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Questions tagged [computational-chemistry]

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Why is the SCF calculation performed after VC-RELAX more energetically stable than the VC-RELAX calculation in QE

Recently, I performed a vc-relax calculation in QE. After vc-relax, I performed an scf calculation, including all the optimized parameters from the vc-relax output file (cell parameters, atomic ...
Thejan Hasaranga's user avatar
4 votes
0 answers
19 views

Which quantum chemistry codes have the capability use point charges in a QM/MM setting?

I came across a few examples like: NWchem : QM/MM Bq charges PySCF : QM/MM with MM charges GPAW : External Point charge potential I wanted to know of other code examples, which had the same ...
Atom's user avatar
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2 votes
0 answers
19 views

Investigation of ferro, ferri, antiferro, para and dia magnetism using QE

Can Quantum ESPRESSO be used to investigate ferromagnetism, ferrimagnetism, antiferromagnetism, diamagnetism, and paramagnetism? If so, could you please elaborate on how these types of magnetism are ...
Thejan Hasaranga's user avatar
5 votes
1 answer
214 views

Calculating structural stability of a doped plane

The following image indicates an equation published on a reserach paper which was used to calculate structural stability in a metal atom-substituted graphene sheet. Can anyone tell me if we should ...
Thejan Hasaranga's user avatar
4 votes
0 answers
34 views

Time efficient way of conducting vc relax calculations while mainting accurate results at the same time

I believe this VC-relaxation calculation will take a significant amount of time to successfully complete. Referring to the literature (which indicates that the vanadium substitution atom is positioned ...
Thejan Hasaranga's user avatar
1 vote
0 answers
35 views

Formation and Optimization of Dimers, Trimers, Tetramers, and Beyond

What is the procedure to follow in order to computationally create clusters such as dimers, trimers, or tetramers using Quantum ESPRESSO?
Thejan Hasaranga's user avatar
7 votes
1 answer
88 views

Does the size of atoms influence the speed of DFT calculations when comparing systems with almost the same number of atoms

How does the size of atoms within a structure influence the speed of DFT (Density Functional Theory) calculations? considering that the calculation speed is known to scale cubically with the number of ...
Joyal sunny's user avatar
19 votes
3 answers
2k views

What major advances in theoretical and computational chemistry have been made in recent decades?

Computational modeling has become a mainstay in chemistry, materials science and physics. However, the methods that are typically employed are already decades old: for instance, the B3LYP and PBE ...
Susi Lehtola's user avatar
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3 votes
1 answer
72 views

How to interpret defect formation energy diagram?

Why are formation energy diagrams typically plotted as a function of Fermi energy, and how should one interpret the changes in the x-axis before the charge state changes in these diagrams? Figure ...
user avatar
7 votes
1 answer
86 views

At what point in the Hartree-Fock formalism is the Fock operator introduced?

I seem to be having a conceptual problem with HF theory as to where the Fock operator comes from. In order to explain the context of my conceptual problem, I will include how HF was derived according ...
Kevin Freddo's user avatar
6 votes
0 answers
117 views

Normalization of the Smooth Overlap of Atomic Positions (SOAP) Kernel

I am using the DScribe implementation (https://singroup.github.io/dscribe/latest/tutorials/descriptors/soap.html) of the Smooth overlap of atomic positions (SOAP) ...
C_Swann22's user avatar
  • 533
7 votes
1 answer
113 views

Stopping an ongoing relax calculation with provision to continuing the calculation later on from that checkpoint

How can I interrupt an ongoing relaxation calculation in Quantum ESPRESSO on my system, while ensuring that I can resume it later from the same point?
Joyal sunny's user avatar
2 votes
1 answer
44 views

Structural stability of Graphene

is it acceptable if I came up with around -8.5ev/atom for cohesive energy of graphene?, Literature is in the range 7.3-7.9 ev/atom The formula used for cohesive energy calculation Codes I have used ...
Thejan Hasaranga's user avatar
4 votes
1 answer
53 views

Can we use formation/ cohesive energy to express the structural stability of a supercell?

I have created a graphene supercell using Quantum Espresso and performed a vc-relaxation on it. Now, I need to verify whether the created structure is stable and demonstrate its stability with ...
Thejan Hasaranga's user avatar
2 votes
0 answers
23 views

Why am I getting wrong information about basis functions on running gaussian calculation using the 6-31G basis set for the krypton atom?

This is the information about basis functions which I am getting on doing Gaussian calculation. But according to the best of my knowledge Kr has six primitive Gaussians for 1s, 2s,2p, 3s, and 3p ...
user avatar
5 votes
2 answers
86 views

Why my Relax calculation is not stopping?

I am conducting a relaxation calculation on a mono-layer of MoS2 with a 3x3x1 super-cell, where one Molybdenum (Mo) atom is substituted with a Palladium (Pd) atom defect. However, the calculation is ...
Joyal sunny's user avatar
4 votes
1 answer
75 views

Introducing a vacuum space in z direction for 2D monolayer calculations

Is the introduction of a vacuum in the z-axis necessary when utilizing a 2D monolayer material for Density Functional Theory (DFT) calculations in Quantum Espresso? (This is due to the fact that only ...
Thejan Hasaranga's user avatar
9 votes
1 answer
284 views

Comparing results of various DFT calculations in Quantum ESPRESSO

To verify the reliability of calculation scheme, I want to compare lattice constants, bond length and band gap calculated by the different functionals with the experimental results. So in order to do ...
Joyal sunny's user avatar
2 votes
0 answers
27 views

Error in 2D Ewald sum for a multipolar expansion

I am attempting to calculate the potential of a particle at the center of an infinite two-dimensional lattice as per the following reference: Reference: Lambin, PH & Senet, P. Ewald Summation of ...
JasonC's user avatar
  • 21
2 votes
1 answer
42 views

vc-relax calculation on two-dimensional slab

Is performing only a relaxation calculation (calculation='relax') sufficient for geometrical optimization in conducting a density functional theory (DFT) study of ...
Joyal sunny's user avatar
5 votes
1 answer
89 views

Non-monotonic behaviour in calculation time with changing 'degauss' value of 'cold' smearing

"I conducted a convergence test for the degauss value in Quantum Espresso input with smearing = 'cold'. The results, ...
Joyal sunny's user avatar
6 votes
1 answer
537 views

Understanding algorithm of Quantum ESPRESSO from scratch

As someone new to this field, what are some effective strategies or resources I can utilize to study and understand the Quantum ESPRESSO algorithm from scratch?
Joyal sunny's user avatar
3 votes
1 answer
89 views

At a particular K-point (Monkhorst Pack) grid, SCF calculation is not converging

During a convergence test of (MoS2 2x2x1) monolayer using Quantum ESPRESSO, I tried several K-point Monkhorst-Pack grids. According to my understanding, the calculation time and computational cost ...
Joyal sunny's user avatar
3 votes
0 answers
38 views

Energy corrections to be added in my DFT input of Quantum ESPRESSO for studying catalytic activity of MoS2 for hydrogen evolution reaction

While investigating 'catalytic activity of MoS2 (monolayer) in hydrogen evolution reaction', what are the energy corrections that I am supposed to add in the DFT input (using Quantum ESPRESSO) to get ...
Joyal sunny's user avatar
7 votes
1 answer
198 views

Convergence testing in DFT calculation

I have done convergence testing for MoS2 (2x2x1) monolayer structure in the following order: ecutwfc ecutrho k_points After setting these values, I would like to include vdW correction to the system ...
Joyal sunny's user avatar
5 votes
1 answer
114 views

Neural Network to predict atomic forces using SOAP descriptors

I am working on neural network in tensorflow to train a model to predict atomic forces from SOAP descriptors (regression problem). I have 64 020 data points (chemical structures), each structure has ...
jessss's user avatar
  • 73
3 votes
1 answer
70 views

How to write .TBTGF files using sisl for TranSIESTA

Good day, I trust you are doing well. I am trying to calculate transport properties for a 3D structure stacked between two gold electrodes along the c-axis. The 3D structure and the electrodes should ...
Lenard Carroll's user avatar
5 votes
1 answer
36 views

How to Model Cations or Anions for Activation Energy Barrier Calculation in VASP for Electron Exchange Reactions?

I am interested in performing activation energy barrier calculations using VASP (Vienna Ab initio Simulation Package) specifically for reactions involving electron exchange. However, I am uncertain ...
Nidhi Tiwari's user avatar
4 votes
0 answers
37 views

Which one of the following showing the correct structure Jsmol or Vesta? Or they are just same

Let me explain. I found that the structure for TiFeSi given in the ICSD database using Jsmol software is a little different from what can be obtained using Vesta software using the same cif file ...
Nilabja Kanti Sarkar's user avatar
4 votes
1 answer
113 views

Help with Geometry Optimization in CASTEP

I am a beginner in CASTEP simulation and I need some guidance on the general steps for geometry optimization. I have tried the following three approaches: (1) Build unit cell > geometry ...
Minhaz Mahmood's user avatar
5 votes
1 answer
152 views

What is the problem in my gaussian input?

I want to obtain the single point energy of a Ni-complex molecule, with a mixed basis set using the Gen keyword. The input is: ...
Saeed Hp's user avatar
3 votes
1 answer
71 views

How to get the HOMO/LUMO from spin up/down eigenvalues?

I'm working with OpenMX and see that I have eigenvalues in the output in two columns: one for spin up and one for spin down. How would I know what the total eigenvalue is? Would I just add them ...
lzzard's user avatar
  • 123
3 votes
1 answer
105 views

Cannot reproduce excitation energies in Orca

I do TD-DFT studies in Orca 5.0.3 on porphyrin system and hence at the very beginning I need to pick functional that reproduce excitation energies. The experimental reported values equal: 691, 656, ...
farmaceut's user avatar
2 votes
1 answer
21 views

Geometry of H2O in the v=1 vibrational state for AIMD simulation

This is a follow-up to my recent question: Algorithm for finding the v=1 state of an H2O molecule I want the geometry (atomic positions) of the H2O molecule in the v=1 state. How are initial ...
Nidhi Tiwari's user avatar
5 votes
0 answers
69 views

What do Negative Atomic Orbital Contributions in a Mulliken Population Analysis mean?

I am performing a Mulliken population analysis (MPA) for a molecular system of interest (calculated with B3LYP/Def2-TZVP). I am analyzing the LCAO-MO coefficients/contributions associated with each &...
Kevin Freddo's user avatar
6 votes
2 answers
398 views

How may I solve the radial Schrödinger equation?

I want to solve the radial Schrodinger equation for a Carbon atom with all six electrons. The equation I want to solve is for $r>0$: $$[\frac{-\hbar^2}{2m}\frac{\partial^2}{\partial r^2}+ \frac{\...
L Maxime's user avatar
3 votes
2 answers
421 views

How do I draw perovskite structure with own without CIF file?

I just wonder if there are any chemistry drawing software to draw a hybrid perovskite structure ?
Cho-Hee's user avatar
  • 31
2 votes
0 answers
36 views

Help with understanding the method of MBD & MBD-NL

I am having a hard time understanding the steps of Tkatchenko's method of many-body dispersion (MBD) and nonlocal many-body dispersion (MBD-NL). I would greatly appreciate a detailed & clear ...
Reut S's user avatar
  • 21
6 votes
0 answers
125 views

Free energy calculation as a function of temperature over phase transition

I've run a molecular dynamics simulation (NVT) of a simple Lennard-Jones system of a few particles and I'm trying to calculate the Helmholtz free energy $\Delta F$ as a function of temperature over ...
napadia's user avatar
  • 121
2 votes
0 answers
17 views

Can I define molecular units on NBO3.1 or NBO6.0?

I'm studying donor-acceptor charge transfer (CT) process between tetrakis(m2-acetato)-di-Wolframium (acceptor) with an acetonitrile (donor) at the B3LYP-D3BJ/def2-TZVPD level of theory. The W···N ...
Juandiego Velasquez Benites's user avatar
2 votes
0 answers
42 views

How to set up a calculation including dummy atoms in Dalton Quantum Chemistry Package?

I want to plot a magnetic shielding isosurface around benzene molecule, for that, I prepared a 100 atom grid keeping benzene at the center. At each grid point there is a dummy atom (X with charge=0.0)....
MeliodusSama's user avatar
4 votes
1 answer
233 views

Finding HOMO/LUMO from SCF calculation: VASP

I'm running some SCF calculations in VASP, and when looking at the OUTCAR, I see that for each KPOINT there is a slightly different value for the HOMO/LUMO (looking at Band No. and Occupation values, ...
lzzard's user avatar
  • 123
6 votes
1 answer
94 views

Is it essential to include solvent cage effect in radical reactions?

My question is straightforward and is outlined in the post title: Is it essential to include the solvent cage effect in radical reactions during the computational estimation of Gibbs free energies and ...
farmaceut's user avatar
4 votes
0 answers
23 views

How to evaluate excited state MO coefficients using Dalton Pacakge?

I need the excited state (T1) wavefunction associated with my benzene molecule, but even after trying multiple times using multiple input formats, I am not able to find the correct input to evaluate ...
compcal's user avatar
  • 93
10 votes
2 answers
97 views

Most detailed molecule representation format

I'd like to represent and save molecules at a more detailed level than an InChI, such that I can include metastable molecules with electrons at specific excitations (for example, singlet vs triplet ...
Gert's user avatar
  • 103
5 votes
1 answer
141 views

How to convert Dalton Output FIle (.out) to Multiwfn input file (.wfn)?

Cross-posted on Chem.SE. I just started with dalton and facing quite a few challenges in visualizing its output. I tried using Chemcraft, though its showing me some of the results like optimization ...
compcal's user avatar
  • 93
4 votes
0 answers
154 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
  • 246
2 votes
1 answer
235 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
38 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
1 vote
1 answer
51 views

When optimizing AMBER molecular dynamics parameters for protein-ligand interactions, how do I balance accuracy and efficiency?

Are there established practices for fine-tuning AMBER MD parameters in scenarios like mine, involving specific factors like mutant proteins or non-standard ligands? Has anyone successfully tackled ...
Don Aborah's user avatar

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