArray
smoothness_kappa: DOFArray
+ smoothness_d: DOFArray
smoothness_beta: DOFArray
@@ -179,6 +181,7 @@ def dependent_vars(
temperature_seed: Optional[DOFArray] = None,
smoothness_mu: Optional[DOFArray] = None,
smoothness_kappa: Optional[DOFArray] = None,
+ smoothness_d: Optional[DOFArray] = None,
smoothness_beta: Optional[DOFArray] = None) -> GasDependentVars:
"""Get an agglomerated array of the dependent variables.
@@ -194,6 +197,8 @@ def dependent_vars(
smoothness_mu = zeros
if smoothness_kappa is None:
smoothness_kappa = zeros
+ if smoothness_d is None:
+ smoothness_d = zeros
if smoothness_beta is None:
smoothness_beta = zeros
@@ -203,6 +208,7 @@ def dependent_vars(
speed_of_sound=self.sound_speed(cv, temperature),
smoothness_mu=smoothness_mu,
smoothness_kappa=smoothness_kappa,
+ smoothness_d=smoothness_d,
smoothness_beta=smoothness_beta
)
@@ -257,6 +263,7 @@ def dependent_vars(
temperature_seed: Optional[DOFArray] = None,
smoothness_mu: Optional[DOFArray] = None,
smoothness_kappa: Optional[DOFArray] = None,
+ smoothness_d: Optional[DOFArray] = None,
smoothness_beta: Optional[DOFArray] = None) -> MixtureDependentVars:
"""Get an agglomerated array of the dependent variables.
@@ -272,6 +279,8 @@ def dependent_vars(
smoothness_mu = zeros
if smoothness_kappa is None:
smoothness_kappa = zeros
+ if smoothness_d is None:
+ smoothness_d = zeros
if smoothness_beta is None:
smoothness_beta = zeros
@@ -282,6 +291,7 @@ def dependent_vars(
species_enthalpies=self.species_enthalpies(cv, temperature),
smoothness_mu=smoothness_mu,
smoothness_kappa=smoothness_kappa,
+ smoothness_d=smoothness_d,
smoothness_beta=smoothness_beta
)
diff --git a/mirgecom/gas_model.py b/mirgecom/gas_model.py
index 4791270a7..46563d2bc 100644
--- a/mirgecom/gas_model.py
+++ b/mirgecom/gas_model.py
@@ -118,6 +118,7 @@ class FluidState:
.. autoattribute:: temperature
.. autoattribute:: smoothness_mu
.. autoattribute:: smoothness_kappa
+ .. autoattribute:: smoothness_d
.. autoattribute:: smoothness_beta
.. autoattribute:: velocity
.. autoattribute:: speed
@@ -169,6 +170,11 @@ def smoothness_kappa(self):
"""Return the smoothness_kappa field."""
return self.dv.smoothness_kappa
+ @property
+ def smoothness_d(self):
+ """Return the smoothness_d field."""
+ return self.dv.smoothness_d
+
@property
def smoothness_beta(self):
"""Return the smoothness_beta field."""
@@ -297,6 +303,7 @@ def make_fluid_state(cv, gas_model,
temperature_seed=None,
smoothness_mu=None,
smoothness_kappa=None,
+ smoothness_d=None,
smoothness_beta=None,
material_densities=None,
limiter_func=None, limiter_dd=None):
@@ -328,6 +335,11 @@ def make_fluid_state(cv, gas_model,
Optional array containing the smoothness parameter for extra thermal
conductivity in the artificial viscosity.
+ smoothness_d: :class:`~meshmode.dof_array.DOFArray`
+
+ Optional array containing the smoothness parameter for extra species
+ diffusivity in the artificial viscosity.
+
smoothness_beta: :class:`~meshmode.dof_array.DOFArray`
Optional array containing the smoothness parameter for extra bulk
@@ -357,6 +369,8 @@ def make_fluid_state(cv, gas_model,
is None else smoothness_kappa)
smoothness_beta = (actx.np.zeros_like(cv.mass) if smoothness_beta
is None else smoothness_beta)
+ smoothness_d = (actx.np.zeros_like(cv.mass) if smoothness_d
+ is None else smoothness_d)
if isinstance(gas_model, GasModel):
temperature = gas_model.eos.temperature(cv=cv,
@@ -373,6 +387,7 @@ def make_fluid_state(cv, gas_model,
speed_of_sound=gas_model.eos.sound_speed(cv, temperature),
smoothness_mu=smoothness_mu,
smoothness_kappa=smoothness_kappa,
+ smoothness_d=smoothness_d,
smoothness_beta=smoothness_beta
)
@@ -384,6 +399,7 @@ def make_fluid_state(cv, gas_model,
speed_of_sound=dv.speed_of_sound,
smoothness_mu=dv.smoothness_mu,
smoothness_kappa=dv.smoothness_kappa,
+ smoothness_d=dv.smoothness_d,
smoothness_beta=dv.smoothness_beta,
species_enthalpies=gas_model.eos.species_enthalpies(cv, temperature)
)
@@ -428,6 +444,7 @@ def make_fluid_state(cv, gas_model,
speed_of_sound=gas_model.eos.sound_speed(cv, temperature),
smoothness_mu=smoothness_mu,
smoothness_kappa=smoothness_kappa,
+ smoothness_d=smoothness_d,
smoothness_beta=smoothness_beta,
species_enthalpies=gas_model.eos.species_enthalpies(cv, temperature),
)
@@ -507,6 +524,10 @@ def project_fluid_state(dcoll, src, tgt, state, gas_model, limiter_func=None,
if state.dv.smoothness_kappa is not None:
smoothness_kappa = op.project(dcoll, src, tgt, state.dv.smoothness_kappa)
+ smoothness_d = None
+ if state.dv.smoothness_d is not None:
+ smoothness_d = op.project(dcoll, src, tgt, state.dv.smoothness_d)
+
smoothness_beta = None
if state.dv.smoothness_beta is not None:
smoothness_beta = op.project(dcoll, src, tgt, state.dv.smoothness_beta)
@@ -519,6 +540,7 @@ def project_fluid_state(dcoll, src, tgt, state, gas_model, limiter_func=None,
temperature_seed=temperature_seed,
smoothness_mu=smoothness_mu,
smoothness_kappa=smoothness_kappa,
+ smoothness_d=smoothness_d,
smoothness_beta=smoothness_beta,
material_densities=material_densities,
limiter_func=limiter_func, limiter_dd=tgt)
@@ -535,6 +557,7 @@ def make_fluid_state_trace_pairs(cv_pairs, gas_model,
temperature_seed_pairs=None,
smoothness_mu_pairs=None,
smoothness_kappa_pairs=None,
+ smoothness_d_pairs=None,
smoothness_beta_pairs=None,
material_densities_pairs=None,
limiter_func=None):
@@ -579,6 +602,8 @@ def make_fluid_state_trace_pairs(cv_pairs, gas_model,
smoothness_mu_pairs = [None] * len(cv_pairs)
if smoothness_kappa_pairs is None:
smoothness_kappa_pairs = [None] * len(cv_pairs)
+ if smoothness_d_pairs is None:
+ smoothness_d_pairs = [None] * len(cv_pairs)
if smoothness_beta_pairs is None:
smoothness_beta_pairs = [None] * len(cv_pairs)
if material_densities_pairs is None:
@@ -590,6 +615,7 @@ def make_fluid_state_trace_pairs(cv_pairs, gas_model,
temperature_seed=_getattr_ish(tseed_pair, "int"),
smoothness_mu=_getattr_ish(smoothness_mu_pair, "int"),
smoothness_kappa=_getattr_ish(smoothness_kappa_pair, "int"),
+ smoothness_d=_getattr_ish(smoothness_d_pair, "int"),
smoothness_beta=_getattr_ish(smoothness_beta_pair, "int"),
material_densities=_getattr_ish(material_densities_pair, "int"),
limiter_func=limiter_func, limiter_dd=cv_pair.dd),
@@ -598,6 +624,7 @@ def make_fluid_state_trace_pairs(cv_pairs, gas_model,
temperature_seed=_getattr_ish(tseed_pair, "ext"),
smoothness_mu=_getattr_ish(smoothness_mu_pair, "ext"),
smoothness_kappa=_getattr_ish(smoothness_kappa_pair, "ext"),
+ smoothness_d=_getattr_ish(smoothness_d_pair, "ext"),
smoothness_beta=_getattr_ish(smoothness_beta_pair, "ext"),
material_densities=_getattr_ish(material_densities_pair, "ext"),
limiter_func=limiter_func, limiter_dd=cv_pair.dd))
@@ -605,10 +632,11 @@ def make_fluid_state_trace_pairs(cv_pairs, gas_model,
tseed_pair,
smoothness_mu_pair,
smoothness_kappa_pair,
+ smoothness_d_pair,
smoothness_beta_pair,
material_densities_pair in zip(
cv_pairs, temperature_seed_pairs,
- smoothness_mu_pairs, smoothness_kappa_pairs,
+ smoothness_mu_pairs, smoothness_kappa_pairs, smoothness_d_pairs,
smoothness_beta_pairs, material_densities_pairs)]
@@ -628,6 +656,10 @@ class _FluidSmoothnessKappaTag:
pass
+class _FluidSmoothnessDiffTag:
+ pass
+
+
class _FluidSmoothnessBetaTag:
pass
@@ -758,6 +790,14 @@ def make_operator_fluid_states(
dcoll, volume_state.smoothness_kappa, volume_dd=dd_vol,
tag=(_FluidSmoothnessKappaTag, comm_tag))]
+ smoothness_d_interior_pairs = None
+ if volume_state.smoothness_d is not None:
+ smoothness_d_interior_pairs = [
+ interp_to_surf_quad(tpair=tpair)
+ for tpair in interior_trace_pairs(
+ dcoll, volume_state.smoothness_d, volume_dd=dd_vol,
+ tag=(_FluidSmoothnessDiffTag, comm_tag))]
+
smoothness_beta_interior_pairs = None
if volume_state.smoothness_beta is not None:
smoothness_beta_interior_pairs = [
@@ -780,6 +820,7 @@ def make_operator_fluid_states(
temperature_seed_pairs=tseed_interior_pairs,
smoothness_mu_pairs=smoothness_mu_interior_pairs,
smoothness_kappa_pairs=smoothness_kappa_interior_pairs,
+ smoothness_d_pairs=smoothness_d_interior_pairs,
smoothness_beta_pairs=smoothness_beta_interior_pairs,
material_densities_pairs=material_densities_interior_pairs,
limiter_func=limiter_func)
@@ -874,6 +915,7 @@ def replace_fluid_state(
temperature_seed=new_tseed,
smoothness_mu=state.smoothness_mu,
smoothness_kappa=state.smoothness_kappa,
+ smoothness_d=state.smoothness_d,
smoothness_beta=state.smoothness_beta,
material_densities=material_densities,
limiter_func=limiter_func,
diff --git a/mirgecom/transport.py b/mirgecom/transport.py
index 4f6e5bf6f..9260488fb 100644
--- a/mirgecom/transport.py
+++ b/mirgecom/transport.py
@@ -16,6 +16,7 @@
.. autoclass:: MixtureAveragedTransport
.. autoclass:: ArtificialViscosityTransportDiv
.. autoclass:: ArtificialViscosityTransportDiv2
+.. autoclass:: ArtificialViscosityTransportDiv3
Exceptions
^^^^^^^^^^
@@ -698,3 +699,134 @@ def species_diffusivity(self, cv: ConservedVars,
eos: Optional[GasEOS] = None) -> DOFArray:
r"""Get the vector of species diffusivities, ${d}_{\alpha}$."""
return self._physical_transport.species_diffusivity(cv, dv, eos)
+
+
+class ArtificialViscosityTransportDiv3(TransportModel):
+ r"""Transport model for add artificial viscosity.
+
+ Inherits from (and implements) :class:`TransportModel`.
+
+ Takes a physical transport model and adds the artificial viscosity
+ contribution to it. Defaults to simple transport with inviscid settings.
+ This is equivalent to inviscid flow with artifical viscosity enabled.
+
+ .. automethod:: __init__
+ .. automethod:: bulk_viscosity
+ .. automethod:: viscosity
+ .. automethod:: volume_viscosity
+ .. automethod:: thermal_conductivity
+ .. automethod:: species_diffusivity
+ """
+
+ def __init__(self,
+ av_mu, av_kappa, av_beta, av_d, av_prandtl,
+ physical_transport=None,
+ av_species_diffusivity=None):
+ """Initialize uniform, constant transport properties."""
+ if physical_transport is None:
+ self._physical_transport = SimpleTransport()
+ else:
+ self._physical_transport = physical_transport
+
+ if av_species_diffusivity is None:
+ av_species_diffusivity = np.empty((0,), dtype=object)
+
+ self._av_mu = av_mu
+ self._av_beta = av_beta
+ self._av_kappa = av_kappa
+ self._av_d = av_d
+ self._av_prandtl = av_prandtl
+
+ def av_mu(self, cv, dv, eos):
+ r"""Get the shear artificial viscosity for the gas."""
+ actx = cv.array_context
+ return (self._av_mu * cv.mass
+ * actx.np.sqrt(np.dot(cv.velocity, cv.velocity)
+ + dv.speed_of_sound**2))
+
+ def av_beta(self, cv, dv, eos):
+ r"""Get the shear artificial viscosity for the gas."""
+ actx = cv.array_context
+ return (self._av_beta * cv.mass
+ * actx.np.sqrt(np.dot(cv.velocity, cv.velocity)
+ + dv.speed_of_sound**2))
+
+ def av_kappa(self, cv, dv, eos):
+ r"""Get the shear artificial viscosity for the gas."""
+ actx = cv.array_context
+ return (self._av_kappa * cv.mass
+ * actx.np.sqrt(np.dot(cv.velocity, cv.velocity)
+ + dv.speed_of_sound**2))
+
+ def av_d(self, cv, dv, eos):
+ r"""Get the shear artificial viscosity for the gas."""
+ actx = cv.array_context
+ return (self._av_d * actx.np.sqrt(np.dot(cv.velocity, cv.velocity)
+ + dv.speed_of_sound**2))
+
+ def bulk_viscosity(self, cv: ConservedVars, # type: ignore[override]
+ dv: GasDependentVars,
+ eos: GasEOS) -> DOFArray:
+ r"""Get the bulk viscosity for the gas, $\mu_{B}$."""
+ actx = cv.array_context
+ smoothness_beta = actx.np.where(
+ actx.np.greater(dv.smoothness_beta, 0.), dv.smoothness_beta, 0.)
+ return (smoothness_beta*self.av_beta(cv, dv, eos)
+ + self._physical_transport.bulk_viscosity(cv, dv))
+
+ def viscosity(self, cv: ConservedVars, # type: ignore[override]
+ dv: GasDependentVars,
+ eos: GasEOS) -> DOFArray:
+ r"""Get the gas dynamic viscosity, $\mu$."""
+ actx = cv.array_context
+ smoothness_mu = actx.np.where(
+ actx.np.greater(dv.smoothness_mu, 0.), dv.smoothness_mu, 0.)
+ return (smoothness_mu*self.av_mu(cv, dv, eos)
+ + self._physical_transport.viscosity(cv, dv))
+
+ def volume_viscosity(self, cv: ConservedVars, # type: ignore[override]
+ dv: GasDependentVars,
+ eos: GasEOS) -> DOFArray:
+ r"""Get the 2nd viscosity coefficent, $\lambda$.
+
+ In this transport model, the second coefficient of viscosity is:
+
+ $\lambda = \left(\mu_{B} - \frac{2\mu}{3}\right)$
+ """
+ actx = cv.array_context
+ smoothness_mu = actx.np.where(
+ actx.np.greater(dv.smoothness_mu, 0.), dv.smoothness_mu, 0.)
+ smoothness_beta = actx.np.where(
+ actx.np.greater(dv.smoothness_beta, 0.), dv.smoothness_beta, 0.)
+
+ return (smoothness_beta*self.av_beta(cv, dv, eos)
+ - 2*smoothness_mu*self.av_mu(cv, dv, eos)/3
+ + self._physical_transport.volume_viscosity(cv, dv))
+
+ def thermal_conductivity(self, cv: ConservedVars, # type: ignore[override]
+ dv: GasDependentVars,
+ eos: GasEOS) -> DOFArray:
+ r"""Get the gas thermal_conductivity, $\kappa$."""
+ cp = eos.heat_capacity_cp(cv, dv.temperature)
+ actx = cv.array_context
+ smoothness_beta = actx.np.where(
+ actx.np.greater(dv.smoothness_beta, 0.), dv.smoothness_beta, 0.)
+ smoothness_kappa = actx.np.where(
+ actx.np.greater(dv.smoothness_kappa, 0.), dv.smoothness_kappa, 0.)
+ av_kappa = (
+ cp*(smoothness_beta*self.av_beta(cv, dv, eos)/self._av_prandtl
+ + smoothness_kappa*self.av_kappa(cv, dv, eos))
+ )
+
+ return (av_kappa
+ + self._physical_transport.thermal_conductivity(cv, dv, eos))
+
+ def species_diffusivity(self, cv: ConservedVars, # type: ignore[override]
+ dv: GasDependentVars,
+ eos: GasEOS) -> DOFArray:
+ r"""Get the vector of species diffusivities, ${d}_{\alpha}$."""
+ actx = cv.array_context
+ smoothness_d = actx.np.where(
+ actx.np.greater(dv.smoothness_d, 0.), dv.smoothness_d, 0.)
+ return (smoothness_d*self.av_d(cv, dv, eos)
+ + self._physical_transport.species_diffusivity(cv, dv, eos))
From d70ac5e23184ad770b18832e881e4a153031ae6b Mon Sep 17 00:00:00 2001
From: Matthias Diener <mdiener@illinois.edu>
Date: Mon, 13 Nov 2023 15:05:22 -0600
Subject: [PATCH 2/2] Clean up temp files on porter before CI runs (#980)
---
.github/workflows/ci.yaml | 11 ++++++++++-
1 file changed, 10 insertions(+), 1 deletion(-)
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index c2d570390..aa0fcc7bf 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -119,12 +119,16 @@ jobs:
- name: Run examples
run: |
+ set -x
MINIFORGE_INSTALL_DIR=.miniforge3
. "$MINIFORGE_INSTALL_DIR/bin/activate" testing
export XDG_CACHE_HOME=/tmp
mamba install vtk # needed for the accuracy comparison
[[ $(hostname) == "porter" ]] && export PYOPENCL_TEST="port:nv" && unset XDG_CACHE_HOME
- # && export POCL_DEBUG=cuda
+
+ # This is only possible because actions run sequentially on porter
+ [[ $(hostname) == "porter" ]] && rm -rf /tmp/githubrunner/pocl-scratch && rm -rf /tmp/githubrunner/xdg-scratch
+
scripts/run-integrated-tests.sh --examples
doc:
@@ -195,8 +199,13 @@ jobs:
fetch-depth: '0'
- name: Prepare production environment
run: |
+ set -x
[[ $(uname) == Linux ]] && [[ $(hostname) != "porter" ]] && sudo apt-get update && sudo apt-get install -y openmpi-bin libopenmpi-dev
[[ $(uname) == Darwin ]] && brew upgrade && brew install mpich
+
+ # This is only possible because actions run sequentially on porter
+ [[ $(hostname) == "porter" ]] && rm -rf /tmp/githubrunner/pocl-scratch && rm -rf /tmp/githubrunner/xdg-scratch
+
MIRGEDIR=$(pwd)
cat scripts/production-testing-env.sh
. scripts/production-testing-env.sh