materialsvirtuallab/matgenb

Jupyter notebooks demonstrating the utilization of open-source codes for the study of materials science.

matgenb's Issues

Notebook for using adsorption.py

Add the tutorial for using adsorption.py from the supplementary material of:

Montoya, J. H., & Persson, K. A. (2017). A high-throughput framework for determining adsorption energies on solid surfaces. Npj Computational Materials, 3(1), 14. https://doi.org/10.1038/s41524-017-0017-z

to matgenb. Will take a pedantic approach to discussing the nuances of modelling adsorption.

`pymacy` package?

The 2018-03-09-Reaction Diagram Construction notebook has the line

from pymacy.bim.thermo import ReactionAnalysis

in the first code cell, but I couldn't find a pymacy package on PyPI. Could you amend the notebook with instructions on how to install that package?

Can developers update files?

Hi, I found that pymatgen has changed a lot change-log, which some modules can not be found in the lastest version. May I request developers update the notebook files for convenience?

Request: Notebook demonstrating pymatgen transformations capabillities

Requesting an example notebook of using the transformations framework in pymatgen to create structures with full provenance of how they were generated.

• using various transformations
• chaining transformations
• the one to many concept
• converting to a SNL
• embedding provenance for original structure into SNL ( e.g. ICSD, MP, OQMD, etc. IDs and info)

Import Error when using "get_pourbaix_entries"

Using python version 3.7.1 I am trying to use the example for producing pourbaix diagrams.
The first errors I receive when importing the packages and calling "get_pourbaix_entries" are resolved upon recompiling.
ValueError: numpy.ufunc has the wrong size, try recompiling. Expected 192, got 216

I then get the following error upon recompiling the code below:
# Get all pourbaix entries corresponding to the Cu-O-H chemical system.
entries = mpr.get_pourbaix_entries(["Cu"])

ImportError: cannot import name 'LinearAssignment' from 'pymatgen.optimization.linear_assignment' (unknown location)

[Missing notebook]: The `2013-01-01-Bandstructure of NiO` is missing

The 2013-01-01-Bandstructure of NiO.ipynb is removed in 013e371 but the hyperlink is still kept in the homepage. I'm not sure if this removal is accidental or intended?

'BandStructure' object has no attribute 'branches'

On the 2013-01-01-Bandstructure of NiO.ipynb notebook 5) Plot Bands and DOS section

bsdosplot = BSDOSPlotter(
    bs_projection="elements",
    dos_projection="elements",
    vb_energy_range=22,
    egrid_interval=2.5,
)
plt = bsdosplot.get_plot(bs, dos=dos)  # error of  'BandStructure' object has no attribute 'branches'

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