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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10
votes
3answers
509 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. ?
8
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0answers
36 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
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0answers
61 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
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1answer
199 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
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0answers
62 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-...
13
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2answers
119 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 ...
10
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1answer
66 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 ...
17
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2answers
285 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
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2answers
965 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 ...
6
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1answer
27 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
votes
4answers
694 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
94 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 ...
11
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1answer
275 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 ...
10
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3answers
341 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, ...
11
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2answers
161 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 ...
8
votes
1answer
63 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 ...
11
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0answers
110 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 BSE Is there a ...
8
votes
1answer
105 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
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3answers
122 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 (...
14
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0answers
88 views

What are the advantages of different point defects calculation tools?

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? pycdt: Python Charge Defects Toolkit (PyCDT) is a ...
10
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3answers
407 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 ...
11
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0answers
64 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 ...
9
votes
1answer
97 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?
9
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2answers
77 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 ...
9
votes
1answer
81 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
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4answers
172 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 ...
14
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2answers
125 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 ...
9
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0answers
46 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 ...
6
votes
2answers
52 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
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0answers
67 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
100 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 ...
11
votes
1answer
128 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
2answers
188 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 modelling ‘real’ materials or solid solutions with dopants, dislocations, grain boundaries and ...
11
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3answers
172 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 ...
18
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5answers
896 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 ...
19
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2answers
198 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 ...
20
votes
2answers
237 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
5answers
356 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 ...
17
votes
3answers
158 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?...
21
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 ...
14
votes
4answers
208 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 ...
18
votes
3answers
483 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 ...
15
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2answers
183 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?
40
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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 ...
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 ...
32
votes
10answers
1k 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 ...
23
votes
8answers
3k 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
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5answers
2k views

Molecular Dynamics simulation software for Windows

Is there a Windows-based Molecular Dynamics simulation software which is easy to use?
21
votes
2answers
1k 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 ...