Overlap Diagnostics
Overlap diagnostics live in the alchemrs::analysis module.
Available functions:
overlap_matrixoverlap_eigenvaluesoverlap_scalar
overlap_matrix
This function:
- computes MBAR log weights from the supplied windows
- constructs the overlap matrix from those weights and state sample counts
- returns an
OverlapMatrix
Input:
- slice of
UNkMatrix - optional
MbarOptions
overlap_eigenvalues
Computes the eigenvalues of the overlap matrix and returns them sorted in descending order.
The implementation rejects eigenvalues with significant imaginary components.
overlap_scalar
Computes:
1 - second_largest_eigenvalue
This is the scalar overlap diagnostic currently surfaced by the CLI.
CLI usage
bar, mbar, exp, and dexp can include overlap diagnostics with:
--overlap-summary
The CLI then reports:
- overlap scalar
- overlap eigenvalues
in text, JSON, or CSV output.