Merge branch 'workflow-fixes' into 'v1.0.0'

Workflow fixes

See merge request !540

fhi-aims @ 2460559c

-Subproject commit c342127e8795ec48238ff7339798b4a6867f514d
+Subproject commit 2460559c7c7b1d2c7c4335bd272717eb1b146141

gaussian @ 87e823af

-Subproject commit 774c4258c1d6b9c63cfe43006eb9bdecb4e7177b
+Subproject commit 87e823af984b0925afb581998a7f905e21b7445f

gpaw @ 1b5f2742

-Subproject commit 19d35f800ceb6c28651decb22f849717808f8859
+Subproject commit 1b5f27421bcde5f6c35d9902df66c048dea908bd

gromacs @ 683b1239

-Subproject commit 7528f94a08f63572ef920e7686672fdf4fccaf81
+Subproject commit 683b1239e07686f4696f0e8eadd04a7396b99c04

lammps @ ea5c3fb5

-Subproject commit 918f29baeceaa0c17b2c5cffd3ef04951c9afdd1
+Subproject commit ea5c3fb51e5d2d4441f9451d78b8cd1593136194

quantum-espresso @ 8aa96aad

-Subproject commit f2e5ddf4e1210a0808454481c5a5a92d25db1820
+Subproject commit 8aa96aadd03ecca3451a6dc8b57025999d58af1a

nomad/normalizing/workflow.py

@@ -17,6 +17,7 @@
 #
 
 import numpy as np
+from ase import Atoms
 from nomad.datamodel.metainfo.simulation.calculation import Calculation
 
 from nomad.normalizing.normalizer import Normalizer
@@ -255,9 +256,14 @@ class GeometryOptimizationNormalizer(TaskNormalizer):
         if not self.section.final_displacement_maximum:
             try:
                 system = self.run.system
+                ase_atoms = [Atoms(
+                    positions=system_i.atoms.positions.magnitude,
+                    cell=system_i.atoms.lattice_vectors.magnitude,
+                    pbc=system_i.atoms.periodic) for system_i in system]
+                _ = [atoms.wrap() for atoms in ase_atoms]
                 displacements = [np.max(np.abs(
-                    system[n].atoms.positions - system[n - 1].atoms.positions)) for n in range(1, len(system))]
-                self.section.final_displacement_maximum = resolve_difference(displacements)
+                    ase_atoms[n].get_positions() - ase_atoms[n - 1].get_positions())) for n in range(1, len(ase_atoms))]
+                self.section.final_displacement_maximum = displacements[np.amax(np.nonzero(displacements))]
             except Exception:
                 pass