Add bug.py

examples/bug.py

@@ -0,0 +1,32 @@
+import os
+from ase.io import read
+import mala
+from mala.datahandling.data_repo import data_repo_path
+data_path = os.path.join(data_repo_path, "Be2")
+
+# Trigger LAMMPS by performing inference on an atomic snapshot.
+parameters, network, data_handler, predictor = mala.Predictor.\
+    load_run("be_model", path="basic")
+atoms = read(os.path.join(data_path, "Be_snapshot3.out"))
+ldos = predictor.predict_for_atoms(atoms)
+ldos_calculator: mala.LDOS = predictor.target_calculator
+ldos_calculator.read_from_array(ldos)
+
+# Test OpenPMD.
+params = mala.Parameters()
+ldos_calculator = mala.LDOS. \
+    from_numpy_file(params,
+                    os.path.join(data_path,
+                                 "Be_snapshot1.out.npy"))
+ldos_calculator. \
+    read_additional_calculation_data(os.path.join(data_path,
+                                                  "Be_snapshot1.out"),
+                                     "espresso-out")
+
+# Write and then read in via OpenPMD and make sure all the info is
+# retained.
+# for key, val in os.environ.items():
+#     print("\t{}:{}".format(key, val))
+ldos_calculator.write_to_openpmd_file("test_openpmd.bp4",
+                                      ldos_calculator.
+                                      local_density_of_states)