Questions tagged [pymatgen]
Pymatgen (Python Materials Genomics) is a robust, open-source Python library for materials analysis.
17
questions
2
votes
0
answers
27
views
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 ...
- 21
1
vote
0
answers
19
views
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 ...
- 243
9
votes
2
answers
499
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,...
- 871
6
votes
2
answers
99
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.
(...
- 211
3
votes
1
answer
86
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 ...
- 1,237
7
votes
1
answer
103
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 ...
- 243
4
votes
1
answer
218
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 ...
- 243
5
votes
1
answer
184
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 ...
- 3,836
2
votes
1
answer
205
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 ...
- 871
7
votes
2
answers
737
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 ...
- 181
5
votes
1
answer
467
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 ...
- 1,938
8
votes
2
answers
209
views
Magnetic Transition Pymatgen Error
I am trying to simulate the change in magnetic moments during a ferromagnetic to antiferromagnetic transition.
...
- 129
18
votes
4
answers
3k
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 ...
- 181
4
votes
0
answers
80
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:
...
- 129
13
votes
2
answers
388
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 ...
- 1,962
16
votes
1
answer
976
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 ...
- 2,763
24
votes
0
answers
463
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 ...
- 501