All Questions
3,601
questions
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 ...
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?
- 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 ...
- 443
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?
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 ...
- 21
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 ...
- 31
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 ...
- 309
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.
- 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 ...
- 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 ...
- 367
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 #
...
- 131
1
vote
2
answers
47
views
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 ...
- 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 ...
- 51
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 ...
- 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 ...
- 53
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 ...
- 181
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.
- 21
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 ...
- 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 ...
- 105
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.
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?
- 11
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 ...
- 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 ...
- 913
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 ...
- 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-...
- 33
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 ...
- 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 ...
- 151
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 ...
- 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 ...
- 133
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?
- 105
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 ...
unit vector
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 ...
- 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.
...
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 ...
- 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 ...
- 913
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 ...
- 31
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 ...
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 ...
- 11
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 ...
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 ...
- 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. ...
- 51
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 ...
- 21
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?
- 105
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 ...
- 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 ...
- 145
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 ...
- 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, ...
- 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 ...
- 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 ...
- 443