Improve output files

[rs028]

• instantaneousRates: change name to reactionRates (solved by Rename instananeousRates globally to reactionRates. #349) add column with reaction number, add header

• lossRates.output and productionRates.output: the current "3D" format is awkward to use. Consider dropping some columns, reformat as "flat" 2D matrix. This may be difficult if the species of interests are 2 or more. Consider multiple files for each species of interest.

• speciesConcentrations.output: currently limited to 100 species. an MCM model can involve thousands of species, but that would make the file very large and a bit unwieldy.

• initialConditionsSetting.output: it's unclear what this is and its purpose. It can get very big (hundred of MB).

• errors.output: make this more useful, maybe convert to a more general log file. Currently, most of the messages are printed to screen (or redirected to the atchem2_error.log file by the HPC system).

• consider switch to binary formats for output files (for example, netcdf). This has advantages and disadvantages.

[spco]

The extra column and header from (1) are implemented by #327 and #328

[rs028]

Cool. For point (2) I am not really sure what is the best approach, but I would leave it for now. I think the testing and numerical stuff should have priority.

[rs028]

Note: the headers of model/output/lossRates.output and model/output/productionRates.output miss one column

[spco]

Note: the headers of model/output/lossRates.output and model/output/productionRates.output miss one column

This is addressed by #366

[spco]

initialConditionsSetting.output is removed by #379