Add Feature: XspectraCrystalWorkChain

pyproject.toml

@@ -118,6 +118,7 @@ aiida-quantumespresso = 'aiida_quantumespresso.cli:cmd_root'
 'quantumespresso.pdos' = 'aiida_quantumespresso.workflows.pdos:PdosWorkChain'
 'quantumespresso.xspectra.base' = 'aiida_quantumespresso.workflows.xspectra.base:XspectraBaseWorkChain'
 'quantumespresso.xspectra.core' = 'aiida_quantumespresso.workflows.xspectra.core:XspectraCoreWorkChain'
+'quantumespresso.xspectra.crystal' = 'aiida_quantumespresso.workflows.xspectra.crystal:XspectraCrystalWorkChain'
 
 [tool.flit.module]
 name = 'aiida_quantumespresso'

src/aiida_quantumespresso/calculations/functions/xspectra/get_spectra_by_element.py

@@ -0,0 +1,88 @@
+# -*- coding: utf-8 -*-
+"""Calcfunction to compile a complete spectrum for each element from multiple powder sample spectra."""
+from aiida import orm
+from aiida.engine import calcfunction
+import numpy as np
+
+
+@calcfunction
+def get_spectra_by_element(elements_list, equivalent_sites_data, **kwargs):
+ """Generate a final spectrum for each element from a dictionary of powder spectra inputs.
+
+ Powder spectra to be processed must be passed in using ``kwargs``, in which the keys must
+ correspond to the keys of ``equivalent_sites_data``.
+
+ :param elements_list: a List object defining the elements to compile spectra for.
+ :param equivalent_sites_data: a Dict object, defining the symmetry properties of the sites associated with each
+ powder spectrum in ``kwargs``. Must be in the format used in the ``equivalent_sites_data`` dictionary of
+ ``get_xspectra_structures.outputs.output_parameters``
+ """
+
+ incoming_spectra_nodes = {key: value for key, value in kwargs.items() if key != 'metadata'}
+ elements = elements_list.get_list()
+ equivalency_data = equivalent_sites_data.get_dict()
+ core_work_chains = {key: value.creator.caller for key, value in incoming_spectra_nodes.items()}
+
+ data_dict = {element: {} for element in elements}
+ for key in incoming_spectra_nodes:
+ core_work_chain = core_work_chains[key]
+ xspectra_out_params = core_work_chain.outputs.parameters_xspectra__xas_0.get_dict()
+ energy_zero = xspectra_out_params['energy_zero']
+ multiplicity = equivalency_data[key]['multiplicity']
+ element = equivalency_data[key]['symbol']
+
+ if 'total_multiplicity' not in data_dict[element]:
+ data_dict[element]['total_multiplicity'] = multiplicity
+ else:
+ data_dict[element]['total_multiplicity'] += multiplicity
+
+ data_dict[element][key] = {
+ 'spectrum_node': incoming_spectra_nodes[key],
+ 'element': element,
+ 'multiplicity': multiplicity,
+ 'energy_zero': energy_zero
+ }
+
+ spectra_by_element = {}
+ for element in elements:
+ spectra_list = []
+ total_multiplicity = data_dict[element].pop('total_multiplicity')
+ for key in data_dict[element]:
+ spectrum_node = data_dict[element][key]['spectrum_node']
+ site_multiplicity = data_dict[element][key]['multiplicity']
+ spectrum_x = spectrum_node.get_x()[1]
+ spectrum_y = spectrum_node.get_y()[0][1]
+ weighted_spectrum = np.column_stack((spectrum_x, (spectrum_y * site_multiplicity) / total_multiplicity))
+ spectra_list.append((weighted_spectrum, float(data_dict[element][key]['energy_zero'])))
+
+ # Sort according to Fermi level, then correct to align all spectra to the
+ # highest value. Note that this is needed because XSpectra automatically aligns the
+ # final spectrum such that the system's Fermi level is at 0 eV.
+ spectra_list.sort(key=lambda entry: entry[1])
+ highest_level = spectra_list[0][-1]
+ energy_zero_corrections = [(entry[0], entry[1] - highest_level) for entry in spectra_list]
+ corrected_spectra = [
+ np.column_stack((entry[0][:, 0] - entry[1], entry[0][:, 1])) for entry in energy_zero_corrections
+ ]
+
+ spectra_by_element[element] = np.column_stack((
+ sum([array[:, 0] for array in corrected_spectra]) / len(corrected_spectra),
+ sum([array[:, 1] for array in corrected_spectra])
+ ))
+
+ all_final_spectra = {}
+ for element in elements:
+ final_spectra = orm.XyData()
+ corrected_spectrum = spectra_by_element[element]
+ final_spectra_y_labels = [f'{element}_dipole']
+ final_spectra_y_units = ['sigma']
+ final_spectra_y_arrays = [corrected_spectrum[:, 1]]
+
+ final_spectra_x_label = 'energy'
+ final_spectra_x_units = 'eV'
+ final_spectra_x_array = corrected_spectrum[:, 0]
+ final_spectra.set_x(final_spectra_x_array, final_spectra_x_label, final_spectra_x_units)
+ final_spectra.set_y(final_spectra_y_arrays, final_spectra_y_labels, final_spectra_y_units)
+ all_final_spectra[f'{element}_xas'] = final_spectra
+
+ return all_final_spectra

src/aiida_quantumespresso/workflows/functions/get_xspectra_structures.py

@@ -256,9 +256,9 @@ def get_xspectra_structures(structure, **kwargs): # pylint: disable=too-many-st
  output_params['spacegroup_number'] = symmetry_dataset['number']
  output_params['international_symbol'] = symmetry_dataset['international']
 
- result['standardized_structure'] = standardized_structure_node
  output_params['structure_is_standardized'] = structure_is_standardized
  if structure_is_standardized:
+ result['standardized_structure'] = standardized_structure_node
  output_params['standardized_structure_num_sites'] = len(standardized_structure_node.sites)
  output_params['standardized_structure_cell_matrix'] = standardized_structure_node.cell
  output_params['standardized_structure_params'] = standardized_structure_node.cell_lengths

src/aiida_quantumespresso/workflows/protocols/xspectra/crystal.yaml

@@ -0,0 +1,14 @@
+default_inputs:
+ abs_atom_marker: X
+ clean_workdir: True
+ return_all_powder_spectra: False
+ core:
+ get_powder_spectrum: True
+default_protocol: moderate
+protocols:
+ moderate:
+ description: 'Protocol to perform XANES dipole calculations at normal precision and moderate computational cost.'
+ precise:
+ description: 'Protocol to perform XANES dipole calculations at high precision and higher computational cost.'
+ fast:
+ description: 'Protocol to perform XANES dipole calculations at low precision and minimal computational cost for testing purposes.'