All Questions
2,911
questions
1
vote
0
answers
7
views
Quantum ESPRESSO installation
People, can someone please help me how to solve this problem with QE 7.0 installation:
- 351
2
votes
0
answers
11
views
Reading DCD files using Python without using third party packages?
I am trying to read a NAMD DCD file using Python. Following the code given at here to read DCD files using Fortran, I have written the following code snippet to read the header section of the DCD file....
- 725
1
vote
0
answers
14
views
Gromacs simulation with 100 copies of same ligand appears weird
I'm a gromacs noob, so I appreciate your patience. I tried simulating the interaction of a protein with 100 copies of the same ligand, in water. The workflow I used is attached here as a picture. The ...
- 51
1
vote
1
answer
33
views
What is the difference between relax and multiple scf calculation in Quantum ESPRESSO?
Relaxation calculation gives us the ionic position of the relaxed structure. Now instead of doing a relaxation calculation, if I do fixed point self-consistent field (scf) calculation for varying ...
- 660
1
vote
0
answers
13
views
ASE: Receiving error on implimenting ase cellpar_to_cell method
I am getting the following error while implementing ase cell method. I am not able to understand where is it going wrong, although I think it has to do something with the values I am getting for cell.
...
- 115
4
votes
1
answer
40
views
Choosing the right basis set for describing vdW-interactions with DFT-D3
I want to do some DFT calculations for structures of protonated alkaloid dimers. I know that a method of choice when vdW interactions are involved is the use of dispersion corrections. But now I am ...
- 489
6
votes
2
answers
205
views
Change cif file into vesta format
I have 100 .cif files.
I want to convert them all to .vesta files through vesta software (https://jp-minerals.org/vesta/en/download.html).
I know I can choose them one by one and convert them.
Is ...
- 61
6
votes
2
answers
62
views
Density Functional Perturbation Theory
What is the difference between density functional perturbation theory (DFPT) and many-body perturbation theory (MBPT)? Also, please help me understand why approximations like PBEsol are considered as ...
- 375
5
votes
2
answers
953
views
How can I run my calculations on a remote server?
I'm going to use a more powerful server to run my simulations on it using a remote control software (The server is in another building). It's my first time to try that.
What are the things that I ...
- 855
4
votes
0
answers
24
views
Comparing stability of phases under constant pressure
I have used DFT to calculate the internal energy of a couple of different phases at 0K. As I would also like to compare the relative stability of the phases at finite temperature, I have also computed ...
- 41
3
votes
0
answers
26
views
Compositional SMILES data
I am interested to know if it is possible to encode compositional information in SMILES strings or other structural identifiers.
For instance, in generating a SMILES string when combining two ...
- 31
3
votes
0
answers
18
views
How are reconstructed surfaces named?
I am trying to understand the terminology of reconstructed surfaces.
Simple surfaces such as 2x2 or 1x1 make sense to me. For instance, figure 1 of the paper https://doi.org/10.1063/1.1574798 shows a ...
- 761
5
votes
1
answer
531
views
Why does my zincblende structure not look cubic?
The structure of my material is zincblende. So normally the structure is cubic. However, when I open the primitive cell with xcrysden it dosen't look 100% cubic. It's a little bit inclined. Also when ...
- 855
4
votes
2
answers
44
views
When and why are torques needed in molecular dynamics simulations?
I have seen that many MD simulations compute the torques due to dipole-dipole interactions and other interactions. I understand that there is a torque on a dipole in an electric field. I don't ...
- 3,299
3
votes
0
answers
12
views
How to change cell shape during calculations in LAMMPS?
I was doing some calculations using LAMMPS and wondered if there was a way to change the cell shape during npt or nvt calculations (in the latter, changing the cell shape while keeping the volume ...
- 689
2
votes
0
answers
24
views
Why do I get very intense picks when I use PBE0 with NC PP?
I used PBE0 to get projected density of states using norm-conserving pseudopotentials with Quantum ESPRESSO. I found very intense picks (scf -> projwfc ) compared to the ones that I found using ...
- 855
2
votes
0
answers
31
views
4
votes
0
answers
36
views
PySCF calcuation of 'one-index' electrostatic (Hartree) potential
I'm trying to calculate the electrostatic (Hartree) potential corresponding to a single (auxiliary) GTO:
$$v_i({\bf r_1}) = \int d{\bf r}_2~ \frac{\phi_i ({\bf r}_2)}{r_{12}}$$
[Please note that $\...
- 41
2
votes
0
answers
39
views
Computation of thermodynamic functions of molecules by molecular parameters
I want to implement in my program Chemcraft the computation of entropy and Gibbs energy of molecules in approximation "rigid rotor - harmonic oscillator", by the molecular parameters (...
- 136
1
vote
0
answers
41
views
How to determine high-symmetry points in case of PBE0 using Quantum ESPRESSO?
Normally when we use PBE-GGA as an approximation we can determine the high symmetry points in x coordinate from the output file of bands.x calculation . But in the ...
- 855
3
votes
1
answer
46
views
VASP calculation error
I got the error when running Vasp Calculation: Error EDDDAV: Call to ZHEGV failed. Returncode = 11 1 1. Can any one help me solve this problem?
- 61
2
votes
0
answers
53
views
DFT calculations [duplicate]
What is the best way to learn DFT (Density Functional Theory) for beginners?
I want to learn DFT (both simulation and theory). I am a beginners in this field. What is the best way to learn it?
- 61
4
votes
2
answers
264
views
What's the meaning of k-points with weight zero?
In a post from the Quantum Espresso mailing list, a user suggests adding k-points with weight zero to an SCF calculation as a workaround to allow bandstructure to be computed using a hybrid functional....
- 855
5
votes
1
answer
94
views
gyration radius of short freely jointed chain with excluded volume
The freely jointed chain model without excluded volume has the following gyration radius,
$$
\langle R_g^2 \rangle=\frac{1}{6}\frac{N+2}{N+1}Na^2
$$
where $N$ is the number of bonds and $a$ their ...
4
votes
0
answers
65
views
How do I get openMPI to run with gromacs?
When I run the command
mpirun -np 48 mdrun_mpi -deffnm md -v, the software works with no error, but it only runs as fast as when I'm using 1 CPU (the computer I'm ...
- 51
3
votes
1
answer
60
views
Energy balance in a molecular dynamics simulation with ghost atoms and periodic boundary conditions?
I am performing a simulation in LAMMPS with granules (DEM) and I had a question regarding the conservation of energy. If an interaction happens where one granule is in the simulation box and the other ...
4
votes
0
answers
52
views
Absorption spectra with Gaussian
I want to calculate the absorption spectra of molecules (and possibly ions) with TD-DFT.
I have used Gaussian in the past and, to my knowledge, the application of TD-DFT is implemented in this code. ...
- 689
5
votes
1
answer
120
views
Extracting band structure data using Boltztrap for Quantum ESPRESSO
I used PBE0 in my calculations using Quantum ESPRESSO . I have ran a scf calculation then I used Boltztrap by running the command btp2 -vv interpolate -m 3 ./ then <...
- 855
6
votes
3
answers
279
views
Using OpenBabel's gen3d in a Python notebook
I want to preface this by saying I am really new to computational chemistry and this kind of programming in general, but I am having real trouble figuring out how to use OpenBabel's ...
- 63
5
votes
1
answer
155
views
Constrained optimisation on a hypersphere
I am currently trying to implement a GS2 (Gonzalez-Schlegel second order) IRC algorithm in a python code. I am following the original paper ref(1).
The main problem is in the constrained optimisation ...
- 6,216
3
votes
0
answers
83
views
Layer detection in a crystal structure
Context
I have two images from a Monte Carlo Basin Hopping where silicon (in yellow) is getting replaced by germanium (in blue). Both have 32 germanium atoms at Si/Ge = 2.5; only the Ge distribution ...
- 783
4
votes
1
answer
78
views
How can I transform my unit cell positions to cartesian coordinates?
I have a structure with the parameters bellow:
...
- 855
4
votes
1
answer
87
views
How can I build the wheels necessary for a quick installation of PySCFad on a "compute node"?
The following is the procedure I have been following:
Install PySCFad
...
- 30.9k
6
votes
2
answers
220
views
Can someone guide me on how to get the k-point file for a VASP simulation?
I have a system with box dimensions of 21.0 * 21.0 * 80.0 for x,y and z directions. How may I generate the KPOINTs mesh for this system for VASP simulation? Any reference on this is hugely appreciated....
- 101
4
votes
1
answer
45
views
Any software that can model eddy currents?
Is there any software on metals that can predicts orbital or induced currents in metals in the presence of a magnetic field or electromagnetic waves?
- 332
4
votes
1
answer
71
views
VASP with VDW dispersion corrections for a large system
I have been trying to find the binding energy of a water molecule with a crystalline silica slab and want to use vasp. whenever I try to use vasp for this purpose i get this error. Also, can someone ...
- 101
5
votes
1
answer
85
views
Calculate deprotonation energy or Gibbs free energy of acids
I'm delving into the world of superacids, acids with an acid strength greater than that of sulfuric acid at 100%. I've recently encountered some computational papers which suggest that the ...
- 343
5
votes
1
answer
236
views
How to model an isolated molecule with Quantum ESPRESSO?
I am trying to model isolated structures such as quantum dots or molecules in Quantum ESPRESSO (QE).
QE uses 3D periodic boundary conditions (PBC) by default. That's why in order to reduce any ...
- 660
2
votes
0
answers
31
views
How to add the scissor operator in Quantum ESPRESSO input?
I want to calculate the optical, transport and electronic properties of my material. GGA underestimate the bandgap.
I tried GGA+U but the bandgap is still underestimated and also when I tried to use ...
- 855
3
votes
0
answers
51
views
Calculation of Carbon Quantum Dots using Quantum ESPRESSO
I have build a carbon quantum dots model based on this paper. The model looks like this.
I have calculated the density of states of the system, but does not get a desired plot as written on the paper,...
- 91
4
votes
0
answers
20
views
Using LAMMPS and VMD to analyze a new structure
I have a new structure that I want to analyze (lets just call it a shape). For the shape, I have the coordinates that make it up. I even have a tcl script in VMD that allows me to create the shape ...
- 41
5
votes
1
answer
166
views
Which Python packages, APIs or online databases may be used for a Python script to find bond dissociation energy between two arbitrary atoms?
Let us say that I wish to create a function that may do the following:
>>> find_bond_energy(atom1="C", atom2="O", order=3)
1072 kJ/mol
...
- 151
4
votes
0
answers
37
views
Where can I find the MASTANI-2014 tutorial files?
There was a two-week summer school on Density Functional Theory using Quantum ESPRESSO in the summer of 2014 organized by The Abdus Salam International Centre for Theoretical Physics (ICTP), jointly ...
- 660
5
votes
1
answer
72
views
Unexpected atoms while working with XYZ files in rdkit
I am processing some XYZ files using the rdkit library in python. I came across some strange/unexpected behaviour.
Consider a sample XYZ file of methanol with ...
- 1,117
5
votes
1
answer
118
views
Can specifications of a second-order phase transition of a solid be obtained with the Hartree-Fock (or DFT) calculation?
At some temperature a crystal lattice of a solid can be rearranged or to say it more precise - got new positions of its cores. This phenomenon is well-known to be called a second-order phase ...
- 601
3
votes
0
answers
43
views
How to calculate the formation energy of a defect using the unit cell?
I want to dope CuI conventional unit cell using Quantum ESPRESSO.
In previous papers they used different formulas of defect formation energies,and they use supercell. So I'm confused.
What's the ...
- 855
5
votes
1
answer
79
views
Regarding SISL package of siesta
I want to visualise MPSH (molecular projected self-consistent Hamiltonian) orbitals using SISL package of siesta, is there any manual or guide for it.
I have searched in internet but didn't get any ...
- 307
3
votes
1
answer
32
views
External magnetic field in magnetic shielding calculations
There is this method called nucleus-independent chemical shift (NICS) to calculate the magnetic shielding values at different spatial coordinates of a molecular system. It can be used to estimate the ...
- 489
3
votes
0
answers
15
views
Issue with getting pw_bands output file for ws2
After running the input pw_bands.in file execution is not stopping even after 10hrs , and the output is not updating anything further after 1 min of the output.
- 31
6
votes
2
answers
74
views
NBO analysis of potentially hypervalent compounds
I know that one can determine which type of bond is present between different atoms in a molecule by analyzing the output of an NBO analysis. Furthermore the second order perturbation theory analysis ...
- 489