"""
This module provides functionality for storing structures and their fit
matrices together with target forces and displacements
"""
import tarfile
import numpy as np
from collections import OrderedDict
from ase.calculators.singlepoint import SinglePointCalculator
from .input_output.read_write_files import (add_items_to_tarfile_hdf5,
add_items_to_tarfile_pickle,
add_items_to_tarfile_custom,
add_list_to_tarfile_custom,
read_items_hdf5,
read_items_pickle,
read_list_custom)
from .cluster_space import ClusterSpace
from .force_constant_model import ForceConstantModel
from .input_output.logging_tools import logger
logger = logger.getChild('structure_container')
[docs]class StructureContainer:
"""
This class serves as a container for structures as well as associated
fit properties and fit matrices.
Parameters
-----------
cs : ClusterSpace
cluster space that is the basis for the container
fit_structure_list : list(FitStructure)
structures to be added to the container
"""
def __init__(self, cs, fit_structure_list=None):
"""
Attributes
-----------
_cs : ClusterSpace
cluster space that is the basis for the container
_structure_list : list(FitStructure)
structures to add to container
_previous_fcm : ForceConstantModel
FCM object used for last fit matrix calculation; check will be
carried out to decide if this FCM can be used for a new structure
or not, which often enables a considerable speed-up
"""
self._cs = cs.copy()
self._previous_fcm = None
# Add atoms from atoms_list
self._structure_list = []
if fit_structure_list is not None:
for fit_structure in fit_structure_list:
if not isinstance(fit_structure, FitStructure):
raise TypeError('Can only add FitStructures')
self._structure_list.append(fit_structure)
def __len__(self):
return len(self._structure_list)
def __getitem__(self, ind):
return self._structure_list[ind]
@property
def data_shape(self):
""" tuple : tuple of integers representing the shape of the fit data
matrix """
n_cols = self._cs.n_dofs
n_rows = sum(len(fs) * 3 for fs in self)
if n_rows == 0:
return None
return n_rows, n_cols
@property
def cluster_space(self):
""" ClusterSpace : copy of the cluster space the structure
container is based on"""
return self._cs.copy()
[docs] @staticmethod
def read(fileobj, read_structures=True):
"""Restore a StructureContainer object from file.
Parameters
----------
f : str or file object
name of input file (str) or stream to load from (file object)
read_structures : bool
if True the structures will be read; if False only the cluster
space will be read
"""
if isinstance(fileobj, str):
tar_file = tarfile.open(mode='r', name=fileobj)
else:
tar_file = tarfile.open(mode='r', fileobj=fileobj)
# Read clusterspace
f = tar_file.extractfile('cluster_space')
cs = ClusterSpace.read(f)
# Read fitstructures
fit_structure_list = None
if read_structures:
fit_structure_list = read_list_custom(tar_file, 'fit_structure', FitStructure.read)
# setup StructureContainer
sc = StructureContainer(cs, fit_structure_list)
# Read previous FCM if it exists
if 'previous_fcm' in tar_file.getnames():
f = tar_file.extractfile('previous_fcm')
fcm = ForceConstantModel.read(f)
sc._previous_fcm = fcm
return sc
[docs] def write(self, f):
"""Write a StructureContainer instance to a file.
Parameters
----------
f : str or file object
name of input file (str) or stream to write to (file object)
"""
if isinstance(f, str):
tar_file = tarfile.open(mode='w', name=f)
else:
tar_file = tarfile.open(mode='w', fileobj=f)
# save cs and previous_fcm (if it exists)
custom_items = dict(cluster_space=self._cs)
if self._previous_fcm is not None:
custom_items['previous_fcm'] = self._previous_fcm
add_items_to_tarfile_custom(tar_file, custom_items)
# save fit structures
add_list_to_tarfile_custom(tar_file, self._structure_list, 'fit_structure')
tar_file.close()
[docs] def add_structure(self, atoms, **meta_data):
"""Add a structure to the container.
Note that custom information about the atoms object may not be
stored inside, for example an ASE
:class:`SinglePointCalculator` will not be kept.
Parameters
----------
atoms : ase.Atoms
the structure to be added; the Atoms object must contain
supplementary per-atom arrays with displacements and forces
meta_data : dict
dict with meta_data about the atoms
"""
atoms_copy = atoms.copy()
# atoms object must contain displacements
if 'displacements' not in atoms_copy.arrays.keys():
raise ValueError('Atoms must have displacements array')
# atoms object must contain forces
if 'forces' not in atoms_copy.arrays.keys():
if isinstance(atoms.calc, SinglePointCalculator):
atoms_copy.new_array('forces', atoms.get_forces())
else:
raise ValueError('Atoms must have forces')
# check if an identical atoms object already exists in the container
for i, structure in enumerate(self._structure_list):
if are_configurations_equal(atoms_copy, structure.atoms):
raise ValueError('Atoms is identical to structure {}'.format(i))
logger.debug('Adding structure')
M = self._compute_fit_matrix(atoms)
structure = FitStructure(atoms_copy, M, **meta_data)
self._structure_list.append(structure)
[docs] def delete_all_structures(self):
""" Remove all current structures in StructureContainer. """
self._structure_list = []
[docs] def get_fit_data(self, structures=None):
"""Return fit data for structures. The fit matrices and target forces
for the structures are stacked into NumPy arrays.
Parameters
----------
structures: list, tuple
list of integers corresponding to structure indices. Defaults to
None and in that case returns all fit data available.
Returns
-------
numpy.ndarray, numpy.ndarray
stacked fit matrices, stacked target forces for the structures
"""
if structures is None:
structures = range(len(self))
M_list, f_list = [], []
for i in structures:
M_list.append(self._structure_list[i].fit_matrix)
f_list.append(self._structure_list[i].forces.flatten())
if len(M_list) == 0:
return None
return np.vstack(M_list), np.hstack(f_list)
def __str__(self):
if len(self._structure_list) > 0:
return self._get_str_structure_list()
else:
return 'Empty StructureContainer'
def __repr__(self):
return 'StructureContainer({!r}, {!r})'.format(
self._cs, self._structure_list)
def _get_str_structure_list(self):
""" Return formatted string of the structure list """
def str_structure(index, structure):
fields = OrderedDict([
('index', '{:^4}'.format(index)),
('num-atoms', '{:^5}'.format(len(structure))),
('avg-disp', '{:7.4f}'
.format(np.mean([np.linalg.norm(d) for d in
structure.displacements]))),
('avg-force', '{:7.4f}'
.format(np.mean([np.linalg.norm(f) for f in
structure.forces]))),
('max-force', '{:7.4f}'
.format(np.max([np.linalg.norm(f) for f in
structure.forces])))])
s = []
for name, value in fields.items():
n = max(len(name), len(value))
if index < 0:
s += ['{s:^{n}}'.format(s=name, n=n)]
else:
s += ['{s:^{n}}'.format(s=value, n=n)]
return ' | '.join(s)
# table width
dummy = self._structure_list[0]
n = len(str_structure(-1, dummy))
# table header
s = []
s.append(' Structure Container '.center(n, '='))
s += ['{:22} : {}'.format('Total number of structures', len(self))]
_, target_forces = self.get_fit_data()
s += ['{:22} : {}'.format('Number of force components', len(target_forces))]
s.append(''.center(n, '-'))
s.append(str_structure(-1, dummy))
s.append(''.center(n, '-'))
# table body
for i, structure in enumerate(self._structure_list):
s.append(str_structure(i, structure))
s.append(''.center(n, '='))
return '\n'.join(s)
def _compute_fit_matrix(self, atoms):
""" Compute fit matrix for a single atoms object """
logger.debug('Computing fit matrix')
if atoms != getattr(self._previous_fcm, 'atoms', None):
logger.debug(' Building new FCM object')
self._previous_fcm = ForceConstantModel(atoms, self._cs)
else:
logger.debug(' Reusing old FCM object')
return self._previous_fcm.get_fit_matrix(atoms.get_array('displacements'))
[docs]class FitStructure:
"""This class holds a structure with displacements and forces as well as
the fit matrix.
Parameters
----------
atoms : ase.Atoms
supercell structure
fit_matrix : numpy.ndarray
fit matrix, `N, M` array with `N = 3 * len(atoms)`
meta_data : dict
any meta data that needs to be stored in the FitStructure
"""
def __init__(self, atoms, fit_matrix, **meta_data):
if 3 * len(atoms) != fit_matrix.shape[0]:
raise ValueError('fit matrix not compatible with atoms')
self._atoms = atoms
self._fit_matrix = fit_matrix
self.meta_data = meta_data
@property
def fit_matrix(self):
""" numpy.ndarray : the fit matrix """
return self._fit_matrix
@property
def atoms(self):
""" ase.Atoms : supercell structure """
return self._atoms.copy()
@property
def forces(self):
""" numpy.ndarray : forces """
return self._atoms.get_array('forces')
@property
def displacements(self):
""" numpy.ndarray : atomic displacements """
return self._atoms.get_array('displacements')
def __getattr__(self, key):
""" Accesses meta_data if possible and returns value. """
if key not in self.meta_data.keys():
return super().__getattribute__(key)
return self.meta_data[key]
def __len__(self):
return len(self._atoms)
def __str__(self):
s = []
s.append(' FitStructure '.center(65, '='))
s.append('Formula: {}'.format(self.atoms.get_chemical_formula()))
s.append(('Cell:' + '\n [{:9.5f} {:9.5f} {:9.5f}]'*3).format(
*self.atoms.cell[0], *self.atoms.cell[1], *self.atoms.cell[2]))
s.append('Atoms (positions, displacements, forces):')
for atom, disp, force in zip(self.atoms, self.displacements, self.forces):
array_fmt = '[ {:9.5f} {:9.5f} {:9.5f} ]'
row_str = '{:3d} {}'.format(atom.index, atom.symbol)
row_str += array_fmt.format(*atom.position)
row_str += array_fmt.format(*disp)
row_str += array_fmt.format(*force)
s.append(row_str)
return '\n'.join(s)
def __repr__(self):
return 'FitStructure({!r}, ..., {!r})'.format(self.atoms, self.meta_data)
[docs] def write(self, fileobj):
""" Write the instance to file.
Parameters
----------
fileobj : str or file object
name of input file (str) or stream to write to (file object)
"""
if isinstance(fileobj, str):
tar_file = tarfile.open(name=fileobj, mode='w')
else:
tar_file = tarfile.open(fileobj=fileobj, mode='w')
items_pickle = dict(atoms=self._atoms, meta_data=self.meta_data)
items_hdf5 = dict(fit_matrix=self.fit_matrix)
add_items_to_tarfile_pickle(tar_file, items_pickle, 'items.pickle')
add_items_to_tarfile_hdf5(tar_file, items_hdf5, 'fit_matrix.hdf5')
tar_file.close()
[docs] @staticmethod
def read(fileobj, read_fit_matrix=True):
""" Read a OrientationFamily instance from a file.
Parameters
----------
fileobj : str or file object
name of input file (str) or stream to read from (file object)
read_fit_matrix : bool
whether or not to read the fit_matrix
Returns
-------
FitStructure instance
"""
if isinstance(fileobj, str):
tar_file = tarfile.open(mode='r', name=fileobj)
else:
tar_file = tarfile.open(mode='r', fileobj=fileobj)
items = read_items_pickle(tar_file, 'items.pickle')
fit_matrix = read_items_hdf5(tar_file, 'fit_matrix.hdf5')['fit_matrix']
return FitStructure(items['atoms'], fit_matrix, **items['meta_data'])
[docs]def are_configurations_equal(atoms1, atoms2, tol=1e-10):
""" Compare if two configurations are equal within some tolerance. This
includes checking all available arrays in the two atoms objects.
Parameters
----------
atoms1 : ase.Atoms
atoms2 : ase.Atoms
Returns
-------
bool
True if atoms are equal, False otherwise
"""
# pbc
if not all(atoms1.pbc == atoms2.pbc):
return False
# cell
if not np.allclose(atoms1.cell, atoms2.cell, atol=tol, rtol=0.0):
return False
# arrays
if not len(atoms1.arrays.keys()) == len(atoms2.arrays.keys()):
return False
for key, array1 in atoms1.arrays.items():
if key not in atoms2.arrays.keys():
return False
if not np.allclose(array1, atoms2.arrays[key], atol=tol, rtol=0.0):
return False
# passed all test, atoms must be equal
return True