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.

Filter by
Sorted by
Tagged with
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 ...
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 ...
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 ...
9
votes
1answer
168 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 ...
4
votes
1answer
53 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.
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?
8
votes
1answer
145 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. ...
8
votes
0answers
60 views

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

Cross-posted on Physics.SE. 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, ...
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 ...
8
votes
1answer
132 views

How do the various programs read or write integrals in FCIDUMP format?

The FCIDUMP format was created by Peter Knowles and Nick Handy circa 1989 and now allows many electronic structure software packages to interact with each other. ...
9
votes
2answers
82 views

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 ...
7
votes
0answers
156 views

What are some DMRG packages with an easy learning curve?

I've been meaning to learn how to use DMRG (density matrix renormalization group) for a long time. Which packages have an easy learning curve? I specifically mean it should be easy to actually learn ...
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 ...
8
votes
2answers
80 views

What packages exist for building quantum Monte Carlo simulations of spin or Hubbard Hamiltonians?

What packages exist that can help someone, especially a new masters/PhD student get started with QMC on spin or Hubbard systems? As an example, for writing a stochastic series expansion QMC program ...
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: $$\...
9
votes
1answer
60 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 ...
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 ...
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
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 ...
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.
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 ...
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 ...
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 ...
8
votes
1answer
109 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
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
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 ...
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 ...
4
votes
1answer
48 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
62 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
70 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
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 ...
10
votes
2answers
127 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
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 ...
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?
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
129 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
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 ...
9
votes
4answers
248 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
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. ?
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 ...
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 ...
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 ...
12
votes
2answers
395 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
112 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
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 ...
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 ...
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
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 ...