Resolve "System links and ASE atoms for results section"

The new to_ase function allows to conviniently generate an ASE Atoms object from a given section syst em based on the data in its atoms sub-section. Here is a simple example:

from nomad.client import ArchiveQuery

query = ArchiveQuery(
    required={
        'run': {
            'system[-1]': {
                'atoms': '*'
            }
        }
    })

result = query.download(1)[0]
atoms = result.run[0].system[-1].atoms.to_ase()

print(atoms.get_chemical_formula(mode='reduce'))

See also the discussion here: https://matsci.org/t/convert-query-result-directly-to-ase-atoms-objects/44513/7

#1074 (closed)

examples/api/to_ase.py

+'''
+Demonstrates how to use requests for a simple query and archive access.
+'''
+
+import requests
+from ase import Atoms
+
+base_url = 'http://nomad-lab.eu/prod/v1/api/v1'
+response = requests.post(
+    f'{base_url}/entries/archive/query',
+    json={
+        'pagination': {
+            'page_size': 1
+        },
+        'required': {
+            'run': {
+                'system[-1]': {
+                    'atoms': '*'
+                }
+            }
+        }
+    })
+response_json = response.json()
+nomad_atoms = response_json['data'][0]['archive']['run'][0]['system'][-1]['atoms']
+atoms = Atoms(
+    symbols=nomad_atoms['labels'],
+    positions=nomad_atoms['positions'],
+    cell=nomad_atoms['lattice_vectors'],
+    pbc=nomad_atoms['periodic']
+)
+
+print(atoms)
+
+
+from nomad.client import ArchiveQuery
+
+query = ArchiveQuery(
+    required={
+        'run': {
+            'system[-1]': {
+                'atoms': '*'
+            }
+        }
+    })
+
+result = query.download(1)[0]
+atoms = result.run[0].system[-1].atoms.to_ase()
+
+print(atoms.get_chemical_formula(mode='reduce'))