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Questions tagged [pymatgen]

Pymatgen (Python Materials Genomics) is a robust, open-source Python library for materials analysis.

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Can MongoDB/Fireworks run on a supercomputing cluster?

I'm trying to set up MongoDB and Fireworks on a supercomputing cluster, but I've encountered several issues. OpenSSL and Shared Libraries: Initially, MongoDB couldn't find the required libcrypto.so.1....
otto's user avatar
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3 votes
0 answers
29 views

Material for learning to use pymatgen?

I was looking for methods to generate the k-path for electronic band calculation in periodic solids. In the article below, the authors presented an algorithm they developed based on the Latimer–Munro (...
Camps's user avatar
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3 votes
0 answers
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Electronic density of states from not the usual VASP outputs

In a very frustrating development, my VASP has decided to hang at the writing of outputs stage. While I troubleshoot that separately, for the moment I need to get an electronic density of states from ...
Andrey Poletayev's user avatar
2 votes
0 answers
45 views

How to choose k grid using pymatgen for VASP? [duplicate]

Before I start; sorry for this lengthy question. I am confused about choosing the correct set of K points for the K-convergence test for VASP calculations. The system of my interest has an ...
Nilabja Kanti Sarkar's user avatar
4 votes
0 answers
58 views

Read pymatgen format from something else other than Python?

It seems that the only way that Materials Project can report structures with the new API is through the Pymatgen JSON format. ...
alfC's user avatar
  • 281
4 votes
1 answer
114 views

How to resolve ModuleNotFoundError: No module named 'pymatgen.analysis.defects'?

Background My goal is to use PyCDT: Python Charged Defect Toolkit (paper, github, pypi). I installed the code by doing: pip3 install pycdt I am not using any ...
Abdul Muhaymin -Free Palestine's user avatar
1 vote
0 answers
49 views

Interstitial and vacancy defects

I'm trying to insert interstitial defects in an FCC crystal with 32 atoms. And also a quick way of inserting a vacancy or doing a substitutional defect. Any code for this would be deeply appreciated. ...
Nana Kofi Boakye's user avatar
2 votes
0 answers
41 views

Calculating geometric features using Zeo++?

I am currently engaged in research involving metal-organic frameworks (MOFs) and I am seeking assistance with calculating specific geometric features using Zeo++. The features I am interested in are ...
harsh's user avatar
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2 votes
1 answer
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Non-Equivalent T-Sites from a cif file

I am trying to find symmetrically inequivalent T-atoms in a crystal structure (zeolite). Does anyone happen to know any package that can help with that? I see that pymatgen does have options for ...
Saha_1994's user avatar
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3 votes
0 answers
81 views

Calculating bulk modulus of aluminum using pymatgen and MLIP

I have an interatomic potential (CHGNet) which is interfaced with pymatgen and can output the stress on any structure. Now, I want to use pymatgen to calculate the bulk modulus for aluminum. The code ...
xlr's user avatar
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2 votes
0 answers
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What is the Miller index of the highest site?

I am trying to use Pymatgen adsorption module for my adsorption site calculations. While going through the documentation, I had a small confusion. It says the following Determine “surface sites” by ...
Ezio's user avatar
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4 votes
1 answer
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Isotropy of Pymatgen Structures

I'm using pymatgen and have a host of structure objects (generated from cif files). How can I judge if the structure is isotropic or not? I took a look at the options associated with structure objects ...
R Walser's user avatar
  • 367
10 votes
3 answers
646 views

Tool to extract rings from zeolite structures

I am trying to reproduce the work done in this paper https://doi.org/10.1021/acscatal.7b00588. In this direction, I have been successful in optimizing the unit cells of the zeolites. For further steps,...
ansonthms's user avatar
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6 votes
2 answers
129 views

Is there any Python library for returning the atoms of a periodic material within a cube?

Is there any Python package that allows to cut defined by the points (0, 0, 0) and (x, y, z)? That is, it should return all the atoms of the unit cell and periodic images inside the shaded region. (...
ado sar's user avatar
  • 211
3 votes
1 answer
136 views

How to generate the remaining sites in a cubic lattice from a given POSCAR/cif in Python?

For example, I intend to generate the remaining sites of the Cr cubic lattice but the POSCAR file provides limited info on the number of atoms present as shown below. Is there a way to implement this ...
Pranoy Ray's user avatar
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7 votes
1 answer
198 views

How to determine dimensionality of a structure with pymatgen?

Is there a neat way to figure out if a crystal structure in pymatgen is 2D or 3D? If we have a molecule we can feed its coordinates to (say) the ConvexHull method in scipy. Is there way to do the same ...
R Walser's user avatar
  • 367
4 votes
1 answer
503 views

Pymatgen structure to rdkit molecule

Context I am trying to convert a pymatgen bonded structure, such as one generated by CrystalNN to an rdkit molecule. So I obtain the pymatgen bonded structure with ...
R Walser's user avatar
  • 367
6 votes
1 answer
229 views

Symmetrization of elastic constants based on rotational symmetry in Pymatgen

I am trying to write a small python script which will symmetrize an elastic tensor based on rotational symmetry of the space group. I started with this link and created a new python script as below. I ...
Pranav kumar's user avatar
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2 votes
1 answer
321 views

How to terminate a surface with hydrogens

I am trying to study surface reconstructions of metal oxides using Quantum ESPRESSO. For this, I am creating slabs using python tools: ASE, Pymatgen, and catgen. However, I am unable to terminate the ...
ansonthms's user avatar
  • 991
8 votes
2 answers
2k views

Convert ase atoms to pymatgen structure

I have atom_row from ase_db. I have tried various methods but they all fail. Seems like I'm missing a lattice, but I don't know what that is and where I can get it ...
Dmitry  Sokolov's user avatar
5 votes
1 answer
693 views

The standard format and parser of VASP output files

I see a lot of post-processing tools for VASP, including ASE, VASPKIT,Pymagten and some other customized codes. They all read the VASP output files like a normal text file. Sometimes I would meet ...
Jack's user avatar
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8 votes
2 answers
218 views

Magnetic Transition Pymatgen Error

I am trying to simulate the change in magnetic moments during a ferromagnetic to antiferromagnetic transition. ...
k2_2009's user avatar
  • 129
18 votes
4 answers
4k views

How to generate the high symmetry paths for band structure calculations?

Suppose I want to calculate the band structure of a material system along a specific high symmetry path in the Brillouin Zone. If the point group of the system is given, how can I easily compute the ...
beginner's user avatar
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4 votes
0 answers
94 views

Predicting the magnetic behaviour of Mn doped SmFeO3 [closed]

I am trying to predict the magnetic order transformations in Mn doped SmFeO3 using the MagneticStructureEnumerator class of pymatgen. Attached is the error message: ...
k2_2009's user avatar
  • 129
13 votes
2 answers
567 views

High throughput tool to quantify the similarity of crystal structures?

Quantifying the similarity of crystal structures is important to understand and predict the properties of less-studied crystals. For example, the inorganic crystal structure database (ICSD) contains ...
Achintha Ihalage's user avatar
16 votes
1 answer
1k views

How to separate the data plot for spin up and spin down band structure into 2 different graphs, in Pymatgen?

I am a beginner user of the Pymatgen package. In order to process the data from VASP DFT calculation software, I use Pymatgen to visualize the output band structure. When I do spin polarised band ...
JensenPang's user avatar
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24 votes
0 answers
489 views

What are the tools available for point defects calculations? [closed]

It would be appreciated if you could explain one of the tools below (or another tool not listed), in the format used here (for example): What software will allow me to combine two images? What ...
Franksays's user avatar
  • 501