Add aiida-core==2.X support

aiida_lsmo/calcfunctions/oxidation_state.py

@@ -22,4 +22,4 @@ def compute_oxidation_states(cif):
         }
 
     results_dict['oximachine_version'] = str(OXIMACHINE_RUNNER)
-    return Dict(dict=results_dict)
+    return Dict(results_dict)

aiida_lsmo/calcfunctions/selectivity.py

@@ -25,4 +25,4 @@ def calc_selectivity(isot_dict_a, isot_dict_b):
         out_dict['selectivity_dev'] = out_dict['selectivity_average'] * sqrt(
             (isot_dict_a['henry_coefficient_dev'] / isot_dict_a['henry_coefficient_average']) +
             (isot_dict_b['henry_coefficient_dev'] / isot_dict_b['henry_coefficient_average']))
-    return Dict(dict=out_dict)
+    return Dict(out_dict)

aiida_lsmo/calcfunctions/working_cap.py

@@ -59,7 +59,7 @@ def calc_ch4_working_cap(isot_dict):
             'wc_65bar_fraction': wc_65bar_fract,
             'wc_65bar_fraction_unit': '-',
         })
-    return Dict(dict=out_dict)
+    return Dict(out_dict)
 
 
 @calcfunction
@@ -112,7 +112,7 @@ def calc_h2_working_cap(isotmt_dict):  # pylint: disable=too-many-locals
                     'case-{}_{}_dev'.format(case, unit): sqrt(load_dev**2 + disc_dev**2) * conv
                 })
 
-    return Dict(dict=out_dict)
+    return Dict(out_dict)
 
 
 @calcfunction
@@ -161,4 +161,4 @@ def calc_o2_working_cap(isot_dict):
             'wc_140bar_fraction': wc_140bar_fract,
             'wc_140bar_fraction_unit': '-',
         })
-    return Dict(dict=out_dict)
+    return Dict(out_dict)

aiida_lsmo/calcfunctions/wrappers.py

@@ -26,7 +26,7 @@ def calc_co2_parasitic_energy(isot_co2, isot_n2, pe_parameters):
     from calc_pe import mainPE
 
     if not isot_co2['is_porous'] or not isot_n2['is_porous']:
-        return Dict(dict={'is_porous': False})
+        return Dict({'is_porous': False})
 
     bar2pa = 1e5  # convert pressure from bar to Pa
     gcm2kgm = 1000  # convert density from g/cm3 to kg/m3
@@ -53,4 +53,4 @@ def calc_co2_parasitic_energy(isot_co2, isot_n2, pe_parameters):
     )
     pe_dict['is_porous'] = True
 
-    return Dict(dict=pe_dict)
+    return Dict(pe_dict)

aiida_lsmo/utils/multiply_unitcell.py

@@ -60,7 +60,7 @@ def angle(vect1, vect2):
         'ny': int(ceil(thr / perpwidth[1])),
         'nz': int(ceil(thr / perpwidth[2]))
     }
-    return Dict(dict=resize)
+    return Dict(resize)
 
 
 @calcfunction

aiida_lsmo/utils/other_utilities.py

@@ -7,6 +7,7 @@
 from aiida.orm import Dict, CifData, StructureData
 from aiida.engine import calcfunction
 
+from collections.abc import Mapping
 
 def dict_merge(dct, merge_dct):
     """ Taken from https://gist.github.com/angstwad/bf22d1822c38a92ec0a9
@@ -19,7 +20,7 @@ def dict_merge(dct, merge_dct):
     :return: None
     """
     for k in merge_dct.keys():
-        if (k in dct and isinstance(dct[k], dict) and isinstance(merge_dct[k], collections.Mapping)):
+        if (k in dct and isinstance(dct[k], dict) and isinstance(merge_dct[k], Mapping)):
             dict_merge(dct[k], merge_dct[k])
         else:
             dct[k] = merge_dct[k]
@@ -35,7 +36,7 @@ def aiida_dict_merge(to_dict, from_dict):
 
     dict_merge(to_dict, from_dict)
 
-    return Dict(dict=to_dict)
+    return Dict(to_dict)
 
 
 def ase_cells_are_similar(ase_a, ase_b, thr=2):

aiida_lsmo/workchains/binding_site.py

@@ -10,8 +10,8 @@
 Cp2kBindingEnergyWorkChain = WorkflowFactory('lsmo.cp2k_binding_energy')  # pylint: disable=invalid-name
 
 # import aiida data
-StructureData = DataFactory('structure')  # pylint: disable=invalid-name
-CifData = DataFactory('cif')  # pylint: disable=invalid-name
+StructureData = DataFactory('core.structure')  # pylint: disable=invalid-name
+CifData = DataFactory('core.cif')  # pylint: disable=invalid-name
 
 
 class BindingSiteWorkChain(WorkChain):

aiida_lsmo/workchains/cp2k_binding_energy.py

@@ -36,7 +36,7 @@ def get_output_parameters(**cp2k_out_dict):
         if key in cp2k_out_dict['bsse'].get_dict():  # "binding_energy_dispersion" may miss
             output_dict[key] = cp2k_out_dict['bsse'][key]
 
-    return Dict(dict=output_dict)
+    return Dict(output_dict)
 
 
 @calcfunction
@@ -185,7 +185,7 @@ def run_geo_opt(self):
         if 'parameters' in self.exposed_inputs(Cp2kBaseWorkChain, 'cp2k_base')['cp2k']:
             dict_merge(self.ctx.cp2k_param,
                        self.exposed_inputs(Cp2kBaseWorkChain, 'cp2k_base')['cp2k']['parameters'].get_dict())
-        self.ctx.base_inp['cp2k']['parameters'] = Dict(dict=self.ctx.cp2k_param)
+        self.ctx.base_inp['cp2k']['parameters'] = Dict(self.ctx.cp2k_param)
         self.ctx.base_inp['metadata'].update({'label': 'geo_opt_molecule', 'call_link_label': 'run_geo_opt_molecule'})
         self.ctx.base_inp['cp2k']['metadata'].update({'label': 'GEO_OPT'})
         self.ctx.base_inp['cp2k']['metadata']['options']['parser_name'] = 'lsmo.cp2k_advanced_parser'
@@ -250,7 +250,7 @@ def run_bsse(self):
         if 'parameters' in self.exposed_inputs(Cp2kBaseWorkChain, 'cp2k_base')['cp2k']:
             dict_merge(self.ctx.cp2k_param,
                        self.exposed_inputs(Cp2kBaseWorkChain, 'cp2k_base')['cp2k']['parameters'].get_dict())
-        self.ctx.base_inp['cp2k']['parameters'] = Dict(dict=self.ctx.cp2k_param)
+        self.ctx.base_inp['cp2k']['parameters'] = Dict(self.ctx.cp2k_param)
         self.ctx.base_inp['cp2k']['structure'] = self.ctx.stages[-1].outputs.output_structure
         self.ctx.base_inp['metadata'].update({'label': 'bsse', 'call_link_label': 'run_bsse'})
         self.ctx.base_inp['cp2k']['metadata'].update({'label': 'BSSE'})

aiida_lsmo/workchains/cp2k_multistage.py

@@ -68,7 +68,7 @@ def apply_initial_magnetization(structure, protocol, oxidation_states=None, with
     cp2k_param = get_kinds_section(atoms=atoms, protocol=protocol_dict, with_ghost_atoms=bool(with_ghost_atoms))
     dict_merge(cp2k_param, get_multiplicity_section(atoms=atoms, protocol=protocol_dict))
 
-    return {'structure': StructureData(ase=atoms), 'cp2k_param': Dict(dict=cp2k_param)}
+    return {'structure': StructureData(ase=atoms), 'cp2k_param': Dict(cp2k_param)}
 
 
 @calcfunction
@@ -137,7 +137,7 @@ def extract_results(resize, **kwargs):
     output_dict['final_bandgap_spin1_au'] = kwarg['bandgap_spin1_au']
     output_dict['final_bandgap_spin2_au'] = kwarg['bandgap_spin2_au']
 
-    return Dict(dict=output_dict)
+    return Dict(output_dict)
 
 
 class Cp2kMultistageWorkChain(WorkChain):

aiida_lsmo/workchains/cp2k_multistage_ddec.py

@@ -14,8 +14,8 @@
 DdecCalculation = CalculationFactory('ddec')  # pylint: disable=invalid-name
 
 # import aiida data
-Dict = DataFactory('dict')  # pylint: disable=invalid-name
-CifData = DataFactory('cif')  # pylint: disable=invalid-name
+Dict = DataFactory('core.dict')  # pylint: disable=invalid-name
+CifData = DataFactory('core.cif')  # pylint: disable=invalid-name
 
 
 class Cp2kMultistageDdecWorkChain(WorkChain):
@@ -50,7 +50,7 @@ def run_cp2kddec(self):
         cp2k_ddec_inputs = AttributeDict(self.exposed_inputs(Cp2kDdecWorkChain))
         cp2k_ddec_inputs['cp2k_base'] = self.exposed_inputs(Cp2kMultistageWorkChain)['cp2k_base']
         cp2k_params_modify = Dict(
-            dict={
+            {
                 'FORCE_EVAL': {
                     'DFT': {
                         'WFN_RESTART_FILE_NAME': './parent_calc/aiida-RESTART.wfn',

aiida_lsmo/workchains/cp2k_phonopy.py

@@ -18,13 +18,13 @@
 Cp2kBaseWorkChain = WorkflowFactory('cp2k.base')  # pylint: disable=invalid-name
 
 # import aiida data
-Str = DataFactory('str')  # pylint: disable=invalid-name
-Int = DataFactory('int')  # pylint: disable=invalid-name
-List = DataFactory('list')  # pylint: disable=invalid-name
-Dict = DataFactory('dict')  # pylint: disable=invalid-name
-CifData = DataFactory('cif')  # pylint: disable=invalid-name
-StructureData = DataFactory('structure')  # pylint: disable=invalid-name
-SinglefileData = DataFactory('singlefile')  # pylint: disable=invalid-name
+Str = DataFactory('core.str')  # pylint: disable=invalid-name
+Int = DataFactory('core.int')  # pylint: disable=invalid-name
+List = DataFactory('core.list')  # pylint: disable=invalid-name
+Dict = DataFactory('core.dict')  # pylint: disable=invalid-name
+CifData = DataFactory('core.cif')  # pylint: disable=invalid-name
+StructureData = DataFactory('core.structure')  # pylint: disable=invalid-name
+SinglefileData = DataFactory('core.singlefile')  # pylint: disable=invalid-name
 
 
 class Cp2kPhonopyWorkChain(WorkChain):
@@ -92,7 +92,7 @@ def collect_cp2k_inputs(self):
 
         # Collect the other inputs for Cp2kBaseWC from the ref_cp2k_calc to self.ctx.base_inp
         self.ctx.base_inp = AttributeDict(self.exposed_inputs(Cp2kBaseWorkChain, 'cp2k_base'))
-        self.ctx.base_inp['cp2k']['settings'] = Dict(dict={'additional_retrieve_list': ['aiida-forces-1_0.xyz']})
+        self.ctx.base_inp['cp2k']['settings'] = Dict({'additional_retrieve_list': ['aiida-forces-1_0.xyz']})
         self.ctx.base_inp['cp2k']['parent_calc_folder'] = ref_cp2k_calc.outputs.remote_folder
         self.ctx.base_inp['cp2k']['file'] = {}
         if 'file' in ref_cp2k_calc.inputs:
@@ -226,7 +226,7 @@ def results(self):
             sets_of_forces.append(forces_parsed)
 
         # Output the forces of the initial structure as a List
-        initial_forces = List(list=sets_of_forces[0])
+        initial_forces = List(sets_of_forces[0])
         initial_forces.store()
         self.out('initial_forces', initial_forces)
         self.report(f'Forces computed on the input structure: List<{initial_forces.pk}>')

aiida_lsmo/workchains/isotherm.py

@@ -20,7 +20,7 @@
 FFBuilder = CalculationFactory('lsmo.ff_builder')  # pylint: disable=invalid-name
 
 # import aiida data
-CifData = DataFactory('cif')  # pylint: disable=invalid-name
+CifData = DataFactory('core.cif')  # pylint: disable=invalid-name
 ZeoppParameters = DataFactory('zeopp.parameters')  # pylint: disable=invalid-name
 
 
@@ -35,7 +35,7 @@ def get_molecule_dict(molecule_name):
         yaml_dict = yaml.safe_load(stream)
         ISOTHERM_MOLECULES_SCHEMA(yaml_dict)
     molecule_dict = yaml_dict[molecule_name.value]
-    return Dict(dict=molecule_dict)
+    return Dict(molecule_dict)
 
 
 @calcfunction
@@ -71,7 +71,7 @@ def get_ff_parameters(molecule_dict, isotparam):
     ff_params['tail_corrections'] = isotparam['ff_tail_corrections']
     ff_params['mixing_rule'] = isotparam['ff_mixing_rule']
     ff_params['separate_interactions'] = isotparam['ff_separate_interactions']
-    return Dict(dict=ff_params)
+    return Dict(ff_params)
 
 
 @calcfunction
@@ -95,7 +95,7 @@ def choose_pressure_points(inp_param, geom, raspa_widom_out):
             else:
                 pressure_points.append(inp_param['pressure_max'])
                 break
-    return List(list=pressure_points)
+    return List(pressure_points)
 
 
 @calcfunction
@@ -107,7 +107,7 @@ def get_geometric_dict(zeopp_out, molecule):
         'Estimated_saturation_loading_unit': 'mol/kg',
         'is_porous': geometric_dict['POAV_A^3'] > 0.000
     })
-    return Dict(dict=geometric_dict)
+    return Dict(geometric_dict)
 
 
 @calcfunction
@@ -172,7 +172,7 @@ def get_output_parameters(geom_out, inp_params, widom_out=None, pressures=None,
                 'conversion_factor_molec_uc_to_mol_kg': gcmc_out_mol['conversion_factor_molec_uc_to_mol_kg'],
             })
 
-    return Dict(dict=out_dict)
+    return Dict(out_dict)
 
 
 class IsothermWorkChain(WorkChain):
@@ -283,7 +283,7 @@ def setup(self):
         # Get the parameters Dict, merging defaults with user settings
         @calcfunction
         def get_valid_dict(dict_node):
-            return Dict(dict=self.parameters_schema(dict_node.get_dict()))
+            return Dict(self.parameters_schema(dict_node.get_dict()))
 
         self.ctx.parameters = get_valid_dict(self.inputs.parameters)
 
@@ -416,7 +416,7 @@ def run_raspa_widom(self):
             self.ctx.inp['raspa']['block_pocket'] = {'block_file': self.ctx.zeopp.outputs.block}
 
         self.ctx.raspa_param = self._get_widom_param()
-        self.ctx.inp['raspa']['parameters'] = Dict(dict=self.ctx.raspa_param)
+        self.ctx.inp['raspa']['parameters'] = Dict(self.ctx.raspa_param)
 
         # Generate the force field with the ff_builder
         ff_params = get_ff_parameters(self.ctx.molecule, self.ctx.parameters)
@@ -502,7 +502,7 @@ def run_raspa_gcmc(self):
             self.ctx.pressures[self.ctx.current_p_index] * 1e5
 
         # Update parameters Dict
-        self.ctx.inp['raspa']['parameters'] = Dict(dict=self.ctx.raspa_param)
+        self.ctx.inp['raspa']['parameters'] = Dict(self.ctx.raspa_param)
 
         # Update restart (if present, i.e., if current_p_index>0)
         if self.ctx.current_p_index > 0:

aiida_lsmo/workchains/isotherm_accurate.py

@@ -20,7 +20,7 @@
 FFBuilder = CalculationFactory('lsmo.ff_builder')  # pylint: disable=invalid-name
 
 # import aiida data
-CifData = DataFactory('cif')  # pylint: disable=invalid-name
+CifData = DataFactory('core.cif')  # pylint: disable=invalid-name
 ZeoppParameters = DataFactory('zeopp.parameters')  # pylint: disable=invalid-name
 
 
@@ -35,7 +35,7 @@ def get_molecule_dict(molecule_name):
         yaml_dict = yaml.safe_load(stream)
         ISOTHERM_MOLECULES_SCHEMA(yaml_dict)
     molecule_dict = yaml_dict[molecule_name.value]
-    return Dict(dict=molecule_dict)
+    return Dict(molecule_dict)
 
 
 @calcfunction
@@ -71,7 +71,7 @@ def get_ff_parameters(molecule_dict, isotparam):
     ff_params['tail_corrections'] = isotparam['ff_tail_corrections']
     ff_params['mixing_rule'] = isotparam['ff_mixing_rule']
     ff_params['separate_interactions'] = isotparam['ff_separate_interactions']
-    return Dict(dict=ff_params)
+    return Dict(ff_params)
 
 
 @calcfunction
@@ -83,7 +83,7 @@ def get_geometric_dict(zeopp_out, molecule):
         'Estimated_saturation_loading_unit': 'mol/kg',
         'is_porous': geometric_dict['POAV_A^3'] > 0.000
     })
-    return Dict(dict=geometric_dict)
+    return Dict(geometric_dict)
 
 
 @calcfunction
@@ -153,7 +153,7 @@ def get_output_parameters(geom_out, inp_params, widom_out=None, **gcmc_out_dict)
                 'conversion_factor_molec_uc_to_mol_kg': gcmc_out_mol['conversion_factor_molec_uc_to_mol_kg'],
             })
 
-    return Dict(dict=out_dict)
+    return Dict(out_dict)
 
 
 class IsothermAccurateWorkChain(WorkChain):
@@ -266,7 +266,7 @@ def setup(self):
         # Get the parameters Dict, merging defaults with user settings
         @calcfunction
         def get_valid_dict(dict_node):
-            return Dict(dict=self.parameters_schema(dict_node.get_dict()))
+            return Dict(self.parameters_schema(dict_node.get_dict()))
 
         self.ctx.parameters = get_valid_dict(self.inputs.parameters)
 
@@ -405,7 +405,7 @@ def run_raspa_widom(self):
             self.ctx.inp['raspa']['block_pocket'] = {'block_file': self.ctx.zeopp.outputs.block}
 
         self.ctx.raspa_param = self._get_widom_param()
-        self.ctx.inp['raspa']['parameters'] = Dict(dict=self.ctx.raspa_param)
+        self.ctx.inp['raspa']['parameters'] = Dict(self.ctx.raspa_param)
 
         # Generate the force field with the ff_builder
         ff_params = get_ff_parameters(self.ctx.molecule, self.ctx.parameters)
@@ -557,7 +557,7 @@ def run_raspa_gcmc(self):
         self.ctx.raspa_param['System']['framework_1']['ExternalPressure'] = self.ctx.pressure * 1e5
 
         # Update parameters Dict
-        self.ctx.inp['raspa']['parameters'] = Dict(dict=self.ctx.raspa_param)
+        self.ctx.inp['raspa']['parameters'] = Dict(self.ctx.raspa_param)
 
         # Update restart (if present, i.e., if current_p_index>0)
         if 'raspa_gcmc' in self.ctx:

aiida_lsmo/workchains/isotherm_calc_pe.py

@@ -14,7 +14,7 @@
 IsothermWorkChain = WorkflowFactory('lsmo.isotherm')  #pylint: disable=invalid-name
 
 # import aiida data
-CifData = DataFactory('cif')  #pylint: disable=invalid-name
+CifData = DataFactory('core.cif')  #pylint: disable=invalid-name
 
 
 class IsothermCalcPEWorkChain(WorkChain):