Add Array<int> to options, additional limiters for grids #2721
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* Previously the second cmake invocation failed, e.g. after some source changes or after changing a configure time option * It also generated many files, some of which overwrite git-tracked files from autotools, and others where not git-ignored.
Squash optional
Fix some warnings and deprecated headers
Not comprehensive, still fails to run successfully on basic input file (zero pivot in cyclic reduce) Fixes: - unused variables - wrong variable names (including case) - creating laplacians from wrong input sections - some issues with staggering
MPI_DOUBLE is a macro, so this check can break, even if there is no mismatch.
Fix versions after release
Improve docs + fix boutpp docs (master)
Fix some warnings
Co-authored-by: Peter Hill <[email protected]>
Get mesh outputs after physics init
No mallocs now needed when setting matrix elements in serial or parallel for 1D-recycling example. Hypre preconditioner type can now be set with pc_hypre_type option. Defaults to pilut, as this seems to give the best performance in parallel.
cvode_nonlinear_convergence_coef
Sets parameter through call to CVodeSetNonlinConvCoef
https://sundials.readthedocs.io/en/latest/cvodes/Usage/SIM.html#c.CVodeSetNonlinConvCoef
cvode_linear_convergence_coef
Sets parameter through call to CVodeSetEpsLin
https://sundials.readthedocs.io/en/latest/cvodes/Usage/SIM.html#c.CVodeSetEpsLin
Add some documentation of new cvode and beuler solver options.
If PETSc is not configured with Hypre then PCHYPRESetType is not defined.
If a step fails, re-calculate the Jacobian and preconditioner. This can be an expensive operation, so doing this on failure allows lag_jacobian to be increased.
Enables `petsc:log_view=true` option to set the PETSc `-log_view` switch correctly.
They are not used anyway
Reverts some of the deling commits and changes _runs to _compiles
Co-authored-by: David Bold <[email protected]>
Co-authored-by: David Bold <[email protected]>
Co-authored-by: David Bold <[email protected]>
Solver improvements
Do not try to run SLEPc or PETSc in configure
Update `make dist` invocation [skip ci]
mesh:paralleltransform is a section [skip ci]
* next: (96 commits) Use petsc version 3.19.1 in examples, on 'Advanced installation options' page of manual. [skip ci] Apply clang-format changes The additional check is not needed provide VectorMetric in vectormetric.hxx Update more example code snippets from make to cmake. Include -S and -B flags, so examples are more consistent. Use <build-directory> to indicate the path to the build directory. [skip ci] Use petsc version 3.17.5 in examples, on 'Advanced installation options' page of manual. (version 3.19 is not compatible) [skip ci] Apply clang-format changes Pull out cached variables to function Mark some functions as const CI: Drop coverage build OS down to ubuntu-20.04 CI: fix petsc path CI: fix slepc path CI: Update paths for ubuntu 20.04 CI: move some runs to ubunutu-latest CI: do not run on removed old ubuntu Change command example from 'make' to 'cmake --build <build-directory>' in 'Compiling BOUT++' section of 'Advanced installation options' page of manual. Clarify example using dnf. Added comma, for clarity. Add /manual/sphinx/_build to gitignore file. Update examples to petsc version 3.19.0 in 'Advanced installation options' page of manual. ...
Enable 1D arrays of integers to be read from NetCDF files, and made available via `Mesh::get()`. Mainly useful for mesh construction.
When reading 1D vector of ints, check that the input is long enough, and resize the output vector.
A short-term fix, allowing extra limiters to be added with inputs: limiter_count : int limiter_yinds : [int], length limiter_count limiter_xstarts : [int], length limiter_count limiter_xends : [int], length limiter_count The limiter(s) are added between yinds[i] and yinds[i] + 1
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This was branched from |
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@bendudson Do you mind rebasing to make the diff more clear? |
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Replaced by #2767 |
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Array<int>to the Options typeArray<int>from NetCDF files (e.g. mesh input file), and makes them available throughMesh::getThe reason this was added is to be able to include additional limiters in the input file. The format is a short-term solution only, though these have a habit of becoming permanent.