python: contextmanager for v.array() and v.array_read()

Merge pull request #491 from CEED/jed/intel-compiler

Jed/intel compiler

tests: relax some FP tolerances for Intel compiler

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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Python tests: Fix t320-basis test and elemrestriction docstrings

python: install libceed.so and headers with Python; make wheels

* Install libceed.so and obtain at run-time via $ORIGIN
* Updates some nonconforming package metadata
* Use Docker with cache for buil

python: install libceed.so and headers with Python; make wheels

* Install libceed.so and obtain at run-time via $ORIGIN
* Updates some nonconforming package metadata
* Use Docker with cache for building manylinux2014 wheels
* qfunction extensions don't call libceed.so directly; can get include
path from libceed module

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python tests: replace hard-coded 1E-14 with TOL based on machine epsilon

Ceed - add CeedView()

Add VLA support for CUDA backends (#481)

* CUDA - add VLA support for CUDA backends

* Navier-Stokes - guard #include math.h for CUDA

* Navier-Stokes - fix struct definitions for code generatio

Add VLA support for CUDA backends (#481)

* CUDA - add VLA support for CUDA backends

* Navier-Stokes - guard #include math.h for CUDA

* Navier-Stokes - fix struct definitions for code generation

* Navier-Stokes - fix file location of mass QFunction

* Navier-Stokes - minor style consistency

* Navier-Stokes - more context sturct fixing

* Navier-Stokes - cast context to stop CUDA errors

* Navier-Stokes - change helper functions to inline to silence CUDA errors

* CUDA - clean up CEED_Q_VLA definition for cuda/gen

* Navier-Stokes - populate TODOs for undocumenced functions

* Doc - document libCEED macros

* CUDA - use -default-device for NVRTC

* Tests - add t507 to test VLA support

* CUDA - fix my bug in dim, Q1d for cuda/gen

* Tests - update tap/junit to reflect current CUDA capabilities

* make style

* CUDA - check output bases for dim, Q1d as well (this fixes multigrid example support)

* CUDA - fix readSliceQuads, not all arguments were defined

* Navier-Stokes - document all functions in Navier-Stokes QFunction files

* make style

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Testing - add OCCA exception for t506

Tests - add t506, test reuse of QFunction across operators

Python - add CEED_ELEMRESTRICTION_NONE

ElemRestriction - add CEED_ELEMRESTRICTION_NONE so we can stop making dummy restrictions for CEED_EVAL_WEIGHT fields

Restriction - expand codecov

Python - convert to strided restrictions

Restriction - replace identity restrictions with strided restrictions

Merge branch 'jed/ns-dmplex' [PR #458]

* jed/ns-dmplex: (73 commits)
NS: remove density_current_primitive (still work in progress)
Remove a bunch of unused variables and update doc
Update READ

Merge branch 'jed/ns-dmplex' [PR #458]

* jed/ns-dmplex: (73 commits)
NS: remove density_current_primitive (still work in progress)
Remove a bunch of unused variables and update doc
Update README: remove density_current_primitive problem option for now
Use const in VLA declaration casts to suppress icc warning also in densitycurrent_primitive
Remove a bunch of unused or double-declared variables
Update README
NS: use const in VLA casts to suppress icc warning
NS: add command-line support for specifying DC center/axis
NS: return to insulated no-slip walls instead of full-Dirichlet
NS: remove dead code for scaling VTK output back to dimensional units
NS: add support for free slip wall boundary conditions
NS density_current: remove redundant initial/boundary condition and trailing whitespace
Some changes in documentation
Update top-level README
Update examples/README
Update examples/navier-stokes/README
Update .gitignore
Update documentation
Initialize *problem pointer as NULL
NS: move nsplex.c to navierstokes.c
...

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test(navierstokes): Remove stdout output for testing

test(nsplex): Remove stdout output during test

nsplex: Update nsplex /tests/output file

ElemRestriction - make lmode a separate enum

ElemRestriction - move lmode to constructor over apply

Enable MAGMA non-tensor basis (#424)

* update magma backend files from magma-dev to new branch

* add skeleton for elem restrictions

* start putting code and files for nontensor case

* more

Enable MAGMA non-tensor basis (#424)

* update magma backend files from magma-dev to new branch

* add skeleton for elem restrictions

* start putting code and files for nontensor case

* more framework for adding magma elem restrictions

* typo/old code error fixes for interface and header file, etc

* add the writedofs kernels

* fix nonconstants - template them for now

* fix bugs in non-tensor basis apply (interp and weight)

* update magma backend files from magma-dev to new branch

* add skeleton for elem restrictions

* start putting code and files for nontensor case

* more framework for adding magma elem restrictions

* typo/old code error fixes for interface and header file, etc

* add the writedofs kernels

* fix nonconstants - template them for now

* fix bugs in non-tensor basis apply (interp and weight)

* fix incorrect merge conflict resolution of header file

* fix bugs in lmode=notranspose elem restrictions
and in copying of indices to device

* test simpler kernels for lmode=transpose elem restrict

* swap element and component ordering in tensor basis actions

* update comments in restriction kernels to match swapped ordering

* fix if statement to work with CEED_VECTOR_NONE instead of NULL

* minor code cleanup

* skip t204-7 for magma after changing E-vector layout

* remove commented old calls for now

* use magma set/get vectors instead of cuda memcopies

* remove dead code

* make style changes

Co-authored-by: Stan Tomov <tomov@eecs.utk.edu>
Co-authored-by: abdelfattah83 <36712794+abdelfattah83@users.noreply.github.com>

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Merge pull request #450 from CEED/tests/remove-implementation-dependent-logic-on-t208

[Tests] Removed testing padded entries