fc_calculation and qpoints_mesh info were moved to postprocess_parame…

…ters.

aiida_phonopy/calcs/base.py

@@ -29,8 +29,8 @@ def define(cls, spec):
                    help='Phonopy parameters')
         spec.input('structure', valid_type=StructureData,
                    help='Unit cell structure')
-        spec.input('qpoint_mesh', valid_type=Dict,
-                   help='Q-point sampling mesh information')
+        spec.input('postprocess_parameters', valid_type=Dict,
+                   help='Parameters to run phonopy')
         spec.input('symmetry_tolerance', valid_type=Float,
                    default=lambda: Float(1e-5))
         spec.input('fc_only', valid_type=Bool,

aiida_phonopy/calcs/phonopy.py

@@ -65,7 +65,7 @@ def _create_additional_files(self, folder):
         self._create_phonopy_yaml(folder)
         self._create_FORCE_SETS(folder)
         mesh_opts, fc_opts = get_phonopy_options(
-            self.inputs.settings.get_dict(), self.inputs.qpoint_mesh.get_dict())
+            self.inputs.postprocess_parameters)
 
         self._internal_retrieve_list = [self._INOUT_FORCE_CONSTANTS, ]
         self._additional_cmd_params = [['--writefc', ] + fc_opts, ]
@@ -90,7 +90,7 @@ def _create_additional_files(self, folder):
     def _create_phonopy_yaml(self, folder):
         phpy_yaml_txt = get_phonopy_yaml_txt(
             self.inputs.structure,
-            self.inputs.settings.get_dict())
+            supercell_matrix=self.inputs.settings['supercell_matrix'])
         with folder.open(self._INPUT_CELL, 'w', encoding='utf8') as handle:
             handle.write(phpy_yaml_txt)
 
@@ -99,9 +99,9 @@ def _create_FORCE_SETS(self, folder):
             force_sets = self.inputs.force_sets
         else:
             force_sets = None
-        if 'displacement_dataset' in self.inputs.settings.attributes:
+        if 'displacement_dataset' in self.inputs.settings.keys():
             dataset = self.inputs.settings['displacement_dataset']
-        elif 'dataset' in self.inputs.settings.attributes:
+        elif 'dataset' in self.inputs.settings.keys():
             dataset = self.inputs.settings['dataset']
         elif ('dataset' in self.inputs and
               'displacements' in self.inputs.dataset.get_arraynames()):

aiida_phonopy/common/file_generators.py

@@ -53,13 +53,12 @@ def get_FORCE_CONSTANTS_txt(force_constants_object):
 
 
 def get_phonopy_yaml_txt(structure,
-                         settings,
                          supercell_matrix=None,
                          primitive_matrix=None,
                          calculator=None):
     unitcell = phonopy_atoms_from_structure(structure)
     ph = Phonopy(unitcell,
-                 supercell_matrix=settings['supercell_matrix'],
+                 supercell_matrix=supercell_matrix,
                  primitive_matrix='auto',
                  calculator=calculator)
     phpy_yaml = PhonopyYaml()
@@ -68,11 +67,11 @@ def get_phonopy_yaml_txt(structure,
     return str(phpy_yaml)
 
 
-def get_phonopy_options(settings, qpoint_mesh):
+def get_phonopy_options(postprocess_parameters):
     """Return phonopy command option strings."""
     mesh_opts = []
-    if 'mesh' in qpoint_mesh:
-        mesh = qpoint_mesh['mesh']
+    if 'mesh' in postprocess_parameters.keys():
+        mesh = postprocess_parameters['mesh']
         try:
             length = float(mesh)
             mesh_opts.append('--mesh=%f' % length)
@@ -81,8 +80,8 @@ def get_phonopy_options(settings, qpoint_mesh):
         mesh_opts.append('--nowritemesh')
 
     fc_opts = []
-    if 'fc_calculator' in settings:
-        if settings['fc_calculator'].lower().strip() == 'alm':
+    if 'fc_calculator' in postprocess_parameters.keys():
+        if postprocess_parameters['fc_calculator'].lower().strip() == 'alm':
             fc_opts.append('--alm')
     return mesh_opts, fc_opts
 

aiida_phonopy/common/utils.py

@@ -29,7 +29,6 @@ def generate_phonopy_cells(phonon_settings,
          'phonon_supercell_matrix',
          'distance',
          'symmetry_tolerance',
-         'fc_calculator',
          'number_of_snapshots',
          'random_seed',
          'is_plusminus',
@@ -73,7 +72,6 @@ def generate_phonopy_cells(phonon_settings,
             'international' : Space group type.
         'phonon_displacement_dataset' : dict
             Phono3py.phonon_dataset.
-         'fc_calculator' : str
          'number_of_snapshots' : int
          'random_seed' : int
          'is_plusminus' : bool
@@ -129,6 +127,7 @@ def generate_phono3py_cells(phonon_settings,
 @calcfunction
 def get_force_constants(structure,
                         phonon_settings,
+                        postprocess_parameters,
                         force_sets,
                         symmetry_tolerance):
     """Calculate force constants."""
@@ -137,7 +136,11 @@ def get_force_constants(structure,
                                    symmetry_tolerance=symmetry_tolerance.value)
     phonon.dataset = phonon_settings['displacement_dataset']
     phonon.forces = force_sets.get_array('force_sets')
-    phonon.produce_force_constants()
+    if 'fc_calculator' in postprocess_parameters.keys():
+        if postprocess_parameters['fc_calculator'].lower().strip() == 'alm':
+            phonon.produce_force_constants(fc_calculator='alm')
+    else:
+        phonon.produce_force_constants()
     force_constants = ArrayData()
     force_constants.set_array('force_constants', phonon.force_constants)
     force_constants.set_array('p2s_map', phonon.primitive.p2s_map)
@@ -645,7 +648,6 @@ def _get_setting_info(phonon_settings, code_name='phonopy'):
                   'phonon_supercell_matrix',
                   'distance',
                   'symmetry_tolerance',
-                  'fc_calculator',
                   'number_of_snapshots',
                   'random_seed',
                   'is_plusminus',

aiida_phonopy/workflows/phonopy.py

@@ -1,8 +1,8 @@
 """WorkChan to run phonon calculation by phonopy and force calculators."""
 
-from aiida.engine import WorkChain
+from aiida.engine import WorkChain, calcfunction
 from aiida.plugins import DataFactory, CalculationFactory
-from aiida.orm import Float, Bool, Str, Code
+from aiida.orm import Code
 from aiida.engine import if_, while_
 from aiida_phonopy.common.builders import get_immigrant_builder
 from aiida_phonopy.common.utils import (
@@ -17,6 +17,9 @@
 # Should be improved by some kind of WorkChainFactory
 # For now all workchains should be copied to aiida/workflows
 
+Float = DataFactory('float')
+Bool = DataFactory('bool')
+Str = DataFactory('str')
 Dict = DataFactory('dict')
 ArrayData = DataFactory('array')
 XyData = DataFactory('array.xy')
@@ -25,6 +28,20 @@
 PhonopyCalculation = CalculationFactory('phonopy.phonopy')
 
 
+@calcfunction
+def get_postprocess_parameters(phonon_settings):
+    """Return phonopy postprocess parameters."""
+    valid_keys = ('mesh', 'fc_calculator')
+    params = {}
+    for key in valid_keys:
+        if key in phonon_settings.keys():
+            params[key] = phonon_settings[key]
+
+    if 'mesh' not in phonon_settings.keys():
+        params['mesh'] = 100.0
+    return Dict(dict=params)
+
+
 class PhonopyWorkChain(WorkChain):
     """Phonopy workchain.
 
@@ -108,7 +125,9 @@ def define(cls, spec):
 
         spec.outline(
             cls.initialize_structures,
-            cls.initialize_postprocess_settings,
+            if_(cls.run_phonopy)(
+                cls.initialize_postprocess_settings,
+            ),
             if_(cls.import_calculations)(
                 if_(cls.import_calculations_from_files)(
                     while_(cls.continue_import)(
@@ -153,7 +172,7 @@ def define(cls, spec):
         spec.output('band_structure', valid_type=BandsData, required=False)
         spec.output('dos', valid_type=XyData, required=False)
         spec.output('pdos', valid_type=XyData, required=False)
-        spec.output('qpoint_mesh', valid_type=Dict, required=False)
+        spec.output('postprocess_parameters', valid_type=Dict, required=False)
         spec.output('phonon_setting_info', valid_type=Dict)
 
     def dry_run(self):
@@ -234,11 +253,8 @@ def initialize_postprocess_settings(self):
         """Set default settings and create supercells and primitive cell."""
         self.report('initialize_postprocess_settings')
 
-        if 'mesh' in self.inputs.phonon_settings.keys():
-            mesh = self.inputs.phonon_settings['mesh']
-        else:
-            mesh = 100.0
-        self.ctx.qpoint_mesh = Dict(dict={'mesh': mesh})
+        params = get_postprocess_parameters(self.inputs.phonon_settings)
+        self.ctx.postprocess_parameters = params
 
     def run_force_and_nac_calculations(self):
         """Run supercell force and NAC params calculations.
@@ -388,7 +404,7 @@ def run_phonopy_remote(self):
         builder.structure = self.inputs.structure
         builder.settings = self.ctx.phonon_setting_info
         builder.symmetry_tolerance = self.inputs.symmetry_tolerance
-        builder.qpoint_mesh = self.ctx.qpoint_mesh
+        builder.postprocess_parameters = self.ctx.postprocess_parameters
         builder.metadata.label = self.inputs.metadata.label
         builder.metadata.options.update(self.inputs.phonon_settings['options'])
         builder.force_sets = self.ctx.force_sets
@@ -413,7 +429,7 @@ def collect_data(self):
         for prop in ph_props:
             if prop in self.ctx.phonon_properties.outputs:
                 self.out(prop, self.ctx.phonon_properties.outputs[prop])
-        self.out('qpoint_mesh', self.ctx.qpoint_mesh)
+        self.out('postprocess_parameters', self.ctx.postprocess_parameters)
 
         self.report('finish phonon')
 
@@ -424,6 +440,7 @@ def create_force_constants(self):
         self.ctx.force_constants = get_force_constants(
             self.inputs.structure,
             self.ctx.phonon_setting_info,
+            self.ctx.postprocess_parameters,
             self.ctx.force_sets,
             self.inputs.symmetry_tolerance)
         self.out('force_constants', self.ctx.force_constants)
@@ -438,13 +455,13 @@ def run_phonopy_locally(self):
         result = get_phonon_properties(self.inputs.structure,
                                        self.ctx.phonon_setting_info,
                                        self.ctx.force_constants,
-                                       self.ctx.qpoint_mesh,
+                                       self.ctx.postprocess_parameters,
                                        self.inputs.symmetry_tolerance,
                                        **params)
         self.out('thermal_properties', result['thermal_properties'])
         self.out('dos', result['dos'])
         self.out('band_structure', result['band_structure'])
-        self.out('qpoint_mesh', self.ctx.qpoint_mesh)
+        self.out('postprocess_parameters', self.ctx.postprocess_parameters)
 
         self.report('finish phonon')