Preparation for adding electrons #207
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If dimension has size 1 for some input it cannot be parallelised, so there is no need to check it (for that case). By skipping size 1 dimensions, we can reduce the number of combinations that need debug tests, which speeds up the tests.
Ensures that a correct region type is being used, rather than relying on the calling site of the derivative_*!() function to have already set a correct region type.
Allows `setindex!()` for DebugMPISharedArray to be used with, for
example, `Float128` values, not just `mk_float`. Any type that is OK for
the underlying `setindex!()` of `Array{mk_float,N}` should be supported.
This makes it easier to add the run_id to multiple output files, which might not be created by the same function.
The separate functions are also called by a single output function so the original call-site does not get more complicated, but the individual functions can be called on their own if necessary.
It can be useful to know how much of a change the 'moment constraint corrections' are having to apply. To help diagnose this, store the values of the coefficients used to apply the constraints (for each species of ion and neutral, at each spatial point) into arrays in the `moments` structs, and write out the most recent values at each output.
…ance!() Will allow them to be passed into init_pdf_and_moments() in future to be used in kinetic electron setup.
Will be useful for boundary conditions for electrons.
Allow passing or returning `nothing` if a coordinate is not present.
Define reload_moments(), etc., functions at the module level instead of locally inside reload_evolving_fields!(). This will allow (some of) these functions to be used separately to reload electron variables.
Previously, the moments of the source term were introduced in vpa/vz 'advection speed' and in source_terms in terms of `external_source_amplitude`. The moments were taken assuming that the source is a Maxwellian with temperature `T_source`. This is not true for "energy_source" (where the source is defined as roughly 'f_M - f' in such a way that no particles are introduced). However, the moments of the source term are already calculated in external_density_source and external_pressure_source, so these can be used instead to support more generic source terms.
The corrected form is similar to the ion one, and has correct dimensions.
Fixes changes from 399e521.
Also avoid division by zero - in a hacky way by just setting the result to zero if we would have divided by zero.
Lets code be run just to write out the initial profiles.
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A lot of minor structural changes, being added now to reduce the number of conflicts when the electron branch (the latest is currently electrons-jto-debug) is added.