Support promolecules with single atom (#135)

atomdb/promolecule.py

@@ -17,16 +17,16 @@
 
 from copy import deepcopy
 from itertools import chain, combinations
-from numbers import Integral
+from numbers import Integral, Number
 from operator import itemgetter
 from warnings import warn
 
 import numpy as np
 from scipy.optimize import linprog
 
-from atomdb.utils import DEFAULT_DATAPATH, DEFAULT_REMOTE, DEFAULT_DATASET, MULTIPLICITIES
 from atomdb.periodic import element_number, element_symbol
 from atomdb.species import load
+from atomdb.utils import DEFAULT_DATAPATH, DEFAULT_DATASET, DEFAULT_REMOTE, MULTIPLICITIES
 
 __all__ = [
     "Promolecule",
@@ -566,6 +566,10 @@ def make_promolecule(
         Promolecule instance.
 
     """
+    # Convert single coord [x, y, z] to list of coords [[x, y, z]]
+    coords = np.asarray(coords, dtype=float)
+    if coords.ndim == 1:
+        coords = coords.reshape(1, -1)
     # Check coordinate units
     if units is None or units.lower() == "bohr":
         coords = [coord / 1 for coord in coords]
@@ -574,13 +578,18 @@ def make_promolecule(
     else:
         raise ValueError(f"Invalid `units` parameter '{units}'; " "must be 'bohr' or 'angstrom'")
 
+    # Convert single atnum to list of atnums [atnum]
+    if isinstance(atnums, (Integral, str)):
+        atnums = [atnums]
     # Get atomic symbols/numbers from inputs
-    atoms = [element_symbol(atom) for atom in atnums]
     atnums = [element_number(atom) for atom in atnums]
+    atoms = [element_symbol(atom) for atom in atnums]
 
     # Handle default charge parameters
     if charges is None:
         charges = [0 for _ in atnums]
+    elif isinstance(charges, Number):
+        charges = [charges]
 
     # Handle default multiplicity parameters
     if mults is None:
@@ -590,6 +599,8 @@ def make_promolecule(
         else:
             # set each multiplicity to None
             mults = [None for _ in atnums]
+    elif isinstance(mults, Number):
+        mults = [mults]
 
     # Construct linear combination of species
     promol = Promolecule()

atomdb/test/test_promolecule.py

@@ -21,13 +21,12 @@
 #
 # --
 
-import pytest
-
 import os
+from numbers import Number
 
 import numpy as np
-
 import numpy.testing as npt
+import pytest
 
 from atomdb import make_promolecule
 
@@ -95,6 +94,16 @@
         },
         id="Be floating point charge/floating point mult",
     ),
+    pytest.param(
+        {
+            "atnums": 4,
+            "charges": 1.2,
+            "mults": 1.2,
+            "coords": np.asarray([0.0, 0.0, 0.0], dtype=float),
+            "dataset": "uhf_augccpvdz",
+        },
+        id="Be floating point charge/floating point mult",
+    ),
     pytest.param(
         {
             "atnums": [4],
@@ -167,6 +176,13 @@ def test_make_promolecule(case):
         remotepath=None,
     )
 
+    if isinstance(atnums, (Number, str)):
+        atnums = [atnums]
+    if isinstance(charges, Number):
+        charges = [charges]
+    if isinstance(mults, Number):
+        mults = [mults]
+
     # Check that coefficients add up to (# centers)
     npt.assert_allclose(sum(promol.coeffs), len(atnums))
 

website/requirements.txt

@@ -1,5 +1,5 @@
 jupyter-book
 sphinx
 matplotlib
-numpy>= 1.10
-scipy>=1.0, <=1.10.1
+numpy>=1.16
+scipy>=1.4