Questions tagged [reference-request]

This tag is for questions looking for a single specific, or a small number of (citable) references.

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5
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0answers
17 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 ...
10
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3answers
526 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 ...
12
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1answer
88 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 ...
4
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1answer
55 views

Has there been any work done on fluid dynamic or acoustic modeling of the human oral (or nasal) cavity?

The purpose is for me to develop a deeper understanding of speech production and how distinct features that identify a phenome are produced. ab initio models based on classical & statistical ...
9
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1answer
55 views

What methods are there to computationally determine the taste of a molecule?

There are a number of molecules which no human should ever have to taste for safety reasons. Still, it could be interesting to know how it interacts with the taste buds. Applications could also ...
18
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1answer
216 views

Promising functionals for transition metal chemistry

I'm looking to get your opinions on the most promising density functionals to use for thermochemistry and kinetics of transition metal complexes. However, as eloquently laid out by Tom Manz on this ...
26
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2answers
407 views

How is Julia used in Materials Modeling?

What are the main uses and applications of Julia in Materials Modeling? Python for example is used in codes such as kwant, ...
15
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3answers
219 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 ...
7
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0answers
64 views

What are some examples where TD-DFT was successful and where it fell short in describing photophysical or photochemical processes?

Time-dependent Density Functional Theory has been around for quite a while now, seeing Density-Functional Theory for Time-Dependent Systems, and so it has been developed extensively, implemented in ...
23
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1answer
132 views

Benchmark Timings of Machine Learning Potentials vs Molecular Mechanics Force Fields

Machine learning is an increasingly common tool for developing force fields for molecular dynamics simulations. It's not totally clear what should be considered a machine-learning potential, but let's ...
10
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1answer
141 views

What novel drugs are developed via CADD?

Virtual screening , protein ligand docking, MD simulation, FEP free energy calculations and the QM/MM approach have all been widely applied in optimization for drug discovery. Which drugs that have ...
20
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2answers
242 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 ...
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0answers
66 views

Formulate the Model Quantum Spin Hamiltonian for low dimensional (1D or 2D) magnetic materials [closed]

Recently I have started studying the properties of low dimensional magnetic materials by solving the MODEL QUANTUM SPIN HAMILTONIAN. I am finding difficulties in formulating the model quantum spin ...
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Is it necessary to terminate the surface ions in a quantum dot?

I was trying to study quantum dots of ZnO. But I'm pretty new to creating and passivating 0 D particles. Is it always necessary to passivate the free surface of the quantum dot? Regarding the studies ...
26
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3answers
291 views

Where is the extended Hückel method (EHM) still used today?

The extended Hückel method (EHM) proved to be very useful through time, but there are better and affordable models today. One interesting thing about the model is the independence of the Hamiltonian ...
14
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1answer
222 views

Software recommendations for passivating structures

I am looking for an open-source library that allows to passivate a structure, ideally starting from a xyz-file. QuantumATK provides a function like this. However, this is not an option at the moment. ...
9
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1answer
61 views

Algorithmic description of implementing path integral molecular dynamics?

Suppose I have a functioning molecular dynamics package for classical MD. I want to extend this code to run path integral MD. I know that a surprisingly small number of new features need to be ...
7
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0answers
293 views

Is there any code for local-orbital ab initio tight binding molecular dynamics other than fireball?

I was searching for a local-orbital ab-initio tight binding implementation of molecular dynamics and Ive found a code called fireball. Ive tried to compile it but the code seems to be buggy and there ...
6
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1answer
53 views

How to calculate Transport coeffiecients for 0 D systems?

I would like to calculate the thermal transport coefficients like Thermal Conductivity, Seebeck coefficient etc for thermoelectric 0 D systems (quantum dots, nanoclusters ..etc). For bulk materials, ...
6
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1answer
66 views

How can I properly represent paramagnetic materials in DFT calculations?

I have seen specific ways of constructing input files for Anti-ferromagnetic materials Ferromagnetic materials. How can I represent a paramagnetic material in plane wave DFT codes like Quantum ...
10
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2answers
128 views

About the surface Greens function method for calculating the surface state

Currently I'm using some software package to do the data analysis from the DFT calculation so that I can study the surface state of some topological insulator. I found that the method they use is ...
9
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1answer
73 views

Where did the “Computational Chemistry Comparison and Benchmark DataBase” find its scaling factors for vibrational specra?

I worked with gaussian to simulate vibrational IR and Raman spectra. For that purpose, I scaled the vibrational frequencies from my gaussian calculation with the scaling factors from this website: ...
20
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6answers
1k views

What are good resources to learn to code for matter modeling?

A little bit of coding can a long way in matter modeling. Coding is not used only to write big programs but can be used for scripting, data processing, automation, and more. But sometimes many ...
13
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2answers
230 views

Hubbard U correction for Copper

I am reviewing some information in the Materials Project and notice that they do not use DFT+U to model copper oxides. Since the methodology for fitting U is largely based on the 2006 Ceder paper, I ...
18
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4answers
592 views

References for Molecular Dynamics?

I am new to the world of Molecular Dynamics (zero practical experience), and I know that a starting point to really go into the back-bone of MD is Statistical Mechanics (took a semester course in ...
10
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1answer
67 views

Calculate Redox Potential

I am interested in calculating some redox potentials of organic compounds (H,C,N,O,F,Cl,Br) in organic solvents such as MeCN. I do not need absolute agreement with experiments since this is just a ...
8
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1answer
61 views

What are the possible applications of DIC (digital image correlation) in mechanical testing and the field of materials science?

I would like to know about possible applications of DIC in mechanical testing and the field of materials science, when I search there is the general topics of DIC usages, but I would like to know ...
12
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1answer
367 views

Are there any good books to learn how to use DFT+U?

I am interested in learning how to do DFT+U calculations and was wondering if anyone has any good recommendations for books or articles.
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3answers
1k views

Introduction to protein folding for mathematicians

My background is mostly in (applied) math with healthy doses of physics and computer science. Are there any good introductions to protein folding and its challenges for someone with that kind of ...
11
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1answer
222 views

What are some of the biggest theoretical and computational challenges in Condensed Phase Chemistry?

What are some of the biggest open-questions / challenges in Condensed Phase theory and computation? What efforts are being done to answer them? I realize Condensed Phase chemistry is a huge field, but ...
15
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1answer
124 views

What is the definition of ergodicity in Monte Carlo?

I've been writing a manuscript about the breakdown of ergodicity in single spin flip Metropolis algorithm Monte Carlo arXiv:2001.09268. The definition I have been using is: a Markov process is ...
10
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0answers
69 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
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2answers
134 views

General Techniques for Smart Sampling in Matter Machine Learning?

This question is somewhat broad, but hopefully I can convey my point and elicit some worthwhile discussion. One of the fundamental difficulties of machine learning is trying to develop a model that ...
11
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2answers
103 views

How reproducible are results from materials modelling? Are there any notable results which could not be reproduced?

One of the key pillars of scientific method is the reproducibility of scientific results. A 2016 survey by Nature revealed that many fields in science suffer from reproducibility crisis. Lejaeghere ...
7
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2answers
112 views

Apply DFT+U to Oxygen/Nitrogen p Orbitals

I often see DFT+U corrections for transition metals with delocalization problems, but a comment about applying a U correction to nitrogen or oxygen's p orbitals also shows up when digging around in ...
8
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1answer
106 views

Gaussian-n test sets in machine readable format?

Gaussian-n theory has been used for a long time to assess the accuracy of density functionals, and for some reason still appears to be used in the literature even though much more accurate ...
16
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3answers
177 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?...
9
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1answer
145 views

Computational biology textbook similar to “Computational Materials Science” by June Gunn Lee

I'm looking for a text for computational biology which is similar in structure to a book called Computational Materials Science by June Gunn Lee. In his book, Lee discusses the theory of MD ...
11
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1answer
201 views

How to use coherent-potential approximation (CPA) method in VASP?

I found there are very few tutorials regarding how to use the CPA method in VASP. Are there any nice materials available? Also what are the pros and cons of CPA and VCA? If CPA is more reliable then ...
18
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5answers
413 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 ...
8
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2answers
137 views

Supercell band structure unfolding advantages

I understand that some codes allow for or have external tools to perform band unfolding in super cell calculations. Normally these codes give band structures that are somewhat grainy and not nearly ...
8
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2answers
92 views

Alanine dipeptide trajectories dataset

I was looking for a dataset of alanine dipeptide trajectories. I was wondering whether there is such dataset available or it is unlikely to find one and I should start running molecular dynamics ...
8
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2answers
181 views

Tools for structural analysis on LAMMPS trajectories

I have a very general question but still quite important since I didn't find convincing tools to get the structural analysis done for LAMMPS dump file (trajectories). I am looking for post processing ...
12
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2answers
466 views

What is Surface termination and how to make surface termination of a crystal structure?

I want to calculate the surface energy of CuO and for that, I've asked CuO (monoclinic) crystallographic plane and their relaxed surface energy. But for the lack of knowledge of the surface ...
9
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2answers
202 views

How to calculate the nuclear energy derivatives in molecular mechanics?

In molecular mechanics, the energy is often written as a sum of bonds, angles and torsion energies, and an electrostatic term, e.g. $V = \sum_{bonds} K_r (r-r_{eq})^2 +\sum_{angles}K_{\theta}(\theta -\...
11
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1answer
83 views

CuO (monoclinic) crystallographic plane and their relaxed surface energy

I want to calculate wulff construction for CuO of space group C2/c. Can any one help me with its crystallographic plane/Miller indices and their corresponding relaxed surface energy? If you can ...
22
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1answer
123 views

Which basis set families were optimized to give the lowest possible variational energy for a given number of orbitals?

Dunning's basis set families (such as cc-pVXZ and aug-cc-pCVXZ) were not optimized to give the lowest variational energy for a given number of orbitals. For example the S-type orbitals are optimized, ...
22
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5answers
366 views

What functions other than Gaussians are used for orbital basis sets?

The Gaussian function $\propto\exp((x-a)^2/b)$ with $b>0$ is one of the most common functions used in molecular modelling (e.g. Gaussian type orbitals). What are some examples of applications of ...
17
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1answer
114 views

Benchmark transition state geometries in condensed phases

I'm seeking references/benchmarks for transition state geometries of reactions in condensed phases like crystals, zeolites, or surfaces. Basically the system just needs to be considered big, yet ...
12
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1answer
91 views

Theoretical origins of stereochemistry

What are the current theories of computational chemistry for studying homochirality (for example the phenomenon discussed here, here and in many other places)? Electroweak chemistry has been developed ...