Run ESPEI via input files, rather than command line arguments about espei

[bocklund]

Some user facing options that could be tuned that are not yet include:

• Standard deviation of the walker initialization from DFT parameters. Currently hardcoded to 10% of the parameter value. The fraction of parameter value should be tunable.
• Which models to use (though this might be in the scope of the input.json)
• Number of walkers, as multiple of number of parameters. Currently hardcoded as the minimum, 2. More walkers helpful for better acceptance fractions, avoiding getting stuck in low likelihood, etc. see emcee troubleshooting docs
• Number of dask cores to run with
• pycalphad point density
• (when implemented) pycalphad solver convergence options? Allows for tunable accuracy/speed tradeoff.

[bocklund]

Regarding the above input file, one thing I do not like is that some parameters only take effect when other parameters are active/inactive. Of course, we can validate this in the software, but it would be nice if the options were more straightforward initially. Not to mention that validating it in the software means that users running ESPEI through schedulers might wait in the queue, only to find out that their input was invalid.

[richardotis]

Looks pretty good. How about a schema for client-side validation?

[bocklund]

Here's a solution to the confusing options.

Right now, we assume a full run and users can turn off single phase fitting by providing an input file and turn off MCMC with the no-mcmc flag. This can be confusing because MCMC runs can start from

1. A single phase fitting from the same run
2. A previous TDB from a single phase or multiphase run
3. A previous TDB and a restart to continue a previous run

And some of these have conflicting options!

Instead, we should have nothing run by default and users have to add exactly what they want. By the specifying the heading key and the desired options: e.g. top level single_phase (needs better name?) and mcmc that control aspects of those runs. If no single_phase key is specified, then the mcmc key will have to specify an input database and a restart file, if desired.

[richardotis]

I like this idea. Maybe call the single phase step generate_parameters?