Questions tagged [terminology]
Questions seeking clarification on the various terminology related to materials modeling.
42
questions
4
votes
1
answer
494
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.
- 1,117
5
votes
1
answer
408
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, ...
- 153
3
votes
1
answer
112
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?
- 2,352
5
votes
1
answer
121
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 ...
- 53
3
votes
1
answer
223
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 ...
- 221
8
votes
1
answer
273
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 ...
- 2,352
3
votes
0
answers
34
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 ...
- 911
6
votes
3
answers
2k
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&...
- 2,025
4
votes
2
answers
149
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 ...
- 2,352
4
votes
0
answers
63
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 ...
- 1,894
4
votes
2
answers
168
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 ...
- 2,352
1
vote
1
answer
105
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, ...
- 2,352
14
votes
1
answer
242
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".
- 2,025
3
votes
3
answers
681
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 ...
- 2,352
4
votes
1
answer
146
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 ...
- 2,352
3
votes
0
answers
95
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?
- 529
7
votes
2
answers
1k
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".
...
- 6,551
3
votes
0
answers
51
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!
- 3,813
13
votes
3
answers
4k
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.
- 1,674
10
votes
1
answer
501
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... ...
- 1,894
6
votes
1
answer
78
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 ...
- 929
5
votes
1
answer
84
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?
- 151
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&...
- 7,957
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),...
- 175
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'...
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 ...
- 1,585
6
votes
1
answer
182
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 ...
- 841
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.
user1263
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 ...
- 10.8k
12
votes
1
answer
135
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 ...
- 375
20
votes
2
answers
995
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 ...
- 33.6k
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 ...
- 161
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 ...
- 1,894
11
votes
1
answer
248
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 ...
- 1,962
10
votes
1
answer
182
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 ...
- 33.6k
11
votes
1
answer
291
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 ...
- 4,719
20
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 ...
- 4,719
32
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 ...
- 33.6k
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 ...
- 22.3k
6
votes
1
answer
252
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 ...
- 6,579
17
votes
6
answers
536
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 ...
- 1,607
31
votes
2
answers
653
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 ...
- 411