fast_forward.constraint_coupling module

fast_forward.constraint_coupling.compute_coupling(u, constraints)[source]

Function to calculate the constraint coupling matrix A used in the LINCS algorithm. Adopted from https://github.com/bio-phys/constraint-coupling-analysis

Parameters:

  • u (Universe)

  • constraints (list) – List of constraints in the system

Returns:

A – Constraint coupling matrix

Return type:

ndarray

fast_forward.constraint_coupling.report_constraint_coupling(u, block, estimate_lincs=False)[source]

Function to check the constraint coupling of a molecule. Will print a warning if the constraint coupling is high.

Parameters:

  • block (Block) – Block containing the molecule of interest.

  • estimate_lincs (bool) – optional. Whether to report the estimated LINCS order required for the constraints, defaults to False