18

You can see it with VESTA software. For example, we can see the different lattice planes of NaCl crystal. [001] plane of NaCl: [101] plane of NaCl: [111] plane of NaCl:


14

Phonon calculations tend to be very expensive to run. That being said, for gas phase molecules it is very common and expected that frequency calculations are run to ensure the molecule is not on a saddle point. In general, you can publish anything if it makes it past peer review. Phonon calculations are something you would do if you fear you are on the ...


13

In general it is not justified to published the geometry of a system without performing a phonon calculation. This is where you may end up in the potential energy surface depending on which type of calculation you perform: Geometry optimization. With a geometry optimization, you may end up at a local minimum or at a saddle point of the potential energy ...


13

Assuming a generic chemistry background I wouldn't assume that knowledge of crystal structure would be too in depth at an undergraduate level. It is definitely encountered, but depending on the type of chemistry you want to go into, you probably never deal with solid state chemistry. I would first explain briefly how crystals are described by periodic ...


12

Easiest free tool to do this (no download necessary): What you are describing, is the conversion from XYZ format to ZMAT format. How to do this, has been asked here on the Chemistry Stack Exchange, and my answer was to use this free tool in which you just copy and paste the 3 spatial coordinates along with the name of the element, for each row of the XYZ ...


11

ASE The ASE library has an atom object with built-in get_angle, get_dihedral and get_distance methods that do just that.


11

I highly recommend reading: Efficient creation and convergence of surface slabs The following answer will assume a reasonable level of VASP knowledge (where keywords can be looked up at the VASP wiki). The best way to optimize a monolayer or surface in VASP follows: First, optimize your bulk structure. This will give you a reasonable estimation. From the ...


10

VESTA I'm an avid user of VESTA and haven't quite used Mercury. So I'll the steps to do it in VESTA (it's quite easy though) Step 1: Open your file in VESTA Step 2: Choose the selection tool in the left panel. (highlighted in blue) Step 3: Click and drag to select the atoms you want to manipulate; Here the three top atoms After selection they are ...


10

What is the best way to optimize monolayer geometry in VASP? For the geometric optimization of the monolayer in VASP, you should use the following key tags: ISIF=4 % firstly using 4 then 2 IBRION=2 NSW=300 EDIFFG=-0.005 You can search the explanation for each tag in VASPWIKI. For completeness, I give an INCAR ...


10

This depends on what you are studying. For molecular systems without periodicity, the simplest approach is to carry out a vibrational frequency analysis and confirm that there are no imaginary modes. It is considered standard to carry out a vibrational frequency analysis for all investigated structures, provided the number of investigated systems is not ...


10

You can probably do it with only OpenBabel or RDKit using SMARTS search strings, but you can get a much easier solution if you combine OpenBabel with checkmol (which you have mentioned in the question). First, convert the .xyz file into a .mol file that checkmol can recognize. This can be done with Openbabel which can automatically detect bonds from 3D ...


9

In the paper you linked, the relevant phrase is "$A_{\mathrm{fu}}$ is the per formula unit total surface area of $\mathrm{TiS_2}$." The "per formula unit surface area" part is equivalent to "surface area per formula unit." So, the full surface area divided by the number of formula units. For the graphene example, it would be ...


8

If you know which atoms correspond to each other in the two structures, you can use a structural superposition method. Least-squares superposition methods find the rotation matrix and translation that minimizes the RMSD between given points. There are a few well-established methods. Recently, I had to use one and I picked QCP (because it comes with BSD-...


8

Open Babel First, the command-line version: obabel c60.xyz -oreport Yields: All interatomic distances All bond angles All connected torsions Also, partial charges e.g. INTERATOMIC DISTANCES C 1 C 2 C 3 C 4 C 5 C 6 ------------------------------------------------------------------ C 1 ...


7

Here is a more concise way of doing the same thing. from ase.io import read bec = read("bec_replaced.vasp").write("bec_replaced.xyz") It is not needed to import ase and import the functions, you want to do one or the other (This is a python thing not ASE). read also returns an atoms object with a write function built in, so there is no ...


6

There is no guaranteed increase in performance if you specify a non-zero value for ibrav. There is an additional layer to this - Whether the atomic positions are specified in cartesian or crystal coordinates (sometimes some symmetries can be missed out on QE). On both points, you would need to run a test calculation and see how many symmetries QE detects. ...


6

Since you know how to use Avogadro to create XYZ files, a very simple solution to your problem is to simply create the XYZ file then use an xyz2gen script to convert fron XYZ format to the GEN format you seek. This is an example of a script that converts from XYZ to DFTB+ format. The beauty of the GEN format of DFTB+ is that with only a few lines, you can &...


5

I would propably explain that there are different planes within a crystal, show some of them in an animation or pyhsical prop and depending on the depth of the presentation just omit the numbering and details.


5

You should do something like this instead: import ase from ase.io import read, write bec = ase.io.read("bec_replaced.vasp") bec_new = ase.io.write("bec_replaced.xyz", bec, format="xyz") according to the documentation page.


5

In order to check if a geometry is a local minimum, it is a necessary and sufficient condition that the Hessian is positive (semi)definite, i.e. that the lowest eigenvalue of the nuclear Hessian is non-negative. Namely, expanding the energy $E({\bf R})$ around the reference point ${\bf R}_0$ you have the Taylor expansion $E({\bf R}) = E({\bf R}_0) - {\bf g} \...


4

There is a patch of vasp used to fix any axis. For a monolayer materials, to fix c-axis is a good choice. https://github.com/Chengcheng-Xiao/VASP_OPT_AXIS When you want to optimize n-layer materials (n=2,3,4,5), Van der Waals (vdW) correction needs to be added in INCAR to condider the interaction between two layers. Usually I use IVDW = 11 to describe van ...


4

Take care in the figure posted by Jack that the [hkl] notation actually represents the vector plane, that is the direction perpendicular to the plane. The plane are indexed as (hkl). for example, the first figure should be read as (001) plane of NaCl, whereas [001] represents the direction along the c-axis.


4

If you're familiar with Python, this can be done using pymatgen fairly easily. To illustrate, let's first define our problem: from pymatgen.core.lattice import Lattice from pymatgen.core.structure import Structure malnac_lattice = Lattice.from_parameters(5.33, 5.14, 11.25, 102.7, 135.17, 85.17) malnac02_lattice = Lattice.from_parameters(5.156, 5.341, 8.407, ...


3

I've never done this before but here is my guess of how you can do it. If the numbers you posted are the unit cell axes vectors with a vector for each column then their direct matrices are. $$\tag{1}\mathbf{A} = \begin{bmatrix}3.31 & 0.00 & 0.00 \\ 0.00 & 10.47 & 0.00 \\ 0.00 & 0.00 & 4.37\end{bmatrix}...


3

It seems to me that there is a discrepancy about the c-axis in the 2 unit cells, producing a significant difference in the unit cell volume (213.1 and 210.8, respectively). If you apply the transformation matrix [-b,-a,c] to the first unit cell 5.156 5.341 8.407 71.48 76.12 85.09 and compare with the second one you obtain: 5.341 5.156 8.407 103.88 108.52 85....


3

The software GLIDE is not used for RMSD calculation. GLIDE is dedicated to do small ligand/protein docking (rigid/rigid and flexible/rigid). You can calculate the RMSD by hand, using MAESTRO, CHIMERA and VMD interfaces (all free for academics) among many other software (also free).


2

The question makes no sense, since a solid state system might have different phases, or a molecule might have different conformers. They may all be proper local minima of the energy functional, and with very small overall total energy differences. For instance, J. Phys. Chem. A 117, 2269 (2013) is a benchmark study for the 52 different conformers of the ...


2

This is not a xyz file. If you have xyz file then you can use numpy.genfromtxt() module to read from the data. create an numpy array having each component as an element of the array. Using eular's method to find the distance


1

You are correct that the optimum geometry for one spin multiplicity will in general be different for another spin multiplicity. Therefore if you want to know the geometry of the lowest-energy state of a molecule, a pre-requisite is to first know the electronic configuration (spin multiplicity and spatial configuration) of the lowest-energy state of the ...


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