Merge pull request #526 from CEED/valeria/petsc-examples-cleaning

PETSc examples: some cleaning

NS solver: remove stray restrictxcoord restriction

NS: Use non_zero_time=false for problem type avection

Since exact solution and error calculation is not currently provided for the 3D advection case, this flag should be set to false for now

With n

NS: Use non_zero_time=false for problem type avection

Since exact solution and error calculation is not currently provided for the 3D advection case, this flag should be set to false for now

With non_zero_time=true the program was always reporting Max Error: 0. for problem type advection

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NS: Rename ICs_PetscMultiplicity() -> ICs_FixMultiplicity()

The name ICs_PetscMultiplicity was misleading, since the multiplicity is not related to PETSc

NS: Fix memory leak

Reported-by @jedbrown

Merge pull request #513 from CEED/jeremy/restriction-no-interlace

Convert restriction to offsets

Fluids - fix omitted indices correction in fluids version of CreateRestrictionFromPlex

Restriction - convert restiction to use offsets instead of interlace mode. CPU and Python impl only, CUDA and MAGMA left to do.

Merge pull request #511 from CEED/valeria/viz-refine

Add support for level of refinements for viz

fluids: fix -viz_refine by composing interpolation matrices

This also changes -petscspace_degree to -degree (using
PetscFECreateLagrange, which is now available).

Example parallel run with -viz_ref

fluids: fix -viz_refine by composing interpolation matrices

This also changes -petscspace_degree to -degree (using
PetscFECreateLagrange, which is now available).

Example parallel run with -viz_refine:

mpiexec -n 2 ./navierstokes -degree 3 -qextra 1 -problem density_current -dm_plex_box_faces 12,1,12 -lx 4000 -ly 200 -lz 4000 -bc_wall 1,2 -bc_slip_x 5,6 -bc_slip_y 3,4 -center 0,0,2000 -dc_axis 0,1,0 -ts_adapt_monitor -ts_adapt_safety 0.8 -implicit -pc_type bjacobi -stab supg -snes_atol 1e-3 -ksp_atol 1e-4 -ksp_rtol 1e-3 -ts_type alpha -ts_dt 5e-3 -ksp_type bcgs -snes_lag_jacobian 100 -snes_lag_jacobian_persists -snes_mf_operator -viz_refine 2

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Add support for level of refinements for viz

Now -viz_refine is not a PetscBool anymore, but a PetscInt

Merge branch 'master' into valeria/jupyter-notebook-tutorials

Solid Mechanics Example (#474)

libCEED + PETSc Solid Mechanics example

Co-authored-by: Jeremy L Thompson <jeremy.thompson@colorado.edu>
Co-authored-by: Arash Mehraban <arashm81@gmail.com>
Co-au

Solid Mechanics Example (#474)

libCEED + PETSc Solid Mechanics example

Co-authored-by: Jeremy L Thompson <jeremy.thompson@colorado.edu>
Co-authored-by: Arash Mehraban <arashm81@gmail.com>
Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: Valeria Barra <valeriabarra21@gmail.com>


* Solids - initial commit of elasticity example

Co-authored-by: Jeremy L Thompson <jeremy.thompson@colorado.edu>
Co-authored-by: Arash Mehraban <arashm81@gmail.com>

* Solids - add VLA macro

* Solids - fix test for mesh file output string

* Solids - update documentation

Co-authored-by: Jeremy L Thompson <jeremy.thompson@colorado.edu>
Co-authored-by: Arash Mehraban <arashm81@gmail.com>

* Solids - update README

* Solids - update ctx struct and casting for CUDA

* Tests - clean up test conditions for GPU backends

* GPU - fix falbacks identified

* CUDA - whitelist FDM Inverse

* make style

* doc: solids editing/correctness

* Solids - separate FE boilerplate into its own function

* Solids - clean up double includes

* doc: add more complete explanation of hyperelasticity and formulation

* Solids - Use ISGetSize for global number of face sets (had no effect on PETSc bug in MR 2615)

* edited docs for hyperFS

* Improve doc of solids example with some constitent notation and fonts

* HyperSS docs modified

* edited typo

* linearization added

* fixed a typo

* Improved doc

* doc: more writing on hyperelasticity and implementation tradeoffs

* Solids - fix typo

* Solids - compute and store C, Cinv, and S as symmetric

* Solids - use new Newton linearization, but its not converging

* Solids - update BC handling

* Solids - update README with new BC options

* removed old notation

* Solids - whitespace changes only in documentation

* doc: adjust differential notation and derive dP(dF)

* Solids - small documentation flow edits

* Solids - simplify setting BCs

* Solids - Symmetritize e in SS

* Solids - set more reasonable default number of steps for nonlinear

* Solids - fix documentation typo

* Solids - clean up computation of deltaS

* Solids - fix sample runs

* Solids - fix hyperSS jacobian

* Solids - fix hyperSS documentation

* Solids - clean up code for hyperSS

* Solids - add file and function docstrings

* doc: commutative diagram of linearization and stable stress expression

* Solids - update hyperSS documentation with linearization

* doc: further tips on stable computation

* Solids - fix typo with trace in hyperSS

* Solids - intro and hyperSS documentation updates

* Solids - update hyperFS for numerical stability with small E and nearly incompressible

* examples/solids: simpler C = I + 2E

* Solids - more compact/readable E computation

* Solids - minor style consistency change

* Solids - replace log1p with series approximation, log1p is not vectorized in libc

* Solids - refactor common components between hyperFSF and hyperFSdF

* examples/solids: use PETSc dependency flags for incremental rebuild

* examples/solids: extend range of log1p_series via shift/scale

* Solids - add bc_clamp_max option to specify maximum displacement for clamped boundary

* make style

* Solids - update with sample run informantion and spellchecking

* Doc - typo fixes

* Solids - homogonize presentation of command line options

* examples/solids: fix -Wmisleading-indentation

* examples/fluids: PETSc 3.13 compatibility

* examples/solids: use log1p for numerical stability in hyperSS

* doc: copy editing in examples/solids

* Solids - update documentation on running the code

* Solids - convert README to rst and include in documentation

* Solids - clean dependency file

* Solids - use log1p approximation in hyperSS as well

* Solids - update README to explain mms

* Solids - switch range on hyperSS log1p series approximation

* Solids - update README to clarify mandatory options

* Solids - add link to sample meshes

* Solids - simplify listing of mesh options

* Travis - use newer PETSc

* Solids - update sample run to list [.exo file] instead of name of sample mesh

* Solids - update make clean to remove src/*.d

* examples/solids: makefile cleanup

* make style

* doc examples/solids: clean up and explain nondimensionalization

* examples/solids: document algebraic solver

* examples/solids: use CG for Chebyshev eig estimation

* doc: fix references to examples/fluids

* Solids - remove mesh folder

* Solids - drop expicit ExodusII requirement, PETSc supports many types of meshes

* doc: mention PETSc --download-exodusii for Exodus

* doc: fix latexpdf

* Fix \longrightarrow rendering in PDF

* Solids - fix toctree link to README for pdflatex

* Examples and BPs Docs: Homogenize math with dS and dV and other tiny esthetics

* Solids - fix unshifted series for hyperSS log1p

* Improve doc of bpssphere: Add differential for consistency with all other examples and explain domain for clarity

* Solids - include sample mesh image

* Move mesh figure after note and slightly rename inclusion marker

Co-authored-by: Arash Mehraban <arashm81@gmail.com>
Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: valeriabarra <valeriabarra21@gmail.com>

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