XspectraCrystalWorkChain: Enable Symmetry Data Inputs

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: