FHI-aims

Introduction

FHI-aims is a all-electron full-potential density functional theory code using a numeric local orbital basis set.

Running the Calculator

The default initialization command for the FHI-aims calculator is

class ase.calculators.aims.Aims(restart=None, ignore_bad_restart_file=False, label='.', atoms=None, cubes=None, radmul=None, tier=None, aims_command=None, outfilename=None, **kwargs)[source]

Construct the FHI-aims calculator.

The keyword arguments (kwargs) can be one of the ASE standard keywords: ‘xc’, ‘kpts’ and ‘smearing’ or any of FHI-aims’ native keywords.

Note

The behavior of command/run_command has been refactored ase X.X.X It is now possible to independently specify the command to call FHI-aims and the outputfile into which stdout is directed. In general, we replaced

<run_command> = <aims_command> + ” > ” + <outfilename

That is,what used to be, e.g.,

>>> calc = Aims(run_command = "mpiexec -np 4 aims.x > aims.out")

can now be achieved with the two arguments

>>> calc = Aims(aims_command = "mpiexec -np 4 aims.x"
>>>             outfilename = "aims.out")

Backward compatibility, however, is provided. Also, the command actually used to run FHI-aims is dynamically updated (i.e., the “command” member variable). That is, e.g.,

>>> calc = Aims()
>>> print(calc.command)
aims.version.serial.x > aims.out
>>> calc.outfilename = "systemX.out"
>>> print(calc.command)
aims.version.serial.x > systemX.out
>>> calc.aims_command = "mpiexec -np 4 aims.version.scalapack.mpi.x"
>>> print(calc.command)
mpiexec -np 4 aims.version.scalapack.mpi > systemX.out

Arguments:

cubes: AimsCube object
Cube file specification.
radmul: int
Set radial multiplier for the basis set of all atomic species.
tier: int or array of ints
Set basis set tier for all atomic species.
aims_command : str
The full command as executed to run FHI-aims without the redirection to stdout. For instance “mpiexec -np 4 aims.x”. Note that this is not the same as “command” or “run_command”. .. note:: Added in ase X.X.X
outfilename : str
The file (incl. path) to which stdout is redirected. Defaults to “aims.out” .. note:: Added in ase X.X.X
run_command : str, optional (default=None)
Same as “command”, see FileIOCalculator documentation. .. note:: Deprecated in ase X.X.X
outfilename : str, optional (default=aims.out)
File into which the stdout of the FHI aims run is piped into. Note that this will be only of any effect, if the <run_command> does not yet contain a ‘>’ directive.
kwargs : dict
Any of the base class arguments.

In order to run a calculation, you have to ensure that at least the following str variables are specified, either in the initialization or as shell environment variables:

keyword description
run_command The full command required to run FHI-aims from a shell, including anything to do with an MPI wrapper script and the number of tasks, e.g.: mpiexec aims.081213.scalapack.mpi.x > aims.out. An alternative way to set this command is via the ASE_AIMS_COMMAND environment variable.
species_dir Directory where the species are located, e.g.: /opt/fhi-aims-081213/species_defaults/light. Can also be specified with the AIMS_SPECIES_DIR environment variable.
xc which exchange-correlation functional is used.

List of keywords

This is a non-exclusive list of keywords for the control.in file that can be addresses from within ASE. The meaning for these keywords is exactly the same as in FHI-aims, please refer to its manual for help on their use.

One thing that should be mentioned is that keywords with more than one option have been implemented as tuples/lists, eg. k_grid=(12,12,12) or relativistic=('atomic_zora','scalar'). In those cases, specifying a single string containing all the options is also possible.

None of the keywords have any default within ASE, but do check the defaults set by FHI-aims.

Example keywords describing the computational method used:

keyword type
xc str
charge float
spin str
relativistic list
use_dipole_correction bool
vdw_correction_hirshfeld str
k_grid list

Note

Any argument can be changed after the initial construction of the calculator, simply by setting it with the method

>>> calc.set(keyword=value)

Volumetric Data Output

The class

class ase.calculators.aims.AimsCube(origin=(0, 0, 0), edges=[(0.1, 0.0, 0.0), (0.0, 0.1, 0.0), (0.0, 0.0, 0.1)], points=(50, 50, 50), plots=None)[source]

Object to ensure the output of cube files, can be attached to Aims object

parameters:

origin, edges, points:
Same as in the FHI-aims output
plots:
what to print, same names as in FHI-aims

describes an object that takes care of the volumetric output requests within FHI-aims. An object of this type can be attached to the main Aims() object as an option.

The possible arguments for AimsCube are:

keyword type
origin list
edges 3x3-array
points list
plots list

The possible values for the entry of plots are discussed in detail in the FHI-aims manual, see below for an example.

Example

Here is an example of how to obtain the geometry of a water molecule, assuming ASE_AIMS_COMMAND and AIMS_SPECIES_DIR are set: ase/test/aims/H2O_aims.py.

from ase import Atoms
from ase.calculators.aims import Aims, AimsCube
from ase.optimize import QuasiNewton

water = Atoms('HOH', [(1, 0, 0), (0, 0, 0), (0, 1, 0)])

water_cube = AimsCube(points=(29, 29, 29),
                      plots=('total_density',
                             'delta_density',
                             'eigenstate 5',
                             'eigenstate 6'))

calc = Aims(xc='PBE',
            output=['dipole'],
            sc_accuracy_etot=1e-6,
            sc_accuracy_eev=1e-3,
            sc_accuracy_rho=1e-6,
            sc_accuracy_forces=1e-4,
            cubes=water_cube)

water.set_calculator(calc)
dynamics = QuasiNewton(water, trajectory='square_water.traj')
dynamics.run(fmax=0.01)