ctx - add context field labels to interface

H(div) basis constructor (#878)

* backends/interface: added H(div) basis constructor

* tests: CEED_EVAL_INTERP/DIV tested for H(div) basis.

* Update interface/ceed-basis.c

Co-authored-by:

H(div) basis constructor (#878)

* backends/interface: added H(div) basis constructor

* tests: CEED_EVAL_INTERP/DIV tested for H(div) basis.

* Update interface/ceed-basis.c

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

* Update interface/ceed-basis.c

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

* Update interface/ceed-basis.c

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

* Update interface/ceed-basis.c

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

* Update interface/ceed-basis.c

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

* interface/ceed-basis.c: delete [-1,1] for non-tensor basis constructor

* Update interface/ceed-basis.c

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

* include/ceed: added CEEDFESpace enum and used it at ceed-basis.c

* tests: added t330-basis.out and changed xhat-->x_hat

* Changed name convention for CeedElemTopology and CeedFESpace enum.

* make style

* interface/ceed-basis.c: Added FE space/topology of the basis to CeedBasisView function

* tests/output: update ...basis.out file

* Changed CEED_FE_TOPO_ ==> CEED_TOPOLOGY_

* backends/ref: delete CeedBasisApplyHdiv_Ref

* Update interface/ceed-basis.c

Co-authored-by: Jeremy L Thompson <jeremy@jeremylt.org>

* Update interface/ceed-basis.c

Co-authored-by: Jeremy L Thompson <jeremy@jeremylt.org>

* Update include/ceed-impl.h

Co-authored-by: Jeremy L Thompson <jeremy@jeremylt.org>

* interface/ceed-bassi.c: update CeedBasisView

* deleted L2 and H(curl) FE spaces

* minor - update output file

* minor - update output file

* style - consistency with main

Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: Jeremy L Thompson <jeremy@jeremylt.org>

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style - make qf/op field names human readable

op - add ctx setting interface for operators

ctx - define interface for updating ctx fields

vec/qf - initial valid/borrowed/owned split for data (#853)

* vec/qf - initial valid/borrowed/owned split for data

* vec/qf - tidy logic for checking active/stale data

* minor - add missing NU

vec/qf - initial valid/borrowed/owned split for data (#853)

* vec/qf - initial valid/borrowed/owned split for data

* vec/qf - tidy logic for checking active/stale data

* minor - add missing NULL

* doc - explain VectorTakeArray update

* minor - update error messages

* test - update error message in junit/tap

* gpu - fix stray CeedScalar vs void for QFunctionContext

* vec/qf - clarify/simplify access logic

* vec - calloc host arrays when no value set to make empty

* style - minor

* style - minor

* minor - fix error messages

* vec/qf - move data validity checking to backend interface

* gpu - add missing sync error checking for qfcontext

* gpu - homogonize use of impl for backend data to reduce confusion

* vec - clarify access conditions

* python - update test for stricter vector access

* vec - minor fixes

* minor - fix ipython change

* vec - add missing declarations in ceed/backend.h

* ctx - mirror vector borrowed data check in ctx interface

* vec - add CeedVectorGetArrayWrite

* vec - consistent use of CeedVectorGetArray vs CeedVectorGetArrayWrite

* python - small vec fixes

* doc - describe vector data semantics

* magma - update restriction

* gpu - fix restr bug I added, need to sum into target

* magma - fix restriction bug

* cpu - fix restriction bug here too

* op - fix evec allocations

* julia - fix ElemRestriction for new vector access rules

* op - double check GetArray vs Read vs Write usage

* doc - small fix

* restr - clean up read/write logic for restr

* python - add vec.array_write

* magma - typo fix

show more ...

gallery - basic testing of vector gallery functions

junit - add optional JUNIT_BATCH for output filename, prevents overwriting in CI

tests - drop unused include in t406

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

qf - add test for multi source support

qf - add function to retreive kernel name, stored path now excludes kernel name

Allow CeedScalar to be single precision (#788)

One can modify `ceed.h` to include `ceed-f32.h` and then use single precision. This is tested for C in CI and has been tested by developers with Rust,

Allow CeedScalar to be single precision (#788)

One can modify `ceed.h` to include `ceed-f32.h` and then use single precision. This is tested for C in CI and has been tested by developers with Rust, Julia, and Python. This interface is evolving and should be considered experimental at this time (thus lack of automated build support).

* Introduce CeedScalarType enum

* WIP changes to allow different definitions of CeedScalar

* Introduce new header files for float and double

* Only use avx tensor contract and MAGMA non-tensor basis if CeedScalar is double

* WIP changes to allow CeedScalar to be float

* WIP start trying to adjust test tolerances for float or double

* fix typos in comments

* install ceed-f32/64 headers

* Fix missing casts for hipMAGMA element restrictions

* make CeedQFunctionContextGetContextSize available for Python bindings

* Changes to Python bindings to allow CeedScalar to be float

* WIP adjust Python tests for float or double

* make style

* remove QFunctionContextGetContextSize from backend header

* Use quotes instead of <> in include statement

* Remove unncessary includes

* Update tolerances for tests

* [Julia] allow CeedScalar to be Float32

* [Julia] Use Preferences instead of custom build configuration

# Conflicts:
# julia/LibCEED.jl/src/C.jl

* [Makefile] Change definition of CC_VENDOR so it works with cross-compilation

* [Julia] Use Preferences in CI

# Conflicts:
# .github/workflows/julia-test-with-style.yml

* [Julia] Update docs about preferences

* [Julia] Add test/Project.toml workaround for Preferences

* Add CeedGetScalarType to get the type of CeedScalar at runtime

* [Julia] Move functions from Ceed.jl to LibCEED.jl

* [Julia] Add support for getting library path and scalar type at runtime

* [Julia] Minor change to checking if CUDA is loaded

* [Julia] Check correct CeedScalar types in basis functions

* [Julia] Fix tests comparing with output file

* [Julia] Change devtests to use CeedScalar instead of Float64

* Update test 402 so context will be same size in double or float

* Update tolerances for ceed examples

* [Julia] CUDA fixes

* remove unused variable in t208

* SchurDecomposition: do not compute tau on final iteration

* Update tolerances for some basis tests (for single precision)

* Make style

* Python style fixes for basis test

* Add single precision output for t300 and t320 and adjust checks; skip t541 in single

* Add LCOV exclusions after moving to new line

* fix spacing

* Python: make CEED_EPSILON available as libceed.EPSILON

* Python: optional parameter to specify different output file for test comparison

* Python: update tests' use of EPSILON and change test_300 output file for single precision

* Python: add convenience function for getting dtype corresponding to CeedScalar

* rust - add single precision support

* [Julia] Fall back on Float64 if CeedGetScalarType is not available

* [Julia] style

* Adjust tolerance for t301

* xsmm - add single precision support

* avx - add single precision support

* Add initial single precision support for MAGMA non-tensor basis

* Skip t300 and t320 in single precision; revert Python t300 changes

* Revert output changes for t300 and t320 in junit

* [Julia] Changes to autogenerated bindings for mixed precision

* [Julia] style

* [Julia] Check scalar type when changing libceed library path

The check is also performed when the package is loaded. This prevents having to
restart the Julia session twice

* [Julia] Require JLLWrappers version 1.3

This is needed to use Preferences to change the library path

* Add documentation page for precision development

Co-authored-by: Will Pazner <will.e.p@gmail.com>

* Cleanup from merge: remove old README

* Return CEED_ALIGN to backend.h

* Make Fortran compiler (FC) optional; empty skips Fortran tests

Use in Python and Rust builds, which may not have a Fortran compiler
installed and thus would produce confusing output.

* Add single precision CI test for Noether

Co-authored-by: Jeremy L Thompson <jeremy@jeremylt.org>

Co-authored-by: Will Pazner <will.e.p@gmail.com>
Co-authored-by: Jeremy L Thompson <jeremy@jeremylt.org>
Co-authored-by: Jed Brown <jed@jedbrown.org>

show more ...

tests: remove unused variable

junit.py: add classname for gitlab-ci junit parser

style - add missing codecov exclusion

tests - refactor t301,302 to not use output

tests - refactor t202,203,208,213 to not use output

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>

show more ...

fdm - accuracy fixes: peturb diff matirx, sort eigenvalues in simultanious diag

Update backends/ref/ceed-ref-operator.c

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

Update backends/ref/ceed-ref-op

fdm - accuracy fixes: peturb diff matirx, sort eigenvalues in simultanious diag

Update backends/ref/ceed-ref-operator.c

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

Update backends/ref/ceed-ref-operator.c

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

show more ...

Python - add basis.get_grad_1d()

tests - add t541, test FDM inv of singular operator with Dirichlet conditions added via Schur complement

test - refactor t304/5 to verify decomposition

test - sync data to device arrays before testing backend vector functions, such as axpy, reciprocal, and scale

Fluids - Refactor and add GPU support (#754)

* Initial commit for using PetscFunctionList in fluids example

* WIP: debugging

* Debug: initialize PetscFunctionList with NULL

* allocate memor

Fluids - Refactor and add GPU support (#754)

* Initial commit for using PetscFunctionList in fluids example

* WIP: debugging

* Debug: initialize PetscFunctionList with NULL

* allocate memory for context problem

* freed allocated memory

* WIP: fluids: split density current into new compilation unit
I have dropped last changes before this commit so there might be some
bugs

* Fixed bugs after dropping the commit containing unnecessary changes

* NS: dropped unused variable from User struct

* WIP: factored out DMAddBoundary() for density_current

* split advection and advection2d into separate compilation units as well

* fluids: added *.o to make clean

* removed bc from problemData

* style

* commented the error handlers and moved petsc options regarding the boundary conditions to each compilation unit

* call bc functions inside SetUpDM()

* Moved all bc related statements from SetUpDM() to each compilation unit

* examples/fluids/advection.h: style

* WIP: modified CeedQFunctionContexts

* FFR: By creating a struct for DC context, one of the last test crushed so I had to reverse it. This should be investigated later.

* style

* examples/navierstokes: Use heap memory for ctxSetup

* examples/fluids: WIP - reading arrays through cl options for DC is enabled by using double pointers but there is still a problem with unit conversions and also need to fix other structs

* style

* WIP: Trying to assign values to context data in each problem function

* bug: there is a problem in pointer to struct

* WIP: Everything seems to be working but it breaks and I haven't figured out the reason ...

* fixed typo

* comment out stuff that have been moved to densitycurrent.c

* WIP: The first two regression test pass. There is a problem with stabilization.

* style

* Fluids: QFContext -> Physics

* WIP: passing StabilizationType to Physics (but PETSc is not happy and it diverges for SU and SUPG)

* Initial commit for refactoring advection(2d)

* WIP: Advection is set up except for wind_type

* WIP: refactored advection2d; need to fix the BCs for translation and also passing implicit to advection correctly

* WIP: pass wind_type to all functions correctly but there is still a problem with BCs in the case of translation (changes are not applied to advection yet)

* Apply the same fixes for BCs in advection

* Fluids - Refactor: Moved warnings to advection(2d)

* Fluids - Refactor: remove dead code

* Fluids - Refactor: Move *.h to /qfunctions and *.c to /src

* style

* Fluids - Refactor: drop the supg regression test for now

We need to debug SU/SUPG for density_current. The test does not work.

* Fluids - Refactor: Fixed the double-pointer issue

* Fluids - Refactor: Assign ctxSetup->time = 0 inside each problem's *.c

* Fluids - Refactor: make implicit a member of Physics

* Fluids - Refactor: Add warning for the usage of explicit and supg

* Some comments and naming

* Merge main after v0.8 (#723)

* Fluids - Five regression tests added for euler_vortex

* Fluids - Drop some of the regression tests for now (Needs to get fixed)

* Fluids - Moved all functions to their corresponding source files

* Fluids - move problem source files to /problems

* Fluids - drop dead regression test reference files

* Fluids - more consistent file names

* Fluids - drop dead code and comments

* Fluids - removed CreateVectorFromPetscVec() since it was only used once

* Fluids - created AppCtx for cl option variables and moved cl options to a cloption.c

* Fluids: change style of AppCtx

* style

* Fluids: /src -> /utils

* Created CreateDistributedDM() and some style

* Fluids - create RegisterProblem()

* style - minor

* style - minor

* Fluids - some more C style

* Fluids - /utils -> /src

* Fluids - create VizRefineDM() for viz_refine

* Fluids: some style and name change

* Fluids - style

* Fluids - remove the second ceed initialization

* Fluids - Created CeedData and SetupLibCEED()

* Fluids - create SetupContextForProblems()

* Fluids - Assign structs after they are created

* Fluids - style, minor

* Fluids - created RegressionTests_NS

* Fluids - created GetError_NS()

* Fluids - created PrintOutput_NS()

This processes bash output except for the problem summary which will be
included after mem_type is managed properly.

* Fluids - remove unused variables

* Fluids - created TSSolve_NS() which creates, sets up, and solves ts

* Fluids: Fixed a bug caused by merging#714

* Fluids - style

* Fluids - created SetupICsFromBinary() for case of -continue

* Fluids - create SetBCsFromICs_NS()

* Fluids - default degree had is 1 not 2

* Fluids: clean-up

* Fluids: style - minor

* Fluids - drop redundant operation

* Fluids: clean-up SetupLibCEED()

* Fluids: style - minor

* Fluids: WIP - C style

* Fluids: style - minor

* Fluids: move ceed vector creation to SetupLibCEED()

* Fluids: WIP - clean-up CreateOperatorForDomain()

* Fluids: major clean-up in CreateOperatorForDomain()

* Fluids: style - minor

* Fluids: drop VectorPlacePetscVec()

* Fluids: move ICs_FixMultiplicity() to misc.c

* Fluids: WIP - C style

* Fluids: fix merge conflict after d63eecaab22a26d3072677a1b66c0cf77aa9009d

* Fluids: drop unused function call DMLocalizeCoordinates()

* Fluids: replace user requested memType with MemTypeP2C()

* Fluids: C style

* Fluids: Q->num_Q (Q (# qpts) and Q (global state vector) were confusing my fresh petsc config)

* Fluids: WIP - add GPU vectors

* Fluids: Fixed the memory leak caused by Physics struct

* Fluids: style -minor

* Fluids: no need for casting

* Fluids: Fix mem leak (q0_ceed had to be destroyed at the end of navierstokes.c)

* Fluids: Fixed all mem leaks

* Fluids: Set VecType for dm_hierarchy

* Fluids/doc: fix style

* Fluids: fix missing VecRestoreArray()

* Fluids: clean-up ComputeLumpedMassMatrix()

* Fluids: Cleanup ICs_FixMultiplicity()

* Fluids: WIP - cleanup setupts.c

* Fluids: style - minor

* Fluids: Create element coord ceed vector locally and drop it from CeedData

* Fluids: fix some todos

* Fluids: drop unused code for EULER BCs

* Fluids: PetscMalloc1 -> PetscCalloc1

* Fluids - Define BCs for ADVECTION(2D) for all cases without having the user specify them and change the regressions accordingly

ToDo: For some reason I can't create new regression tests for explicit scheme.

* Fluids - Define problem->print_info() for each problem

* Fluids: Shorten some problem specific command line variables & style

* Fluids - Cleanup BCs in the translation mode

* Fluids - cleanup

* Fluids - more cleanup in BCs

* Fluids - Updated doc, README, and cleanup in the code and cl options

* Fluids - add more regression tests

* Fluids - Define tolerance for the convergence test

* Fluids: include x_coord in CeedData

* wip - gpu

Revert "Fluids: include x_coord in CeedData"

I had to revert this commit since it crashes DC

* style

* Fluids - remove unused variables

* Fluids - fix unused function warnings

* Fluids - fix the remaining warnings

* Fluids - style

* Fluids - add missing licence

* Fluids - bring back contexts to the QFunction header files

* Fluids - transfer QFunctions for boundary integral to their corresponding setupgeo(2d).h header files and add description for Setup2d

* fluids - fix context data sizes

* GPU - add helper function macro

* ex - use consistent MPI info output

* GPU - improve CEED_QFUNCTION_HELPER macro, more flexible

* Fluids - turn on some gpu tests

* Fluids - bring back element coordinate to CeedData

* Fluids - cleanup

* qfunction - clean up helper function macro

* Fixed the remaining conflicts from #769 (helped-by: @rezgarshakeri)

Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: jeremylt <thompson.jeremy.luke@gmail.com>

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junit - skip t506 for cuda/shared, some testing env don't have enough resources to run kernels of that size