Merge branch 'main' into ph-initialization

pyproject.toml

@@ -47,7 +47,7 @@ docs = [
     'sphinx-click~=4.4.0',
     'sphinx-design~=0.4.1',
     'sphinxcontrib-details-directive~=0.1.0',
-    'sphinx-autoapi~=3.0',
+    'sphinx-autoapi~=3.0.0',
     'myst_parser~=1.0.0',
 ]
 pre-commit = [
@@ -86,6 +86,7 @@ aiida-quantumespresso = 'aiida_quantumespresso.cli:cmd_root'
 'quantumespresso.seekpath_structure_analysis' = 'aiida_quantumespresso.calculations.functions.seekpath_structure_analysis:seekpath_structure_analysis'
 'quantumespresso.xspectra' = 'aiida_quantumespresso.calculations.xspectra:XspectraCalculation'
 'quantumespresso.open_grid' = 'aiida_quantumespresso.calculations.open_grid:OpenGridCalculation'
+'quantumespresso.bands' = 'aiida_quantumespresso.calculations.bands:BandsCalculation'
 
 [project.entry-points.'aiida.data']
 'quantumespresso.force_constants' = 'aiida_quantumespresso.data.force_constants:ForceConstantsData'
@@ -105,6 +106,7 @@ aiida-quantumespresso = 'aiida_quantumespresso.cli:cmd_root'
 'quantumespresso.pw2wannier90' = 'aiida_quantumespresso.parsers.pw2wannier90:Pw2wannier90Parser'
 'quantumespresso.xspectra' = 'aiida_quantumespresso.parsers.xspectra:XspectraParser'
 'quantumespresso.open_grid' = 'aiida_quantumespresso.parsers.open_grid:OpenGridParser'
+'quantumespresso.bands' = 'aiida_quantumespresso.parsers.bands:BandsParser'
 
 [project.entry-points.'aiida.tools.calculations']
 'quantumespresso.pw' = 'aiida_quantumespresso.tools.calculations.pw:PwCalculationTools'
@@ -125,6 +127,7 @@ aiida-quantumespresso = 'aiida_quantumespresso.cli:cmd_root'
 'quantumespresso.xps' = 'aiida_quantumespresso.workflows.xps:XpsWorkChain'
 'quantumespresso.xspectra.core' = 'aiida_quantumespresso.workflows.xspectra.core:XspectraCoreWorkChain'
 'quantumespresso.xspectra.crystal' = 'aiida_quantumespresso.workflows.xspectra.crystal:XspectraCrystalWorkChain'
+'quantumespresso.bands.base' = 'aiida_quantumespresso.workflows.bands.base:BandsBaseWorkChain'
 
 [tool.flit.module]
 name = 'aiida_quantumespresso'

src/aiida_quantumespresso/calculations/bands.py

@@ -0,0 +1,39 @@
+# -*- coding: utf-8 -*-
+"""`CalcJob` implementation for the bands.x code of Quantum ESPRESSO."""
+
+from aiida import orm
+
+from aiida_quantumespresso.calculations.namelists import NamelistsCalculation
+
+
+class BandsCalculation(NamelistsCalculation):
+    """`CalcJob` implementation for the bands.x code of Quantum ESPRESSO.
+
+    bands.x code of the Quantum ESPRESSO distribution, re-orders bands, and computes band-related properties.
+
+    It computes for instance the expectation value of the momentum operator:
+    <Psi(n,k) | i * m * [H, x] | Psi(m,k)>. For more information, refer to http://www.quantum-espresso.org/
+    """
+
+    _MOMENTUM_OPERATOR_NAME = 'momentum_operator.dat'
+    _BANDS_NAME = 'bands.dat'
+
+    _default_namelists = ['BANDS']
+    _blocked_keywords = [
+        ('BANDS', 'outdir', NamelistsCalculation._OUTPUT_SUBFOLDER),  # pylint: disable=protected-access
+        ('BANDS', 'prefix', NamelistsCalculation._PREFIX),  # pylint: disable=protected-access
+        ('BANDS', 'filband', _BANDS_NAME),
+        ('BANDS', 'filp', _MOMENTUM_OPERATOR_NAME),  # Momentum operator
+    ]
+
+    _internal_retrieve_list = []
+    _default_parser = 'quantumespresso.bands'
+
+    @classmethod
+    def define(cls, spec):
+        """Define the process specification."""
+        # yapf: disable
+        super().define(spec)
+        spec.input('parent_folder', valid_type=(orm.RemoteData, orm.FolderData), required=True)
+        spec.output('output_parameters', valid_type=orm.Dict)
+        # yapf: enable

src/aiida_quantumespresso/cli/workflows/pw/base.py

@@ -42,6 +42,9 @@ def launch_workflow(
     cutoff_wfc, cutoff_rho = pseudo_family.get_recommended_cutoffs(structure=structure, unit='Ry')
 
     parameters = {
+        'CONTROL': {
+            'calculation': 'scf',
+        },
         'SYSTEM': {
             'ecutwfc': ecutwfc or cutoff_wfc,
             'ecutrho': ecutrho or cutoff_rho,

src/aiida_quantumespresso/parsers/bands.py

@@ -0,0 +1,27 @@
+# -*- coding: utf-8 -*-
+from aiida.orm import Dict
+
+from aiida_quantumespresso.utils.mapping import get_logging_container
+
+from .base import BaseParser
+
+
+class BandsParser(BaseParser):
+    """``Parser`` implementation for the ``BandsCalculation`` calculation job class."""
+
+    def parse(self, **kwargs):
+        """Parse the retrieved files of a ``BandsCalculation`` into output nodes."""
+        logs = get_logging_container()
+
+        _, parsed_data, logs = self.parse_stdout_from_retrieved(logs)
+
+        base_exit_code = self.check_base_errors(logs)
+        if base_exit_code:
+            return self.exit(base_exit_code, logs)
+
+        self.out('output_parameters', Dict(parsed_data))
+
+        if 'ERROR_OUTPUT_STDOUT_INCOMPLETE'in logs.error:
+            return self.exit(self.exit_codes.ERROR_OUTPUT_STDOUT_INCOMPLETE, logs)
+
+        return self.exit(logs=logs)

src/aiida_quantumespresso/workflows/bands/base.py

@@ -0,0 +1,61 @@
+# -*- coding: utf-8 -*-
+"""Workchain to run a Quantum ESPRESSO bands.x calculation with automated error handling and restarts."""
+from aiida.common import AttributeDict
+from aiida.engine import BaseRestartWorkChain, ProcessHandlerReport, process_handler, while_
+from aiida.plugins import CalculationFactory
+
+BandsCalculation = CalculationFactory('quantumespresso.bands')
+
+
+class BandsBaseWorkChain(BaseRestartWorkChain):
+    """Workchain to run a Quantum ESPRESSO bands.x calculation with automated error handling and restarts."""
+
+    _process_class = BandsCalculation
+
+    @classmethod
+    def define(cls, spec):
+        """Define the process specification."""
+        # yapf: disable
+        super().define(spec)
+        spec.expose_inputs(BandsCalculation, namespace='bands')
+        spec.expose_outputs(BandsCalculation)
+        spec.outline(
+            cls.setup,
+            while_(cls.should_run_process)(
+                cls.run_process,
+                cls.inspect_process,
+            ),
+            cls.results,
+        )
+        spec.exit_code(300, 'ERROR_UNRECOVERABLE_FAILURE',
+            message='The calculation failed with an unrecoverable error.')
+        # yapf: enable
+
+    def setup(self):
+        """Call the `setup` of the `BaseRestartWorkChain` and then create the inputs dictionary in `self.ctx.inputs`.
+
+        This `self.ctx.inputs` dictionary will be used by the `BaseRestartWorkChain` to submit the calculations in the
+        internal loop.
+        """
+        super().setup()
+        self.ctx.restart_calc = None
+        self.ctx.inputs = AttributeDict(self.exposed_inputs(BandsCalculation, 'bands'))
+
+    def report_error_handled(self, calculation, action):
+        """Report an action taken for a calculation that has failed.
+
+        This should be called in a registered error handler if its condition is met and an action was taken.
+
+        :param calculation: the failed calculation node
+        :param action: a string message with the action taken
+        """
+        arguments = [calculation.process_label, calculation.pk, calculation.exit_status, calculation.exit_message]
+        self.report('{}<{}> failed with exit status {}: {}'.format(*arguments))
+        self.report(f'Action taken: {action}')
+
+    @process_handler(priority=600)
+    def handle_unrecoverable_failure(self, node):
+        """Handle calculations with an exit status below 400 which are unrecoverable, so abort the work chain."""
+        if node.is_failed and node.exit_status < 400:
+            self.report_error_handled(node, 'unrecoverable error, aborting...')
+            return ProcessHandlerReport(True, self.exit_codes.ERROR_UNRECOVERABLE_FAILURE)

src/aiida_quantumespresso/workflows/functions/get_xspectra_structures.py

@@ -360,6 +360,7 @@ def get_xspectra_structures(structure, **kwargs):  # pylint: disable=too-many-st
             new_supercell = get_supercell_result['new_supercell']
             output_params['supercell_factors'] = multiples
 
+        result['supercell'] = new_supercell
         output_params['supercell_num_sites'] = len(new_supercell.sites)
         output_params['supercell_cell_matrix'] = new_supercell.cell
         output_params['supercell_cell_lengths'] = new_supercell.cell_lengths

src/aiida_quantumespresso/workflows/xspectra/crystal.py

@@ -4,7 +4,7 @@
 Uses QuantumESPRESSO pw.x and xspectra.x.
 """
 from aiida import orm
-from aiida.common import AttributeDict, ValidationError
+from aiida.common import AttributeDict
 from aiida.engine import ToContext, WorkChain, if_
 from aiida.orm import UpfData as aiida_core_upf
 from aiida.plugins import CalculationFactory, DataFactory, WorkflowFactory
@@ -173,6 +173,19 @@ def define(cls, spec):
             help=('Input namespace to provide core wavefunction inputs for each element. Must follow the format: '
                    '``core_wfc_data__{symbol} = {node}``')
         )
+        spec.input_namespace(
+            'symmetry_data',
+            valid_type=(orm.Dict, orm.Int),
+            dynamic=True,
+            required=False,
+            help=(
+                'Input namespace to define equivalent sites and spacegroup number for the system. If defined, will '
+                'skip symmetry analysis and structure standardization. Use *only* if symmetry data are known '
+                'for certain. Requires ``spacegroup_number`` (Int) and ``equivalent_sites_data`` (Dict) to be '
+                'defined separately. All keys in `equivalent_sites_data` must be formatted as "site_<site_index>". '
+                'See docstring of `get_xspectra_structures` for more information about inputs.'
+            )
+        )
         spec.inputs.validator = cls.validate_inputs
         spec.outline(
             cls.setup,
@@ -370,7 +383,7 @@ def get_builder_from_protocol( # pylint: disable=too-many-statements
 
 
     @staticmethod
-    def validate_inputs(inputs, _):
+    def validate_inputs(inputs, _): # pylint: disable=too-many-return-statements
         """Validate the inputs before launching the WorkChain."""
         structure = inputs['structure']
         kinds_present = [kind.name for kind in structure.kinds]
@@ -382,54 +395,92 @@ def validate_inputs(inputs, _):
             if element not in elements_present:
                 extra_elements.append(element)
         if len(extra_elements) > 0:
-            raise ValidationError(
+            return (
                 f'Some elements in ``elements_list`` {extra_elements} do not exist in the'
                 f' structure provided {elements_present}.'
             )
 
         abs_atom_marker = inputs['abs_atom_marker'].value
         if abs_atom_marker in kinds_present:
-            raise ValidationError(
+            return (
                 f'The marker given for the absorbing atom ("{abs_atom_marker}") matches an existing Kind in the '
                 f'input structure ({kinds_present}).'
             )
 
         if not inputs['core']['get_powder_spectrum'].value:
-            raise ValidationError(
+            return (
                 'The ``get_powder_spectrum`` input for the XspectraCoreWorkChain namespace must be ``True``.'
             )
 
         if 'upf2plotcore_code' not in inputs and 'core_wfc_data' not in inputs:
-            raise ValidationError(
+            return (
                 'Neither a ``Code`` node for upf2plotcore.sh or a set of ``core_wfc_data`` were provided.'
             )
 
         if 'core_wfc_data' in inputs:
             core_wfc_data_list = sorted(inputs['core_wfc_data'].keys())
             if core_wfc_data_list != absorbing_elements_list:
-                raise ValidationError(
+                return (
                     f'The ``core_wfc_data`` provided ({core_wfc_data_list}) does not match the list of'
                     f' absorbing elements ({absorbing_elements_list})'
                 )
-            else:
-                empty_core_wfc_data = []
-                for key, value in inputs['core_wfc_data'].items():
-                    header_line = value.get_content()[:40]
-                    try:
-                        num_core_states = int(header_line.split(' ')[5])
-                    except Exception as exc:
-                        raise ValidationError(
-                            'The core wavefunction data file is not of the correct format'
-                        ) from exc
-                    if num_core_states == 0:
-                        empty_core_wfc_data.append(key)
-                if len(empty_core_wfc_data) > 0:
-                    raise ValidationError(
-                        f'The ``core_wfc_data`` provided for elements {empty_core_wfc_data} do not contain '
-                        'any wavefunction data.'
-                    )
+            empty_core_wfc_data = []
+            for key, value in inputs['core_wfc_data'].items():
+                header_line = value.get_content()[:40]
+                try:
+                    num_core_states = int(header_line.split(' ')[5])
+                except: # pylint: disable=bare-except
+                    return (
+                        'The core wavefunction data file is not of the correct format'
+                    ) # pylint: enable=bare-except
+                if num_core_states == 0:
+                    empty_core_wfc_data.append(key)
+            if len(empty_core_wfc_data) > 0:
+                return (
+                    f'The ``core_wfc_data`` provided for elements {empty_core_wfc_data} do not contain '
+                    'any wavefunction data.'
+                )
+
+        if 'symmetry_data' in inputs:
+            spacegroup_number = inputs['symmetry_data']['spacegroup_number'].value
+            equivalent_sites_data = inputs['symmetry_data']['equivalent_sites_data'].get_dict()
+            if spacegroup_number <= 0 or spacegroup_number >= 231:
+                return (
+                    f'Input spacegroup number ({spacegroup_number}) outside of valid range (1-230).'
+                )
 
+            input_elements = []
+            required_keys = sorted(['symbol', 'multiplicity', 'kind_name', 'site_index'])
+            invalid_entries = []
+            # We check three things here: (1) are there any site indices which are outside of the possible
+            # range of site indices (2) do we have all the required keys for each entry,
+            # and (3) is there a mismatch between `absorbing_elements_list` and the elements specified
+            # in the entries of `equivalent_sites_data`. These checks are intended only to avoid a crash.
+            # We assume otherwise that the user knows what they're doing and has set everything else
+            # to their preferences correctly.
+            for site_label, value in equivalent_sites_data.items():
+                if not set(required_keys).issubset(set(value.keys())) :
+                    invalid_entries.append(site_label)
+                elif value['symbol'] not in input_elements:
+                    input_elements.append(value['symbol'])
+                    if value['site_index'] < 0 or value['site_index'] >= len(structure.sites):
+                        return (
+                            f'The site index for {site_label} ({value["site_index"]}) is outside the range of '
+                            + f'sites within the structure (0-{len(structure.sites) -1}).'
+                        )
+
+            if len(invalid_entries) != 0:
+                return (
+                    f'The required keys ({required_keys}) were not found in the following entries: {invalid_entries}'
+                )
+
+            sorted_input_elements = sorted(input_elements)
+            if sorted_input_elements != absorbing_elements_list:
+                return (f'Elements defined for sites in `equivalent_sites_data` ({sorted_input_elements}) '
+                 f'do not match the list of absorbing elements ({absorbing_elements_list})')
 
+
+    # pylint: enable=too-many-return-statements
     def setup(self):
         """Set required context variables."""
         if 'core_wfc_data' in self.inputs.keys():
@@ -489,6 +540,12 @@ def get_xspectra_structures(self):
         if 'spglib_settings' in self.inputs:
             inputs['spglib_settings'] = self.inputs.spglib_settings
 
+        if 'symmetry_data' in self.inputs:
+            inputs['parse_symmetry'] = orm.Bool(False)
+            input_sym_data = self.inputs.symmetry_data
+            inputs['equivalent_sites_data'] = input_sym_data['equivalent_sites_data']
+            inputs['spacegroup_number'] = input_sym_data['spacegroup_number']
+
         if 'relax' in self.inputs:
             result = get_xspectra_structures(self.ctx.optimized_structure, **inputs)
         else:

tests/calculations/test_bands.py

@@ -0,0 +1,27 @@
+# -*- coding: utf-8 -*-
+"""Tests for the `BandsCalculation` class."""
+# pylint: disable=protected-access
+from aiida.common import datastructures
+
+from aiida_quantumespresso.calculations.bands import BandsCalculation
+
+
+def test_bands_default(fixture_sandbox, generate_calc_job, generate_inputs_bands, file_regression):
+    """Test a default `BandsCalculation`."""
+    entry_point_name = 'quantumespresso.bands'
+
+    inputs = generate_inputs_bands()
+    calc_info = generate_calc_job(fixture_sandbox, entry_point_name, inputs)
+
+    retrieve_list = [BandsCalculation._DEFAULT_OUTPUT_FILE] + BandsCalculation._internal_retrieve_list
+
+    # Check the attributes of the returned `CalcInfo`
+    assert isinstance(calc_info, datastructures.CalcInfo)
+    assert sorted(calc_info.retrieve_list) == sorted(retrieve_list)
+
+    with fixture_sandbox.open('aiida.in') as handle:
+        input_written = handle.read()
+
+    # Checks on the files written to the sandbox folder as raw input
+    assert sorted(fixture_sandbox.get_content_list()) == sorted(['aiida.in'])
+    file_regression.check(input_written, encoding='utf-8', extension='.in')

tests/calculations/test_bands/test_bands_default.in

@@ -0,0 +1,6 @@
+&BANDS
+  filband = 'bands.dat'
+  filp = 'momentum_operator.dat'
+  outdir = './out/'
+  prefix = 'aiida'
+/