Questions tagged [periodic-boundary-conditions]

Questions regarding periodic boundary conditions in materials.

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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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13 votes
1 answer
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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 ...
Camps's user avatar
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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: ...
fireball.1's user avatar
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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/...
fireball.1's user avatar
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8 votes
1 answer
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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 ...
prananna's user avatar
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7 votes
1 answer
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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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7 votes
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Coupled cluster and periodic systems

I recently found that PySCF supports coupled cluster calculations for periodic systems (link to the documentation: https://pyscf.org/user/pbc/mix_mol.html). That seems pretty unique: of course DFT in ...
Alex I's user avatar
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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 ...
dtg67's user avatar
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6 votes
1 answer
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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 ...
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5 votes
1 answer
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Unwrapping particle coordinates in MD simulations to remove effects of periodic boundary condition

While calculating various quantities that involves particle positions ( for example, radial distribution function, mean square displacement etc.) using Molecular Dynamics simulation, the effects of ...
bubucodex's user avatar
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5 votes
1 answer
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How to model an isolated molecule with Quantum ESPRESSO?

I am trying to model isolated structures such as quantum dots or molecules in Quantum ESPRESSO (QE). QE uses 3D periodic boundary conditions (PBC) by default. That's why in order to reduce any ...
Abdul Muhaymin's user avatar
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How to draw periodic bonds in Visual Molecular Dynamics (VMD)?

I have the LAMMPS DUMP file of a salt solution, and I am investigating the Oligomerization of the salt ions in solution. However, when I am trying to visualize the trajectory, I can only draw bonds ...
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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 ...
Suslik's user avatar
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4 votes
2 answers
307 views

What is the difference between a "periodic image" and a "nearest image" in MD simulation?

As far as I understand - In MD, when a particle or coordinate moves beyond one face of the simulation box, it reappears on the opposite face as if the box were replicated infinitely in all directions....
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4 votes
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Periodic boundary conditions or spherical potential? [closed]

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 ...
Paul Logan's user avatar
3 votes
2 answers
167 views

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 ...
user366312's user avatar
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3 votes
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Verifying periodicity of crystalline orbital modulus in PySCF

I'm trying to verify that the modulus of the crystalline atomic/molecular orbitals computed by PySCF satisfy the correct periodicity condition for the supercell. I'm considering a hydrogen chain ...
phonon's user avatar
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Miller indices and periodic boundary conditions

I want to implement building the Miller indeces in my program Chemcaft. Currently I need to understand more the computations with periodic boundary conditions (PBC) needed for crystallographers. The ...
Linkey's user avatar
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3 votes
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Is it possible to find a cubic supercell for a non-cubic crystal structure?

Suppose that we have a crystal material with a non-cubic unit cell. E.g. $\alpha \neq \beta \neq \gamma \neq 90^{\circ}$. Is it possible to find a supercell such that $\alpha = \beta = \gamma = 90^{\...
ado sar's user avatar
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2 votes
1 answer
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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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Is there any effect on the physical properties when the size of the system increases in DFT?

I am using Quantum ESPRESSO to do some DFT calculations. I want to know if the optoelectronic properties obtained by a unit cell would remain the same when the properties are obtained by using a ...
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Issue regarding self repeated .vasp structure of engineered graphite/graphene

When engineers the graphite and save it as.vasp format, it will give self periodically repeated structure. Still, the size of the cell is the same, but the structure repeated itself by huge numbers in ...
vikas's user avatar
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2 votes
0 answers
27 views

How to find the scaling factors for minimum image convention?

Suppose that we have an arbitrary (not necessarily cubic) unit cell with cell parameters $\mathbf{a}$, $\mathbf{b}$, $\mathbf{c}$ (lattice vectors) and $\alpha$, $\beta$, $\gamma$ (lattice angles). We ...
ado sar's user avatar
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How to access Unit Cell Dimensions inside tclForces Script (NAMD)? [closed]

I have a NAMD system with PBCs (FlexibleCell on) and I need to access the unit cell information to manually apply wrapping to some atoms in the system such that i may apply custom restraints to them. ...
Byotik's user avatar
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1 answer
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Symmetric issue about the Gaussian basis Hamiltonian

The material system is described by the Hamiltonian and overlap matrice, with the Gaussian basis set. At Gamma point in the reciprocal space, the upper triangle block and the lower triangle block in ...
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