Source code for molsysmt.third_party.openmm.forces.add_forbidden_z_region
from molsysmt import pyunitwizard as puw
from molsysmt._private.argdigest import arg_digest
[docs]
@arg_digest()
def add_forbidden_z_region(
molecular_system,
selection="all",
z0="0.0 nm",
width="1.0 nm",
force_constant="5000 kilojoules_per_mole/nm**2",
pbc=False,
return_force=False,
syntax="MolSysMT",
skip_digestion=False,
):
"""
Adding repulsive boundary restraints preventing particles from entering a z-slab in OpenMM.
Parameters
----------
molecular_system : molecular system
Molecular system in any supported MolSysMT format.
selection : str, list, tuple, or numpy.ndarray, default='all'
Selection string or boolean/integer array specifying elements.
z0 : object, default='0.0 nm'
Argument z0.
width : object, default='1.0 nm'
Argument width.
force_constant : object, default='5000 kilojoules_per_mole/nm**2'
Argument force_constant.
pbc : bool, default=False
Whether to take periodic boundary conditions into account.
return_force : object, default=False
Argument return_force.
syntax : str, default='MolSysMT'
Selection syntax used to evaluate `selection` (e.g., 'MolSysMT', 'MDTraj').
skip_digestion : bool, default=False
Whether to skip MolSysMT's internal argument digestion mechanism.
Returns
-------
openmm.CustomExternalForce
The added barrier force instance.
.. versionadded:: 1.0.0
"""
from .add_forbidden_plane_region import add_forbidden_plane_region
z0, unit = puw.get_value_and_unit(z0)
point = [[0.0, 0.0, z0]]
point = puw.quantity(point, unit)
return add_forbidden_plane_region(
molecular_system,
selection=selection,
force_constant=force_constant,
point=point,
normal_vector=[0, 0, 1],
width=width,
pbc=pbc,
return_force=return_force,
syntax=syntax,
skip_digestion=True,
)
