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10 views

Deriving pressure in a pair-wise additive system

I am studying pairwise-additive systems in statistical mechanics. These are systems with particles which only have a 2-body potential defined. When trying to find the pressure of such a system, we do $...
3
votes
0answers
10 views

How to analyze the band symmetry with Quantum ESPRESSO?

This question is related to this paper: J. Phys. Chem. Lett. 2017, 8, 13, 2999–3007 The above figure shows symmetry analysis for the band structure. The author writes: The band symmetry and parity ...
6
votes
0answers
15 views

Relax vs VC-Relax for interstitial incorporation energy

In order to model an interstitial trapped in a metal lattice, and the associated incorporation energy, which should be used - "relax" or "vc-relax"? I want to understand the ...
5
votes
0answers
14 views

Algorithmic description of implementing path integral molecular dynamics?

Suppose I have a functioning molecular dynamics package for classical MD. I want to extend this code to run path integral MD. I know that a surprisingly small number of new features need to be ...
7
votes
1answer
49 views

Calculating hyperpolarizability in NWChem

I'm trying to make a pipeline geometry optimization -> calculation of polarizability/hyperpolarizability. And NWChem seems pretty good for it, the only thing I can't understand its how to calculate ...
4
votes
0answers
36 views

How do I reconstruct the surface with known Miller indices?

I'm trying to reconstruct the surface $(1\bar{1}01)$ in an hexagonal material and the reconstruction is described by the matrix $\begin{pmatrix} \hspace{3mm}3 \hspace{2mm}1 \\-1 \hspace{2mm}2 \end{...
8
votes
1answer
266 views

Density of States of Supercells

Are there any important considerations to make for density of state calculations for supercells? With band structures typically band unfolding schemes make things easier to understand but is there ...
5
votes
0answers
32 views

How do I identify an oblique surface mesh?

I have drawn three surface meshes from a hexagonal material for the $(0001)$, $(1\bar{1}00)$ and $(1\bar{1}01)$ . The first one would be the top horizontal surface of the hexagonal structure, the ...
2
votes
0answers
24 views

Is there a difference in performance when the symmetry is specified via ibrav in Quantum ESPRESSO?

I have been using cif2cell for converting CIF files into quantum ESPRESSO input files. But cif2cell always keeps the ibrav value to be zero and indicates the CELL_PARAMETERS. As per the quantum ...
4
votes
1answer
76 views

How can I find the area of an overlayer structure?

What sources would you recommend (or if you could instead explain it to me that would be great). I have never studied crystallography but must do a module on it and in some of the questions we were ...
2
votes
0answers
31 views

Are there other kinds of stability of materials? How to demonstrate that with computation approaches?

I have known some kinds of stability of materials, such as: Mechanical stability; Dynamical stability; Thermal stability In particular, they can be studied with first-principles computational ...
10
votes
0answers
55 views

Deciding the number of CPUs for a DFT calculation

If I am using Quantum ESPRESSO for my work, how can I know the number of CPUs necessary for a certain DFT calculation?
7
votes
0answers
54 views

How can we make a mechanically unstable cubic system, stable

I have to calculate the elastic constants of a Cubic system using a Density functional theory-based software. A cubic system will be mechanically stable if it satisfies the Born-stability condition (...
4
votes
0answers
37 views

Equations related to the first order derivative of the wave function

I have two brakets (the angular momentum matrix elements) that are $$ \langle \partial_\mathbf{k} \psi_{n \mathbf{k}} | \times \mathbf{p} | \psi_{m \mathbf{k}} \rangle \tag{1} $$ $$ \langle \psi_{n \...
9
votes
1answer
61 views

Pattern X-Ray Diffraction Fitting

Assuming I have an experimental powder XRD spectra and I have a number of computational structures without any knowledge of which is correct, how can I simulate the powder XRD spectra? Once I have ...
7
votes
0answers
39 views

CP2K vs BigDFT comparison

I typically run DFT calculations with 1000 to 5000 atoms using CP2K. This works fine but I'm interested in BigDFT also. Is there anyone here that has experience using BigDFT and is able to compare ...
2
votes
1answer
43 views

BSE and IQP oscillator strength from VASP

Recently I am trying to calculate the BSE and IQP transition dipole based on VASP lecture on BSE and BSE fatband. However, I have a few questions regarding the BSE and IQP oscillator strength. From ...
9
votes
3answers
733 views

Which software is good with generally contracted basis sets?

Recently, I learnt that basis sets can be contracted as segmented (like def2 or 6-31G) or general (like cc-PVTZ, or ANO). The general contraction allows all the primitives to appear in all shells, ...
7
votes
0answers
81 views

Is there an upper limit of temperature after which the quasi-harmonic approximation (QHA) fails?

I can't seem to articulate what made me ask this question but it sprang up when I asked: What does it mean to say a material is 'anharmonic'?. I've heard before that the electronic entropy ...
14
votes
2answers
896 views

What does it mean to say a material is 'anharmonic'?

I understand that a harmonic picture of the potential in a material isn't enough to study lattice dynamics thoroughly. The quasi-harmonic approximation is a good workaround and helps incorporate ...
13
votes
1answer
278 views

Why is CPHF/CPKS necessary for calculating second derivatives?

This question is coming from an answer to one of my previous questions. During optimizations, QM programs usually compute the gradient(first derivative) analytically, and take a guess of the hessian (...
10
votes
1answer
86 views

How many GB of RAM would be needed for VASP to evaluate optical properties of a material?

Even though it is a powerful tool, Quantum ESPRESSO's hardware requirements are very high. For instance, to evaluate optical properties, even for structures with tens of atoms, Quantum ESPRESSO can ...
8
votes
0answers
34 views

How to get order constitution data for single equilibrium calculation in Thermo-Calc's TC Python module?

I know that it is possible to get order constitution data for phases when using Thermo-Calc's GUI (e.g. to get "BCC_B2 DISORD" instead of just "BCC_B2") for a single equilibrium ...
11
votes
1answer
206 views

What are some of the biggest theoretical and computational challenges in Condensed Phase Chemistry?

What are some of the biggest open-questions / challenges in Condensed Phase theory and computation? What efforts are being done to answer them? I realize Condensed Phase chemistry is a huge field, but ...
6
votes
1answer
47 views

How to choose starting magnetization while doing spin polarised calculation in Quantum ESPRESSO?

I am trying to run spin polarised DFT calculation in Quantum ESPRESSO on system Co2MnSi. I kept starting magnetization for all these three species as, ...
7
votes
1answer
50 views

For ergodicity, what is the significance of the R value and slope?

I am calculating MSDs for the first time and have been struggling to find newbie-level resources on understanding them. If anyone could please suggest any resources or provide guidance on how to ...
2
votes
0answers
58 views

Soft Material for life indication [migrated]

I have a mechanism where two parts are screwed and unscrewed and I wish to incorporate a system by which the number of screwing and unscrewing can be indicated. I have thought of a method using the ...
6
votes
1answer
32 views

How can I assign spins to an non-planar Anti-Ferro Magnetic system (CoO in this case)?

I have been working with an anti-ferromagnetic material Cobalt Oxide. And in the image given below the blue spheres are Co ions. The blue spheres form a tetrahedron shape. And I've assigned the spin ...
12
votes
1answer
202 views

What material will expand after being compressed?

The theory of elasticity is essential in engineering. The most basic law is that any piece becomes smaller if one compresses it. My question is: How can a piece of material expand (some minutes, hours,...
7
votes
1answer
30 views

How To make 2D Quantum dots in VESTA

I want to know how to make 2D Quantum dots in Vesta?
7
votes
1answer
77 views

What differences are there when modeling metal-organic-frameworks as isolated clusters or periodic solids?

Should I take MOF (metal-organic framework) as a periodic structure or an isolated cluster? What's the difference between them? If it's periodic, can I do an analysis of the electronic structure, such ...
6
votes
1answer
141 views

Where to obtain MOF structures suitable for carrying out DFT simulations?

For bulk and two-dimensional materials, we can download the structures from many databases, such as Materials Project and CMR. Are there also similar databases for MOF (metal-organic framework) ...
5
votes
0answers
47 views

Why does Thermo-Calc one axis equilibrium calculation get stuck in never ending loop?

I've been trying to run a Thermo-Calc one axis equilibrium calculation on some quaternary alloys in the TCHEA4 database. Most of the calculations work fine, but for some alloys it gets stuck in a loop ...
8
votes
1answer
129 views

What are the pitfalls for the simulation of MOF materials with VASP?

I want to study the properties of metal-organic framework (MOF) materials with DFT implemented in VASP. What's the pitfall for this kind of simulation? Which points should I take special care of? I ...
2
votes
1answer
106 views

Would the increase in cost, of a double-sided whiteboard, make it worth it to engineer such a device?

I wonder whether or not it would be useful to design and construct a double-sided Whiteboard (i.e. the front and back sides can both be used)? The cost of the Whiteboard product would increase, but ...
9
votes
0answers
63 views

Geometric optimization taking a long time. Are my convergence criteria too tight in CP2K?

I have been having trouble with the VIBRATIONAL_ANALYSIS routine. Namely, the routine keeps timing out. I am trying to find the vibrational modes of Pyridine in a non periodic system, as well as Mo2C ...
9
votes
1answer
67 views

Are there any conventions or guidelines to prepare images of molecular/crystal structures?

Preparing good figures is an important part of reporting molecular modeling results. There are many programs that can be used to visualize and generate images from all sorts of programs and approaches....
14
votes
1answer
139 views

Which codes can perform density functional perturbation theory (DFPT) calculations for a van der Waals (vdW) material?

I notice that most codes can only perform finite difference calculations when including van der Waals interaction. Are there any codes that can apply density functional perturbation theory (DFPT) in ...
12
votes
1answer
99 views

What's the physics contained in the exchange-correlation functional in the framework of KS-DFT?

This question is inspired by this post. In the Kohn-Sham framework of density functional theory, the total energy is expressed as: $$E=E_{kin}^{non}+E_{ext}+E_{H}+E_{xc}$$ in which The first term is ...
9
votes
0answers
117 views

Phonon density of states as a function of frequency vs energy

This question might seem more suited for the Physics SE but I'm asking it here because of its many applications in materials modelling. Lattice dynamics codes like ...
11
votes
1answer
48 views

Modelling nitrogen interstitial barrier to oxygen diffusion in metals

I want to study the effect of nitrogen interstitials on oxygen diffusion in metals and vice-versa. Would you suggest MSD calculations in LAMMPS to be a viable method for this? There aren't many ...
9
votes
1answer
52 views

How can I simulate the work function given by Ultraviolet Photoelectron Spectrum (UPS)?

How can I simulate the work function given by Ultraviolet Photoelectron Spectrum (UPS) of a molecule or a molecular crystal? I thought it is an easy job: Just do a geometry optimization and get the ...
12
votes
2answers
137 views

Optimization of Gaussian basis sets within the Hartree-Fock Method

I am revisiting some exercises in Thijssen's Computational Physics book, particularly chapter 4 on the Hartree-Fock method. I am interested in the method of nonlinear optimisation for its own purposes,...
13
votes
2answers
2k views

High-Performance Computing: What does “Mio CPUh” mean?

Sorry if this question is too simple for the community but I really could not find an explanation. A detailed answer would be appreciated.
10
votes
1answer
165 views

How to calculate the energy of conduction band and valence band with respect to vacuum in quantum espresso?

I was able to calculate band energies in quantum espresso. How to convert them to values that are in terms of difference from vacuum energy?
10
votes
1answer
54 views

How to define a nonconventional geometry to obtain exchange spring hysteresis loop structure using MuMax3?

I have tried to simulate the hysteresis loop for the exchange spring structure using Mumax3. I have already simulated the hysteresis loop for the conventional bilayer soft-hard structure. Please find ...
10
votes
1answer
62 views

Generating SOAP descriptors in python

What is the best python package to construct Smooth Overlap of Atomic Positions (SOAP) descriptors given SMILES representation of a molecule? Is this even possible without providing 3D geometry? An ...
14
votes
1answer
136 views

How can you separate the data plot for spin up and spin down band structure into 2 different graphs, in Pymatgen?

I am a beginner user of Pymatgen package. In order to process the data from VASP DFT calculation software, I use Pymatgen to visualise the output band structure. When I do spin polarised band ...
12
votes
2answers
105 views

Are there any codes to study magnetic materials?

I have used a few codes for studying magnetic materials (specifically core-shell nanoparticles with an AFM shell and an FM core). These are: Vampire: For the calculation of curie temperature via ...
7
votes
1answer
37 views

What's the difference between charge density and the electron localization function (ELF)?

The following figure is the electron localization function (ELF) for monolayer LaBr$_2$. The ELF is calculated to reflect the bonding character in SL LaBr$_2$. As shown in the figure, ELF shows two ...

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