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.

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40
votes
14answers
6k views

Supercomputers around the world

For a matter modelling person, the most valuable resource is computing power. For many of us, computing power at hand limits the scale of problems we can solve. There are many national supercomputing ...
39
votes
16answers
2k views

What are some recent developments in density functional theory?

In the book Materials Modelling Using Density Functional Theory: Properties and Predictions by Feliciano Giustino, a timeline of milestones in DFT was given for achievements between 1964 and 1996: $$\...
34
votes
13answers
2k views

What is a good programming language for matter modeling?

What is a good programming language for matter (e.g. molecular or materials) modeling? Since this is a broad field, I don't expect there to be only one answer.
31
votes
10answers
2k views

What are the types of charge analysis?

I am evaluating the atomic charge of a system using inter-atomic potentials and comparing with using DFT. I know about the following types of partial charge: Mulliken, Bader, Qeq. I wonder what are ...
28
votes
9answers
678 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.
27
votes
9answers
4k views

Which Linux distribution is best for Matter Modeling?

In some science fields there are efforts to provide customized distributions, so you can get a productive environment with minimum set-up overhead. For example, in high energy particle physics, we ...
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 ...
24
votes
5answers
1k views

What are the types of DFT?

Similar to: What are the types of charge analysis?, What are the types of bond orders?, and What are some recent developments in density functional theory?, I would like to ask: What are the different ...
22
votes
2answers
248 views

What are the different ways of calculating dispersion constants?

There are many different dispersion corrections out there. The most famous is D3 [1] (and the new D4 [2]), but there's probably other approaches too. The dispersion energy can be written as: $$ E_{\...
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
4answers
1k views

What are the pitfalls for new users of DFT?

This question is inspired from a post in another SE. Many users these days use density functional theory codes as 'black boxes' and hence its natural to expect that they would have made many mistakes ...
20
votes
2answers
259 views

What are the great unsolved questions in Matter Modeling?

This is inspired from an amazingly successful question on Operations Research Stack Exchange: What are the great unsolved problems in operations research? Wikipedia has some huge lists of: Unsolved ...
19
votes
3answers
3k views

Solving the Schrödinger equation as a service?

Does anyone know of a company with a cloud-based service which takes some representation of a molecule as an input, and then somehow solves the Schrödinger equation to some level of accuracy and ...
19
votes
4answers
520 views

What are the types of bond orders?

I am studying the interaction of a metal with a nanostructure. As we can not trust graphical software about the bond formation, I decided to analyze them using the software Multiwfn. It happens that ...
19
votes
2answers
278 views

What methods are available for excited state calculations in solids?

In the spirit of a succint answer (3 paragraphs maximum) to create a useful resource, what are the types of excited state calculation available for solids? Please add to the list: Quasiparticle ...
19
votes
2answers
409 views

What is a chemputer?

I first saw the term "chemputer" when reading about the work of Neil Ostlund (who you may know as one of the authors of the famous book "Modern Quantum Chemistry"). Based on the ...
19
votes
2answers
224 views

Special quasirandom structures vs virtual crystal approach

What are the advantages and disadvantages in using special quasirandom structures (SQS) vs virtual-crystal approximation (VCA) to simulate electronic properties of disordered alloys? You do not need ...
19
votes
0answers
249 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 ...
18
votes
5answers
1k views

Tools for high-throughput DFT studies?

High-throughput density functional theory (DFT) calculations are used to screen for new materials and conduct fundamental research in materials science and materials innovation. It involves ...
18
votes
5answers
484 views

What are the types of SCF?

Many of us know the most common types of SCF (though we can do better than Wikipedia at explaining them): RHF (Restricted Hartree-Fock), RKS (Restricted Kohn-Sham) [link to answer] UHF (Unrestricted ...
18
votes
3answers
584 views

What are the types of ab initio Molecular Dynamics?

I am new to the world of Molecular Dynamics, and am curious to know exactly what is considered to be an ab initio Molecular Dynamics (AIMD) method, and how do they work? The seminal work by Roberto ...
16
votes
3answers
191 views

What are the types of MCSCF?

Similar to: What are the types of SCF? What are the types of Quantum Monte Carlo? What are the types of ab initio Molecular Dynamics? What are the types of pseudopotentials? What are the types of DFT?...
15
votes
4answers
2k views

How can I visualize the trajectory of a VASP simulation?

Which software package(s) can be used to visualize the trajectory of VASP MD simulation? VMD claims that there is a plugin to read the VASP output, while in the last version for Linux, I did not find ...
15
votes
3answers
307 views

What are some codes available for Dynamical Mean Field Theory (DMFT)?

One particularly field of matter modeling is that of strongly correlated materials, heavy-fermion compounds with partially filled 4f or 5f orbitals. In brief, these are materials whose complex ...
15
votes
3answers
138 views

Candidate structures for global minimum determination

What are the best packages that can generate candidate structures for quantum chemical optimization (DFT or CCSD) to find the global minimum? I am working on the gas-phase small inorganic clusters (...
15
votes
3answers
224 views

What ab initio methods are better suited to modelling disorder in materials?

In contrast to the perfect periodic bulk materials, now computational approaches are moving towards modeling ‘real’ materials or solid solutions with dopants, dislocations, grain boundaries, and ...
14
votes
5answers
972 views

What are some cloud services for computing?

A group of researchers in my university (including me), started to study the possibility to move to cloud computing services in order to run our simulations. The simulation areas include condensed ...
14
votes
8answers
2k views

What are some free programs to do docking?

I'm interested in doing molecular docking. What are some free programs for it and what are their pros and cons?
14
votes
2answers
133 views

Order of scaling for different algorithms

There are many different computational methods used in matter modelling. For example: solving multi-electron Schroedinger equation, DFT with different approximations, Quantum Monte Carlo, etc. How ...
14
votes
2answers
277 views

What are the types of pseudopotentials?

I would like to know what are the different types of pseudopotentials, the pro and cons, and what properties can/cannot be calculated with them?
14
votes
1answer
175 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
4answers
280 views

What are some open-source all-electron DFT alternatives to Wien2K?

Since the beginning of the century, Wien2K has proven to be a very powerful player in computational condensed matter and materials physics. Wien2K is an all-electron periodic DFT code based on the ...
13
votes
3answers
188 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
268 views

Software for Exact Diagonalization of quantum spin Hamiltonians in 1D and 2D

I'm looking for software (which can also run in parallel) for Exact Diagonalization of Quantum Spin Hamiltonians in 1D and 2D (e.g. Heisenberg Model) consisting of a large number of spin sites. There ...
13
votes
1answer
135 views

Semi-empirical software for bands calculations

In Semiconductor Physics, one of the main parameters of interest is the band gap. It is known that, in DFT, there are functionals that underestimate it. I came across the MOPAC program, a semi-...
13
votes
1answer
115 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)...
12
votes
5answers
388 views

What are the common acronyms in Materials Modelling?

Many abbreviations are used in Materials Modelling. For example, we have DFT (density functional theory/discrete Fourier transform), TST (transition state theory) and MD (molecular dynamics). Which ...
12
votes
3answers
227 views

What are the types of Quantum Monte Carlo?

Similar to: What are the types of SCF? What are the types of MCSCF? What are the types of ab initio Molecular Dynamics? What are the types of pseudopotentials? What are the types of DFT? What are the ...
12
votes
3answers
144 views

Citizen science projects in Matter Modeling

According to Wikipedia, Volunteer computing is a type of distributed computing in which people donate their computers' unused resources to a research-oriented project An example of a volunteer ...
12
votes
2answers
394 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
1answer
110 views

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 ...
12
votes
1answer
311 views

Suggestions for a good crystal structure visualization workflow

Following up on this question about freely available crystal structure visualization codes, I wish to know what procedures people follow from start to finish in preparing images of their materials for ...
12
votes
1answer
92 views

Recent developments in QM/MM for Molecular Dynamics

I am looking for new QM/MM methodologies which have recently developed and implemented into MD packages. Any applications or molecular systems studies with these methods can be used as an example as ...
12
votes
0answers
87 views

What are the recent developments of GW@BSE to simulate the excited properties of materials?

The time-dependent density functional theory (TDDFT) and the many-body perturbation theory (GW@BSE) methods are considered as the two most popular and successful methods to describe the excited-stated ...
11
votes
3answers
752 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
112 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?
10
votes
3answers
1k views

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 ...
10
votes
3answers
546 views

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 ...
10
votes
3answers
650 views

Codes for post-processing Gaussian cube files?

I have generated MOs of a molecular system and I need to recreate its electronic density via $\rho(r)=\sum_{A_i}|\psi_i(\mathbf{r})|^2$ where $A$ is a set of occupied MOs. I am trying to do this via ...