Merge branch 'main' into gbd

Author: tschaume

mp_api/client/mprester.py

@@ -783,17 +783,22 @@ def get_entries(
 
     def get_pourbaix_entries(
         self,
-        chemsys: str | list,
+        chemsys: str | list[str] | list[ComputedEntry | ComputedStructureEntry],
         solid_compat="MaterialsProject2020Compatibility",
         use_gibbs: Literal[300] | None = None,
     ):
         """A helper function to get all entries necessary to generate
         a Pourbaix diagram from the rest interface.
 
         Args:
-            chemsys (str or [str]): Chemical system string comprising element
+            chemsys (str or [str] or Computed(Structure)Entry):
+                Chemical system string comprising element
                 symbols separated by dashes, e.g., "Li-Fe-O" or List of element
                 symbols, e.g., ["Li", "Fe", "O"].
+
+                Can also be a list of Computed(Structure)Entry objects to allow
+                for adding extra calculation data to the Pourbaix Diagram.
+                If this is set, the chemsys will be inferred from the entries.
             solid_compat: Compatibility scheme used to pre-process solid DFT energies prior
                 to applying aqueous energy adjustments. May be passed as a class (e.g.
                 MaterialsProject2020Compatibility) or an instance
@@ -816,6 +821,27 @@ def get_pourbaix_entries(
         )
         from pymatgen.entries.computed_entries import ComputedEntry
 
+        thermo_types = ["GGA_GGA+U"]
+        user_entries: list[ComputedEntry | ComputedStructureEntry] = []
+        if isinstance(chemsys, list) and all(
+            isinstance(v, ComputedEntry | ComputedStructureEntry) for v in chemsys
+        ):
+            user_entries = [ce.copy() for ce in chemsys]
+
+            elements = set()
+            for entry in user_entries:
+                elements.update(entry.elements)
+            chemsys = [ele.name for ele in elements]
+
+            user_run_types = set(
+                [
+                    entry.parameters.get("run_type", "unknown").lower()
+                    for entry in user_entries
+                ]
+            )
+            if any("r2scan" in rt for rt in user_run_types):
+                thermo_types = ["GGA_GGA+U_R2SCAN"]
+
         if solid_compat == "MaterialsProjectCompatibility":
             solid_compat = MaterialsProjectCompatibility()
         elif solid_compat == "MaterialsProject2020Compatibility":
@@ -851,9 +877,13 @@ def get_pourbaix_entries(
         # TODO - would be great if the commented line below would work
         # However for some reason you cannot process GibbsComputedStructureEntry with
         # MaterialsProjectAqueousCompatibility
-        ion_ref_entries = self.get_entries_in_chemsys(
-            list([str(e) for e in ion_ref_elts] + ["O", "H"]),
-            # use_gibbs=use_gibbs
+        ion_ref_entries = (
+            self.get_entries_in_chemsys(
+                list([str(e) for e in ion_ref_elts] + ["O", "H"]),
+                additional_criteria={"thermo_types": thermo_types}
+                # use_gibbs=use_gibbs
+            )
+            + user_entries
         )
 
         # suppress the warning about supplying the required energies; they will be calculated from the

mp_api/client/routes/materials/robocrys.py

@@ -15,7 +15,7 @@ def search(
         self,
         keywords: list[str],
         num_chunks: int | None = None,
-        chunk_size: int | None = 100,
+        chunk_size: int | None = 1000,
     ):
         """Search text generated from Robocrystallographer.