Hi,
I am trying to compute matminer feature using
cf.ElementProperty.from_preset(“matminer”)
It work fine for other features, but for ‘PymatgenData mean bulk_modulus’ for composition such as Al0.25NbTaTiZr (writes NaN), but it works for Al0.25NbTaTiV
I figured from /utils/data_files/magpie_elementdata/BulkModulus.table that the data for Zr is missing. I found out the value from literature and filled the “Missing” Zr value.
It still does not work.
Is there a way to fix it?
Thanks
Debasis
Hello Debasis,
The error here stems from the “matminer” present of ElementProperty using data from pymatgen, and not the tables in the “magpie_elementdata” folder.
You can edit the Pymatgen data by changing the value in Pymatgen before computing features. See code example below.
Best,
Logan
from pymatgen import Element, Composition
x = Element(‘Zr’)
x.bulk_modulus
x = Element(‘Fe’)
x.bulk_modulus
170.0
x = Element(‘Zr’)
from matminer.featurizers.composition import ElementProperty
e = ElementProperty(‘pymatgen’, [‘bulk_modulus’], [‘mean’])
e.featurize(Composition(‘Zr’))
[nan]
x.bulk_modulus = 10
e.featurize(Composition(‘Zr’))
[10.0]
···
From: Debasis Sengupta
Sent: Wednesday, July 17, 2019 10:28 AM
To: matminer
Subject: Bulk modulus missing data
Hi,
I am trying to compute matminer feature using
cf.ElementProperty.from_preset(“matminer”)
It work fine for other features, but for ‘PymatgenData mean bulk_modulus’ for composition such as Al0.25NbTaTiZr (writes NaN), but it works for Al0.25NbTaTiV
I figured from /utils/data_files/magpie_elementdata/BulkModulus.table that the data for Zr is missing. I found out the value from literature and filled the “Missing” Zr value.
It still does not work.
Is there a way to fix it?
Thanks
Debasis
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Hi Logan,
Thanks for the tips.
Is there a way I can directly edit that data file in pymatgen instead of assigning value by scripting? Where should I look for the pymatgen bulk modulus data file that I can edit and save?
Thanks
Debasis
···
On Wednesday, July 17, 2019 at 11:28:50 AM UTC-4, Debasis Sengupta wrote:
Hi,
I am trying to compute matminer feature using
cf.ElementProperty.from_preset(“matminer”)
It work fine for other features, but for ‘PymatgenData mean bulk_modulus’ for composition such as Al0.25NbTaTiZr (writes NaN), but it works for Al0.25NbTaTiV
I figured from /utils/data_files/magpie_elementdata/BulkModulus.table that the data for Zr is missing. I found out the value from literature and filled the “Missing” Zr value.
It still does not work.
Is there a way to fix it?
Thanks
Debasis
Yes, you can edit the “periodic_table.json” file associated with Pymatgen.
See: https://github.com/materialsproject/pymatgen/blob/master/pymatgen/core/periodic_table.json
Logan
···
From: Debasis Sengupta
Sent: Thursday, July 18, 2019 10:12 AM
To: matminer
Subject: Re: Bulk modulus missing data
Hi Logan,
Thanks for the tips.
Is there a way I can directly edit that data file in pymatgen instead of assigning value by scripting? Where should I look for the pymatgen bulk modulus data file that I can edit and save?
Thanks
Debasis
On Wednesday, July 17, 2019 at 11:28:50 AM UTC-4, Debasis Sengupta wrote:
Hi,
I am trying to compute matminer feature using
cf.ElementProperty.from_preset(“matminer”)
It work fine for other features, but for ‘PymatgenData mean bulk_modulus’ for composition such as Al0.25NbTaTiZr (writes NaN), but it works for Al0.25NbTaTiV
I figured from /utils/data_files/magpie_elementdata/BulkModulus.table that the data for Zr is missing. I found out the value from literature and filled the “Missing” Zr value.
It still does not work.
Is there a way to fix it?
Thanks
Debasis
–
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/80cccacd-8165-4ec7-b043-90ed2e09429f%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.