Fixed wrong imports

Author: RandomDefaultUser

test/align_ldos_test.py

@@ -3,7 +3,10 @@
 import numpy as np
 
 import mala
-from mala.datahandling.data_repo import data_path_be
+from mala.datahandling.data_repo import data_path_be, data_path_bao
+
+accuracy_band_energy = 1
+accuracy_strict = 1e-16
 
 
 class TestSplitting:
@@ -96,9 +99,9 @@ def test_ldos_alignment(self):
         # initialize and add snapshots to workflow
         ldos_aligner = mala.LDOSAligner(parameters)
         ldos_aligner.clear_data()
-        ldos_aligner.add_snapshot("Be_snapshot0.out.npy", data_path)
-        ldos_aligner.add_snapshot("Be_snapshot1.out.npy", data_path)
-        ldos_aligner.add_snapshot("Be_snapshot2.out.npy", data_path)
+        ldos_aligner.add_snapshot("Be_snapshot0.out.npy", data_path_be)
+        ldos_aligner.add_snapshot("Be_snapshot1.out.npy", data_path_be)
+        ldos_aligner.add_snapshot("Be_snapshot2.out.npy", data_path_be)
 
         # align and cut the snapshots from the left and right-hand sides
         ldos_aligner.align_ldos_to_ref(
@@ -107,6 +110,7 @@ def test_ldos_alignment(self):
 
         try:
             import openpmd_api
+
             use_openpmd = True
         except ImportError:
             use_openpmd = False
@@ -115,24 +119,95 @@ def test_ldos_alignment(self):
             # initialize and add snapshots to workflow
             ldos_aligner = mala.LDOSAligner(parameters)
             ldos_aligner.clear_data()
-            ldos_aligner.add_snapshot("Be_snapshot0.out.h5",
-                                      data_path, snapshot_type='openpmd')
-            ldos_aligner.add_snapshot("Be_snapshot1.out.h5",
-                                      data_path, snapshot_type='openpmd')
-            ldos_aligner.add_snapshot("Be_snapshot2.out.h5",
-                                      data_path, snapshot_type='openpmd')
+            ldos_aligner.add_snapshot(
+                "Be_snapshot0.out.h5", data_path_be, snapshot_type="openpmd"
+            )
+            ldos_aligner.add_snapshot(
+                "Be_snapshot1.out.h5", data_path_be, snapshot_type="openpmd"
+            )
+            ldos_aligner.add_snapshot(
+                "Be_snapshot2.out.h5", data_path_be, snapshot_type="openpmd"
+            )
 
             # align and cut the snapshots from the left and right-hand sides
             ldos_aligner.align_ldos_to_ref(
-                left_truncate=True, right_truncate_value=11, number_of_electrons=4
+                left_truncate=True,
+                right_truncate_value=11,
+                number_of_electrons=4,
             )
 
             parameters = mala.Parameters()
             data_handler = mala.DataHandler(parameters)
             for i in range(1, 4):
-                data_openpmd = data_handler.target_calculator.read_from_openpmd_file(
-                    f"{data_path}/aligned/Be_snapshot0.out.h5")
-                data_numpy = data_handler.target_calculator.read_from_numpy_file(
-                    f"{data_path}/aligned/Be_snapshot0.out.npy")
+                data_openpmd = (
+                    data_handler.target_calculator.read_from_openpmd_file(
+                        f"{data_path_be}/aligned/Be_snapshot0.out.h5"
+                    )
+                )
+                data_numpy = (
+                    data_handler.target_calculator.read_from_numpy_file(
+                        f"{data_path_be}/aligned/Be_snapshot0.out.npy"
+                    )
+                )
                 if not np.allclose(data_numpy, data_openpmd):
                     raise Exception("Inconsistency in snapshot", i)
+
+    def test_ldos_splitting_multiple_elements(self):
+        """
+        Test that the LDOS splitting works both on LDOS and DOS level.
+
+        We compute the band energy with splitted and unsplitted DOS and
+        compare both to splitted LDOS band energy.
+        """
+        params = mala.Parameters()
+
+        params.targets.ldos_gridsize = [12, 13, 14, 28]
+        params.targets.ldos_gridspacing_ev = [0.5, 0.5, 0.5, 0.5]
+        params.targets.ldos_gridoffset_ev = [-19, -10.5, -4.5, 3.5]
+        params.targets.pseudopotential_path = "."
+
+        dos_calculator = mala.DOS(params)
+        dos_calculator.read_additional_calculation_data(
+            os.path.join(data_path_bao, "BaO_snapshot0.out")
+        )
+        dos_calculator.read_from_qe_out(
+            os.path.join(data_path_bao, "BaO_snapshot0.out"),
+            smearing_factor=[2, 2, 2, 2],
+        )
+
+        params2 = mala.Parameters()
+        params2.targets.ldos_gridsize = 73
+        params2.targets.ldos_gridspacing_ev = 0.5
+        params2.targets.ldos_gridoffset_ev = -19
+        params2.targets.pseudopotential_path = "."
+        dos_calculator_unsplitted = mala.DOS(params2)
+        dos_calculator_unsplitted.read_additional_calculation_data(
+            os.path.join(data_path_bao, "BaO_snapshot0.out")
+        )
+
+        dos_calculator_unsplitted.read_from_qe_out(
+            os.path.join(data_path_bao, "BaO_snapshot0.out"),
+            smearing_factor=2,
+        )
+
+        params3 = mala.Parameters()
+        params3.targets.ldos_gridsize = [12, 13, 14, 28]
+        params3.targets.ldos_gridspacing_ev = [0.5, 0.5, 0.5, 0.5]
+        params3.targets.ldos_gridoffset_ev = [-19, -10.5, -4.5, 3.5]
+
+        ldos_calculator = mala.LDOS.from_numpy_file(
+            params3, os.path.join(data_path_bao, "BaO_snapshot0.out.npy")
+        )
+        ldos_calculator.read_additional_calculation_data(
+            os.path.join(data_path_bao, "BaO_snapshot0.info.json")
+        )
+        assert np.isclose(
+            dos_calculator.band_energy,
+            ldos_calculator.band_energy,
+            atol=accuracy_strict,
+        )
+        assert np.isclose(
+            dos_calculator.band_energy,
+            dos_calculator_unsplitted.band_energy,
+            atol=accuracy_band_energy,
+        )

test/workflow_test.py

@@ -120,6 +120,13 @@ def test_preprocessing(self):
             "correct_output_shape": (48, 48, 48, 64),
         }
 
+        # Multiple elements only work with LAMMPS.
+        systems = (
+            ["Be", "BaO"]
+            if importlib.util.find_spec("lammps") is not None
+            else ["Be"]
+        )
+
         for system in ["Be", "BaO"]:
             configuration = (
                 configuration_be if system == "Be" else configuration_bao
@@ -314,66 +321,6 @@ def test_postprocessing_from_dos(self):
             atol=accuracy_band_energy,
         )
 
-    def test_ldos_splitting(self):
-        """
-        Test that the LDOS splitting works both on LDOS and DOS level.
-
-        We compute the band energy with splitted and unsplitted DOS and
-        compare both to splitted LDOS band energy.
-        """
-        params = mala.Parameters()
-
-        params.targets.ldos_gridsize = [12, 13, 14, 28]
-        params.targets.ldos_gridspacing_ev = [0.5, 0.5, 0.5, 0.5]
-        params.targets.ldos_gridoffset_ev = [-19, -10.5, -4.5, 3.5]
-        params.targets.pseudopotential_path = "."
-
-        dos_calculator = mala.DOS(params)
-        dos_calculator.read_additional_calculation_data(
-            os.path.join(data_path_bao, "BaO_snapshot0.out")
-        )
-        dos_calculator.read_from_qe_out(
-            os.path.join(data_path_bao, "BaO_snapshot0.out"),
-            smearing_factor=[2, 2, 2, 2],
-        )
-
-        params2 = mala.Parameters()
-        params2.targets.ldos_gridsize = 73
-        params2.targets.ldos_gridspacing_ev = 0.5
-        params2.targets.ldos_gridoffset_ev = -19
-        params2.targets.pseudopotential_path = "."
-        dos_calculator_unsplitted = mala.DOS(params2)
-        dos_calculator_unsplitted.read_additional_calculation_data(
-            os.path.join(data_path_bao, "BaO_snapshot0.out")
-        )
-
-        dos_calculator_unsplitted.read_from_qe_out(
-            os.path.join(data_path_bao, "BaO_snapshot0.out"),
-            smearing_factor=2,
-        )
-
-        params3 = mala.Parameters()
-        params3.targets.ldos_gridsize = [12, 13, 14, 28]
-        params3.targets.ldos_gridspacing_ev = [0.5, 0.5, 0.5, 0.5]
-        params3.targets.ldos_gridoffset_ev = [-19, -10.5, -4.5, 3.5]
-
-        ldos_calculator = mala.LDOS.from_numpy_file(
-            params3, os.path.join(data_path_bao, "BaO_snapshot0.out.npy")
-        )
-        ldos_calculator.read_additional_calculation_data(
-            os.path.join(data_path_bao, "BaO_snapshot0.info.json")
-        )
-        assert np.isclose(
-            dos_calculator.band_energy,
-            ldos_calculator.band_energy,
-            atol=accuracy_strict,
-        )
-        assert np.isclose(
-            dos_calculator.band_energy,
-            dos_calculator_unsplitted.band_energy,
-            atol=accuracy_band_energy,
-        )
-
     def test_postprocessing(self):
         """
         Test whether MALA can postprocess data (from LDOS)
@@ -671,13 +618,13 @@ def test_predictions(self):
 
     def test_model_copying(self):
         parameters, network, data_handler, tester = mala.Tester.load_run(
-            "Be_model", path=data_path
+            "Be_model", path=data_path_be
         )
         data_handler.add_snapshot(
             "Be_snapshot3.in.npy",
-            data_path,
+            data_path_be,
             "Be_snapshot3.out.npy",
-            data_path,
+            data_path_be,
             "te",
         )
         parameters.manual_seed = 123456252
@@ -686,7 +633,7 @@ def test_model_copying(self):
         actual_ldos, predicted_ldos = tester.predict_targets(0)
         ldos_calculator = data_handler.target_calculator
         ldos_calculator.read_additional_calculation_data(
-            os.path.join(data_path, "Be_snapshot3.out"), "espresso-out"
+            os.path.join(data_path_be, "Be_snapshot3.out"), "espresso-out"
         )
         band_energy_1 = ldos_calculator.get_band_energy(predicted_ldos)
 
@@ -696,7 +643,7 @@ def test_model_copying(self):
         actual_ldos, predicted_ldos = tester.predict_targets(0)
         ldos_calculator = data_handler.target_calculator
         ldos_calculator.read_additional_calculation_data(
-            os.path.join(data_path, "Be_snapshot3.out"), "espresso-out"
+            os.path.join(data_path_be, "Be_snapshot3.out"), "espresso-out"
         )
         band_energy_2 = ldos_calculator.get_band_energy(predicted_ldos)
         print(