ASE calculators

Calorine provides two ASE calculators for NEP calculations, one that uses the GPU implementation and one that uses the CPU implementation of NEP. The former is better tested but is likely to be slow if many calculations are to performed, since it relies on reading and writing files.

GPU calculator

class calorine.gpunep_calculator.GPUNEP(potential_filename, maximum_neighbors=None, directory=None, cutoff=None, label='GPUNEP', atoms=None, command='gpumd < PREFIX.txt', prefix='to_run')[source]

This class provides an ASE calculator for NEP calculations with GPUMD.

This calculator writes files that are input to the gpumd executable. It is thus likely to be slow if many calculations are to be performed.

Parameters
  • potential_filename (str) – Path to nep.txt potential

  • directory (str) – Directory to run GPUMD in. If None, a temporary directory will be created and removed once the calculations are finished. If specified, the directory will not be deleted. In the latter case, it is advisable to do no more than one calculation with this calculator (unless you know exactly what you are doing).

  • maximum_neighbors (int) – Maximum number of neighbors any atom can ever have. If None, the code will try to come up with a reasonable estimate. 1024 is always safe.

  • cutoff (float) – Initial cutoff distance used for building the neighbor list. Defaults to force cutoff + 1 Angstrom

  • label (str) – Label for this calculator

  • atoms (Atoms) – atoms to attach this calculator to

  • command (str) – Command to run GPUMD with. Default: gpumd < PREFIX.txt

  • prefix (str) – Filename (excluding file ending) for run script. Default: to_run

Example

>>> calc = GPUNEP('nep.txt')
>>> atoms.calc = calc
>>> atoms.get_potential_energy()
run_custom_md(parameters, return_last_atoms=False, only_prepare=False)[source]

Run a custom MD simulation.

Parameters
  • parameters (List[Tuple[str, float]]) –

    Parameters to be specified in the run.in file. The potential keyword is set automatically, all other keywords need to be set via this argument. Example:

    [('dump_thermo', 1000),
     ('dump_position', 1000),
     ('velocity', 300),
     ('time_step', 1),
     ('ensemble', ['nvt_ber', 300, 300, 100]),
     ('neighbor', 1),
     ('run', 100000)]
    

  • return_last_atoms (Atoms) – If True, the last saved snapshot will be returned. Default: False

  • only_prepare (bool) – If True, the necessary input files will be written but the MD run will not be executed. Default: False

Return type

The last snapshot (if return_last_atoms = True)

set_atoms(atoms)[source]

Set Atoms object. Used also when attaching calculator to Atoms object.

set_directory(directory)[source]

Set path to a new directory. This makes it possible to run several calculations with the same calculator while saving all results

CPU calculator

class calorine.nepy.cpunep_calculator.CPUNEP(potential_filename, atoms=None, label=None, debug=False)[source]

This class provides an ASE calculator for nep_cpu, the in-memory CPU implementation of GPUMD.

Parameters
  • potential_filename (str) – Path to nep.txt potential

  • atoms (Atoms) – Atoms to attach the calculator to

  • label (str) – Label for this calculator

  • debug (bool, optional) – Flag to toggle debug mode. Prints GPUMD output. Defaults to False.

Raises
  • FileNotFoundError – Raises FileNotFoundError if potential_filename does not point to a valid file.

  • ValueError – Raises ValueError atoms are not defined when trying to get energies and forces.

Example

>>> calc = CPUNEP('nep.txt')
>>> atoms.calc = calc
>>> atoms.get_potential_energy()
set_atoms(atoms)[source]

Updates the Atoms object.

Parameters

atoms (Atoms) – Atoms to attach the calculator to