Questions tagged [software-recommendations]

Questions of the form "Is there a software that can do...?" and similar.

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7 votes
1 answer
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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
9 votes
0 answers
59 views

Software recommendation for drawing atomic structures

Anyone familiar what kind of software is used for drawing the atomic strucutres shown in the attached figure?
Jaafar Mehrez's user avatar
6 votes
2 answers
222 views

Are there scripts available for AIMD?

I need to determine which of two electrolyte is the best for a hydrogen fuel cell. As far as I understand, the first thing to do is to compute their ionic diffusion coefficient and to compare (the ...
Mjf T's user avatar
  • 61
5 votes
0 answers
37 views

How to determine the unit cell in heterostructure?

I’ve to create a heterostructure from two monolayers, for example, two graphene sheets or two metal layers. And then I want to rotate the first layer relative to another one by some angle. The ...
Victor's user avatar
  • 51
2 votes
1 answer
62 views

Building Fullerenes using scikit-nano package

I am trying to use scikit-nano package to build the various isomers of fullerenes. However, none of the methods that is presented in the manual seem to work for installing the package. These are the ...
Hemanth Haridas's user avatar
7 votes
1 answer
236 views

Better SIESTA workflows system?

Normally, I run all my SIESTA calculations manually and then go to post-processing the results, also manually. I would like to know which of the tools below is "better" (more complete?) in ...
Camps's user avatar
  • 23.3k
12 votes
2 answers
172 views

Are there any free or free quantum chemistry codes which can apply an external field gradient?

I wanted to apply a field gradient on my molecule and study some associated property. I'm able use MM point charges w.r.t a QM/MM scheme of doing things to produce a field gradient. But I was ...
Atom's user avatar
  • 945
2 votes
1 answer
52 views

How to write the REBO force field

I want to use the REBO-CHO force field to study graphene oxide using lammps. But I don't know how to create the input file with the parameters by reading the article or if there is a tutorial or ...
Matías Eduardo González Ozuna's user avatar
7 votes
1 answer
315 views

Why use PySCF/OpenMolcas instead of VASP/QuantumESPRESSO

While I am aware that VASP and QE are widely used for solid-state materials and PySCF/OpenMolcas are primarily designed for molecular systems. I want to know why should I use PySCF/OpenMolcas for ...
Jaafar Mehrez's user avatar
3 votes
0 answers
46 views

Running molecular docking simulation between two proteins

i did run docking simulation between two proteins on HADDOCK server but now i want to run a simulation of complex (protein+ligand and protein) is it possible with HADDOCK and how can i use it best ...
Imane Yamari's user avatar
5 votes
0 answers
46 views

Error correction software for VASP calculations

I am looking for error correction packages for VASP calculations that can be integrated into a high-throughput worfklow. Ideally the software would both find and propose fixes for errors at runtime, ...
kpoint's user avatar
  • 139
6 votes
3 answers
766 views

Which MD software is preferable for protein simulation?

I see that some free MD simulation software are available online. VMD NAMD LAMMPS OpenMM GROMACS Amber CHARMM Which one above is the most appropriate for protein simulation?
user366312's user avatar
  • 2,506
9 votes
1 answer
3k views

Software for quantum electrodynamics?

I've been reading some beginner books about quantum electrodynamics / quantum field theory (e.g. Feynman's QED book), and basically everything is done at the paper and pencil level. I'm curious if ...
Alex I's user avatar
  • 1,038
4 votes
1 answer
300 views

What's the best code for getting 1-particle and 2-particle density matrices with CCSD(T) in Python?

I have been using PySCF to calculate the 1-particle and 2-particle density matrix from ccsd(T) wavefunction using these modules in-built in PySCF make_rdm1() and <...
Pro's user avatar
  • 964
5 votes
0 answers
83 views

Packages that can model effects of intense electric fields from femtosecond compressed IR and EUV laser pulses on surfaces?

Laser-based and time-resolved ARPES are relatively1 new techniques to study atomic and especially electronic structure (necessarily) near crystal surfaces and of adsorbed 2D materials on those ...
uhoh's user avatar
  • 1,964
3 votes
1 answer
152 views

Script to draw one-dimensional PES comparing harmonic and anharmonic vibrational modes

This is an extension of a question I asked a little while ago: Software to draw one-dimensional PES including vibrational energy levels. I am asking the followup here based on advice received after ...
isolated matrix's user avatar
5 votes
1 answer
337 views

Python library to obtain atomic orbitals of atoms in the lowest energy state

I want to code an UHF code. Hence for each atom I need the lowest energy electronic configuration. Is there a python package/library that already does it?
mle's user avatar
  • 1,021
4 votes
1 answer
60 views

Software for storing information of large number of atomic structures into database file

Say I have a MD trajectory that contains a million snapshots (i.e. a million atomic structures). Each snapshot contains some calculated information (either by DFT or some force field) such as energy, ...
Shaun Han's user avatar
  • 1,845
5 votes
1 answer
88 views

What codes exist to calculate the second order susceptibility tensor (SHG) using DFT?

I was asked by a collaborator if I could calculate the second order susceptibility tensor for a structure. I have been principally using Vasp which includes linear response and hence the first order ...
user2155952's user avatar
4 votes
1 answer
194 views

How to do molecular dynamics with different isotopes of the same element?

In this paper, they separated knock-on damage (originating from the collision of the beam electrons with the nucleus of the target atom) from other radiation damage mechanisms (e.g., ionization damage ...
Vladislav Gladkikh's user avatar
3 votes
0 answers
44 views

Quantum ESPRESSO vs AMS [closed]

Both Quantum ESPRESSO and AMS (Amsterdam Modeling Suite) can be used to perform simulations of the materials and their properties. What are the differences between AMS and Quantum ESPRESSO? Is it ...
Zeina 's user avatar
  • 31
3 votes
0 answers
145 views

Electronic Structure Calculation with External Field

There are various programs for calculating energy states for molecules (ORCA, Gaussian, ...). Is there also software that allows the same simulations with an additional external potential (e.g. ...
Johny Dow's user avatar
4 votes
0 answers
90 views

Are there any open-source or free softwares for covalent docking of multiple ligands?

I am currently screening more than 2000 compounds virtually on Vina, but I would like to perform covalent docking. Unfortunately, Vina's functionality is limited as its requires manual designation of ...
biryaniboi's user avatar
6 votes
1 answer
129 views

Software for computing heat of formation

What are the the options available for software to compute heat of formation ($\Delta_f H$) of a given compound in your own system? (Preferably at no cost, like GAMESS.)
nightcod3r's user avatar
6 votes
1 answer
92 views

Which DFT code allows 'nonuniform grids for Brillouin zone integration'?

In this Phys. Rev. B article, Chen, Salzbrenner & Monserrat provide a [n]onuniform grids for Brillouin zone integration and interpolation. According to them, they were able to accelerate the ...
Abdul Muhaymin's user avatar
5 votes
1 answer
369 views

Which applications can convert multiple CIF files to multiple XYZ files all at once

I have tried a bunch of apps such as Mercury, OpenLabel but they cannot convert CIF files to XYZ files in bulk. I am also thinking of doing it in Python but just want to know if there's an app for ...
Rose Vanilla's user avatar
8 votes
3 answers
777 views

Duplicate structure in PDB format?

I have a PDB file. I want to duplicate this pdb file automatically instead of doing it manually. For example, if I visualize my PDB, I will find only one structure in (x,y,z). I want to have more ...
Abd-Elazeem Mohamed's user avatar
2 votes
0 answers
59 views

Figure-of-merit with Transiesta/TBtrans [closed]

Would it be possible to calculate the figure-of-merit: $$ZT =\frac{S^2\sigma}{\kappa}T,\tag{1}$$ with Transiesta and TBTrans? If not, which other programs can be used? I've only read about Gollum.
Laura's user avatar
  • 1,187
8 votes
1 answer
1k views

Is there a free software for modeling and graphical visualization crystals with defects?

At real situation, it can happen, that a crystal can have defects, for instance, some of them are point defects — Schottky, Frenkel defects, line defects — dislocations, planar defects — grain ...
SFriendly's user avatar
  • 897
8 votes
1 answer
199 views

Quantum Chemistry software that can calculate nonadiabatic coupling vectors between excited states using DFT/TDDFT

I am looking for software that can calculate the first-order non-adiabatic coupling vector $$\vec \tau_{ij}=\langle \varphi_i|\nabla_R\varphi_j\rangle$$ between excited electronic singlet states using ...
Hans Wurst's user avatar
3 votes
1 answer
924 views

Why Windows is not showing in the Dual-Boot menu and boot into Ubuntu directly? [closed]

It's been more than a month that I installed Ubuntu 20.04 on a desktop along side with windows (Probably 10 or 11) that was already on the desktop. Now I noticed that the computer boot directly into ...
Camilla's user avatar
  • 2,119
10 votes
2 answers
831 views

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. I do not have any clue to explain why ...
M06-2x's user avatar
  • 906
7 votes
0 answers
69 views

Get kinetic diameter of a molecule [closed]

I want to calculate the kinetic diameter of a molecule to estimate if it can fit inside a pore/channel of a microporous material. Do you know any software that would allow me to do this? I've seen a ...
cbornes's user avatar
  • 91
6 votes
1 answer
575 views

How can I predict the time of a simulation using Quantum ESPRESSO?

I performed a vc-relax calculation with hybrid functional on a 2 atoms material using the command ...
Camilla's user avatar
  • 2,119
4 votes
1 answer
81 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?
Jellium mind's user avatar
6 votes
1 answer
241 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 ...
Alexander Kalian's user avatar
4 votes
1 answer
78 views

Program to classify structures of different composition?

Is there a program to classify and compare structures with different composition? I want to compare e.g. structure_1 with composition [2,1,4] and structure_2 with composition [16,8,32]. Maybe both ...
leire's user avatar
  • 183
3 votes
1 answer
52 views

What package do I use to model a material and get the LAMMPS data file as an output?

VMD has a nanotube builder that I can use to build CNT and then using topotools I am able to produce the data file for LAMMPS. For my specific research I need to create a fake CNT with triangular ...
Delaram Nematollahi's user avatar
5 votes
1 answer
270 views

What is a good software for computational electrochemistry?

I am thinking about working on computational electrochemistry for a limited subject and don't have a huge amount of time I can invest to explore different software. The JDFTx software seems like a ...
Elie H's user avatar
  • 1,412
7 votes
1 answer
289 views

Ab-initio molecular dynamics of liquid systems: best tools and resources

I have been studying liquid systems (particularly deep eutectic solvents) using classical molecular dynamics (MD) simulations. The main drawback of classical MD is the arbitrariness of the potential ...
user35952's user avatar
  • 333
4 votes
1 answer
303 views

Is there any free software that helps to know specific charge densities or ELFs at any position of the material?

Can anyone suggest some free software that can visualize the charge density and/or electron localization function (ELF)? More importantly, can we determine/know those values (charge density and/or ELF)...
Sak's user avatar
  • 889
11 votes
1 answer
422 views

Software recommendations to construct band structures using tight binding

I am at the beginning of computational materials modeling. My objective is to calculate the electrical conductivity of a system that consists of several thousand atoms, and running DFT calculations is ...
wenu's user avatar
  • 113
6 votes
1 answer
315 views

Is it possible to recover the protein structure after conversions PDB->XYZ->PDB?

Let suppose that, for a given reason, a PDB file (with all the residues/chains/heteratom/cofactor/ligand information inside) is converted to a XYZ file. Doing that, all protein information is lost. ...
Camps's user avatar
  • 23.3k
6 votes
2 answers
1k views

A python compatible GUI chemical drawing library/software

So, I am developing a GUI for a python computational chemistry software (with PyQt5). The Qt part of the GUI will handle running the python software (calling the proper functions with proper arguments ...
S R Maiti's user avatar
  • 6,841
3 votes
0 answers
95 views

How to get started modeling liquid crystals? [closed]

I am an experimentalist who is interested in getting hands on experience with how simulations play into our understanding of liquid crystal formation. I have tried to read several reviews on the topic ...
Yetinsyny's user avatar
6 votes
1 answer
491 views

Free Graphical User Interface to prepare inputs for LAMMPS

Searching the LAMMPS site, I found some software capable to prepare LAMMPS inputs but they are not free and other software to analyze the output. I would like to know other package (with Graphical ...
Camps's user avatar
  • 23.3k
6 votes
1 answer
325 views

Software for Molecular Dynamics in Material Science

I would like to know available software that can do Molecular Dynamics (MD) simulations for any type of system, specifically inorganic and organic ones. The must cited MD packages (GROMACS, AMBER, ...
Camps's user avatar
  • 23.3k
3 votes
1 answer
67 views

Perform energy minimization of multiple models of protein-dna complexes

Is there a software/standalone tool that can perform energy minimization of a large number of protein-dna complex models (more than 1000)? I know of GROMACS or Chimera or the online servers but is ...
Lily Sharpton's user avatar
7 votes
0 answers
176 views

How to make an idealized infinite alpha helix or beta sheet?

I'm interested in studying some simple periodic model systems representing proteins. For that I'd like to make pdb files of an alpha helix or beta sheet with idealized coordinates which is infinitely ...
Alex I's user avatar
  • 1,038
15 votes
3 answers
1k views

Is there a simple free working code that implements Hartree–Fock or DFT?

Is there somewhere in the internet a good simple free working code (with a minimal number of lines in its presentation) that implements a calculation of eigenvalues with Hartree–Fock (or DFT) ...
SFriendly's user avatar
  • 897