Molcas Forum

hrgrimsl

Member

Registered: 2018-07-16

Posts: 8

Obtaining Data from Log File

Is there a generally accepted way to pull energies/gradients from a file from within a python script?  Something similar to awk but that willl give me the gradient as a numpy array, and doesn't require me to know the exact preceding string?

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,079

Re: Obtaining Data from Log File

No, but if you compiled with HDF5 support, you read energies and gradients from the .h5 files using the h5py python module.

valera

Administrator

Registered: 2015-11-03

Posts: 127

Re: Obtaining Data from Log File

hrgrimsl,
the idea of internally markup-ed output was never fully implemented. but for energies you may rely on the fact that grep '^::' should spot them. The gradient is another matter - it is a big data, so stored either in runfile or in hdf5.

hrgrimsl

Member

Registered: 2018-07-16

Posts: 8

Re: Obtaining Data from Log File

Thank you both; it looks like the default is to throw gradients in the log file.  Is there a keyword in the input to specify that I want them in HDF5 form or  something?

EDIT:   I did compile with HDF5 support, and I'm getting an scf.h5 file when I run that calculation, just not Alaska.

Last edited by hrgrimsl (2018-12-05 22:57:18)

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,079

Re: Obtaining Data from Log File

Gradients are stored in the slapaf.h5 file (if you run SLAPAF).

hrgrimsl

Member

Registered: 2018-07-16

Posts: 8

Re: Obtaining Data from Log File

I don't actually need to do a geometry update; does SLAPAF slow the code down significantly?

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,079

Re: Obtaining Data from Log File

No, but it may be easier to actually read the gradient from the log file.