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
votes
1answer
50 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 ...
5
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0answers
53 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
votes
1answer
51 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, ...
9
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0answers
45 views

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

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 ...
10
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2answers
101 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 ...
5
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0answers
32 views

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 ...
9
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1answer
64 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: ...
14
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2answers
220 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 ...
11
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1answer
57 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
54 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 ...
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 ...
12
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1answer
354 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 ...
9
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0answers
36 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 ...
12
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1answer
218 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 ...
19
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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 ...
7
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0answers
31 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 ...
8
votes
2answers
89 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 ...
15
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0answers
152 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 ...
9
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1answer
137 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
147 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 ...
15
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0answers
50 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 ...
9
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2answers
124 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 ...
9
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2answers
124 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
388 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
81 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 ...
9
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2answers
198 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
79 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 ...
8
votes
1answer
102 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 ...
11
votes
1answer
88 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 ...
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)?
8
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0answers
90 views

Coupling between 1st and 2nd order phase transitions?

I am seeking some models or references on how to couple, or what to take into consideration, while coupling first-order phase transitions (for magnetic systems) and second-order phase transitions, in ...
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 ...
11
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2answers
122 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 ...
19
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4answers
495 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 ...
8
votes
0answers
59 views

Orbital-free DFT and Density Functional Tight-Binding: Comparison

There are many flavors of DFT that are alternative or go beyond the formulation of Kohn and Sham (KS-DFT). Some of these are based on approximations that sacrifice accuracy when compared to KS-DFT, ...
9
votes
1answer
73 views

What are the top journals that focus on or cover matter modeling?

What are the top journals that focus on or cover matter modeling? For context: I am a physicist, which is a small field, so I find it difficult to navigate the much-larger space of materials science ...
10
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2answers
392 views

Can Machine Learning lead to the more accurate theories and methods for matter modeling?

There's no doubt about it. Machine Learning (ML) is one of the hottest topics out there and it plays an important role in computational science. One application I have seen is to use ML and Density ...
14
votes
1answer
114 views

What progress has been made in modelling photocatalytic reactions on semiconductor surfaces?

For example, are there any methods to allow for modeling of photo-oxidation or photo-reduction of a compound on a semiconductor surface? It appears there has been a lot of work on the bulk properties ...
12
votes
2answers
88 views

What are real examples where fractals were used in Matter Modeling?

A fractal is, accordingly Oxford English Dictionary: A curve or geometric figure, each part of which has the same statistical character as the whole. Fractals are useful in modeling structures (such ...
11
votes
1answer
133 views

Examples of matter modeling in fiction

Can you remember any example of a work of fiction, for example, movie, book, short story, anime, et cetera, where computational matter modeling was an important plot device? I'm looking for examples ...
12
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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 ...
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 ...
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
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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?...
6
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0answers
52 views

Do we have authorship rankings in our field or related fields? [closed]

I was reading about the field of "energy economics" and found it fascinating that there is a list of "top 20" authors: At first this seemed strange: What does it even mean to be ...
7
votes
1answer
84 views

Bond Order: When and how is it used today?

We all learned about single vs double vs triple bonds in high school chemistry and biology. We learned that unsaturated fats have double bonds whereas saturated fats have only single bonds, which ...
22
votes
2answers
443 views

Create a new DFT functional from experimental data

This is my first time here and I think you can help me. I would like to try (just for fun) to create a new DFT functional starting from experimental data. Do you have any manual, procedure or ...
17
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6answers
282 views

What are the applications of chemical graph theory?

Graph theory was originally introduced in computer science to study data structure. Chemists also introduced graph theory to study the relation between structure and properties for molecular compounds....