Questions tagged [software-recommendations]

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

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31
votes
5answers
3k 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 ...
28
votes
9answers
756 views

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.
26
votes
3answers
2k 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 ...
22
votes
6answers
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 ...
21
votes
5answers
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.
21
votes
5answers
2k 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?
20
votes
0answers
269 views

What are the tools available for point defects calculations?

As far as I know, there are mainly PyCDT, PyDEF, pylada and some part of pymatgen. As a new user to those tools, which one would be a good choice? It would be appreciated if you could explain one of ...
17
votes
2answers
547 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 ...
16
votes
2answers
408 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,...
16
votes
2answers
402 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? ...
15
votes
1answer
245 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. ...
15
votes
1answer
90 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?
15
votes
0answers
129 views

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

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 ...
14
votes
2answers
267 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. ...
14
votes
1answer
177 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 ...
14
votes
1answer
178 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 ...
13
votes
5answers
494 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 (...
13
votes
3answers
195 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 ...
13
votes
1answer
118 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)...
13
votes
1answer
147 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. ...
13
votes
1answer
314 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 ...
12
votes
2answers
497 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 ...
12
votes
2answers
134 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 ...
12
votes
2answers
129 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?
12
votes
1answer
191 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 ...
12
votes
1answer
150 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 ...
12
votes
1answer
215 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 ...
11
votes
2answers
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?
11
votes
4answers
394 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 ...
11
votes
3answers
771 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. ?
11
votes
2answers
355 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 ...
11
votes
2answers
113 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 ...
11
votes
1answer
98 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\...
11
votes
0answers
77 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 ...
10
votes
3answers
809 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 ...
10
votes
2answers
148 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)...
10
votes
1answer
144 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 ...
10
votes
1answer
156 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....
10
votes
1answer
237 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 ...
10
votes
0answers
50 views

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

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 ...
10
votes
0answers
85 views

Periodic polarizable QM/MM embedding

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 ...
9
votes
4answers
294 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 ...
9
votes
3answers
94 views

Which non-commercial softwares can be used to model amorphous carbon?

I have a fair idea of generating and modeling crystalline materials but what non commercial software programs can be used to model amorphous carbon of a specific dimension, say a $6\times6\times6$ Å ...
9
votes
1answer
212 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 ...
9
votes
2answers
220 views

How to calculate the nuclear energy derivatives in molecular mechanics?

In molecular mechanics, the energy is often written as a sum of bonds, angles and torsion energies, and an electrostatic term, e.g. $V = \sum_{bonds} K_r (r-r_{eq})^2 +\sum_{angles}K_{\theta}(\theta -\...
9
votes
1answer
182 views

Freely available constrained DFT implementations

What free quantum chemistry packages that have constrained DFT (CDFT) implemented? A google search does not reveal anything, perhaps there may exist a better resource to find the packages.
9
votes
1answer
63 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 ...
9
votes
1answer
64 views

What software is a software for RNA tertiary structure prediction?

It seems that the prediction of protein folding is a pretty advanced area. Are there options based on some GDT-like measure? For me, it has relevance in connection with the origin of life (cf. RNA ...
9
votes
1answer
62 views

Finding conformations of peptide based on dihedral angles

I was trying to look at the alanine dipeptide trajectories from this link and track the trajectories in a Ramachandran plot. Below is a plot based on dihedral angles at each timestep for all ...
9
votes
2answers
152 views

How to build a simulation model for a molecular dynamics simulation

I have got aggregate of 4 non-protein compounds I would submit for molecular dynamics simulation. The problem is I can't find software capable to do that. Amber, GROMACS, LAMMPS, all of them require ...