Questions tagged [periodic-boundary-conditions]

Questions regarding periodic boundary conditions in materials.

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7
votes
1answer
50 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 ...
13
votes
1answer
147 views

Minimum image convention for non-orthorhombic unit cells

I am trying to take into account periodic boundary conditions for non-orthorhombic unit cells. I have the atomic coordinates for a monoclinic super cell with the following lattice vectors output by ...
5
votes
0answers
33 views

Kinetic energy cut-off for Gaussian-type orbitals when applying periodic boundary conditions

I have a solid with PBC (periodic boundary conditions) and I want to perform a DFT simulation. I use GTO as the basis. In a paper I read, I can transform the GTO to a Bloch function (crystalline ...
7
votes
0answers
43 views

CP2K Spherical Cell [closed]

I'm trying to run a gas phase cluster calculation in CP2K. I want to create an outside force to constrain water molecules that are in the simulation within a radius of a central ion. I want to create ...
11
votes
2answers
234 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: ...
11
votes
2answers
205 views

Recalculate atom positions to account for periodic boundary conditions

I have the output of a simulation done using Periodic boundary conditions (PBC), however, the atom positions have been resolved, i.e. there are atoms outside the PBC-box now. Is there a software/...
11
votes
1answer
67 views

What is the meaning of periodic boundary condition for molecular systems?

Reading some Gaussian related documents (inputs, manuals, books), I found the possibility to setup periodic boundary conditions (PBC) in Gaussian. As Gaussian is developed only for molecular systems ...