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Splitting Artificial viscosity out of hydrodynamics packages into its own physics package #317

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Splitting Artificial viscosity out of hydrodynamics packages into its own physics package #317

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Summary

  • This PR is a feature/refactoring
  • It does the following:
    • Make the ArtificialViscosity it's own physics package, working alongside the hydrodynamics package.
    • Cleans up some state usage, particularly being more rigorous about some of the artificial viscosity logic correctly time centering it's dependent state during a time advancement cycle.

ToDo :

  • Annotate RELEASE_NOTES.md with notable changes.
  • Create LLNLSpheral PR pointing at this branch. (PR#)
  • LLNLSpheral PR has passed all tests.

@jmikeowen
Moving grad-h corrections to SPH::postStateUpdate to avoid mixing tim…
30d1444 
…e-levels in multi-stage integrators
@jmikeowen
Parameter change in interpolation kernel (no real change)
af2c1b1
@jmikeowen
Converted NodePairList storage in ConnectivityMap to be a shared_ptr
9a22af9
@jmikeowen
Convert NodePairList to use size_t
faf2546
@jmikeowen
Split up the NodePairIdxType and NodePairList into separate headers,
e510788 
and adding an index of NodePair->index lookup map.
@jmikeowen
Initial introduction of PairwiseField. Also split out NodePairIdxType
d83759d 
from the NodePairList header.
@jmikeowen
Using the pair->index lookup computed by NodePairList
d3093c2
@jmikeowen
Interim checkin
f8ac3a9
@jmikeowen
Lot of renaming
6a5c976
@jmikeowen
Converting SPH classes to use PairwiseField for pair-accelerations.
7b55da6 
And some other cleanup...
@jmikeowen
Updating Python front-end constructor
f41931e
@jmikeowen
Initial conversion of SPH PYB11 package (untested)
56c4dd8
@jmikeowen
Updating thermal energy policies for PairwiseField use
04af076
@jmikeowen
Fixing some DataTypeTraits zeros, and making Python better respect co…
7f339ad 
…nfiguration choices such as which hydros to build.
@jmikeowen
SPH can now run using PairwiseField for pair accelerations, but the i…
0a08b64 
…nitialization order is not great
@jmikeowen
Merge branch 'develop' into bugfix/EvalDerivCleanup
b47d696
@jmikeowen
Making State and StateDerivatives not default constructable
83c46a1
@jmikeowen
Changing initialization order in Integrators and DataBase such that
92f85b8 
the ConnectivtyMap is available during construction of the State and
StateDerivatives. This is necessary to support pair-wise fields as
state members.
@jmikeowen
Clean up unused method
11d4e8a
@jmikeowen
Fixing a comment in SPH, and starting to convert CRK
89bd714
@jmikeowen
Simplifying dependencies for postion update, eps, and RZ cases
844414a
@jmikeowen
Initial conversion of CRKSPH to newer interface with PairwiseField
da23e11
@jmikeowen
Some SPH fixes with new interface
6cc6e02
@jmikeowen
PSPH needs to start inconsistently (need to fix this)
e576f2e
@jmikeowen
Got PSPH functioning
28625e3
@jmikeowen
FSISPH converted to PairwiseFields
2aa7d14
@jmikeowen
Converted GSPH to PairwiseField
09fc429
@jmikeowen
Moved how we build the State to be robust when not running a full
909bacb 
problem using the SpheralController
@jmikeowen
Removed unused option filter
2f09aeb
@jmikeowen
Fixed incorrect contract
6ebdba6
@jmikeowen
Checkpoint
24bdd33
@jmikeowen
- Converted all viscosities to Physics packages
3d68c02 
- Updated our ArtificialViscosity interface to allow Scalar and Tensor viscosity return types
- Cleaned up a lot of old code, removed unused AV types
@jmikeowen
Rearranging a bit
5d0c2f2
@jmikeowen
Missed some necessary overrides for TensorCRKSPHViscosity
c797ebf
@jmikeowen
Initial update of Python bindings -- not compiled yet
01a29ea
@jmikeowen
Introducing ArtficialViscosityHandle to split off QPiType template
f7ed821 
parameter for classes consuming an AV
@jmikeowen
Adding back effective viscous pressure
d7f5414
@jmikeowen
FSI conversion
0020b93
@jmikeowen
Initial conversion of SPH
1eb7d44
@jmikeowen
Converted CRK C++
99c2cd7
@jmikeowen
Compiles and links
3ba2735
@jmikeowen
Planar Noh tests are passing
e548163
@jmikeowen
Working through failing tests
47d0b1a
@jmikeowen
Fixed outdated graphics
1cc320e
@jmikeowen
Moving initialization of AV FieldList sizes to initializeProblemStartup
ee65a90
@jmikeowen
Updating for interface change to Morris-Monaghan and Cullen-Dehnen
5268d73 
reducing viscosity packages
@jmikeowen
Fix for spherical geometry
f66f675
@jmikeowen
Clean up warnings in optimized build
db68a19
@jmikeowen
Removing redundant Q constructor in test
fc6b8c4
@jmikeowen
Updated release notes
9b04100
@jmikeowen
Merge branch 'develop' into feature/ArtificialViscosityPackage
f43682c
@jmikeowen
Cleaning up State and StateDerivatives a bit, and allowing default co…
f2c49dd 
…nstruction
@jmikeowen
Changing DataBase::nodeListIndex to use size_t
dc02ef4
@jmikeowen
During initialization we have to be careful about recreating
a9b825b 
derivatives if connectivity has updated
@jmikeowen
On BlueOS with gcc we have some problem with using "any" without the
fed1318 
std:: prefix
@jmikeowen
Cleaning up warnings
77ef956
@jmikeowen
More warning cleanup
8cd72bf
@jmikeowen
Compile fix for blueos
4c3963e
@jmikeowen
Making NodePairList::Pair2Index lazy evaluation gets back most of the
c93a65a 
performance vs develop (about 90%)
@jmikeowen
Making PairwiseField allow more than one Value per pair as an optional
2b06fd7 
template parameter.  Let's us avoid using fields of std::pair or std::tuple.
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@jmikeowen