Name: JEMS crystal file
Extension: .txt
Specification: Website of JEMS
Visualization programs: JEMS
JEMS is a software for simulating high-resolution scanning or transmission electron microscopy (HRTEM) images. Atomsk can read and write JEMS files, with the restrictions below.
To write this file format, the occupancy, thermal vibration, and absorption coefficients should be defined as auxiliary properties for each atom. They can be defined e.g. with the option -properties. If they are not set, Atomsk will use default values of 1, 0, and 0.03, respectively.
When reading JEMS files, if a space group is specified (in a line starting with "HMSymbol"), then the symmetry operations associated with it are applied immediately to all atoms.
It should be noted that Atomsk does not perform any implicit conversion of units. By default JEMS files use nanometers as unit of length (and nm2 for thermal vibration). When reading JEMS files, Atomsk stores these values as-is. It is up to the user to convert them to Å (or any other unit) if he wishes to do so after reading the file, e.g. with the option -unit. Similarly, if data is read in Å (or any other unit), it is up to the user to convert them into nm before writing a JEMS file. The examples below illustrate these points.
atomsk my_system.xsf -unit A nm JEMS
This will read the file my_system.xsf, convert the units from Angströms to nanometers, and write it to my_system.txt. The latter file can be opened in JEMS.