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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9
votes
1answer
190 views

How can we calculate the Gibbs free energy from first principles?

I am trying to calculate the Gibbs free energy for a bulk material. Since DFT ground state calculations give the energy at 0K, a temperature dependent part has to be added in this to obtain correct ...
6
votes
1answer
53 views

Where can I find/generate force-field parameters for common inorganic anions in water?

I have to do simulations of some inorganic anions, specifically $\ce{PO4^3-}$ (ortho-phosphate), $\ce{CO3^2-}$ (carbonate), $\ce{SO4^2-}$ (sulfate), in an aqueous enviornment. However, I am having a ...
5
votes
0answers
33 views

References for Electrostatics Calculations Used in Molecular Dynamics

I'm looking for classic references that describe the usual electrostatic contributions which have to be calculated in molecular dynamics simulations. I find it very hard to apprehend what different ...
6
votes
0answers
41 views

Large compound/material dataset with physical and chemical properties?

I'm looking for a fairly large (>100k) dataset of chemical compounds (and materials) that also has physical and chemical properties (such as boiling point, conductivity, solubility, etc.). I've ...
6
votes
1answer
54 views

How can scanning tunneling microscopy images (constant current and dI/dV conductivity) be simulated? What's under the hood in software packages?

Scanning tunneling microscopy comes in several flavors; vanilla (traditional STM) is constant current where the tip height is varied to maintain a constant current at a set constant bias1 and the ...
17
votes
4answers
363 views

Good books about computational chemistry of solid state materials for newbie

At the University, I chose the organic chemistry path and to better understand my experimental works I started studying computational chemistry on my own. There are a lot of books in this field, but I ...
8
votes
0answers
73 views

References related to the molecular distance geometry problem (estimating true distances based on noisy distances)

One aspect of the molecular distance geometry problem (MDGP) described in this PDF, can be written as follows: "Given observations of noisy distances between atoms in a molecule, estimate the ...
15
votes
1answer
142 views

Linearized Augmented Plane Wave Method vs. Pseudopotential Methods

While reviewing some DFT literature, I have come across a few papers utilizing the LAPW (Linearized Augmented Plane Wave) method, but I am interested in understanding why exactly one would use these ...
11
votes
1answer
301 views

Choice of coordinate system for geometry optimization

For geometry optimization, most QM codes tend to use internal coordinates. Most codes also support Cartesian coordinates. I have always heard the usual "use Cartesian as a last resort, always use ...
11
votes
1answer
222 views

What units are used in Gaussian 16 for dipole derivatives output?

I ran a frequency analysis employing Gaussian 16 on MP2/6-31+G(d,p) level of theory with the keyword iop(7/33=1) in order to have access to dipole derivatives with ...
12
votes
1answer
112 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
votes
3answers
547 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 ...
4
votes
1answer
62 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 ...
8
votes
0answers
69 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 ...
10
votes
1answer
147 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 ...
14
votes
1answer
229 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. ...
6
votes
1answer
97 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 ...
7
votes
0answers
304 views

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

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
58 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, ...
12
votes
2answers
164 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 ...
6
votes
0answers
55 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-dimensional particles. Is it always necessary to passivate the free surface of the quantum dot? Regarding ...
9
votes
1answer
102 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: ...
13
votes
2answers
290 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 ...
10
votes
1answer
77 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
votes
1answer
67 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
votes
1answer
99 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
votes
1answer
385 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.
20
votes
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
votes
1answer
64 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 ...
11
votes
1answer
238 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 ...
20
votes
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 ...
8
votes
1answer
56 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 ...
7
votes
2answers
166 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 ...
18
votes
1answer
235 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
votes
1answer
151 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
votes
1answer
263 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 ...
23
votes
1answer
143 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
votes
2answers
145 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
votes
2answers
228 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
votes
2answers
581 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
votes
2answers
105 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
votes
2answers
218 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
votes
1answer
90 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
107 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 ...
12
votes
1answer
96 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 ...
10
votes
0answers
71 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
124 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)?
9
votes
0answers
100 views

Coupling between 1st and 2nd order phase transitions? [closed]

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
102 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 ...
10
votes
2answers
138 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 ...