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wfl.calculators.orca package

wfl.calculators.orca package#

Submodules#

wfl.calculators.orca.basinhopping module#

class wfl.calculators.orca.basinhopping.BasinHoppingORCA(atoms=None, n_hop=10, n_run=3, scratchdir=None, n_missing_tolerance=1, energy_tol=0.001, forces_tol=0.05, seed='orca', n_orb=10, max_angle=60.0, smearing=5000.0, maxiter=500, chained_hops=True, orcasimpleinput='UHF PBE def2-SVP tightscf', orcablocks=None, orca_command='orca', rng=None, keep_files=False, uhf=True, **kwargs)#

Bases: Calculator

ORCA calculator with basin hopping in wavefunction space for smooth PES of radicals

Call n_runs (3 <= recommended) instances of calculation on each frame. If all agree in energy within a given margin, then it is a successful.

calculations:

  1. no rotation, only smearing calculation

  2. n_hop - 1 number of calculations with random rotations

Parameters

  • atoms (ase.Atoms) – molecule for calculation

  • n_hop (int) – number of hopping steps

  • n_run (int) – number of independent runs to perform, resultant energy/force is checked to be the same

  • scratchdir (path_like) – put temporary directories here for the calculations, one per task very efficient if you have an SSD scratch disk on nodes that perform the tasks

  • n_missing_tolerance (int) – number of files allowed to be missing

  • energy_tol (float) – energy tolerance in eV/atom

  • force_tol (float) – force tolerance in eV/Angstrom per component

  • seed (str) – file name seed

  • n_orb (int) – number of orbital pairs to rotate

  • max_angle (float) – maximal angle to rotate orbitals to

  • smearing (float, default 5000.) – smearing temperature in K, recommended is 5000 K

  • maxiter (int, default 500) – maximum number of SCF iterations to do

  • chained_hops (bool, default True) – chain hops, ie. to take the previous wavefunction result or the very initial one

  • orcasimpleinput (str) – What you’d put after the “!” in an orca input file.

  • orcablocks (str) – What you’d put in the “% … end”-blocks.

  • orca_command (str) – command of ORCA calculator as in path

  • rng (np.random.Generator) – random number generator

  • keep_files (bool) – to keep the resultant files from each calculation

  • uhf (bool, default True) – to use Unrestricted HF/KS method. This is advised to be used at all times, implemented for development purposes.

  • kwargs –

calculate(atoms=None, properties=None, system_changes=['positions', 'numbers', 'cell', 'pbc', 'initial_charges', 'initial_magmoms'], keep_raw_results=False, verbose=False)#

Do the calculation.

properties: list of str

List of what needs to be calculated. Can be any combination of ‘energy’, ‘forces’, ‘stress’, ‘dipole’, ‘charges’, ‘magmom’ and ‘magmoms’.

system_changes: list of str

List of what has changed since last calculation. Can be any combination of these six: ‘positions’, ‘numbers’, ‘cell’, ‘pbc’, ‘initial_charges’ and ‘initial_magmoms’.

Subclasses need to implement this, but can ignore properties and system_changes if they want. Calculated properties should be inserted into results dictionary like shown in this dummy example:

self.results = {'energy': 0.0,
                'forces': np.zeros((len(atoms), 3)),
                'stress': np.zeros(6),
                'dipole': np.zeros(3),
                'charges': np.zeros(len(atoms)),
                'magmom': 0.0,
                'magmoms': np.zeros(len(atoms))}

The subclass implementation should first call this implementation to set the atoms attribute and create any missing directories.

get_homo()#

Get the index of the HOMO.

ORCA counts form 0 and fills the alpha (indexed 0) spin more than the beta (indexed 1) for odd n_elec.

Returns

i_homo_alpha, i_homo_beta

Return type

int

get_multiplicity()#

Gets the multiplicity of the atoms object.

ORCA format: singlet = 1, doublet = 2, etc.

Returns

multiplicity

Return type

int

implemented_properties: List[str] = ['energy', 'forces']#

Properties calculator can handle (energy, forces, …)

process_results(energy_array, force_array)#

Compares the resultant energies and forces

Maximal difference between energy minima per atom and corresponding force components are checked against the set thresholds.

Parameters

  • energy_array (array, shape(n_runs, n_hop)) –

  • force_array (array, shape(n_runs, n_hop, len_atoms, 3)) –

Returns

  • energy

  • forces

wfl.calculators.orca.basinhopping.evaluate_basin_hopping(*args, **kwargs)#

Evaluate with BasinHoppingORCA calculator

Parameters

  • inputs (list(Atoms) / ConfigSet) – input atomic configs, needs to be iterable

  • outputs (OutputSpec) – output atomic configs

  • workdir_root (path-like, default os.getcwd()) – directory to put calculation directories into

  • rundir_prefix (str, default 'ORCA_') – directory name prefix for calculations

  • keep_files ("default" / bool) –

    what kind of files to keep from the run

    • ”default : .out, .inp, .ase, .engrad is kept – ase can read the results again

    • True : all files kept

    • False: none kept

  • orca_kwargs (dict) – kwargs for BasinHoppingORCA calculator

  • output_prefix (str, default None) – prefix for keys in the

Returns

results – ConfigSet(outputs)

Return type

ConfigSet

Module contents#

class wfl.calculators.orca.ORCA(keep_files='default', rundir_prefix='ORCA_', scratchdir=None, workdir=None, calculator_exec=None, post_process=None, **kwargs)#

Bases: WFLFileIOCalculator, ORCA

Extension of ASE’s ORCA calculator that can be used by wfl.calculators.generic

Notes

  • “directory” argument cannot be present. Use rundir_prefix and workdir instead.

  • Unless specified, multiplicity is set to singlet/doublet for closed-/open-shell structures

  • Results from additional optimisation task (set to “opt” or “copt”) are stored in extra_results dictionary.

Parameters

  • keep_files (bool / None / "default" / list(str), default "default") –

    what kind of files to keep from the run

    • True : everything kept

    • None, False : nothing kept, unless calculation fails

    • ”default” : only ones needed for NOMAD uploads (‘*.pwo’)

    • list(str) : list of file globs to save

  • rundir_prefix (str / Path, default 'ORCA_') – Run directory name prefix

  • workdir (str / Path, default . at calculate time) – Path in which rundir will be created.

  • scratchdir (str / Path, default None) – temporary directory to execute calculations in and delete or copy back results (set by “keep_files”) if needed. For example, directory on a local disk with fast file I/O.

  • calculator_exec (str, default "orca") – command for ORCA, without any prefix or redirection set. for example: “/path/to/orca” mutually exclusive with “command”

  • post_process (function that takes the current instance of the calculator and is to be) – executed after reading back results from file, but before all the files are deleted. For example, a localisation scheme that uses the wavefunction files and saves local charges to ORCA.extra_results.

  • **kwargs (arguments for ase.calculators.espresso.Espresso) –

calculate(atoms=None, properties=['energy', 'forces'], system_changes=['positions', 'numbers', 'cell', 'pbc', 'initial_charges', 'initial_magmoms'])#

Does the calculation. Handles the working directories in addition to regular ASE calculation operations (writing input, executing, reading_results)

cleanup()#

Clean all (empty) directories that could not have been removed immediately after the calculation, for example, because other parallel process might be using them.

default_parameters = {'charge': 0, 'mult': None, 'orcablocks': '%scf maxiter 200 end', 'orcasimpleinput': 'tightscf PBE def2-SVP', 'task': 'engrad'}#
static get_default_multiplicity(atoms, charge=0)#

Gets the multiplicity of the atoms object.

ORCA format: singlet = 1, doublet = 2, etc.

Parameters

  • atoms (ase.Atoms) –

  • charge (int) –

Returns

multiplicity

Return type

int

implemented_properties: List[str] = ['energy', 'forces', 'dipole']#

Properties calculator can handle (energy, forces, …)

is_converged()#

checks for warnings about SCF/wavefunction not converging.

Returns

None if “FINAL SINGLE POINT ENERGY” is not in the output False if “Wavefunction not fully converged” is in the file True otherwise

Based on ase.calculators.orca.read_energy().

pick_task()#
read_dipole()#

Note

Dipole is calculated by default, though only written up to 0.00001 so the rest of the digits are not meaningful in the output.

read_frequencies()#

Reads frequencies (dynamical matrix eigenvalues) and normal modes (eigenvectors) from output. Currently broken.

read_opt_atoms()#

Reads the result of the geometry optimisation

read_results()#

Reads all results

read_trajectory()#

Reads the trajectory of the geometry optimisation

Notes

Each comment line in output xyz has “Coordinates from ORCA-job orca E -154.812399026326”; # TODO parse out forces as well

wfl_generic_default_autopara_info = {'num_inputs_per_python_subprocess': 1}#
write_input(atoms, properties=None, system_changes=None)#

Writes orca.inp, based on the wfl ORCA calculator parameters

wfl.calculators.orca.natural_population_analysis(janpa_home_dir, orca_calc)#

https://sourceforge.net/p/janpa/wiki/Home/

wfl.calculators.orca.parse_npa_output(fname)#
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