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5
votes
0answers
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 ...
3
votes
0answers
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 ...
4
votes
0answers
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 ...
5
votes
1answer
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): ...
6
votes
0answers
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 ...
4
votes
0answers
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 ...
4
votes
0answers
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 ...
6
votes
1answer
40 views

Is this notation for single and double excited Slater determinants correct?

Is the following notation $\Phi^\mathrm{HF}_0 \equiv | \phi_1, \phi_2, \cdots, \phi_i, \phi_j, \cdots, \phi_N \rangle$ $\Phi_{ia} \equiv | \phi_1, \phi_2, \cdots, \phi_a, \phi_j, \cdots, \phi_N \...
6
votes
0answers
30 views

Frequency error in Gaussian CASSCF(10,10)

I am stuck in calculating the frequencies of one optimised geometry for naphthalene CASSCF(10,10) with Gaussian 16. I have optimised its geometry and checked the active space is the pi system of it, ...
7
votes
1answer
40 views

Does PySCF support CAS-SCF calculation?

Does PySCF support CAS-SCF calculations? If not, it is possible to implement it based on their GTO integral library?
5
votes
1answer
79 views

Modify ORCA orbitals for CASSCF

I have run a HF calculation on naphthalene and I have checked the MOs that have been obtained. Now, I have to select my active and inactive orbitals for CASCF(10,10). As there are 34 occupied orbitals,...
5
votes
0answers
46 views

Why am I getting DOS like this in Quantum ESPRESSO?

I am working on $\ce{GeHfTe}$ and in the case of a non-collinear calculation, I am getting the DOS in the attached photo. I have already relaxed my structure with VC-relax and it is converged with ...
12
votes
1answer
81 views

How to find reviewers for your paper?

When you submit a paper to be published, the journal will ask you to suggest at least three reviewers. My question is how to search for appropriate reviewers for your paper?
6
votes
1answer
53 views

Doubt about K point selection for 2x2x1 supercell

I have one doubt about K points selection for a supercell. I construct one 2X2X1 supercell with 64 atoms having a=11.19, b=11.19, c=5.59. For checking K points convergence test with energy should I ...
6
votes
1answer
44 views

Eigen-values not converged, warning in Quantum espresso

I am running a simple example of vc-relax/scf for aluminum using PBE pseudo-potential.Setting are given below ...
4
votes
0answers
30 views

What are Crystal Electric Field Parameters?

What does the following notation mean? $$A_{20}\left<r^2\right> = -100 \mathrm{K}$$ Where $A_{20}$ is termed a Crystal Electric Field Parameter. I often see this notation when reading papers on ...
7
votes
2answers
452 views

Why can MD simulations not handle "exotic" materials?

We are all aware of the fact that MD Simulations using force fields can treat very big systems. But they cannot handle "exotic" materials. Why?
4
votes
0answers
48 views

Gaussian warning

I am running an ONIOM optimization calculation on GAUSSIAN software and when I open the LOG file I get a warnig saying: ...
4
votes
1answer
43 views

How to run hp.x command in Quantum ESPRESSO 6.8?

How to run hp.x command in QuantumEspresso v6.8? It is saying command not found. After doing ...
7
votes
1answer
52 views

How to perform linear response theory calculation of U Hubbard parameter in VASP?

Following to this post, I would like to know how to perform linear response theory for calculation of U Hubbard parameter in VASP?
7
votes
0answers
39 views

How might inclusion of a Grimme dispersion correction influence a simulation of a dense liquid that is not water?

I adapted an example first-principles water simulation to do simulations of liquid SiO2, but did not know what I was doing and did not remove a Grimme dispersion correction term. It would be great to ...
8
votes
0answers
54 views
+100

Simulation of charged species with plane-waves in Quantum Espresso

I am using Quantum Espresso to simulate a platinum surface with ligands, so far everything is working ok. I now need to introduce a solvated hydronium $H_3O^+(H_2O)_2$. Is there something I should be ...
10
votes
2answers
184 views

Non-Convergence of the XC functional in the sense of a Taylor series

When it comes to improving the accuracy of DFT calculations, there is a well known hierarchy: starting from LDA using $E_{xc}[n]$, proceeding with GGA and its $E_{xc}[ n, \nabla n]$ dependency and ...
4
votes
0answers
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 ...
8
votes
1answer
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 ...
6
votes
1answer
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 ...
4
votes
0answers
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/...
12
votes
1answer
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 ...
4
votes
0answers
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 ...
5
votes
0answers
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 ...
8
votes
0answers
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 ...
6
votes
0answers
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 ...
10
votes
1answer
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 ...
5
votes
1answer
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 ...
4
votes
1answer
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 ...
5
votes
1answer
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 ...
8
votes
1answer
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 ...
4
votes
0answers
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) ...
5
votes
1answer
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 ...
5
votes
0answers
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 ...
11
votes
0answers
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 ...
3
votes
0answers
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 ...
27
votes
2answers
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 ...
8
votes
0answers
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 ...
5
votes
1answer
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 ...
10
votes
2answers
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 ...
6
votes
2answers
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?
9
votes
0answers
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 ...
8
votes
1answer
94 views

How to eliminate imaginary frequencies during a Gaussian geometry optimization?

When conducting a minimization on Gaussian software, What are the procedures used to eliminate imaginary frequencies if we have already found a stationary point? Are there any keywords that would help ...
8
votes
1answer
50 views

How is SYMPREC used to determine symmetries compatible with local magnetic moments in VASP?

In DFT calculations using vasp, symmetry analysis are performed to determine space group symmetries at first, if symmetrization is turned on, such as ISYM = 2. When magmoms are set in INCAR, ...

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