How to run Dacapo from CamposASE2
Let's try to set up a CO dimer calculation. This is about as simple as it may get:
"""CO dimer in a box.""" import os from Dacapo import Dacapo from ASE import Atom, ListOfAtoms atoms = ListOfAtoms([Atom('C', (2, 2, 2)), Atom('O', (3.1, 2, 2))], cell=(4, 4, 4), periodic=1) calc = Dacapo(planewavecutoff=300, # in eV nbands=10, # 5 extra empty bands out='CO_in_a_box.nc', txtout='CO_in_a_box.txt') atoms.SetCalculator(calc) energy = atoms.GetPotentialEnergy()
If you have completed the installation of Dacapo and CamposASE2, you may save the code piece above in a file (CO.py) and execute it with the command python CO.py.
OK, what is going on here? Let's go through this first script, line by line:
from Dacapo import Dacapo from ASE import Atom, ListOfAtoms
will define the classes Dacapo, ListOfAtoms and Atom. A class is sort of a template for creating objects - like here:
atoms = ListOfAtoms([Atom('C', (4, 4, 4)), Atom('O', (5.1, 4, 4))], cell=(8, 8, 8), periodic=1)
Here we create a ListOfAtoms object from a list of Atom objects and a cell keyword argument giving the size of the unit cell. The periodic=1 argument indicates that periodic boundary conditions are used. A plane wave calculations needs to have periodic boundary conditions. In the example above, this is a dummy box that contains the CO molecule.
calc = Dacapo(planewavecutoff=300, # in eV nbands=10, # 5 extra empty bands out='CO_in_a_box.nc', txtout='CO_in_a_box.txt')
will create a Dacapo calculator using a planewave cutoff of 300 eV, 10 electronic bands, and the file 'CO_in_a_box.nc' for output. By default, the CamposASE units are Angstrom and eV. All lines starting with "#" are comments, similarly to common shell languages. More precisely, "#" means that the rest of the line is a comment, so that you may also put comments after statements.
The plane wave cutoff and the number of bands are - apart from specifying the atoms - the only calculational parameters you as a minimum need to provide.