# -*- coding: utf-8 -*-
"""
Control parameters for the Atomic Charges step in a SEAMM flowchart
"""
import logging
import seamm
logger = logging.getLogger(__name__)
[docs]
class AtomicChargesParameters(seamm.Parameters):
"""The control parameters for the Atomic Charges step.
Parameters
----------
parameters : {str: {str: str}}
A dictionary describing each control parameter, keyed by the parameter
name. See ``seamm.Parameters`` for the full description of each field
("default", "kind", "default_units", "enumeration", "format_string",
"description", "help_text").
See Also
--------
AtomicCharges, TkAtomicCharges
"""
parameters = {
"method": {
"default": "DDEC6",
"kind": "enum",
"default_units": "",
"enumeration": (
"DDEC6",
"Bader",
"DDEC6 and Bader",
),
"format_string": "",
"description": "Charge method:",
"help_text": (
"The density-partitioning scheme used to assign atomic charges. "
"DDEC6 (via Chargemol) gives ESP-faithful, transferable charges; "
"Bader (via the Henkelman code) gives a rigorous topological "
"partition. Both work for molecular and periodic systems."
),
},
"charge label": {
"default": "<method>",
"kind": "string",
"default_units": "",
"enumeration": ("<method>",),
"format_string": "",
"description": "Store charges as:",
"help_text": (
"Label for the charge set written onto the atoms. The charges are "
"stored in the configuration as the attribute 'charges_<label>', "
"so several schemes can coexist on the same structure. The default "
"'<method>' uses the method name, e.g. 'charges_DDEC6'."
),
},
"density source": {
"default": "from the previous step in the flowchart",
"kind": "enum",
"default_units": "",
"enumeration": (
"from the previous step in the flowchart",
"from files",
),
"format_string": "",
"description": "Electron density:",
"help_text": (
"Where to obtain the electron density. Normally it is taken from "
"the quantum-chemistry step immediately preceding this one, which "
"must have been told to write its (all-electron) density."
),
},
"density files": {
"default": "",
"kind": "string",
"default_units": "",
"enumeration": tuple(),
"format_string": "",
"description": "Density file(s):",
"help_text": (
"Explicit path(s) to the density grid/cube file(s) when not taking "
"them from the previous step. For VASP this is the directory holding "
"CHGCAR plus AECCAR0/AECCAR2; for molecular codes a .cube or .wfx."
),
},
"atomic densities directory": {
"default": "~/SEAMM/atomic_charges/atomic_densities",
"kind": "string",
"default_units": "",
"enumeration": tuple(),
"format_string": "",
"description": "DDEC reference densities:",
"help_text": (
"Directory containing the reference atomic densities required by "
"Chargemol for DDEC6. If this path does not exist, the copy "
"bundled in the seamm-chargemol conda environment is used "
"automatically. Ignored for the Bader method."
),
},
"enforce net charge": {
"default": "yes",
"kind": "enum",
"default_units": "",
"enumeration": ("yes", "no"),
"format_string": "",
"description": "Enforce the total charge:",
"help_text": (
"Shift the charges uniformly so they sum exactly to the known net "
"charge of the system, removing the small residual left by grid / "
"numerical integration. The residual is reported. Turn off to keep "
"the raw charges from the partitioning program."
),
},
"apply to structure": {
"default": "no",
"kind": "enum",
"default_units": "",
"enumeration": ("no", "yes"),
"format_string": "",
"description": "Set as the atomic charges on the structure:",
"help_text": (
"Also store the computed charges as the structure's per-atom "
"charge (the standard 'charge' attribute), in addition to the "
"labeled 'charges_<label>' column. Turn this on to have the "
"charges written out with the structure -- e.g. to an extended "
"XYZ (extxyz) file for machine-learning training. With more than "
"one charge method, the last one applied wins."
),
},
"results": {
"default": {},
"kind": "dictionary",
"default_units": "",
"enumeration": tuple(),
"format_string": "",
"description": "results",
"help_text": "The results to save to variables or in tables.",
},
}
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.
"""
logger.debug("AtomicChargesParameters.__init__")
super().__init__(
defaults={**AtomicChargesParameters.parameters, **defaults}, data=data
)
