integration_param dictionary input deletes existing defaults

[ZacaroniMacaroni]

When specifying an integration_param input dictionary manually for a HOPS trajectory calculation, the default dictionary is completely overwritten, removing any non-specified settings entirely. For example, in the quickstart guide, integration parameters are set in the following dictionary:

integration_param = {"INTEGRATOR": "RUNGE_KUTTA"}

However, if running a hops trajectory:

from mesohops.dynamics.hops_trajectory import HopsTrajectory as HOPS

hops = HOPS(
    sys_param,
    noise_param=noise_param,
    hierarchy_param=hierarchy_param,
    eom_param=eom_param,
    integration_param=integration_param,
    )

in which all other dictionaries are satisfied, this will result in a key error for a missing "EARLY_ADAPTIVE_INTEGRATOR" dictionary entry rather than maintaining the default dictionary

integration_param=dict(
    INTEGRATOR="RUNGE_KUTTA",
    EARLY_ADAPTIVE_INTEGRATOR='INCH_WORM',
    EARLY_INTEGRATOR_STEPS=5,
    INCHWORM_CAP=5,
    STATIC_BASIS=None,
    EFFECTIVE_NOISE_INTEGRATION=False,
)

in any portion.

[digbennett]

Thank you for raising this issue. The error here is in the hops_trajectory.py. The problem is that unlike all of the other dictionaries, we don't define a default for the integration_param dictionary. It looks like this was an oversight when we implemented all of the extensions on the integration options.

The simplest solution would probably be to construct a default dictionary in the hops_trajectory.py file and then use the dictionary update() method to override the default values with the user selections. It might be worth putting out a small patch to fix this specific problem since it should be a pretty minimal change and - as you noted - the tutorials don't currently work. We should also add a couple of tests to make sure the defaults are working for each of the input dictionaries.

[CaptainExasperated]

MesoHOPS 1.4.2 solves the issue using the default dictionary solution and adds a test!