Improve Keep Redundant Spaces algorithm for PatchedPhaseDiagram (mate…

…rialsproject#3900)

* fix: old algorithm to deduplicate spaces didn't find the minimum subset

* test: direct test for remove_redundant_spaces static method

* doc: clean up old comments, add details explaining why patchedphasediagram as_dict doesn't save computations due to shared memory id issue.

* pre-commit auto-fixes

* lint: spelling

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/pymatgen/analysis/phase_diagram.py

@@ -903,7 +903,6 @@ def get_decomp_and_phase_separation_energy(
             }
 
             # NOTE calling PhaseDiagram is only reasonable if the composition has fewer than 5 elements
-            # TODO can we call PatchedPhaseDiagram here?
             inner_hull = PhaseDiagram(reduced_space)
 
             competing_entries = inner_hull.stable_entries | {*self._get_stable_entries_in_space(entry_elems)}
@@ -1036,8 +1035,6 @@ def get_critical_compositions(self, comp1, comp2):
         if np.all(c1 == c2):
             return [comp1.copy(), comp2.copy()]
 
-        # NOTE made into method to facilitate inheritance of this method
-        # in PatchedPhaseDiagram if approximate solution can be found.
         intersections = self._get_simplex_intersections(c1, c2)
 
         # find position along line
@@ -1619,29 +1616,21 @@ def __init__(
         # Add the elemental references
         inds.extend([min_entries.index(el) for el in el_refs.values()])
 
-        self.qhull_entries = tuple(min_entries[idx] for idx in inds)
+        qhull_entries = tuple(min_entries[idx] for idx in inds)
         # make qhull spaces frozensets since they become keys to self.pds dict and frozensets are hashable
         # prevent repeating elements in chemical space and avoid the ordering problem (i.e. Fe-O == O-Fe automatically)
-        self._qhull_spaces = tuple(frozenset(entry.elements) for entry in self.qhull_entries)
+        qhull_spaces = tuple(frozenset(entry.elements) for entry in qhull_entries)
 
         # Get all unique chemical spaces
-        spaces = {s for s in self._qhull_spaces if len(s) > 1}
+        spaces = {s for s in qhull_spaces if len(s) > 1}
 
         # Remove redundant chemical spaces
-        if not keep_all_spaces and len(spaces) > 1:
-            max_size = max(len(s) for s in spaces)
-
-            systems = set()
-            # NOTE reduce the number of comparisons by only comparing to larger sets
-            for idx in range(2, max_size + 1):
-                test = (s for s in spaces if len(s) == idx)
-                refer = (s for s in spaces if len(s) > idx)
-                systems |= {t for t in test if not any(t.issubset(r) for r in refer)}
-
-            spaces = systems
+        spaces = self.remove_redundant_spaces(spaces, keep_all_spaces)
 
         # TODO comprhys: refactor to have self._compute method to allow serialization
-        self.spaces = sorted(spaces, key=len, reverse=False)  # Calculate pds for smaller dimension spaces first
+        self.spaces = sorted(spaces, key=len, reverse=True)  # Calculate pds for smaller dimension spaces last
+        self.qhull_entries = qhull_entries
+        self._qhull_spaces = qhull_spaces
         self.pds = dict(self._get_pd_patch_for_space(s) for s in tqdm(self.spaces, disable=not verbose))
         self.all_entries = all_entries
         self.el_refs = el_refs
@@ -1675,7 +1664,19 @@ def __contains__(self, item: frozenset[Element]) -> bool:
         return item in self.pds
 
     def as_dict(self) -> dict[str, Any]:
-        """
+        """Write the entries and elements used to construct the PatchedPhaseDiagram
+        to a dictionary.
+
+        NOTE unlike PhaseDiagram the computation involved in constructing the
+        PatchedPhaseDiagram is not saved on serialisation. This is done because
+        hierarchically calling the `PhaseDiagram.as_dict()` method would break the
+        link in memory between entries in overlapping patches leading to a
+        ballooning of the amount of memory used.
+
+        NOTE For memory efficiency the best way to store patched phase diagrams is
+        via pickling. As this allows all the entries in overlapping patches to share
+        the same id in memory when unpickling.
+
         Returns:
             dict[str, Any]: MSONable dictionary representation of PatchedPhaseDiagram.
         """
@@ -1688,7 +1689,18 @@ def as_dict(self) -> dict[str, Any]:
 
     @classmethod
     def from_dict(cls, dct: dict) -> Self:
-        """
+        """Reconstruct PatchedPhaseDiagram from dictionary serialisation.
+
+        NOTE unlike PhaseDiagram the computation involved in constructing the
+        PatchedPhaseDiagram is not saved on serialisation. This is done because
+        hierarchically calling the `PhaseDiagram.as_dict()` method would break the
+        link in memory between entries in overlapping patches leading to a
+        ballooning of the amount of memory used.
+
+        NOTE For memory efficiency the best way to store patched phase diagrams is
+        via pickling. As this allows all the entries in overlapping patches to share
+        the same id in memory when unpickling.
+
         Args:
             dct (dict): dictionary representation of PatchedPhaseDiagram.
 
@@ -1699,9 +1711,23 @@ def from_dict(cls, dct: dict) -> Self:
         elements = [Element.from_dict(elem) for elem in dct["elements"]]
         return cls(entries, elements)
 
+    @staticmethod
+    def remove_redundant_spaces(spaces, keep_all_spaces=False):
+        if keep_all_spaces or len(spaces) <= 1:
+            return spaces
+
+        # Sort spaces by size in descending order and pre-compute lengths
+        sorted_spaces = sorted(spaces, key=len, reverse=True)
+
+        result = []
+        for i, space_i in enumerate(sorted_spaces):
+            if not any(space_i.issubset(larger_space) for larger_space in sorted_spaces[:i]):
+                result.append(space_i)
+
+        return result
+
     # NOTE following methods are inherited unchanged from PhaseDiagram:
     # __repr__,
-    # as_dict,
     # all_entries_hulldata,
     # unstable_entries,
     # stable_entries,
@@ -1771,8 +1797,6 @@ def get_equilibrium_reaction_energy(self, entry: Entry) -> float:
         """
         return self.get_phase_separation_energy(entry, stable_only=True)
 
-    # NOTE the following functions are not implemented for PatchedPhaseDiagram
-
     def get_decomp_and_e_above_hull(
         self,
         entry: PDEntry,
@@ -1787,6 +1811,20 @@ def get_decomp_and_e_above_hull(
             entry=entry, allow_negative=allow_negative, check_stable=check_stable, on_error=on_error
         )
 
+    def _get_pd_patch_for_space(self, space: frozenset[Element]) -> tuple[frozenset[Element], PhaseDiagram]:
+        """
+        Args:
+            space (frozenset[Element]): chemical space of the form A-B-X.
+
+        Returns:
+            space, PhaseDiagram for the given chemical space
+        """
+        space_entries = [e for e, s in zip(self.qhull_entries, self._qhull_spaces) if space.issuperset(s)]
+
+        return space, PhaseDiagram(space_entries)
+
+    # NOTE the following functions are not implemented for PatchedPhaseDiagram
+
     def _get_facet_and_simplex(self):
         """Not Implemented - See PhaseDiagram."""
         raise NotImplementedError("_get_facet_and_simplex() not implemented for PatchedPhaseDiagram")
@@ -1835,18 +1873,6 @@ def get_chempot_range_stability_phase(self):
         """Not Implemented - See PhaseDiagram."""
         raise NotImplementedError("get_chempot_range_stability_phase() not implemented for PatchedPhaseDiagram")
 
-    def _get_pd_patch_for_space(self, space: frozenset[Element]) -> tuple[frozenset[Element], PhaseDiagram]:
-        """
-        Args:
-            space (frozenset[Element]): chemical space of the form A-B-X.
-
-        Returns:
-            space, PhaseDiagram for the given chemical space
-        """
-        space_entries = [e for e, s in zip(self.qhull_entries, self._qhull_spaces) if space.issuperset(s)]
-
-        return space, PhaseDiagram(space_entries)
-
 
 class ReactionDiagram:
     """

tests/analysis/test_phase_diagram.py

@@ -3,6 +3,7 @@
 import collections
 import unittest
 import unittest.mock
+from itertools import combinations
 from numbers import Number
 from unittest import TestCase
 
@@ -709,6 +710,7 @@ def setUp(self):
 
         self.pd = PhaseDiagram(entries=self.entries)
         self.ppd = PatchedPhaseDiagram(entries=self.entries)
+        self.ppd_all = PatchedPhaseDiagram(entries=self.entries, keep_all_spaces=True)
 
         # novel entries not in any of the patches
         self.novel_comps = [Composition("H5C2OP"), Composition("V2PH4C")]
@@ -756,7 +758,11 @@ def test_dimensionality(self):
 
         # test dims of sub PDs
         dim_counts = collections.Counter(pd.dim for pd in self.ppd.pds.values())
-        assert dim_counts == {3: 7, 2: 6, 4: 2}
+        assert dim_counts == {4: 2, 3: 2}
+
+        # test dims of sub PDs
+        dim_counts = collections.Counter(pd.dim for pd in self.ppd_all.pds.values())
+        assert dim_counts == {2: 8, 3: 7, 4: 2}
 
     def test_get_hull_energy(self):
         for comp in self.novel_comps:
@@ -772,7 +778,7 @@ def test_get_decomp_and_e_above_hull(self):
             assert np.isclose(e_above_hull_pd, e_above_hull_ppd)
 
     def test_repr(self):
-        assert repr(self.ppd) == str(self.ppd) == "PatchedPhaseDiagram covering 15 sub-spaces"
+        assert repr(self.ppd) == str(self.ppd) == "PatchedPhaseDiagram covering 4 sub-spaces"
 
     def test_as_from_dict(self):
         ppd_dict = self.ppd.as_dict()
@@ -810,7 +816,8 @@ def test_getitem(self):
         pd = self.ppd[chem_space]
         assert isinstance(pd, PhaseDiagram)
         assert chem_space in pd._qhull_spaces
-        assert str(pd) == "V-C phase diagram\n4 stable phases: \nC, V, V6C5, V2C"
+        assert len(str(pd)) == 186
+        assert str(pd).startswith("V-H-C-O phase diagram\n25 stable phases:")
 
         with pytest.raises(KeyError, match="frozenset"):
             self.ppd[frozenset(map(Element, "HBCNOFPS"))]
@@ -830,6 +837,19 @@ def test_setitem_and_delitem(self):
         assert self.ppd[unlikely_chem_space] == self.pd
         del self.ppd[unlikely_chem_space]  # test __delitem__() and restore original state
 
+    def test_remove_redundant_spaces(self):
+        spaces = tuple(frozenset(entry.elements) for entry in self.ppd.qhull_entries)
+        # NOTE this is 5 not 4 as "He" is a non redundant space that gets dropped for other reasons
+        assert len(self.ppd.remove_redundant_spaces(spaces)) == 5
+
+        test = (
+            list(combinations(range(1, 7), 4))
+            + list(combinations(range(1, 10), 2))
+            + list(combinations([1, 4, 7, 9, 2], 5))
+        )
+        test = [frozenset(t) for t in test]
+        assert len(self.ppd.remove_redundant_spaces(test)) == 30
+
 
 class TestReactionDiagram(TestCase):
     def setUp(self):