All Questions

Filter by
Sorted by
Tagged with
1 vote
0 answers
14 views

Diagnosing faulty bands calculation

Using QE v6.7, I computed the bands structure of CsPbI3 and I am not happy with the results. The Problem While performing the nscf calculation I kept getting the ...
R Walser's user avatar
  • 315
4 votes
0 answers
28 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
4 votes
0 answers
29 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
  • 613
5 votes
1 answer
70 views

Comprehensive tutorial for CASTEP without Material Studio Visualizer

I started using CASTEP (academic license). I have a little experience with Material Studio Visualizer, but now I cannot afford it. Would you please suggest nice tutorial(s) for beginners to CASTEP on ...
heartfield's user avatar
2 votes
0 answers
31 views

Why do constrained geometry scans behave differently based on the starting conformation?

In relation to my previous questions here and here, I figured that orca would be a better choice for my calculations. This was partly due to the inability of psi4 to converge to a minimum at many of ...
Hemanth Haridas's user avatar
5 votes
1 answer
155 views

What is a good material to use in a blood vessel model? [closed]

I'm trying to create a training model for neurosurgery that utilizes 3D printed bones and associated vessels. I intend to use a pump to run artifical blood through these vessels. So they need to be ...
Bilal Bahadır Akbulut's user avatar
3 votes
0 answers
35 views

t2g-eg resolved PDOS analysis

I was attempting to analyze the t2g-eg resolved PDOS for transition metal-containing systems. Here, I have taken an example where three types of transition metals are present in octahedral geometry: $...
Kratos1611's user avatar
2 votes
0 answers
12 views

Colour coding modifier in Ovito

I have what is probably a silly question about the colour coding modifier. I am using it to begin the analysis of my LAMMPS trajectory files by colour coding the potential energy per atom and entropy ...
Baba Booey's user avatar
5 votes
3 answers
160 views

Different results from MP2 calculations on same geometry in ORCA

I am trying to do a segmented potential energy scan around a dihedral for a molecule. I have optimized the geometry to a minima, and the scan runs from [-180, 180] in steps of two points at a time. ...
Hemanth Haridas's user avatar
3 votes
0 answers
39 views

Number of atoms is different in xyz file and POSCAR file. Some atom positions of listed in the xyz are missing too in POSCAR. Why?

I am trying to make POSCAR file and xyz file using vasp for NbReSi compound using VESTA. However, I notice that the number of atoms for xyz file is given as 41 whereas for POSCAR is it 36. Further, I ...
Nilabja Kanti Sarkar's user avatar
7 votes
1 answer
107 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
36 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
2 votes
1 answer
35 views

Tool for plotting spin texture

Is there a tool that can plot a spin texture graph like these two examples below: Or does anyone know an example using matplotlib?
Gabriel Elyas's user avatar
2 votes
0 answers
18 views

Making a mirror structure of a structure from Quantum ESPRESSO input file

I have two Quantum ESPRESSO input files. They are supposed to be mirror like. I want to check whether they are actually mirror or not. Is there any tool or way to convert one structure to it's mirror ...
Sak's user avatar
  • 909
1 vote
0 answers
17 views

ASE GPAW variable cell relaxation

Ive been trying to do a vc relax using GPAW and ASE on the BaTiO3 unitcell. The input file is as below: ...
Atom's user avatar
  • 1,015
0 votes
0 answers
29 views

Weird time-averaged temperature v.s. distance figure result

I am computing the thermal conductance for the structure 'Al2O3-bilayer graphene-Al2O3' along the z axis, with the following input file. ...
Kieran's user avatar
  • 571
4 votes
1 answer
63 views

Causes of Straight Bands in Phonon Dispersion Calculations

In my phonon calculation utilizing DFPT in VASP for a monolayer material with space group 187, I've noticed that while most of the phonon bands are positive, two of them appear to be straight. What ...
Farah Shehzadi's user avatar
4 votes
1 answer
85 views

Cut off convergence with Hubbard and long-range interactions on VASP

I have a multilayer structure formed by C,O,H,N and Cu, for a total of 174 atoms. I am thus using U+J Hubbard methodology as well as Grimme corrections within VASP code. I am doing some convergence ...
Laura's user avatar
  • 1,227
3 votes
0 answers
36 views

Hydrogen bonding rate of relaxation on molecular dynamics

I am studying the works of Alenka Luzar on the hydrogen bonding kinetics in liquid water. Luzar defines an autocorrelation function c(t) that gives the probability that an hydrogen bond is intact at ...
horlust's user avatar
  • 163
4 votes
1 answer
47 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
3 votes
0 answers
11 views

Diblock building in Biovia material studio

I am trying to build polystyrene and polyethylenepropylene diblock chains. When I assign head and tail and build diblock chain I could see that the atom numbers get flipped, meaning that head and tail ...
Princy David's user avatar
4 votes
1 answer
40 views

Optimum number of CPUs to use for an efficient LAMMPS simulation

Are there any rules of thumb to optimize the number of CPUs to perform a LAMMPS simulation of a given size efficiently? For example, there are 32 cores under each node in my computational resource. ...
Kieran's user avatar
  • 571
2 votes
0 answers
15 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
0 answers
21 views

How can calculate length or coordinate of any molecule in different quantum state [like (rotational quantum state)j=2] with any software or code?

How can one determine the bond length of a diatomic or tri-atomic molecule(rot. state J=3 and vib. state v=2) from its ground state bond length (x angstrom) using computational tools or programming ...
Rubi Agrawal's user avatar
5 votes
2 answers
71 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
3 votes
0 answers
23 views

Installing Material Studio on Linux (CentOs cluster) for a non-root user

I am a beginner and want to install Material Studio in CentOs (version 7) cluster. Is there anyone have detailed tutorial or information for installing Material Studio in linux? My tries: I used ...
Martin's user avatar
  • 31
2 votes
1 answer
23 views

Problem with 'Thermo and fix ave not computed at compatible times' in LAMMPS

I followed the tutorial (https://github.com/lammps/lammps/blob/develop/examples/KAPPA/in.heat) to compute the thermal conductance of bilayer graphene sandwiched by Al2O3 on both sides along the z axis....
Kieran's user avatar
  • 571
3 votes
0 answers
34 views

'Invalid value encountered in scalar power' error in psi4 calculation

I am trying to do a potential energy scan across a dihedral angle of interest using psi4. The input file that I am using is copied below: ...
Hemanth Haridas's user avatar
3 votes
0 answers
46 views

Lost atoms in a lammps simulation

I am simulating the thermal conductance along the z axis for bilayer graphene sandwiched by Al2O3 system. This is my input setting. ...
Kieran's user avatar
  • 571
2 votes
0 answers
41 views

How to use interatomic potential in LAMMPS

This is my input file for the lammps simulation. ...
Kieran's user avatar
  • 571
3 votes
1 answer
52 views

what determines the 'Estimated total dynamical RAM ' in a Quantum Espresso calculation

As per my understandings the computer resources required for a DFT calculation increases by an order of three with the number of atoms. But as you can see in the output files given below the ...
Joyal sunny's user avatar
0 votes
1 answer
39 views

In which irreducible representations shall I put the electrons in an F atom in PySCF?

I’m looking to complete ROHF energy calculations in PySCF for the F atom. I need to update the irrep_nelec dictionary for F. I know that the one for the O atom is: ...
TheorVHP's user avatar
5 votes
1 answer
65 views

How to convert all structure coordinates in .traj file to separate .txt files (e.g. POSCAR format files)?

I am using the ACAT code for generating the structures. ...
Rubi Agrawal's user avatar
4 votes
0 answers
35 views

CDD on the surface of a slab and in other types of (finite) systems

What would be the appropriate method of calculating the difference in charges for this type of system? For composite systems it is usually something like: $$ \Delta\rho = \rho_{system}-\sum_{i=1}^{N}\...
Gabriel Elyas's user avatar
7 votes
1 answer
93 views

Calculated adsorption energy is too high in VASP

I am trying to calculate the adsorption energy of benzoic acid into a PtRu surface, but the energy that I am finding is too high (around 40eV). The reported values are around -2.0eV for this. Also, I ...
César Catizane's user avatar
7 votes
2 answers
190 views

How to add atom attribute molecule for each layer in LAMMPS?

I want to model several layers of hBN in LAMMPS. First, for two layers, I created a lammps data file from vasp POSCAR using atomsk. It is like this: ...
Vladislav Gladkikh's user avatar
7 votes
1 answer
226 views

Is there any software or Python library for visualizing higher-order Brillouin Zones of standard lattices?

I am looking for a software or Python library to help me visualize higher-order Brillouin Zones (BZs) of standard lattices like FCC, BCC, etc. I have already plotted the first BZ of an FCC lattice ...
Puspendu Rana's user avatar
5 votes
0 answers
14 views

Compound Bioactivity classification

I am trying to train a model to classify whether a compound is active or inactive looking at its SMILES. I have a table with 3 columns-InchiKey, SMILES, and activity-5300 rows in total -35 % of which ...
furkat's user avatar
  • 51
3 votes
1 answer
105 views

Is it possible to do a vc-relax calculation using GPAW?

I wanted to do a variable-cell relaxation calculation using GPAW (similar to the one present in quantum ESPRESSO). It would be nice if I could get pointers on how to approach this. ...
Atom's user avatar
  • 1,015
4 votes
1 answer
45 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
3 votes
0 answers
32 views

How to undo the periodic boundary conditions for supercell calculations

I am using Quantum Espresso to study defects in III-V materials, and recently I relaxed my defect system in a 64-atom supercell. Currently, I am trying to determine the ionic displacements relative to ...
Austin's user avatar
  • 61
2 votes
0 answers
15 views

Issue regarding self repeated .vasp structure of engineered graphite/graphene

When engineers the graphite and save it as.vasp format, it will give self periodically repeated structure. Still, the size of the cell is the same, but the structure repeated itself by huge numbers in ...
vikas's user avatar
  • 21
2 votes
0 answers
26 views

PDoS using mBJ in vasp

I have calculated the band structure of a compound using mBJ-LDA potential and plotted it using the p4vasp package. However, i am not able to get Partial DoS from these calculations. I have followed ...
Vivek Gusain's user avatar
4 votes
1 answer
118 views

Can we use Density Functional Theory (DFT) to calculate the second and third-order force constants of a slab?

If we aim to compute the surface phonon lifetime of a Cu(111) surface, the second and third-order force constants are essential (to put in Boltzmann transport equation). However, to my knowledge, it ...
James's user avatar
  • 41
1 vote
0 answers
38 views

How to Converge the CUTOFF and REL_CUTOFF

I'm doing the "How to Converge the CUTOFF and REL_CUTOFF" tutorial, but I can't get the results after cutoff_run.sh using .ssmp . The calculation cashes and end with the message below: ...
Inna's user avatar
  • 19
8 votes
3 answers
313 views

Hydrogen bonding autocorrelations

I am currently analyzing hydrogen bonding behaviour and kinetics with molecular dynamics simulations. I've been trying to compute autocorrelation functions for hydrogen bonds in a water system. Some ...
horlust's user avatar
  • 163
4 votes
2 answers
96 views

Options for automated Q-Chem input file generation

I have a big number of .xyz files which I plan to run using Q-Chem, and I was wondering if there were any options for automatically generating Q-Chem input files from these .xyz files. I know that ...
frobenius's user avatar
  • 133
3 votes
1 answer
134 views

Potential for LAMMPS Simulation

The system I want to simulate is a benzene ring molecule sandwiched by Al2O3 nano-rod on both sides along the z axis. There is no chemical bonding between benzene ring and the Al2O3 compound. I want ...
Kieran's user avatar
  • 571
4 votes
1 answer
59 views

Exploring Electronic Properties: Density of States (DOS) and Band Structure Analysis with Gnuplot?

How can one plot Density of States (DOS) and Band Structure using Gnuplot, and could you provide a sample script to accomplish this task effectively?
Farah Shehzadi's user avatar
2 votes
0 answers
43 views

how to do 2D material supercell convergence?

I do not have lattice parameter of my 2D MXene material, so i am doing convergence test of lattice parameter for a supercell 221 using the INCAR file. Firstly am I using the correct approach for ...
Khushi's user avatar
  • 21

15 30 50 per page
1
2 3 4 5
80