Merge branch 'master' into lauri_restructure

common/python/nomadcore/atoms2nomad.py

+import numpy as np
+
+from nomadcore.unit_conversion.unit_conversion import convert_unit
+
+
+def ase_atoms_to_section_system(backend, atoms, new_section=True):
+    """Add ASE Atoms object as metainfo to section_system.
+
+    If new_section is True, open and close a new section_system,
+    returning its gIndex."""
+
+    if new_section:
+        gIndex = backend.openSection('section_system')
+
+    backend.addArrayValues('atom_labels',
+                           np.array(atoms.get_chemical_symbols()))
+    backend.addArrayValues('atom_positions',
+                           convert_unit(atoms.positions, 'angstrom'))
+    backend.addArrayValues('simulation_cell',
+                           convert_unit(atoms.cell, 'angstrom'))
+    backend.addArrayValues('configuration_periodic_dimensions',
+                           np.array(atoms.pbc))
+
+    # Return system ref if we opened it, else None:
+    if new_section:
+        backend.closeSection('section_system', gIndex)
+        return gIndex

common/python/nomadcore/cube_reader.py

+import numpy as np
+from ase.io import read
+
+from nomadcore.atoms2nomad import ase_atoms_to_section_system
+
+class CubeError(OSError):
+    pass
+
+
+def read_cube_file(backend, file_name):
+    try:
+        d = read(file_name, format = 'cube', full_output = True)
+
+    except Exception as err:
+        raise CubeError(err)
+
+    data = d['data']
+    atoms = d['atoms']
+    origin = d['origin']
+    nx, ny, nz = data.shape
+    displacements = np.array([atoms.cell[i]/data.shape[i] for i in range(3)])
+
+    system = ase_atoms_to_section_system(backend, atoms)
+
+    singleconfig = backend.openSection('section_single_configuration_calculation')
+    volumetric = backend.openSection('section_volumetric_data')
+
+    backend.addValue('volumetric_data_nx', nx)
+    backend.addValue('volumetric_data_ny', ny)
+    backend.addValue('volumetric_data_nz', nz)
+
+    backend.addArrayValues('volumetric_data_origin', origin)
+    backend.addArrayValues('volumetric_data_displacements', displacements)
+
+    backend.addValue('volumetric_data_multiplicity', 1)
+    backend.addArrayValues('volumetric_data_values', data[None])
+    backend.closeSection('section_volumetric_data', volumetric)
+
+    backend.addValue('single_configuration_calculation_to_system_ref', system)
+    backend.closeSection('section_single_configuration_calculation', singleconfig)

nomadcore/constants/structure_types.py

@@ -4001,7 +4001,7 @@ structure_types_by_spacegroup = {1: [{'Notes': '-',
        'Strukturbericht Designation': 'A11',
        'Wyckoff Positions': 'f',
        'aflow_prototype_id': 'A_oC8_64_f',
-       'aflow_prototype_url': 'http://www.aflowlib.org/CrystalDatabase/A_oC8_64_f.html',
+       'aflow_prototype_url': 'http://www.aflowlib.org/CrystalDatabase/A_oC8_64_f.alpha-Ga.html',
        'atom_labels': ['Ga', 'Ga', 'Ga', 'Ga'],
        'atom_positions': [[0.0, 1.18658047e-10, 3.665979e-11],
                           [0.0, -1.18658047e-10, -3.665979e-11],
@@ -5728,7 +5728,7 @@ structure_types_by_spacegroup = {1: [{'Notes': '-',
         'Strukturbericht Designation': 'A6',
         'Wyckoff Positions': 'a',
         'aflow_prototype_id': 'A_tI2_139_a',
-        'aflow_prototype_url': 'http://www.aflowlib.org/CrystalDatabase/A_tI2_139_a.html',
+        'aflow_prototype_url': 'http://www.aflowlib.org/CrystalDatabase/A_tI2_139_a.In.html',
         'atom_labels': ['In'],
         'atom_positions': [[0.0, 0.0, 0.0]],
         'lattice_vectors': [[3.2512769800000005e-10, 0.0, 0.0],
@@ -5854,7 +5854,7 @@ structure_types_by_spacegroup = {1: [{'Notes': '-',
         'Strukturbericht Designation': 'Aa',
         'Wyckoff Positions': 'a',
         'aflow_prototype_id': 'A_tI2_139_a',
-        'aflow_prototype_url': 'http://www.aflowlib.org/CrystalDatabase/A_tI2_139_a.html',
+        'aflow_prototype_url': 'http://www.aflowlib.org/CrystalDatabase/A_tI2_139_a.alpha-Pa.html',
         'atom_labels': ['Pa'],
         'atom_positions': [[0.0, 0.0, 0.0]],
         'lattice_vectors': [[3.925e-10, 0.0, 0.0],
@@ -7518,7 +7518,7 @@ structure_types_by_spacegroup = {1: [{'Notes': '-',
         'Strukturbericht Designation': 'A7',
         'Wyckoff Positions': 'c',
         'aflow_prototype_id': 'A_hR2_166_c',
-        'aflow_prototype_url': 'http://www.aflowlib.org/CrystalDatabase/A_hR2_166_c.html',
+        'aflow_prototype_url': 'http://www.aflowlib.org/CrystalDatabase/A_hR2_166_c.alpha-As.html',
         'atom_labels': ['As', 'As'],
         'atom_positions': [[1.37328129e-10, 1.37328129e-10, 1.37328129e-10],
                            [-1.37328129e-10, -1.37328129e-10, -1.37328129e-10]],
@@ -7977,7 +7977,7 @@ structure_types_by_spacegroup = {1: [{'Notes': '-',
         'Strukturbericht Designation': '-',
         'Wyckoff Positions': 'c',
         'aflow_prototype_id': 'A_hR2_166_c',
-        'aflow_prototype_url': 'http://www.aflowlib.org/CrystalDatabase/A_hR2_166_c.html',
+        'aflow_prototype_url': 'http://www.aflowlib.org/CrystalDatabase/A_hR2_166_c.C.html',
         'atom_labels': ['C', 'C'],
         'atom_positions': [[0.0, 0.0, 1.6740000000000337e-10],
                            [0.0, 0.0, 8.369999999999966e-10]],
@@ -8113,7 +8113,7 @@ structure_types_by_spacegroup = {1: [{'Notes': '-',
         'Strukturbericht Designation': 'A10',
         'Wyckoff Positions': 'a',
         'aflow_prototype_id': 'A_hR1_166_a',
-        'aflow_prototype_url': 'http://www.aflowlib.org/CrystalDatabase/A_hR1_166_a.html',
+        'aflow_prototype_url': 'http://www.aflowlib.org/CrystalDatabase/A_hR1_166_a.alpha-Hg.html',
         'atom_labels': ['Hg'],
         'atom_positions': [[0.0, 0.0, 0.0]],
         'lattice_vectors': [[2.9288947099999997e-10,
@@ -8135,7 +8135,7 @@ structure_types_by_spacegroup = {1: [{'Notes': '-',
         'Strukturbericht Designation': '-',
         'Wyckoff Positions': 'c',
         'aflow_prototype_id': 'A_hR2_166_c',
-        'aflow_prototype_url': 'http://www.aflowlib.org/CrystalDatabase/A_hR2_166_c.html',
+        'aflow_prototype_url': 'http://www.aflowlib.org/CrystalDatabase/A_hR2_166_c.beta-O.html',
         'atom_labels': ['O', 'O'],
         'atom_positions': [[0.0, 0.0, 6.125583e-11], [0.0, 0.0, -6.125583e-11]],
         'lattice_vectors': [[1.6445e-10, -9.4945252e-11, 3.76033333e-10],
@@ -8151,7 +8151,7 @@ structure_types_by_spacegroup = {1: [{'Notes': '-',
         'Strukturbericht Designation': 'Ai',
         'Wyckoff Positions': 'a',
         'aflow_prototype_id': 'A_hR1_166_a',
-        'aflow_prototype_url': 'http://www.aflowlib.org/CrystalDatabase/A_hR1_166_a.html',
+        'aflow_prototype_url': 'http://www.aflowlib.org/CrystalDatabase/A_hR1_166_a.beta-Po.html',
         'atom_labels': ['Po'],
         'atom_positions': [[0.0, 0.0, 0.0]],
         'lattice_vectors': [[2.98911671e-10, -2.1818147e-11, -2.1818147e-11],