Implement writing of single step Structure

Also write scaling factor to POSCAR file

src/py4vasp/_data/structure.py

@@ -27,8 +27,8 @@ class _Format:
     def comment_line(self, topology, step_string):
         return f"{topology}{step_string}{self.newline}"
 
-    def scaling_factor(self):
-        return f"1.0{self.newline}"
+    def scaling_factor(self, scale):
+        return f"{self._element_to_string(scale)}{self.newline}".lstrip()
 
     def ion_list(self, topology):
         return f"{topology.to_POSCAR(self.newline)}{self.newline}"
@@ -98,10 +98,10 @@ def _repr_html_(self):
         return self._create_repr(format_)
 
     def _create_repr(self, format_=_Format()):
-        step = self._last_step_in_slice
+        step = self._get_last_step()
         lines = (
             format_.comment_line(self._topology(), self._step_string()),
-            format_.scaling_factor(),
+            format_.scaling_factor(self._raw_data.cell.scale),
             format_.vectors_to_table(self._raw_data.cell.lattice_vectors[step]),
             format_.ion_list(self._topology()),
             format_.coordinate_system(),
@@ -288,7 +288,7 @@ def _topology(self):
 
     def _lattice_vectors(self):
         lattice_vectors = _LatticeVectors(self._raw_data.cell.lattice_vectors)
-        return lattice_vectors[self._get_steps()]
+        return self._raw_data.cell.scale * lattice_vectors[self._get_steps()]
 
     def _positions(self):
         return self._raw_data.positions[self._get_steps()]
@@ -306,6 +306,9 @@ def _viewer_from_trajectory(self):
     def _get_steps(self):
         return self._steps if self._is_trajectory else ()
 
+    def _get_last_step(self):
+        return self._last_step_in_slice if self._is_trajectory else ()
+
     def _step_string(self):
         if self._is_slice:
             range_ = range(len(self._raw_data.positions))[self._steps]
@@ -315,6 +318,12 @@ def _step_string(self):
         else:
             return f" (step {self._steps + 1})"
 
+    def __getitem__(self, steps):
+        if not self._is_trajectory:
+            message = "The structure is not a Trajectory so accessing individual elements is not allowed."
+            raise exception.IncorrectUsage(message)
+        return super().__getitem__(steps)
+
     @property
     def _is_trajectory(self):
         return self._raw_data.positions.ndim == 3

tests/conftest.py

@@ -608,7 +608,7 @@ def _Sr2TiO4_cell():
         [-0.839055341042049, -0.367478859090843, 0.401180037874301],
     ]
     return raw.Cell(
-        lattice_vectors=scale * np.array(number_steps * [lattice_vectors]), scale=scale
+        lattice_vectors=np.array(number_steps * [lattice_vectors]), scale=scale
     )
 
 

tests/data/test_structure.py

@@ -12,10 +12,10 @@
 
 REF_POSCAR = """\
 Sr2TiO4
-1.0
-   6.9229000000000003    0.0000000000000000    0.0000000000000000
-   4.6945030167999979    5.0880434191000035    0.0000000000000000
-  -5.8086962205000017   -2.5440193935999971    2.7773292841999986
+6.9229000000000003
+   1.0000000000000000    0.0000000000000000    0.0000000000000000
+   0.6781122097386930    0.7349583872510080    0.0000000000000000
+  -0.8390553410420490   -0.3674788590908430    0.4011800378743010
 Sr Ti O
 2 1 4
 Direct
@@ -29,11 +29,11 @@
 
 REF_HTML = """\
 Sr2TiO4<br>
-1.0<br>
+6.9229000000000003<br>
 <table>
-<tr><td>   6.9229000000000003</td><td>   0.0000000000000000</td><td>   0.0000000000000000</td></tr>
-<tr><td>   4.6945030167999979</td><td>   5.0880434191000035</td><td>   0.0000000000000000</td></tr>
-<tr><td>  -5.8086962205000017</td><td>  -2.5440193935999971</td><td>   2.7773292841999986</td></tr>
+<tr><td>   1.0000000000000000</td><td>   0.0000000000000000</td><td>   0.0000000000000000</td></tr>
+<tr><td>   0.6781122097386930</td><td>   0.7349583872510080</td><td>   0.0000000000000000</td></tr>
+<tr><td>  -0.8390553410420490</td><td>  -0.3674788590908430</td><td>   0.4011800378743010</td></tr>
 </table>
 Sr Ti O<br>
 2 1 4<br>
@@ -48,6 +48,22 @@
 <tr><td>   0.0000000000000000</td><td>   0.5000000000000000</td><td>   0.5000000000000000</td></tr>
 </table>"""
 
+REF_Ca3AsBr3 = """Ca3AsBr3
+5.9299999999999997
+   1.0000000000000000    0.0000000000000000    0.0000000000000000
+   0.0000000000000000    1.0000000000000000    0.0000000000000000
+   0.0000000000000000    0.0000000000000000    1.0000000000000000
+Ca As Br Ca Br
+2 1 1 1 2
+Direct
+   0.5000000000000000    0.0000000000000000    0.0000000000000000
+   0.0000000000000000    0.5000000000000000    0.0000000000000000
+   0.0000000000000000    0.0000000000000000    0.0000000000000000
+   0.0000000000000000    0.5000000000000000    0.5000000000000000
+   0.0000000000000000    0.0000000000000000    0.5000000000000000
+   0.5000000000000000    0.0000000000000000    0.5000000000000000
+   0.5000000000000000    0.5000000000000000    0.0000000000000000"""
+
 
 @pytest.fixture
 def Sr2TiO4(raw_data):
@@ -67,7 +83,8 @@ def Ca3AsBr3(raw_data):
 def make_structure(raw_structure):
     structure = Structure.from_data(raw_structure)
     structure.ref = types.SimpleNamespace()
-    structure.ref.lattice_vectors = raw_structure.cell.lattice_vectors
+    cell = raw_structure.cell
+    structure.ref.lattice_vectors = cell.scale * cell.lattice_vectors
     structure.ref.positions = raw_structure.positions
     return structure
 
@@ -107,12 +124,13 @@ def test_read_Ca3AsBr3(Ca3AsBr3, Assert):
     assert actual["names"] == ["Ca_1", "Ca_2", "As_1", "Br_1", "Ca_3", "Br_2", "Br_3"]
 
 
-def test_to_poscar(Sr2TiO4):
+def test_to_poscar(Sr2TiO4, Ca3AsBr3):
     assert Sr2TiO4.to_POSCAR() == REF_POSCAR
     assert Sr2TiO4[0].to_POSCAR() == REF_POSCAR.replace("Sr2TiO4", "Sr2TiO4 (step 1)")
     for steps in (slice(None), slice(1, 3)):
         with pytest.raises(exception.NotImplemented):
             Sr2TiO4[steps].to_POSCAR()
+    assert Ca3AsBr3.to_POSCAR() == REF_Ca3AsBr3
 
 
 def test_from_poscar(Sr2TiO4, Assert, not_core):
@@ -303,11 +321,13 @@ def check_plot_structure(structure):
         cell.assert_called_once()
 
 
-def test_incorrect_step(Sr2TiO4):
+def test_incorrect_step(Sr2TiO4, Ca3AsBr3):
     with pytest.raises(exception.IncorrectUsage):
         Sr2TiO4[100].read()
     with pytest.raises(exception.IncorrectUsage):
         Sr2TiO4[[0, 1]].read()
+    with pytest.raises(exception.IncorrectUsage):
+        Ca3AsBr3[0]
 
 
 def test_print_final(Sr2TiO4, format_):
@@ -319,6 +339,7 @@ def test_print_specific(Sr2TiO4, format_):
     actual, _ = format_(Sr2TiO4[0])
     ref_plain = REF_POSCAR.replace("Sr2TiO4", "Sr2TiO4 (step 1)")
     ref_html = REF_HTML.replace("Sr2TiO4", "Sr2TiO4 (step 1)")
+    assert actual["text/plain"] == ref_plain
     assert actual == {"text/plain": ref_plain, "text/html": ref_html}
 
 
@@ -329,6 +350,11 @@ def test_print_trajectory(Sr2TiO4, format_):
     assert actual == {"text/plain": ref_plain, "text/html": ref_html}
 
 
+def test_print_Ca3AsBr3(Ca3AsBr3, format_):
+    actual, _ = format_(Ca3AsBr3)
+    assert actual["text/plain"] == REF_Ca3AsBr3
+
+
 def test_factory_methods(raw_data, check_factory_methods):
     data = raw_data.structure("Sr2TiO4")
     check_factory_methods(Structure, data)