PETTT Feature #1: Model Reconstruction

[zhang-alvin]

First of a series of PRs for various features that have been implemented. The primary feature of this PR is geometric model reconstruction from Proteus mesh data structures with proper topology but not shape information.

The model reconstruction handles 3D geometries and identifies external boundaries by the material flags.
The reconstruction capability is handled in SCOREC/core and assembling the requisite inputs are the primary modifications to Proteus.

• add in 2D model reconstruction for jupyter notebook
• update jupyter notebook to show capability

[zhang-alvin]

The number of files/commits are a lot larger than they should be.

[zhang-alvin]

History of feature branch was modified via cherry-picking of commits on top of master.

[zhang-alvin]

@cekees hashdist/hashstack#998 needs to be pulled in before compilation can pass on Travis CI.

[codecov]

Codecov Report

Merging #708 into master will increase coverage by <.01%.
The diff coverage is 7.5%.

@@            Coverage Diff             @@
##           master     #708      +/-   ##
==========================================
+ Coverage   48.12%   48.13%   +<.01%     
==========================================
  Files         380      380              
  Lines       85753    85729      -24     
==========================================
- Hits        41272    41269       -3     
+ Misses      44481    44460      -21

Impacted Files	Coverage Δ
proteus/config/default.py	80.99% <0%> (-0.68%)	⬇️
proteus/MeshTools.py	54.38% <22.22%> (-0.07%)	⬇️
proteus/NumericalSolution.py	52.86% <3.57%> (+1.4%)	⬆️
proteus/tests/test_boundaryconditions.py	97.58% <0%> (-0.66%)	⬇️

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[zhang-alvin]

Merging hashdist/hashstack#999 and updating the .hashstack_default commit should resolve the build issues after the most recent commits.

[zhang-alvin]

Whenever this PR is ready, it would be helpful to add the following to the merge commit message for bookkeeping purposes:

"PETTT Project (Number: PP-CFD-KY09-011-P3) Deliverable D2: Provide VMS-based error estimation, smoothed inputs to anisotropic mesh adaptation, and 3D discrete model reconstruction; (Task 2A) – anisotropic indicators at the interface."

[cekees]

Thanks.