Questions tagged [periodic-boundary-conditions]

Questions regarding periodic boundary conditions in materials.

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What is the relationship between periodic boundary and the simulation box?

Suppose, the size of my simulation box is: Width = 200 Height = 100 Where, Top-left corner = (0, 0) Bottom-right corner = (200,100) Center of the coordinate is at (100, 50) What would be the size ...
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2 votes
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Why do we even need periodic boundary conditions?

According to Wikipedia - Periodic boundary conditions (PBCs) are a set of boundary conditions that are often chosen for approximating a large (infinite) system by using a small part called a unit ...
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Periodic boundary conditions or spherical potential?

I was wondering whether you know if there is any sort of literature discussing whether periodic boundary conditions or spherical potentials could be better or worse for QM/MM or MM simulations, their ...
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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 ...
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7 votes
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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 ...
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14 votes
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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 ...
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5 votes
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Kinetic energy cut-off for Gaussian-type orbitals when applying periodic boundary conditions [duplicate]

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 ...
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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 ...
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11 votes
2 answers
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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: ...
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11 votes
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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/...
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13 votes
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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 ...
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