Refactor coordinates #2873

…ers.

…ties.

…t be marked explicit to avoid unintentional implicit conversions.

…ometry().

…FakeMesh has no 'source', which causes a crash when the constructor leads to initialisation of FieldMetric objects).

…reference.

…void unintentional implicit conversions.

…ntMetricTensor in Coordinates::setBoundaryCells method, to avoid recalculation of the christoffel symbols, which would (at this stage) involve field data at different locations (specifically the metric tensor and jacobian).

…constructor that is used with FakeMesh.

…ather than the metric tensor, dx, dy, etc.

…istoffel_symbols.

… input source).

…bols constructor.

…ransform().

…and the remaining two uses of it.

…y have been set.

…sing it in as a parameter or re-fetching.

(So now we can directly replace jacobian() with recalculateJacobian(); no longer a special case).

… outside of if-else statement.

… they are for the other variables.

Set after comparing calculated and loaded values, otherwise there will be no difference. Rename Jcalc to J_from_file.

…x, y indices.

…alised fully (no mesh)).

…we know what the name should be) and implement with same pattern as Christoffel symbols.

…trapolateGValues(). Make GValues constructor take a reference to Coordinates (so that it can call methods on the Coordinates class (DDX, DDY, DDZ, communicate). Make communicate() a (public) method of Coordinates so that it can be called by the GValues constructor. This means fixZShiftGuards() also has to be a (private) method of Coordinates.

…eRepresentation" to "MetricTensor::inverse".

…ensor that inherit from MetricTensor.

…e only used by Coordinates class (i.e. put back dependency on bout/derivs).

…s class onto DifferentialOperators.

…r file.

…Tensor class to header file.

… construct a MetricTensor. Co-authored-by: Ben Dudson <[email protected]>

…ent with a single scalar value).

…version).

… duplicating the type name"

…r in 'interpolateFieldsFromOtherCoordinates' method.

…-coordinates

…uctor.

…ling ChristoffelSymbols::applyToComponents() directly).

This reverts commit 5d2a9dd. (Return value could be either Field2D or Field3D).

…s' into refactor-coordinates

…tters.

…or (immediately before calling the differential operator functions).

…void unintentional implicit conversions.

…instead of 'length'.

…t be marked explicit to avoid unintentional implicit conversions.

This reverts commit 37c90c5. It now has to be a class method, as it's called by other functions that are now member functions.

…-coordinates

…not Field2D (as it could be either Field2D or Field3D).

…d be FieldMetric, not Field2D (as it could be either Field2D or Field3D).

(as it could be either Field2D or Field3D).

…D case.

…to set to arbitrary values in the tests. Also the constructor calls the differential operators, which (in the BOUT_USE_METRIC_3D case) require that the ParallelTransform has already been set.

…dReset(). Otherwise calculation of the Christoffel symbols and metric tensor will cause Mesh::getCoordinates() to be called (and fail). (This is because of the circular dependency between Mesh and Coordinates).

… attempting to use it in Coordinates::DDY().

…e constructor that takes no Options (Use the basic type, ParallelTransformIdentity, in this case).

…s are used (and setParallelTransform() requires that dz is already set!)

…ATIBLE(lhs, rhs) failing in Field3D operator/(const Field3D& lhs, const Field3D& rhs).

…that gives a valid inverse metric (i.e. all diagonal components positive). This became a problem once setting the contra- or co-variant metric tensor was made to trigger the calculation of the other representation.

…-coordinates

…ntravariant components.

…multiple parameters are sent.

…rameters.

Some duplication of methods because there are still cases where it has to take non-const items.

…fied parameters.

…eld2D& f) and void communicate(const Field3D& f).

…structableFromInt`.

…pies are still in scope when they are used.

…the copies are still in scope when they are used.

…t reference to the actual data to Mesh::communicate(), so that it can modify it.

…->communicate(), so that it will be able to modify it.

…ms() and Coordinates::communicateGValues().

… to be able to modify it.

(removed in commit 62dcf21)

This reverts commit c7b70a9.

This reverts commit 0235449.

This reverts commit 77231a6.

… suite.

…-coordinates

…oth co- and contravariant components in the tests and examples.

Other clang-tidy suggestions.

…ment must be marked explicit to avoid unintentional implicit conversions." This reverts commit befabd5.

This reverts commit ac9cad6.

This reverts commit b2a3dad.

…cit to avoid unintentional implicit conversions." This reverts commit 9adbfda.

This reverts commit 40de3ee.

This reverts commit e37d6fe.

This reverts commit b719ad1.

…ptiness instead of 'length'." This reverts commit 2718250.

This reverts commit 07078ed.

This reverts commit 0dfafd4.

…mOtherCoordinates() to interpolateFromCoordinates().

…mesh->get().

…ensor because it will invalidate the (cached) jacobian, which will then be recalculated from the metric tensor).

…ticular x, y (or x, y, z) position.

…-coordinates

…ue at a particular x, y (or x, y, z) position.

…and a reference otherwise).

…lue at a particular x, y (or x, y, z) position.

…and a reference otherwise).

…IC_3D.

…articular x, y (or x, y, z) position.

… y (or x, y, z) position

…lar x, y (or x, y, z) position

…cular x, y (or x, y, z) position

This reverts commit 541ff17. Issue is fixed in separate PR

* next: (72 commits) Make function signature match implementation in example Fix some clang-tidy issues in dalf3 Apply suggestions from code review Apply clang-format changes prefer `auto *` for pointer types Fix: preserve regionID Fix exception message Ensure pointer is checked before dereferencing Try to do the right thing for linking netCDF::netcdf Add LC gitlab CI for GPU build/run tests BoutMask: Add non-const operator[](Ind3D) Use consistently signed char Apply clang-format changes naulin laplace: Acceptance tolerances after maxits CI: Remove test of deleted example CI: Bump all ubuntu images Read 2D variables into Field3D Fix "call to deleted constructor of 'Options' [clang-diagnostic-error]" Apply clang-format changes Revert change to reference for 'datadir'. ...

Location will already be set from initialising using `emptyFrom`

Commits on May 10, 2024

include <functional>

Tom C authored and Tom C committed May 10, 2024

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Refactor coordinates #2873

Refactor coordinates #2873

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Refactor coordinates #2873

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Refactor coordinates #2873

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