Questions tagged [one-topic-per-answer]
Special tag for certain big-list questions. Answers should only go into detail about one specific topic related to the question. The original question will often present a template format for submitting answers.
122
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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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0
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27
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Types of pseudopotential for calculating optical properties?
What types of pseudopotential should I use for calculating optical properties in Quantum ESPRESSO?
- 61
5
votes
1
answer
290
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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?
- 495
4
votes
1
answer
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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, ...
- 1,257
5
votes
1
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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 ...
- 91
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votes
0
answers
30
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What factors determine the selection of a specific type of MC move?
There are several types of Monte Carlo (MC) moves that can be used in simulations:
Metropolis-Hastings: a sampling technique used to generate a Markov chain of states with desired probabilities by ...
- 2,212
3
votes
0
answers
140
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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
4
votes
0
answers
60
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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 ...
- 41
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votes
3
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626
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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 ...
- 1,285
4
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0
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How realistic is the use of classical analog electronic computers in solving the Schrödinger, Hartree-Fock, and Kohn-Sham equations?
Classical binary computer
The classical binary computers, on which a Hartree-Fock (or density functional theory) calculation can be executed, already allows seeing a limit in their progress, mainly in ...
- 857
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vote
0
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46
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Figure-of-merit with Transiesta/TBtrans
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.
- 907
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votes
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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 ...
- 857
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votes
3
answers
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What would be the preferred format for a geometry database?
Introduction (analogy to basis set database files)
Many programs have a database of basis sets stored in a file such as the following (so that users can just specify in their input file something like ...
- 33.1k
4
votes
1
answer
55
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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?
- 404
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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
...
- 151
1
vote
0
answers
40
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 ...
- 153
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Is there a free software to build a crystal shape that is cut with a specific angle plane (like 40 degrees), which is not implemented in Vesta?
I would like to cut $\ce{SrTiO3}$ with a specific angle of 40 degrees, or to choose an angle plane which is not implemented in the Vesta software.
Could you please recommend a free software to build ...
- 51
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answers
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What software can simulate bulk magnetism?
I am interested in investigating bulk magnetism computationally. What are the packages available for it? Any help in this direction will be appreciated.
Please answer with the format of the answer in ...
- 494
5
votes
1
answer
187
views
What is a good software for computational electrochemistry?
I am thinking about working on computational electrochemistry for a limited subject and don't have a huge amount of time I can invest to explore different software. The JDFTx software seems like a ...
- 1,347
7
votes
1
answer
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Ab-initio molecular dynamics of liquid systems: best tools and resources
I have been studying liquid systems (particularly deep eutectic solvents) using classical molecular dynamics (MD) simulations. The main drawback of classical MD is the arbitrariness of the potential ...
- 331
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votes
2
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575
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A python compatible GUI chemical drawing library/software
So, I am developing a GUI for a python computational chemistry software (with PyQt5). The Qt part of the GUI will handle running the python software (calling the proper functions with proper arguments ...
- 6,436
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votes
1
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250
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Software for Molecular Dynamics in Material Science
I would like to know available software that can do Molecular Dynamics (MD) simulations for any type of system, specifically inorganic and organic ones.
The must cited MD packages (GROMACS, AMBER, ...
- 21.9k
6
votes
0
answers
93
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Methods to build tight-binding models for realistic materials [closed]
I am aware that a standard way to build tight-binding models for realistic crystalline systems is by using the Maximally-localized Wannier Functions (MLWFs) as implemented in the Wannier90 Fortran ...
user5405
14
votes
3
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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) ...
- 857
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1
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Alternatives to OpenBabel for converting *large* files?
I have been using OpenBabel as a handy-tool for converting small files without any issues.
Now, I am working with graphene-like systems with hundreds or even ...
- 21.9k
2
votes
0
answers
96
views
What are the types of density matrix mixing methods?
I would like to know what are the different types of mixing procedures to be applied to the density matrix (Broyden mixing, Pulay mixing) and their pros and cons?
- 1,561
2
votes
1
answer
100
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What do we simulate with molecular simulation of proteins in the theoretical research?
I know that the following can be simulated:
secondary/tertiary structure prediction
protein-surface/protein-protein interaction tests
protein-ligand binding test
I wonder if references or ...
- 2,212
7
votes
1
answer
410
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List of programs for post-CCSD(T) calculations
Implementations of CCSD(T) are almost too numerous to list, but CCSDT and CCSDT(Q) are much more rare. I have compiled a list of such programs below, and I would be interested to hear if anyone is ...
- 375
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88
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What are some recent significant developments/studies in theoretical nonlinear chemical dynamics?
During my undergraduate studies, I was introduced to oscillatory and nonlinear reactions, which are essentially chemical reactions oscillating far away from equilibrium conditions - A very visual ...
- 2,252
17
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4
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I am considering to purchase a GPU. What calculations would need FP32, and what would need FP64?
I would like to know how to choose the best GPU on the basis of its FP32 or FP64 efficiency, depending on different types of simulations.
In brief I would like to know what types of simulations work ...
- 1,459
8
votes
1
answer
95
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What software should I use for an MD study of a temperature-dependent crystallographic phase transition?
I want to study the crystallographic phase transitions of crystals with increasing temperature. Which freely available MD package should I choose, which has easily available tutorials/example-input-...
- 181
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votes
2
answers
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Which methods are size-consistent / size-extensive, and why?
This is a follow up question from another question I posted here. I am looking for an explanation (or a mathematical proof, if possible) of the size extensivity and size consistency of the following ...
- 6,436
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votes
5
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Recommended software to open NetCDF files?
I found plenty of packages that open .nc files but all specifically catered to climate (meteorological) and geo-maps data. I would like to get suggestions of ...
- 21.9k
7
votes
2
answers
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What software can be used for Crystal Surface Calculations?
I have been unable to find software for making surface calculations, so I currently perform surface calculations in LAMMPS by creating crystal structures in python, before rotating and cutting them ...
- 929
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votes
3
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458
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Open source FCI solvers for exact diagonalization of the many-electron Hamiltonian
What open source solvers (according to the generally accepted Open Source Definition i.e. licensed under a valid open source license) are available for full configuration interaction calculations? ...
- 17.6k
13
votes
1
answer
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views
How are structure descriptors used in regression or machine learning?
I am currently working on prediction of UV-vis spectra from structure of molecules. I have read multiple papers where structure descriptors were used as inputs for machine learning to find various ...
- 6,436
13
votes
1
answer
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Are there any benchmark test sets for UV-vis absorption maxima?
In computational chemistry, I have come across many test sets which are used to benchmark a new method. For example, the G2 test set for thermochemical calculations (heats of formation). There is the ...
- 6,436
4
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1
answer
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Is there a site to obtain or create membranes?
I am interested in creating an enterocyte intestinal basal membrane.
So, I wonder if there is a database or site where the membrane could be downloaded or created.
- 21.9k
16
votes
2
answers
752
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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. ...
- 17.6k
12
votes
3
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How can I submit jobs to an HPC scheduler?
It is my first time trying to use an HPC system and I am a bit overwhelmed. I have gone through a course on using HPC systems on Coursera and have a basic idea about using Linux. Could you guys tell ...
- 1,631
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votes
1
answer
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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 ...
- 1,376
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votes
1
answer
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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.
- 3,836
9
votes
1
answer
966
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. ...
- 4,306
9
votes
1
answer
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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 ...
- 99
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votes
2
answers
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Classes of Graphs used in Chemistry
I am looking for common categories of graphs used in chemistry, for math research I am doing in graph theory.
When I write categories, the meaning is not for graphs design or types of design, but for ...
- 191
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votes
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84
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Software for calculating the mirror Chern number of 2D systems? [closed]
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 ...
- 651
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1
answer
354
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What are the databases of semiconductor properties?
Is there any database listing the experimentally-determined properties of semiconductor materials - things like Band Gap and Electron Mobility. These are easily found for common materials like ...
- 281
12
votes
2
answers
487
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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?
- 121
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3
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571
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Which DFT functional should I use to simulate spectra of pesticides?
I am mainly searching for functionals to calculate spectra of pesticides. I found the benchmark test from Goerigk and Grimme$^1$, but don't understand which of the functionals suits my purpose the ...
- 589
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What are some types of topologically-relevant band degeneracies in contemporary 2D condensed matter research? [closed]
In the study of 2D condensed matter systems, I have seen several kinds of band degeneracies. I call 'bands' the eigenvalues to the time-independent Schrodinger equation, solved over 2D k-space. By '...
- 2,131