NEP interface

calorine.nep.get_descriptors(structure, model_filename=None, debug=False)

Calculates the NEP descriptors for a given structure. A NEP model defined by a nep.txt can additionally be provided to get the NEP3 model specific descriptors.

Parameters:

• structure (Atoms) – Input structure

• model_filename (Optional[str]) – Path to NEP model in nep.txt format. Defaults to None.

• debug (bool) – Flag to toggle debug mode. Makes the generated dummy NEP2 model available in a local tmp directory, as well as prints GPUMD output. Defaults to False.

Return type:

Descriptors for the supplied structure, with shape (number_of_atoms, descriptor components)

calorine.nep.get_dipole(structure, model_filename=None, debug=False)

Calculates the dipole for a given structure. A NEP model defined by a nep.txt file needs to be provided.

Parameters:

• structure (Atoms) – Input structure

• model_filename (Optional[str]) – Path to NEP model in nep.txt format. Defaults to None.

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

Return type:

dipole with shape (3,)

calorine.nep.get_dipole_gradient(structure, model_filename=None, backend='c++', method='central difference', displacement=0.01, charge=1.0, nep_command='nep', debug=False)

Calculates the dipole gradient for a given structure using finite differences. A NEP model defined by a nep.txt file needs to be provided.

Parameters:

• structure (Atoms) – Input structure

• model_filename (Optional[str]) – Path to NEP model in nep.txt format. Defaults to None.

• backend (str) – Backend to use for computing dipole gradient with finite differences. One of 'c++' (CPU), 'python' (CPU) and 'nep' (GPU). Defaults to 'c++'.

• method (str) – Method for computing gradient with finite differences. One of ‘forward difference’ and ‘central difference’. Defaults to ‘central difference’

• displacement (float) – Displacement in Å to use for finite differences. Defaults to 0.01.

• charge (float) – System charge in units of the elemental charge. Used for correcting the dipoles before computing the gradient. Defaults to 1.0.

• nep_command (str) – Command for running the NEP executable. Defaults to 'nep'.

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

Return type:

ndarray

Returns:

dipole gradient with shape (N, 3, 3)

calorine.nep.get_latent_space(structure, model_filename=None, debug=False)

Calculates the latent space representation of a structure, i.e, the activiations in the hidden layer. A NEP model defined by a nep.txt file needs to be provided.

Parameters:

• structure (Atoms) – Input structure

• model_filename (Optional[str]) – Path to NEP model. Defaults to None.

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

Return type:

Activation with shape (natoms, N_neurons)

calorine.nep.get_parity_data(structures, property, selection=None, flatten=True)

Returns the predicted and target energies, forces, virials or stresses from a list of structures in a format suitable for generating parity plots.

The structures should have been read using read_structures, such that the info-object is populated with keys on the form <property>_<type> where <property> is one of energy, force, virial, and stress, and <type> is one of predicted or target.

The resulting parity data is returned as a tuple of dicts, where each entry corresponds to a list.

Parameters:

• structures (List[Atoms]) – List of structures as read with read_structures.

• property (str) – One of energy, force, virial, stress, polarizability, dipole.

• selection (Optional[List[str]]) – A list containing which components to return, and/or the absolute value. Possible values are x, y, z, xx, yy, zz, yz, xz, xy, abs, pressure.

• flatten (bool) – if True return flattened lists; this is useful for flattening the components of force or virials into a simple list

Return type:

DataFrame

calorine.nep.get_polarizability(structure, model_filename=None, debug=False)

Calculates the polarizability tensor for a given structure. A NEP model defined by a nep.txt file needs to be provided. The model must be trained to predict the polarizability.

Parameters:

• structure (Atoms) – Input structure

• model_filename (Optional[str]) – Path to NEP model in nep.txt format. Defaults to None.

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

Return type:

polarizability with shape (3, 3)

calorine.nep.get_polarizability_gradient(structure, model_filename=None, displacement=0.01, component='full', debug=False)

Calculates the dipole gradient for a given structure using finite differences. A NEP model defined by a nep.txt file needs to be provided. This function computes the derivatives using the second-order central difference method with a C++ backend.

Parameters:

• structure (Atoms) – Input structure.

• model_filename (Optional[str]) – Path to NEP model in nep.txt format. Defaults to None.

• displacement (float) – Displacement in Å to use for finite differences. Defaults to 0.01.

• component (Union[str, List[str]]) – Component or components of the polarizability tensor that the gradient should be computed for. The following components are available: x`, ``y, z, full. Option full computes the derivative whilst moving the atoms in each Cartesian direction, which yields a tensor of shape (N, 3, 6). Multiple components may be specified. Defaults to full.

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

Return type:

ndarray

Returns:

polarizability gradient with shape (N, C, 6) where C is the number of components chosen.

calorine.nep.get_potential_forces_and_virials(structure, model_filename=None, debug=False)

Calculates the per-atom potential, forces and virials for a given structure. A NEP model defined by a nep.txt file needs to be provided.

Parameters:

• structure (Atoms) – Input structure

• model_filename (Optional[str]) – Path to NEP model. Defaults to None.

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

Return type:

Tuple[ndarray, ndarray, ndarray]

Returns:

• potential with shape (natoms,)

• forces with shape (natoms, 3)

• virials with shape (natoms, 9)

calorine.nep.read_loss(filename)

Parses a file in loss.out format from GPUMD and returns the content as a data frame. More information concerning file format, content and units can be found here.

Parameters:

filename (str) – input file name

Return type:

DataFrame

calorine.nep.read_model(filename)

Parses a file in nep.txt format and returns the content in the form of a Model object.

Parameters:

filename (str) – Input file name.

Return type:

Model

calorine.nep.read_nepfile(filename)

Returns the content of a configuration file (nep.in) as a dictionary.

Parameters:

filename (str) – input file name

Return type:

Dict[str, Any]

calorine.nep.read_structures(dirname)

Parses the energy_*.out, force_*.out, virial_*.out, polarizability_*.out and dipole_*.out files from a nep run and returns their content as lists. The first and second list contain the structures from the training and test sets, respectively. Each list entry corresponds to an ASE Atoms object, which in turn contains predicted and target energies, forces and virials/stresses or polarizability/diople stored in the info property.

Parameters:

dirname (str) – directory from which to read output files

Return type:

Tuple[List[Atoms], List[Atoms]]

calorine.nep.setup_training(parameters, structures, enforced_structures=[], rootdir='.', mode='kfold', n_splits=None, train_fraction=None, seed=42, overwrite=False)

Sets up the input files for training a NEP via the nep executable of the GPUMD package.

Parameters:

• parameters (NamedTuple) – dictionary containing the parameters to be set in the nep.in file; see here for an overview of these parameters

• structures (List[Atoms]) – list of structures to be included

• enforced_structures (List[int]) – structures that _must_ be included in the training set, provided in the form of a list of indices that refer to the content of the structures parameter

• rootdir (str) – root directory in which to create the input files

• mode (str) – how the test-train split is performed. Options: 'kfold' and 'bagging'

• n_splits (Optional[int]) – number of splits of the input structures in training and test sets that ought to be performed; by default no split will be done and all input structures will be used for training

• train_fraction (Optional[float]) – fraction of structures to use for training when mode 'bagging' is used

• seed (int) – random number generator seed to be used; this ensures reproducability

• overwrite (bool) – if True overwrite the content of rootdir if it exists

Return type:

None

calorine.nep.write_nepfile(parameters, dirname)

Writes parameters file for NEP construction.

Parameters:

• parameters (NamedTuple) – input parameters; see here

• dirname (str) – directory in which to place input file and links

Return type:

None

calorine.nep.write_structures(outfile, structures)

Writes structures for training/testing in format readable by nep executable.

Parameters:

• outfile (str) – output filename

• structures (List[Atoms]) – list of structures with energy, forces, and (possibly) stresses

Return type:

None

class calorine.nep.model.Model(version, model_type, types, radial_cutoff, angular_cutoff, n_basis_radial, n_basis_angular, n_max_radial, n_max_angular, l_max_3b, l_max_4b, l_max_5b, n_descriptor_radial, n_descriptor_angular, n_neuron, n_parameters, n_descriptor_parameters, n_ann_parameters, ann_parameters, q_scaler, radial_descriptor_weights, angular_descriptor_weights, zbl=None, zbl_typewise_cutoff_factor=None, max_neighbors_radial=None, max_neighbors_angular=None, radial_typewise_cutoff_factor=None, angular_typewise_cutoff_factor=None)

Objects of this class represent a NEP model in a form suitable for inspection and manipulation. Typically a Model object is instantiated by calling the read_model function.

version

NEP version.

Type:

int

model_type

One of potential, dipole or polarizability.

Type:

str

types

Chemical species that this model represents.

Type:

Tuple[str, …]

radial_cutoff

The radial cutoff parameter in Å.

Type:

float

angular_cutoff

The angular cutoff parameter in Å.

Type:

float

max_neighbors_radial

Maximum number of neighbors in neighbor list for radial terms.

Type:

int

max_neighbors_angular

Maximum number of neighbors in neighbor list for angular terms.

Type:

int

radial_typewise_cutoff_factor

The radial cutoff factor if use_typewise_cutoff is used.

Type:

float

angular_typewise_cutoff_factor

The angular cutoff factor if use_typewise_cutoff is used.

Type:

float

zbl

Inner and outer cutoff for transition to ZBL potential.

Type:

Tuple[float, float]

zbl_typewise_cutoff_factor

Typewise cutoff when use_typewise_cutoff_zbl is used.

Type:

float

n_basis_radial

Number of radial basis functions \(n_\mathrm{basis}^\mathrm{R}\).

Type:

int

n_basis_angular

Number of angular basis functions \(n_\mathrm{basis}^\mathrm{A}\).

Type:

int

n_max_radial

Maximum order of Chebyshev polymonials included in radial expansion \(n_\mathrm{max}^\mathrm{R}\).

Type:

int

n_max_angular

Maximum order of Chebyshev polymonials included in angular expansion \(n_\mathrm{max}^\mathrm{A}\).

Type:

int

l_max_3b

Maximum expansion order for three-body terms \(l_\mathrm{max}^\mathrm{3b}\).

Type:

int

l_max_4b

Maximum expansion order for four-body terms \(l_\mathrm{max}^\mathrm{4b}\).

Type:

int

l_max_5b

Maximum expansion order for five-body terms \(l_\mathrm{max}^\mathrm{5b}\).

Type:

int

n_descriptor_radial

Dimension of radial part of descriptor.

Type:

int

n_descriptor_angular

Dimension of angular part of descriptor.

Type:

int

n_neuron

Number of neurons in hidden layer.

Type:

int

n_parameters

Total number of parameters including scalers (which are not fit parameters).

Type:

int

n_descriptor_parameters

Number of parameters in descriptor.

Type:

int

n_ann_parameters

Number of neural network weights.

Type:

int

ann_parameters

Neural network weights.

Type:

Dict[Tuple[str, Dict[str, np.darray]]]

q_scaler

Scaling parameters.

Type:

List[float]

radial_descriptor_weights

Radial descriptor weights by combination of species; the array for each combination has dimensions of \((n_\mathrm{max}^\mathrm{R}+1) \times (n_\mathrm{basis}^\mathrm{R}+1)\).

Type:

Dict[Tuple[str, str], np.ndarray]

angular_descriptor_weights

Angular descriptor weights by combination of species; the array for each combination has dimensions of \((n_\mathrm{max}^\mathrm{A}+1) \times (n_\mathrm{basis}^\mathrm{A}+1)\).

Type:

Dict[Tuple[str, str], np.ndarray]

write(filename)

Write NEP model to file in nep.txt format.

Return type:

None