tqchem.ttconf.electronic_structure_interfaces¶

Attributes¶

DielectricConstant

Classes¶

`ElectronicStructureInterface`	Interface to electronic structure codes
`TBliteInterface`	Interface/Wrapper for ASE/TBLite library to calculate energies
`OpenFFInterface`	Interface to OpenFF
`CrestEnsembleInterface`

Functions¶

`sageFF_interface`(→ OpenFFInterface)	Set up OpenMM simulation environment for the Sage OpenFF forcefield
`amberFF_interface`(→ OpenFFInterface)	Set up OpenMM Simulation environment for Amber Forcefield

Module Contents¶

tqchem.ttconf.electronic_structure_interfaces.DielectricConstant: _typeshed.Incomplete¶

class tqchem.ttconf.electronic_structure_interfaces.ElectronicStructureInterface¶

Bases: abc.ABC

Interface to electronic structure codes

Needs to implement a single point calculation and a gradient optimization

__call__:: Calculate energy for ase.Atoms object (i.e. the molecule)

_single_point_calculation:: Calculate energy for the current structure of the ase.Atoms object

_local_optimization:: Perform gradient optimization for ase.Atoms object and return energy for the optimized structure

_morse_energy:: Calculate energy based on a simple morse potential

__call__(molecule: ase.Atoms) → float¶

Calculate energy for molecule

Parameters:: molecule (ase.Atoms) – Molecule object containing atom types and positions
Returns:: energy – Single point energy in eV
Return type:: float

class tqchem.ttconf.electronic_structure_interfaces.TBliteInterface(method: str, ref_mol: ase.Atoms, charge: int = 0, accuracy: float = 1.0, solvent: str = None, local_optimization: bool = True)¶

Bases: ElectronicStructureInterface

Interface/Wrapper for ASE/TBLite library to calculate energies

https://tblite.readthedocs.io/en/latest/users/ase.html

calculator¶: TBLite calculator to perform single point calculations.

__call__:: Calculate energy for ase.Atoms object (i.e. the molecule)

_single_point_calculation:: Calculate energy for the current structure of the ase.Atoms object

_local_optimization:: Perform gradient optimization for ase.Atoms object and return energy for the optimized structure

calculator: _typeshed.Incomplete¶

local_optimization: _typeshed.Incomplete¶

adjacency: _typeshed.Incomplete¶

class tqchem.ttconf.electronic_structure_interfaces.OpenFFInterface(simulation: openmm.app.Simulation, ref_mol: ase.Atoms, local_optimization: bool = True)¶

Bases: ElectronicStructureInterface

Interface to OpenFF

Different Force Fields are supported by changing the OpenMM simulation object from which this interface is constructed

Implementing functions for single point calculations, optimization and extracting of coordinates from the openMM system

simulation¶

OpenMM simulation class for calculating energies and optimized structures

Type:: Simulation

adjacency¶

Adjacency matrix of the molecular system

Type:: np.array

local_optimization: _typeshed.Incomplete¶

simulation: _typeshed.Incomplete¶

adjacency: _typeshed.Incomplete¶

tqchem.ttconf.electronic_structure_interfaces.sageFF_interface(molecule: ase.Atoms, local_optimization: bool = True, charge: int = 0, solvent: str = None) → OpenFFInterface¶

Set up OpenMM simulation environment for the Sage OpenFF forcefield

Parameters:

molecule (ase.Atoms) – Molecule to create openMM simulation object from
local_optimization (bool, default=True) – Enable gradient optimziation
charge (int, default=0) – Formal charge of the molecule
solvent (str, default=None) – Add implicit solvation using solvent specified by name

tqchem.ttconf.electronic_structure_interfaces.amberFF_interface(molecule: ase.Atoms, local_optimization: bool = True, charge: int = 0, solvent: str = None) → OpenFFInterface¶

Set up OpenMM Simulation environment for Amber Forcefield

Parameters:

molecule (ase.Atoms) – Molecule to create openMM simulation object
local_optimization (bool, default=True) – Enable gradient optimziation
charge (int, default=0) – Formal charge of the molecule
solvent (str, default=None) – Add implicit solvation using solvent specified by name

class tqchem.ttconf.electronic_structure_interfaces.CrestEnsembleInterface(method: str, ref_mol: ase.Atoms, charge: int = 0, solvent: str = None, threads: int = 4)¶

optlevel: str¶

threads: _typeshed.Incomplete¶

charge: _typeshed.Incomplete¶

solvent: _typeshed.Incomplete¶

adjacency: _typeshed.Incomplete¶

method: _typeshed.Incomplete¶

__call__(molecules: list[ase.Atoms]) → numpy.ndarray¶: Prepare ensemble of molecules whithout collided atoms and optimize with CREST