PhBaseWorkChain: Add a first draft for the protocols (#810)

Add a first draft for the `PhBaseWorkChain` protocols. These have not
been tested rigorously, but can serve as an initial setup that can be
easily adapted after using the `get_builder_from_protocol()` method.

This is also necessary to allow higher-level work chains to develop
protocols.

src/aiida_quantumespresso/workflows/ph/base.py

@@ -2,14 +2,17 @@
 """Workchain to run a Quantum ESPRESSO ph.x calculation with automated error handling and restarts."""
 from aiida import orm
 from aiida.common import AttributeDict
+from aiida.common.lang import type_check
 from aiida.engine import BaseRestartWorkChain, ProcessHandlerReport, process_handler, while_
 from aiida.plugins import CalculationFactory
 
+from aiida_quantumespresso.workflows.protocols.utils import ProtocolMixin
+
 PhCalculation = CalculationFactory('quantumespresso.ph')
 PwCalculation = CalculationFactory('quantumespresso.pw')
 
 
-class PhBaseWorkChain(BaseRestartWorkChain):
+class PhBaseWorkChain(ProtocolMixin, BaseRestartWorkChain):
  """Workchain to run a Quantum ESPRESSO ph.x calculation with automated error handling and restarts."""
 
  _process_class = PhCalculation
@@ -45,6 +48,50 @@ def define(cls, spec):
  message='The calculation failed with an unrecoverable error.')
  # yapf: enable
 
+ @classmethod
+ def get_protocol_filepath(cls):
+ """Return ``pathlib.Path`` to the ``.yaml`` file that defines the protocols."""
+ from importlib_resources import files
+
+ from ..protocols import ph as ph_protocols
+ return files(ph_protocols) / 'base.yaml'
+
+ @classmethod
+ def get_builder_from_protocol(cls, code, parent_folder=None, protocol=None, overrides=None, **_):
+ """Return a builder prepopulated with inputs selected according to the chosen protocol.
+
+ :param code: the ``Code`` instance configured for the ``quantumespresso.ph`` plugin.
+ :param structure: the ``StructureData`` instance to use.
+ :param protocol: protocol to use, if not specified, the default will be used.
+ :param overrides: optional dictionary of inputs to override the defaults of the protocol.
+ :return: a process builder instance with all inputs defined ready for launch.
+ """
+ if isinstance(code, str):
+ code = orm.load_code(code)
+
+ type_check(code, orm.Code)
+
+ inputs = cls.get_protocol_inputs(protocol, overrides)
+
+ qpoints_mesh = inputs['ph'].pop('qpoints')
+ qpoints = orm.KpointsData()
+ qpoints.set_kpoints_mesh(qpoints_mesh)
+
+ # pylint: disable=no-member
+ builder = cls.get_builder()
+ builder.ph['code'] = code
+ if parent_folder is not None:
+ builder.ph['parent_folder'] = parent_folder
+ builder.ph['parameters'] = orm.Dict(inputs['ph']['parameters'])
+ builder.ph['metadata'] = inputs['ph']['metadata']
+ if 'settings' in inputs['ph']:
+ builder.ph['settings'] = orm.Dict(inputs['ph']['settings'])
+ builder.clean_workdir = orm.Bool(inputs['clean_workdir'])
+ builder.ph['qpoints'] = qpoints
+ # pylint: enable=no-member
+
+ return builder
+
  def setup(self):
  """Call the `setup` of the `BaseRestartWorkChain` and then create the inputs dictionary in `self.ctx.inputs`.
 

src/aiida_quantumespresso/workflows/protocols/ph/base.yaml

@@ -0,0 +1,36 @@
+default_inputs:
+ clean_workdir: True
+ ph:
+ metadata:
+ options:
+ resources:
+ num_machines: 1
+ max_wallclock_seconds: 43200 # Twelve hours
+ withmpi: True
+ parameters:
+ INPUTPH:
+ tr2_ph: 1.0e-18
+ qpoints:
+ - 3
+ - 3
+ - 3
+default_protocol: moderate
+protocols:
+ moderate:
+ description: 'Protocol to perform the computation at normal precision at moderate computational cost.'
+ precise:
+ description: 'Protocol to perform the computation at high precision at higher computational cost.'
+ ph:
+ parameters:
+ INPUTPH:
+ tr2_ph: 1.0e-20
+ fast:
+ description: 'Protocol to perform the computation at low precision at minimal computational cost for testing purposes.'
+ ph:
+ parameters:
+ INPUTPH:
+ tr2_ph: 1.0e-16
+ qpoints:
+ - 2
+ - 2
+ - 2