Detach Tensor3D from MATLAB

[willGraham01]

Context/Description

Detaches Tensor3D class from MATLAB. This class is now robust enough to read from either standard C++ buffers or from MATLAB data of the appropriate shape. We also no longer need to use malloc for memory management.

The dependant classes still depend on MATLAB for reading/writing from the input file, which can be addressed in another pull request.

• Continues Classes to detach from MATLAB #285 : Resolves Tensor3D task and addresses dependant classes.
• Depends on DispersiveMultiLayer no longer uses MATLAB #324 : This will target main once this goes in.

More details

Tensor3D wraps a std::vector.

• operator() is used to index/reference the data with three indices.
• We cannot use the operator[] since this can only take 1 argument unless we up our C++ standard to 23.
• The operator[] can still be invoked if passed an ijk struct from cell_coordinate.h, but this simply unpacks and passes the information to operator().
• This causes these changes to be noisy, since we have to change the call methods for all classes that have Tensor3D members or parents.

Data is stored as a strided vector

• Row-major format is used since C and hdf5 use this convention. IE Later dimensions have faster-varying indices.
• Using a strided vector means that zero(), frobenius(), and any other all-element operations can be carried out using std::vector methods.
• The class stores the "3D" dimensions that it is mimicking when they are set.

Reading 3D buffers

• Tensor3D::initialise allows us to read from ***T buffers.
• To comply with std::vector ownership laws and avoid memory leaks, data is copied into Tensor3Ds storage rather than reassigning the underlying pointer.

File restructuring

In an attempt to curb the rampant expansion of the arrays.h file, classes and structs within this file have begun to be broken out into separate files within the arrays directory.

Testing

Unit tests for Tensor3D, DTilde, and IncidentField have been preserved, and continue to pass. Tensor3D unit tests have been updated slightly to reflect the new call syntax.

[codecov]

Codecov Report

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Additional details and impacted files

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[samcunliffe]

Can this be targetted at main yet? Or do we need all of #250 's changes to go in first?

[willGraham01]

Can this be targetted at main yet? Or do we need all of #250 's changes to go in first?

Need all of #250 I'm afraid. However this, #303 <- #307, and my current attempts to deal with XYZVector (#315) are all parallel from there on out.

[samcunliffe]

V. minor suggestions: a bit more docs and one thing you might want to rename.