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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14
votes
3answers
261 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 ...
12
votes
3answers
222 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
1answer
104 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 ...
13
votes
4answers
873 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 ...
28
votes
9answers
637 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.
19
votes
0answers
229 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 ...
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 ...
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 ...
9
votes
0answers
65 views

Is there some free software to do some computation of Frank-Condon analysis?

I know Gaussian 16 can do it, but are there some free software to do? For simple excited state calculations using TD-DFT, we can use NWChem and Octopus.
10
votes
3answers
539 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 ...
7
votes
0answers
49 views

What are some types of topologically-relevant band degeneracies in contemporary 2D condensed matter research?

Cross-posted the question here: https://physics.stackexchange.com/q/633457/49107 In the study of 2D condensed matter systems, I have seen several kinds of band degeneracies. I call 'bands' the ...
8
votes
1answer
108 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
113 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
1answer
91 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 ...
14
votes
1answer
172 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 ...
4
votes
1answer
46 views

Optical anisotropy from first-principles

I am interested in the theoretical study of optical anisotropy (birefringence, dichroism etc.) of different materials. I have seen DFT works studying optical anisotropy from the calculation of ...
9
votes
1answer
61 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 ...
9
votes
1answer
67 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 ...
15
votes
3answers
221 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 ...
10
votes
2answers
121 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)...
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.
20
votes
2answers
247 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
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?
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 ...
9
votes
1answer
119 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-...
12
votes
0answers
84 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 ...
9
votes
4answers
232 views

What programs can do electron integrals and SCF calculations with more than one CPU?

Similar to this question which asks for each answer to provide one software that can do CASSCF: I am interested in software that can do integrals, SCF (Hartree-Fock), and the integral transformation, ...
11
votes
3answers
745 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. ?
39
votes
15answers
1k 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: $$\...
19
votes
2answers
269 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 ...
39
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 ...
13
votes
1answer
244 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 ...
12
votes
2answers
340 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 ...
9
votes
1answer
103 views

Fermi energy in density functional theory

Disclaimer: Assume the questioner is a novice in DFT and condensed matter physics in general. How reliable are DFT based estimates of the fermi energy? Do different flavours of DFT affect the accuracy ...
12
votes
1answer
302 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 ...
13
votes
4answers
267 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 ...
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.
15
votes
4answers
1k 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 ...
13
votes
2answers
129 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 ...
12
votes
2answers
131 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 ...
18
votes
2answers
377 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 ...
9
votes
1answer
70 views

Can you list some useful code snippets for processing quantum ESPRESSO output files?

I know that this is quite general. But we have all written code for processing output files from various dft codes. The functionality of which, may range from analysing time traces to finding ...
10
votes
0answers
70 views

What are the methods of modeling Jahn-Teller effects in a solid-state material? [closed]

The Jahn-Teller effect arises from the symmetry breaking (distortion) of the local environment for the crystal field of 3d transitional metal ions.The distortion result in energy saving of electronic ...
7
votes
2answers
966 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 ...
5
votes
1answer
29 views

What are some ways to model disequilibrium processes with current software?

Its normally that case that most material modeling techniques rely on energy minimizations, which result in the equilibrium solutions for most chemical of physical processes. While this is great for ...
9
votes
1answer
113 views

What are the types of Quantum Molecular Dynamics (QMD)?

In similar spirit to recent questions on Quantum Monte Carlo, ab-initio Molecular Dynamics, types of SCF, and others, I would like to ask: What are the types of Quantum Molecular Dynamics (QMD)? As I ...
8
votes
4answers
223 views

Tools for electronic transport calculations

Electronic transport calculations play an important role in device simulation. What tools can do electronic transport calculation? I am familiar with TranSIESTA (a module of SIESTA program) and ...
9
votes
3answers
588 views

Molecular visualization software in Jupyter (IPython) Notebooks

Jupyter notebooks have always been a great way for me to create high-quality graphs, and write code. The features also continue to improve with packages such as Jupyter Lab, and now Jupyter Books, ...
16
votes
3answers
184 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?...
19
votes
4answers
464 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 ...