15
votes
How to generate the high symmetry paths for band structure calculations?
If you are really interested in learning how to generate the path, I strongly advice you to avoid using any automatic tool like suggested in previous answers.
In the Wiki page entitle Brillouin zone ...
- 24k
14
votes
Accepted
How to separate the data plot for spin up and spin down band structure into 2 different graphs, in Pymatgen?
Here I provide an example with my own python scripts to realize your purpose rather than using Pymatgen (You can save data firstly with Pymatgen and plot with python). I assume that you can perform ...
- 15.3k
14
votes
How to generate the high symmetry paths for band structure calculations?
If the crystal unit cell is in a format readable by ASE, then you can use code that looks approximately like so:
...
- 1,436
11
votes
Accepted
High throughput tool to quantify the similarity of crystal structures?
As Thomas mentioned, there are tools from Materials Project that we use for structure similarity. See for example this paper, with code available in pymatgen. This works by creating local environment &...
- 1,541
10
votes
How to generate the high symmetry paths for band structure calculations?
Pymatgen can definitely do what you are asking for. You can find several algorithms under the pymatgen.symmetry.kpath module here. I include a minimal example below ...
- 7,401
8
votes
High throughput tool to quantify the similarity of crystal structures?
Not sure what your input files are, but there's a technique based on spherical harmonics that is relevant described here: High Throughput Profiling of Molecular Shapes in Crystals https://doi.org/10....
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8
votes
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How to determine dimensionality of a structure with pymatgen?
Yes you can indeed identify a crystsal structure's dimensionality in pymatgen. This is done by pymatgen.analysis.dimensionality.get_dimensionality_gorai, which ...
- 1,970
8
votes
Is there any Python library for returning the atoms of a periodic material within a cube?
You can use a python library called ASE (Atomic Simulation Environment) to achieve your requirement.
Here is a sample code:
...
- 3,145
7
votes
Convert ase atoms to pymatgen structure
Try AseAtomsAdaptor.get_structure method from pymatgen.io.ase, it actually serves exactly this purpose.
- 346
6
votes
Tool to extract rings from zeolite structures
R.I.N.G.S. code
The RINGS code can generate a number of ring statistics, including the number of rings (with many supported definitions).
Among its multiple outputs are the list of atom indices of ...
- 1,675
6
votes
Tool to extract rings from zeolite structures
While there might not be a dedicated tool that directly extracts rings of different sizes from zeolite structures, you can achieve this using graph theory and network analysis libraries that can be ...
- 3,145
6
votes
Magnetic Transition Pymatgen Error
Oddly, despite the name, the class doesn't specifically implement any methods to do iteration directly on the object to access the structures. You can see in the source code, you can see the class ...
- 15.7k
5
votes
Magnetic Transition Pymatgen Error
I suspect this is not an error, but just an issue with how you are trying to print it. The enumerator object is an object, so when you print it attempts to give you information about the enumerator ...
- 11.4k
4
votes
Accepted
The standard format and parser of VASP output files
If by "standard", you mean an "official" VASP-supported program, then the answer is no. VASP gives you the raw text output for you to deal with on your own. That being said, the <...
- 7,401
3
votes
Accepted
Isotropy of Pymatgen Structures
As mentioned in the first comment, you need to check the symmetries and spacegroups. You can refer to the following sample code:
...
- 3,535
3
votes
Accepted
How to generate the remaining sites in a cubic lattice from a given POSCAR/cif in Python?
I sort of get what OP wants to achieve based on the comment section, but what a strange request! Nonetheless, this can be easily done by both pymatgen and the Atomic Simulation Environment (ASE).
The ...
- 1,970
3
votes
Pymatgen structure to rdkit molecule
Since you have not mentioned the CIF ID of your crystal, I took a random crystal structure from Crystallography Open Database with CIF ID: 2008748 with which I will answer both your questions 1 and 2....
- 3,145
2
votes
How to generate the high symmetry paths for band structure calculations?
Here are a couple of extra links that might be helpful in your (now 5months old) quest: [1], [2].
It would be helpful for all of us if you could put up that green chekmarck on the answers you found ...
- 1,411
2
votes
Accepted
Symmetrization of elastic constants based on rotational symmetry in Pymatgen
Solution
On Line 21 of your code, where you initialize the elastic tensor, if the .symmetrized part is removed, then you get the desired output.
Modified Code:
<...
- 3,145
2
votes
Accepted
How to terminate a surface with hydrogens
Phil Hasnip:
"I don't know any tools to automate this, but as an opening guess I would create a slab with one extra atomic layer on the surface. Then I would remove all oxygen in the extra layer,...
2
votes
Accepted
How to resolve ModuleNotFoundError: No module named 'pymatgen.analysis.defects'?
They break backwards compatibility all the time! I have run into different but equally frustrating problems before. It seems your problem may have solutions. See here: https://materialsproject.github....
- 1,668
2
votes
Non-Equivalent T-Sites from a cif file
I guess that T refers to 'tetrahedral'; this site is occupied by Si and Al. In the cif file these atoms have exactly the same coordinates because Al substitutes Si. So you have one single T site ...
- 671
2
votes
Is there any Python library for returning the atoms of a periodic material within a cube?
You can also use sisl to achieve this.
Best shown with an example:
...
- 3,959
1
vote
Tool to extract rings from zeolite structures
RingsStatisticsMatter.jl
If you prefer your rings to be returned as a python list to do further analysis with, there's code available at https://github.com/MorrowChem/RingsStatisticsMatter.jl
With a ...
- 11
1
vote
Convert ase atoms to pymatgen structure
This is how I wound up getting things working.
I saved atom as xyz:
atoms = row.toatoms()
atoms.write(f"./{dir_}/{i}_{str(atoms.symbols)}.xyz")
Then, I ...
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Only top scored, non community-wiki answers of a minimum length are eligible