ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

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ASE Manual, Release 3.6.1.2828 An other example showing how to change colors and textures in pov can be found here: doc/tutorials/saving_graphics.py 7.7 ASE-GUI The graphical user-interface allows users to visualize, manipulate, and render molecular systems and atoms objects. It also allows to setup and run a number of calculations and can be used to transfer between different file formats. 72 Chapter 7. Documentation for modules in ASE
7.7.1 ag basics and command line options General use ASE Manual, Release 3.6.1.2828 Visualizing a system with ag is straight-forward using a regular mouse. The scroll function allows to change the magnification, the left mouse button selects atoms, the right mouse button allows to rotate, and the middle button allows to translate the system on the screen. Depending on the number of selected atoms, ag automatically measures different quantities: Selection measurement single atom xyz position and atomic symbol two atoms interatomic distance and symbols three atoms all three internal angles and symbols four atoms, selected sequentially Measures the dihedral angle, e.g. the angle between bonds 12 and 34 more than four atoms chemical composition of selection. ag can save the following file formats: File format Comment xyz XYZ file traj ASE trajectory pdb PDB file cube Gaussian cube file py Python script vnl VNL file png Portable Network Graphics pov Persistance of Vision eps Encapsulated PostScript in FHI-aims geometry input POSCAR VASP geometry input bundle ASE bundle trajectory cif Crystallographic Information File Files The ag program can read all the file formats the ASE’s read() function can understand. $ ag N2Fe110-path.traj Selecting part of a trajectory A Python-like syntax for selecting a subset of configurations can be used. Instead of the Python syntax list[start:stop:step], you use filaname@start:stop:step: $ ag x.traj@0:10:1 # first 10 images $ ag x.traj@0:10 # first 10 images $ ag x.traj@:10 # first 10 images $ ag x.traj@-10: # last 10 images $ ag x.traj@0 # first image $ ag x.traj@-1 # last image $ ag x.traj@::2 # every second image If you want to select the same range from many files, the you can use the -n or --image-number option: $ ag -n -1 *.traj # last image from all files $ ag -n 0 *.traj # first image from all files Tip: Type ag -h for a description of all command line options. 7.7. ASE-GUI 73
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