Newest Questions
4,593 questions
4
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answers
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How to plot orbitals for S1->T1 transition in Orca
I use TD-DFT and want to examine how molecular orbital changes upon ISC from S1 to Tx state and refer to confirm El Sayed rule. How to achieve it if NTO are not generated for S1->Tx transitions? If ...
- 563
3
votes
0
answers
19
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Partial Hessian vibrational analysis (PHVA) of adsorption in MOFs
I have been probing acid sites in metal-organic frameworks (MOFs) by performing the partial Hessian vibrational analysis (PHVA) which provides information about characteristic vibrational modes that ...
3
votes
0
answers
24
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When performing the transiesta calculation, the device does not converge
I am attempting to perform an electronic transport calculation, where the electrode calculations are converging normally, but the device as a whole is not converging.
...
- 31
3
votes
0
answers
25
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How to determine the direct band gap for a semi-metal (bismuth) in Quantum Espresso/BURAI Interface
I have run the Self-Consistent Field calculations and found the highest unoccupied and lowest unoccupied energy level for Bismuth (hR2) crystal structure. Now, bismuth is a semi metal with Fermi level ...
- 141
6
votes
3
answers
690
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Is converting values from reduced units to physical units a good idea?
I have written a program for MC simulation or LJ particles in NVT.
I have used reduced units to run simulations.
My professor wants me to show him data and plot it in physical units.
Is converting ...
- 2,708
2
votes
0
answers
24
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Mismatch between acceptance rate and phase transition
I have written a program for performing MC simulation of LJ (Lennard-Jones) particles.
Simulation literature says that the acceptance rate should be 20–60%.
However, I see that the position where the ...
- 2,708
5
votes
1
answer
113
views
Galfenol (FeGa) structure
I am currently engaged with a first principles calculation based project. I was wondering can anyone share .cif file or lattice parameters (primitive lattice vectors/atomic positions) of Galfenol at ...
- 731
3
votes
0
answers
17
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NaN result using ShengBTE
I tried using ShengBTE t get the thermal conductivity of PE after performing phonon calculations using quantum espresso. When I used version 1.5.0 ShengBTE I got some numbers at the beginning of the ...
- 31
4
votes
1
answer
71
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How should I apply the 2.5σ rule of cut-off distance in the case of reduced units?
According to the book of Frenken & Smit, Page 35-37, the cut-off distance in the case of LJ (Lennard-Jones) particles:
Equal to $2.5 \sigma$; where $\sigma$ is the equilibrium distance in the LJ ...
- 2,708
3
votes
0
answers
23
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How to Analyze the Effect of a Dopant Atom on the Band Gap Using Supercell and Band Structure Calculations?
I want to study the impact of a dopant atom on the band gap of a material.
For a 2x1x1 supercell, is it necessary to perform band unfolding especially when I study the undoped in a similar super cell?
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4
votes
0
answers
25
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Creating a surface with ASE (Atomic simulation Environment)
I want to create the (4×2) Rutile TiO2(110) surface and the surface slab consisting of five TiO2 trilayers (or 15 atomic layers)
I did that, but I don't if it is correct or not!
...
- 41
2
votes
0
answers
10
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quantum espresso ESM relax calculation
Is it possible to relax a slab with ESM bc1 conditions in Quantum Espresso?
The slab has vacuum regions on each side in the z direction. The relaxation is performed on the z direction only. The x and ...
- 313
2
votes
0
answers
25
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Crystallographic Specific Mean Free Path (MFP) Derivations: High-Symmetry Direction Mapping and Band Slope Selection
In the given paper,(Paper Link) Figure 4 describes the Mean Free Path (MFP) for the three crystallographic directions (100, 110, and 111). The Methods section mentions that the MFPs are obtained using ...
- 21
4
votes
1
answer
45
views
When using M062x is it preferable to introduce the dispersion correction explicitly or not?
The London dispersion forces are analogous to the interactions observed at long range. From the computational perspective, these dispersion forces can be modeled by directly incorporating any ...
- 129
2
votes
0
answers
22
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Dataset of 2D/3D potential energy surfaces, excited states
I see several research papers with excited and ground state PES of different molecules showing level crossings and intersections. But, I do not find any database publicly available. Is there any ...
- 21
2
votes
0
answers
80
views
How to adapt Einstein summation subscripts from 3-Index to 4-Index tensors in Numpy's einsum?
I am trying to apply frozen core approximation in order to get the effect of the forzen core orbitals on the 1-electron and 2-electron Hamiltonian. According to the notes on Page 28, the electronic ...
- 3,770
0
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0
answers
25
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VASP Molecular Dynamics Simulation
I want to study some physical properties of methane under high temperature and high density. However, when running molecular dynamics simulations, I noticed that the POTCAR pseudopotential file I used ...
- 9
3
votes
2
answers
69
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Why converge energy vs. Ecut when k-points is the bottleneck?
I'm writing a report for a university modelling class where we have to determine equilibrium lattice parameters for various materials using DFT (Castep).
The first of these is Aluminium. What I am ...
- 31
1
vote
0
answers
28
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Vasp encut convergence [closed]
which encut value should I choose considering this plot
2
votes
0
answers
60
views
Adsorption energy calculations using quantum espresso through BURAI
I'm currently working on a CO2 capture project and would love some guidance as I'm not super confident about what I'm doing and am in sore need of some mentorship. I want to test different zeolite ...
- 21
1
vote
0
answers
20
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How to compute the magnetic permeability
Is there any code computing the magetic permeability of the magnetic materials?
Is there any other way to compute the magnetic permeability property for the magnetic materials with different shapes?
...
- 833
4
votes
1
answer
174
views
How to perform phonon convergence?
I am conducting phonon calculations for the CsPbI3₃ perovskite structure. How can a convergence test be performed for phonons? Which parameter should be checked in the output file to ensure ...
- 403
2
votes
0
answers
21
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MD calculation of hexagonal boron nitride using LAMMPS
I use LAMMPS to perform MD calculations for hBN. However, I can't find a suitable tersoff potential file. Where can I get it?
- 21
1
vote
0
answers
15
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Impact of Symmetry Preservation on Accurate Elastic Constant(Modulus) Calculations in Cubic Lattice Systems with Aliovalent Doping
I am currently working on calculating the bulk modulus of a 3D bulk structure with a cubic crystal system using VASP. The structure contains alkali ions, and my goal is to evaluate how the bulk ...
- 71
3
votes
0
answers
34
views
Software for calculation of polyhedral packing fractions of crystal structures?
I know how to calculate the polyhedral packing fraction of simple crystal structures, but in a lot cases, the structure is not cubic and the polyhedra are irregular, and it becomes very tedious to ...
- 379
1
vote
0
answers
20
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RDKit SetScale method for drawing
I am trying to figure out thisn old SO question RDKit SetScale method for drawing:
I can have this code running (from comment below the original SO question : There is a C++ example of using the ...
- 143
1
vote
0
answers
9
views
Retis evaluation with Openpathsampling
Dear Users of Openpathsamling !
I am an old user of OPS, and I need to evaluate my RETIS calculation. I have done this before, back in 2021, but I was back then still using the old NETCDF (.nc) ...
3
votes
1
answer
35
views
Formation energy AXO3 - free atoms or elemental solids?
I am trying to calculate the formation energy of a perovskite compound with, say, $\ce{AXO3}$-structure. The formation energy is given as
$E_\mathrm{form}=E_\mathrm{\ce{AXO3}}-\sum_in_iE_i$
with $i$ ...
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3
votes
0
answers
28
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Wannier orbital shape and bonding
In the Wannierization of CsPbBr3, xsf files have been generated. One of these files displays an orbital centered on a Pb atom. How can I interpret this orbital's shape and spatial spread? Additionally,...
- 403
2
votes
0
answers
18
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Convergence issue for ions with GPAW
How best to do relaxation on charged molecules (plus and minus one electron) from the initial geometry of the relaxed neutral system? Two examples are CCOCCOCC(F)F and CCS(=O)(=O)C=C, where the former ...
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1
vote
0
answers
49
views
How can I fix the SI units in this program?
I have written the following script to run an MC simulation of polymers.
The script is producing very small total energies.
What am I doing incorrectly? My suspect is that the unit conversion is ...
- 2,708
1
vote
0
answers
50
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What is the proper approach to optimize a 3D cubic crystal structure after applying Biaxial Strain in QE?
What is the proper approach to optimize a 3D cubic crystal structure after applying Biaxial Strain in QE ?
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2
votes
0
answers
41
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PySCF: Frozen Core FCI calculation
PySCF gives the option to freeze orbitals in CISD calculations by:
myci = ci.CISD(mf, frozen=2).run()
However, for FCI calculations
...
- 2,207
0
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0
answers
20
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Biaxial Strain under Quantum Espresso
for a strain effect on 3D cubic materials, when studying the unstrained structure, its properties then applying the strain pourcentage in order to compare, changing the a and b values and keeping the ...
- 11
0
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0
answers
20
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How can i calculate Total density of state from DOSCAR file
I am trying to draw a DOS-energy graph in python and excel.
And I know that the sum of orbitals does not match the overall DOS.
For example, I drew a Si DOS graph.
I added the s and d orbitals of Si. ...
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2
votes
1
answer
51
views
Effect of number of component and How to plot DOS
I'm studying DOS these days.
I followed some examples from YouTube and other papers,
but I have some questions.
Does the number of components affect the DOS?
At first, I thought so. But I changed my ...
- 91
4
votes
1
answer
42
views
How to find the number of plane waves considered for the wavefunctions on Abinit?
I am working on a tutorial of crystalline cubic silicon of an abinit based software where
I have to find the number of plane waves but I don't really know what I should look for in my input or output ...
- 43
2
votes
1
answer
45
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How to Optimize Atomic Positions and Volume While Preserving Cell Shape in VASP?
I’m working on optimizing a crystal structure using VASP 6.3.2, and I need a method to optimize both atomic positions and cell volume while keeping the cell shape fixed, in order to preserve the ...
- 71
3
votes
1
answer
33
views
Overcoming forces and pressure in SCF step for relaxed slab system
The vc-relax calculation (cell and position optimisation) using quantum ESPRESSO for 2D slab system has printed the end final coordinates and corresponding cell parameters. Using these, the next SCF ...
- 939
3
votes
0
answers
24
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Ideas to obtain projection matrix Amn(K) from QE
in a nutshell, I want to have access to the projection matrix that QE uses to calculate the orbital contributions/weights for each n and k (with &PROJWFC). Knowing that $w_{n,\mathbf{k},\alpha} = |...
- 103
5
votes
1
answer
160
views
What is the proper interpretation of the output 'HF' energy of a ground-state Gaussian 16 calculation using the opt keyword (B3LYP)?
I am running calculations to find optimized ground states with Gaussian 16 such as
#opt=(MaxCyc=100) b3lyp/3-21g Pop=reg
for which I get the following output (...
- 51
1
vote
0
answers
23
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How to calculate ionic charge density in Quantum Espresso?
I am trying to calculate total charge density of surface slab along z axis. I am using from QUantum Espresso. I know that using plot_num=0, I can calculate the electronic charge density in pp.x. Now, ...
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5
votes
1
answer
54
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What software can we use to plot magnetically induced currents in aromatic compounds?
I am investigating some polyaromatic compounds, and I wish to plot the ring currents to gain further insights into their aromaticity. Is there any software (other than AICD) that may be employed to do ...
- 153
3
votes
0
answers
43
views
Lattice Constant Optimization for Janus Monolayers
How can I optimize the lattice constant for a Janus monolayer material like FeBrCl using VASP, ensuring accuracy in capturing its unique structural properties and potential symmetry breaking? Could ...
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1
vote
1
answer
22
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Band structure using NEGF method in Transiesta
I have used transiesta to calculate electronic transmission functions using NEGF approach. Is there any way to calculate the band structure of the central scattering region in transiesta supercell? So,...
- 369
3
votes
0
answers
13
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How to optimize the structure of the HEMO group
I have used the GAMESS program to try to optimize the structure of an iron complex with oxidation state +3 with porphyrin. I have doubts about whether the charge and the multiplicity assigned to the ...
- 41
1
vote
2
answers
68
views
Why do my phonons look so bad?
I have been working on CsCl using Quantum ESPRESSO, and I calculated both the electronic band structure and phonons using Ultrasoft Pseudopotentials (USPP) and GGA.
Surprisingly, the electronic ...
- 457
0
votes
1
answer
22
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Number of orbitals per atom in the electrode does not match the system electrode
I had the following question during transiesta calculation.
...
- 167
0
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0
answers
28
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Quantum espresso pseudopotential convergence test
I generated a pseudopotential using atomic code(Quantum_espresso_6.7/atomic/src/ld1.x) and conducted convergence test. But as below, total energy tends to oscillation as ecut goes up.
(I performed a ...
- 44
2
votes
0
answers
36
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Why end final positions don't appear?
I am running relax calculation for a 2D material using Quantum ESPRESSO code. However, after job is done the "end final coordinates" don't appear. What can I addjust?
Greetings.
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