Source code for hiphive.structure_container

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 .io.read_write_files import (add_items_to_tarfile_hdf5,

from .cluster_space import ClusterSpace
from .force_constant_model import ForceConstantModel
from .io.logging 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 object cluster space that is the basis for the container fit_structure_list : list of FitStructure objects (optional) structures to be added to the container """ def __init__(self, cs, fit_structure_list=None): """ Attributes ----------- _cs : ClusterSpace object ClusterSpace object which is the basis for the container _structure_list : list List of FitStructure objects _previous_fcm : ForceConstantModel object FCM object used for last fit matrix calculation _previous_atoms: ASE Atoms object atoms object used in last fit_matrix calculation; it is used to decided if the previous 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 self._previous_atoms = 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.number_of_dofs n_rows = sum(len(fs) * 3 for fs in self if fs.fit_ready) if n_rows == 0: return None return n_rows, n_cols @property def cluster_space(self): """ ClusterSpace object : copy of the cluster space the structure container is based on""" return self._cs.copy()
[docs] def get_structure_indices(self, user_tag): """ Get structure indices via user tag. Parameters ---------- user_tag : string user tag used for selecting structures Returns ------- list list of structures with specified user tag """ return [i for i, s in enumerate(self) if s.user_tag == user_tag]
[docs] def read(fileobj, read_fit_matrices=True): """Restore a StructureContainer object from file. Parameters ---------- f : string or file object name of input file (string) or stream to load from (file object) read_fit_matrices : bool Whether or not to load the fit matrices. """ if isinstance(fileobj, str): tar_file ='r', name=fileobj) else: tar_file ='r', fileobj=fileobj) # Read clusterspace f = tar_file.extractfile('cluster_space') cs = # Read fitstructures fit_structure_list = read_list_custom( tar_file, 'fit_structure',, read_fit_matrix=read_fit_matrices) return StructureContainer(cs, fit_structure_list)
[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 ='w', name=f) else: tar_file ='w', fileobj=f) # save cs custom_items = dict(cluster_space=self._cs) 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, user_tag=None, compute_fit_matrix=True): """Add a structure to the container. Note that custom information about the atoms object may not be stored inside, for example a SinglePointCalculator will not be kept. Parameters ---------- atoms : ASE Atoms object the structure to be added; the Atoms object must contain supplementary per-atom arrays with displacements and forces user_tag : string custom user tag to identify structure compute_fit_matrix : boolean if True the fit matrix of the structure is computed """ atoms_copy = atoms.copy() # atoms object must contain displacements and forces if 'displacements' not in atoms_copy.arrays.keys(): logger.warning('Skipping structure; no displacements found') return if 'forces' not in atoms_copy.arrays.keys(): if isinstance(atoms.calc, SinglePointCalculator): atoms_copy.new_array('forces', atoms.get_forces()) else: logger.warning('Skipping structure; no forces found') return # check if an identical atoms object already exists in the container for i, structure in enumerate(self._structure_list): if atoms_equals(atoms_copy, structure.atoms): logger.warning('Skipping structure; is equal to structure' ' {}'.format(i)) return'Adding structure') structure = FitStructure(atoms_copy, user_tag) if compute_fit_matrix: M = self._compute_fit_matrix(structure.atoms) structure.set_fit_matrix(M) self._structure_list.append(structure)
[docs] def update_fit_data(self): """Compute the fit matrices for structures for which they are not yet available.""" for structure in self._structure_list: if not structure.fit_ready: M = self._compute_fit_matrix(structure.atoms) structure.set_fit_matrix(M)
[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 array, NumPy array stacked fit matrices, stacked target forces for the structures """ if structures is None: M_list = [s.fit_matrix for s in self._structure_list if s.fit_ready] f_list = [s.forces.flatten() for s in self._structure_list if s.fit_ready] else: M_list, f_list = [], [] for i in structures: if not self._structure_list[i].fit_ready: raise ValueError('Structure {} is not fit ready'.format(i)) M_list.append(self._structure_list[i].fit_matrix) f_list.append(self._structure_list[i].forces.flatten()) if len(M_list) == 0: logger.warning('No available fit data for {}'.format(structures)) return None return np.vstack(M_list), np.hstack(f_list)
[docs] def print_cluster_space(self, include_orbits=False): """Print information concerning the cluster space this structure container is based on. Parameters ---------- include_orbits : boolean if True also print the list of orbits associated with the cluster space """ print(self._cs) if include_orbits: self._cs.print_orbits()
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)), ('user-tag', '{:^16}'.format(structure.user_tag)), ('num-atoms', '{:^5}'.format(len(structure))), ('fit-ready', '{:^5}'.format(str(structure.fit_ready))), ('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))] 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 """'Computing fit matrix') if atoms != self._previous_atoms:' Building new FCM object') self._previous_atoms = atoms.copy() self._previous_fcm = ForceConstantModel(atoms, self._cs) else:' 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 object supercell structure user_tag : string custom user tag fit_matrix : NumPy array fit matrix; NumPy (N, M) array with `N = 3 * len(atoms)` """ def __init__(self, atoms, user_tag=None, fit_matrix=None): self._fit_ready = False self._atoms = atoms self._user_tag = user_tag self.set_fit_matrix(fit_matrix) @property def fit_matrix(self): """NumPy array : the fit matrix""" return self._fit_matrix @property def atoms(self): """ASE Atoms object : supercell structure""" return self._atoms @property def forces(self): """NumPy array : forces""" return self._atoms.get_array('forces') @property def displacements(self): """NumPy array : atomic displacements""" return self._atoms.get_array('displacements') @property def fit_ready(self): """boolean : True if the structure is prepared for fitting, i.e. the fit matrix is available""" return self._fit_ready @property def user_tag(self): return str(self._user_tag)
[docs] def set_fit_matrix(self, fit_matrix): """Set the fit matrix. Parameters ---------- fit_matrix : NumPy array fit matrix for this structure; NumPy (N, M) array with `N = 3 * len(atoms)` """ if fit_matrix is not None: if fit_matrix.shape[0] == len(self._atoms) * 3: self._fit_matrix = fit_matrix self._fit_ready = True else: logger.warning('fit matrix not compatible with atoms') else: self._fit_matrix = None self._fit_ready = False
def __len__(self): return len(self._atoms) def __str__(self): s = [] s.append('atoms: {}'.format(self.atoms)) s.append('user_tag: {}'.format(self.user_tag)) s.append('fit_ready: {}'.format(self.fit_ready)) return '\n'.join(s) def __repr__(self): return 'FitStructure({!r}, {!r})'.format(self.atoms, self.user_tag)
[docs] def write(self, fileobj): if isinstance(fileobj, str): tar_file =, mode='w') else: tar_file =, mode='w') items_pickle = dict(atoms=self._atoms, user_tag=self.user_tag, fit_ready=self.fit_ready) items_hdf5 = dict(fit_matrix=self.fit_matrix) add_items_to_tarfile_pickle(tar_file, items_pickle, 'items.pickle') if self.fit_ready: add_items_to_tarfile_hdf5(tar_file, items_hdf5, 'fit_matrix.hdf5') tar_file.close()
[docs] def read(fileobj, read_fit_matrix=True): if isinstance(fileobj, str): tar_file ='r', name=fileobj) else: tar_file ='r', fileobj=fileobj) items = read_items_pickle(tar_file, 'items.pickle') if items['fit_ready'] and read_fit_matrix: fit_matrix = read_items_hdf5( tar_file, 'fit_matrix.hdf5')['fit_matrix'] else: fit_matrix = None return FitStructure(items['atoms'], user_tag=items['user_tag'], fit_matrix=fit_matrix)
def atoms_equals(atoms1, atoms2, tol=1e-10): """ Compare if two atoms are equals within some tolerance Parameters ---------- atoms1 : ASE Atoms object atoms object 1 atoms2 : ASE Atoms object atoms object 2 Returns ------- bool True if atoms are equal, else False """ # 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