Questions tagged [software-recommendations]

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

Filter by
Sorted by
Tagged with
5 votes
1 answer
48 views

How to create the vector image of crystal structure?

I am trying to create a vector image of TiO2 crystal because all journals require vector images. When I build the model for calculation, I use ...
user avatar
  • 1,427
8 votes
4 answers
1k views

DFT code for simulating thousands of atoms in a supercell

I'm trying to simulate a supercell that contains thousands of atoms with the DFT method, but it seems VASP couldn't handle such a large system, its parallel efficiency is relatively low, when I try to ...
user avatar
  • 1,427
8 votes
2 answers
58 views

Any software that could do surface hopping?

I am trying to understand how to do the time-dependent simulation of the electron transfer, I find that the popular method is surface hopping, but I am not sure if there is any software that could ...
user avatar
  • 1,427
6 votes
1 answer
79 views

What software implements UFF

I am looking for common software packages that implement UFF ideally with an example of how to run it to calculate forces and energies. I see that Rdkit should be capable of doing this for example, ...
user avatar
3 votes
0 answers
39 views

EPR spectrum simulation

Can anyone recommend code (preferably open-source) for the simulation of EPR spectra from electronic structure calculations? I found EasySpin: EasySpin is an open-source MATLAB toolbox for simulating ...
user avatar
6 votes
1 answer
111 views

List of programs for post-CCSD(T) calculations

Implementations of CCSD(T) are almost too numerous to list, but CCSDT and CCSDT(Q) are much more rare. I have compiled a list of such programs below, and I would be interested to hear if anyone is ...
user avatar
  • 150
5 votes
1 answer
32 views

Which software can I use to model a nanotube with a triangular lattice shape and extract from it the lammps input file?

I am looking for a software to build my own chice of lattice nanotube and get the lammps input file for it. Do you have any suggestions?
user avatar
8 votes
1 answer
50 views

Any molecular codes to calculate non-local susceptibility?

I am interested in calculating the non-interacting non-local susceptibility for simple molecules. In principle, if you have a single Slater determinant, then you should just take a sum over the ...
user avatar
11 votes
0 answers
74 views

Calculating Core-Level Binding Energies (XPS) using DFT

I'm pretty new to DFT calculations but I'm trying to learn how XPS calculations are set up, particularly for open-shell molecular systems in common non-periodic DFT codes. A highly related secondary ...
user avatar
6 votes
2 answers
117 views

Similar (and still ongoing) services like TeleSpek IR simulator on the web?

A question about the IR absorption modi of diiron nonacarbonyl on chemistry.se found two answers. One of them provided an illustration with animated vibrations. In the 1990s, the Gasteiger group ...
user avatar
  • 1,457
6 votes
0 answers
46 views

Any Open-Source, Free Software That Can Be Used to Computationally Calculate Binding Affinity Between Two Molecules?

There are programs out there which calculate the binding affinity between a ligand and a target protein (Autodock 4, Autodock Vina, Chimera... etc). Is there any analogous program that can be used to ...
user avatar
  • 211
10 votes
1 answer
102 views

Recommendation of open source software that could build Heterostructure models visually?

I am looking for open-source software that could help me to build Heterostructure models visually, I've been working with BIOVIA Materials Studio before, but I got no valid license now, so I'd like to ...
user avatar
  • 1,427
6 votes
0 answers
65 views

Are there tools to calculate the electrical conductivity of nanostructures

Are there any free to use tools which can be used to calculate the electrical conductivity of nanostructured materials. The systems that I am interested in consist of several thousand atoms, and ...
user avatar
  • 2,454
10 votes
1 answer
191 views

Tools to Visualize Phonons

Software such as ChemCraft or GaussView is easy to find for vibrational calculations in gas phase, but I am finding it much more difficult to find good visualization software for phonons. I have ...
user avatar
10 votes
3 answers
300 views

How to plot molecules with angles and bond lengths

There are many programs out there where you pass an XYZ coordinate file and the program will give you a visualization of the molecule. I want to make a plot like the one in the picture, with bond ...
user avatar
9 votes
5 answers
268 views

Recommended software to open NetCDF files?

I found plenty of packages that open .nc files but all specifically catered to climate (meteorological) and geo-maps data. I would like to get suggestions of ...
user avatar
  • 18.5k
7 votes
2 answers
128 views

What software can be used for Crystal Surface Calculations?

I have been unable to find software for making surface calculations, so I currently perform surface calculations in LAMMPS by creating crystal structures in python, before rotating and cutting them ...
user avatar
  • 869
6 votes
0 answers
61 views

Simple code for polarizable force-field molecular dynamics?

I am interested in writing my own molecular dynamics code that uses a polarizable force-field. I am wondering if there are relatively simple "toy repositories" for these models such as is ...
user avatar
  • 1,040
4 votes
0 answers
65 views

A structural transformation package? [duplicate]

What are some of the structural (protein) transformation packages available, which can change a bond length, angle or dihedral?
user avatar
  • 1,301
8 votes
1 answer
92 views

Which software is suitable for visualizing the electron wavefunctions in a crystal?

I'd like to use the tight-binding model with a linear combination of atomic orbitals. It should show the full energy bands, as well as the spatial probability distribution for each eigenfunction of ...
user avatar
5 votes
1 answer
104 views

Software for generating ensembles of dimer pairs of organic molecules

For two organic molecules of essentially unlimited size (up to and including, and sometimes exceeding MW = 1000 g/mol), I would like to generate all possible dimer pairs in vacuum. The pairs may be ...
user avatar
  • 1,040
8 votes
2 answers
275 views

Building model of Graphene Oxide

I used to build some small molecules using Avogadro. Now, I want to build a large molecule, Graphene oxide which unfortunately doesn't have a definite structure with different levels of oxidation. Can ...
user avatar
9 votes
1 answer
201 views

What software can I use for gas adsorption calculations?

We are from a new research group working on matter modelling. Currently our work has focused mainly on classical Molecular Dynamics (MD), Lattice Dynamics (LD) and ab-initio methods. For these, we ...
user avatar
  • 2,454
6 votes
1 answer
70 views

How can I build an MoS2 nanoribbon?

Are there any codes available? What is the easiest way?
user avatar
  • 139
11 votes
1 answer
109 views

Guess cell parameters from atomic coordinates

I have a xyz file of a system that doesn't contain any cell information, but which has all its coordinates wrapped inside the same (triclinic) cell. I would like to ...
user avatar
  • 1,363
14 votes
1 answer
138 views

Looking for crystal generator library

I am looking for a C or a C++ library that can do crystal generation, that is, multiply unit cells in one or more directions with symmetry information. (in other words, generate supercells). I have ...
user avatar
  • 241
4 votes
0 answers
29 views

Discrete lattice polymer simulations

I am trying to develop phase coexistence curves for generic polymers. Of course, I can use standard Flory theory free energy functionals to do this, but I want to define my nearest neighbor polymer-...
user avatar
  • 3,697
5 votes
2 answers
335 views

Soil Modelling: Getting accurate Thermal Conductivity values

Context: We perform a lot of CFD (Computational Fluid Dynamics) modelling for our clients (geothermal, construction, general underground engineering, etc) where we have to model temperature flows and ...
user avatar
8 votes
1 answer
396 views

Given the adjacency matrix of a molecule, how can I get a graphical representation using only open source software?

In Huckel Method, by numbering the sp2 carbons in a molecule with conjugated double bonds, we can assemble its secular determinant in a form similar to the adjacency matrix of a graph. Taking trans-...
user avatar
  • 3,696
10 votes
3 answers
839 views

How can I learn LaTeX?

I have no experience in using Latex, but I am planning to use it for publishing purposes. Could you please recommend any resources that help me to learn in less time (at least the basics on how to ...
user avatar
  • 5,546
11 votes
2 answers
2k views

Which image format is best to use in a scientific paper?

When submitting a scientific paper written using LaTeX, to a journal, which high-quality image format do you usually use?
user avatar
  • 5,546
8 votes
1 answer
230 views

Structure visualization software for Windows

I have been using Quantum ESPRESSO for my calculations and I do most of my processing in Linux. Recently I bought a new laptop and it came with Windows and I need to keep it like that for several ...
user avatar
  • 181
15 votes
2 answers
371 views

What's the best quantum chemistry output parser for the command line?

This question is about tools like Open Babel. Are there any good command-line parsers for quantum chemistry program outputs? A good Python library could come in as a close second. I am interested e.g. ...
user avatar
  • 14.2k
9 votes
1 answer
589 views

How can we calculate the Gibbs free energy from first principles?

I am trying to calculate the Gibbs free energy for a bulk material. Since DFT ground state calculations give the energy at 0K, a temperature dependent part has to be added in this to obtain correct ...
user avatar
8 votes
0 answers
95 views

Tools for symbolic calculations of quantum transport using the Keldysh NEGF formalism [closed]

I am looking for tools for symbolic calculation of quantum transport or quantum mechanics that involves Keldysh NEGF (non-equilibrium Green's function) formalism. The closest tool I heard/seen is <...
user avatar
  • 181
5 votes
1 answer
79 views

List of software for creating random multi-component alloy inputs for DFT or MD

I'm looking for a list of tools similar to ATAT which are available for creating random multi-component alloy inputs for DFT/MD.
user avatar
  • 3,054
10 votes
0 answers
62 views

How to generate a complete set of doped (substituted) structures? [duplicate]

I'm trying to analyse doping in a certain material in low concentrations. I'm approaching the problem by taking crystallographic unit cell of that material, then expanding that to a 2x2x2 supercell ...
user avatar
6 votes
2 answers
465 views

Analytic Hessian at the level of full CI?

This is a follow-up question to my previous question: Computing analytic derivatives of molecular Hamiltonians obtained from solving Hartree-Fock equations. After looking at various quantum chemistry ...
user avatar
7 votes
0 answers
65 views

Molecular dynamics to reproduce dispersion interactions [closed]

I'm trying to simulate the behavior of chromophore molecules incorporated into a polymer under an external electric field. I've tried to use classical molecular dynamics (GROMACS) but it's unable to ...
user avatar
  • 2,293
8 votes
1 answer
348 views

Functional group detection for group contribution methods

I would like to be able to parse a molecule into its functional groups, and, also, know the number of occurrences of each. A similar question was asked on matter modelling specifically for xyz files. ...
user avatar
  • 3,810
9 votes
1 answer
70 views

Package for computing properties of excited vibrational states

We're starting to develop some calculations of the hyperfine parameters (electric field gradient, spin-rotation coupling, spin-spin coupling) with CFOUR, and we reached a limitation of the public ...
user avatar
  • 99
13 votes
1 answer
198 views

Generating numpy-compatible electron density from Molden / QC calculation

I'd like to use a variety of Python tools (e.g., matplotlib and Mayavi) to analyze orbitals plot electron density contours, etc. ...
user avatar
8 votes
1 answer
132 views

What are open source options to simulate kinematical electron diffraction patterns?

I tried using the python package diffsims. I get an image, but not a diffraction pattern I was expecting. ...
user avatar
  • 179
9 votes
0 answers
68 views

Software for calculating the mirror Chern number of 2D systems? [closed]

Can anyone please explain to me how can I calculate the mirror Chern number of a 2D system? I will be very thankful if you can refer me to a package or software which can directly perform mirror Chern ...
user avatar
  • 641
16 votes
2 answers
424 views

How should I organize and keep track of a huge number of calculations systematically?

Doing matter modeling generates vast amounts of data. We might most probably be working on different projects simultaneously. We definitely will have to revisit old data for revisions, post-processing,...
user avatar
  • 8,362
14 votes
1 answer
614 views

GUI for DFT calculations

I am a beginner in DFT. Can someone suggest a good DFT software with a GUI for simulating dipole moments and optical absorption spectra in an organic crystal? I have tried the Burai GUI of Quantum ...
user avatar
12 votes
2 answers
218 views

Is there some free software to do Frank-Condon analysis?

I know Gaussian 16 can do it, but are there some free programs that can? For simple excited state calculations using TD-DFT, we can use NWChem and Octopus. Can these do Franck-Condon factors?
user avatar
17 votes
2 answers
607 views

What are good tools for visualizing glide planes and screw axes?

While there are a few tools for visualizing crystal structures, I'm particularly curious to know tools for visualizing space group symmetry, including: screw axes glide planes I teach a class on ...
user avatar
8 votes
4 answers
1k views

How to create a lookup table of ϵ and σ values for Lennard-Jones Potentials?

So in my last question How may I calculate the bond length between two atoms? I mentioned that I want to use Lennard-Jones Potential to simulate atom/molecule interaction for my sandbox-game-like ...
user avatar
  • 552
8 votes
1 answer
166 views

Chimera or other software to perform protonation states of a protein

I want to perform a Molecular Docking between some ligands and a protein in different pH conditions. For this, I calculated the distance between atoms in different pH concentrations for the ligands, ...
user avatar
  • 367