Add Array/Matrix/Tensor<int> to options, additional limiters for grids (rebase) by bendudson · Pull Request #2767 · boutproject/BOUT-dev

bendudson · 2023-10-12T15:32:07Z

Rebase of #2721 on next

Adds Array to the Options type
Reads Array from NetCDF files (e.g. mesh input file), and makes them available through Mesh::get

The 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.

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

github-actions

clang-tidy made some suggestions

github-actions · 2023-10-12T15:40:46Z

+  int limiter_count = 0;
+  Mesh::get(limiter_count, "limiter_count", 0);
+  if (limiter_count > 0) {
+    std::vector<int> limiter_yinds, limiter_xstarts, limiter_xends;


warning: multiple declarations in a single statement reduces readability [readability-isolate-declaration]

Suggested change

std::vector<int> limiter_yinds, limiter_xstarts, limiter_xends;

std::vector<int> limiter_yinds;

std::vector<int> limiter_xstarts;

std::vector<int> limiter_xends;

dschwoerer

Test would be nice 😊

Enable Options to store index arrays

Without these the build fails at link time when building with ADIOS2.

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* next: (247 commits) Remove vagrant config Remove makefiles Remove configure left overs Avoid mpi-compatibility issues BoutComm::get() might return int Bump bundled fmt Delete v5 header shims CI: Fedora container is already fully setup Apply clang-format changes Add `has_hypre` to python `boutconfig` Update examples for LaplaceXY factory Fix call to virtual function in ctor CI: Don't warn about including PETSc or MPI symbols directly Try to appease clang-tidy `misc-include-cleaner` Remove private variables from base class Bump soname Fix typo in define Apply clang-format changes Add factory for LaplaceXY, LaplaceXY2, LaplaceXY2Hypre Enable non-const iteration over `Options` ...

github-actions

clang-tidy made some suggestions

github-actions

clang-tidy made some suggestions

github-actions · 2025-11-18T17:59:38Z

+
+/// Create a `std::index_sequence` with the length of a tuple ``T``
+template <typename T>
+using tuple_index_sequence = std::make_index_sequence<std::tuple_size_v<T>>;


warning: no header providing "std::make_index_sequence" is directly included [misc-include-cleaner]

include/bout/traits.hxx:5:

+ #include <utility>

github-actions · 2025-11-18T17:59:38Z

@@ -1,4 +1,5 @@
 #include "bout/build_defines.hxx"
+#include "bout/traits.hxx"



warning: included header traits.hxx is not used directly [misc-include-cleaner]

Suggested change

github-actions · 2025-11-18T17:59:38Z


+using bout::utils::tuple_index_sequence;
+
+template <class Tuple, std::size_t... I>


warning: no header providing "std::size_t" is directly included [misc-include-cleaner]

template <class Tuple, std::size_t... I> ^

github-actions · 2025-11-18T17:59:38Z

+using bout::utils::tuple_index_sequence;
+
+template <class Tuple, std::size_t... I>
+auto make_dims_impl(NcGroup& group, Tuple&& t, std::index_sequence<I...> /* index */) {


warning: no header providing "std::index_sequence" is directly included [misc-include-cleaner]

src/sys/options/options_netcdf.cxx:1:

+ #include <utility>

github-actions · 2025-11-18T17:59:38Z

+template <class Tuple, std::size_t... I>
+auto make_dims_impl(NcGroup& group, Tuple&& t, std::index_sequence<I...> /* index */) {
+  return std::vector{findDimension(group, fmt::format("dim_{}", I),
+                                   std::get<I>(std::forward<Tuple>(t)))...};


warning: 't' used after it was forwarded [bugprone-use-after-move]

std::get<I>(std::forward<Tuple>(t)))...}; ^

Additional context

src/sys/options/options_netcdf.cxx:307: forward occurred here

std::get<I>(std::forward<Tuple>(t)))...}; ^

github-actions · 2025-11-18T17:59:38Z

+  return "Array<int>";
+}
+template <>
+std::string typeName<Array<BoutReal>>() {


warning: no header providing "Array" is directly included [misc-include-cleaner]

std::string typeName<Array<BoutReal>>() { ^

github-actions · 2025-11-18T17:59:39Z

+      }
+    }
+
+    Options fields{{"f2d", Field2D(1.0)},


warning: no header providing "Field2D" is directly included [misc-include-cleaner]

tests/integrated/test-options-adios/test-options-adios.cxx:3:

- #include "bout/options_io.hxx" + #include "bout/field2d.hxx" + #include "bout/options_io.hxx"

github-actions · 2025-11-18T17:59:39Z

+      }
+    }
+
+    Options fields{{"f2d", Field2D(1.0)},


warning: variable 'fields' of type 'Options' can be declared 'const' [misc-const-correctness]

Suggested change

Options fields{{"f2d", Field2D(1.0)},

Options const fields{{"f2d", Field2D(1.0)},

github-actions · 2025-11-18T17:59:39Z

+    }
+
+    Options fields{{"f2d", Field2D(1.0)},
+                   {"f3d", Field3D(2.0)},


warning: no header providing "Field3D" is directly included [misc-include-cleaner]

tests/integrated/test-options-adios/test-options-adios.cxx:3:

- #include "bout/options_io.hxx" + #include "bout/field3d.hxx" + #include "bout/options_io.hxx"

github-actions · 2025-11-18T17:59:39Z

+
+    Options fields{{"f2d", Field2D(1.0)},
+                   {"f3d", Field3D(2.0)},
+                   {"fperp", FieldPerp(3.0)},


warning: no header providing "FieldPerp" is directly included [misc-include-cleaner]

{"fperp", FieldPerp(3.0)}, ^

ZedThree · 2025-11-19T11:52:09Z

Spotted some bugs in the adios implementation when adding some unit tests to this PR -- will merge this first, and make a new PR for tests + fixes.

bendudson and others added 4 commits October 12, 2023 08:26

Add Array<int> to Options

cc1672d

Enable 1D arrays of integers to be read from NetCDF files, and made available via `Mesh::get()`. Mainly useful for mesh construction.

GridFile: Check sizes, allocate vector ints

e654af6

When reading 1D vector of ints, check that the input is long enough, and resize the output vector.

Apply clang-format changes

1c1d834

bendudson mentioned this pull request Oct 12, 2023

Add Array<int> to options, additional limiters for grids #2721

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github-actions Bot reviewed Oct 12, 2023

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dschwoerer previously approved these changes Oct 13, 2023

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dschwoerer and others added 4 commits October 18, 2023 14:20

Merge branch 'next' into options-array-ints-rebase

0156c0e

Merge branch 'next' into options-array-ints-rebase

c1c1b70

Merge branch 'next' into options-array-ints-rebase

9a2637c

Options: Add Matrix<int> and Tensor<int>

eeb3426

Enable Options to store index arrays

bendudson dismissed dschwoerer’s stale review via eeb3426 May 30, 2025 18:54

Apply black changes

979cce8

bendudson changed the title ~~Add Array<int> to options, additional limiters for grids (rebase)~~ Add Array/Matrix/Tensor<int> to options, additional limiters for grids (rebase) May 30, 2025

bendudson and others added 5 commits June 4, 2025 11:59

ADIOS2: Add Array/Matrix/Tensor<int> types

21e964c

Without these the build fails at link time when building with ADIOS2.

Apply clang-format changes

020d879

Apply suggestions from code review

a32390e

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

Apply clang-format changes

bfedcc3

ZedThree previously approved these changes Nov 18, 2025

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github-actions Bot reviewed Nov 18, 2025

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ZedThree added 5 commits November 18, 2025 17:50

Add helper function for Options::as for Array/Matrix/Tensor

cdaa626

Remove unnecessary template argument from specialisations

da418b1

Reduce duplication in ADIOSPutVarVisitor for Array/Matrix/Tensor

1adfb2f

Support Array/Matrix/Tensor<int> in OptionsNetCDF

f09c14c

Fix a bunch of clang-tidy warnings

134eb2b

ZedThree dismissed their stale review via 134eb2b November 18, 2025 17:55

ZedThree force-pushed the options-array-ints-rebase branch from b5663ca to 134eb2b Compare November 18, 2025 17:55

ZedThree approved these changes Nov 18, 2025

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github-actions Bot reviewed Nov 18, 2025

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ZedThree merged commit aae67a5 into next Nov 19, 2025
35 of 36 checks passed

ZedThree deleted the options-array-ints-rebase branch November 19, 2025 16:06

-    std::vector<int> limiter_yinds, limiter_xstarts, limiter_xends;
+    std::vector<int> limiter_yinds;
+    std::vector<int> limiter_xstarts;
+    std::vector<int> limiter_xends;

		@@ -1,4 +1,5 @@
		#include "bout/build_defines.hxx"
		#include "bout/traits.hxx"


		using bout::utils::tuple_index_sequence;

		template <class Tuple, std::size_t... I>

	Options fields{{"f2d", Field2D(1.0)},
	Options const fields{{"f2d", Field2D(1.0)},

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ZedThree commented Nov 19, 2025

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