Hubbard: add useful utility functions

docs/source/conf.py

@@ -50,6 +50,7 @@
     'python': ('https://docs.python.org/3.8', None),
     'aiida': ('https://aiida.readthedocs.io/projects/aiida-core/en/latest/', None),
     'aiida_pseudo': ('http://aiida-pseudo.readthedocs.io/en/latest/', None),
+    'pymatgen': ('https://pymatgen.org/', None),
 }
 
 # Settings for the `autoapi.extenstion` automatically generating API docs

src/aiida_quantumespresso/data/hubbard_structure.py

@@ -120,9 +120,11 @@ def append_hubbard_parameter(
         parameters = HubbardParameters.from_tuple(hp_tuple)
         hubbard = self.hubbard
 
-        if parameters not in hubbard.parameters:
-            hubbard.parameters.append(parameters)
-            self.hubbard = hubbard
+        if parameters in hubbard.parameters:
+            hubbard.parameters.remove(parameters)
+
+        hubbard.parameters.append(parameters)
+        self.hubbard = hubbard
 
     def pop_hubbard_parameters(self, index: int):
         """Pop Hubbard parameters in the list.

src/aiida_quantumespresso/workflows/protocols/pw/base.yaml

@@ -5,7 +5,7 @@ default_inputs:
     meta_parameters:
         conv_thr_per_atom: 0.2e-9
         etot_conv_thr_per_atom: 1.e-5
-    pseudo_family: 'SSSP/1.2/PBEsol/efficiency'
+    pseudo_family: 'SSSP/1.3/PBEsol/efficiency'
     pw:
         metadata:
             options:

tests/conftest.py

@@ -168,7 +168,7 @@ def sssp(aiida_profile, generate_upf_data):
                 'cutoff_rho': 240.0,
             }
 
-        label = 'SSSP/1.2/PBEsol/efficiency'
+        label = 'SSSP/1.3/PBEsol/efficiency'
         family = SsspFamily.create_from_folder(dirpath, label)
 
     family.set_cutoffs(cutoffs, stringency, unit='Ry')

tests/fixtures/structures/Fe3O4.cif

@@ -0,0 +1,263 @@
+#------------------------------------------------------------------------------
+#$Date: 2017-10-13 02:32:00 +0300 (Fri, 13 Oct 2017) $
+#$Revision: 201954 $
+#$URL: file:///home/coder/svn-repositories/cod/cif/1/01/03/1010369.cif $
+#------------------------------------------------------------------------------
+#
+# This file is available in the Crystallography Open Database (COD),
+# http://www.crystallography.net/
+#
+# All data on this site have been placed in the public domain by the
+# contributors.
+#
+data_1010369
+loop_
+_publ_author_name
+'Montoro, V'
+_publ_section_title
+;
+Miscibilita fra gli ossidi salini di ferro e di manganese
+;
+_journal_coden_ASTM              GCITA9
+_journal_name_full               'Gazzetta Chimica Italiana'
+_journal_page_first              728
+_journal_page_last               733
+_journal_volume                  68
+_journal_year                    1938
+_chemical_formula_structural     'Fe3 O4'
+_chemical_formula_sum            'Fe3 O4'
+_chemical_name_systematic        'Iron diiron(III) oxide'
+_space_group_IT_number           227
+_symmetry_cell_setting           cubic
+_symmetry_space_group_name_Hall  'F 4d 2 3 -1d'
+_symmetry_space_group_name_H-M   'F d -3 m :1'
+_cell_angle_alpha                90
+_cell_angle_beta                 90
+_cell_angle_gamma                90
+_cell_formula_units_Z            8
+_cell_length_a                   8.384
+_cell_length_b                   8.384
+_cell_length_c                   8.384
+_cell_volume                     589.3
+_cod_original_sg_symbol_H-M      'F d -3 m S'
+_cod_database_code               1010369
+loop_
+_symmetry_equiv_pos_as_xyz
+x,y,z
+y,z,x
+z,x,y
+x,z,y
+y,x,z
+z,y,x
+x,-y,-z
+y,-z,-x
+z,-x,-y
+x,-z,-y
+y,-x,-z
+z,-y,-x
+-x,y,-z
+-y,z,-x
+-z,x,-y
+-x,z,-y
+-y,x,-z
+-z,y,-x
+-x,-y,z
+-y,-z,x
+-z,-x,y
+-x,-z,y
+-y,-x,z
+-z,-y,x
+1/4-x,1/4-y,1/4-z
+1/4-y,1/4-z,1/4-x
+1/4-z,1/4-x,1/4-y
+1/4-x,1/4-z,1/4-y
+1/4-y,1/4-x,1/4-z
+1/4-z,1/4-y,1/4-x
+1/4-x,1/4+y,1/4+z
+1/4-y,1/4+z,1/4+x
+1/4-z,1/4+x,1/4+y
+1/4-x,1/4+z,1/4+y
+1/4-y,1/4+x,1/4+z
+1/4-z,1/4+y,1/4+x
+1/4+x,1/4-y,1/4+z
+1/4+y,1/4-z,1/4+x
+1/4+z,1/4-x,1/4+y
+1/4+x,1/4-z,1/4+y
+1/4+y,1/4-x,1/4+z
+1/4+z,1/4-y,1/4+x
+1/4+x,1/4+y,1/4-z
+1/4+y,1/4+z,1/4-x
+1/4+z,1/4+x,1/4-y
+1/4+x,1/4+z,1/4-y
+1/4+y,1/4+x,1/4-z
+1/4+z,1/4+y,1/4-x
+x,1/2+y,1/2+z
+1/2+x,y,1/2+z
+1/2+x,1/2+y,z
+y,1/2+z,1/2+x
+1/2+y,z,1/2+x
+1/2+y,1/2+z,x
+z,1/2+x,1/2+y
+1/2+z,x,1/2+y
+1/2+z,1/2+x,y
+x,1/2+z,1/2+y
+1/2+x,z,1/2+y
+1/2+x,1/2+z,y
+y,1/2+x,1/2+z
+1/2+y,x,1/2+z
+1/2+y,1/2+x,z
+z,1/2+y,1/2+x
+1/2+z,y,1/2+x
+1/2+z,1/2+y,x
+x,1/2-y,1/2-z
+1/2+x,-y,1/2-z
+1/2+x,1/2-y,-z
+y,1/2-z,1/2-x
+1/2+y,-z,1/2-x
+1/2+y,1/2-z,-x
+z,1/2-x,1/2-y
+1/2+z,-x,1/2-y
+1/2+z,1/2-x,-y
+x,1/2-z,1/2-y
+1/2+x,-z,1/2-y
+1/2+x,1/2-z,-y
+y,1/2-x,1/2-z
+1/2+y,-x,1/2-z
+1/2+y,1/2-x,-z
+z,1/2-y,1/2-x
+1/2+z,-y,1/2-x
+1/2+z,1/2-y,-x
+-x,1/2+y,1/2-z
+1/2-x,y,1/2-z
+1/2-x,1/2+y,-z
+-y,1/2+z,1/2-x
+1/2-y,z,1/2-x
+1/2-y,1/2+z,-x
+-z,1/2+x,1/2-y
+1/2-z,x,1/2-y
+1/2-z,1/2+x,-y
+-x,1/2+z,1/2-y
+1/2-x,z,1/2-y
+1/2-x,1/2+z,-y
+-y,1/2+x,1/2-z
+1/2-y,x,1/2-z
+1/2-y,1/2+x,-z
+-z,1/2+y,1/2-x
+1/2-z,y,1/2-x
+1/2-z,1/2+y,-x
+-x,1/2-y,1/2+z
+1/2-x,-y,1/2+z
+1/2-x,1/2-y,z
+-y,1/2-z,1/2+x
+1/2-y,-z,1/2+x
+1/2-y,1/2-z,x
+-z,1/2-x,1/2+y
+1/2-z,-x,1/2+y
+1/2-z,1/2-x,y
+-x,1/2-z,1/2+y
+1/2-x,-z,1/2+y
+1/2-x,1/2-z,y
+-y,1/2-x,1/2+z
+1/2-y,-x,1/2+z
+1/2-y,1/2-x,z
+-z,1/2-y,1/2+x
+1/2-z,-y,1/2+x
+1/2-z,1/2-y,x
+1/4-x,3/4-y,3/4-z
+3/4-x,1/4-y,3/4-z
+3/4-x,3/4-y,1/4-z
+1/4-y,3/4-z,3/4-x
+3/4-y,1/4-z,3/4-x
+3/4-y,3/4-z,1/4-x
+1/4-z,3/4-x,3/4-y
+3/4-z,1/4-x,3/4-y
+3/4-z,3/4-x,1/4-y
+1/4-x,3/4-z,3/4-y
+3/4-x,1/4-z,3/4-y
+3/4-x,3/4-z,1/4-y
+1/4-y,3/4-x,3/4-z
+3/4-y,1/4-x,3/4-z
+3/4-y,3/4-x,1/4-z
+1/4-z,3/4-y,3/4-x
+3/4-z,1/4-y,3/4-x
+3/4-z,3/4-y,1/4-x
+1/4-x,3/4+y,3/4+z
+3/4-x,1/4+y,3/4+z
+3/4-x,3/4+y,1/4+z
+1/4-y,3/4+z,3/4+x
+3/4-y,1/4+z,3/4+x
+3/4-y,3/4+z,1/4+x
+1/4-z,3/4+x,3/4+y
+3/4-z,1/4+x,3/4+y
+3/4-z,3/4+x,1/4+y
+1/4-x,3/4+z,3/4+y
+3/4-x,1/4+z,3/4+y
+3/4-x,3/4+z,1/4+y
+1/4-y,3/4+x,3/4+z
+3/4-y,1/4+x,3/4+z
+3/4-y,3/4+x,1/4+z
+1/4-z,3/4+y,3/4+x
+3/4-z,1/4+y,3/4+x
+3/4-z,3/4+y,1/4+x
+1/4+x,3/4-y,3/4+z
+3/4+x,1/4-y,3/4+z
+3/4+x,3/4-y,1/4+z
+1/4+y,3/4-z,3/4+x
+3/4+y,1/4-z,3/4+x
+3/4+y,3/4-z,1/4+x
+1/4+z,3/4-x,3/4+y
+3/4+z,1/4-x,3/4+y
+3/4+z,3/4-x,1/4+y
+1/4+x,3/4-z,3/4+y
+3/4+x,1/4-z,3/4+y
+3/4+x,3/4-z,1/4+y
+1/4+y,3/4-x,3/4+z
+3/4+y,1/4-x,3/4+z
+3/4+y,3/4-x,1/4+z
+1/4+z,3/4-y,3/4+x
+3/4+z,1/4-y,3/4+x
+3/4+z,3/4-y,1/4+x
+1/4+x,3/4+y,3/4-z
+3/4+x,1/4+y,3/4-z
+3/4+x,3/4+y,1/4-z
+1/4+y,3/4+z,3/4-x
+3/4+y,1/4+z,3/4-x
+3/4+y,3/4+z,1/4-x
+1/4+z,3/4+x,3/4-y
+3/4+z,1/4+x,3/4-y
+3/4+z,3/4+x,1/4-y
+1/4+x,3/4+z,3/4-y
+3/4+x,1/4+z,3/4-y
+3/4+x,3/4+z,1/4-y
+1/4+y,3/4+x,3/4-z
+3/4+y,1/4+x,3/4-z
+3/4+y,3/4+x,1/4-z
+1/4+z,3/4+y,3/4-x
+3/4+z,1/4+y,3/4-x
+3/4+z,3/4+y,1/4-x
+loop_
+_atom_site_label
+_atom_site_type_symbol
+_atom_site_symmetry_multiplicity
+_atom_site_Wyckoff_symbol
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+_atom_site_occupancy
+_atom_site_attached_hydrogens
+_atom_site_calc_flag
+Fe1 Fe2+ 16 d 0.625 0.625 0.625 0.5 0 d
+Fe2 Fe3+ 16 d 0.625 0.625 0.625 0.5 0 d
+Fe3 Fe3+ 8 a 0. 0. 0. 1. 0 d
+O1 O2- 32 e 0.375 0.375 0.375 1. 0 d
+loop_
+_atom_type_symbol
+_atom_type_oxidation_number
+Fe2+ 2.000
+Fe3+ 3.000
+O2- -2.000
+loop_
+_cod_related_entry_id
+_cod_related_entry_database
+_cod_related_entry_code
+1 ChemSpider 4937312

tests/fixtures/structures/LMT.cif

@@ -0,0 +1,30 @@
+# generated using pymatgen
+data_LiMnTe2
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   4.31097682
+_cell_length_b   4.31097682
+_cell_length_c   5.22251802
+_cell_angle_alpha   90.00000000
+_cell_angle_beta   90.00000000
+_cell_angle_gamma   120.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   LiMnTe2
+_chemical_formula_sum   'Li1 Mn1 Te2'
+_cell_volume   84.05469084
+_cell_formula_units_Z   1
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Mn  Mn0  1  0.33333333  0.66666667  0.47975861  1.0
+  Te  Te1  1  0.33333333  0.66666667  -0.01976285  1.0
+  Te  Te2  1  0.66666667  0.33333333  0.45389956  1.0
+  Li  Li3  1  -0.00000000  -0.00000000  0.73880468  1.0

tests/fixtures/structures/MnCoS.cif

@@ -0,0 +1,28 @@
+data_image0
+_chemical_formula_structural       MnCoS
+_chemical_formula_sum              "Mn1 Co1 S1"
+_cell_length_a       4.02254
+_cell_length_b       4.02254
+_cell_length_c       4.02254
+_cell_angle_alpha    60
+_cell_angle_beta     60
+_cell_angle_gamma    60
+
+_space_group_name_H-M_alt    "P 1"
+_space_group_IT_number       1
+
+loop_
+  _space_group_symop_operation_xyz
+  'x, y, z'
+
+loop_
+  _atom_site_type_symbol
+  _atom_site_label
+  _atom_site_symmetry_multiplicity
+  _atom_site_fract_x
+  _atom_site_fract_y
+  _atom_site_fract_z
+  _atom_site_occupancy
+  Mn  Mn1       1.0  0.00000  0.00000  0.00000  1.0000
+  Co  Co1       1.0  0.75000  0.75000  0.75000  1.0000
+  S   S1        1.0  0.50000  0.50000  0.50000  1.0000