Calculator interface proposal

All ASE calculators should behave similarly if there is no good reason for them not to. This should make it simpler for both users and developers.

This proposal tries to define how a good ASE calculator should behave. The goal is to have ASE calculators:

  • that share more code
  • are more uniform to use
  • are better tested
  • are portable

Setting some standards is a good thing, but we should also be careful not to set too strict rules that could limit each calculator to the lowest common denominator.

Behavior

When a calculator calculates the energy, forces, stress tensor, total magnetic moment, atomic magnetic moments or dipole moment, it should store a copy of the system (atomic numbers, atomic positions, unit cell and boundary conditions). When asked again, it should return the value already calculated if the system hasn’t been changed.

If calculational parameters such as plane wave cutoff or XC-functional has been changed the calculator should throw away old calculated values.

Standards parameters

The standard keywords that all calculators must use (if they make sense) are: xc, kpts, smearing, charge and nbands. Each calculator will have its own default values for these parameters — see recommendations below. In addition, calculators will typically have many other parameters. The units are eV and Å.

Initial magnetic moments are taken from the Atoms object.

xc:

It is recommended that 'LDA' and 'PBE' are valid options.

kpts:
  • (1,1,1): Gamma-point
  • (n1,n2,n3): Monkhorst-Pack grid
  • (n1,n2,n3,'gamma'): Shifted Monkhorst-Pack grid that includes \(\Gamma\)
  • [(k11,k12,k13),(k21,k22,k23),...]: Explicit list in units of the reciprocal lattice vectors
  • kpts=3.5: \(\vec k\)-point density as in 3.5 \(\vec k\)-points per Å\(^{-1}\)
smearing:

The smearing parameter must be given as a tuple:

  • ('Fermi-Dirac', width)
  • ('Gaussian', width)
  • ('Methfessel-Paxton', width, n), where \(n\) is the order (\(n=0\) is the same as 'Gaussian')

Lower-case strings are also allowed. The width parameter used for the chosen smearing method is in eV units.

charge:

Charge of the system in units of \(|e|\) (charge=1 means one electron has been removed).

nbands:

Each band can be occupied by two electrons.

ABC calculator example

The constructor will look like this:

ABC(restart=None, ignore_bad_restart=False, label=None,
    atoms=None, **kwargs)

A calculator should be able to prefix all output files with a given label or run the calculation in a directory with a specified name. This is handled by the label argument. There are three possibilities:

  • Name of a file containing all results of a calculation (possibly containing a directory).
  • A prefix used for several files containing results. The label may have both a directory part and a prefix part like 'LDA/mol1'.
  • Name of a directory containing result files with fixed names.

Each calculator can decide what the default value is: None for no output, '-' for standard output or something else.

If the restart argument is given, atomic configuration, input parameters and results will be read from a previous calculation from the file(s) pointed to by the restart argument. It is an error if those files don’t exist and are corrupted. This error can be ignored bu using ignore_bad_restart=True.

The atoms argument is discussed below. All additional parameters are given as keyword arguments.

Example: Do a calculation with ABC calculator and write results to si.abc:

>>> atoms = ...
>>> atoms.calc = ABC(label='si.abc', xc='LDA', kpts=3.0)
>>> atoms.get_potential_energy()
-1.2

Read atoms with ABC calculator attaced from a previous calculation:

>>> atoms = ABC.read_atoms('si.abc')
>>> atoms.calc
<ABC-calculator>
>>> atoms.get_potential_energy()
-1.2

The ABC.read_atoms('si.abc') statement is equivalent to:

ABC(restart='si.abc', label='si.abc').get_atoms()

If we do:

>>> atoms = ABC.read_atoms('si.abc')
>>> atoms.rattle()            # change positions and/or
>>> atoms.calc.set(xc='PBE')  # change a calculator-parameter
>>> atoms.get_potential_energy()
-0.7

then the si.abc will be overwritten or maybe appended to.

An alternative way to connect atoms and calculator:

>>> atoms = ...
>>> calc = ABC(restart='si.abc', label='si.abc', atoms=atoms)
>>> atoms.get_potential_energy()
-0.7

This will automatically attach the calculator to the atoms and the atoms will be updated form the file. If you add ignore_bad_restart=True, you will be able to use the same script to do the initial calculation where si.abc does not exist and following calculations where atoms may have been moved around by an optimization algorithm.

The command used to start the ABC code can be given in an environment variable called ASE_ABC_COMMAND or as a command keyword. The command can look like this:

mpiexec abc PREFIX.input > PREFIX.output

or like this:

~/bin/start_abc.py PREFIX

The PREFIX strings will be substituted by the label keyword.

Implementation

  • Portability (Linux/Windows): os.system('Linux commands') not allowed.
  • Common base class for all calculators: Calculator. Takes care of restart from file logic, handles setting of parameters and checks for state changes.
  • A FileIOCalculator for the case where we need to:
    • write input file(s)
    • run Fortran/C/C++ code
    • read output file(s)
  • Helper function to deal with kpts keyword.

Testing

An interface must pass the tests located under ase/test/calculator/.