Add calcjob, parser and base workchain plugin for bands.x (aiidatea…

…m#1033)

An implementation that wraps the binary `bands.x` was missing.
This program is used to find the symmetries of wavefunctions,
to re-order the bands, and to perform basic post-processings,
such as the calculation of the momentum operator.

The current parser only performs basic parsing, with no specialized
outputs for k-point wavefunction symmetries, nor momentum operator,
nor bands. This can be, for instance, implemented over time depending
on user request.

pyproject.toml

@@ -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/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)

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'
+/

tests/conftest.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# pylint: disable=redefined-outer-name,too-many-statements
+# pylint: disable=redefined-outer-name,too-many-statements,too-many-lines
 """Initialise a text database and profile for pytest."""
 from collections.abc import Mapping
 import io
@@ -594,6 +594,27 @@ def _generate_inputs_q2r():
     return _generate_inputs_q2r
 
 
+@pytest.fixture
+def generate_inputs_bands(fixture_sandbox, fixture_localhost, fixture_code, generate_remote_data):
+    """Generate default inputs for a `BandsCalculation."""
+
+    def _generate_inputs_bands():
+        """Generate default inputs for a `BandsCalculation."""
+        from aiida_quantumespresso.utils.resources import get_default_options
+
+        inputs = {
+            'code': fixture_code('quantumespresso.bands'),
+            'parent_folder': generate_remote_data(fixture_localhost, fixture_sandbox.abspath, 'quantumespresso.pw'),
+            'metadata': {
+                'options': get_default_options()
+            }
+        }
+
+        return inputs
+
+    return _generate_inputs_bands
+
+
 @pytest.fixture
 def generate_inputs_ph(
     generate_calc_job_node, generate_structure, fixture_localhost, fixture_code, generate_kpoints_mesh

tests/parsers/fixtures/bands/default/aiida.out

@@ -0,0 +1,22 @@
+
+     Program BANDS v.7.1 starts on 12Jun2024 at 18:53:54 
+
+     This program is part of the open-source Quantum ESPRESSO suite
+     for quantum simulation of materials; please cite
+         "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
+         "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
+         "P. Giannozzi et al., J. Chem. Phys. 152 154105 (2020);
+          URL http://www.quantum-espresso.org", 
+     in publications or presentations arising from this work. More details at
+     http://www.quantum-espresso.org/quote
+
+   # many lines deleted
+
+     BANDS        :      0.68s CPU      0.72s WALL
+
+
+   This run was terminated on:  18:53:55  12Jun2024            
+
+=------------------------------------------------------------------------------=
+   JOB DONE.
+=------------------------------------------------------------------------------=

tests/parsers/test_bands.py

@@ -0,0 +1,24 @@
+# -*- coding: utf-8 -*-
+"""Tests for the `BandsParser`."""
+from aiida import orm
+
+
+def generate_inputs():
+    """Return only those inputs that the parser will expect to be there."""
+    return {}
+
+
+def test_bands_default(fixture_localhost, generate_calc_job_node, generate_parser, data_regression):
+    """Test a default `bands.x` calculation."""
+    entry_point_calc_job = 'quantumespresso.bands'
+    entry_point_parser = 'quantumespresso.bands'
+
+    node = generate_calc_job_node(entry_point_calc_job, fixture_localhost, 'default', generate_inputs())
+    parser = generate_parser(entry_point_parser)
+    results, calcfunction = parser.parse_from_node(node, store_provenance=False)
+
+    assert calcfunction.is_finished, calcfunction.exception
+    assert calcfunction.is_finished_ok, calcfunction.exit_message
+    assert not orm.Log.collection.get_logs_for(node)
+    assert 'output_parameters' in results
+    data_regression.check(results['output_parameters'].get_dict())

tests/parsers/test_bands/test_bands_default.yml

@@ -0,0 +1,2 @@
+code_version: '7.1'
+wall_time_seconds: 0.72

tests/workflows/bands/test_base.py

@@ -0,0 +1,54 @@
+# -*- coding: utf-8 -*-
+# pylint: disable=no-member,redefined-outer-name
+"""Tests for the `BandsBaseWorkChain` class."""
+from aiida.common import AttributeDict
+from aiida.engine import ProcessHandlerReport
+from plumpy import ProcessState
+import pytest
+
+from aiida_quantumespresso.calculations.bands import BandsCalculation
+from aiida_quantumespresso.workflows.bands.base import BandsBaseWorkChain
+
+
+@pytest.fixture
+def generate_workchain_bands(generate_workchain, generate_inputs_bands, generate_calc_job_node):
+    """Generate an instance of a `BandsBaseWorkChain`."""
+
+    def _generate_workchain_bands(exit_code=None):
+        entry_point = 'quantumespresso.bands.base'
+        process = generate_workchain(entry_point, {'bands': generate_inputs_bands()})
+
+        if exit_code is not None:
+            node = generate_calc_job_node()
+            node.set_process_state(ProcessState.FINISHED)
+            node.set_exit_status(exit_code.status)
+
+            process.ctx.iteration = 1
+            process.ctx.children = [node]
+
+        return process
+
+    return _generate_workchain_bands
+
+
+def test_setup(generate_workchain_bands):
+    """Test `BandsBaseWorkChain.setup`."""
+    process = generate_workchain_bands()
+    process.setup()
+
+    assert process.ctx.restart_calc is None
+    assert isinstance(process.ctx.inputs, AttributeDict)
+
+
+def test_handle_unrecoverable_failure(generate_workchain_bands):
+    """Test `BandsBaseWorkChain.handle_unrecoverable_failure`."""
+    process = generate_workchain_bands(exit_code=BandsCalculation.exit_codes.ERROR_NO_RETRIEVED_FOLDER)
+    process.setup()
+
+    result = process.handle_unrecoverable_failure(process.ctx.children[-1])
+    assert isinstance(result, ProcessHandlerReport)
+    assert result.do_break
+    assert result.exit_code == BandsBaseWorkChain.exit_codes.ERROR_UNRECOVERABLE_FAILURE
+
+    result = process.inspect_process()
+    assert result == BandsBaseWorkChain.exit_codes.ERROR_UNRECOVERABLE_FAILURE