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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9
votes
1answer
50 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 ...
9
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2answers
53 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 ...
12
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1answer
107 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 ...
9
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0answers
66 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
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3answers
540 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
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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, ...
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 ...
19
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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 ...
13
votes
1answer
114 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
68 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 ...
13
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4answers
915 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 ...
9
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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 ...
21
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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.
10
votes
2answers
124 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)...
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. ?
12
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0answers
85 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 ...
12
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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 ...
13
votes
1answer
248 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 ...
9
votes
1answer
121 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
3answers
179 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 ...
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 ...
18
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2answers
383 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 ...
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
30 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 ...
15
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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 ...
9
votes
1answer
107 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
306 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 ...
9
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3answers
619 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, ...
12
votes
2answers
350 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 ...
7
votes
1answer
65 views

What are the methods for calculating interaction energies of layered materials, and where are they implemented?

What are the available methods for the calculation of reference interaction energies of layered materials and in which codes they are implemented? For example, I know RPA-ACFDT in the DFT concept. But ...
14
votes
1answer
173 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 ...
8
votes
1answer
116 views

Are there other custom chemistry programming languages besides SVL?

I must confess some ignorance... I just became aware of the Scientific Vector Language (SVL) which has been around since 1994 and was created solely for computational chemistry. It has a large ...
15
votes
3answers
134 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 (...
19
votes
0answers
233 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 ...
10
votes
3answers
583 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 ...
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 ...
10
votes
1answer
116 views

What resources are available to learn how to do something in VASP?

Apart from what is obvious (from a Google Search), what are the various resources available if I want to learn how to do something in VASP (for example, starting an HSE06 calculation)?
14
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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?
8
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2answers
90 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 ...
8
votes
1answer
98 views

What are the types of DMRG?

The following questions have worked out very well 😊 : What are the types of Quantum Monte Carlo? What are the types of SCF? What are the types of MCSCF? What are the types of ab initio Molecular ...
8
votes
4answers
229 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 ...
7
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0answers
145 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 ...
7
votes
2answers
78 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 ...
13
votes
2answers
131 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 ...
8
votes
0answers
58 views

What are the ways to add dynamic correlation to an MCSCF wavefunction?

We recently learned about the many types of MCSCF, which treat "static" electron correlation. There are then many ways to treat further "dynamic" electron correlation to try and ...
5
votes
2answers
65 views

For software that does not support FCIDUMP format, what format is used and how can we get the software to interact with FCIDUMP integrals?

Complementary to this question: How do the various programs read or write integrals in FCIDUMP format? which attempts to list all electronic structure packages that support the ...
7
votes
1answer
117 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
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 ...
15
votes
3answers
278 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 ...