Massive speed up of extract cluster.

materialsproject · Nov 30, 2017 · d95488e · d95488e
1 parent d412dcf
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diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,6 +1,13 @@
 Change log
 ==========
 
+v2017.11.30
+-----------
+* Fix for severe enumlib_caller bug. This causes enumerations not to be carried
+  out properly due to bad accounting of symmetry of ordered sites. It results
+  in too few orderings.
+* New method to extract clusters of atoms from a Molecule based on bonds.
+
 v2017.11.27
 -----------
 * Improvements to FEFF

diff --git a/pymatgen/core/structure.py b/pymatgen/core/structure.py
@@ -2227,15 +2227,19 @@ def extract_cluster(self, target_sites, **kwargs):
             (Molecule) Cluster of atoms.
         """
         cluster = list(target_sites)
+        others = [site for site in self if site not in cluster]
         size = 0
         while len(cluster) > size:
             size = len(cluster)
-            for site in self:
-                if site not in cluster:
-                    for site2 in cluster:
-                        if CovalentBond.is_bonded(site, site2, **kwargs):
-                            cluster.append(site)
-                            break
+            new_others = []
+            for site in others:
+                for site2 in cluster:
+                    if CovalentBond.is_bonded(site, site2, **kwargs):
+                        cluster.append(site)
+                        break
+                else:
+                    new_others.append(site)
+            others = new_others
         return Molecule.from_sites(cluster)