Merge pull request #981 from pyiron/load_sparse_list

Remove sparse list
pyiron · Jul 11, 2023 · 1211fd3 · 1211fd3
2 parents aee21f2 + a4d43dd
commit 1211fd3
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Showing 18 changed files with 136 additions and 971 deletions.
diff --git a/pyiron_atomistics/atomistics/job/atomistic.py b/pyiron_atomistics/atomistics/job/atomistic.py
@@ -759,7 +759,7 @@ def _get_structure(self, frame=-1, wrap_atoms=True):
             if cell is not None:
                 snapshot.cell = cell
             if indices is not None:
-                snapshot.indices = indices
+                snapshot.set_array("indices", indices)
         if self.output.positions is not None:
             if wrap_atoms:
                 snapshot.positions = self.output.positions[frame]
@@ -882,7 +882,7 @@ def __getitem__(self, item):
             if self._cells is not None:
                 new_structure.cell = self._cells[item]
             if self._indices is not None:
-                new_structure.indices = self._indices[item]
+                new_structure.set_array("indices", self._indices[item])
             new_structure.positions = self._positions[item]
             # This step is necessary for using ase.io.write for trajectories
             new_structure.arrays["positions"] = new_structure.positions

diff --git a/pyiron_atomistics/atomistics/master/phonopy.py b/pyiron_atomistics/atomistics/master/phonopy.py
@@ -111,7 +111,7 @@ def _restore_magmoms(self, structure):
         Returns:
             structure (pyiron_atomistics.atomistics.structure.atoms): output structure with magnetic moments
         """
-        if any(self._master.structure.get_initial_magnetic_moments() != None):
+        if self._master.structure.has("initial_magmoms"):
             magmoms = self._master.structure.get_initial_magnetic_moments()
             magmoms = np.tile(
                 magmoms,

diff --git a/pyiron_atomistics/atomistics/structure/atom.py b/pyiron_atomistics/atomistics/structure/atom.py
@@ -7,7 +7,6 @@
     PeriodicTable,
     ChemicalElement,
 )
-from pyiron_atomistics.atomistics.structure.sparse_list import SparseArrayElement
 from ase.atom import Atom as ASEAtom
 
 __author__ = "Sudarsan Surendralal"
@@ -22,7 +21,7 @@
 __date__ = "Aug 1, 2020"
 
 
-class Atom(ASEAtom, SparseArrayElement):
+class Atom(ASEAtom):
     """
     Class for representing a single atom derived from the `ASE atom class`_.
 
@@ -59,22 +58,19 @@ def __init__(
         if element is None:
             element = symbol
 
-        SparseArrayElement.__init__(self, **qwargs)
-        # super(SparseArrayElement, self).__init__(**qwargs)
-        # verify that element is given (as string, ChemicalElement object or nucleus number
         if pse is None:
             pse = PeriodicTable()
 
         if element is None or element == "X":
             if "Z" in qwargs:
                 el_symbol = pse.atomic_number_to_abbreviation(qwargs["Z"])
-                self._lists["element"] = pse.element(el_symbol)
+                qwargs["element"] = pse.element(el_symbol)
         else:
             if isinstance(element, str):
                 el_symbol = element
-                self._lists["element"] = pse.element(el_symbol)
+                qwargs["element"] = pse.element(el_symbol)
             elif isinstance(element, ChemicalElement):
-                self._lists["element"] = element
+                qwargs["element"] = element
             else:
                 raise ValueError("Unknown element type")
 
@@ -111,6 +107,9 @@ def __init__(
         for key, val in qwargs.items():
             self.data[key] = val
 
+    def __getattr__(self, key):
+        return self.data[key]
+
     @property
     def mass(self):
         """