Fix concentrations in nanoparticle generation

BlauGroup · Oct 4, 2023 · 7f8a428 · 7f8a428
1 parent 7046c74
commit 7f8a428
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Showing 2 changed files with 10 additions and 10 deletions.
diff --git a/src/NanoParticleTools/inputs/nanoparticle.py b/src/NanoParticleTools/inputs/nanoparticle.py
@@ -378,18 +378,15 @@ def __init__(self,
                              'The result will be zero intensity for everything')
 
         if prune_hosts:
-            for dopants_dict, constraint in zip(conc_by_layer_and_species,
-                                                constraints):
+            replaced_els = []
+            for dopants_dict in conc_by_layer_and_species:
+                replaced_els.extend(list(dopants_dict.keys()))
+            replaced_els = list(set(replaced_els))
+            for constraint in constraints:
                 _sites = [
                     site for site in constraint.get_host_structure().sites
-                    if site.species_string in dopants_dict.keys()
+                    if site.species_string in replaced_els
                 ]
-
-                if len(_sites) == 0:
-                    # Need at least one site for a valid pymatgen structure.
-                    # Just keep the first site from the host structure
-                    _sites = [constraint.get_host_structure().sites[0]]
-
                 constraint.host_structure = Structure.from_sites(_sites)
 
         self._sites = None

diff --git a/tests/inputs/test_nanoparticle.py b/tests/inputs/test_nanoparticle.py
@@ -77,7 +77,10 @@ def test_nanoparticle_with_empty():
                             prune_hosts=True)
     dnp.generate()
     assert len(dnp.dopant_sites) == 18015
-    assert len(dnp.sites) == 39579
+    assert len(dnp.sites) == 59790
+    assert dnp.dopant_concentrations()['Yb'] == 0.24609466465964208
+    assert dnp.dopant_concentrations()['Er'] == 0.011975246696772036
+    assert dnp.dopant_concentrations()['Nd'] == 0.04323465462451915
 
 
 def test_empty_nanoparticle():