Fixes workshop (#58)

* Bump patch version number
* Read all scalar data
* Deal with missing data in dielectric tensor

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "py4vasp"
-version = "0.5.0"
+version = "0.5.1"
 description = "Tool for assisting with the analysis and setup of VASP calculations."
 authors = [
     "VASP Software GmbH <py4vasp@vasp.at>",

src/py4vasp/__init__.py

@@ -4,5 +4,5 @@
 from py4vasp._third_party.interactive import set_error_handling
 from py4vasp._third_party.graph import plot
 
-__version__ = "0.5.0"
+__version__ = "0.5.1"
 set_error_handling("Minimal")

src/py4vasp/data/dielectric_tensor.py

@@ -19,7 +19,7 @@ def to_dict(self):
         """
         return {
             "clamped_ion": self._raw_data.electron[:],
-            "relaxed_ion": self._raw_data.electron[:] + self._raw_data.ion[:],
+            "relaxed_ion": self._read_relaxed_ion(),
             "independent_particle": self._read_independent_particle(),
             "method": _convert.text_to_string(self._raw_data.method),
         }
@@ -35,14 +35,22 @@ def __str__(self):
 {_dielectric_tensor_string(data["relaxed_ion"], "relaxed-ion")}
 """.strip()
 
+    def _read_relaxed_ion(self):
+        if self._raw_data.ion.is_none():
+            return None
+        else:
+            return self._raw_data.electron[:] + self._raw_data.ion[:]
+
     def _read_independent_particle(self):
-        if self._raw_data.independent_particle is None:
+        if self._raw_data.independent_particle.is_none():
             return None
         else:
             return self._raw_data.independent_particle[:]
 
 
 def _dielectric_tensor_string(tensor, label):
+    if tensor is None:
+        return ""
     row_to_string = lambda row: 6 * " " + " ".join(f"{x:12.6f}" for x in row)
     rows = (row_to_string(row) for row in tensor)
     return f"{label:^55}".rstrip() + "\n" + "\n".join(rows)

src/py4vasp/raw/_access.py

@@ -131,13 +131,13 @@ def _get_dataset(self, h5f, key):
 
     def _parse_dataset(self, dataset):
         result = raw.VaspData(dataset)
-        if _scalar_string(result):
-            result = result.data
+        if _is_scalar(result):
+            result = result[()]
         return result
 
 
-def _scalar_string(data):
-    return not data.is_none() and data.ndim == 0 and data.dtype.type == np.str_
+def _is_scalar(data):
+    return not data.is_none() and data.ndim == 0
 
 
 def _error_message(quantity, source):

tests/conftest.py

@@ -88,7 +88,9 @@ def dielectric_function(selection):
 
     @staticmethod
     def dielectric_tensor(selection):
-        return _dielectric_tensor(selection)
+        method, with_ion = selection.split()
+        with_ion = with_ion == "with_ion"
+        return _dielectric_tensor(method, with_ion)
 
     @staticmethod
     def dos(selection):
@@ -243,13 +245,15 @@ def _ion_dielectric_function():
     )
 
 
-def _dielectric_tensor(method):
+def _dielectric_tensor(method, with_ion):
     shape = (3, axes, axes)
     data = np.arange(np.prod(shape)).reshape(shape)
+    ion = raw.VaspData(data[1] if with_ion else None)
+    independent_particle = raw.VaspData(data[2] if method in ("dft", "rpa") else None)
     return raw.DielectricTensor(
-        electron=data[0],
-        ion=data[1],
-        independent_particle=data[2] if method in ("dft", "rpa") else None,
+        electron=raw.VaspData(data[0]),
+        ion=ion,
+        independent_particle=independent_particle,
         method=method.encode(),
     )
 
@@ -373,7 +377,7 @@ def _single_band(projectors):
     eigenvalues = np.array([np.linspace([0], [1], len(kpoints.coordinates))])
     return raw.Band(
         dispersion=raw.Dispersion(kpoints, eigenvalues),
-        fermi_energy=_make_data(0.0),
+        fermi_energy=0.0,
         occupations=np.array([np.linspace([1], [0], len(kpoints.coordinates))]),
         projectors=_Sr2TiO4_projectors(use_orbitals=False),
     )
@@ -386,7 +390,7 @@ def _multiple_bands(projectors):
     use_orbitals = projectors == "with_projectors"
     raw_band = raw.Band(
         dispersion=raw.Dispersion(kpoints, eigenvalues),
-        fermi_energy=_make_data(0.5),
+        fermi_energy=0.5,
         occupations=np.arange(np.prod(shape)).reshape(shape),
         projectors=_Sr2TiO4_projectors(use_orbitals),
     )
@@ -403,7 +407,7 @@ def _line_band(labels):
     eigenvalues = np.arange(np.prod(shape)).reshape(shape)
     return raw.Band(
         dispersion=raw.Dispersion(kpoints, eigenvalues),
-        fermi_energy=_make_data(0.5),
+        fermi_energy=0.5,
         occupations=np.arange(np.prod(shape)).reshape(shape),
         projectors=_Sr2TiO4_projectors(use_orbitals=False),
     )
@@ -417,7 +421,7 @@ def _spin_polarized_bands(projectors):
     use_orbitals = projectors in ["with_projectors", "excess_orbitals"]
     raw_band = raw.Band(
         dispersion=raw.Dispersion(kpoints, eigenvalues),
-        fermi_energy=_make_data(0.0),
+        fermi_energy=0.0,
         occupations=np.arange(np.prod(shape)).reshape(shape),
         projectors=_Fe3O4_projectors(use_orbitals),
     )

tests/data/test_dielectric_tensor.py

@@ -7,32 +7,40 @@
 
 @pytest.fixture
 def dft_tensor(raw_data):
-    return make_reference(raw_data, "dft")
+    expected_description = "including local field effects in DFT"
+    return make_reference(raw_data, "dft with_ion", expected_description)
 
 
 @pytest.fixture
 def rpa_tensor(raw_data):
-    return make_reference(raw_data, "rpa")
+    expected_description = "including local field effects in RPA (Hartree)"
+    return make_reference(raw_data, "rpa without_ion", expected_description)
 
 
 @pytest.fixture
 def scf_tensor(raw_data):
-    return make_reference(raw_data, "scf")
+    expected_description = "including local field effects"
+    return make_reference(raw_data, "scf with_ion", expected_description)
 
 
 @pytest.fixture
 def nscf_tensor(raw_data):
-    return make_reference(raw_data, "nscf")
+    expected_description = "excluding local field effects"
+    return make_reference(raw_data, "nscf without_ion", expected_description)
 
 
-def make_reference(raw_data, method):
+def make_reference(raw_data, method, expected_description):
     raw_tensor = raw_data.dielectric_tensor(method)
     tensor = DielectricTensor.from_data(raw_tensor)
     tensor.ref = types.SimpleNamespace()
     tensor.ref.clamped_ion = raw_tensor.electron
-    tensor.ref.relaxed_ion = raw_tensor.ion + raw_tensor.electron
+    if raw_tensor.ion.is_none():
+        tensor.ref.relaxed_ion = None
+    else:
+        tensor.ref.relaxed_ion = raw_tensor.ion + raw_tensor.electron
     tensor.ref.independent_particle = raw_tensor.independent_particle
-    tensor.ref.method = method
+    tensor.ref.method = method.split()[0]
+    tensor.ref.expected_description = expected_description
     return tensor
 
 
@@ -64,45 +72,47 @@ def check_read_dielectric_tensor(dielectric_tensor, Assert):
 
 def test_print_dft_tensor(dft_tensor, format_):
     actual, _ = format_(dft_tensor)
-    expected_description = "including local field effects in DFT"
-    check_print_dielectric_tensor(actual, expected_description)
+    check_print_dielectric_tensor(actual, dft_tensor.ref)
 
 
 def test_print_rpa_tensor(rpa_tensor, format_):
     actual, _ = format_(rpa_tensor)
-    expected_description = "including local field effects in RPA (Hartree)"
-    check_print_dielectric_tensor(actual, expected_description)
+    check_print_dielectric_tensor(actual, rpa_tensor.ref)
 
 
 def test_print_scf_tensor(scf_tensor, format_):
     actual, _ = format_(scf_tensor)
-    expected_description = "including local field effects"
-    check_print_dielectric_tensor(actual, expected_description)
+    check_print_dielectric_tensor(actual, scf_tensor.ref)
 
 
 def test_print_dft_tensor(nscf_tensor, format_):
     actual, _ = format_(nscf_tensor)
-    expected_description = "excluding local field effects"
-    check_print_dielectric_tensor(actual, expected_description)
+    check_print_dielectric_tensor(actual, nscf_tensor.ref)
 
 
-def check_print_dielectric_tensor(actual, expected_description):
-    reference = f"""
+def check_print_dielectric_tensor(actual, reference):
+    if reference.relaxed_ion is None:
+        relaxed_ion = ""
+    else:
+        relaxed_ion = """\
+                      relaxed-ion
+          9.000000    11.000000    13.000000
+         15.000000    17.000000    19.000000
+         21.000000    23.000000    25.000000
+"""
+    expected = f"""
 Macroscopic static dielectric tensor (dimensionless)
-  {expected_description}
+  {reference.expected_description}
 ------------------------------------------------------
                       clamped-ion
           0.000000     1.000000     2.000000
           3.000000     4.000000     5.000000
           6.000000     7.000000     8.000000
-                      relaxed-ion
-          9.000000    11.000000    13.000000
-         15.000000    17.000000    19.000000
-         21.000000    23.000000    25.000000
+{relaxed_ion}
 """.strip()
-    assert actual == {"text/plain": reference}
+    assert actual == {"text/plain": expected}
 
 
 def test_factory_methods(raw_data, check_factory_methods):
-    data = raw_data.dielectric_tensor("dft")
+    data = raw_data.dielectric_tensor("dft with_ion")
     check_factory_methods(DielectricTensor, data)