waccmToMusicBox.py should output CSV column titles as PREFIX.name.unit

[carl-drews]

This issue is a follow-up for Pull Request: #413

waccmToMusicBox.py defines this function:
def writeInitCSV(initValues, filename):

About halfway through that function we have this line of code:
fp.write("{}.{} [{}]".format(reaction_type, key, value[unitIndex]))

To do: That line of code needs to be changed for the new format for CSV columns titles:
Column naming convention: PREFIX.name.unit (e.g., CONC.A.mol m-3)
Updated all test configs and CSV files to new format with mandatory time.s column

Ideally we could call Conditions.formatReactionVarUnits() to create each column title. Is there such a function defined in the Conditions class? If not, then we can either create that new virtual function or simply change the code here.

To do: writeInitCSV() takes a dictionary of initial values. That incoming list should have time.s with a value of 0.0 as the first element (because these are initial conditions). Make sure that time.s ends up in the first column.

[carl-drews]

This PR is now merged into the main branch:
#413

[carl-drews]

@K20shores commented on PR #413:

•    assert conds["species_concentrations"]["A"] == 1.0
  

•    assert conds["species_concentrations"]["B"] == 2.0
  

• def test_surf_rate_parameter_format(self):

•    """Test SURF rate parameter format handling."""
  

•    manager = ConditionsManager()
  

•    manager.set_condition(time=0, rate_parameters={
  

•        "SURF.surface.particle number concentration.# m-3": 1e12,
  

•        "SURF.surface.effective radius.m": 1e-7
  

•    })
  

Oh, SURF is the reaction type and surface is the name of the reaction specified by the name parameter. It might be more easy to understand if we called it my surface. Also, the particle number concentration and effective particle radius are specified in mechanism configuration, but we didn't document them there well enough so we need to fix that. But, whether or not they have spaces is determined by mechanism configuration since we take those values and call set_user_defiend_rate_paramters using the labels provided here

Also tagging @boulderdaze .

Idea for the default parameters:
Conditions.formatReactionVarUnits(name, units, prefix=None, particle=None)
That order appears to correspond with our required/optional status of parameters and Python syntax. There will always be a name and units, usually a prefix, and sometimes particle information.

However, those values will be written on the lines of the CSV file in this order:
f"{prefix}.{name}.{particle}.{units}"
with appropriate coding for None parameters, of course.