petsc - set minimum version for examples

Merge pull request #801 from CEED/jeremy/no-switches

Refactoring Solids to Remove Switches

solids - refactor to separate problem formulations

Mooney-Rivlin model (#794)

* refactored MR to work with current version of main. Updated doc with dS for MR

* fixed documentation formatting

* update dS for MR in documentation

* cleaning u

Mooney-Rivlin model (#794)

* refactored MR to work with current version of main. Updated doc with dS for MR

* fixed documentation formatting

* update dS for MR in documentation

* cleaning up MR dS equations and wording

* minor changes in doc

* MR dS draft 1"

* MR coded, jacobian diverging

* added FSInitial-MR1.h

* fixed call option

* NH no longer needs mu_1 option

* processphysics and upated naming scheme

* WIP: Notes on using finite differencing for dS

* added print strain at every increment cl option

* MR cleaned. started CSV file but not quite there

* examples/solids: write csv file

can be read using pandas:

In [2]: pd.read_csv('test.csv')
Out[2]:
increment energy
0 0.000000 0.000000
1 0.066667 0.002402
[...]

* examples/solids: add targets for CSV logging and Altair chart

The MR data is currently hacked because it isn't converging as I'd expect.

* fixed style

* solids/doc: added derivation of dS for MR

* added analytical dS in Jacobian evaluation

* fixed style

* updated doc and energy plot for MR

* MR almost done

* started removing integer division

* got rid of all integer divisions

* missed some 1/3

* remove extra print statement

* added coulped MR FSInitial-MRc qfunction

* MR coupled version doc update

* refactored MR to work with current version of main. Updated doc with dS for MR

* fixed documentation formatting

* update dS for MR in documentation

* cleaning up MR dS equations and wording

* minor changes in doc

* MR dS draft 1"

* MR coded, jacobian diverging

* added FSInitial-MR1.h

* fixed call option

* NH no longer needs mu_1 option

* processphysics and upated naming scheme

* added print strain at every increment cl option

* MR cleaned. started CSV file but not quite there

* examples/solids: write csv file

can be read using pandas:

In [2]: pd.read_csv('test.csv')
Out[2]:
increment energy
0 0.000000 0.000000
1 0.066667 0.002402
[...]

* examples/solids: add targets for CSV logging and Altair chart

The MR data is currently hacked because it isn't converging as I'd expect.

* fixed style

* solids/doc: added derivation of dS for MR

* added analytical dS in Jacobian evaluation

* fixed style

* updated doc and energy plot for MR

* MR almost done

* started removing integer division

* got rid of all integer divisions

* missed some 1/3

* fixed some typo

* rerunning plot files

* Mooney-Rivlin coupled model

* some minor changes

* Mooney-Rivlin coupled model

* some clean-up and update

* clean-up, rebased

* examples/solids: revise docs/derivation and fix Newton

The (fixed) Newton linearization yields an indefinite operator causing
Newton to fail (so output/MR-strain1.csv is broken). This can be handled
by switching to minres, but a better solution would be nice.

* format: added newlines and removed unused/commented code blocks

* doc: removed GP model dropdown.

* examples/solids: Mooney-Rivlin docs/notation

* examples/solids: Mooney-Rivlin notation and experimental configuration

* examples/solids: process -dm_plex_box_faces with PETSc main

* make style

* examples/solids: syntax fix and minor cleanup

* make style

* doc: fixing Holzapfel ref in Mooney-Rivlin

* added TESTARGS for Mooney-Rivlin

* fixed TESTARGS for MR

* tests/tap.sh: make test for solids examples with names

* WIP: adding test option. added -expect_final_strain_energy and RegressionTests_solids function but not sure how to actually pull the reference strain energy from the reference file

* examples/solids: add regression tests using expected strain energy

* examples/solids: error on MMS with model that does not provide manufactured solutions

* examples/solids: fix HIP via CEED_QFUNCTION_HELPER

* update in-line comments

* changed as Jeremy suggested

* examples/solids: make style

Co-authored-by: Rezgar Shakeri <Rezgar.Shakeri@colorado.edu>
Co-authored-by: Jed Brown <jed@jedbrown.org>

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examples/solids: rewrite Cauchy-Green (b-I) in terms of grad(u)/Green-Euler strain for better stability (#769)

* FSCurrent-NH1.h: rewrite (b-I3) in terms of Grad(u)

* fixed the error

* rewrite

examples/solids: rewrite Cauchy-Green (b-I) in terms of grad(u)/Green-Euler strain for better stability (#769)

* FSCurrent-NH1.h: rewrite (b-I3) in terms of Grad(u)

* fixed the error

* rewrite (b-I3) in terms of Grad(u) in FSCurrent-NH2.h

* update documentation

* doc: defined Green_Euler strain tensor

* Update examples/solids/index.rst

Co-authored-by: Jed Brown <jed@jedbrown.org>

* added eq numbers in tip

* Update examples/solids/index.rst

Co-authored-by: Jed Brown <jed@jedbrown.org>

Co-authored-by: Jed Brown <jed@jedbrown.org>

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Merge pull request #745 from CEED/jeremy/test-order

gitlab - rearange the script for clearer output

examples: fix DMAddBoundary for petsc-3.16 (next release) API change

petsc - new compatibility macro for DMAddBoundary

Merge pull request #735 from CEED/jeremy/style-guide

Style Unification

style - updating C variable style

Merge pull request #708 from CEED/Add_ftr_cur_config

examples/solids: add current configuration for residual and Jacobian

* Add_ftr_cur_config:
examples/solids: Add residual and Jacobian in curre

Merge pull request #708 from CEED/Add_ftr_cur_config

examples/solids: add current configuration for residual and Jacobian

* Add_ftr_cur_config:
examples/solids: Add residual and Jacobian in current configuration
Stricter field checking and better error messages

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examples/solids: Add residual and Jacobian in current configuration

There are some benefits to evaluating residuals and/or Jacobians in
current configuration. This includes simpler representation of

examples/solids: Add residual and Jacobian in current configuration

There are some benefits to evaluating residuals and/or Jacobians in
current configuration. This includes simpler representation of body
forces and contact, as well as lower storage and lower arithmetic in the
Jacobian action. We add these implementations as well documentation to
derive their representations via linearize-then-pushforward and
pushforward-then-linearize.

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

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Merge pull request #714 from CEED/leila/ex-output-dir

Fluids & Solids | add/modify cl options for viz output folder

Command line option for viz in Fluids and Solids examples

examples/fluids: change the cl option -of to -output_dir for the output folder

examples/solids: add cl option -output_dir for the viz outpu

Command line option for viz in Fluids and Solids examples

examples/fluids: change the cl option -of to -output_dir for the output folder

examples/solids: add cl option -output_dir for the viz output

change: output folder -> output directory

Co-authored-by: Jed Brown <jed@jedbrown.org>

examples: change variable name outputfolder -> outputdir

examples: update the README files

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WIP: Solids-GivensBC (#702)

* Givens boundary condition added.

Co-authored with: @jedbrown and @jeremylt

* Comments first letter capitalized

headers - clearify includes to not rely on transitive includes (#701)

* headers - clearify includes to not rely on transitive includes

* style - add header recommendations from 'include-what-you-

headers - clearify includes to not rely on transitive includes (#701)

* headers - clearify includes to not rely on transitive includes

* style - add header recommendations from 'include-what-you-use'

* style - apply 'include-what-you-use' changes to CUDA backends

* style - 'include-what-you-use' for hip backends

* style - drop ceed.h includes in gallery qf source

* docs - add dev notes for header files

* style - header style and alphabetize

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Merge pull request #679 from CEED/jed/petsc-hip

examples/petsc: use VecGetArrayAndMemType() to support CUDA/HIP/Kokkos

examples/petsc: use VecGetArrayAndMemType() to support CUDA/HIP/Kokkos

We resolve default VECCUDA or VECHIP based on /gpu/cuda or /gpu/hip. For
others, one should pass -dm_vec_type kokkos or -dm_vec

examples/petsc: use VecGetArrayAndMemType() to support CUDA/HIP/Kokkos

We resolve default VECCUDA or VECHIP based on /gpu/cuda or /gpu/hip. For
others, one should pass -dm_vec_type kokkos or -dm_vec_type standard.

There is no longer a "libCEED User Requested MemType" field in the
output.

Enable CI testing using PETSc built locally with HIP. This should be
converted to building a specified version once some bugs are fixed and
the branch merges.

Exclude automatic selection of VECHIP for /gpu/hip/occa due to SEGV:
https://github.com/CEED/libCEED/issues/678

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Merge pull request #655 from CEED/jeremy/solid-bcs

Solids - new BCs

solids - traction BCs

QFunction Context Data Object (#596)

* Ctx - create context object for QFunction context data

* Context - rename UserContext -> QFunctionContext

* Ctx - add lcov markers

* Ctx - fix leak in

QFunction Context Data Object (#596)

* Ctx - create context object for QFunction context data

* Context - rename UserContext -> QFunctionContext

* Ctx - add lcov markers

* Ctx - fix leak in identity QFunctions

* Hip/Cuda - rename sync functions for vector/context

* Tests - lcov marker update

* QFunction - drop unused function

* Python - fix copy-paste errors

* Ctx - update notes for Fortran usage

* Fortran - drop unneeded cast

Co-authored-by: Jed Brown <jed@jedbrown.org>

* Interface - use void* for SetData interfaces

* Make - use call quiet for NVCC

* Interface - use void* for GetData interfaces

* Make - add quiet call option for examples

* Makefile - create common makefile to reduce duplication/complexity in example makefiles

Co-authored-by: Jed Brown <jed@jedbrown.org>

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PETSc examples: Update DMPlexCreateSphereMesh() and DMAddBoundary() calls after changes in PETSc's API (#600)

* PETSc examples: Update DMPlexCreateSphereMesh call after change in API

* PETSc bps:

PETSc examples: Update DMPlexCreateSphereMesh() and DMAddBoundary() calls after changes in PETSc's API (#600)

* PETSc examples: Update DMPlexCreateSphereMesh call after change in API

* PETSc bps: Update DMAddBoundary() call after change in API

* Add compatibility macros

* solids/ and fluids/ : Update DMAddBoundary() call and add compatibility macros

* Travis: Update PETSc ref with latest hash from master

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Op - add interface for multigrid level creation (#579)

* Op - add interface for multigrid level creation

* Op - add implementation for OperatorMultigridLevelCreate

* make style

* make tidy

Op - add interface for multigrid level creation (#579)

* Op - add interface for multigrid level creation

* Op - add implementation for OperatorMultigridLevelCreate

* make style

* make tidy

* Op - add test t550, fix errors

* Tests - add Fortran version of t550

* Tests - add t511 for testing tensor basis multigrid level setup

* make style and tidy

* Tests - fix t55* memory leaks

* Tests - add t552 for non-tensor basis multigrid levels

* CUDA - use CeedIntMax in shared CUDA backend

* Tests - add OCCA test exception for t55*

* Op - add lvector global prolongation multiplicity, simplifies user interface

* Solids - convert example to new interface

* make style

* Tests - convert t550 to multicomponent

* Solids - drop unused ceed_fine

* Python - add new multigrid level interface

* Python - fix operator wrap, use ceed python obj rather than ceed pointer

* Gallery - update comment slightly

* Tests - remove accidental duplicate test

* Multigrid - add size=2 case as well

* Operator - drop unneeded inline

* QFunction - simplify context ownership to match vector

* make style

* Python - update multigrid function signature

* Operator - refactor prolong/restrict qfunctions as scaling qfunctions

* Vector - add testing for reciprocal and add to Fortran/Python interfaces

* CUDA - add VectorReciprocal on device

* Gallery - drop specalized versions for 'Scale', wil fix performance hit later

* Hip - add vector reciprocal

* Operator - add more flexible prologation basis creation interface

* Vec - make sure data is set for VectorReciprocal

* Tests - drop ncomp for t550/1 so kernel is not too large for Magma backend

* Tests - add missing lcov markers

* make style

* Travis - allow ARM job to fail

* Travis - fix intel install

* Travis - try different install dir name for inteloneapi

* Travis - add ifort, ipp packages

* Tests - add missing lcov marker

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Merge branch 'main' into natalie/hip-ref-v2

Merge branch 'master' into yohann/nameKernels