Merge pull request #324 from duartegroup/v1.4.2

V1.4.2

Author: t-young31

README.md

@@ -94,3 +94,4 @@ If **autodE** is used in a publication please consider citing the [paper](https:
 - Domen Pregeljc ([@dpregeljc](https://github.com/dpregeljc))
 - Jonathon Vandezande ([@jevandezande](https://github.com/jevandezande))
 - Shoubhik Maiti ([@shoubhikraj](https://github.com/shoubhikraj))
+- Daniel Hollas ([@danielhollas](https://github.com/danielhollas))

autode/atoms.py

@@ -1041,9 +1041,10 @@ def angle(self, i: int, j: int, k: int) -> Angle:
                 f"least one zero vector"
             )
 
-        value = np.arccos(np.dot(vec1, vec2) / norms)
+        # Cos(theta) must lie within [-1, 1]
+        cos_value = np.clip(np.dot(vec1, vec2) / norms, a_min=-1, a_max=1)
 
-        return Angle(value)
+        return Angle(np.arccos(cos_value))
 
     def dihedral(self, w: int, x: int, y: int, z: int) -> Angle:
         r"""

autode/config.py

@@ -198,6 +198,9 @@ class ORCA:
         #
         # Path can be unset and will be assigned if it can be found in $PATH
         path = None
+        #
+        # File extensions to copy when a calculation completes
+        copied_output_exts = [".out", ".hess", ".xyz", ".inp", ".pc"]
 
         optts_block = (
             "\n%geom\n"

autode/mol_graphs.py

@@ -115,6 +115,15 @@ def node_matcher(self):
 
         return matcher
 
+    @property
+    def is_connected(self) -> bool:
+        """Is this graph fully connected (i.e. not separate parts)"""
+        return nx.is_connected(self)
+
+    def connected_components(self):
+        """Generate the separate connected components"""
+        return nx.connected_components(self)
+
 
 def make_graph(
     species: "Species",

autode/neb/original.py

@@ -3,7 +3,6 @@
 Henkelman and H. J ́onsson, J. Chem. Phys. 113, 9978 (2000)
 """
 import numpy as np
-import matplotlib.pyplot as plt
 
 from typing import Optional, Sequence, List, Any, TYPE_CHECKING, Union, Type
 from copy import deepcopy
@@ -361,6 +360,8 @@ def plot_energies(
         self, save=False, name="None", color=None, xlabel="NEB coordinate"
     ):
         """Plot the NEB surface"""
+        import matplotlib.pyplot as plt
+
         blues = plt.get_cmap("Blues")
 
         color = (
@@ -673,6 +674,8 @@ def calculate(
             etol_per_image: Energy tolerance per image to use in the L-BFGS-B
                             minimisation
         """
+        import matplotlib.pyplot as plt
+
         self.print_geometries(name=f"{name_prefix}neb_init")
 
         # Calculate energy on the first and final points as these will not be recalc-ed

autode/opt/coordinates/__init__.py

@@ -1,3 +1,3 @@
-from autode.opt.coordinates.base import OptCoordinates, CartesianComponent
+from autode.opt.coordinates.base import OptCoordinates
 from autode.opt.coordinates.cartesian import CartesianCoordinates
 from autode.opt.coordinates.dic import DIC, DICWithConstraints