Unanswered Questions
124 questions with no upvoted or accepted answers
11
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Have FDTD methods made inroads into dynamical simulation of electron and/or X-ray scattering by crystals?
I'm afraid this question might be too basic or too naive or both, but here goes!
For optical diffraction by periodic nano-structures (gratings, semiconductor manufacturing metrology) the rigorous ...
9
votes
0
answers
133
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How to go from zero to hero in Machine Learning for materials modelling
I am interested in exploring the use of machine learning tools to accelerate molecular dynamics simulation probably by training machine learning potentials. While I have found some papers that apply ...
- 453
9
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118
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DIY molecular dynamics for Xenes on crystal surfaces; where can I get applicable open-source force field parameters that I can use in my scripts?
The linked question(s) below describes a DIY project to simulate how Xenes (honeycomb nets of atoms like graphehe) behave on single crystal surfaces. Behaviors include rotation, strain, and heigh ...
- 2,074
8
votes
0
answers
258
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Contribution in action from collisions for a gas?
So if I write the action for a gas:
$$ S = \int (T -U) dt \tag{1}$$
where $T$ is the kinetic energy and $U$ is potential energy.
I suspect there is a constant term (which does not affect the equations ...
8
votes
0
answers
70
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How to calculate small and wide-angle X-ray scattering spectra for the hydration shell restricted by a distance radius criteria
My main aim is to extract the SWAXS spectra for the hydration shell surrounding a solvated molecule and I am unfamiliar with the idea of excluded solvent volume. I tried looking online but many ...
- 2,362
8
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96
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How do I identify an oblique surface mesh?
I have drawn three surface meshes from a hexagonal material for the $(0001)$, $(1\bar{1}00)$ and $(1\bar{1}01)$.
The first one would be the top horizontal surface of the hexagonal structure, the ...
- 15.9k
7
votes
0
answers
32
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Question about Constructing Supercell Layers for MD Simulations for Solid-Solid Phase Transitions
I am a newcomer to MD simulations,
so my questions may be at a basic level,
but I appreciate your understanding.
I would like to simulate solid-solid phase transitions using MD simulations.
To begin ...
- 3,770
7
votes
0
answers
57
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Database (or table) of functions obeying symmetry properties of space groups
I'm looking for a table or database containing mathematical functions that belong to crystallographic space groups by having the same symmetry elements.
Imagine a 2D square planar lattice. It has a 4-...
7
votes
0
answers
231
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Apparent conservation of potential energy in NPT simulation?
I was examining a system with a problematic equilibration (more details given at the end, but probably unnecessary to answer the question), and came upon what is presumably a pretty basic conceptual ...
7
votes
0
answers
176
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How to analyse structure factors calculated from a mixture of isotropic amorphous substrates
I am looking for a way to computationally analyse the interactions between two molecular species (as solute and solvent) in an isotropic mixture using X-ray scattering. Is there a guideline as to how ...
7
votes
0
answers
448
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Straightforward formalism to get sets of lattice vectors of fcc (111), (110) and (100) facet surfaces that I can also cite?
I am simulating low energy electron diffraction (LEED) from a polyfaceted sample. Usually it's a single, well-defined flat crystalline surface.
Since low energy electrons (below a few hundred eV) only ...
- 2,074
7
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0
answers
201
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How to convert lab frame quaternions and plane normal to misorientation quaternion and crystal plane normal for grain boundaries?
Background
Let qA and qB represent unit, orientation quaternions of grain A and grain B of a grain boundary in the lab reference ...
- 15.9k
6
votes
0
answers
132
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Free energy calculation as a function of temperature over phase transition
I've run a molecular dynamics simulation (NVT) of a simple Lennard-Jones system of a few particles and I'm trying to calculate the Helmholtz free energy $\Delta F$ as a function of temperature over ...
- 121
6
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229
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Regarding use of GCMC to add water molecules
I am working on a goethite system, and wish to fill the unit cell with water molecules for AIMD simulation using quantum espresso. For this, some papers[1],[2] indicated the use of Grand Canonical ...
5
votes
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answers
90
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What kind of simulation should I run to find out the temperature at which a crystal would melt?
I have learned some basics as far as performing molecular dynamics simulations, but struggle to figure out big-picture issues.
I would like to know if it's possible to find out the temperature at ...