schrodinger.application.matsci.mlip.constraint module

Constraint terms for the MLIP nanoreactor MD engine.

Provides soft harmonic constraints for fixing atom positions or preserving relative distances between atoms.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.matsci.mlip.constraint.PairwiseHarmonicConstraint(indices_to_constrain, init_r=None, k_constraint=1.0, return_zero_energy=True)

Bases: object

Soft constraint preserving relative distances between selected atoms.

Applies harmonic potentials between each pair of constrained atoms, following the approach from xTB: https://xtb-docs.readthedocs.io/en/latest/xcontrol.html#fixing-constraining-and-confining

atom_behavior = 'relative'
__init__(indices_to_constrain, init_r=None, k_constraint=1.0, return_zero_energy=True)
Parameters:

  • indices_to_constrain (list) – Zero-based atom indices to constrain

  • init_r (torch.Tensor or None) – Initial positions of shape (M, N, 3) in Angstrom. If None, reference distances are set on first call.

  • k_constraint (float) – Force constant in eV/Angstrom^2

  • return_zero_energy (bool) – If True, return zero energy and only apply forces

buildReferenceDistances(r_tensor)

Build reference pairwise distances from the given positions.

Parameters:

r_tensor (torch.Tensor) – Positions of shape (M, N, 3) in Angstrom

class schrodinger.application.matsci.mlip.constraint.FixPositionConstraint(indices_to_constrain, init_r=None, k_constraint=1.0, return_zero_energy=True)

Bases: object

Fix the position of selected atoms at their initial positions using a harmonic restraint potential.

If the initial position is not given, it is captured on the first call.

atom_behavior = 'absolute'
__init__(indices_to_constrain, init_r=None, k_constraint=1.0, return_zero_energy=True)
Parameters:

  • indices_to_constrain (list) – Zero-based atom indices to constrain

  • init_r (torch.Tensor or None) – Initial positions of shape (M, N, 3) in Angstrom. If None, reference positions are set on first call.

  • k_constraint (float) – Force constant in eV/Angstrom^2

  • return_zero_energy (bool) – If True, return zero energy and only apply forces