# All Questions

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28 views

### How to implement a toy DFT

I want to learn DFT for research purposes and I need to implement a toy DFT for pedagogical reasons. I would like some recommendations regarding resources like books, articles, or any other thing that ...
14 views

### Can electron-phonon coupling be extracted from measurements of the dielectric function?

Electron-phonon coupling, and more generally electron-ion coupling, is highly important for all sorts of things from superconductivity to heat transport and thermoelectrics. Computationally, there are ...
20 views

### How to identify localized surface states in the band structure

After calculating the band diagram of a structure, is there a way to identify localized surface states? I am working with Si nanowires with different cross sections. I want to determine the band gap ...
62 views

### How to create molecule image similar with molconvert using RDKit

I have the following molecule in SMILE format (saved as my_molecule.smi): ...
18 views

### How are structure descriptors used in regression or machine learning?

I am currently working on prediction of UV-vis spectra from structure of molecules. I have read multiple papers where structure descriptors were used as inputs for machine learning to find various ...
19 views

### There are two different fermi energy calculated in the two steps(SC and NSC) of the calculation of band structure using VASP, which is correct one?

While calculating the band structure using VASP, we usually take two steps: one is about self-consistent run to get the right CHGCAR file; and the other is about non self-consistent calculation ...
18 views

### How to look for specific structural motifs in proteins?

Is there a way to search to search for specific structural motifs in proteins? For example can a database where we can find structures with zing finger motif or an hairpin... PDBeMotif (ebi.ac.uk) has ...
40 views

46 views

### Guidelines for determining k-mesh

If I need to draw the band structure of a semiconductor, like when I do CFD simulations, I am guessing I will need a lot of k-points to form a fine mesh in the k-space, but in reality, it seems the ...
56 views

### Quantum mechanical antireflection coating; what quantity would be analogous to index of refraction?

Background Quasiparticle interference (QPI) is a technique that can be used to study 2D surface state band structure; carrier reflections at boundaries or impurity sites will interfere producing ...
44 views

### How accurate is ALGO= All in VASP?

I was facing convergence problems in my 2D system, but after I have used the ALGO = All tag the convergence problems have gone. I would like to know how accurate is ...
39 views

### Calculate FF interaction energy of small molecular dimers

I have a set of molecular dimers (~25 atoms) for which DFT-D3 interaction energies are calculated by Psi4 and Turbomole program. Now I want to compare these values against Force-Field methods like UFF/...
222 views

### Are there any benchmark test sets for UV-vis absorption maxima?

In computational chemistry, I have come across many test sets which are used to benchmark a new method. For example, the G2 test set for thermochemical calculations (heats of formation). There is the ...
43 views

### Spin-orbit coupling in Siesta

I am going to simulate the electronic structure of the Au 111 surface including Fe-centered porphyrin on top. Since the molecule includes Fe, I first did spin-polarized calculations. Using converged ...
35 views

### How to calculate electronic circular dichroism (ECD) spectra from MCTDH?

electronic circular dichroism (ECD) spectra is commonly used in organic chemistry to characterize chiral molecules. Here the question is how to simulate ECD spectra using MCTDH (Multi-configurational ...
62 views

### Steps to obtain ionic diffusivity using AIMD

I read a paper and the authors wrote they use AIMD to estimate the ionic diffusivity of materials. I wonder steps to obtain the value at different temperatures. What are the input and output of ...
26 views

### How to efficiently adjust the AMIX_MAG and BMIX_MAG parameter in VASP calculations?

I'm trying to calculate the magnetic anisotropy energy of Cr2O3 by comparing the total energy difference of the system in different spin configurations (in-plane and out-of-plane). However, when ...
266 views

### Accuracy trade-off between energy and density in DFT calculations

Consider the following situation that the exchange-correlation term (e.g., B3LYP) overestimates the energy in a system (i.e., a simpler one (e.g., LDA) is sufficient in the system). In this case, my ...
102 views

### What's the Difference between Lattice Statics and Lattice Dynamics?

For example, in something like the General Utility Lattice Program, you perform structural optimisation and then use phonons to calculate properties like elastic constants etc. The latter part seems ...
27 views

### In VASP, how to perform putting normal stress , with the parameter -PSTRESS?

I found the only parameter related to pressure is Pstress tag in VASP. But the pressure of Pstress tag is Hydrostatic pressure, while I only want to put stress along z-axis. Could you please help me ...
41 views

### Tool to saturate the dangling bonds at the surface of nanostructures

When it comes to studying 2D, 1D or 0D nanomaterials, saturating the dangling bonds in the surface helps remove unwanted localized surface states from the band structure 1. However, so far I have not ...
56 views

### How to use VEDA to analyze vibrational energy distribution?

In my bachelor thesis, I am trying to use the VEDA program to analyze the vibrational energy distribution to associate different vibrations to the calculated modes from gaussian. I am stuck now ...
30 views

### Changing orientation of SQS structure generated from ATAT

I generated the following SQS cell using ATAT (the sructure is converted to POSCAR format) ...
51 views

### How to convert a hexagonal unit cell to rhombohedral unit cell?

Hexagonal unit cells can be converted to rhombohedral unit cells, and the latter unit cells have fewer atoms. But how can I convert them? Is there any software or codes that are able to do this ...
18 views

### How to change the magnetization direction in Quantum ESPRESSO?

I have a magnetic crystal system. I want to calculate the total energy of the system if the magnetization direction is aligned in different directions such as [110], [010]. By default Quantum ESPRESSO ...
80 views

### Looking for crystal generator library

I am looking for a C or a C++ library that can do crystal generation, that is, multiply unit cells in one or more directions with symmetry information. (in other words, generate supercells). I have ...
26 views

### Smearing values for different codes

I am using Quantum Espresso along with a different code, I am performing calculations on Platinum bulk. After choosing the "cold" smearing (which I read is a good choice for metals) with a ...
4k views

### Can a highly-cited published paper have this type of error?

I know the title sounds opinion-based (and admitedly, part of my question is), but I will try to bring more practical elements to the question: Here is my problem: I have been testing a force field ...
70 views

### Geometry optimization using DFT

I have been attempting to optimize the structure of a Si nanowire using SIESTA. The original structure fed into the optimization is as follows. Once it is optimized, the structure would change to ...
39 views

### What is the meaning of Coulomb Subtraction?

Specifically, in the General Utility Lattice Program (GULP) 2003 paper, in the methods section on Two-body Short-range Interactions we have the following: For covalently bonded atoms, it is often ...
2k views

### How can I use a GUI on a supercomputer?

I am trying to make plots based to VASP simulation results, but I am struggling with how to download so much data from the server. A lot of examples on the internet are taught using the local desktop ...
267 views

### Geometry optimization with Moller-Plesset MP4

Can we optimize a molecular structure using Moller-Plesset MP4 method on GAUSSIAN software? If yes what keyword do we have to add?
101 views

### How to plot a Gaussian cube file with python/matplotlib?

I know there are programs that can automatically visualize .cube files (like VMD), but I'm trying to do it myself in python/matplotlib (or equivalent) to better understand what the numbers mean. I ...