options port was moved in phonon_settings port as a dict

aiida_phonopy/calcs/base.py

@@ -48,7 +48,6 @@ def define(cls, spec):
                    help='Primitive cell structure')
         spec.input('dataset', valid_type=(Dict, ArrayData), required=False,
                    help='Displacements and forces dataset')
-        spec.inputs['metadata']['options']['withmpi'].default = False
 
     def prepare_for_submission(self, folder):
         """Create the input files from the input nodes passed to this instance of the `CalcJob`.
@@ -81,6 +80,8 @@ def prepare_for_submission(self, folder):
             for params in self._additional_cmd_params:
                 params.append('--nac')
 
+        self.inputs.metadata.options.withmpi = False
+
         # ============================ calcinfo ===============================
 
         local_copy_list = []

aiida_phonopy/common/utils.py

@@ -3,8 +3,10 @@
 from aiida.plugins import DataFactory
 from aiida.orm import Float, Bool, Str, Int, load_node
 from phonopy.structure.atoms import PhonopyAtoms
-from phonopy.interface.calculator import get_default_displacement_distance
+from phonopy.interface.calculator import (get_default_displacement_distance,
+                                          get_default_physical_units)
 from phonopy.structure.symmetry import symmetrize_borns_and_epsilon
+from phonopy import Phonopy
 
 
 Dict = DataFactory('dict')
@@ -19,10 +21,17 @@ def generate_phonopy_cells(phonon_settings,
                            structure,
                            symmetry_tolerance,
                            dataset=None):
-    ph_settings = _get_setting_info(phonon_settings,
-                                    symmetry_tolerance)
+    """Generate supercells and primitive cell.
+
+    Returns
+    -------
+
+
+
+    """
+    ph_settings = _get_setting_info(phonon_settings, symmetry_tolerance)
 
-    ph = get_phonopy_instance(structure, ph_settings, {})
+    ph = _get_phonopy_instance(structure, ph_settings, {})
     if dataset is None:
         supported_keys = (
             'distance', 'is_plusminus', 'is_diagonal', 'is_trigonal',
@@ -49,7 +58,7 @@ def generate_phono3py_cells(phonon_settings,
     ph_settings = _get_setting_info(phonon_settings,
                                     symmetry_tolerance)
 
-    ph = get_phono3py_instance(structure, ph_settings, {})
+    ph = _get_phono3py_instance(structure, ph_settings, {})
     if dataset is None:
         ph.generate_displacements(distance=ph_settings['distance'])
     else:
@@ -156,7 +165,7 @@ def get_nac_params(born_charges, epsilon, nac_structure, symmetry_tolerance,
 @calcfunction
 def get_force_constants(structure, phonon_settings, force_sets):
     params = {}
-    phonon = get_phonopy_instance(structure, phonon_settings, params)
+    phonon = _get_phonopy_instance(structure, phonon_settings, params)
     phonon.dataset = phonon_settings['displacement_dataset']
     phonon.forces = force_sets.get_array('force_sets')
     phonon.produce_force_constants()
@@ -171,7 +180,7 @@ def get_force_constants(structure, phonon_settings, force_sets):
 @calcfunction
 def get_phonon(structure, phonon_settings, force_constants, **params):
     phonon_settings_dict = phonon_settings.get_dict()
-    ph = get_phonopy_instance(structure, phonon_settings_dict, params)
+    ph = _get_phonopy_instance(structure, phonon_settings_dict, params)
     ph.force_constants = force_constants.get_array('force_constants')
     mesh = phonon_settings_dict['mesh']
 
@@ -339,15 +348,14 @@ def get_bands(qpoints, frequencies, labels, path_connections, label=None):
     return bs
 
 
-def get_phonopy_instance(structure, phonon_settings_dict, params):
-    from phonopy import Phonopy
+def _get_phonopy_instance(structure, phonon_settings_dict, params):
+    """Create Phonopy instance"""
     phonon = Phonopy(
         phonopy_atoms_from_structure(structure),
         supercell_matrix=phonon_settings_dict['supercell_matrix'],
         primitive_matrix='auto',
         symprec=phonon_settings_dict['symmetry_tolerance'])
     if 'nac_params' in params:
-        from phonopy.interface.calculator import get_default_physical_units
         units = get_default_physical_units('vasp')
         factor = units['nac_factor']
         nac_params = {'born': params['nac_params'].get_array('born_charges'),
@@ -358,7 +366,8 @@ def get_phonopy_instance(structure, phonon_settings_dict, params):
     return phonon
 
 
-def get_phono3py_instance(structure, phonon_settings_dict, params):
+def _get_phono3py_instance(structure, phonon_settings_dict, params):
+    """Create Phono3py instance"""
     from phono3py import Phono3py
     if 'phonon_supercell_matrix' in phonon_settings_dict:
         ph_smat = phonon_settings_dict['phonon_supercell_matrix']
@@ -382,44 +391,26 @@ def get_phono3py_instance(structure, phonon_settings_dict, params):
     return ph3py
 
 
-def get_primitive(structure, ph_settings):
-    from phonopy import Phonopy
-
-    phonon = Phonopy(
-        phonopy_atoms_from_structure(structure),
-        supercell_matrix=ph_settings.get_dict()['supercell_matrix'],
-        primitive_matrix=ph_settings.get_dict()['primitive_matrix'],
-        symprec=ph_settings.get_dict()['symmetry_tolerance'])
-    primitive_phonopy = phonon.get_primitive()
-
-    primitive_cell = primitive_phonopy.get_cell()
-    symbols = primitive_phonopy.get_chemical_symbols()
-    positions = primitive_phonopy.get_positions()
-
-    primitive_structure = StructureData(cell=primitive_cell)
-    for symbol, position in zip(symbols, positions):
-        primitive_structure.append_atom(position=position, symbols=symbol)
-
-    return {'primitive_structure': primitive_structure}
-
-
 def phonopy_atoms_to_structure(cell):
-    symbols = cell.get_chemical_symbols()
-    positions = cell.get_positions()
-    structure = StructureData(cell=cell.get_cell())
+    """Convert PhonopyAtoms to StructureData"""
+    symbols = cell.symbols
+    positions = cell.positions
+    structure = StructureData(cell=cell.cell)
     for symbol, position in zip(symbols, positions):
         structure.append_atom(position=position, symbols=symbol)
     return structure
 
 
 def phonopy_atoms_from_structure(structure):
+    """Convert StructureData to PhonopyAtoms"""
     cell = PhonopyAtoms(symbols=[site.kind_name for site in structure.sites],
                         positions=[site.position for site in structure.sites],
                         cell=structure.cell)
     return cell
 
 
 def from_node_id_to_aiida_node_id(node_id):
+    """Convert PK or UUID to an AiiDA data type"""
     if type(node_id) is int:
         return Int(node_id)
     elif type(node_id) is str:
@@ -430,6 +421,25 @@ def from_node_id_to_aiida_node_id(node_id):
 
 
 def collect_vasp_forces_and_energies(ctx, ctx_supercells, prefix="force_calc"):
+    """Collect forces and energies from calculation outputs.
+
+
+    Parameters
+    ----------
+    ctx : AttributeDict-like
+        AiiDA workchain context.
+    ctx_supercells : dict of StructDict
+        Supercells. For phono3py, this can be phonon_supercells.
+    prefix : str
+        Prefix string of dictionary keys of ctx.
+
+    Returns
+    -------
+    dict
+        Forces and energies.
+
+    """
+
     forces_dict = {}
     for key in ctx_supercells:
         # key: e.g. "supercell_001", "phonon_supercell_001"
@@ -530,6 +540,21 @@ def _generate_phonon_structures(ph):
     Designed to be shared by phonopy and phono3py.
     ph is either an instance of Phonopy or Phono3py.
 
+    Returns
+    -------
+    dict of StructureData
+        'supercell'
+            Perfect supercell.
+        'supercell_001', 'supercell_002', ...
+            Supercells with displacements
+        'primitive':
+            Primitive cell.
+        'phonon_supercell'
+            For phono3py. Perfect supercell for harmonic phonon calculation.
+        'phonon_supercell_001', 'phonon_supercell_002', ...
+            For phono3py. Supercells with displacements for harmonic phonon
+            calculation.
+
     """
 
     structures_dict = {}

aiida_phonopy/version.py

@@ -0,0 +1 @@
+__version__ = "0.4"

aiida_phonopy/workflows/phonopy.py

@@ -1,5 +1,5 @@
 from aiida.engine import WorkChain
-from aiida.plugins import DataFactory
+from aiida.plugins import DataFactory, CalculationFactory
 from aiida.orm import Float, Bool, Str, Code
 from aiida.engine import if_, while_
 from aiida_phonopy.common.builders import (
@@ -20,6 +20,7 @@
 XyData = DataFactory('array.xy')
 StructureData = DataFactory('structure')
 BandsData = DataFactory('array.bands')
+PhonopyCalculation = CalculationFactory('phonopy.phonopy')
 
 
 class PhonopyWorkChain(WorkChain):
@@ -53,6 +54,9 @@ class PhonopyWorkChain(WorkChain):
             False.
         displacement_dataset : dict
             Atomic displacement dataset that phonopy can understand.
+        options : dict
+            AiiDA calculation options for phonon calculation used when both of
+            run_phonopy and remote_phonopy are True.
     subtract_residual_forces : Bool, optional
         Run a perfect supercell force calculation and subtract the residual
         forces from forces in supercells with displacements. Default is False.
@@ -63,9 +67,6 @@ class PhonopyWorkChain(WorkChain):
     code_string : Str, optional
         Code string of phonopy needed when both of run_phonopy and
         remote_phonopy are True.
-    options : Dict
-        AiiDa calculation options for phonon calculation used when both of
-        run_phonopy and remote_phonopy are True.
     symmetry_tolerance : Float, optional
         Symmetry tolerance. Default is 1e-5.
     immigrant_calculation_folders : Dict, optional
@@ -98,7 +99,6 @@ def define(cls, spec):
         spec.input('calculation_nodes', valid_type=Dict, required=False)
         spec.input('calculator_settings', valid_type=Dict, required=False)
         spec.input('code_string', valid_type=Str, required=False)
-        spec.input('options', valid_type=Dict, required=False)
 
         spec.outline(
             cls.initialize,
@@ -156,7 +156,7 @@ def run_phonopy(self):
         return self.inputs.run_phonopy
 
     def is_nac(self):
-        if 'is_nac' in self.inputs.phonon_settings.attributes:
+        if 'is_nac' in self.inputs.phonon_settings.dict:
             return self.inputs.phonon_settings['is_nac']
         else:
             False
@@ -186,12 +186,10 @@ def initialize(self):
         self.report('initialize')
 
         if self.inputs.run_phonopy and self.inputs.remote_phonopy:
-            if ('code_string' not in self.inputs or
-                'options' not in self.inputs):
-                raise RuntimeError(
-                    "code_string and options have to be specified.")
+            if 'code_string' not in self.inputs:
+                raise RuntimeError("code_string has to be specified.")
 
-        if 'supercell_matrix' not in self.inputs.phonon_settings.attributes:
+        if 'supercell_matrix' not in self.inputs.phonon_settings.dict:
             raise RuntimeError(
                 "supercell_matrix was not found in phonon_settings.")
 
@@ -381,8 +379,8 @@ def run_phonopy_remote(self):
         builder = Code.get_from_string(code_string).get_builder()
         builder.structure = self.inputs.structure
         builder.settings = self.ctx.phonon_setting_info
-        builder.metadata.options.update(self.inputs.options)
         builder.metadata.label = self.inputs.metadata.label
+        builder.metadata.options.update(self.inputs.phonon_settings['options'])
         builder.force_sets = self.ctx.force_sets
         if 'nac_params' in self.ctx:
             builder.nac_params = self.ctx.nac_params

setup.json

@@ -1,6 +1,6 @@
 {
     "name": "aiida-phonopy",
-    "version": "0.3",
+    "version": "0.4",
     "description": "AiiDA plugin for running phonon calculations using phonopy",
     "author": "Atsushi Togo",
     "author_email": "atz.togo@gmail.com",
@@ -12,7 +12,7 @@
         "Programming Language :: Python :: 3.8",
         "Topic :: Scientific/Engineering :: Physics",
         "Topic :: Scientific/Engineering :: Chemistry",
-	"Development Status :: 5 - Production/Stable",
+        "Development Status :: 5 - Production/Stable",
         "Framework :: AiiDA"
     ],
     "license": "MIT license",