All Questions
5 questions
10
votes
3
answers
172
views
Is there a scriptable tool to determine whether two periodic structures are the same?
I'm doing some material search, in which I remove 2-4 atoms from a medium sized (~20 atoms) unit cell. I need to find all different combinations that are unique with respect to the translational, ...
- 658
6
votes
1
answer
311
views
Clustering Algorithms with Periodic Boundary Conditions
I've been working on a project that involves the clustering of data with periodic boundary conditions. Like simulation of extra-framework water species.
Specifically, I am looking for clustering ...
- 1,970
8
votes
1
answer
387
views
Periodic Boundary Conditions in Atomistic Simulation Environment
Consider the following atoms object.
atoms_al = ase.build.fcc111('Al', size=(1,2,2), vacuum=16.0, orthogonal=True)
To set the periodic boundary conditions along the ...
- 15.9k
7
votes
1
answer
783
views
How to discard molecules at the boundary in the Atomic Simulation Environment (ASE)?
When building a supercell for a molecular crystal with the Atomic Simulation Environment, it seems that the program takes into account periodic boundary conditions when replicating the unit cell. How ...
- 1,154
11
votes
2
answers
2k
views
How to include individual PBC box dimensions in xyz file format compatible with VMD
I am using ASE to write an xyz file. Each frame in the file has a different PBC (periodic boundary condition). Currently, a frame starts like this:
...
- 15.9k