SpectralSynthesisModel with fixed element abundances

[alexji]

Looking at the code, it appears that this will fit all elements in the synth_model.elements list (this is good and what I've assumed in the chemical abundances tab). However, there is currently no way to include elements whose abundances you want to remain fixed for a particular synthesis.

@andycasey I'm happy to implement this, but if you have a master plan for how this should go I'll leave it up to you.

[andycasey]

Yeah these will be separate things (elements in the line list and elements to fit). Assign this to me and I will get to it ASAP

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On 1 Jun 2016, at 8:05 pm, Alex Ji notifications@github.com wrote:

Looking at the code, it appears that this will fit all elements in the synth_model.elements list (this is good and what I've assumed in the chemical abundances tab). However, there is currently no way to include elements whose abundances you want to remain fixed for a particular synthesis.

@andycasey I'm happy to implement this, but if you have a master plan for how this should go I'll leave it up to you.

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[alexji]

@andycasey I can get the needed elements from model.transitions, but how do I give those elements abundances to be used in the synthesis? Ideally for me, it's a dict of element -> logeps stored in metadata (so it is also saved/regenerated), and this dict is automatically used when calling model.fit().

[andycasey]

In 3f4c0be I have implemented an optional keyword argument of rt_abundances to model.fit(). This is expected to be a dictionary where keys are elements (or species) and values are abundances in log_epsilon format.

[alexji]

Modified so that rt_abundances is in spectral_model metadata (presumably this will then be saved and loaded with the spectral models): 3cffef43b01c9665f42cbb28dc0478caa98fd16b