Questions tagged [crystallography]
Questions concerning crystallography, the science of determining the arrangement of atoms in crystalline solids.
108
questions
6
votes
0answers
36 views
Any Open-Source, Free Software That Can Be Used to Computationally Calculate Binding Affinity Between Two Molecules?
There are programs out there which calculate the binding affinity between a ligand and a target protein (Autodock 4, Autodock Vina, Chimera... etc). Is there any analogous program that can be used to ...
10
votes
1answer
77 views
Recommendation of open source software that could build Heterostructure models visually?
I am looking for open-source software that could help me to build Heterostructure models visually, I've been working with BIOVIA Materials Studio before, but I got no valid license now, so I'd like to ...
7
votes
0answers
21 views
XANES simulation software/code besides FEFF for Pt L3 edge?
I need to generate the XANES region spectra of the Pt L3 edge of a theoretical Pt6 crystal with adsorbed atoms/molecules, such as $\ce{Pt(H^*), Pt(O^*), Pt(OH^*),Pt(CO^*)}$. It is for generating ...
6
votes
1answer
34 views
How to determine the right k-points for the band structure of a slab?
I am trying to compare the band structure of a slab and the bulk phase, just like the example on the VASP wiki. In the example of VASP, it calculates the band structure of the slab of Ni metal.
A slab ...
6
votes
0answers
44 views
Compute bulk electrical conducitivity from single-crystal measurements
If I have single-crystal measurements of electrical conductivity along 3D axes (considering for example anisotropic materials), is there any straightforward way to compute the bulk (global) electrical ...
6
votes
1answer
58 views
How to transform lattice in VESTA
Can anyone please help me transform $\ce{LiCoO2}$ hexagonal cell ($a \times a \times c$) to orthorhombic cell ($a \times a \sqrt{3} \times 1$) and hexagonal cell ($a \sqrt{3} \times a \sqrt{3}\times 1$...
8
votes
1answer
63 views
How to choose a proper rotation matrix and apply it to rotate unit cell about Cartesian axis
In this paper, they have rotated the unit cell using a rotation matrix, so the axes are aligned with the atomic bonds. I would like to know how they calculated that rotation matrix, and which software ...
2
votes
0answers
66 views
Visualizing Crystal Structures [duplicate]
I would like to know if there are any free alternatives to VESTA for visualizing crystal structures.
Thanks
9
votes
1answer
339 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... ...
10
votes
0answers
73 views
How to implement a toy DFT [duplicate]
I want to learn DFT for research purposes and I need to implement a toy DFT for pedagogical reasons.
I would like some recommendations regarding resources like books, articles, or any other thing that ...
14
votes
1answer
136 views
Looking for crystal generator library
I am looking for a C or a C++ library that can do crystal generation, that is, multiply unit cells in one or more directions with symmetry information. (in other words, generate supercells).
I have ...
29
votes
2answers
4k views
Can a highly-cited published paper have this type of error?
Related cross-network post: Have there been instances in physics where different scientists have interpreted the same data differently?
Here is my problem: I have been testing a force field published ...
5
votes
1answer
56 views
Variable Cell Optimization of Halfnium Crystal
Reference: Density Functional Theory: A Practical Introduction, David Sholl, Janice A. Steckel, Chapter 2, Page No. 46
Hf is experimentally observed to be an hcp metal with c/a 1.58. Perform ...
8
votes
3answers
116 views
Cu FCC vc-relax method error
Reference: Density Functional Theory: A Practical Introduction, David Sholl, Janice A. Steckel, Chapter 2, Page No. 48
Section 2.2 The fcc Cu calculations in Fig. 2.3 used a cubic supercell
with 4 Cu ...
6
votes
0answers
52 views
How to create a CIF using VESTA? [closed]
I am looking into double perovskite materials. One of the possible materials is $\ce{Cs4CuSb2Cl12}$. Now, although there are a few papers which have done ab intio calculations but none of the common ...
5
votes
0answers
29 views
DOS projection in alternate axis for eg and t2g contributions
I am studying doping in 0D and 2D perovskites which present tilted octahedra. It is important for me to analyze the contributions in the PDOS in terms of $e_g$ and $t_{2g}$ levels for d orbital in the ...
4
votes
1answer
40 views
wurtzite unit cell of ZnO
am looking to draw wurtzite unit cell of ZnO, and i find two of them
and the second one
how can I draw the first one in software like vesta?
5
votes
0answers
59 views
Space group will not change in VESTA
I have one unit cell of 16 atoms (4 formula unit cells) 2x2x2 unit cells. I want to construct the supercell with 32 and 64 atoms. I went in the transform and I changed the rotation matrix 4x2x2 and ...
5
votes
1answer
195 views
1T and 1H CIF file for MoS2
On the COD website, only 2-layer hexagonal (2H) and 3-layer orthorhombic (3R) $\ce{MoS2}$ are available. I can't find the 1-layer tetragonal (1T) and 1H CIF for $\ce{MoS2}$. Where can I find them, or ...
6
votes
2answers
79 views
How can I make a CIF file for Monoclinic MoO2?
A CIF file of Monoclinic $\ce{MoO2}$ is not available in the Crystallography Open Database website. How can I make it myself or find it elsewhere?
9
votes
0answers
72 views
Crystallography: How to sample *unique* structures from configuration space? (binary alloy supercell) [closed]
I'm working with a binary alloy system (call it 'AB'), and I'd like to generate a few unique configurations for DFT purposes.
My primitive cubic unit cell consists of 4 atoms; i.e. 4 positions. Thus, ...
10
votes
0answers
62 views
How to generate a complete set of doped (substituted) structures? [duplicate]
I'm trying to analyse doping in a certain material in low concentrations. I'm approaching the problem by taking crystallographic unit cell of that material, then expanding that to a 2x2x2 supercell ...
6
votes
0answers
151 views
Straightforward formalism to get four sets of 2D hexagonal lattice vectors of fcc(111) planes 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 ...
10
votes
2answers
116 views
High throughput tool to quantify the similarity of crystal structures?
Quantifying the similarity of crystal structures is important to understand and predict the properties of less-studied crystals. For example, the inorganic crystal structure database (ICSD) contains ...
9
votes
0answers
51 views
Is there a script that will suggest (hkl) indices based on distances in an electron diffraction pattern for a known crystal structure? [closed]
I am looking for a script (preferably in Python) that will suggest (hkl) indices based on distances in an electron diffraction pattern. The crystal structure is known,i.e. I have the CIF file and know ...
6
votes
0answers
84 views
How to optimize the geometry of beta PHB in VASP? [closed]
I would like to calculate the elastic constants of beta PHB. From this paper. I know that it has P3221 space group. The beta PHB has upward and downward chains, which exist at one lattice site with 50%...
9
votes
1answer
104 views
Problems with finding the unit cell from a CIF file and extracting XYZ coordinates using a software
I got hold of a CIF file for a material that I am interested in. I am trying to isolate the xyz coordinates of the molecules. However, when I open the CIF file in VESTA, I get a near-infinite periodic ...
11
votes
1answer
135 views
Extracting molecular strucutre from CIF file using VESTA or Mercury
I am trying to extract XYZ coordinates from a CIF file for a molecule to use in DFT calculations. I have Mercury and Vesta installed on my computer. Whenever I open the files, I get the following ...
16
votes
6answers
2k views
How to make a python code that can read a .xyz file and find the distance between atoms?
I want to make a python script that will load an xyz file. From the xyz parameters, I need to find the distance between atoms, angle and dihedral between atoms.
The file xyz have this structure:
...
7
votes
1answer
62 views
How to discard molecules at the boundary in the Atomic Simulation Environment (ASE)?
When building a supercell for a molecular crystal with the Atomic Simulation Environment, it seems that the program takes into account periodic boundary conditions when replicating the unit cell. How ...
13
votes
1answer
168 views
Minimum image convention for non-orthorhombic unit cells
I am trying to take into account periodic boundary conditions for non-orthorhombic unit cells.
I have the atomic coordinates for a monoclinic super cell with the following lattice vectors output by ...
13
votes
1answer
547 views
How do you write an .xyz file in the Atomic Simulation Environment?
I built a supercell of a molecular crystal and wish to write an .xyz file in ASE. How do I do that? The molecule has three different types of elements, C, H, and N.
5
votes
1answer
171 views
How do I extract the wave function from a VASP calculation?
We can obtain a energy band structure of a crystal from a DFT calculation in Vasp. Each point in each band represents an energy eigenvalue with a corresponding wave function from the Schrödinger ...
10
votes
1answer
314 views
How to import a .cif file into Avogadro 2?
I downloaded the latest version of Avogadro2 (1.91.0), but it appears I can't open a .cif file in this software. Is there a way around this? In an earlier version of Avogadro, I remember being able to ...
12
votes
1answer
150 views
How to cut properly a slab from a cif file?
I am trying to do DFT calculations on ethanol adsorbed on Pd, both surfaces 111 and 100. I have the cif file from the database and also I have built the new unit ...
12
votes
2answers
276 views
How to sort a supercell for a molecular crystal?
I am trying to build a supercell of the following (below) molecular crystal from its .cif file. How do I sort a supercell here according to each molecule in the supercell? I'm not tethered to a ...
5
votes
1answer
194 views
ASE: why do I get warnings about "monoclinic" and "orthorhombic" not being interpreted?
I am trying to use ASE (Atomic Simulation Environment) to build a supercell of some molecular crystals and then output the result to a file with the atoms given in a specified order for each molecule, ...
6
votes
0answers
34 views
Atomic Packing Fraction [closed]
I need to calculate excess entropy of mixing for a particular system of alloy. The excess entropy of mixing is dependent on temperature and it takes into account this temperature dependence by using ...
5
votes
0answers
42 views
What's the difference between dynamic and static strain aging? [closed]
I do understand how static strain aging occurs and why the yield point comes back if ample time is allotted after a loading and unloading cycles primarily due to diffusion of substitutional and ...
5
votes
1answer
174 views
Order of diffraction pattern confusion in XRD experiment
Somewhere I came across this phrase:
"expected diffraction angle for first order reflection."
With respect to XRD do I take this as a rule of thumb that the diffraction will always be a ...
11
votes
3answers
139 views
Rotation of crystal structure to match another structure of the same compound/polymorph
Say, I have two crystal structures of a particular organic molecule, the crystal structures are basically identical, apart from a rotation and redefinition of the lattice vectors/angles, a simple ...
