Questions tagged [software-recommendations]
Questions of the form "Is there a software that can do...?" and similar.
78
questions
8
votes
1answer
307 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-...
10
votes
3answers
789 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 ...
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?
8
votes
1answer
86 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 ...
14
votes
2answers
253 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. ...
9
votes
1answer
190 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 ...
8
votes
0answers
71 views
Tools for symbolic calculations of quantum transport using the Keldysh NEGF formalism
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 <...
5
votes
1answer
61 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.
9
votes
0answers
49 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 ...
6
votes
2answers
440 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 ...
6
votes
0answers
42 views
Molecular dynamics to reproduce dispersion interactions
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 ...
8
votes
1answer
176 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. ...
9
votes
1answer
61 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 ...
13
votes
1answer
142 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. ...
8
votes
1answer
113 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.
...
7
votes
0answers
55 views
Software for calculating the mirror Chern number of 2D systems?
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 ...
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,...
13
votes
1answer
303 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
122 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?
17
votes
2answers
541 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 ...
7
votes
4answers
728 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 ...
8
votes
1answer
120 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, ...
13
votes
1answer
117 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)...
9
votes
1answer
79 views
What software can do RNA secondary structure prediction?
This question is a follow-up to this previous question.
I have learnt there that there are reasonable ways to predict RNA tertiary structure. Here I inquire about how to predict RNA secondary ...
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 ...
12
votes
1answer
178 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 ...
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 ...
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.
6
votes
0answers
73 views
Is there a software package to analyse interactions in crystals?
I have been using Quantum ESPRESSO, specifically the pp.x module to
study interactions via charge density plots. The process is slow as
for crystals containing ...
10
votes
2answers
139 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)...
6
votes
2answers
99 views
Symmetry-preserving low-level structural relaxation
I would like some suggestions on how to do structural relaxation (while I'm at it, let me list some synonyms for search exposure - geometry optimization, structural refinement, energy minimization etc)...
5
votes
1answer
45 views
SiC surface reconstruction
I know how to cleave surfaces with integer Miller indices, however I wonder how I could cleave a $(\sqrt{3} \times \sqrt{3}) R30$ reconstruction of $(001)\,\, 4H-SiC$.
I have found a nice link to O-...
6
votes
0answers
23 views
Is it possible to calculate the variation of magnetization M(T) for a diluted magnetic semiconductor?
Is there any simulation program (for example a DFT package) to determine the variation of magnetization M(T) for dilute magnetic semiconductors or doped semiconductors with different concentrations of ...
5
votes
0answers
30 views
Fitting of mesostructure diffraction peaks [closed]
I've got synchrotron X-ray powder diffraction data where nice mesostructure diffraction peaks are observed at a very low angles. Does anybody know how to gain relevant information from these data? ...
14
votes
1answer
229 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.
...
12
votes
1answer
143 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 ...
11
votes
3answers
758 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. ?
7
votes
0answers
304 views
Is there any code for local-orbital ab initio tight binding molecular dynamics other than fireball? [closed]
I was searching for a local-orbital ab-initio tight binding implementation of molecular dynamics and Ive found a code called fireball. Ive tried to compile it but the code seems to be buggy and there ...
7
votes
0answers
39 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 ...
10
votes
1answer
143 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 ...
13
votes
1answer
300 views
Software for solving quantum spin Hamiltonians in 1D and 2D
I'm looking to solve quantum spin Hamiltonians in 1D and 2D (e.g. Heisenberg Model) consisting of a large number of spin sites.
What are the pros and cons of each package, and which package is more ...
13
votes
1answer
172 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 ...
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
1answer
146 views
A good software for DFT optimization and nonlinear optical properties
I'm running a series of calculation for nonlinear chromophores. The general pipeline is geometry optimization (B3LYP/def2-TZVP) -> Frequencies -> Hyperpolarizability calculation (M06-2X (or CAM-...
13
votes
3answers
191 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 ...
11
votes
2answers
341 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 ...
7
votes
2answers
972 views
Computer simulation of squeezing flexible objects with force
I am looking for any software, or scientific works, or search phrase in the field of simulating graphic modeling of squeezing objects. I would like to simulate packing very oddly shaped soft elastic ...
11
votes
4answers
383 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
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 ...
7
votes
1answer
84 views
Software to generate compound library
I'm trying to perform a QSPR research and for it I need to generate a library of compounds.
Now I'm using a plugin for MarvinSkectch for enumerating Markush structures but it doesn't work properly (...