Octopus is a density functional theory code focusing on time-dependent simulations. It supports several other calculation modes as well.
This page documents the ASE interface to Octopus. The interface is written for Octopus tetricus (svn version 14450 or newer) but may be compatible with older versions as well.
Structure optimization of ethanol molecule:
from ase.collections import g2 from ase.calculators.octopus import Octopus from ase.optimize import QuasiNewton # Ethanol molecule with somewhat randomized initial positions: system = g2['CH3CH2OH'] system.rattle(stdev=0.1, seed=42) system.center(vacuum=3.0) calc = Octopus(label='ethanol', Spacing=0.25, BoxShape='parallelepiped') system.set_calculator(calc) opt = QuasiNewton(system, logfile='opt.log', trajectory='opt.traj') opt.run(fmax=0.05)
Numerical parameters can be specified as strings as well.
The Octopus default
BoxShape is used unless specified otherwise.
This means that the cell of non-periodic Atoms is ignored unless
BoxShape = parallelepiped. In the calculation above, if
BoxShape is removed, the calculation will default to
minimum and the specified vacuum will have no effect.
Calculate density of states of silicon:
from ase.calculators.octopus import Octopus from ase.build import bulk system = bulk('Si', orthorhombic=True) calc = Octopus(label='silicon', Spacing=0.25, KPointsGrid=[[4, 4, 4]], KPointsUseSymmetries=True, Output='dos + density + potential', OutputFormat='xcrysden', DosGamma=0.1) system.set_calculator(calc) system.get_potential_energy()
Note how a block such as
KPointsGrid is specified as a list of
lists. In general, a block is a list of lists of strings. Numerical
datatypes are converted to strings.
Time-dependent density functional theory¶
TODO Write script
The interface works by reading and writing files. When triggering a calculation, ASE writes an input file and proceeds to run Octopus. Almost any keywords can be given to the Octopus calculator, and they will be passed almost uncritically to Octopus. This results in mostly predictable but at times non-user-friendly behaviour.
ASE always works with
Units = ev_angstrom. Keywords that attempt
to interfere with this will result in an error, or unspecified
behaviour if there are unhandled cases.
By default, Octopus output is written under the directory
label keyword can be used to specify a
Octopus input files can be loaded by the ASE GUI. You can visualize
an Octopus input file by running
ase gui inp.
Bugs and misbehaviour¶
Please report misbehaviour to the ASE-developers unless you are certain that the behaviour is linked to Octopus and not the ASE interface.
Below are listed some known bugs, issues, and limitations. These may or may not be fixed, depending on user response.
When parsing input files, arithmetic, calls to GNU GSL, or assignments from keywords are presently unsupported. Only statements of the form
keyword = valueor blocks are supported.
Most Octopus keywords are passed directly to Octopus. The ASE interface itself is not logically aware of their meaning. Only those necessary to construct the Atoms are handled individually. There may exist keywords that affect the Atoms (the cell or geometry) which are not handled by the interface, and therefore result in confusing behaviour. In particular, avoid changing the units.
Subsequent calculations always overwrite files. This is probably fine for densities in a structure optimization (the density is reused on each step), but not useful for text output. Therefore, avoid keywords like
stdout='"out.log"'and redirect stdout and stderr by other means.