ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
printput: Basis input ----------------------------------------------
Tip 2: You can look at the shape of the orbitals by plotting the contents of the ORB* files generated by SIESTA.
Tip 3: You will find a lot of information on the run in the .txt output file
Tip 4: In ag you can select View → VMD to start the VMD viewer. There you can change the atom representation
to what you feel is more convenient. Do that by selecting Graphics → Representations in the top bar.
Tip 5: SIESTA will store basis functions in ORB.* files. These files can be plotted using the xmgrace command
on the GBAR like this:
$ xmgrace ORB.S1.1.O ORB.S2.1.O
Siesta 2: Molecular Dynamics
This exercise is intended to illustrate a Molecular Dynamics run with the SIESTA calculator. The system is a
Si(001) surface, in the 2x1 reconstruction with asymmetric dimers. The simulation cell contains two dimers. An
H2 molecule approaches the surface, above one of the dimers, and dissociates, ending up with a H atom bonded
to each of the Si atoms in the dimer (and thus leading to a symmetric dimer). You can get the xyz file with the
initial geometry doc/exercises/siesta2/geom.xyz.
#!/usr/bin/env python
from ase.io import read
from ase.constraints import FixAtoms
from ase.calculators.siesta import Siesta
from ase.md import VelocityVerlet
from ase import units
# Read in the geometry from a xyz file, set the cell, boundary conditions and center
atoms = read(’geom.xyz’)
atoms.set_cell([7.66348,7.66348,7.66348*2])
atoms.set_pbc((1,1,1))
atoms.center()
# Set initial velocities for hydrogen atoms along the z-direction
p = atoms.get_momenta()
p[0,2]= -1.5
p[1,2]= -1.5
atoms.set_momenta(p)
# Keep some atoms fixed during the simulation
atoms.set_constraint(FixAtoms(indices=range(18,38)))
# Set the calculator and attach it to the system
calc = Siesta(’si001+h2’,basis=’SZ’,xc=’PBE’,meshcutoff=50*units.Ry)
calc.set_fdf(’PAO.EnergyShift’, 0.25 * units.eV)
calc.set_fdf(’PAO.SplitNorm’, 0.15)
atoms.set_calculator(calc)
# Set the VelocityVerlet algorithm and run it
dyn = VelocityVerlet(atoms,dt=1.0 * units.fs,trajectory=’si001+h2.traj’)
dyn.run(steps=100)
Note that both H atoms are given an initial velocity towards the surface through the lines:
p = atoms.get_momenta()
p[0,2]= -1.5
p[1,2]= -1.5
atoms.set_momenta(p)
Run the program, and check the results. You can visualize the dynamics using the trajectory file with the help of
the ASE gui. For example you can visualize the behaviour of the potential and total energies during the dynamics
50 Chapter 6. Tutorials