dscribe package

Subpackages

• dscribe.core package
  • Submodules
  • dscribe.core.lattice module
    • Lattice
      • Lattice.abc
      • Lattice.get_cartesian_coords()
      • Lattice.get_fractional_coords()
      • Lattice.get_points_in_sphere()
      • Lattice.inv_matrix
      • Lattice.lengths
      • Lattice.matrix
      • Lattice.reciprocal_lattice
      • Lattice.reciprocal_lattice_crystallographic
  • dscribe.core.system module
    • System
      • System.from_atoms()
      • System.get_cell_inverse()
      • System.get_displacement_tensor()
      • System.get_distance_matrix()
      • System.get_distance_matrix_within_radius()
      • System.get_inverse_distance_matrix()
      • System.set_cell()
      • System.set_pbc()
      • System.set_positions()
      • System.set_scaled_positions()
      • System.to_cartesian()
      • System.to_scaled()
  • Module contents
• dscribe.descriptors package
  • Submodules
  • dscribe.descriptors.acsf module
    • ACSF
      • ACSF.create()
      • ACSF.create_single()
      • ACSF.g2_params
      • ACSF.g3_params
      • ACSF.g4_params
      • ACSF.g5_params
      • ACSF.get_number_of_features()
      • ACSF.r_cut
      • ACSF.species
      • ACSF.validate_derivatives_method()
  • dscribe.descriptors.coulombmatrix module
    • CoulombMatrix
      • CoulombMatrix.create()
      • CoulombMatrix.create_single()
      • CoulombMatrix.derivatives_numerical()
  • dscribe.descriptors.descriptor module
    • Descriptor
      • Descriptor.check_atomic_numbers()
      • Descriptor.create()
      • Descriptor.create_parallel()
      • Descriptor.derivatives_parallel()
      • Descriptor.format_array()
      • Descriptor.get_number_of_features()
      • Descriptor.periodic
      • Descriptor.sparse
      • Descriptor.validate_derivatives_method()
  • dscribe.descriptors.descriptorglobal module
    • DescriptorGlobal
      • DescriptorGlobal.derivatives()
      • DescriptorGlobal.derivatives_numerical()
      • DescriptorGlobal.derivatives_single()
  • dscribe.descriptors.descriptorlocal module
    • DescriptorLocal
      • DescriptorLocal.derivatives()
      • DescriptorLocal.derivatives_numerical()
      • DescriptorLocal.derivatives_single()
      • DescriptorLocal.init_derivatives_array()
      • DescriptorLocal.init_descriptor_array()
      • DescriptorLocal.validate_derivatives_method()
  • dscribe.descriptors.descriptormatrix module
    • DescriptorMatrix
      • DescriptorMatrix.create_single()
      • DescriptorMatrix.get_eigenspectrum()
      • DescriptorMatrix.get_matrix()
      • DescriptorMatrix.get_number_of_features()
      • DescriptorMatrix.sort()
      • DescriptorMatrix.sort_randomly()
      • DescriptorMatrix.unflatten()
      • DescriptorMatrix.zero_pad()
  • dscribe.descriptors.ewaldsummatrix module
    • EwaldSumMatrix
      • EwaldSumMatrix.create()
      • EwaldSumMatrix.create_single()
      • EwaldSumMatrix.get_matrix()
  • dscribe.descriptors.lmbtr module
    • LMBTR
      • LMBTR.create()
      • LMBTR.create_single()
      • LMBTR.geometry
      • LMBTR.get_location()
      • LMBTR.get_number_of_features()
      • LMBTR.grid
      • LMBTR.normalization
      • LMBTR.species
      • LMBTR.weighting
  • dscribe.descriptors.mbtr module
    • MBTR
      • MBTR.create()
      • MBTR.create_single()
      • MBTR.derivatives_analytical()
      • MBTR.geometry
      • MBTR.get_location()
      • MBTR.get_number_of_features()
      • MBTR.grid
      • MBTR.normalization
      • MBTR.species
      • MBTR.validate_derivatives_method()
      • MBTR.weighting
    • check_geometry()
    • check_grid()
    • check_weighting()
  • dscribe.descriptors.sinematrix module
    • SineMatrix
      • SineMatrix.create()
      • SineMatrix.get_matrix()
  • dscribe.descriptors.soap module
    • SOAP
      • SOAP.compression
      • SOAP.create()
      • SOAP.create_single()
      • SOAP.derivatives_analytical()
      • SOAP.derivatives_numerical()
      • SOAP.get_basis_gto()
      • SOAP.get_basis_poly()
      • SOAP.get_cutoff_padding()
      • SOAP.get_location()
      • SOAP.get_number_of_features()
      • SOAP.init_internal_array()
      • SOAP.init_internal_dev_array()
      • SOAP.prepare_centers()
      • SOAP.species
      • SOAP.validate_derivatives_method()
  • dscribe.descriptors.valleoganov module
    • ValleOganov
  • Module contents
• dscribe.kernels package
  • Submodules
  • dscribe.kernels.averagekernel module
    • AverageKernel
      • AverageKernel.get_global_similarity()
  • dscribe.kernels.localsimilaritykernel module
    • LocalSimilarityKernel
      • LocalSimilarityKernel.create()
      • LocalSimilarityKernel.get_global_similarity()
      • LocalSimilarityKernel.get_pairwise_matrix()
  • dscribe.kernels.rematchkernel module
    • REMatchKernel
      • REMatchKernel.get_global_similarity()
  • Module contents
• dscribe.utils package
  • Submodules
  • dscribe.utils.dimensionality module
    • is1d()
    • is2d()
  • dscribe.utils.geometry module
    • get_adjacency_list()
    • get_adjacency_matrix()
    • get_extended_system()
  • dscribe.utils.species module
    • get_atomic_numbers()
    • symbols_to_numbers()
  • dscribe.utils.stats module
    • system_stats()
  • Module contents

Submodules

dscribe.ext module

class dscribe.ext.ACSFWrapper(*args, **kwargs)

Bases: pybind11_object

Overloaded function.

1. __init__(self: dscribe.ext.ACSFWrapper, arg0: float, arg1: List[List[float]], arg2: List[float], arg3: List[List[float]], arg4: List[List[float]], arg5: List[int]) -> None

2. __init__(self: dscribe.ext.ACSFWrapper) -> None

property atomic_numbers

create(self: dscribe.ext.ACSFWrapper, arg0: List[List[float]], arg1: List[int], arg2: List[List[float]], arg3: List[List[int]], arg4: List[int]) → List[List[float]]

property g3_params

property g4_params

property g5_params

get_g2_params(self: dscribe.ext.ACSFWrapper) → List[List[float]]

property n_g2

property n_g3

property n_g4

property n_g5

property n_type_pairs

property n_types

property r_cut

set_g2_params(self: dscribe.ext.ACSFWrapper, arg0: List[List[float]]) → None

class dscribe.ext.CellList(self: dscribe.ext.CellList, arg0: numpy.ndarray[numpy.float64], arg1: float)

Bases: pybind11_object

get_neighbours_for_index(self: dscribe.ext.CellList, arg0: int) → CellListResult

get_neighbours_for_position(self: dscribe.ext.CellList, arg0: float, arg1: float, arg2: float) → CellListResult

class dscribe.ext.CellListResult(self: dscribe.ext.CellListResult)

Bases: pybind11_object

property distances

property distances_squared

property indices

class dscribe.ext.CoulombMatrix(self: dscribe.ext.CoulombMatrix, arg0: int, arg1: str, arg2: float, arg3: int)

Bases: pybind11_object

create(self: dscribe.ext.CoulombMatrix, arg0: numpy.ndarray[numpy.float64], arg1: numpy.ndarray[numpy.float64], arg2: numpy.ndarray[numpy.int32], arg3: numpy.ndarray[numpy.float64], arg4: numpy.ndarray[bool]) → None

derivatives_numerical(self: dscribe.ext.CoulombMatrix, arg0: numpy.ndarray[numpy.float64], arg1: numpy.ndarray[numpy.float64], arg2: numpy.ndarray[numpy.float64], arg3: numpy.ndarray[numpy.int32], arg4: numpy.ndarray[numpy.float64], arg5: numpy.ndarray[bool], arg6: numpy.ndarray[numpy.int32], arg7: bool) → None

class dscribe.ext.ExtendedSystem(self: dscribe.ext.ExtendedSystem)

Bases: pybind11_object

property atomic_numbers

property indices

property positions

class dscribe.ext.MBTRWrapper(self: dscribe.ext.MBTRWrapper, arg0: Dict[int, int], arg1: int, arg2: List[List[int]])

Bases: pybind11_object

get_k1(self: dscribe.ext.MBTRWrapper, arg0: numpy.ndarray[numpy.float64], arg1: List[int], arg2: str, arg3: str, arg4: Dict[str, float], arg5: float, arg6: float, arg7: float, arg8: int) → None

get_k2(self: dscribe.ext.MBTRWrapper, arg0: numpy.ndarray[numpy.float64], arg1: numpy.ndarray[numpy.float64], arg2: bool, arg3: bool, arg4: List[int], arg5: List[List[float]], arg6: List[List[float]], arg7: List[List[int]], arg8: str, arg9: str, arg10: Dict[str, float], arg11: float, arg12: float, arg13: float, arg14: int) → None

get_k2_local(self: dscribe.ext.MBTRWrapper, arg0: List[int], arg1: List[int], arg2: List[List[float]], arg3: List[List[int]], arg4: str, arg5: str, arg6: Dict[str, float], arg7: float, arg8: float, arg9: float, arg10: int) → List[Dict[str, List[float]]]

get_k3(self: dscribe.ext.MBTRWrapper, arg0: numpy.ndarray[numpy.float64], arg1: numpy.ndarray[numpy.float64], arg2: bool, arg3: bool, arg4: List[int], arg5: List[List[float]], arg6: List[List[float]], arg7: List[List[int]], arg8: str, arg9: str, arg10: Dict[str, float], arg11: float, arg12: float, arg13: float, arg14: int) → None

get_k3_local(self: dscribe.ext.MBTRWrapper, arg0: List[int], arg1: List[int], arg2: List[List[float]], arg3: List[List[int]], arg4: str, arg5: str, arg6: Dict[str, float], arg7: float, arg8: float, arg9: float, arg10: int) → List[Dict[str, List[float]]]

class dscribe.ext.SOAPGTO(self: dscribe.ext.SOAPGTO, arg0: float, arg1: int, arg2: int, arg3: float, arg4: dict, arg5: str, arg6: float, arg7: numpy.ndarray[numpy.int32], arg8: numpy.ndarray[numpy.float64], arg9: bool, arg10: str, arg11: numpy.ndarray[numpy.float64], arg12: numpy.ndarray[numpy.float64])

Bases: pybind11_object

create(*args, **kwargs)

Overloaded function.

1. create(self: dscribe.ext.SOAPGTO, arg0: numpy.ndarray[numpy.float64], arg1: numpy.ndarray[numpy.float64], arg2: numpy.ndarray[numpy.int32], arg3: numpy.ndarray[numpy.float64]) -> None

2. create(self: dscribe.ext.SOAPGTO, arg0: numpy.ndarray[numpy.float64], arg1: numpy.ndarray[numpy.float64], arg2: numpy.ndarray[numpy.int32], arg3: numpy.ndarray[numpy.float64], arg4: numpy.ndarray[bool], arg5: numpy.ndarray[numpy.float64]) -> None

3. create(self: dscribe.ext.SOAPGTO, arg0: numpy.ndarray[numpy.float64], arg1: numpy.ndarray[numpy.float64], arg2: numpy.ndarray[numpy.int32], arg3: numpy.ndarray[numpy.float64], arg4: CellList) -> None

derivatives_analytical(self: dscribe.ext.SOAPGTO, arg0: numpy.ndarray[numpy.float64], arg1: numpy.ndarray[numpy.float64], arg2: numpy.ndarray[numpy.float64], arg3: numpy.ndarray[numpy.float64], arg4: numpy.ndarray[numpy.float64], arg5: numpy.ndarray[numpy.float64], arg6: numpy.ndarray[numpy.int32], arg7: numpy.ndarray[numpy.float64], arg8: numpy.ndarray[bool], arg9: numpy.ndarray[numpy.float64], arg10: numpy.ndarray[numpy.int32], arg11: numpy.ndarray[numpy.int32], arg12: bool, arg13: bool) → None

derivatives_numerical(self: dscribe.ext.SOAPGTO, arg0: numpy.ndarray[numpy.float64], arg1: numpy.ndarray[numpy.float64], arg2: numpy.ndarray[numpy.float64], arg3: numpy.ndarray[numpy.int32], arg4: numpy.ndarray[numpy.float64], arg5: numpy.ndarray[bool], arg6: numpy.ndarray[numpy.float64], arg7: numpy.ndarray[numpy.int32], arg8: numpy.ndarray[numpy.int32], arg9: bool, arg10: bool) → None

class dscribe.ext.SOAPPolynomial(self: dscribe.ext.SOAPPolynomial, arg0: float, arg1: int, arg2: int, arg3: float, arg4: dict, arg5: str, arg6: float, arg7: numpy.ndarray[numpy.int32], arg8: numpy.ndarray[numpy.float64], arg9: bool, arg10: str, arg11: numpy.ndarray[numpy.float64], arg12: numpy.ndarray[numpy.float64])

Bases: pybind11_object

create(*args, **kwargs)

Overloaded function.

1. create(self: dscribe.ext.SOAPPolynomial, arg0: numpy.ndarray[numpy.float64], arg1: numpy.ndarray[numpy.float64], arg2: numpy.ndarray[numpy.int32], arg3: numpy.ndarray[numpy.float64]) -> None

2. create(self: dscribe.ext.SOAPPolynomial, arg0: numpy.ndarray[numpy.float64], arg1: numpy.ndarray[numpy.float64], arg2: numpy.ndarray[numpy.int32], arg3: numpy.ndarray[numpy.float64], arg4: numpy.ndarray[bool], arg5: numpy.ndarray[numpy.float64]) -> None

3. create(self: dscribe.ext.SOAPPolynomial, arg0: numpy.ndarray[numpy.float64], arg1: numpy.ndarray[numpy.float64], arg2: numpy.ndarray[numpy.int32], arg3: numpy.ndarray[numpy.float64], arg4: CellList) -> None

derivatives_numerical(self: dscribe.ext.SOAPPolynomial, arg0: numpy.ndarray[numpy.float64], arg1: numpy.ndarray[numpy.float64], arg2: numpy.ndarray[numpy.float64], arg3: numpy.ndarray[numpy.int32], arg4: numpy.ndarray[numpy.float64], arg5: numpy.ndarray[bool], arg6: numpy.ndarray[numpy.float64], arg7: numpy.ndarray[numpy.int32], arg8: numpy.ndarray[numpy.int32], arg9: bool, arg10: bool) → None

dscribe.ext.extend_system(arg0: numpy.ndarray[numpy.float64], arg1: numpy.ndarray[numpy.int32], arg2: numpy.ndarray[numpy.float64], arg3: numpy.ndarray[bool], arg4: float) → ExtendedSystem

Create a periodically extended system.

Module contents

Copyright 2019 DScribe developers

Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.