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[pre-commit.ci] auto fixes from pre-commit.com hooks
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pre-commit-ci[bot] committed Jul 27, 2024
1 parent ce84c04 commit 8e5915e
Showing 1 changed file with 11 additions and 11 deletions.
22 changes: 11 additions & 11 deletions mosdef_dihedral_fit/dihedral_fit/fit_dihedral_with_gomc.py
Original file line number Diff line number Diff line change
Expand Up @@ -194,33 +194,33 @@ def fit_dihedral_with_gomc(
named 'dihedral.txt' for the energy and dihedral angle values (one 1 per directory).
combining_rule: str ('geometric' or 'lorentz'), default = None
The combining_rule in the foyer or GMSO XML file for the Lennard-Jones or VDW sigmas
(Rmin --> sigmas for Exp6). If this is None, it will use whatever is specified in
the XML file, or the default foyer or GMSO values. BEWARE, if it is not specified
XML file, it has a default. If this is None, it will use whatever is specified in
The combining_rule in the foyer or GMSO XML file for the Lennard-Jones or VDW sigmas
(Rmin --> sigmas for Exp6). If this is None, it will use whatever is specified in
the XML file, or the default foyer or GMSO values. BEWARE, if it is not specified
XML file, it has a default. If this is None, it will use whatever is specified in
the XML file, or the default foyer or GMSO values.
'geometric' is the geometric mean used to combine the
Lennard-Jones or VDW sigmas (Rmin --> sigmas for Exp6), as required by OPLS force field.
'lorentz' is the arithmetic mean used to combine the
Lennard-Jones or VDW sigmas (Rmin --> sigmas for Exp6), as required by
Lennard-Jones or VDW sigmas (Rmin --> sigmas for Exp6), as required by
TraPPE, Amber, or CHARMM force fields.
'None', the default setting used to combine the Lennard-Jones or VDW sigmas
(Rmin --> sigmas for Exp6), is pulled from the force field XML, but if it is
'None', the default setting used to combine the Lennard-Jones or VDW sigmas
(Rmin --> sigmas for Exp6), is pulled from the force field XML, but if it is
not present it defaults to 'geometric' via MoSDeF's default settings.
NOTE: The mixing rules for the other non-Lennard-Jones or non-VDW sigmas forces are
listed below for reference, which applicable in GOMC and here:
"NOTE: epsilon_ij = 'geometric' for All FFs --> epsilon_ij = (epsilon_ii * epsilon_jj)**0.5."
"NOTE: n_ij = 'lorentz' for Mie FFs --> n_ij = (n_ii + n_jj)/2."
"NOTE: alpha_ij = 'geometric' for Exp FFs --> alpha_ij = (alpha_ii * alpha_jj)**0.5."
atom_type_naming_style: str, optional, default='all_unique', ('general' or 'all_unique')
* 'general'
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