Questions tagged [software-recommendations]

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

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34 votes
9 answers
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Is there a free package with robust CASSCF functionality?

Among free software packages, which one has robust CASSCF functionality? The FCI solver can be implemented in either way, e.g., direct solver, DMRG, etc.
Yingzhou Li's user avatar
  • 1,076
34 votes
5 answers
9k views

What is a good replacement for Gaussian?

When I started studying computational chemistry (circa 2007), my supervisor used to tell me about the controversy surrounding Gaussian, Inc. regarding the banning of researchers involved in the ...
1__'s user avatar
  • 503
28 votes
3 answers
3k views

How to "get my feet wet" in Density Functional Theory by simulating a water molecule using Python

I just saw I am a beginner in Density Functional Theory. What are some resources that could help me to learn the basics? and it reminded me that few years ago I'd asked How can I calculate the charge ...
uhoh's user avatar
  • 1,904
24 votes
0 answers
482 views

What are the tools available for point defects calculations? [closed]

It would be appreciated if you could explain one of the tools below (or another tool not listed), in the format used here (for example): What software will allow me to combine two images? What ...
Franksays's user avatar
  • 501
23 votes
6 answers
5k views

Is ARM64 the next big thing?

Considering how GPUs in matter modeling was first recognized in gaming devices like PlayStation, it is also interesting to consider whether ARM64 chips, which are the type of chips in modern smart ...
Cody Aldaz's user avatar
  • 7,997
22 votes
6 answers
4k views

What software is available to do molecular dynamics on Windows?

Is there a Windows-based molecular dynamics simulation software which is easy to use?
Papia Chowdhury's user avatar
21 votes
5 answers
4k views

What software will allow me to combine two images?

I have seen in many presentations and publications, things like a human on a molecule (for example). What software can do this? It's for a presentation I'm doing.
Savir's user avatar
  • 1,051
19 votes
0 answers
229 views

Is there a software that can do derivatives with respect to user defined vibrational modes?

I'm doing some property calculations that depend on a sum of derivatives of some quantity with respect to normal vibrational modes. I was hoping to find some physical intuition relating the type of ...
Tyberius's user avatar
  • 15.4k
17 votes
2 answers
668 views

Software for solving quantum systems in 1D and 2D

I'm looking to solve quantum system in 1D and 2D consisting of a large number of sites. What are the pros and cons of each package, and which package is more suitable for what type of calculations? ...
quanta's user avatar
  • 474
16 votes
2 answers
459 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,...
Thomas's user avatar
  • 8,952
16 votes
2 answers
893 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. ...
Susi Lehtola's user avatar
  • 18.4k
16 votes
2 answers
764 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 ...
Geoff Hutchison's user avatar
16 votes
1 answer
124 views

Which modelling package currently implements an AI derived force field?

I would like to use an AI-derived force field as they seemed to have lesser computational cost. Which simulation package (Gromacs, Amber, NAMD...) currently implement some of them?
BND's user avatar
  • 1,341
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
  • 877
15 votes
1 answer
493 views

Software recommendations for passivating structures

I am looking for an open-source library that allows to passivate a structure, ideally starting from a xyz-file. QuantumATK provides a function like this. However, this is not an option at the moment. ...
random01's user avatar
  • 171
14 votes
5 answers
3k views

DFT software package for a beginner?

I would like to do start doing some basic calculations using DFT. I am interested in solid state physics of strongly correlated materials in 3D (for example high temperature superconductors) or 2D (...
sintetico's user avatar
  • 241
14 votes
1 answer
503 views

Visualizing MD generated electron density cubes as trajectories

During an ab-inito MD simulation one can generate the electron density cube file which basically provides the electronic density data in a standard volumetric format as shown here. The file consists ...
mykd's user avatar
  • 2,282
14 votes
1 answer
168 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 ...
alfC's user avatar
  • 281
14 votes
1 answer
286 views

Is there a software that has implemented forces of TDDFT calculations for solids?

I'd like to investigate the structural relaxations of the excited state for periodic systems. BSE and TDDFT are two promising methods for this purpose. While there is a discussion on forces with BSE ...
Xiaoming Wang's user avatar
13 votes
3 answers
369 views

Are there any codes to study magnetic materials?

I have used a few codes for studying magnetic materials (specifically core-shell nanoparticles with an AFM shell and an FM core). These are: Vampire: For the calculation of curie temperature via ...
Anoop A Nair's user avatar
  • 4,458
13 votes
1 answer
152 views

GUI-based force field optimization with bond-typing

I am looking for a list of programs that support structure relaxations via molecular mechanics (e.g. via UFF) with the following conditions: The program is free (free with an academic license is okay)...
Andrew Rosen's user avatar
  • 7,301
13 votes
1 answer
377 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. ...
Geoff Hutchison's user avatar
13 votes
1 answer
922 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 ...
Aswin Alex's user avatar
12 votes
5 answers
1k views

Create doped structures to POSCAR files for vasp

I have a perfect supercell structure Ni fcc. And I would like to dope another element O or N with a ratio of O:Ni=8:100 to the supercell of 3x3x3 and find the most stable ordering structure. The ...
Binh Thien's user avatar
  • 2,035
12 votes
2 answers
2k views

What software can be used to do QTAIM analysis?

I have a rather general question of what software packages exist to do Quantum Theory Atom in Molecule (QTAIM) analysis of periodic and non-periodic systems. Working with Gaussian I have previously ...
Tristan Maxson's user avatar
12 votes
2 answers
892 views

3D Visualization of Molecule / Surface by 3D Model (.stl)

I am looking for a software that is capable of converting some generic atomic format such as .xyz or POSCAR into a .stl format. Ideally it would support automatic generation of bonds so that the ...
Tristan Maxson's user avatar
12 votes
2 answers
321 views

How to classify structures and identify duplicates from a set of .xyz files?

Does there exist a program that can compare a series of (ideally.xyz) files to each other to identify duplicate structures, and then identify the structures in some ...
kskinnerx16's user avatar
  • 1,536
12 votes
2 answers
606 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?
user779130's user avatar
12 votes
1 answer
772 views

Analyzing MD trajectory: molecule orientation

I'm running a MD simulation (in Gromacs) of dye molecules incorporated into polymer to determine how that system responds to external electric field. There are two order parameters that are used to ...
Roman's user avatar
  • 2,373
12 votes
2 answers
690 views

Recommended code to do XAS/XES/RIXS calculations with?

I am a grad student looking to simulate several XAS/XES and potentially RIXS spectra for some strongly correlated metal-oxides. The materials in question will likely require solving the Bethe-Salpeter ...
Haru Fujimura's user avatar
12 votes
1 answer
422 views

What is the best program to manipulate numerical DFT wavefunctions to calculate custom matrix elements?

For pedagogical reasons, I am looking for ways to calculate quantum-mechanical quantities such as $\langle m | \dot{m}\rangle, \langle m | \dot{n}\rangle, \langle m | \ddot{n}\rangle$ using ...
TribalChief's user avatar
  • 2,321
12 votes
1 answer
583 views

Is there a software that can calculate collision cross-sections involving molecules with several atoms?

What software currently can be accessibly used to calculate collision cross section using the geometries obtained from DFT? In my case, Q-Chem is used for geometry optimization. The goal is to compute ...
Dmitry Eremin's user avatar
12 votes
0 answers
151 views

Periodic polarizable QM/MM embedding [closed]

Are there any standalone open source software codes available for periodic polarizable QM/MM embedding MD simulations? In my knowledge, CP2K only has the option for electrostatic embedding and other ...
mykd's user avatar
  • 2,282
11 votes
2 answers
6k 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?
Chi Kou's user avatar
  • 5,713
11 votes
3 answers
552 views

Programs/Libraries for calculating solvent excluded surface and excluded volume

Given the 3D structure of a molecule (e.g. as *.mol) and a probe radius r, I want to calculate the solvent excluded surface (SES)...
Kexanone's user avatar
  • 523
11 votes
3 answers
1k views

How to build a nanocluster?

What are the software tools (if possible open source) or methods we can use for constructing a nanocluster, most preferably with high symmetry such as icosahedron, octahedron, cuboctahedron etc. ?
Niraja moharana's user avatar
11 votes
2 answers
143 views

What are some available software packages for automated finding of local and absolute minima on PES?

I have never used any AI driven calculation package before and to be honest don't fully understand the ins and outs of it. To be more specific I'm looking for something that can find local minima for ...
Cavenfish's user avatar
  • 1,222
11 votes
1 answer
415 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
11 votes
1 answer
198 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 ...
Hebo's user avatar
  • 1,665
11 votes
1 answer
212 views

adaptive k-mesh

Are there any known codes or scripts to generate an adaptive k-mesh for DFT calculations? For example, I'd like to make the k-mesh near the $\Gamma$ point (e.g., half the zone) more denser ($20\...
Xiaoming Wang's user avatar
11 votes
1 answer
404 views

How do I predict the structure of a nanoparticle with Calypso and Quantum ESPRESSO?

I want to create a nanoparticle of CuO and predict it's structure. I've done unit cell relaxation with Quantum ESPRESSO. One tool to predict nanocluster structure is Calypso which is PSO-based. I'm ...
Shafayet Rahat's user avatar
11 votes
0 answers
265 views

Calculating Core-Level Binding Energies (XPS) using DFT

I'm pretty new to DFT calculations but I'm trying to learn how to do X-ray photoelectron spectroscopy (XPS) calculations, particularly for open-shell molecular systems in common non-periodic DFT codes....
Ademola Soyemi's user avatar
10 votes
3 answers
873 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 ...
Chi Kou's user avatar
  • 5,713
10 votes
3 answers
965 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 ...
Carlos Andrés del Valle's user avatar
10 votes
4 answers
795 views

Tools for electronic transport calculations

Electronic transport calculations play an important role in device simulation. What tools can do electronic transport calculation? I am familiar with TranSIESTA (a module of SIESTA program) and ...
Camps's user avatar
  • 22.9k
10 votes
2 answers
804 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
  • 896
10 votes
1 answer
235 views

Calculating/Visualizing electronic density from orbital information written in the Molden format

I'm trying to obtain an electron density from orbital information written in the Molden format by the formula, $$ \rho(\mathbf{r}) = \sum_{i}^{occ} |\phi_{i}(\mathbf{r})|^{2}. \tag{1} $$ Is there any ...
Patche's user avatar
  • 400
10 votes
1 answer
189 views

Is there a software that has implemented forces of BSE calculations for solids?

I'd like to investigate the structural relaxations of the excited state for periodic systems. It seems BSE is a practical method that has already been implemented in many codes for static calculations....
Xiaoming Wang's user avatar
10 votes
1 answer
1k 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 ...
Tristan Maxson's user avatar
10 votes
1 answer
540 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 ...
Jack's user avatar
  • 1,997