Dev (#119)

* minor updates

* cover

* first pass at x-rich (#118)

pymatgen/analysis/defects/thermo.py

@@ -15,7 +15,7 @@
 from pymatgen.analysis.chempot_diagram import ChemicalPotentialDiagram
 from pymatgen.analysis.phase_diagram import PhaseDiagram
 from pymatgen.analysis.structure_matcher import ElementComparator, StructureMatcher
-from pymatgen.core import Composition, Structure
+from pymatgen.core import Composition, Element, Structure
 from pymatgen.electronic_structure.dos import Dos, FermiDos
 from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
 from pymatgen.io.vasp import Locpot, Vasprun
@@ -558,6 +558,53 @@ def as_dataframe(self):
         df = DataFrame(l_)
         return df
 
+    def get_chempot(self, rich_element: Element, en_tol: float = 0.01):
+        """Get the chemical potential for a desired growth condition.
+
+        Choose an element to be rich in, require the chemical potential of that element
+        to be near zero (en_tol, 0), then sort the remaining elements by:
+            1. Are they in the bulk structure:
+                elements in the bulk structure are prioritized.
+            2. how similar they in electron affinity to the rich element:
+                dis-similar elements are prioritized.
+
+        .. note::
+            Priority 2 is pretty arbitrary, but it is a good starting point.
+
+
+        Based on that priority list, take the minimum chemical potential extrema.
+
+        Args:
+            rich_element: The element that are rich in the growth condition.
+            en_tol: Energy tolerance for the chemical potential of the rich element.
+
+        Returns:
+            A dictionary of the chemical potentials for the growth condition.
+        """
+        rich_conditions = list(
+            filter(lambda cp: abs(cp[rich_element]) < en_tol, self.chempot_limits)
+        )
+        if len(rich_conditions) == 0:
+            raise ValueError(
+                f"Cannot find a chemical potential condition with {rich_element} near zero."
+            )
+        defect = self.defect_entries[0].defect
+        in_bulk = defect.structure.composition.elements
+        # make sure they are of type Element
+        in_bulk = list(map(lambda x: Element(x.symbol), in_bulk))
+        not_in_bulk = list(set(self.chempot_limits[0].keys()) - set(in_bulk))
+        in_bulk = list(filter(lambda x: x != rich_element, in_bulk))
+
+        def el_sorter(element):
+            return -abs(element.electron_affinity - rich_element.electron_affinity)
+
+        el_list = sorted(in_bulk, key=el_sorter) + sorted(not_in_bulk, key=el_sorter)
+
+        def chempot_sorter(chempot_dict):
+            return (chempot_dict[el] for el in el_list)
+
+        return min(rich_conditions, key=chempot_sorter)
+
 
 @dataclass
 class MultiFormationEnergyDiagram(MSONable):

tests/test_thermo.py

@@ -5,7 +5,7 @@
 import pytest
 from matplotlib import pyplot as plt
 from pymatgen.analysis.phase_diagram import PhaseDiagram
-from pymatgen.core import PeriodicSite
+from pymatgen.core import Element, PeriodicSite
 
 from pymatgen.analysis.defects.core import Interstitial
 from pymatgen.analysis.defects.corrections.freysoldt import plot_plnr_avg
@@ -172,6 +172,9 @@ def test_formation_energy(data_Mg_Ga, defect_entries_Mg_Ga, stable_entries_Mg_Ga
     # dataframe conversion
     fed.as_dataframe()
 
+    # test that you can get the Ga-rich chempot
+    fed.get_chempot(Element("Ga"))
+
 
 def test_multi(data_Mg_Ga, defect_entries_Mg_Ga, stable_entries_Mg_Ga_N):
     bulk_vasprun = data_Mg_Ga["bulk_sc"]["vasprun"]