Removed old versions of atoms2nomad and cube_reader.

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)