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3 votes
0 answers
14 views

Steps to remove upper tics in the x-axis in winplotr in Fullprof

I am facing difficulty in removing the upper tic in the winplotr in fullprof software. I just want the tics to be below where angles are measured as shown in the image and not above. I tried playing ...
Anshul Sharma's user avatar
2 votes
0 answers
36 views

Do post-hartree fock calculation with localized Molecular orbitals in PySCF

I have localized the canonical Hartree-Fock orbitals for a molecule in PySCF. Now I want to perform ccsd calculations with these localized orbitals. Is it possible with pyscf?
Pro's user avatar
  • 830
4 votes
1 answer
61 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 ...
user1420303's user avatar
1 vote
0 answers
11 views

Removing "say XYZ.PRF:" name in winplotr in Fullprof?

I am facing difficulty on removing text like XYZ.PRF:, when we run fullprof in External applications in winplotr. Is there some way to remove it?
Anshul Sharma's user avatar
2 votes
0 answers
24 views

DFPT vs analytical nuclear gradient

I have read some literatures about the gradient wrt. atom positions of the DFT energy, and find different methods one commonly used in MD(analytical nuclear gradient,pulay's paper), and another ...
Fadelis Hu's user avatar
3 votes
0 answers
25 views

Carbon Capture Research - Force Constants & Basis Sets

Greetings Matter Modeling, I'm researching carbon capture dynamics in the context of sorbent regeneration. The UN IPCC Net-Zero goal requires 75 Mt-CO₂/year captured by 2030. According to the IEA, we ...
Phill McGee's user avatar
0 votes
0 answers
20 views

What (executable) command to calculate charge density using quantum espresso? [duplicate]

I'm trying to calculate the charge density of a structure using quantum espresso, I've already used the DENS.X and DEN.X commands, but in both tests the executable not found error appears. Can someone ...
Caroline Santos 's user avatar
1 vote
1 answer
32 views

Number of electrons per cell

I aim to do a HF-like calculation on a 2D graphene layer. What is the number of electrons per cell? Edit: There are six carbon atoms per cell.
mle's user avatar
  • 733
1 vote
0 answers
15 views

Relax calculation in Wien2k

Can someone help me with the steps to take to perform Relax calculation of a structure in WIEN2k? Then further what to keep in mind while performing strain calculation on the structure for the relax ...
epsilon02fft's user avatar
  • 1,127
1 vote
0 answers
15 views

Free energy calculation

I want to plot the relationship between free energy and temperature. I want to consider two plots, when phonons are considered and when phonons are not considered how the free energy changes with ...
Nana Kofi Boakye's user avatar
1 vote
1 answer
19 views

ASE reading cell dimensions from XYZ file generated by I-Py

I have an xyz file formatted in the following way (just a snapshot of the 192 atoms is shown) its cell information is given in # ...
KugelBlitz's user avatar
1 vote
2 answers
47 views

GAUSSIAN 16 Error with CCSD(T)

My input file is: ...
Another.Chemist's user avatar
2 votes
0 answers
46 views

Wrong lattice parameter of CeO2 after structure relaxation with VASP

I am calculating the lattice parameter of CeO2 with VASP, but the optimized lattice parameter is wrong according to many references (Physical Review B 75, 035109 (2007); The Journal of Chemical ...
FaDA's user avatar
  • 121
2 votes
0 answers
17 views

Strange change in total energy when lattice relaxing of EuTiO3 material and then atomic relaxing in a specific direction using Quantum Espresso

These days, I'm having a trouble in atomic relaxing of "EuTiO3" with tetragonal symmetry using Quantum espresso 7.1 for a period of more that a week. This material have a transverse optical ...
Y. S. Lym's user avatar
4 votes
0 answers
46 views

How do you run Gaussian's cubegen with multiple processes/threads?

The cubegen manual gives the signature of cubegen as: cubegen nprocs kind fchkfile cubefile npts format cubefile2 Where: nprocs Number of shared memory ...
leeman's user avatar
  • 141
2 votes
0 answers
18 views

Finding optical properties (epsilon) by Quantum ESPRESSO

I am calculating the dielectric (Epsilon) for ZnO by quantum espresso, when I run the eps.in file, I always get this error. Reading namelist energy_grid' How do I ...
user307903's user avatar
4 votes
0 answers
20 views

QE - transition state SCF not converging

Background Using Quantum Espresso examining a porous material, that has a ligand with an aromatic group. The aim is to rotate the aromatic group and determine an energy profile for the rotation. The ...
Xavier Phillips's user avatar
2 votes
0 answers
19 views

Creating nanocomposite with material studio

I need to create ZnO/ graphene sheet nanocomposite with material studio and i dont know how. Please, help me or guide me to some one who can help me. I'm blocked.
rihem jemi's user avatar
5 votes
1 answer
110 views

Gaussian 18: Relaxed scan using Jacobi coordinates expressed using generalized internal coordinates

For teaching porpouses, I would like to make a relaxed scan for an A-BC system (for example, the isomerization of of H-NC to H-CN or CH3-NC to CH3-CN) with Gaussian 16 using generalized internal ...
PAEP's user avatar
  • 195
4 votes
1 answer
171 views

Random velocity generation

How to generate random velocities in the geometry coordinates of a surface (POSCAR file) using the Boltzmann distribution law with Atomic Simulation Environment (ASE) or other codes for Molecular ...
Rubi Agrawal's user avatar
3 votes
0 answers
32 views

Where can I read about Valleytronics?

Where can I read about Valleytronics? Are there any good books or review papers or influential papers on this topic? The question was also posted at the Physics site.
Rich Hard Fine Man's user avatar
1 vote
0 answers
22 views

LBFGS -- Incomplete Convergence due to BadIntpln

I am doing energy minimization of a molecular system in TINKER. While doing so, I am getting the error in the title of this question. What might be my problem?
Himanshu's user avatar
2 votes
1 answer
34 views

Non-Equivalent T-Sites from a cif file

I am trying to find symmetrically inequivalent T-atoms in a crystal structure (zeolite). Does anyone happen to know any package that can help with that? I see that pymatgen does have options for ...
Saha_1994's user avatar
  • 969
4 votes
1 answer
43 views

The Appearance of Imaginary Frequencies in Lattice Vibration Calculations with Increasing KPOINTS

I have been conducting lattice vibration calculations using the Density Functional Perturbation Theory (DFPT) method. While investigating the convergence behavior, I noticed that when I increase the ...
Jaafar Mehrez's user avatar
4 votes
1 answer
165 views

Syntax Error in ORCA

I keep getting the following error for my orca code: [file orca_main/maininp1.cpp, line 17547]: ERROR: expect a '$', '!', '%', '*' or '[' in the input [file ...
znc204's user avatar
  • 63
2 votes
1 answer
55 views

Is there a way to force GROMACS to keep a certain density for water?

I am trying to fully populate my GROMACS simulation, but the water density in the bulk is too low. Here are the steps I used: Add organic monolayer into 9x9x9 box Solvate with water equilibrate t-...
Peter Yang's user avatar
5 votes
1 answer
72 views

Bader charge calculation in Quantum ESPRESSO DFT

I am searching for calculating Bader charge using Quantum ESPRESSO. I am using pseudopotential based DFT calculation. And I have charge density files (cube and XSF formats). My objective is to ...
Sak's user avatar
  • 859
4 votes
1 answer
44 views

What are the types of solvation models?

Similar to: What are the types of DFT?, What are the types of charge analysis?, What are the types of bond orders?, and What are some recent developments in density functional theory?, I would like ...
Another.Chemist's user avatar
4 votes
1 answer
155 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 ...
mle's user avatar
  • 733
2 votes
1 answer
35 views

Exclusion of Lennard-Jones potential between O-H and H-H in water models

In reading Jorgensen's 1983 paper comparing the properties of 6 water models it was mentioned that there is the inclusion of an L-J potential between pairs of oxygen molecules, but no mention of ...
KashmirWalla's user avatar
2 votes
1 answer
65 views

Absorption enthaply at different temprature in VASP software via ab initio molecular dynamics

Can we calculate the absorption enthalpy at different temperature in VASP software via ab initio molecular dynamics? If yes, how?
Rubi Agrawal's user avatar
2 votes
0 answers
23 views

How do you determine the Pull Direction for a GROMACS umbrella sampling simulation to generate the most accurate free energy value?

I am trying to calculate the free energy between a protein and aptamer using GROMACS. Literature has indicated that one of the best way to do so is by performing an umbrella sampling MD simulation ...
user avatar
3 votes
0 answers
27 views

Constrained geometry optmization: Molecule interacts with its surroundings

I have a water cluster(suppose) generated from MD run. Now, I want to optimize the geometry of only one water molecule of interest using QC methods (e.g. B3LYP/6-31+G(d,p)). I intend that the water ...
Pro's user avatar
  • 830
2 votes
0 answers
18 views

How to define new 2D-structure in Quantum ATK?

I will define a new structure in Quantum ATK that is unavailable in the database. I tried this file to give information to the application, but it didn't work. ...
ashkan rajabi maram's user avatar
1 vote
0 answers
47 views

Free energy calculations for lammps

Is there any tutorial or reference available to perform free enegy calculations (umbrella sampling; thermodynamic integration; free energy perturbation; widom's particle insertion method) etc. With ...
Robin's user avatar
  • 11
1 vote
0 answers
50 views

Understanding the Interaction Between Phonons and Electrons in Solid-State Systems

How does the wave-particle duality exhibited by electrons and the wave-like nature of phonons enable their interaction in solid-state systems? Can you explain the underlying mechanisms that allow for ...
Jaafar Mehrez's user avatar
3 votes
0 answers
24 views

How to perform atomistic spin dynamics (ASD) Ab Initio Molecular Dynamics (AIMD) using VASP?

I have tried normal AIMD simulation using VASP for Non magnetic materials. Now, I am interested to perform the molecular dynamics simulations for the finite temperature for Magnetic materials to ...
prakash g's user avatar
4 votes
0 answers
23 views

Why am I observing spin-orbit coupling in only one direction (spin up or spin down) in SIESTA (DFT)?

Can someone provide guidance on how to include Spin-orbit Coupling (SoC) for the band structure calcualtion using SIESTA? I have used the #Flag #Spin spin-orbit, but I only obtained spin dependence in ...
Abhishek Chandel's user avatar
1 vote
0 answers
11 views

Thermal conductivity and diffusivity of diatomite (also known as diatomaceous earth or kieselguhr)

Does anyone know where can I find measured thermal conductivity and thermal diffusivity of diatomite for different temperatures? I'm looking for the temperature dependency for temperatures higher than ...
Bambino005's user avatar
3 votes
1 answer
155 views

Is a D-Wave quantum computer able to do TD-DFT calculations?

I was reading this paper (Computing molecular excited states on a D‑Wave quantum annealer) and wondering if I can make a QUBO model for the equations used in the TD-DFT energy calculation for the ...
Hadeel Moustafa's user avatar
3 votes
1 answer
101 views

What are the observables when a quantum system is comprised of orthogonal spacetimes? [closed]

We are given a system of three quantum domains A, B, and C with the following properties: (1) domains A and B are independent Hilbert spaces, each with their own space and time dimensions. Both are ...
RalphW's user avatar
  • 39
3 votes
1 answer
53 views

Is there a way to add 4f-oribital information in Pseudopotential?

Now, I'm calculating with a Quantum Espresso program I want to need Eu pseudopotential file with 4f orbital information. But I couldn't find that file, no matter how much I search on the internet. ...
Y. S. Lym's user avatar
2 votes
0 answers
23 views

How to define the space group of a new material?

I am preparing the following strcture of CdAlCRO4 using Material Studio to further study its properties. However, I am facing difficulty in deciding the space group it belongs to. How to find the ...
Habib Arshad's user avatar
4 votes
1 answer
67 views

How to make Pd(111) supercell (√3×√3)R30 via VESTA

How to make Pd(111) super-cell (√3×√3)R30 via VESTA or Avogadro software?
Rubi Agrawal's user avatar
1 vote
0 answers
55 views

Is it possible to generate an input file for band structure calculations for multiple KPaths at once?

I need to generate an input file for band structure calculation along the following k path. how do I input the k path in the "bands.in" file? here, i need to calculate the band gap along all ...
Prasad's user avatar
  • 11
1 vote
0 answers
33 views

VASP - DOS and band structure with different bandgap (PBE and PBE+SOC)

I did some calculations for the bulk of t-Tellurium, and got some strange results. I calculated the bandgap using the outputs of the SCF calculations and the band gap (~0.5 eV) corresponded with other ...
Gabriel Elyas's user avatar
4 votes
1 answer
96 views

Spin-orbit coupling and lattice constant

Cross-posted on Chem.SE. Is there any evidence that spin-orbit coupling (SOC) leads to a crystal lattice distortion? Using Quantum Espresso and DFT, I am getting different relaxed lattice constants ...
freude's user avatar
  • 342
3 votes
0 answers
120 views

Question about determining Fermi energy in Quantum espresso

I used QE to calculate DOS for hBN. I expect to get results as shown here. The behavior of the computed DOS is as expected but QE gives Fermi energy = 1.974 eV. So, when I plot DOS concerning E-Ef, ...
Bekaso's user avatar
  • 233
2 votes
0 answers
25 views

Non-analytical correction for dielectric constant calculation in VASP

I am calculating the static (low-frequency) dielectric constant for a polar material in VASP. Due to the LO-TO splitting, I need to apply a non-analytical correction. My question is how to do this ...
random01's user avatar
  • 171
5 votes
2 answers
72 views

Reintegrate calculation results from ORCA using finer grid?

I have made a bunch of calculations in ORCA to compare them to results from this paper. The original calculations from this paper were done in TurboMole. I tried to recreate the method as best I could ...
J.Doe's user avatar
  • 443

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