pymatgen

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This mainly concerns the `MaterialsProject2020Compatibility` scheme, so I'm CC'ing @rkingsbury here. https://github.com/materialsproject/pymatgen/blob/dcc4576fb8fb89b7adc2f31158654392348e6498/pymatgen/entries/compatibility.py#L941-L944 The above codeblock checks the POTCAR symbols when getting a correction. While this is a very useful tool,...

Andrew-S-Rosen

Pymatgen Zeo++ installation help

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I am following the directions on the pymatgen documentation site on installing and setting up Zeo++ and Voro++ (https://pymatgen.org/pymatgen.io.zeopp.html#zeo-installation-steps). When I do the svn chackout command I get an "Access...

cwaitt

Outcar parsing for vasp 6.2.0 is broken

3

**Describe the bug** I recently used VASP version 6.2.0 (newest official release afaik) and found that the Outcar parser of pymatgen (class `Outcar`, `__init__` method, in pymatgen.io.vasp.outputs.py) is not compatible...

MichaelWolloch

analysis/adsorption.py add_adsorbate is not working

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**Describe the bug** add_adsorbate function is not working properly. **To Reproduce** Steps to reproduce the behavior: atoms = read(contcar) pym_slab = pym_ase.get_structure(atoms) mol = molecule('N2') pym_mol = Molecule(species=[atom.symbol for atom...

zuhalcakir

[WIP] Relaxation Transformation

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Sometimes, we have calculations with continue from a previous calculation. For example, you run a coarse relaxation followed by a fine relaxation in separate fireworks. In that case, it would...

nwinner

Structure.get_sorted_structure does not preserve magmom site property

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**Describe the bug** The `Structure.get_sorted_structure` method seems to clobber `magmom` attributes. As a consequence, all `DictSet` subclasses don't allow setting magnetic moments using site properties by default, since the default...

bocklund

I have a POSCAR file of Na3Zr2Si2PO12 (mp-532695). I'd like to substitute Zr2 -> HfZr at POSCAR file and get a minimum Ewald sum structure by using pymatgen. So I...

Juo-kim

PDplotter plotly backend ternary diagram default colors are terrible

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Hi, Black font on black markers, completely invisible!  It's nowhere near publication quality plot, please change default look or allow customisation by arguments of PDPlotter.

Youjin1985

**Describe the bug** I noticed that some of the lattice matches I was getting with MPInterfaces' matching algorithm were missing in pymatgen's implementation with the same matching parameters. After a...

fyalcin

Quasi-RRHO Thermochemistry Analysis Module

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## Summary Added quasirrho.py to the analysis subpackage to calculate the Quasi-RRHO free energy from a Gaussian or QChem frequency calculation. * Calculates Grimme's Quasi-RRHO free energy * Option for...

arepstein