In this tutorial we will use Avogadro to create the pyrrole molecule, relax the structure with a force-field optimization, and then perform an accurate geometry optimization using quantum-ESPRESSO.
The below tutorial works with the original version of Avogadro, at https://avogadro.cc/
If you are using Avogadro2 (at https://two.avogadro.cc/), which has slightly different menus, follow instead this tutorial for Avogadro2
- Launch Avogadro. There is detailed Documentation on their website at https://avogadro.cc/docs/getting-started/drawing-molecules/
- If you like, first play with the menu options: Draw: add/delete atoms and bonds, change bond order; Move/Manipulate: move atoms; etc. When finished, clear the window by hitting "Delete" on your keyboard.
- Now using the first "Draw" tab, create the pyrrole molecule.
- Click on the "Optimize" tab and relax the molecule using a simple force-field optimization.
- Click "Save as.." and save the geometry in XYZ format as pyrrole.xyz. In this format, the atoms are specified in Angstrom.
- Check it with Xcrysden
% xcrysden --xyz pyrrole.xyz
- It is advisable to shift the molecule so that it fits neatly inside a box (for the next step).
% head pyrrole.xyz
10
Energy: 32.5376008
N 2.35756 0.26815 -8.46372
C 1.29444 0.14487 -7.64867
...
% awk '{if (NR>2) {print $1,$2,$3+5,$4+10} else print}' pyrrole.xyz > pyrrole_shifted.xyz (choose suitable values)
You can also do this using the main Avogadro menus "Build -> Cartesian Editor" and then translate using the Manipulate submenu.
- Now create an input file for PWscf. The easiest thing is to copy and modify a previous file, i.e. one from the CO tutorial.
cp ../../3_CO/3_HomoLumo/co.relax.in .
cp co.relax.in pyrrole.relax.in
- At this point you need to edit the file: insert the atoms for pyrrole_shifted.xyz, modify appropriately the number and type of atoms, define an appropriate supercell, etc.
- Download suitable pseudopotentials from the quantum-ESPRESSO website. For simplicity, let's choose PBE kinds for N,C,H from http://www.pseudo-dojo.org/ (they are also in the Ref and Pseudo folders)
- At this point you should perform the same convergence tests as we demonstrated for the CO molecule.
- If time is short, take the cutoff from the pseudo-DOJO site and define a cubic box so that molecules are separated by at least 10 angstrom.
- Relax the structure.
- Plot the HOMO using pp.x, and check it looks reasonable using a Google search.
Note that the LUMO, in comparison, looks terrible compared to published work. This is due to several factors, including over-delocalization with PBE and LDA functionals.