WARNING when using CIOVERLAP

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Rafael Souza

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May 12, 2026, 5:59:27 AM (yesterday) May 12
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Dear all,

We noticed a faulty default option when calling CIOVERLAP from NX-NS regarding the phase correction of the overlap matrix. This will lead to noise in the signs of the overlap matrices and improper time-derivative couplings.

This only affects calculations using CIOVERLAP.This does not affect COLUMBUS dynamics.

The default will be modified in future releases of Newton-X, but for now, you can fix this via input (user_config.nml). Add or edit the &cioverlap section with the cio_options:

&cioverlap
  cio_options = -s transmomin -b -t 5e-4 -e -1
/

The important 
thing here is the -b option, but by default, NX-NS was using -a. This assumes the wrong order of old and new geometries in the overlap matrix: https://light-and-molecules.gitlab.io/newton-x-package/manual/theo_background/#cioverlap-program

-a: phases of "new" w.f. in rows (bras); use file "phases.old" to patch phases of wavefunctions from previous step
-b: phases of "new" w.f. in columns (kets); use file "phases.old" to patch phases of wavefunctions from previous step

Best regards,
Rafael
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