# -*- coding: utf-8 -*-
"""
Control parameters for the Ionic Conductivity step in a SEAMM flowchart
"""
import logging
import seamm
from seamm_md_analysis.step_support import source_parameters
logger = logging.getLogger(__name__)
[docs]
class IonicConductivityParameters(seamm.Parameters):
"""
The control parameters for Ionic Conductivity.
The MD to analyze is run earlier in the flowchart -- in a Loop for independent
runs -- or in other jobs (see seamm_md_analysis.step_support.source_parameters).
"""
# Dropped with the own-MD route (phase 8): ignored in older flowcharts
retired = ("nruns", "errors")
parameters = {
**source_parameters("the ionic conductivity"),
"frame interval": {
"default": 1.0,
"kind": "float",
"default_units": "ps",
"enumeration": tuple(),
"format_string": ".2f",
"description": "Longest interval between frames:",
"help_text": "The positions must be sampled at least this often.",
},
"fit start": {
"default": 0.1,
"kind": "float",
"default_units": "",
"enumeration": tuple(),
"format_string": ".2f",
"description": "Fit from:",
"help_text": (
"Where the fit of the mean square displacements starts, as a "
"fraction of their length."
),
},
"fit end": {
"default": 0.5,
"kind": "float",
"default_units": "",
"enumeration": tuple(),
"format_string": ".2f",
"description": "Fit to:",
"help_text": (
"Where the fit ends, as a fraction of the length: the late part has "
"few time origins and is noisy."
),
},
"Yeh-Hummer correction": {
"default": "with the viscosity from a Viscosity step",
"kind": "enumeration",
"default_units": "",
"enumeration": ("with the viscosity from a Viscosity step", "no"),
"format_string": "s",
"description": "Yeh-Hummer correction:",
"help_text": (
"Correct the self-diffusion coefficients, and so the Nernst-Einstein "
"conductivity, for the size of the cell, using the viscosity from a "
"Viscosity step earlier in the flowchart (skipped, with a note, if "
"there is none)."
),
},
}
def __init__(self, defaults={}, data=None):
"""
Initialize the parameters, by default with the parameters defined above
Parameters
----------
defaults: dict
A dictionary of parameters to initialize. The parameters
above are used first and any given will override/add to them.
data: dict
A dictionary of keys and a subdictionary with value and units
for updating the current, default values.
Returns
-------
None
"""
logger.debug("IonicConductivityParameters.__init__")
super().__init__(
defaults={**IonicConductivityParameters.parameters, **defaults}, data=data
)
