Merge pull request mala-project#574 from timcallow/ldos_align

Align LDOS vectors to a reference

examples/advanced/ex09_align_ldos.py

@@ -0,0 +1,32 @@
+import os
+
+import mala
+
+from mala.datahandling.data_repo import data_path
+
+"""
+Shows how to align the energy spaces of different LDOS vectors to a reference.
+This is useful when the band energy spectrum starts at different values, e.g.
+when MALA is trained for snapshots of different mass densities.
+
+Note that this example is only a proof-of-principle, because the alignment
+algorithm has no effect on the Be test snapshots (apart from truncation).
+"""
+
+
+parameters = mala.Parameters()
+parameters.targets.ldos_gridoffset_ev = -5
+parameters.targets.ldos_gridsize = 11
+parameters.targets.ldos_gridspacing_ev = 2.5
+
+# 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)
+
+# 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
+)

mala/__init__.py

@@ -26,6 +26,7 @@
     DataConverter,
     Snapshot,
     DataShuffler,
+    LDOSAligner,
 )
 from .network import (
     Network,

mala/datahandling/__init__.py

@@ -5,3 +5,4 @@
 from .data_converter import DataConverter
 from .snapshot import Snapshot
 from .data_shuffler import DataShuffler
+from .ldos_aligner import LDOSAligner