Hot answers tagged

18

It depends somewhat on the properties you are interested in. Meaningful vibrational modes, for example, require that your geometry is an energy minimum for the method you are using. Since the experimental structure is unlikely to be energy minimum for an arbitrary electronic structure method, you should optimize starting from the experimental structure. Its ...


18

The XYZ format provides a list of atoms with minimal content: element and coordinates. This is often not sufficient, so people need other formats. In particular, XYZ cannot describe a crystal -- it doesn't include unit cell parameters. The PDB format was designed with proteins and nucleic acids is mind. The format is old (from 1970's) and popular, so ...


17

You can use the free software VESTA for creating a new structure by following steps From the file menu choose New structure Go to Unit cell panel and choose the space group of the structure Enter the lattice parameters in the same panel Change to Structure parameters panel and enter x,y,z and Ueq of each atom one by one Save the structure and after ...


12

You can use for example pymatgen in python to do this. The tricky part of your question is to find a unit cell in step 2. I outline the steps here: Read your xyz file into a pymatgen structure. Use the SpacegroupAnalyzer class to determine the unit cell. Write the cif file using the class CifWriter.


12

This is a very intriguing question. I'll answer assuming that your CIF is formed by a molecule-based crystal. The structure in such CIF has been obtained usually by the X-ray diffraction technique. With it, you can obtain a single cell that, repeated in the 3 spatial directions, forms the total crystal structure. Considering this, if you isolate just one ...


11

This is due to an unfortunate code-change in some versions of Open Babel. AFAIK, versions 3.0 and later have a heuristic to detect if the CIF contains a molecule, or is a traditional solid-state crystal structure (e.g., NaCl, YBCO, etc.). These versions are used by the latest development versions of Avogadro (1.93 / 1.94 at the moment). Based on your ...


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

A command line package I use very often to convert between structure formats (and other things) is c2x. You can download the code from their website, and a quick "c2x --formats" suggests that it supports both cif files and xyz files.


10

Well, to answer properly this question first we would need a clarification about the nature of the CIF file. This type of file is Crystallographic Information File, which means that it is devoted to periodic, crystalline, and symmetric materials. In my opinion a core-shell nanostructure (CNS) is not fullfilling this requirements. In particular, the symmetry ...


9

I tried out a few programs. It seems like Jmol and Molden do resolve the CIF structure and directly show me one molecule with all its bonds without requiring any further input. Other programs like Avogadro or a command-line conversion with OpenBabel just produce the raw data of atoms scattered in the unit cell.


8

Two things are mixed in the question. How to create atomistic model of a core-shell nanoparticle? Are both the core and the shell assumed to be crystalline? Most likely you will need is to write a small program that generates the required configuration by calculating atomic positions. You can create the first approximation of a (uniform) nanoparticle by ...


8

The journal requires that the data is deposited in CCDC, ICSD or CRYSTMET. This one was apparently deposited in ICDC with the depository number CSD-417100 (the number is given in the paper, I don't have access to the database). If you also don't have access to ICDC write an e-mail to the author asking for the CIF file. Most academics are happy to answer ...


8

If you're not tethered to Avogadro You can use Mercury to change the system size by going to calculate, packing, and adjusting the cell size.


7

One option is to use the Atomic Simulation Environment's sort function. The function ase.build.sort() takes a required Atoms object (e.g. the supercell of the original CIF) and an optional tags argument that allows you to sort however you wish. It's then just up to you to find out how to flag each individual molecule in the order that you'd like.


7

As far as I understand, this warning can be safely ignored. While parsing a cif structure, the get_spacegroup() function in the cif parser of ASE, checks whether the space group evaluated by ASE is consistent with the cell symmetry mentioned in the cif file. The relevant part of the function is shown below: if setting_name: no = Spacegroup(...


6

I don't know if this is exactly what you want to do, but pymatgen may be able to help (disclosure, I am a developer of this package). See this example code below for your example input file: from pymatgen.core.structure import Structure, Molecule from pymatgen.analysis.graphs import StructureGraph from pymatgen.analysis.local_env import JmolNN # load the ...


6

If one has access to CCDC's Mercury app, the unique molecules (Z') can be easily written as mol2 or xyz files by the Save As option. Of course, this requires completely written CIF file (with metadata). Often times, some codes lazily output all coordinates in the unit cell.


5

There is a way around it you can include a NULL database code [using the _cod_database_code keyword ]under the data_global keyword in CIF and it will work. example: data_global _cod_database_code None This worked for me. Since the cod_databse_code is just for printing the first few comments in the input file created by cif2cell it will resolve ...


5

If the content of the .cif in question is fairly molecule-like, my recommendation are the cod-tools collection by the Crystallography Open Database. These may be obtained directly from their web site; if you use Debian 10/buster or Ubuntu 18.10LTS and higher, you equally find them in the the repositories (DebiChem tracker). A typical extraction follows the ...


5

In the case of Avogadro, the process is really straightforward. Go to File -> Save As In the pop-up window, you can save the data as .xyz or .mol (among many others) types.


4

I was able to find a CIF for this compound through the Materials Project. You can download the CIF, along with viewing other properties of this structure, here: Monoclinic MoO2 In general, the Materials Project is a good place to look for CIFs, along with any of the databases listed by the IUCR (International Union of Crystallography).


3

There are probably quite a few software packages that automate this process. One I like to use is c2x, which provides support for structure files for multiple DFT packages (VASP, QE, Abinit, Castep, etc.) and visualization tools (VESTA, XCrysDen, JMol, etc.). You can download it from their website: https://www.c2x.org.uk


3

ASE can be used to achieve what you require. Basically we need to: Read the structure. Determine the molecules using neighborlist class in ASE. Sort each of the molecules in the required manner using ase.build.sort. The following code does this: import numpy as np from ase.io import read, write from ase import Atoms, neighborlist from ase.build import sort ...


3

This is in Avogadro 1.2.0. I will check behavior on Avogadro 2 later: File -> Open -> Choose your cif file Build -> Super Cell Builder -> Choose the number of repeats File -> Save As -> Choose desired file type (XYZ and PDB work. Avogadro 1.2.0 seems to lock up on my system when I try to write mol2 files by this procedure. I would guess ...


3

While a CIF is not a suitable file format for handling volumetric charge density data, you may find Henkelman's chg2cube.pl script to achieve what you're looking for. It will convert a VASP CHGCAR file into a Cube format, the latter of which many programs can also read and is fairly easy to understand.


3

1H MoS$_2$ without inversion symmetry (I assume you want to MoS$_2$ monolayer) can be built from 2H bulk MoS$_2$. The following is a raw model (saved as MoS2.vasp and open with VESTA software). MoS2 1.00000000000000 3.1828219313310346 0.0002029835391965 0.0000002023172743 -1.5914442249239205 2.7566628171638539 0.0000005369011847 0....


2

You can download structures freely from the database of Materials Project. For example, the monoclinic MoO$_2$ can be found from this link: https://materialsproject.org/materials/mp-559140/


2

You can upload your .xyz file into VESTA, then under the Edit -> Edit Data, you can find the Unit Cell option. Then you can export your data to a .cif format under the File tab.


Only top voted, non community-wiki answers of a minimum length are eligible