From 7046c7493cfb051d7cd3b2f21f72268b9ecda3e9 Mon Sep 17 00:00:00 2001
From: Eric Sivonxay <esivonxay@lbl.gov>
Date: Tue, 3 Oct 2023 14:51:54 -0700
Subject: [PATCH] Fix case and add test

---
 src/NanoParticleTools/inputs/nanoparticle.py |  6 ++
 tests/inputs/test_nanoparticle.py            | 81 ++++++++++----------
 2 files changed, 47 insertions(+), 40 deletions(-)

diff --git a/src/NanoParticleTools/inputs/nanoparticle.py b/src/NanoParticleTools/inputs/nanoparticle.py
index 1bff167..f5dbdc3 100644
--- a/src/NanoParticleTools/inputs/nanoparticle.py
+++ b/src/NanoParticleTools/inputs/nanoparticle.py
@@ -384,6 +384,12 @@ def __init__(self,
                     site for site in constraint.get_host_structure().sites
                     if site.species_string in dopants_dict.keys()
                 ]
+
+                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
index a2bfae4..d79a0a1 100644
--- a/tests/inputs/test_nanoparticle.py
+++ b/tests/inputs/test_nanoparticle.py
@@ -1,31 +1,22 @@
 from NanoParticleTools.inputs.nanoparticle import (
-    SphericalConstraint,
-    PrismConstraint,
-    CubeConstraint,
-    DopedNanoparticle,
-    get_nayf4_structure,
-    get_wse2_structure
-)
+    SphericalConstraint, PrismConstraint, CubeConstraint, DopedNanoparticle,
+    get_nayf4_structure, get_wse2_structure)
 import numpy as np
 import pytest
 
 
 def test_spherical_constraint():
     constraint = SphericalConstraint(30)
-    points = [[30, 0, 0],
-              [0, 30, 0],
-              [0, 0, 30],
-              [0, 30, 30],
-              [30, 30, 30],
-              [17, 17, 17],
-              [18, 18, 18]]
+    points = [[30, 0, 0], [0, 30, 0], [0, 0, 30], [0, 30, 30], [30, 30, 30],
+              [17, 17, 17], [18, 18, 18]]
 
     assert constraint.get_host_structure() == get_nayf4_structure()
     assert constraint.radius == 30
     assert constraint.bounding_box() == [30, 30, 30]
 
-    assert np.all(constraint.sites_in_bounds(points) ==
-                  np.array([True, True, True, False, False, True, False]))
+    assert np.all(
+        constraint.sites_in_bounds(points) == np.array(
+            [True, True, True, False, False, True, False]))
 
     structure = get_wse2_structure()
     constraint = SphericalConstraint(20, structure)
@@ -34,31 +25,24 @@ def test_spherical_constraint():
 
 def test_prism_constraint():
     constraint = PrismConstraint(60, 60, 80)
-    points = [[30, 0, 0],
-              [0, 30, 0],
-              [0, 0, 40],
-              [0, 0, 41],
-              [31, 0, 0],
+    points = [[30, 0, 0], [0, 30, 0], [0, 0, 40], [0, 0, 41], [31, 0, 0],
               [30, 30, 40]]
     assert constraint.bounding_box() == [60, 60, 80]
 
-    assert np.all(constraint.sites_in_bounds(points) ==
-                  np.array([True, True, True, False, False, True]))
+    assert np.all(
+        constraint.sites_in_bounds(points) == np.array(
+            [True, True, True, False, False, True]))
 
 
 def test_cube_constraint():
     constraint = CubeConstraint(60)
-    points = [[30, 0, 0],
-              [0, 30, 0],
-              [0, 0, 30],
-              [0, 30, 30],
-              [30, 30, 30],
-              [31, 31, 31],
-              [0, 0, 31]]
+    points = [[30, 0, 0], [0, 30, 0], [0, 0, 30], [0, 30, 30], [30, 30, 30],
+              [31, 31, 31], [0, 0, 31]]
     assert constraint.bounding_box() == [60, 60, 60]
 
-    assert np.all(constraint.sites_in_bounds(points) ==
-                  np.array([True, True, True, True, True, False, False]))
+    assert np.all(
+        constraint.sites_in_bounds(points) == np.array(
+            [True, True, True, True, True, False, False]))
 
 
 def test_doped_nanoparticle():
@@ -79,6 +63,23 @@ def test_doped_nanoparticle():
     assert len(dnp.sites) == 56
 
 
+def test_nanoparticle_with_empty():
+    constraints = [
+        SphericalConstraint(40),
+        SphericalConstraint(85),
+        SphericalConstraint(102.5)
+    ]
+    dopant_specifications = [(0, 0.5, 'Yb', 'Y'), (0, 0.2, 'Er', 'Y'),
+                             (2, 0.5, 'Yb', 'Y'), (2, 0.1, 'Nd', 'Y')]
+
+    dnp = DopedNanoparticle(constraints,
+                            dopant_specifications,
+                            prune_hosts=True)
+    dnp.generate()
+    assert len(dnp.dopant_sites) == 18015
+    assert len(dnp.sites) == 39579
+
+
 def test_empty_nanoparticle():
     """
     All of these tests are expected to throw an error
@@ -120,11 +121,11 @@ def test_empty_nanoparticle():
 def test_get_nayf4_structure():
     struct = get_nayf4_structure()
 
-    assert ([str(el) for el in struct.species] ==
-            ['Na', 'Na', 'Na', 'Y', 'Y', 'Y', 'F', 'F', 'F',
-             'F', 'F', 'F', 'F', 'F', 'F', 'F', 'F', 'F'])
-    lattice = np.array([[6.067, 0.0, 0.0],
-                        [-3.0335, 5.25417612, 0.0],
+    assert ([str(el) for el in struct.species] == [
+        'Na', 'Na', 'Na', 'Y', 'Y', 'Y', 'F', 'F', 'F', 'F', 'F', 'F', 'F',
+        'F', 'F', 'F', 'F', 'F'
+    ])
+    lattice = np.array([[6.067, 0.0, 0.0], [-3.0335, 5.25417612, 0.0],
                         [0.0, 0.0, 7.103]])
     assert np.allclose(struct.lattice.matrix, lattice)
 
@@ -132,9 +133,9 @@ def test_get_nayf4_structure():
 def test_get_wse2_structure():
     struct = get_wse2_structure()
 
-    assert ([str(el) for el in struct.species] == ['Se', 'Se', 'Se', 'Se', 'W', 'W'])
+    assert ([str(el)
+             for el in struct.species] == ['Se', 'Se', 'Se', 'Se', 'W', 'W'])
 
-    lattice = np.array([[3.327, 0.0, 0],
-                        [-1.6635, 2.88126652, 0],
+    lattice = np.array([[3.327, 0.0, 0], [-1.6635, 2.88126652, 0],
                         [0.0, 0.0, 15.069]])
     assert np.allclose(struct.lattice.matrix, lattice)