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Questions tagged [software-recommendations]

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

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4 votes
0 answers
36 views

Rich editing of ASE images

I want to produce some images related to graphene-like materials. I was able to draw them using ASE visualize module after constructing the atomistic model. However ...
4 votes
0 answers
22 views

Which quantum chemistry codes have the capability use point charges in a QM/MM setting?

I came across a few examples like: NWchem : QM/MM Bq charges PySCF : QM/MM with MM charges GPAW : External Point charge potential I wanted to know of other code examples, which had the same ...
13 votes
1 answer
424 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. ...
1 vote
0 answers
61 views

Code to build the monoclinic crystal lattice

Benzoic acid exists as a solid at room temperature. So, I want to build a monoclinic crystal structure of this molecule. Is there any code available to do that? Thanks. Edit: Is there any way to build ...
2 votes
2 answers
68 views

Tool for plotting spin texture

Is there a tool that can plot a spin texture graph like these two examples below: Or does anyone know an example using matplotlib?
9 votes
1 answer
238 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 ...
6 votes
2 answers
70 views

Exploring Band Structure and Density of States Visualization Tools for VASP Calculations

I'm currently working with VASP and need recommendations for the best tools to effectively plot band structures and density of states obtained from VASP calculations. Could you please share your ...
7 votes
1 answer
240 views

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 ...
2 votes
1 answer
71 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 ...
9 votes
0 answers
71 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?
6 votes
2 answers
231 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 ...
5 votes
0 answers
41 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 ...
12 votes
2 answers
184 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 ...
15 votes
3 answers
507 views

What is the best program to manipulate plane-wave 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 ...
7 votes
1 answer
261 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 ...
2 votes
1 answer
58 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 ...
7 votes
1 answer
368 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 ...
11 votes
1 answer
436 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 ...
6 votes
3 answers
1k 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?
7 votes
0 answers
195 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 ...
12 votes
2 answers
808 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 ...
3 votes
0 answers
48 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 ...
5 votes
0 answers
48 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, ...
4 votes
1 answer
348 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 <...
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 ...
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 ...
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 ...
3 votes
1 answer
188 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 ...
4 votes
1 answer
61 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, ...
5 votes
1 answer
343 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?
5 votes
1 answer
95 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 ...
3 votes
1 answer
72 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 ...
5 votes
3 answers
142 views

Is generating conformers necessary for molecular docking studies?

I have seen some research papers on molecular docking studies using some conformer-generating softwares like CORINA, OMEGA, etc. and they used these softwares to generate conformers of a molecule and ...
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 ...
4 votes
1 answer
201 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 ...
3 votes
0 answers
48 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 ...
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. ...
4 votes
0 answers
91 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 ...
6 votes
1 answer
145 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.)
6 votes
1 answer
95 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 ...
5 votes
1 answer
461 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 ...
11 votes
3 answers
614 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)...
8 votes
3 answers
830 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 ...
2 votes
0 answers
61 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.
10 votes
2 answers
862 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 ...
3 votes
1 answer
959 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 ...
6 votes
1 answer
667 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 ...
7 votes
0 answers
74 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 ...
6 votes
1 answer
460 views

Lennard Jones Clusters in Python

I would like to explore the global optimisation of Lennard-Jones clusters in Python. I do not come from a physical chemistry background. I would like to be able to calculate the cluster energy ...
5 votes
1 answer
92 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?