In the context of linear gyrokinetic simulations, an analysis of the application of field-aligned coordinate systems generated numerically from magnetohydrodynamic equilibria is presented. This family of systems allows some flexibility in the choice of the coordinates, and gyrokinetic solvers often differ in this respect. Certain transformations are therefore required in order to compare physics results. Accordingly, benchmarks of a linear microinstability are carried out between two similar gyrokinetic codes. Effort is also put on the verification of the special properties of the generated systems through certain diagnostics.

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