hyteg merge requestshttps://i10git.cs.fau.de/hyteg/hyteg/-/merge_requests2024-04-18T12:24:53+02:00https://i10git.cs.fau.de/hyteg/hyteg/-/merge_requests/732TerraNeo - parameter handling, initialization, radial profiles2024-04-18T12:24:53+02:00Nils KohlTerraNeo - parameter handling, initialization, radial profilesThis MR is a continuation of !712 (and !707 which is a subset of !712).
The MR rebases and refactors what has been implemented in !712.
Introduces:
* parameter handling for the TN app
* radial profile computation
* IO for radial profil...This MR is a continuation of !712 (and !707 which is a subset of !712).
The MR rebases and refactors what has been implemented in !712.
Introduces:
* parameter handling for the TN app
* radial profile computation
* IO for radial profiles
* temperature initialization functions
Major edits compared to !712:
* refactored temperature initialization functions (now just a "library" of functions that create lambdas for `interpolate()`)
* refactored the radial profile tool (much more efficient as all relevant values are computed in a single loop, [free your functions](https://github.com/CppCon/CppCon2017/blob/master/Presentations/Free%20Your%20Functions/Free%20Your%20Functions%20-%20Klaus%20Iglberger%20-%20CppCon%202017.pdf))
* refactored parameter IO (using json with better error handling, no more global variables, etc.)Nils KohlNils Kohlhttps://i10git.cs.fau.de/hyteg/hyteg/-/merge_requests/727[Rebased] Integrating Stokes solvers from branch burk/ELWMS.2024-03-20T15:56:34+01:00Nils Kohl[Rebased] Integrating Stokes solvers from branch burk/ELWMS.Rebased - see !718.Rebased - see !718.Nils KohlNils Kohlhttps://i10git.cs.fau.de/hyteg/hyteg/-/merge_requests/723Generated Stokes operators with annulus blending2024-03-15T14:49:45+01:00Nils KohlGenerated Stokes operators with annulus blendingNils KohlNils Kohlhttps://i10git.cs.fau.de/hyteg/hyteg/-/merge_requests/716GEMV2024-03-21T21:55:14+01:00Nils KohlGEMVThis MR implements the `gemv` as described in detail in #253.
It turns out that only minor changes have to applied to the `apply()` method to make this work (at least for the elementwise operators).This MR implements the `gemv` as described in detail in #253.
It turns out that only minor changes have to applied to the `apply()` method to make this work (at least for the elementwise operators).Nils KohlNils Kohlhttps://i10git.cs.fau.de/hyteg/hyteg/-/merge_requests/713Extend geometry getter functions of Face and Cell class2024-02-29T15:25:13+01:00Marcus MohrExtend geometry getter functions of Face and Cell classThis MR adds three new functions:
- `Face::getIncircleRadius()`
- `Cell::getVolume()`
- `Cell::getInsphereRadius()`
We test these together with the existing `Face::getArea()` function in the new **Face+CellGeometryTest**.This MR adds three new functions:
- `Face::getIncircleRadius()`
- `Cell::getVolume()`
- `Cell::getInsphereRadius()`
We test these together with the existing `Face::getArea()` function in the new **Face+CellGeometryTest**.Marcus MohrMarcus Mohrhttps://i10git.cs.fau.de/hyteg/hyteg/-/merge_requests/710New generated Stokes operators2024-03-06T08:34:39+01:00Nils KohlNew generated Stokes operatorsSee #246 for extended discussion
----
## Checklist:
- [x] `hyteg-operators` submodule needs to be updated as soon as https://i10git.cs.fau.de/hyteg/hyteg-operators/-/merge_requests/3 is merged
- [x] fix unused variable warnings in gen...See #246 for extended discussion
----
## Checklist:
- [x] `hyteg-operators` submodule needs to be updated as soon as https://i10git.cs.fau.de/hyteg/hyteg-operators/-/merge_requests/3 is merged
- [x] fix unused variable warnings in generated operators
- [x] [move divergence, gradient, viscous directories out of the stokes directory and under `hyteg_operators_composites` instead](https://i10git.cs.fau.de/hyteg/hyteg/-/issues/246#note_28717)
- [x] fix issues for `real_t = float` (single precision builds)
- [x] blending operators test
----
## New module `hyteg_operators_composites`
This MR adds a new module `hyteg_operators_composites` that contains composite operators that are built from generated operators.
For now, three variants of Stokes operators have been added:
* P2P1StokesConstantOperator
* P2P1StokesEpsilonOperator
* P2P1StokesFullOperator
including the necessary viscous, divergence and gradient operators plus their `IcosahedralShellMap` blending versions.
The new module also comes with a short README.
## Testing
The MR extends and modifies
* P2P1ElementwiseStokesOperatorTest (Stokes constant, 2D + 3D)
* P2P1ElementwiseStokesOperatorTest (full Stokes w/ blending, 3D)
* ElementwiseEpsilonMinResConvergenceTest (Stokes epsilon, 2D + 3D)
* DivergenceOperatorTest (divergence, 2D + 3D)
* ViscousOperatorsTest (epsilon + full viscous block, 2D )
to test the new composites.
At least the 2D versions of all non-blending Stokes operators are now tested to some extent.Nils KohlNils Kohlhttps://i10git.cs.fau.de/hyteg/hyteg/-/merge_requests/705Add Stokes benchmarks for annulus and thick spherical shell settings2024-02-22T13:47:51+01:00Marcus MohrAdd Stokes benchmarks for annulus and thick spherical shell settingsThe benchmarks are based on and extend, w.r.t. boundary conditions, those described in [Analytical solutions for mantle flow in cylindrical and spherical shells](https://doi.org/10.5194/gmd-14-1899-2021) by Kramer et al.
Also noteworthy...The benchmarks are based on and extend, w.r.t. boundary conditions, those described in [Analytical solutions for mantle flow in cylindrical and spherical shells](https://doi.org/10.5194/gmd-14-1899-2021) by Kramer et al.
Also noteworthy is the addition of a `PythonCallingWrapper` class.https://i10git.cs.fau.de/hyteg/hyteg/-/merge_requests/676Add continues outputting to LaTeX Table printer2024-01-19T17:58:21+01:00Michael ZikeliAdd continues outputting to LaTeX Table printerThe header `LaTeX/Table.hpp` provides the possibility to log rows of a tabulated `.dat` file that can later be used to, e.g. print graphs with pgfplots or also just tables in LaTeX.
This MR introduces a `writeUpdate` Method, that allows...The header `LaTeX/Table.hpp` provides the possibility to log rows of a tabulated `.dat` file that can later be used to, e.g. print graphs with pgfplots or also just tables in LaTeX.
This MR introduces a `writeUpdate` Method, that allows for intermediate printing of the tables rows, that have not been printed yet, instead of printing the entire table all the time.Michael ZikeliMichael Zikelihttps://i10git.cs.fau.de/hyteg/hyteg/-/merge_requests/671Enable float16 support for the P1 functionspace2024-02-13T18:29:24+01:00Michael ZikeliEnable float16 support for the P1 functionspaceHyTeG was not able to work with float16 types. This merge request fixes this by adding the missing functionality for the P1 functionspace.
Necessary changes:
- [x] Template and explicit instantiate the following kernels that have been ...HyTeG was not able to work with float16 types. This merge request fixes this by adding the missing functionality for the P1 functionspace.
Necessary changes:
- [x] Template and explicit instantiate the following kernels that have been generated at some point <add, apply, assign, communicate>. The other two kernel types <GS and SOR> have not been templated yet, since they are not used for the generated operators.
- [x] Set standard to C++23 if half precision support is enabled, otherwise some basic asserts like `is_floating_point` will fail.
- [x] Add test that check if all necessary functionality of float16 is working properly.
- [x] Update walberla to support float16 support.
- [x] Make sure that `WALBERLA_BUILD_WITH_HALF_PRECISION_SUPPORT` is enabled in the pipeline.
- [x] Make sure that the remote on the submodule walberla is the walberla repo and not a local fork.
- [x] Test the implementation and float16SupportTest for older compilers as well.
- [x] Some of the now templated kernels use copy by value, while reference is sufficient. Go back and add references.
- [x] Update the license in the modified files.
---
This merge request is dependent on the walberla merge request [!643](https://i10git.cs.fau.de/walberla/walberla/-/merge_requests/643).Michael ZikeliMichael Zikelihttps://i10git.cs.fau.de/hyteg/hyteg/-/merge_requests/659Eigen sparse solver wrapper2024-02-12T18:33:32+01:00Nils KohlEigen sparse solver wrapperTo be introduced after !658.To be introduced after !658.Nils KohlNils Kohlhttps://i10git.cs.fau.de/hyteg/hyteg/-/merge_requests/658Eigen sparse matrix and vector assembly (proxies and helper) from HyTeG's FE operators functions.2023-11-09T10:07:10+01:00Nils KohlEigen sparse matrix and vector assembly (proxies and helper) from HyTeG's FE operators functions.See #233
Solver wrappers still left to be implemented.See #233
Solver wrappers still left to be implemented.Nils KohlNils Kohlhttps://i10git.cs.fau.de/hyteg/hyteg/-/merge_requests/657Include multiple-precision floating-point library MPFR to HyTeG2023-11-06T12:38:45+01:00Michael ZikeliInclude multiple-precision floating-point library MPFR to HyTeGMPFR is a C library for simulating arbitrary whole number precision for floating-point variables, hence enabling multiple-precision floating-point computations with correct rounding. The precision requested by the user is the number of b...MPFR is a C library for simulating arbitrary whole number precision for floating-point variables, hence enabling multiple-precision floating-point computations with correct rounding. The precision requested by the user is the number of bits used to represent the mantissa.
For more information about MPFR compare: [mpfr.org](http://www.mpfr.org/)
For better usage in HyTeG, two external C++ wrapper libraries are included as well to enable e.g. operator overloading, automatic memory management, ...
One of these is using compile time definition of the variable precision. Compare the distributor website: [mpfr::real<>](http://chschneider.eu/programming/mpfr_real/)
The other one uses a runtime definition of the variable precision. Compare the distributor website: [mpfr::mpreal](http://www.holoborodko.com/pavel/mpfr/)Dominik Thoennesdominik.thoennes@fau.deDominik Thoennesdominik.thoennes@fau.dehttps://i10git.cs.fau.de/hyteg/hyteg/-/merge_requests/653Particles2023-10-19T12:20:24+02:00Nils KohlParticlesThis MR implements unresolved particles via the MESA-PD particle code generation framework.
The objective is the implementation of **fluid (<)-> particle** and later **particle <-> particle** interactions. Since the particles are assume...This MR implements unresolved particles via the MESA-PD particle code generation framework.
The objective is the implementation of **fluid (<)-> particle** and later **particle <-> particle** interactions. Since the particles are assumed to be smaller than the elements, the module is referred to as _unresolved particles_. Thus fluid-particle interactions are not meant to be fully resolved but are modeled instead. At this point, only the one-way coupling (fluid acts on particles, not vice versa) is considered.
This is sufficient to, e.g., implement tracer particles.
Some notes:
* The implementation is already fully parallelized.
* There is a new tutorial (no. 12) including some images.
* The particle properties are subject to change and probably need to be discussed in the future. As of now, it is possible to flexibly add custom real and integer scalars to particles if needed.
* Direct application of velocity and force fields is possible. For tracer particles, the former is sufficient and can be interpreted as a extremely simplified form of Faxén's law (https://en.wikipedia.org/wiki/Fax%C3%A9n%27s_law). Force fields are also already supported, and naturally involve the particle mass for the computation of the resulting translational velocity.
* Theoretically, all features that are available in MESA-PD can be used. This includes, for instance, other integrators. However, using them involves generating the corresponding C++ code via MESA-PD through the python script in the `data/codegen/unresolved_particles/` directory.
* I had in mind that there has been a temporary(?) tracer particle implementation in the TerraNeo module. I cannot find it right now (could be on a branch) - and I might be wrong. If there is one, we should consider replacing it (and add required features to this new version - if possible).
* Blended domains are not yet supported.Nils KohlNils Kohlhttps://i10git.cs.fau.de/hyteg/hyteg/-/merge_requests/642First version of parallel PrimitiveStorage setup from file.2023-10-23T13:54:07+02:00Nils KohlFirst version of parallel PrimitiveStorage setup from file.This MR realizes a two-step process. First, in a serial (offline) run, the SetupPrimitiveStorage is built and passed to a load balancer, followed by serialization to a file. During the actual, parallel run, the file is read via MPIIO suc...This MR realizes a two-step process. First, in a serial (offline) run, the SetupPrimitiveStorage is built and passed to a load balancer, followed by serialization to a file. During the actual, parallel run, the file is read via MPIIO such that only the portion that is necessary has to be viewed by the respective process. From that binary string, the entire PrimitiveStorage is created in parallel.
There are numerous possible optimizations - most notably, it is not clear to me right now if the current approach of simply writing all neighbor primitives to file is preferable, or if alternatively, such data should be communicated after only reading the locally allocated primitives. Maybe it does not even make a difference at all. Also, this implementation has not been tested with large setups yet.Nils KohlNils Kohlhttps://i10git.cs.fau.de/hyteg/hyteg/-/merge_requests/635Enhance functionality of FEFunctionRegistry and FunctionMultiStore2023-07-28T14:21:17+02:00Marcus MohrEnhance functionality of FEFunctionRegistry and FunctionMultiStoreThe `FEFunctionRegistry` and `FunctionMultiStore` classes are extended to
- allow to remove functions again; note: this technically touches on issues #172 and #186
- only store functions once, where uniqueness is based on the function's...The `FEFunctionRegistry` and `FunctionMultiStore` classes are extended to
- allow to remove functions again; note: this technically touches on issues #172 and #186
- only store functions once, where uniqueness is based on the function's name
This MR supersedes !634.Marcus MohrMarcus Mohrhttps://i10git.cs.fau.de/hyteg/hyteg/-/merge_requests/600Allow asking a Primitive for its type2023-05-19T17:19:54+02:00Marcus MohrAllow asking a Primitive for its typeIn most of our current algorithms we (implicitely) know what type of primitive we are dealing with, i.e. whether we are working on a `Cell`, `Face`, `Edge` or `Vertex`. This largely results from the fact that we ask a `PrimitiveStorage` ...In most of our current algorithms we (implicitely) know what type of primitive we are dealing with, i.e. whether we are working on a `Cell`, `Face`, `Edge` or `Vertex`. This largely results from the fact that we ask a `PrimitiveStorage` object to provide us with all local primitives of a certain type, e.g. via `PrimitiveStorage::getFaces()`.
Still to me it feels strange that we can neither query an object of type `Primitive` to obtain its type, nor that this is encoded in its associated `PrimitiveID`. There are some situations, where we might not (implicitely) know what kind of primitive we are dealing with. An example at the moment would be the migration of primitives between MPI processes. As a consequence of this the `PrimitiveStorage` class defines its own `PrimitiveTypeEnum` and provides a `getPrimitiveType()` method, which, presented with a `PrimitiveID` will return the type of the primitive, if this is either present locally, or in the immediate neighbourhood. If not, it will return `INVALID`.
The idea of this MR is to equip the `Primitive` class itself with a `PrimitiveTypeEnum` type that only has the values `CELL`, `FACE`, `EDGE` and `VERTEX` and a pure virtual function `Primitive::getType()` that can be used to query this. The latter is then easily implemented in the child classes.
The MR preserves `PrimitiveStorage::PrimitiveTypeEnum`, because I did not want to add a special situation `INVALID` enum to `Primitive::PrimitiveTypeEnum`. The former quasi extends the latter, based on fixed int values, so that we can cast the former into the latter.
That feels not ideal, but I am too unfamiliar with the details of primitive migration to understand, why we might want to send a nullptr together with an `INVALID` from one process to another, to change that.
Cheers
MarcusMarcus MohrMarcus Mohrhttps://i10git.cs.fau.de/hyteg/hyteg/-/merge_requests/597Add function for writing blended coarse mesh2023-05-12T10:04:52+02:00Daniel BauerAdd function for writing blended coarse meshWith this MR we can visualize meshes on the physical domain.
![image](/uploads/2412529a9f21b3c4d7b2c3d6cacd1f7a/image.png)
Edit: Now, VTP and poly lines are used.With this MR we can visualize meshes on the physical domain.
![image](/uploads/2412529a9f21b3c4d7b2c3d6cacd1f7a/image.png)
Edit: Now, VTP and poly lines are used.Daniel BauerDaniel Bauerhttps://i10git.cs.fau.de/hyteg/hyteg/-/merge_requests/594Allow use of isoparametric elements in VTKOutput for P2Functions2023-06-22T17:38:46+02:00Marcus MohrAllow use of isoparametric elements in VTKOutput for P2FunctionsThe merge introduces a change to the functionality of the `VTKOutput` class. When writing `P2(Vector)Function`s the default now is to use *VTK_QUADRATIC_TRIANGLE* or *VTK_QUADRATIC_TETRA* as cell type.
The old way to export these functi...The merge introduces a change to the functionality of the `VTKOutput` class. When writing `P2(Vector)Function`s the default now is to use *VTK_QUADRATIC_TRIANGLE* or *VTK_QUADRATIC_TETRA* as cell type.
The old way to export these functions as `P1Function`s on a refined mesh is for the moment still supported and can be activated by calling
- `setUseVTKQuadraticTriangle( false )` or
- `setUseVTKQuadraticTetra( false )`
on the corresponding `VTKOutput` object.
Comparison of the old versus the new approach looks good so far. In the following figures the left part shows a visualisation with the old and the right with the new approach:
![VTK_Quadratic_Triangle-partialAnnulus](/uploads/7fc7c7ed185be1f2fd4bd6ab77057d21/VTK_Quadratic_Triangle-partialAnnulus.png)
![VTK_QUADRATIC_TETRA_3TETS_LVL2-v2](/uploads/3a5ce647b6dca79acc120c590bca1df5/VTK_QUADRATIC_TETRA_3TETS_LVL2-v2.png)Marcus MohrMarcus Mohrhttps://i10git.cs.fau.de/hyteg/hyteg/-/merge_requests/585Add isIdentity and isAffine to GeometryMap2023-04-20T17:38:29+02:00Daniel BauerAdd isIdentity and isAffine to GeometryMapFixes hyteg/hyteg#208.Fixes hyteg/hyteg#208.Daniel BauerDaniel Bauerhttps://i10git.cs.fau.de/hyteg/hyteg/-/merge_requests/584Enriched Galerkin functionspace2023-04-19T19:31:44+02:00Fabian BöhmEnriched Galerkin functionspaceAdds the Enriched Galerkin discretization to HyTeG, contained in directory src/hyteg/egfunctionspace:
- Forms for mass, div, divt, Laplacian and epsilon
- corresponding operators with and without Nitsche-type boundary conditions (Nits...Adds the Enriched Galerkin discretization to HyTeG, contained in directory src/hyteg/egfunctionspace:
- Forms for mass, div, divt, Laplacian and epsilon
- corresponding operators with and without Nitsche-type boundary conditions (Nitsche-operators are preferred due to their symmetry)
- a Stokes-function and operators in directory src/hyteg/composites
- interpolation operators between DG and CG of first degree with P1toDGOperator in directory src/hyteg/dgfunctionspace
- additional addVolumeGhostlayer functionality in vertexDoFFunction required in P1toP0Operator and P0toP1Operator
Two benchmarks with strongy varying viscosity from literature reside in apps/2022-eg-varvisc.
tests/hyteg/egfunctionspace contains tests for operator symmetry, forms, matvec/apply, basic operations of EGFunction and convergence tests.