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#1 2018-11-30 16:52:24

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?

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#2 2018-11-30 17:19:48

Ignacio
Administrator
From: Uppsala
Registered: 2015-11-03
Posts: 506

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.

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#3 2018-11-30 22:06:47

valera
Administrator
Registered: 2015-11-03
Posts: 94

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.


The main reason of my preference with respect to operating systems: cp is two characters, but copy is four.

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#4 2018-12-05 22:21:35

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)

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#5 2018-12-06 09:25:49

Ignacio
Administrator
From: Uppsala
Registered: 2015-11-03
Posts: 506

Re: Obtaining Data from Log File

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

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#6 2018-12-06 15:16:01

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?

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#7 2018-12-06 16:17:38

Ignacio
Administrator
From: Uppsala
Registered: 2015-11-03
Posts: 506

Re: Obtaining Data from Log File

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

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