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add excitation to the hydrogen radiation sink term - copied from SD1D#43

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hahahasan wants to merge 6 commits intobendudson:masterfrom
hahahasan:add_excitation_upstream
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add excitation to the hydrogen radiation sink term - copied from SD1D#43
hahahasan wants to merge 6 commits intobendudson:masterfrom
hahahasan:add_excitation_upstream

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@hahahasan
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The radiation sink term in the neutral model for hydrogen was missing the temperature dependent electron-neutral excitation. This has now been added, where the code is copy and pasted from SD1D.

…me of the numerical diffusion terms to be variable instead of just 1; also have re-introduced slab_radial_buffers because the 3D sims seem to require this ... need to figure out why more thorughly
…tes and included the option to reverse the Curl(b/B) vector. Also had some small code tidy ups
@johnomotani
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Qian (@Vandoo) was looking at the excitation energy loss after talking to Hasan. We think the excitation energy may not be quite right on this branch. In SD1D, the excitation rate/energy-loss is only added to the energy loss
https://github.com/boutproject/SD1D/blob/b85ba131d1c223e526b7080889331b374d8c1923/sd1d.cxx#L1140-L1144

In Hermes that would seem to correspond to Rp
https://github.com/hahahasan/hermes-2/blob/594136490cafa4889cc944f6e09c412170ec1124/src/hermes-2.cxx#L4039
which is set in NeutralModel::neutral_rates() (named in there as the local variable R, which is a reference to Rp passed as an argument to the method) and so there should be something like

R(i, j, k) += Rex(i, j, k);

after
https://github.com/hahahasan/hermes-2/blob/974d2baaac0cac679ac95cefc241bb5d28034637/src/neutral-model.cxx#L227-L229

Instead, in this PR, Rex is added to Dnn
https://github.com/hahahasan/hermes-2/blob/594136490cafa4889cc944f6e09c412170ec1124/src/mixed.cxx#L178
and Fperp
https://github.com/hahahasan/hermes-2/blob/594136490cafa4889cc944f6e09c412170ec1124/src/mixed.cxx#L258
which we think should be related to momentum-transfer terms, not energy-transfer, and so should not include excitation energy loss.

@hahahasan, @bendudson could you re-check?

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