soprano.calculate.gulp.w99

Classes and functions for using the W99 force field in GULP. This force field only applies to organic molecules. More information can be found in the original paper by Donald E. Williams:

D.E. Williams, Improved Intermolecular Force Field for Molecules Containing H, C, N, and O Atoms, with Application to Nucleoside and Peptide Crystals - Journal of Computational Chemistry, Vol. 22, No. 11, 1154-1166 (2001)

Functions

find_w99_atomtypes(s[, force_recalc])	Calculate the W99 force field atom types for a given structure.
get_w99_energy(s[, charge_method, Etol, ...])	Calculate the W99 force field energy using GULP.

Exceptions

W99Error

exception soprano.calculate.gulp.w99.W99Error

Bases: Exception

add_note()

Exception.add_note(note) – add a note to the exception

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

soprano.calculate.gulp.w99._w99_field_definition(s, etol)

Output the W99 field definition for GULP input. System must already have w99 types calculated

soprano.calculate.gulp.w99.find_w99_atomtypes(s, force_recalc=False)

Calculate the W99 force field atom types for a given structure.

Parameters:

s (ase.Atoms): the structure to calculate the atomtypes on

force_recalc (bool): whether to recalculate the molecules even if

already present. Default is False.

soprano.calculate.gulp.w99.get_w99_energy(s, charge_method='eem', Etol=1e-06, gulp_command='gulp', gulp_path=None, save_charges=False)

Calculate the W99 force field energy using GULP.

Parameters:

s (ase.Atoms): the structure to calculate the energy of

charge_method (Optional[str]): which method to use for atomic partial

charge calculation. Can be any of

‘eem’, ‘qeq’ and ‘pacha’.

Default is ‘eem’.

Etol (Optional[float]): tolerance on energy for intermolecular

potential cutoffs (relative to single

interaction energy). Default is 1e-6 eV.

gulp_command (Optional[str]): command required to call the GULP

executable.

gulp_path (Optional[str]): path where the GULP executable can be

found. If not present, the GULP command

will be invoked directly (assuming the

executable is in the system PATH).

save_charges (Optional[bool]): whether to retrieve also the charges

and save them in the Atoms object.

False by default.

Returns:

energy (float): the calculated energy