Name: Dr Probe Cell File
Extension: .cel
Specification: Website of Dr Probe
Visualization programs: Dr Probe
Dr Probe is a software for simulating high-resolution scanning or transmission electron microscopy (HRTEM) images. Atomsk can read and write CEL files, with the restrictions below.
To write this file format, it is recommended that the occupancy and thermal vibration are 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 and 0, respectively.
It should be noted that Atomsk does not perform any implicit conversion of units. By default CEL files use nanometers as unit of length (and nm2 for thermal vibration). When reading CEL 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 CEL file. The examples below illustrate these points.
atomsk my_system.xsf -unit A nm cel
This will read the file my_system.xsf (where atom positions are stored in Å), convert atom positions into nanometers, and write the final result into my_system.cel.
atomsk supercell.cel -unit nm A cfg
This will read the file supercell.cel (where atom positions are stored in nanometers), convert atom positions into Å, and write the final result into supercell.cfg.
atomsk unitcell.cel -dupplicate 1 1 3 supercell.cel
This will read the file unitcell.cel, duplicate the system three times along Z, and write the final result into into supercell.cel. Note that since both input and output files use the same convention of units (i.e. nanometers) it is not necessary to convert the units.