XCrysden ASESMA 2015 Andrea Greco, Florian Thöle, Mehmet Topsakal Some slides are adapted from here: hCp://caribeictp.uis.edu.co/lectures/A.Hernandez/Xcrysden.pdf What is XCrysDen? •  XCrysDen is a program to visualize crystal structures and isosurfaces of 3D data •  It can load many formats: –  XYZ, XSF, PDB, Quantum Espresso input/output, … •  Runs on Linux (and Mac OS X; Win via cygwin) Launch xcrysden •  Launch by typing $ xcrysden Ge`ng the example files •  Download example structures: hCps://sites.google.com/site/asesma2015/
tutorials Loading a file •  Open the file si.rho.xsf: File -­‐> Open Structure… -­‐> Open XSF Changing the display •  Use the mouse to: –  Rotate (lee click) –  Zoom (scroll wheel) –  Translate (click middle buCon) Changing the display •  Try the different display opgons •  Try all opgons in Display menu Changing the display •  Tasks: –  modify the number of displayed cells (Modify-­‐
>Number of Units Drawn) –  change the unit of repeggon (Display -­‐> Unit of repeggon) –  display Wigner-­‐Seitz cell (Display -­‐> Wigner-­‐Seitz Cells) –  display Brillouin Zone (Tools -­‐> k-­‐path Selecgon) –  Lighgng mode off (Display -­‐> Lighgng off) Lighgng mode off •  Faster mode for large systems Saving figures Select menu “Print”: File -­‐> Print Set filename and file format (by extension) • file.png -­‐-­‐ PNG format • file.gif -­‐-­‐ GIF format • file.eps -­‐-­‐ EPS format, etc. XCrysDen takes a screenshot of your structure. So before pringng to file is recommended to: • maximize the XCrysDen window • enlarge the structure to fill the window • increase tesselagon factor (menu Modify -­‐
> Tessellagon Factor) to 40-­‐50 Opgons for pringng •  Modify -­‐> Angaliasing parameters: Increase degree of mulg-­‐sample angaliasing •  Increase tesselagon factor (Modify -­‐> Tessellagon Factor) to 40-­‐50 Using xcrysden for analyses •  Use the funcgons to: –  Informagon about single atom –  Distance between two atoms –  Angle between three atoms –  Dihedral angle between four atoms •  Task: Do all of the above for the Si structure (also with more than one unit cell displayed) Atom info Distances Angles Isosurfaces •  The file si.rho.xsf contains data for the charge density of silicon. •  Select Tools -­‐> Data Grid, then press OK •  Enter a value for the isosurface, then “Submit” 2D planes •  In the same window as for the isosurfaces: –  Plane #1/#2/#3 –  Check “Display color planes” –  Click “Submit” Isosurfaces •  Tasks: –  Play around with the different opgons for isosurfaces –  What can you see in the display? –  Display 2D planes along one direcgon, play around with all the available opgons Checking input files for Quantum Espresso •  You can open input/output fies for QE: –  File -­‐> Open PWscf -­‐> … •  Now load the file BaTiO3.scf.in (in this case, choose “Do not reduce dimensionality” in the next window) and check its structure, bond lengths, angles, etc. Brillouin zone path •  Go to Tools -­‐> k-­‐path selecgon •  Select the path Γ-­‐X-­‐M-­‐Γ-­‐
R-­‐X •  Save it: Set the total number of points to 100, then click ok •  Choose file type: PWscf K_POINTS file •  Look at the saved file in an editor (vi, gedit, …) Animagon •  Load the file geom_opt.xyz •  Click the arrows (“>>”) to run the animagon of a high-­‐
pressure experiment •  Click Animated GIF/
MPEG/AVI for more opgons That’s all, folks!