10
votes
Accepted
Software for quantum electrodynamics?
GRASP
Allow me to introduce you to GRASP, a software that was written largely by now 92-year-old Ian Grant and now 94-year old (5 days from now) Charlotte Froese Fischer whose PhD supervisor was ...
- 33.6k
9
votes
Accepted
Duplicate structure in PDB format?
You can use Packmol to achieve this. Below is an example script
...
- 1,291
9
votes
Accepted
What is a good software for computational electrochemistry?
I'm a computational electrochemistry researcher and I collaborate with the developers of JDFTx and use it as my main driver. The primary reason to use JDFTx is its built-in support for grand canonical ...
- 106
8
votes
Free and optimized code for Hartree-Fock calculation in solids
Quantum ESPRESSO (QE) is a plane wave basis and various types of pseudopotential-based density functional theory (DFT) code. The PWscf package in it can perform both DFT and Hartree-Fock calculations. ...
- 2,101
8
votes
Duplicate structure in PDB format?
This can also be done in VMD using Tcl scripts. The only requirements are that you have a PSF and PDB file for the structure that you want to replicate.
...
- 2,762
8
votes
Accepted
Python library to obtain atomic orbitals of atoms in the lowest energy state
Mendeleev
You can use a python library called Mendeleev. Below is an example of a Silicon atom.
...
- 2,895
8
votes
Accepted
Is there a free software for modeling and graphical visualization crystals with defects?
For point defects like a Schottky pair, you can get the defect formation energies from DFT calculations at 0 K or from AIMD calculations at finite temperatures. For these, you can use codes like VASP ...
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7
votes
Duplicate structure in PDB format?
This can be achieved with Python. I will demonstrate it with a simple molecule : methanol.
The PDB file of methanol I used looks like this:
...
- 2,895
6
votes
Which DFT code allows 'nonuniform grids for Brillouin zone integration'?
CASTEP allows you to give it any k-points you like, and I expect other simulations codes do as well. All you need are the k-point coordinates and the integration weights, and the DFT software should ...
- 6,582
6
votes
A python compatible GUI chemical drawing library/software
You can use RDkit to draw 2D structures of molecules.
You can use RDkit + py3Dmol to draw 3d structures of molecules.
You can install them with pip like this:
...
- 2,895
6
votes
Free and optimized code for Hartree-Fock calculation in solids
I am looking for a free code for Hartree-Fock calculations in solids especially a code optimized (quite fast) compared to Pyscf which is quite slow and unstable.
PySCF is in general one of the ...
- 18k
5
votes
Accepted
How can I predict the time of a simulation using Quantum ESPRESSO?
TL;DR
There were a few issues with the input file and the way OP was running the code.
Longer Answer
OP had been using --oversubscribe flag hoping to use all the 16 virtual processors available on ...
- 2,762
5
votes
Ab-initio molecular dynamics of liquid systems: best tools and resources
CP2K
CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially ...
- 890
5
votes
Accepted
Software for storing information of large number of atomic structures into database file
One of the more recent options for the xyz file format is bqbtool by Martin Brehm, which significantly compresses the trajectory files by factor of 20~30 using a lossless compression scheme. One of ...
- 2,262
5
votes
Accepted
Quantum Chemistry software that can calculate nonadiabatic coupling vectors between excited states using DFT/TDDFT
The BDF program (https://bdf-manual.readthedocs.io/en/latest/; the English manual is under ongoing translation from Chinese. For a purely English but older version, see http://182.92.69.169:7226/...
- 9,076
5
votes
Which MD software is preferable for protein simulation?
There is no one size fits all answer here. The best answer depends on exactly what kind of protein simulation you'd like to perform. In particular, a few points to consider:
What force field you want ...
- 890
4
votes
Accepted
How to do molecular dynamics with different isotopes of the same element?
The answer is relatively simple, the neutrons do not directly contribute to anything electronically in the calculation, so the different isotopes are only different in terms of their masses / motion. ...
- 10.8k
4
votes
Is there any free software that helps to know specific charge densities or ELFs at any position of the material?
Yes, for example the Python package chemtools gives several examples of calculating the ELF from a Gaussian cube or similar wavefunction file.
At the moment, it will generate a Gaussian-compatible ...
- 9,045
4
votes
Script to draw one-dimensional PES comparing harmonic and anharmonic vibrational modes
A script that works for arbitrary potentials
My script has produced the following figures for this paper.
Simple single-well potential:
Double-minimum potential with a small barrier and a "shelf&...
- 33.6k
3
votes
Which Python packages, APIs or online databases may be used for a Python script to find bond dissociation energy between two arbitrary atoms?
PySCF
Bond dissociation energies are either found by laboratory experiments followed by spectroscopic analysis, or by ab initio calculations. Secondary research could be done to find bond dissociation ...
- 33.6k
3
votes
What package do I use to model a material and get the LAMMPS data file as an output?
First, can you clarify what you mean by "it explodes"? Have you ensured that there are no overlaps in your simulation and that the force-field parameters are correct?
Moltemplate is another ...
- 101
3
votes
Lennard Jones Clusters in Python
Potential
The Lennard-Jones potential has a simple form:
$$ V_{\rm LJ} (r) = 4\epsilon \left[ \left( \frac \sigma r \right)^{12} - \left( \frac \sigma r \right)^{6} \right]. $$
In python, this could ...
- 18k
3
votes
Programs/Libraries for calculating solvent excluded surface and excluded volume
Gepol93 is a FORTRAN library which computes three kinds of envelope surfaces :
Van Der Waals molecular surface
Accessible molecular surface
Solvent Excluding surface
There is also a python library ...
- 2,895
2
votes
Recommended code to do XAS/XES/RIXS calculations with?
Adding to wzkchem5's answer, you might also consider using Quanty. The program is a many body script language based on Lua that allows you to calculate XAS, NIXS and RIXS spectra, among other things. ...
- 31
2
votes
What software is available to do molecular dynamics on Windows?
NAMD
A MD simulation software which can run any system but has been particularly developed for the target audience that study biomolecular systems (proteins, lipid bilayers, etc.)
They have multiple ...
- 331
2
votes
Any software that can model eddy currents?
I found couple of tools online. Here I collate the ones I think are relevant:
MEMEP3Dtool:
Three-dimensional (3D) electro-magnetic modeling tool for superconductors and normal conductors using the ...
- 2,895
2
votes
Program to classify structures of different composition?
You may want to look into cluster expansion codes because they generally have a robust structure generation/mapping system. The general idea with this type of code is that you start with a particular ...
- 139
2
votes
Software for computing heat of formation
Gaussian and ORCA can calculate the heat as well as free energies of formation of a given system.
- 306
2
votes
Accepted
Which applications can convert multiple CIF files to multiple XYZ files all at once
ASE
You can use the ase python library to achieve this.
I tested the following code with 3 CIF files obtained from the Crystallographic Open Data: 1569089, 1000017, 1000003 and it produces their ...
- 2,895
2
votes
Why Windows is not showing in the Dual-Boot menu and boot into Ubuntu directly?
You can try this tool to regenerate GRUB :
https://help.ubuntu.com/community/Boot-Repair
And fix the dual boot. For Windows only :
MBR Repair!
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Only top scored, non community-wiki answers of a minimum length are eligible