Merge pull request #546 from pyiron/vasp_vol

Store VASP volumes as numpy arrays

pyiron_atomistics/vasp/base.py

@@ -2075,9 +2075,7 @@ def collect(self, directory=os.getcwd(), sorted_indices=None):
         if vasprun_working:
             log_dict["forces"] = self.vp_new.vasprun_dict["forces"]
             log_dict["cells"] = self.vp_new.vasprun_dict["cells"]
-            log_dict["volume"] = [
-                np.linalg.det(cell) for cell in self.vp_new.vasprun_dict["cells"]
-            ]
+            log_dict["volume"] = np.linalg.det(self.vp_new.vasprun_dict["cells"])
             # log_dict["total_energies"] = self.vp_new.vasprun_dict["total_energies"]
             log_dict["energy_tot"] = self.vp_new.vasprun_dict["total_energies"]
             if "kinetic_energies" in self.vp_new.vasprun_dict.keys():

tests/vasp/test_vasp_import.py

@@ -98,6 +98,11 @@ def test_output(self):
         ham = self.project.inspect("full_job_sample")
         self.assertEqual(ham["output/generic/dft/energy_free"][-1], -17.7379867884)
         self.assertIsInstance(ham["output/charge_density"].to_object(), VaspVolumetricData)
+        with ham.project_hdf5.open("output/generic") as h_gen:
+            for node in h_gen.list_nodes():
+                if h_gen[node] is not None:
+                    self.assertIsInstance(h_gen[node], np.ndarray,
+                                          f"output/generic/{node} is not stored as a numpy array")
 
 
 if __name__ == "__main__":