System
- class mlptrain.system.System(*args: Molecule, box: Box | Sequence[float] | None)
Bases:
objectSystem with molecules but without any coordinates
- __init__(*args: Molecule, box: Box | Sequence[float] | None)
System containing a set of molecules.
e.g. pd_1water = (Pd, water, box_size=[10, 10, 10], charge=2) for a system containing a Pd(II) ion and one water in a 1 nm^3 box
10 Å cubic box.
- add_molecules(molecule: Molecule, num: int = 1) None
Add multiple versions of a molecule to this sytem
- Keyword Arguments:
num – Number of molecules of this type to add
- property atoms: List[Atom]
Constituent atoms of this system
- property charge: int
Get the total charge on the system
- property configuration: Configuration
Single configuration for this system
- property mult: int
Get the total spin multiplicity on the system
- random_configuration(min_dist: float = 2.0, with_intra: bool = False, intra_sigma: float = 0.01) Configuration
Generate a random configuration of this system, where all the molecules in the system have been randomised
- Parameters:
intra_sigma – Variance of the normal distribution used to displace each atom_pair_list of the molecules in the system
- Return type:
(mlptrain.Configuration)
- Raises:
(RuntimeError) – If all the molecules cannot be randomised while maintaining the required min. distance between them
- random_configurations(num: int, **kwargs) ConfigurationSet
Generate a number of random configurations of this system
See also
mlptrain.system.System.random_configuration for keyword arguments
- Return type:
(mlptrain.configurations.configuration_set.ConfigurationSet)
- property unique_atomic_symbols: List[str]
Unique atomic symbols in this system