Questions tagged [periodic-system]
Refers to a model which is treated as infinitely repeating, for example so as to use plane-wave basis functions and capture long-range electrostatic interactions.
37 questions
3 votes
0 answers
78 views
Pymatgen: make molecules whole?
Is there any way in Pymatgen (or some similar python library such as ASE or whatever) to make all molecules read from a .cif whole (i.e. not broken due to PBC)? This is useful for organic molecules ...
- 211
5 votes
0 answers
91 views
Occupations and number of k points in periodic DFT
I'm trying to make sense of what the relationship is between number of k points, number of electrons, and occupations in a plane wave DFT code like Quantum Espresso. Taking the zero temperature case ...
- 151
4 votes
0 answers
81 views
Periodic crystal editors and visualizer
I'm trying to find a visualizer and editor for my periodic crystals (in .cif format) for my tasks. I have used VESTA before and now to view the periodic structure, but I need an editing functionality (...
- 81
11 votes
3 answers
324 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, ...
- 718
1 vote
0 answers
42 views
Using descriptors to compare oxide-phase bulk phase (crystal)
I have the xyz coordinates for multiple oxidized Pt nanoparticles (~ 2.5 nm diameter) at different oxygen content. I would like to find the closest oxide phase match (PtO, PtO2, Pt3O6...). I think a ...
- 1,507
6 votes
1 answer
285 views
Periodic CCSD(T) software?
I'm curious about which quantum chemistry software packages support periodic CCSD(T), and preferably also faster versions such as PNO-CCSD(T) and LNO-CCSD(T). I've recently been rather frustrated by ...
- 1,332
4 votes
1 answer
266 views
What are some good references for periodic Hartree-Fock calculations?
I am looking to implement a Hartree-Fock program to study periodic, condensed matter system, however, I literally cannot find a single reference or example anywhere for how to do this. In the past, I ...
- 141
3 votes
1 answer
372 views
what determines the 'Estimated total dynamical RAM ' in a Quantum Espresso calculation
As per my understandings the computer resources required for a DFT calculation increases by an order of three with the number of atoms. But as you can see in the output files given below the ...
- 804
7 votes
1 answer
987 views
Why use PySCF/OpenMolcas instead of VASP/QuantumESPRESSO
While I am aware that VASP and QE are widely used for solid-state materials and PySCF/OpenMolcas are primarily designed for molecular systems. I want to know why should I use PySCF/OpenMolcas for ...
- 4,076
7 votes
0 answers
222 views
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 ...
- 1,332
5 votes
1 answer
173 views
Large energy differences across successive geometry optimization steps in SIESTA
I am trying to calculate adsorption energies of acetophenone on a 6x6x3 nickel surface with about 12 Angstrom of vacuum above it using SIESTA 5. I have arranged the molecule so that the ring plane is ...
- 463
4 votes
1 answer
188 views
Computing proton-proton potentials for infinite periodic materials
For electronic structure calculation, when optimizing the wavefunction for an infinite periodic material, the proton-proton energy is needed to monitor the convergence of the SCF loop. How is the ...
- 1,061
4 votes
1 answer
123 views
Plane wave expansion of the wavefunction for periodic material modelling
The aim is to do an electronic calculation with static nucleus with Plane wave (PW) basis functions for an infinite periodic material. The number of functions is given by the pairs of reciprocal ...
- 1,061
2 votes
1 answer
96 views
Plane-wave basis expansion for periodic material modelling: cutoff energy inequality and number of atoms in the simulation
The calculation of electronic structure of infinite periodic material using Plane-waves is the object of study here. The cutoff energy $E_{cutoff}$ provides information about the accuracy of the ...
- 1,061
0 votes
1 answer
140 views
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 ...
- 1,103