OpenMMCalculator

class narupatools.ase.openmm.calculator.OpenMMCalculator(simulation: openmm.app.simulation.Simulation, atoms: Optional[ase.atoms.Atoms] = None, **kwargs: Any)

Simple implementation of a ASE calculator for OpenMM.

The context of the OpenMM simulation is used to compute forces and energies given a set of positions. When the ASE Atoms object has its positions changed by an integrator, these changes are pushed to the OpenMM context to enable the calculation of new forces and energies.

Inheritance

Methods

__init__	Create a calculator for the given simulation.
band_structure	Create band-structure object for plotting.
calculate	Do the calculation.
calculate_numerical_forces	Calculate numerical forces using finite difference.
calculate_numerical_stress	Calculate numerical stress using finite difference.
calculate_properties	This method is experimental; currently for internal use.
calculation_required
check_state	Check for any system changes since last calculation.
export_properties
get_atoms
get_charges
get_default_parameters
get_dipole_moment
get_forces
get_magnetic_moment
get_magnetic_moments	Calculate magnetic moments projected onto atoms.
get_potential_energies
get_potential_energy
get_property	Get the named property.
get_stress
get_stresses	the calculator should return intensive stresses, i.e., such that stresses.sum(axis=0) == stress
read	Read atoms, parameters and calculated properties from output file.
read_atoms
reset	Clear all information from old calculation.
set	Set parameters like set(key1=value1, key2=value2, …).
set_atoms	Called when this is assigned using set_calculator().
set_label	Set label and convert label to directory and prefix.
todict

__init__(simulation: openmm.app.simulation.Simulation, atoms: Optional[ase.atoms.Atoms] = None, **kwargs: Any)

Create a calculator for the given simulation.

Parameters

• simulation – OpenMM simulation to use as a calculator.

• atoms – Atoms object to which this calculator will be attached.

• kwargs – Dictionary of keywords to pass to the base ASE calculator.

band_structure()

Create band-structure object for plotting.

calculate(atoms: Optional[ase.atoms.Atoms] = None, properties: Collection[str] = ('energy', 'forces'), system_changes: List[str] = ['positions', 'numbers', 'cell', 'pbc', 'initial_charges', 'initial_magmoms']) → None

Do the calculation.

properties: list of str

List of what needs to be calculated. Can be any combination of ‘energy’, ‘forces’, ‘stress’, ‘dipole’, ‘charges’, ‘magmom’ and ‘magmoms’.

system_changes: list of str

List of what has changed since last calculation. Can be any combination of these six: ‘positions’, ‘numbers’, ‘cell’, ‘pbc’, ‘initial_charges’ and ‘initial_magmoms’.

Subclasses need to implement this, but can ignore properties and system_changes if they want. Calculated properties should be inserted into results dictionary like shown in this dummy example:

self.results = {'energy': 0.0,
                'forces': np.zeros((len(atoms), 3)),
                'stress': np.zeros(6),
                'dipole': np.zeros(3),
                'charges': np.zeros(len(atoms)),
                'magmom': 0.0,
                'magmoms': np.zeros(len(atoms))}

The subclass implementation should first call this implementation to set the atoms attribute and create any missing directories.

calculate_numerical_forces(atoms, d=0.001)

Calculate numerical forces using finite difference.

All atoms will be displaced by +d and -d in all directions.

calculate_numerical_stress(atoms, d=1e-06, voigt=True)

Calculate numerical stress using finite difference.

calculate_properties(atoms, properties)

This method is experimental; currently for internal use.

calculation_required(atoms, properties)

check_state(atoms, tol=1e-15)

Check for any system changes since last calculation.

export_properties()

get_atoms()

get_charges(atoms=None)

get_default_parameters()

get_dipole_moment(atoms=None)

get_forces(atoms=None)

get_magnetic_moment(atoms=None)

get_magnetic_moments(atoms=None)

Calculate magnetic moments projected onto atoms.

get_potential_energies(atoms=None)

get_potential_energy(atoms=None, force_consistent=False)

get_property(name, atoms=None, allow_calculation=True)

Get the named property.

get_stress(atoms=None)

get_stresses(atoms=None)

the calculator should return intensive stresses, i.e., such that stresses.sum(axis=0) == stress

read(label)

Read atoms, parameters and calculated properties from output file.

Read result from self.label file. Raise ReadError if the file is not there. If the file is corrupted or contains an error message from the calculation, a ReadError should also be raised. In case of succes, these attributes must set:

atoms: Atoms object

The state of the atoms from last calculation.

parameters: Parameters object

The parameter dictionary.

results: dict

Calculated properties like energy and forces.

The FileIOCalculator.read() method will typically read atoms and parameters and get the results dict by calling the read_results() method.

classmethod read_atoms(restart, **kwargs)

reset()

Clear all information from old calculation.

set(**kwargs)

Set parameters like set(key1=value1, key2=value2, …).

A dictionary containing the parameters that have been changed is returned.

Subclasses must implement a set() method that will look at the chaneged parameters and decide if a call to reset() is needed. If the changed parameters are harmless, like a change in verbosity, then there is no need to call reset().

The special keyword ‘parameters’ can be used to read parameters from a file.

set_atoms(atoms: ase.atoms.Atoms) → None

Called when this is assigned using set_calculator().

Parameters

atoms – ASE atoms object this calculator has been assigned to.

set_label(label)

Set label and convert label to directory and prefix.

Examples:

• label=’abc’: (directory=’.’, prefix=’abc’)

• label=’dir1/abc’: (directory=’dir1’, prefix=’abc’)

• label=None: (directory=’.’, prefix=None)

todict(skip_default=True)

Attributes

default_parameters	Default parameters
directory
discard_results_on_any_change	Whether we purge the results following any change in the set() method.
ignored_changes	Properties of Atoms which we ignore for the purposes of cache
implemented_properties	Properties calculator can handle (energy, forces, …)
label

default_parameters: Dict[str, Any] = {}

Default parameters

directory

discard_results_on_any_change = False

Whether we purge the results following any change in the set() method.

ignored_changes: Set[str] = {}

Properties of Atoms which we ignore for the purposes of cache

implemented_properties: List[str] = ['energy', 'forces']

Properties calculator can handle (energy, forces, …)

label