Fix Vasprun not interpreting float overflow as nan (#3452)

* fix vasprun not interpreting float overflow as nan * add test * pre-commit auto-fixes * rename and cleanup test_float_overflow introduce artificial overflow in <varray name="forces"> in vasprun.xml.sc_overflow rm tests/files/vasprun.xml.force_overflow --------- Co-authored-by: Eric Taw <[email protected]> Co-authored-by: Janosh Riebesell <[email protected]>
materialsproject · Nov 8, 2023 · 52d6b8c · 52d6b8c
1 parent 9e27ca8
commit 52d6b8c
Show file tree

Hide file tree

Showing 4 changed files with 11 additions and 7 deletions.
diff --git a/pymatgen/io/vasp/outputs.py b/pymatgen/io/vasp/outputs.py
@@ -1301,7 +1301,7 @@ def _parse_chemical_shielding_calculation(self, elem):
 
     def _parse_calculation(self, elem):
         try:
-            istep = {i.attrib["name"]: float(i.text) for i in elem.find("energy").findall("i")}
+            istep = {i.attrib["name"]: _vasprun_float(i.text) for i in elem.find("energy").findall("i")}
         except AttributeError:  # not all calculations have an energy
             istep = {}
         esteps = []

diff --git a/tests/files/.pytest-split-durations b/tests/files/.pytest-split-durations
@@ -2169,7 +2169,7 @@
     "tests/io/vasp/test_outputs.py::TestVasprun::test_potcar_not_found": 0.1334625000017695,
     "tests/io/vasp/test_outputs.py::TestVasprun::test_projected_magnetisation": 4.4185712080216035,
     "tests/io/vasp/test_outputs.py::TestVasprun::test_runtype": 14.43198950093938,
-    "tests/io/vasp/test_outputs.py::TestVasprun::test_sc_step_overflow": 1.980604083975777,
+    "tests/io/vasp/test_outputs.py::TestVasprun::test_float_overflow": 1.980604083975777,
     "tests/io/vasp/test_outputs.py::TestVasprun::test_search_for_potcar": 0.2289056670269929,
     "tests/io/vasp/test_outputs.py::TestVasprun::test_selective_dynamics": 1.798271125066094,
     "tests/io/vasp/test_outputs.py::TestVasprun::test_smart_efermi": 2.6953831250430085,

diff --git a/tests/files/vasprun.xml.sc_overflow b/tests/files/vasprun.xml.sc_overflow
@@ -891,7 +891,7 @@
    </varray>
   </structure>
   <varray name="forces" >
-   <v>       0.41466569      -0.04234049       0.05092706 </v>
+   <v>       **********      -0.04234049       0.05092706 </v>
    <v>       0.23840217       0.09338135      -0.08187019 </v>
    <v>      -0.45497113       0.03109806      -0.23055151 </v>
    <v>      -0.41847023       0.03902084      -0.19336882 </v>

diff --git a/tests/io/vasp/test_outputs.py b/tests/io/vasp/test_outputs.py
@@ -578,13 +578,17 @@ def test_smart_efermi(self):
         smart_fermi = vrun.calculate_efermi()
         assert smart_fermi == approx(6.0165)
 
-    def test_sc_step_overflow(self):
+    def test_float_overflow(self):
+        # test we interpret VASP's *********** for overflowed values as NaNs
+        # https://github.com/materialsproject/pymatgen/pull/3452
         filepath = f"{TEST_FILES_DIR}/vasprun.xml.sc_overflow"
         with pytest.warns(UserWarning, match="Float overflow .* encountered in vasprun"):
             vasp_run = Vasprun(filepath)
-        vasp_run = Vasprun(filepath)
-        estep = vasp_run.ionic_steps[0]["electronic_steps"][29]
-        assert np.isnan(estep["e_wo_entrp"])
+        first_ionic_step = vasp_run.ionic_steps[0]
+        elec_step = first_ionic_step["electronic_steps"][29]
+        assert np.isnan(elec_step["e_wo_entrp"])
+        assert np.isnan(elec_step["e_fr_energy"])
+        assert np.isnan(first_ionic_step["forces"]).any()
 
     def test_update_potcar(self):
         filepath = f"{TEST_FILES_DIR}/vasprun.xml"