Merge pull request #17 from aiida-phonopy/phonopy-base

Phonopy base

README.md

@@ -1,6 +1,7 @@
-AiiDA Phonopy plugin
-====================
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/aiida-phonopy/aiida-phonopy/develop.svg)](https://results.pre-commit.ci/latest/github/aiida-phonopy/aiida-phonopy/develop)
 
-This a phonopy plugin for AiiDA. This plugin includes workflows to
-calculate phonons with supercell and finite displacement approaches.
-Currently it provides interfaces only to VASP.
+# AiiDA Phonopy plugin
+
+This a phonopy plugin for AiiDA. This plugin includes workflows to calculate
+phonons with supercell and finite displacement approaches. Currently VASP and QE
+are supported.

aiida_phonopy/calcs/base.py

@@ -25,8 +25,8 @@ class BasePhonopyCalculation(CalcJob):
     def define(cls, spec):
         """Define inputs, outputs, and outline."""
         super().define(spec)
-        spec.input("settings", valid_type=Dict, help="Phonopy parameters")
-        spec.input("structure", valid_type=StructureData, help="Unit cell structure")
+        spec.input("settings", valid_type=Dict, help="Phonopy parameters.")
+        spec.input("structure", valid_type=StructureData, help="Unit cell structure.")
         spec.input("symmetry_tolerance", valid_type=Float, default=lambda: Float(1e-5))
         spec.input(
             "fc_only",
@@ -41,19 +41,19 @@ def define(cls, spec):
             help="Sets of forces in supercells",
         )
         spec.input(
-            "nac_params", valid_type=ArrayData, required=False, help="NAC parameters"
+            "nac_params", valid_type=ArrayData, required=False, help="NAC parameters."
         )
         spec.input(
             "primitive",
             valid_type=StructureData,
             required=False,
-            help="Primitive cell structure",
+            help="Primitive cell structure only necessary NAC is applied.",
         )
         spec.input(
             "dataset",
             valid_type=(Dict, ArrayData),
             required=False,
-            help="Displacements and forces dataset",
+            help="Displacements and forces dataset.",
         )
 
     def prepare_for_submission(self, folder):
@@ -73,8 +73,7 @@ def prepare_for_submission(self, folder):
             not self.inputs.fc_only
             and "nac_params" in self.inputs
             and "primitive" in self.inputs
-            and "symmetry_tolerance" in self.inputs
-        ):  # noqa: E129
+        ):
             born_txt = get_BORN_txt(
                 self.inputs.nac_params,
                 self.inputs.primitive,

aiida_phonopy/calcs/phonopy.py

@@ -33,31 +33,6 @@ def define(cls, spec):
         """Define inputs, outputs, and outline."""
         super().define(spec)
 
-        spec.input(
-            "projected_dos_filename",
-            valid_type=Str,
-            default=lambda: Str(cls._OUTPUT_PROJECTED_DOS),
-        )
-        spec.input(
-            "total_dos_filename",
-            valid_type=Str,
-            default=lambda: Str(cls._OUTPUT_TOTAL_DOS),
-        )
-        spec.input(
-            "thermal_properties_filename",
-            valid_type=Str,
-            default=lambda: Str(cls._OUTPUT_THERMAL_PROPERTIES),
-        )
-        spec.input(
-            "band_structure_filename",
-            valid_type=Str,
-            default=lambda: Str(cls._OUTPUT_BAND_STRUCTURE),
-        )
-        spec.input(
-            "force_constants_filename",
-            valid_type=Str,
-            default=lambda: Str(cls._INOUT_FORCE_CONSTANTS),
-        )
         # parser_name has to be set to invoke parsing.
         spec.inputs["metadata"]["options"]["parser_name"].default = "phonopy"
         spec.inputs["metadata"]["options"]["output_filename"].default = "phonopy.yaml"

aiida_phonopy/common/raw_parsers.py

@@ -97,7 +97,7 @@ def parse_band_structure(f, label=None):
                 .replace("\\", "")
                 .replace("mathrm{", "")
                 .replace("}", "")
-                .upper()  # noqa E501
+                .upper()
                 for x in pair
             ]
         )

aiida_phonopy/common/utils.py

@@ -573,7 +573,10 @@ def collect_forces_and_energies(ctx, ctx_supercells, prefix="force_calc"):
         else:
             calc_dict = calc.outputs
         forces_dict["forces_%s" % num] = calc_dict["forces"]
-        forces_dict["energy_%s" % num] = calc_dict["energy"]
+        if "energy" in calc_dict:
+            forces_dict["energy_%s" % num] = calc_dict["energy"]
+        elif "total_energy" in calc_dict:  # For CommonWorkflow
+            forces_dict["energy_%s" % num] = calc_dict["total_energy"]
 
     return forces_dict
 
@@ -649,7 +652,10 @@ def _get_force_set(**forces_dict):
             else:
                 force_sets[num - 1] = forces - forces_0
         elif "energy" in key:
-            energies[num - 1] = value.get_array("energy")[-1]
+            if isinstance(value, Float):  # For CommonWorkflow
+                energies[num - 1] = value.value
+            else:
+                energies[num - 1] = value.get_array("energy")[-1]
 
     return force_sets, energies, forces_0_key, energy_0_key
 

aiida_phonopy/parsers/phonopy.py

@@ -3,6 +3,7 @@
 from aiida.engine import ExitCode
 from aiida.common.exceptions import NotExistent
 from aiida.parsers.parser import Parser
+from aiida.plugins import CalculationFactory
 from aiida_phonopy.common.raw_parsers import (
     parse_thermal_properties,
     parse_FORCE_CONSTANTS,
@@ -15,6 +16,7 @@
 
 
 Str = DataFactory("str")
+PhonopyCalculation = CalculationFactory("phonopy.phonopy")
 
 
 class PhonopyParser(Parser):
@@ -38,27 +40,27 @@ def parse(self, **kwargs):
         # check what is inside the folder
         list_of_files = output_folder.list_object_names()
 
-        fc_filename = self.node.inputs.force_constants_filename.value
+        fc_filename = PhonopyCalculation._INOUT_FORCE_CONSTANTS
         if fc_filename in list_of_files:
             with output_folder.open(fc_filename, "rb") as f:
                 self.out("force_constants", parse_FORCE_CONSTANTS(f))
 
-        projected_dos_filename = self.node.inputs.projected_dos_filename.value
+        projected_dos_filename = PhonopyCalculation._OUTPUT_PROJECTED_DOS
         if projected_dos_filename in list_of_files:
             with output_folder.open(projected_dos_filename) as f:
                 self.out("pdos", parse_projected_dos(f))
 
-        total_dos_filename = self.node.inputs.projected_dos_filename.value
+        total_dos_filename = PhonopyCalculation._OUTPUT_TOTAL_DOS
         if total_dos_filename in list_of_files:
             with output_folder.open(total_dos_filename) as f:
                 self.out("dos", parse_total_dos(f))
 
-        tp_filename = self.node.inputs.thermal_properties_filename.value
+        tp_filename = PhonopyCalculation._OUTPUT_THERMAL_PROPERTIES
         if tp_filename in list_of_files:
             with output_folder.open(tp_filename) as f:
                 self.out("thermal_properties", parse_thermal_properties(f))
 
-        band_filename = self.node.inputs.band_structure_filename.value
+        band_filename = PhonopyCalculation._OUTPUT_BAND_STRUCTURE
         if band_filename in list_of_files:
             if "symmetry" in self.node.inputs.settings.attributes:
                 sym_dataset = self.node.inputs.settings["symmetry"]

aiida_phonopy/workflows/forces.py

@@ -34,7 +34,7 @@ def _get_forces(outputs, code_string):
         if (
             "output_trajectory" in outputs
             and "forces" in outputs.output_trajectory.get_arraynames()
-        ):  # noqa: E129 E501
+        ):
             forces_data = get_qe_forces(outputs.output_trajectory)
         else:
             return None
@@ -73,7 +73,7 @@ def _get_energy(outputs, code_string):
         if (
             "output_parameters" in outputs
             and "energy" in outputs.output_parameters.keys()
-        ):  # noqa: E129
+        ):
             energy_data = get_qe_energy(outputs.output_parameters)
     return energy_data