ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
h = 1.85
add_adsorbate(slab, molecule, h, ’ontop’)
In order to speed up the relaxation, let us keep the Cu atoms fixed in the slab by using FixAtoms from the
constraints module. Only the N2 molecule is then allowed to relax to the equilibrium structure:
from ase.constraints import FixAtoms
constraint = FixAtoms(mask=[a.symbol != ’N’ for a in slab])
slab.set_constraint(constraint)
Now attach the QuasiNewton minimizer to the system and save the trajectory file. Run the minimizer with the
convergence criteria that the force on all atoms should be less than some fmax:
from ase.optimize import QuasiNewton
dyn = QuasiNewton(slab, trajectory=’N2Cu.traj’)
dyn.run(fmax=0.05)
Note: The general documentation on structure optimizations contains information about different algorithms,
saving the state of an optimizer and other functionality which should be considered when performing expensive
relaxations.
Input-output
Writing the atomic positions to a file is done with the write() function:
from ase.io import write
write(’slab.xyz’, slab)
This will write a file in the xyz-format. Possible formats are:
format description
xyz Simple xyz-format
cube Gaussian cube file
pdb Protein data bank file
traj ASE’s own trajectory format
py Python script
Reading from a file is done like this:
from ase.io import read
slab_from_file = read(’slab.xyz’)
If the file contains several configurations, the default behavior of the write() function is to return the last
configuration. However, we can load a specific configuration by doing:
read(’slab.traj’) # last configuration
read(’slab.traj’, -1) # same as above
read(’slab.traj’, 0) # first configuration
Visualization
The simplest way to visualize the atoms is the view() function:
from ase.visualize import view
view(slab)
This will pop up a gui window. Alternative viewers can be used by specifying the optional keyword
viewer=... - use one of ‘ase.gui’, ‘gopenmol’, ‘vmd’, or ‘rasmol’. (Note that these alternative viewers are not
a part of ASE and will need to be installed by the user separately.) The VMD viewer can take an optional data
argument to show 3D data:
20 Chapter 6. Tutorials