Questions tagged [software-recommendations]
Questions of the form "Is there a software that can do...?" and similar.
180
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Is there a software/code that generates Brillouin zone k-points of FCC lattice?
tldr:
I am new to working with 3D lattices and am wondering if there are any well-developed methods for generating all $\mathbf{k}$-points inside the first Brillouin zone (BZ) of an FCC lattice.
My (...
- 143
8
votes
1
answer
70
views
What would be the best tool to simulate FTIR spectra of molecules?
I tried to simulate a spectrum of a porphyrin using the orca 5.0.4 program, calculating the frequencies and simulating the spectrum with the orca_mapspc program from the orca package, however the ...
- 355
6
votes
1
answer
136
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Periodic CCSD(T) software?
I'm curious about which quantum chemistry software packages support periodic CCSD(T), and preferably also faster versions such as PNO-CCSD(T) and LNO-CCSD(T). I've recently been rather frustrated by ...
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2
votes
0
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35
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Which programs can read an FCIDUMP file for a UHF wavefunction?
Around 4 years ago, a question was asked about which programs can interact with an FCIDUMP file: How do the various programs read or write integrals in FCIDUMP format?
In the design of Knowles and ...
- 71
2
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0
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27
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DOS calculation with QE
I am doing a DOS calculation via QE and the following is my SCF file :
<I'll add it later>
My nscf file :
<I'll add it later>
My DOS file:
<I'll add it later>
My SLURM submission ...
- 61
1
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0
answers
15
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Software to simulate doing electrolysis with sodium in aqueous solution where one can see electron flow from battery/all redox
I am requesting a picture/simulation or software that can show me the electron flow of the battery's electron flow as well as the electron flow of the metal in reducing anything it reduces in aqueous ...
- 131
5
votes
1
answer
166
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Is there a tool for generating nanotube from an arbitrary 2D structure?
I'm working on creating a specific nanotube structure with a non-hexagonal surface lattice. I have the 2D structure of the walls (basically a 3-atom-width structure, alike, but not, a layer of MoS2) ...
- 385
7
votes
1
answer
67
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Tight-binding computer program with electron thermodynamics
Does anyone know of a computer program which implements the Slater-Koster tight-binding scheme and which uses the resultant band structure to calculate thermodynamic state functions for the electrons (...
- 373
4
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0
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39
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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 ...
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29
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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 ...
- 1,105
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62
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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 ...
- 1,404
2
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2
answers
107
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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?
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7
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1
answer
257
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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 ...
6
votes
2
answers
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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 ...
- 741
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1
answer
136
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Software recommendation for drawing these atomic structures?
Anyone familiar what kind of software is used for drawing the atomic strucutres shown in the attached figure?
- 3,535
6
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2
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246
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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 ...
- 61
5
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0
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43
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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 ...
- 49
2
votes
1
answer
74
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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 ...
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295
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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 ...
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12
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2
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194
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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 ...
- 1,105
2
votes
1
answer
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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
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1
answer
486
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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 ...
- 3,535
3
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0
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48
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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 ...
- 31
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0
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49
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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, ...
- 159
6
votes
3
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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?
- 2,556
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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 ...
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1
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398
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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 <...
- 1,056
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83
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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 ...
- 2,054
3
votes
1
answer
214
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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 ...
- 485
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348
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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?
- 1,031
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votes
1
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63
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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, ...
- 1,970
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votes
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108
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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 ...
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213
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
52
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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 ...
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148
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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. ...
- 31
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0
answers
101
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 ...
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votes
1
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171
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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.)
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1
answer
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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 ...
7
votes
2
answers
594
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 ...
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votes
3
answers
895
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 ...
- 1,592
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0
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63
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.
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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 ...
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303
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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 ...
- 951
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votes
1
answer
1k
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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 ...
- 2,209
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votes
2
answers
935
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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 ...
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7
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0
answers
78
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 ...
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733
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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 ...
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votes
1
answer
118
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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?
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265
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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
...
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4
votes
1
answer
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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 ...
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