# -*- coding: utf-8 -*-
###############################################################################
# Copyright (c), Forschungszentrum Jülich GmbH, IAS-1/PGI-1, Germany. #
# All rights reserved. #
# This file is part of the Masci-tools package. #
# (Material science tools) #
# #
# The code is hosted on GitHub at https://github.com/judftteam/masci-tools. #
# For further information on the license, see the LICENSE.txt file. #
# For further information please visit http://judft.de/. #
# #
###############################################################################
"""
This module defines commonly used recipes for the :py:class:`~masci_tools.io.parsers.hdf5.reader.HDF5Reader`
Available are:
- Recipe for bandstructure calculations with Fleur
- Recipes for almost all DOS calculation modes of Fleur
A Recipe is a python dictionary in a specific format.
A Template Example:
.. code-block:: python
from masci_tools.io.parser.hdf5.readers import Transformation, AttribTransformation
RecipeExample = {
'datasets': {
'example_dataset': {
'h5path': '/path/in/hdf/file',
'transforms': [Transformation(name='get_first_element')]
},
'example_attrib_transform': {
'h5path': '/other/path/in/hdf/file',
'transforms': [AttribTransformation(name='multiply_by_attribute', attrib_name='example_attribute')]
}
},
'attributes': {
'example_attribute': {
'h5path':
'/path/in/hdf/file',
'transforms':
[Transformation(name='get_attribute', args=('attribName',)),
Transformation(name='get_first_element')]
}
}
}
The Recipe consists of two sections 'datasets' and 'attributes'. All data from these two sections will be returned
in separate python dictionaries by the :py:class:`~masci_tools.io.parsers.hdf5.reader.HDF5Reader` class
Each entry in those sections has to have a `h5path` entry, which will specify the dataset to initially
read from the hdf file. Then each entry can define a entry `transforms` with a list of the namedtuples
imported at the top of the code example. These correponds to function calls to functions in
:py:mod:`~masci_tools.io.parsers.hdf5.transforms` to transform the read in data
Entries in the `attributes` section are read and transformed first and can subsequently be used in transformations
for the `datasets`. These correpsond to the transforms created with the :py:class:`~masci_tools.io.parsers.hdf5.reader.AttribTransformation`
namedtuple instead of :py:class:`~masci_tools.io.parsers.hdf5.reader.Transformation`.
"""
from masci_tools.util.constants import HTR_TO_EV, BOHR_A
from masci_tools.io.parsers.hdf5.reader import Transformation, AttribTransformation
def dos_recipe_format(group):
if group == 'Local':
atom_prefix = 'MT'
elif group == 'jDOS':
atom_prefix = 'jDOS'
elif group == 'Orbcomp':
atom_prefix = 'ORBCOMP'
elif group == 'mcd':
atom_prefix = 'MCD'
else:
raise ValueError(f'Unknown group: {group}')
return {
'datasets': {
'dos': {
'h5path':
f'/{group}/DOS',
'transforms': [
Transformation(name='get_all_child_datasets', args=(), kwargs={'ignore': 'energyGrid'}),
AttribTransformation(name='add_partial_sums',
attrib_name='atoms_groups',
args=('{atom_prefix}:{{}}'.format(atom_prefix=atom_prefix).format,),
kwargs={'make_set': True}),
Transformation(name='multiply_scalar', args=(1.0 / HTR_TO_EV,), kwargs={}),
Transformation(
name='split_array',
args=(),
kwargs={'suffixes': ['up', 'down']},
)
],
'unpack_dict':
True,
},
'energy_grid': {
'h5path': f'/{group}/DOS/energyGrid',
'transforms': [Transformation(name='multiply_scalar', args=(HTR_TO_EV,), kwargs={})]
}
},
'attributes': {
'dos_group': {
'h5path': f'/{group}',
'transforms': [
Transformation(name='get_name', args=(), kwargs={}),
],
},
'n_types': {
'h5path':
'/atoms',
'description':
'Number of atom types',
'transforms': [
Transformation(name='get_attribute', args=('nTypes',), kwargs={}),
Transformation(name='get_first_element', args=(), kwargs={})
]
},
'atoms_elements': {
'h5path': '/atoms/atomicNumbers',
'description': 'Atomic numbers',
'transforms': [Transformation(name='periodic_elements', args=(), kwargs={})]
},
'atoms_groups': {
'h5path': '/atoms/equivAtomsGroup'
},
'fermi_energy': {
'h5path':
'/general',
'description':
'fermi_energy of the system',
'transforms': [
Transformation(name='get_attribute', args=('lastFermiEnergy',), kwargs={}),
Transformation(name='get_first_element', args=(), kwargs={})
]
},
'spins': {
'h5path':
'/general',
'description':
'number of distinct spin directions in the system',
'transforms': [
Transformation(name='get_attribute', args=('spins',), kwargs={}),
Transformation(name='get_first_element', args=(), kwargs={})
]
}
}
}
#DOS Recipes
FleurDOS = dos_recipe_format('Local')
FleurJDOS = dos_recipe_format('jDOS')
FleurORBCOMP = dos_recipe_format('Orbcomp')
FleurMCD = dos_recipe_format('mcd')
#Recipe for bandstructures
FleurBands = {
'datasets': {
'weights': {
'h5path':
'/Local/BS',
'transforms': [
Transformation(name='get_all_child_datasets', args=(), kwargs={'ignore': ['eigenvalues', 'kpts']}),
AttribTransformation(name='add_partial_sums',
attrib_name='atoms_groups',
args=('MT:{}'.format,),
kwargs={'make_set': True}),
Transformation(name='split_array', args=(), kwargs={'suffixes': ['up', 'down']}),
Transformation(name='flatten_array', args=(), kwargs={})
],
'unpack_dict':
True
},
'eigenvalues': {
'h5path':
'/Local/BS/eigenvalues',
'transforms': [
AttribTransformation(name='shift_by_attribute',
attrib_name='fermi_energy',
args=(),
kwargs={
'negative': True,
}),
Transformation(name='multiply_scalar', args=(HTR_TO_EV,), kwargs={}),
Transformation(name='split_array', args=(), kwargs={
'suffixes': ['up', 'down'],
'name': 'eigenvalues'
}),
Transformation(name='flatten_array', args=(), kwargs={})
],
'unpack_dict':
True
},
'kpath': {
'h5path':
'/kpts/coordinates',
'transforms': [
AttribTransformation(name='multiply_by_attribute',
attrib_name='reciprocal_cell',
args=(),
kwargs={'transpose': True}),
Transformation(name='calculate_norm', args=(), kwargs={'between_neighbours': True}),
Transformation(name='cumulative_sum', args=(), kwargs={}),
AttribTransformation(name='repeat_array_by_attribute', attrib_name='nbands', args=(), kwargs={}),
]
},
},
'attributes': {
'n_types': {
'h5path':
'/atoms',
'description':
'Number of atom types',
'transforms': [
Transformation(name='get_attribute', args=('nTypes',), kwargs={}),
Transformation(name='get_first_element', args=(), kwargs={})
]
},
'kpoints': {
'h5path': '/kpts/coordinates',
},
'nkpts': {
'h5path':
'/Local/BS/eigenvalues',
'transforms': [
Transformation(name='get_shape', args=(), kwargs={}),
Transformation(name='index_dataset', args=(1,), kwargs={})
]
},
'nbands': {
'h5path':
'/Local/BS/eigenvalues',
'transforms': [
Transformation(name='get_shape', args=(), kwargs={}),
Transformation(name='index_dataset', args=(2,), kwargs={})
]
},
'atoms_elements': {
'h5path': '/atoms/atomicNumbers',
'description': 'Atomic numbers',
'transforms': [Transformation(name='periodic_elements', args=(), kwargs={})]
},
'atoms_position': {
'h5path': '/atoms/positions',
'description': 'Atom coordinates per atom',
},
'atoms_groups': {
'h5path': '/atoms/equivAtomsGroup'
},
'bravais_matrix': {
'h5path': '/cell/bravaisMatrix',
'description': 'Coordinate transformation internal to physical for atoms',
'transforms': [Transformation(name='multiply_scalar', args=(BOHR_A,), kwargs={})]
},
'reciprocal_cell': {
'h5path': '/cell/reciprocalCell'
},
'special_kpoint_indices': {
'h5path': '/kpts/specialPointIndices',
'transforms': [Transformation(name='shift_dataset', args=(-1,), kwargs={})]
},
'special_kpoint_labels': {
'h5path': '/kpts/specialPointLabels',
'transforms': [Transformation(name='convert_to_str', args=(), kwargs={})]
},
'fermi_energy': {
'h5path':
'/general',
'description':
'fermi_energy of the system',
'transforms': [
Transformation(name='get_attribute', args=('lastFermiEnergy',), kwargs={}),
Transformation(name='get_first_element', args=(), kwargs={})
]
},
'spins': {
'h5path':
'/general',
'description':
'number of distinct spin directions in the system',
'transforms': [
Transformation(name='get_attribute', args=('spins',), kwargs={}),
Transformation(name='get_first_element', args=(), kwargs={})
]
}
}
}
#Recipe for bandstructures without reading in weights
FleurSimpleBands = {
'datasets': {
'eigenvalues': {
'h5path':
'/Local/BS/eigenvalues',
'transforms': [
AttribTransformation(name='shift_by_attribute',
attrib_name='fermi_energy',
args=(),
kwargs={
'negative': True,
}),
Transformation(name='multiply_scalar', args=(HTR_TO_EV,), kwargs={}),
Transformation(name='split_array', args=(), kwargs={
'suffixes': ['up', 'down'],
'name': 'eigenvalues'
}),
Transformation(name='flatten_array', args=(), kwargs={})
],
'unpack_dict':
True
},
'kpath': {
'h5path':
'/kpts/coordinates',
'transforms': [
AttribTransformation(name='multiply_by_attribute',
attrib_name='reciprocal_cell',
args=(),
kwargs={'transpose': True}),
Transformation(name='calculate_norm', args=(), kwargs={'between_neighbours': True}),
Transformation(name='cumulative_sum', args=(), kwargs={}),
AttribTransformation(name='repeat_array_by_attribute', attrib_name='nbands', args=(), kwargs={}),
]
},
},
'attributes': {
'kpoints': {
'h5path': '/kpts/coordinates',
},
'nkpts': {
'h5path':
'/Local/BS/eigenvalues',
'transforms': [
Transformation(name='get_shape', args=(), kwargs={}),
Transformation(name='index_dataset', args=(1,), kwargs={})
]
},
'nbands': {
'h5path':
'/Local/BS/eigenvalues',
'transforms': [
Transformation(name='get_shape', args=(), kwargs={}),
Transformation(name='index_dataset', args=(2,), kwargs={})
]
},
'bravais_matrix': {
'h5path': '/cell/bravaisMatrix',
'description': 'Coordinate transformation internal to physical for atoms',
'transforms': [Transformation(name='multiply_scalar', args=(BOHR_A,), kwargs={})]
},
'reciprocal_cell': {
'h5path': '/cell/reciprocalCell'
},
'special_kpoint_indices': {
'h5path': '/kpts/specialPointIndices',
'transforms': [Transformation(name='shift_dataset', args=(-1,), kwargs={})]
},
'special_kpoint_labels': {
'h5path': '/kpts/specialPointLabels',
'transforms': [Transformation(name='convert_to_str', args=(), kwargs={})]
},
'fermi_energy': {
'h5path':
'/general',
'description':
'fermi_energy of the system',
'transforms': [
Transformation(name='get_attribute', args=('lastFermiEnergy',), kwargs={}),
Transformation(name='get_first_element', args=(), kwargs={})
]
},
'spins': {
'h5path':
'/general',
'description':
'number of distinct spin directions in the system',
'transforms': [
Transformation(name='get_attribute', args=('spins',), kwargs={}),
Transformation(name='get_first_element', args=(), kwargs={})
]
}
}
}
[docs]def get_fleur_bands_specific_weights(weight_name):
"""
Recipe for bandstructure calculations only retrieving one
additional weight besides the eigenvalues and kpath
:param weight_name: key or list of keys of the weight(s) to retrieve
:returns: dict of the recipe to retrieve a simple bandstructure
plus the one specified weight
"""
recipe = {
'datasets': {
'eigenvalues': {
'h5path':
'/Local/BS/eigenvalues',
'transforms': [
AttribTransformation(name='shift_by_attribute',
attrib_name='fermi_energy',
args=(),
kwargs={
'negative': True,
}),
Transformation(name='multiply_scalar', args=(HTR_TO_EV,), kwargs={}),
Transformation(name='split_array',
args=(),
kwargs={
'suffixes': ['up', 'down'],
'name': 'eigenvalues'
}),
Transformation(name='flatten_array', args=(), kwargs={})
],
'unpack_dict':
True
},
'kpath': {
'h5path':
'/kpts/coordinates',
'transforms': [
AttribTransformation(name='multiply_by_attribute',
attrib_name='reciprocal_cell',
args=(),
kwargs={'transpose': True}),
Transformation(name='calculate_norm', args=(), kwargs={'between_neighbours': True}),
Transformation(name='cumulative_sum', args=(), kwargs={}),
AttribTransformation(name='repeat_array_by_attribute', attrib_name='nbands', args=(), kwargs={}),
]
},
},
'attributes': {
'n_types': {
'h5path':
'/atoms',
'description':
'Number of atom types',
'transforms': [
Transformation(name='get_attribute', args=('nTypes',), kwargs={}),
Transformation(name='get_first_element', args=(), kwargs={})
]
},
'kpoints': {
'h5path': '/kpts/coordinates',
},
'nkpts': {
'h5path':
'/Local/BS/eigenvalues',
'transforms': [
Transformation(name='get_shape', args=(), kwargs={}),
Transformation(name='index_dataset', args=(1,), kwargs={})
]
},
'nbands': {
'h5path':
'/Local/BS/eigenvalues',
'transforms': [
Transformation(name='get_shape', args=(), kwargs={}),
Transformation(name='index_dataset', args=(2,), kwargs={})
]
},
'atoms_elements': {
'h5path': '/atoms/atomicNumbers',
'description': 'Atomic numbers',
'transforms': [Transformation(name='periodic_elements', args=(), kwargs={})]
},
'atoms_position': {
'h5path': '/atoms/positions',
'description': 'Atom coordinates per atom',
},
'atoms_groups': {
'h5path': '/atoms/equivAtomsGroup'
},
'bravais_matrix': {
'h5path': '/cell/bravaisMatrix',
'description': 'Coordinate transformation internal to physical for atoms',
'transforms': [Transformation(name='multiply_scalar', args=(BOHR_A,), kwargs={})]
},
'reciprocal_cell': {
'h5path': '/cell/reciprocalCell'
},
'special_kpoint_indices': {
'h5path': '/kpts/specialPointIndices',
'transforms': [Transformation(name='shift_dataset', args=(-1,), kwargs={})]
},
'special_kpoint_labels': {
'h5path': '/kpts/specialPointLabels',
'transforms': [Transformation(name='convert_to_str', args=(), kwargs={})]
},
'fermi_energy': {
'h5path':
'/general',
'description':
'fermi_energy of the system',
'transforms': [
Transformation(name='get_attribute', args=('lastFermiEnergy',), kwargs={}),
Transformation(name='get_first_element', args=(), kwargs={})
]
},
'spins': {
'h5path':
'/general',
'description':
'number of distinct spin directions in the system',
'transforms': [
Transformation(name='get_attribute', args=('spins',), kwargs={}),
Transformation(name='get_first_element', args=(), kwargs={})
]
}
}
}
if isinstance(weight_name, str):
weight_name = [weight_name]
for name in weight_name:
if 'MT:' in name and not any(c in name for c in ('s', 'p', 'd', 'f')):
#We need to get all orbitals and calculate the atom sum
recipe['datasets'][name] = {
'h5path':
'/Local/BS',
'transforms': [
Transformation(name='get_all_child_datasets', args=(), kwargs={'contains': name}),
Transformation(name='sum_over_dict_entries', args=(), kwargs={'overwrite_dict': True}),
Transformation(name='split_array', args=(), kwargs={
'suffixes': ['up', 'down'],
'name': name
}),
Transformation(name='flatten_array', args=(), kwargs={})
],
'unpack_dict':
True
}
else:
recipe['datasets'][name] = {
'h5path':
f'/Local/BS/{name}',
'transforms': [
Transformation(name='split_array', args=(), kwargs={
'suffixes': ['up', 'down'],
'name': name
}),
Transformation(name='flatten_array', args=(), kwargs={})
],
'unpack_dict':
True
}
return recipe