Minor fixes

aiida_phonopy/common/utils.py

@@ -63,32 +63,6 @@ def generate_phono3py_cells(phonon_settings,
     return return_vals
 
 
-@calcfunction
-def check_imported_supercell_structure(supercell_ref,
-                                       supercell_calc,
-                                       symmetry_tolerance):
-    symprec = symmetry_tolerance.value
-    cell_diff = np.subtract(supercell_ref.cell, supercell_calc.cell)
-    if (np.abs(cell_diff) > symprec).any():
-        succeeded = Bool(False)
-        succeeded.label = "False"
-        return succeeded
-
-    positions_ref = [site.position for site in supercell_ref.sites]
-    positions_calc = [site.position for site in supercell_calc.sites]
-    diff = np.subtract(positions_ref, positions_calc)
-    diff -= np.rint(diff)
-    dist = np.sqrt(np.sum(np.dot(diff, supercell_ref.cell) ** 2, axis=1))
-    if (dist > symprec).any():
-        succeeded = Bool(False)
-        succeeded.label = "False"
-        return succeeded
-
-    succeeded = Bool(True)
-    succeeded.label = "True"
-    return succeeded
-
-
 @calcfunction
 def get_vasp_force_sets_dict(**forces_dict):
     forces = []
@@ -239,6 +213,29 @@ def get_data_from_node_id(node_id):
         raise RuntimeError("Forces or NAC params were not found.")
 
 
+def compare_structures(cell_ref, cell_calc, symmetry_tolerance):
+    symprec = symmetry_tolerance.value
+    cell_diff = np.subtract(cell_ref.cell, cell_calc.cell)
+    if (np.abs(cell_diff) > symprec).any():
+        succeeded = Bool(False)
+        succeeded.label = "False"
+        return succeeded
+
+    positions_ref = [site.position for site in cell_ref.sites]
+    positions_calc = [site.position for site in cell_calc.sites]
+    diff = np.subtract(positions_ref, positions_calc)
+    diff -= np.rint(diff)
+    dist = np.sqrt(np.sum(np.dot(diff, cell_ref.cell) ** 2, axis=1))
+    if (dist > symprec).any():
+        succeeded = Bool(False)
+        succeeded.label = "False"
+        return succeeded
+
+    succeeded = Bool(True)
+    succeeded.label = "True"
+    return succeeded
+
+
 def get_mesh_property_data(ph, mesh):
     ph.set_mesh(mesh)
     ph.run_total_dos()

aiida_phonopy/workflows/phono3py.py

@@ -1,13 +1,13 @@
 from aiida.engine import WorkChain
 from aiida.plugins import WorkflowFactory, DataFactory
-from aiida.orm import Float, Bool, Str, Code
+from aiida.orm import Float, Bool
 from aiida.engine import if_
 from aiida_phonopy.common.builders import (
     get_calcjob_builder, get_immigrant_builder)
 from aiida_phonopy.common.utils import (
     generate_phono3py_cells, get_nac_params,
     get_vasp_force_sets_dict, collect_vasp_forces_and_energies,
-    check_imported_supercell_structure)
+    compare_structures)
 
 
 PhonopyWorkChain = WorkflowFactory('phonopy.phonopy')
@@ -37,7 +37,7 @@ def define(cls, spec):
             cls.initialize,
             if_(cls.import_calculations_from_files)(
                 cls.read_force_and_nac_calculations_from_files,
-                cls.check_imported_supercell_structures,
+                cls.check_imported_structures,
             ).else_(
                 cls.run_force_and_nac_calculations,
             ),
@@ -244,7 +244,7 @@ def read_force_and_nac_calculations_from_files(self):
             self.report('{} pk = {}'.format(label, future.pk))
             self.to_context(**{label: future})
 
-    def check_imported_supercell_structures(self):
+    def check_imported_structures(self):
         self.report('check imported supercell structures')
 
         msg = ("Immigrant failed because of inconsistency of supercell"
@@ -259,7 +259,7 @@ def check_imported_supercell_structures(self):
                 calc_dict = calc.inputs
             supercell_ref = self.ctx.supercells["supercell_%s" % num]
             supercell_calc = calc_dict['structure']
-            if not check_imported_supercell_structure(
+            if not compare_structures(
                     supercell_ref,
                     supercell_calc,
                     self.inputs.symmetry_tolerance):
@@ -275,10 +275,9 @@ def check_imported_supercell_structures(self):
             supercell_ref = self.ctx.phonon_supercells[
                 "phonon_supercell_%s" % num]
             supercell_calc = calc_dict['structure']
-            if not check_imported_supercell_structure(
-                    supercell_ref,
-                    supercell_calc,
-                    self.inputs.symmetry_tolerance):
+            if not compare_structures(supercell_ref,
+                                      supercell_calc,
+                                      self.inputs.symmetry_tolerance):
                 raise RuntimeError(msg)
 
     def create_force_sets(self):
@@ -319,7 +318,7 @@ def create_nac_params(self):
                 "in the calculation. Please check the calculation setting.")
 
         kwargs = {}
-        if self.import_calculations():
+        if self.import_calculations_from_files():
             kwargs['primitive'] = self.ctx.primitive
         self.ctx.nac_params = get_nac_params(
             calc_dict['born_charges'],

aiida_phonopy/workflows/phonopy.py

@@ -6,7 +6,7 @@
     get_calcjob_builder, get_immigrant_builder)
 from aiida_phonopy.common.utils import (
     get_force_constants, get_nac_params, get_phonon,
-    generate_phonopy_cells, check_imported_supercell_structure,
+    generate_phonopy_cells, compare_structures,
     from_node_id_to_aiida_node_id, get_data_from_node_id,
     get_vasp_force_sets_dict, collect_vasp_forces_and_energies)
 
@@ -108,7 +108,7 @@ def define(cls, spec):
                 if_(cls.import_calculations_from_nodes)(
                     cls.read_calculation_data_from_nodes,
                 ),
-                cls.check_imported_supercell_structures,
+                cls.check_imported_structures,
             ).else_(
                 cls.run_force_and_nac_calculations,
             ),
@@ -274,7 +274,7 @@ def read_calculation_data_from_nodes(self):
             # self.ctx[label]['dielectrics'] -> ArrayData()('epsilon')
             self.ctx[label] = get_data_from_node_id(aiida_node_id)
 
-    def check_imported_supercell_structures(self):
+    def check_imported_structures(self):
         self.report('check imported supercell structures')
 
         msg = ("Immigrant failed because of inconsistency of supercell"
@@ -289,10 +289,9 @@ def check_imported_supercell_structures(self):
                 calc_dict = calc.inputs
             supercell_ref = self.ctx.supercells["supercell_%s" % num]
             supercell_calc = calc_dict['structure']
-            if not check_imported_supercell_structure(
-                    supercell_ref,
-                    supercell_calc,
-                    self.inputs.symmetry_tolerance):
+            if not compare_structures(supercell_ref,
+                                      supercell_calc,
+                                      self.inputs.symmetry_tolerance):
                 raise RuntimeError(msg)
 
     def postprocess_of_dry_run(self):