fixed reading aims input files with no lattice

Author: zerothi

changes/orphan.1.fix.rst

@@ -0,0 +1,5 @@
+reading fhiaims input geometries for molecules
+
+Previously it failed when the lattice was not
+defined in the file. Now it reads but puts
+an arbitrary lattice.

src/sisl/_core/geometry.py

@@ -223,7 +223,7 @@ def _init_lattice(self, lattice: Optional[LatticeLike]) -> None:
 
         # First create an initial guess for the supercell
         # It HAS to be VERY large to not interact
-        closest = self.close(0, R=(0.0, 0.4, 5.0))[2]
+        closest = self.close(0, R=(0.4, 5.0))[1]
         if len(closest) < 1:
             # We could not find any atoms very close,
             # hence we simply return and now it becomes

src/sisl/io/fhiaims/_geometry.py

@@ -88,7 +88,7 @@ def write_geometry(
                 self._write(_fmtm.format(moment[ia]))
 
     @sile_fh_open()
-    def read_lattice(self) -> Lattice:
+    def read_lattice(self) -> Lattice | None:
         """Reads supercell object from the file"""
         self.fh.seek(0)
 
@@ -98,7 +98,9 @@ def read_lattice(self) -> Lattice:
             if line.startswith("lattice_vector"):
                 cell.append([float(f) for f in line.split()[1:]])
 
-        return Lattice(cell)
+        if cell:
+            return Lattice(cell)
+        return None
 
     @sile_fh_open()
     @deprecate_argument(

src/sisl/io/fhiaims/tests/test_in.py

@@ -23,6 +23,23 @@ def test_in_simple(sisl_tmp, sisl_system):
     assert sisl_system.g.atoms.equal(g.atoms, R=False)
 
 
+def test_in_no_lattice(sisl_tmp, sisl_system):
+    # test when the input geometry does not have any lattice.
+    # In this case it shouldn't be used.
+    f = sisl_tmp("gr.in")
+    g = sisl_system.g
+    with open(f, "w") as fh:
+        for atom, xyz in zip(g.atoms, g.xyz):
+            fh.write(f"atom {xyz[0]} {xyz[1]} {xyz[2]} {atom.symbol}\n")
+
+    gr = inSileFHIaims(f).read_geometry()
+
+    # Assert they are the same
+    assert not np.allclose(gr.cell, g.cell)
+    assert np.allclose(gr.xyz, g.xyz)
+    assert gr.atoms.equal(g.atoms, R=False)
+
+
 def test_in_velocity(sisl_tmp, sisl_system):
     f = sisl_tmp("gr.in")
     g = sisl_system.g.copy()