Questions tagged [crystallography]
Questions concerning crystallography, the science of determining the arrangement of atoms in crystalline solids.
122
questions
5
votes
1
answer
71
views
How easy is it to distinguish water from ions in xray crystallography?
I'm interested in bound ions in protein xray crystal structures. Of course a lot of structures include biologically significant ions, such as Mg2+ in the active site of an enzyme. But a lot of ...
5
votes
0
answers
47
views
How can I properly plot this .cube file in Python?
Motivation for Post: I saw a question about how to plot a .cube file recently on the Mathematica & Wolfram Language Stack Exchange. It was marked "off-...
2
votes
1
answer
42
views
Energy of formation Vs Formation Energy Vs Heat of Formation Vs Energy Above Hull differences
I work in the field of materials science. While exploring the concepts related to material stability, I have come across terms such as "Energy of Formation," "Formation Energy," &...
3
votes
1
answer
70
views
Computing lattice coordinates starting from lengths and angles
I've been reading this interesting paper and I'm trying to understand the following: it is known that a crystal lattice can be represented by 6 parameters corresponding to lattice vectors lengths ($a,...
1
vote
0
answers
44
views
How to model an interface between two solids
I have two solid surfaces that I want to combine to study the interface as seen in the attached image. What I know is the lower part of the bottom structure is fixed to mimic the bulk. However, do I ...
5
votes
0
answers
38
views
How to transform a perturbed surface structure to a reference surface structure?
Say I have a bulk FCC Pt structure obtained from Materials Project with a lattice constant a = 3.94 Å. I first did DFT to relax the bulk structure, and the optimized lattice constant becomes for ...
2
votes
0
answers
26
views
How to find the scaling factors for minimum image convention?
Suppose that we have an arbitrary (not necessarily cubic) unit cell with cell parameters $\mathbf{a}$, $\mathbf{b}$, $\mathbf{c}$ (lattice vectors) and $\alpha$, $\beta$, $\gamma$ (lattice angles).
We ...
3
votes
0
answers
44
views
Is it possible to find a cubic supercell for a non-cubic crystal structure?
Suppose that we have a crystal material with a non-cubic unit cell. E.g. $\alpha \neq \beta \neq \gamma \neq 90^{\circ}$. Is it possible to find a supercell such that $\alpha = \beta = \gamma = 90^{\...
0
votes
0
answers
69
views
Do the Miller indices <100> and <001> represent different families of directions?
In Miller indices, <100> is known to represent a family of directions:
Source
Does the <001> notation represent a different set of directions? I often see <001> in reference to the ...
3
votes
1
answer
253
views
Why the relaxation of my material in Quantum ESPRESSO wasn't achieved?
I did a vc-relax calculation using HSE by Quantum ESPRESSO and after 22h time WALL the job was complete and JOB DONE was mentionned in the end of the output file ...
2
votes
0
answers
26
views
Is it a good idea to always read charge and orbitals if I am working on similar systems?
For example, if I am investigating of the elastic properties of a crystal by doing a lot of computations of crystals applied with small strain.
Also, is it a good idea to read charge and orbitals when ...
2
votes
1
answer
97
views
Why I got more atoms than expected when generating POSCAR from VESTA
I tried to generate a perovskite structure with VESTA, and the following are my settings:
The generated structure seems to be correct. However, when I tried to export it as POSCAR I got the following:...
4
votes
1
answer
234
views
What is the best method to compute crystal structures?
I am rather new to VASP and I have seen people using different methods to compute crystal structure:
Using Birch-Murnaghan equation to find optimal lattice volume, and then adjust the structure ...
1
vote
0
answers
19
views
How to generate pole figures from limited amounts of area detector X-ray diffraction from thin films (explain it like I'm five years old)
Historically powder X-ray diffraction was the go-to method for reconstructing crystal structure. X-ray sources were limited in intensity and emittance and so to collect data in a reasonable amount of ...
3
votes
0
answers
24
views
What determines if a material tends to undergo transgranular or intergranular fracure?
As an example, why does glass tend to break by means of intergranular fracture?
My analysis so far led me to believe that the tendency can be related to the intermolecular bond strength in a given ...
9
votes
1
answer
125
views
How to stack graphene and hBN on top of each other?
I read in papers (e.g. link) about AA stacking, where C atoms are above the B and N atoms, and AB stacking where one C atom is above the N or B atom, while the other C atom is above the h-BN hexagon.
...
7
votes
0
answers
34
views
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 showing the same symmetry elements.
Let me provide an example since it might at ...
5
votes
0
answers
66
views
What is the ibrav value of a rhombohedral structure?
I have a rhombohedral structure
The SYSTEM and CELL_PARAMETERS blocks looks like this:
&SYSTEM
ibrav = 0
A = 6.058435171
...
2
votes
0
answers
125
views
A Question about ISIF Tag in VASP
I apologize for asking this stupid question, but I am a bit confused with the ISIF tag.
Doesn't a cell's shape and cell's volume depend on the atoms' positions?
If so, why can the cell's volume/shape ...
5
votes
1
answer
568
views
Why does my zincblende structure not look cubic?
The structure of my material is zincblende. So normally the structure is cubic. However, when I open the primitive cell with xcrysden it dosen't look 100% cubic. It's a little bit inclined. Also when ...
3
votes
1
answer
142
views
Layer detection in a crystal structure
Context
I have two images from a Monte Carlo Basin Hopping where silicon (in yellow) is getting replaced by germanium (in blue). Both have 32 germanium atoms at Si/Ge = 2.5; only the Ge distribution ...
7
votes
2
answers
297
views
Generate structure using atomic coordinates
I am trying to write a Python/C++ code that reads in a *.xyz file and varies the interatomic distances, angles etc. between distinct atoms in a molecule. In other words, a complete new structure with ...
5
votes
0
answers
95
views
Which crystal structure I have to choose for DFT calculations?
I want to study the properties of NiO as a hole transporting material adapted for perovskite solar cells using Quantum ESPRESSO.
From Materials Project website, I saw that NiO can exist in different ...
2
votes
1
answer
42
views
How is it possible for amorphous metal to have good magnetic properties with randomly arranged atoms?
Cross-posted on Physics.SE.
It makes sense that something like grain-oriented electrical steel would have good magnetic properties (e.g., magnetic permeability). I'm envisioning magnetic field lines ...
4
votes
1
answer
65
views
Program to classify structures of different composition?
Is there a program to classify and compare structures with different composition?
I want to compare e.g. structure_1 with composition [2,1,4] and structure_2 with composition [16,8,32]. Maybe both ...
1
vote
0
answers
25
views
Can CrystalFp library be used to compare structures with different number of atoms? [duplicate]
Can I use CrystalFp library to analyze different structures (e.g. of Ca2Si04) that don't have the same number of atoms?
I want to compare e.g. structure_1 with composition [2,1,4] and structure_2 with ...
4
votes
1
answer
238
views
Should this phenolic hydroxyl be rotatable?
Looking at nelfinavir, I get variable results from different compchem packages on whether the phenol hydroxyl oxygen should be rotatable (SP3) or non-rotatable (SP2). Which one is it?
Feasibly, there ...
2
votes
0
answers
21
views
Difference and meaning of isopointal and isoconfigurational structures [closed]
These are the meanings I`ve found, but I do not completely understand them.
Isopointal: Two structures that have the same space-group type or belong to a pair of enantiomorphic space groups. And that ...
5
votes
0
answers
55
views
Is there a free software to build a crystal shape that is cut with a specific angle plane (like 40 degrees), which is not implemented in Vesta?
I would like to cut $\ce{SrTiO3}$ with a specific angle of 40 degrees, or to choose an angle plane which is not implemented in the Vesta software.
Could you please recommend a free software to build ...
2
votes
1
answer
142
views
How do I know which is the asymmetric unit of a unit cell?
I need the number of independent atoms in the asymmetric unit
I have to introduce them in this form:
...
4
votes
1
answer
373
views
Maximum bond length in Vesta
I need some cutoff radii to count bonds between different atoms in my system. When a .cif file is opened in Vesta, there are some default values of min and max bond lengths between two atomic species. ...
3
votes
1
answer
257
views
How do the notions of Crystal structure, unit cell and supercell fit together?
I'm trying to fully understand the notion of crystal structures with some basic implications. I understand that it is conveniently described by a lattice which is the infinite repetition of points in ...
4
votes
1
answer
348
views
Measuring distance with ASE
I wish to calculate the distance of all the atoms from a particular atom(atom A) in my cell. But I also want to include the atoms that might lie just beyond the periodic unit cell boundary.( In figure,...
3
votes
0
answers
44
views
Tilting Octahedra of Perovskite structures in structure file
Perovskite materials form as a combination of $\ce{BX_6}$ octahdera along with A cation. Some perovskites display tilted octahedras. I am currently trying to run calculations for different tilted ...
2
votes
0
answers
28
views
How to create doped possible structures for the calculation in VASP [duplicate]
I want to find the doped structure of a compound. So i need to know how we can find the possible structures after substitution or interstitial doping? for example i want the possible structures for 6:...
3
votes
0
answers
151
views
How to transform the conventional cell to primitive cell, by hand?
I am following this tutorial to transform a conventional cell to a primitive cell, but I am not sure how to determine the primitive copy of some atom in the conventional cell.
For example, in the ...
3
votes
0
answers
35
views
How to visualize the basis in the unit cell of crystals?
Usually, the unit-cell of a crystal is made up of lattice points and basis, but all the crystallography software like VESTA doesn't show the basis, is there any ...
2
votes
0
answers
184
views
Confusion in primitive, conventional and supercell crystal structure
I am doing the DFT calculations in Quantum ESPRESSO code. I have 2 different pwscf input file of the same crystal. I am confused which one is representing primitive, conventional and supercell ...
5
votes
2
answers
284
views
How does one make sure that the [hkl] direction in ab-inito calculations is the same as in experimental calculations?
I am currently looking at isotropic properties and let's say I want to determine my property in the [100] direction. Now, I basically want that my [100] direction be the same as the [100] direction in ...
5
votes
0
answers
80
views
How to find the most stable facet for a crystal?
I am trying to find the most stable facet for a crystal, but since there are many possible choices, like (1 0 0),(1 1 0),(1 1 1),(2 1 0), etc. My questions is:
I am wondering how should I determine ...
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 ...
7
votes
1
answer
300
views
How does one decide the directions in which they will calculate effective mass?
I have been working on trying to calculate the effective mass in different directions by fitting a parabola to the VBM and CBM and using the fitted parameters to calculate $\frac{d^2E}{dk^2}$. And ...
1
vote
1
answer
61
views
Is there a robust and reliable software to change the lattice vectors of unit cells?
I am working with Heusler and Half Heusler materials on LAMMPS. Currently the study follows the properties in individual lattice directions such as [100] [110] etc. As of now, I am obtaining the unit ...
3
votes
1
answer
164
views
How to determine the concrete value for the wavenumber in tight-binding approximation
As a simple problem setting,
consider a one-dimensional linear crystal of NaCl with only 1s orbitals,
where the atomic distance between Na and Cl is also assumed to be 0.5 Å
for simplicity (Fig. 1).
...
3
votes
0
answers
330
views
How to fix outliers in Ramachandran plot using Coot [closed]
I have the following Ramachandran plot generated by Coot:
Notice that it has high outliers content (red dots). I want to manually drag those
red dots into some part of the region. Eventually, I ...
6
votes
1
answer
77
views
Repository of Common Surfaces
Are there any repositories of crystal surfaces? Due to orientation / termination of surfaces, occasionally it is non-trivial to decide how exactly to cut a surface for things such as oxides. I ...
9
votes
1
answer
329
views
Stability using Phonon Calculation
While performing phonon calculation using finite difference method, we get normal modes printed in the outcar file. Now there is a distinction between two different types of modes in the outcar file.
...
3
votes
1
answer
37
views
Spacing issues about multiple-layer bcc structure
I am trying to make Hartree potential of bcc Tungsten(001).
My software is VASP.
5-layer should have 5 bound states.
But I don't have them
I heard it is a layer-layer spacing issue.
I built slab of ...
2
votes
0
answers
87
views
Slab rotation with ASE, unexpected behaviour [closed]
I am trying to generate the $\sqrt{3}\times\sqrt{3}R30^\circ$ representation of a Pt111 slab, I start by generating the $1\times1$ using ASE:
...
2
votes
0
answers
68
views
Continuous Coordination Number Definition
I am interesting in quantifying the coordination number of some atoms in metals and am curious what approaches to defining a coordination number are possible for an atom. In particular, I am curious ...