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Questions tagged [terminology]

Questions seeking clarification on the various terminology related to materials modeling.

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22 votes
3 answers
2k 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 ...
4 votes
1 answer
688 views

What is the difference between computation and simulation?

I would like to know some examples too, if you could use them in explaining in the words.
5 votes
1 answer
553 views

What are alpha and beta electrons?

Question The mwfn filetype includes fields for alpha and beta electrons/orbitals/density matrices. What is the definition of alpha and beta electrons; what distinguishes them? For future research, ...
4 votes
1 answer
137 views

Are MD and MC both parts of statistical physics?

Are MD (Molecular Dynamics) and MC (Monte Carlo) both parts of statistical physics or is only one of them? If so, which branch (e.g., mechanics, thermodynamics, etc.) and why?
5 votes
1 answer
127 views

A terminology for QM calculation methods

I wonder if there is any terminology (or name of classification) that refers to ab-initio QM methods based on the Schrodinger equation and basis functions, such as HF and post-HF methods, but not DFT ...
4 votes
1 answer
378 views

What is the difference, if any, between an effective core potential (ECP) and a pseudopotential?

I've used these terms interchangeably for a while, but have noticed that in PySCF they are separate attributes. Are there any crucial differences between an effective core potential (ECP) and a ...
9 votes
1 answer
351 views

Difference between Statistical Physics, Statistical Mechanics, and Molecular Modeling?

I am looking for relevant books to study the modeling and Monte Carlo simulation of protein chains. I see that books related to Statistical Physics, Statistical Mechanics, and Molecular Modeling have ...
14 votes
1 answer
268 views

What are differences between Mott and Anderson transitions?

Can anyone please explain the differences between Anderson and Mott insulator-metal transition? I found some information in the book named "The_Physics_of_Amorphous_Solids".
18 votes
6 answers
563 views

What are the common acronyms in Materials Modelling?

Many abbreviations are used in Materials Modelling. For example, we have DFT (density functional theory/discrete Fourier transform), TST (transition state theory) and MD (molecular dynamics). Which ...
3 votes
0 answers
40 views

How are reconstructed surfaces named? [closed]

I am trying to understand the terminology of reconstructed surfaces. Simple surfaces such as 2x2 or 1x1 make sense to me. For instance, figure 1 of the paper https://doi.org/10.1063/1.1574798 shows a ...
13 votes
3 answers
5k views

What does "force field" mean?

In MD simulations we often hear the term force field. What is it? We know, for example that, Gromacs provides various types of forcefields.
13 votes
1 answer
2k views

What does a density of states (DOS) plot show?

I have plotted the density of states using GGA-PBE exchange correlation functional for magnesium silcide but I really do not know what the equations involved are in this process, and how they relate ...
12 votes
1 answer
2k views

What does capital sigma followed by an integer (Σn) mean in the context of grain boundaries?

I've just run across a nomenclature for coincidence lattices at grain boundaries which uses a capital greek letter sigma followed by an integer. For example A.D. Rollett's 2016 Grain Boundary ...
4 votes
2 answers
162 views

What is a "transient" state?

I was analyzing this source code of the Ising model. I found the term "transient state". I also found the term in this text: There are two absorbing states in this Markov chain because once ...
6 votes
3 answers
3k views

Difference between "electrical" and "electronic"?

I found that people often measure "electrical conductivity", but some may say "electronic conductivity". Can anyone explain the terms "electrical" and "electronic&...
4 votes
0 answers
65 views

Basic principles (and vocabulary) necessary to begin modeling the rate of atom surface diffusion and thermal planarization of ground metal surfaces?

Background: Surface science experiments very often start with atomically smooth crystal surfaces as substrates. After one experiment ends the surface is sputter cleaned with cycles of keV energy argon ...
4 votes
2 answers
181 views

What does it mean by "scale mismatch" and "bridging of scales"?

As far as I understood, molecular simulation works in two types of scales: temporal scale - how much time is required to simulate the model. spatial scale - how much memory-space is required to ...
1 vote
1 answer
107 views

What does "dynamics" mean in matter modeling?

As an example, I have seen the phrase "dynamics of proteins" or "dynamics of biomolecules". The review paper "Protein Dynamics" by J A McCammon has the word in its title, ...
3 votes
3 answers
683 views

Is it correct to say "in molecular dynamics we are faced with..." or should it be "in molecular modeling we are faced with"?

In the paper "DeePCG: Constructing coarse-grained models via deep neural networks", it says: "In molecular dynamics (MD), we are often faced with two types of coarse-graining tasks. In ...
4 votes
1 answer
161 views

Definition of the terms "modeling" and "simulation" in the context of biomolecules and/or proteins

What are the definitions of the terms "modeling" and "simulation" in the context of biomolecules and/or proteins? Examples will be highly appreciated. Also, please, back them up ...
33 votes
6 answers
4k 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 ...
3 votes
0 answers
105 views

Interpreting Phonon calculations for 2D materials [closed]

What is the meaning of phonon calculation in 2D materials? And is it enough to predict the stability of materials based on positive phonon only?
9 votes
2 answers
2k views

Different types of transition dipole moment in ORCA output

In the ORCA output for a TD-DFT calculation, there are two types of spectra printed. One is called "transition electric dipole moment" and "transition velocty dipole moment". ...
3 votes
0 answers
52 views

Cutoff energy in Quantum ESPRESSO calculation [duplicate]

What is cutoff energy in solid state calculations? I would just like a detailed explanation and the applicable formulas!
31 votes
2 answers
820 views

What is Materials Modeling?

I'm a noob with zero knowledge of the subject. Materials Modeling is so specialized that it's not even on Wikipedia yet. Help orient a newcomer. What do you use it for? Can you use it to model ...
10 votes
1 answer
531 views

Proposing a 2D quasicrystal; what are the necessary and sufficient conditions? (If it looks like a duck and quacks like a duck, or...?)

Quasicrystals show repeating motifs or patterns but are not periodic. And yet their Fourier transforms invariably demonstrate a pattern of sharp peaks revealing that there is still an underlying... ...
6 votes
1 answer
81 views

What is the meaning of Coulomb Subtraction?

Specifically, in the General Utility Lattice Program (GULP) 2003 paper, in the methods section on Two-body Short-range Interactions we have the following: For covalently bonded atoms, it is often ...
5 votes
1 answer
99 views

What does the "pn" column mean in this pseudopotential file?

In this SSSP pseudopotential file for Quantum ESPRESSO, what does the "pn" column mean?
6 votes
1 answer
1k views

What is the polarization catastrophe?

I heard about the polarization catastrophe in a talk about polarizable force fields. The speaker talked about how the dipole induction is damped at short range to avoid the “polarization catastrophe&...
20 votes
2 answers
1k 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 ...
6 votes
1 answer
256 views

How is the material $\ce{\alpha-NaMnO2}$ pronounced?

I am a theoretical physicist, so I am not very familiar with chemical names. The material I am interested in is $\ce{\alpha-NaMnO2}$. Would that be pronounced alpha sodium manganese dioxide? Is it ...
11 votes
2 answers
1k views

Is there any specific name for non-ferrous metals which are not noble metals?

In German there is the name "Buntmetalle" which means "colorful metals" for non-ferrous metals which are also not noble metals: Cadmium (Cd), Cobalt (Co), Copper (Cu), Nickel (Ni),...
30 votes
2 answers
1k views

What is matter modeling?

Perhaps a stupid question, but.. what is matter modeling? I've never heard of it, and a google search just returns news articles about this site that seem to assume you already know what it is. I can'...
6 votes
1 answer
203 views

What is the meaning of energy-consistent and shape-consistent in the context of pseudopotentials?

I am trying to use pseudopotentials to model scattering from heavy molecules. However, I am confused by some of the terminologies of pseudopotentials/ECPs: Norm-conserving according to Wikipedia and ...
19 votes
4 answers
1k views

How to explain Miller indices to someone outside nanomaterials?

I often find that when talking to experimentalists outside of the field of nanomaterials, it is nearly impossible to explain Miller indices concisely. As this often comes up during talks from other ...
12 votes
1 answer
136 views

What does it mean to assign group operations to distinct sets for space groups?

I am trying to understand space groups in crystallography. In International tables for crystallography, for a nonsymmorphic space group, they list some symmetry operations. 8 of them are listed under ...
14 votes
2 answers
3k views

High-Performance Computing: What does "Mio CPUh" mean?

Sorry if this question is too simple for the community but I really could not find an explanation. A detailed answer would be appreciated.
12 votes
1 answer
350 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 ...
16 votes
1 answer
3k views

What are "first principles" calculations?

A newcomer to density functional theory calculations is exposed to jargon which sounds rather non-technical at first. For instance, 'charge density' is something that is actually a term in the ...
11 votes
1 answer
258 views

How would you report the lattice parameters of an alloy, modelled using a supercell

There is a whole lot of literature behind ab initio modelling of alloys with statistical site occupancies. These include VCA, SQS, CPA, supercell approach, etc. This question does not aim to compare ...
11 votes
1 answer
192 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 votes
1 answer
2k views

What is the meaning of fat bands?

I came across the band structure colored as bellow1: As you can see, each band was colored depending of the atom contribution to each band. Googling, I found it was done using the concept of fat ...