stko.GulpUFFMDOptimizer

class stko.GulpUFFMDOptimizer(gulp_path, metal_FF=None, metal_ligand_bond_order=None, output_dir=None, integrator='stochastic', ensemble='nvt', temperature=300, equilbration=1.0, production=10.0, timestep=1.0, N_conformers=10, opt_conformers=True, save_conformers=False)[source]

Bases: GulpUFFOptimizer

Applies forcefield MD that can handle metal centres.

Parameters:

gulp_path (Path | str) – Path to GULP executable.
metal_FF (dict[int, str] | None) – Dictionary with metal atom forcefield assignments. Key: int : atomic number. Value: str : UFF4MOF forcefield type.
metal_ligand_bond_order (str | None) – Bond order to use for metal-ligand bonds. Defaults to half, but using resonant can increase the force constant for stronger metal-ligand interactions.
output_dir (Path | str | None) – The name of the directory into which files generated during the calculation are written, if None then uuid.uuid4() is used.
integrator (str) – Integrator for GULP to use. Defaults to ‘stochastic’.
ensemble (str) – Ensemble for GULP to use. Defaults to ‘nvt’.
temperature (float) – Temperature to run simulation at in Kelvin. Defaults to 300.
equilbration (float) – Time spent equilibrating system in ps. Defaults to 1.0.
production (float) – Time spent running production simulation of system in ps. Defaults to 10.0.
timestep (float) – Timestep of simulation in fs. Defaults to 1.0.
N_conformers (int) – Number of conformers to sample. Defaults to 10.
opt_conformers (bool) – Whether or not to optimise each conformer using UFF4MOF. Defaults to True.
save_conformers (bool) – Whether or not to save to file each conformer. Defaults to False.

Notes

By default, optimize() will run a MD run using the UFF4MOF. This forcefield requires some explicit metal atom definitions, which are determined by the user.

This code was originally written for use with Gulp 5.1 on Linux and has not been officially tested on other versions and operating systems. Make sure to sanity check the output.

Examples

Conformer searching is often useful, so we have provided an interface to MD simulations using GULP and UFF4MOF. A conformer search can be run at high temperature, where N conformers are extracted at constant intervals throughtout the simulation and optimized using UFF4MOF. The lowest energy conformer is returned. After these MD steps, it is crucial to reoptimize the resultant structure using a better forcefield or a more robust method!

gulp_MD = stko.GulpUFFMDOptimizer(
    gulp_path='path/to/gulp',
    metal_FF={46: 'Pd4+2'},
    temperature=300,
    N_conformers=10,
    opt_conformers=True,
)
gulp_MD.assign_FF(cage)
cage = gulp_MD.optimize(cage)

Methods

`assign_FF`	Assign forcefield types to molecule.
`extract_final_energy`
`optimize`	Optimize mol.
`p_optimize`	Optimize mol and unit_cell.

assign_FF(mol)

Assign forcefield types to molecule.

Parameters:: mol (Molecule) – The molecule to be optimized.
Return type:: None

extract_final_energy(out_file)

Parameters:: out_file (Path)
Return type:: float

optimize(mol)[source]

Optimize mol.

Parameters:: mol (MoleculeT) – The molecule to be optimized.
Returns:: The optimized molecule.
Return type:: MoleculeT

p_optimize(mol, unit_cell)[source]

Optimize mol and unit_cell.

Parameters:

mol (MoleculeT) – The molecule to be optimized.
unit_cell (UnitCell) – The unit_cell to be optimized if optimization is periodic.

Returns:

The optimized molecule and the optimized cell.

Return type:

tuple[MoleculeT, UnitCell]