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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7
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2answers
62 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 ...
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1answer
132 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
97 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 ...
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0answers
42 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 ...
8
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2answers
113 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
67 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
346 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 ...
8
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2answers
79 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
195 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
71 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
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1answer
100 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
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1answer
85 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 ...
7
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0answers
40 views

What are the methods of modeling Jahn-Teller effects in a solid-state material?

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 ...
8
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1answer
89 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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88 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 ...
8
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1answer
74 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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1answer
71 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 ...
16
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3answers
435 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 ...
7
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0answers
47 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, ...
8
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1answer
62 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 ...
9
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2answers
378 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 ...
13
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1answer
113 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
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2answers
85 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 ...
10
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1answer
131 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
186 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 ...
18
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2answers
171 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 ...
18
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5answers
316 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 ...
16
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3answers
148 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?...
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0answers
50 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
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1answer
65 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 ...
21
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2answers
434 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 ...
16
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6answers
270 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....
12
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1answer
206 views

How does the atomic arrangement look like in a compound that has partial/mixed site occupancies

I am working on modelling of a material that has partial/mixed site occupancies. For example consider the tetragonal (P4mm) compound $\ce{(Ba_{0.67}Sr_{0.33})TiO3}$. Following is the atomic ...
16
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1answer
109 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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3answers
489 views

Is the DYNAMO code developed by LAMMPS still available?

In 2013 it was stated that v8.8 of DYNAMO was the version mostly used for the last 10-12 years. However I am struggling to find the code repository. It was developed by the LAMMPS developers and is ...
15
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1answer
92 views

Types of Discrete molecular models

It is often assumed in cheminformatics that molecules with similar physical structure tend to have similar chemical properties [1]. Based on this, our group has used discrete graphs as a model for the ...
9
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0answers
74 views

Is there any literature that systematically analyzes current quantum chemistry algorithms using Big O notation for time and memory cost? [closed]

Big O notation is commonly seen in the papers on novel computational methods. However, only a few of them include rigorous analysis of the algorithm. Is there any literature that summarizes current ...
16
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3answers
823 views

I am a beginner in DFT. What are some resources that could help me to learn the basics?

I am a beginner in DFT. Please suggest me some good material to understand the basics.
21
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1answer
108 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, ...
16
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2answers
151 views

State of the art in computational materials design

With the advent of more computational power than ever in the recent years, interest in in silico design of interesting compounds has grown as well. I am wondering about the state of the art for the ...
16
votes
1answer
99 views

What are typical RPA capabilities of plane-wave codes?

Plenty of standard plane-wave codes are able to compute correlation energies on top of DFT solutions using the random-phase approximation (RPA). I was wondering what the typical capabilities are in ...
13
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1answer
116 views

TS-search with explicit solvent

I'm looking for an advice how the best to set up the system and optimize a transition state with explicit solvent. I believe that solvent molecules are participating in the reaction by specific ...
10
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1answer
70 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 ...
11
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1answer
49 views

What methods are there to simulate microscopic cracking of materials?

When a material forms a crack (say, for example, a disk that is getting old, or a fresh bread where force is applied to), on the microscopic/atomic level, atomic bonds break and forces are overcome. ...
15
votes
1answer
56 views

What are good resources to study crystallographic defects in different dimensional systems and their topological dimensionality?

I wonder if there are any books or resources that may address one or more of the following questions: What kinds of defects are important for topology? Especially crystallographic defects. How do ...
14
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2answers
109 views

What is the largest system for which vibrationally resolved electronic spectra have been simulated using ML-MCTDH?

Multi-layer Multi-configuration time-dependent Hartree (ML-MCTDH) is a method widely used for simulation of vibrationally resolved electronic spectra that incorporate the coupling between vibrational ...
21
votes
5answers
318 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 ...
23
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2answers
231 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, ...
9
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1answer
91 views

Is there any recent beginner's reference on materials informatics?

I wonder if anyone might save me several clicks and hours of scrolling and point me to a good recent survey/book on materials informatics to get me acquainted with the field?
12
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0answers
44 views

What are good references to learn how to model heterostructures using DFT? [closed]

I am interested in modeling heterostructures using DFT. What are some good references to start learning?