Ewald featurization

I am struggling to use EwaldSiteEnergy function. How can I get ‘charges that are already-defined for the structure’ on the notes? I would appreciate if you can provide some of example script.

Thanks in advance,

Sung Beom Cho

Hello,

One way you can get the charges on each site by first using the structure_to_oxidstructure function in matminer’s utility functions (link).

The code would be something like

from matminer.utils.conversions import structure_to_oxidstructure

structure_to_oxidstructure(data[‘structure’], inplace=True)

This code will attempt to guess oxidation states for each atom based on the composition of the structure, and save that oxidation state in the structure so that EwaldSiteEnergy could use it.

If your data is not in a pandas DataFrame, you can call the add_oxidation_state_by_guess function directly (see pymatgen’s documentation, and an example in matminer’s unit tests).

Best,

Logan

···

From: 조성범
Sent: Wednesday, July 25, 2018 4:43 PM
To: matminer
Subject: Ewald featurization

I am struggling to use EwaldSiteEnergy function. How can I get ‘charges that are already-defined for the structure’ on the notes? I would appreciate if you can provide some of example script.

Thanks in advance,

Sung Beom Cho


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Just a note that there are other ways also to get oxidation states including BVAnalyzer in pymatgen (bond valence method) if you are familiar with how to use pymatgen.

This notebook in matminer examples tells you how to use the default guessing strategy:

https://github.com/hackingmaterials/matminer_examples/blob/master/notebooks/intro_predicting_bulk_modulus.ipynb

see section 2.2

···

On Wed, Jul 25, 2018 at 2:51 PM Logan Ward [email protected] wrote:

Hello,

One way you can get the charges on each site by first using the structure_to_oxidstructure function in matminer’s utility functions (link).

The code would be something like

from matminer.utils.conversions import structure_to_oxidstructure

structure_to_oxidstructure(data[‘structure’], inplace=True)

This code will attempt to guess oxidation states for each atom based on the composition of the structure, and save that oxidation state in the structure so that EwaldSiteEnergy could use it.

If your data is not in a pandas DataFrame, you can call the add_oxidation_state_by_guess function directly (see pymatgen’s documentation, and an example in matminer’s unit tests).

Best,

Logan

From: 조성범
Sent: Wednesday, July 25, 2018 4:43 PM
To: matminer
Subject: Ewald featurization

I am struggling to use EwaldSiteEnergy function. How can I get ‘charges that are already-defined for the structure’ on the notes? I would appreciate if you can provide some of example script.

Thanks in advance,

Sung Beom Cho


You received this message because you are subscribed to the Google Groups “matminer” group.
To unsubscribe from this group and stop receiving emails from it, send an email to [email protected].
To view this discussion on the web visit https://groups.google.com/d/msgid/matminer/91ad06a6-3aa7-4ff1-8ec4-987d685021eb%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

You received this message because you are subscribed to the Google Groups “matminer” group.

To unsubscribe from this group and stop receiving emails from it, send an email to [email protected].

To view this discussion on the web visit https://groups.google.com/d/msgid/matminer/5b58f0c6.1c69fb81.77cbe.bee9%40mx.google.com.

For more options, visit https://groups.google.com/d/optout.


Best,
Anubhav

Thank you very much. It solved.

2018년 7월 25일 수요일 오후 4시 43분 52초 UTC-5, 조성범 님의 말:

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I am struggling to use EwaldSiteEnergy function. How can I get ‘charges that are already-defined for the structure’ on the notes? I would appreciate if you can provide some of example script.

Thanks in advance,

Sung Beom Cho