Summary and synthesis updates (#333)

* Bump emmet core in reqs

* Rename search to summary

* Bump emmet core again

* Bump emmet in reqs

* Fix dielectric, elasticity and electrode

* Rename to summary, and synthesis test fixes

app.py

@@ -42,7 +42,7 @@
 )
 molecules_store_json = os.environ.get("MOLECULES_STORE", "molecules_store.json")
 oxi_states_store_json = os.environ.get("OXI_STATES_STORE", "oxi_states_store.json")
-search_store_json = os.environ.get("SEARCH_STORE", "search_store.json")
+summary_store_json = os.environ.get("SUMMARY_STORE", "summary_store.json")
 
 es_store_json = os.environ.get("ES_STORE", "es_store.json")
 
@@ -222,11 +222,11 @@
         collection_name="oxi_states",
     )
 
-    search_store = MongoURIStore(
+    summary_store = MongoURIStore(
         uri=f"mongodb+srv://{db_uri}",
         database="mp_core",
         key="material_id",
-        collection_name="search",
+        collection_name="summary",
     )
 
     es_store = MongoURIStore(
@@ -320,7 +320,7 @@
     insertion_electrodes_store = loadfn(insertion_electrodes_store_json)
     molecules_store = loadfn(molecules_store_json)
     oxi_states_store = loadfn(oxi_states_store_json)
-    search_store = loadfn(search_store_json)
+    ssummary_store = loadfn(summary_store_json)
 
     es_store = loadfn(es_store_json)
 
@@ -394,7 +394,7 @@
 # Phonon
 from mp_api.routes.phonon.resources import phonon_bsdos_resource
 
-resources.update({"phonon": [phonon_bsdos_resource(phonon_bs_store),]})
+resources.update({"phonon": [phonon_bsdos_resource(phonon_bs_store)]})
 
 # EOS
 from mp_api.routes.eos.resources import eos_resource
@@ -485,15 +485,14 @@
 resources.update({"charge_density": [charge_density_resource(s3_chgcar)]})
 
 # Search
-from mp_api.routes.search.resources import search_resource, search_stats_resource
+from mp_api.routes.summary.resources import summary_resource, summary_stats_resource
 
 resources.update(
-    {"search": [search_stats_resource(search_store), search_resource(search_store)]}
+    {"search": [summary_stats_resource(summary_store), summary_resource(summary_store)]}
 )
 
 # Electronic Structure
 from mp_api.routes.electronic_structure.resources import (
-    dos_obj_resource,
     es_resource,
     bs_resource,
     bs_obj_resource,

requirements.txt

@@ -4,5 +4,5 @@ typing-extensions==3.10.0.0
 maggma==0.30.2
 requests==2.25.1
 monty==2021.7.8
-emmet-core==0.5.0
+emmet-core==0.8.2
 ratelimit==2.2.1

src/mp_api/matproj.py

@@ -461,6 +461,8 @@ def query(
         total_magnetization_normalized_formula_units: Optional[
             Tuple[float, float]
         ] = None,
+        num_magnetic_sites: Optional[Tuple[int, int]] = None,
+        num_unique_magnetic_sites: Optional[Tuple[int, int]] = None,
         k_voigt: Optional[Tuple[float, float]] = None,
         k_reuss: Optional[Tuple[float, float]] = None,
         k_vrh: Optional[Tuple[float, float]] = None,
@@ -471,13 +473,14 @@ def query(
         poisson_ratio: Optional[Tuple[float, float]] = None,
         e_total: Optional[Tuple[float, float]] = None,
         e_ionic: Optional[Tuple[float, float]] = None,
-        e_static: Optional[Tuple[float, float]] = None,
+        e_electronic: Optional[Tuple[float, float]] = None,
         n: Optional[Tuple[float, float]] = None,
         piezoelectric_modulus: Optional[Tuple[float, float]] = None,
         weighted_surface_energy: Optional[Tuple[float, float]] = None,
         weighted_work_function: Optional[Tuple[float, float]] = None,
-        surface_anisotropy: Optional[Tuple[float, float]] = None,
+        surface_energy_anisotropy: Optional[Tuple[float, float]] = None,
         shape_factor: Optional[Tuple[float, float]] = None,
+        has_reconstructed: Optional[bool] = None,
         has_props: Optional[List[str]] = None,
         theoretical: Optional[bool] = None,
         sort_field: Optional[str] = None,
@@ -516,6 +519,9 @@ def query(
                 normalized by volume to consider.
             total_magnetization_normalized_formula_units (Tuple[float,float]): Minimum and maximum total magnetization
                 values normalized by formula units to consider.
+            num_magnetic_sites (Tuple[int,int]): Minimum and maximum number of magnetic sites to consider.
+            num_unique_magnetic_sites (Tuple[int,int]): Minimum and maximum number of unique magnetic sites
+                to consider.
             k_voigt (Tuple[float,float]): Minimum and maximum value in GPa to consider for
                 the Voigt average of the bulk modulus.
             k_reuss (Tuple[float,float]): Minimum and maximum value in GPa to consider for
@@ -534,7 +540,7 @@ def query(
                 Poisson's ratio.
             e_total (Tuple[float,float]): Minimum and maximum total dielectric constant to consider.
             e_ionic (Tuple[float,float]): Minimum and maximum ionic dielectric constant to consider.
-            e_static (Tuple[float,float]): Minimum and maximum electronic dielectric constant to consider.
+            e_electronic (Tuple[float,float]): Minimum and maximum electronic dielectric constant to consider.
             n (Tuple[float,float]): Minimum and maximum refractive index to consider.
             piezoelectric_modulus (Tuple[float,float]): Minimum and maximum piezoelectric modulus to consider.
             weighted_surface_energy (Tuple[float,float]): Minimum and maximum weighted surface energy in J/m² to
@@ -543,6 +549,7 @@ def query(
             surface_energy_anisotropy (Tuple[float,float]): Minimum and maximum surface energy anisotropy values to
                 consider.
             shape_factor (Tuple[float,float]): Minimum and maximum shape factor values to consider.
+            has_reconstructed (bool): Whether the entry has any reconstructed surfaces.
             has_props: (List[str]): The calculated properties available for the material.
             theoretical: (bool): Whether the material is theoretical.
             sort_field (str): Field used to sort results.
@@ -554,9 +561,10 @@ def query(
                 Default is material_id if all_fields is False.
 
         Returns:
-            ([SearchDoc]) List of SearchDoc documents
+            ([SummaryDoc]) List of SummaryDoc documents
         """
-        return self.search.search_docs(  # type: ignore
+
+        return self.summary.search_summary_docs(  # type: ignore
             material_ids=material_ids,
             chemsys_formula=chemsys_formula,
             nsites=nsites,
@@ -580,6 +588,8 @@ def query(
             total_magnetization=total_magnetization,
             total_magnetization_normalized_vol=total_magnetization_normalized_vol,
             total_magnetization_normalized_formula_units=total_magnetization_normalized_formula_units,
+            num_magnetic_sites=num_magnetic_sites,
+            num_unique_magnetic_sites=num_unique_magnetic_sites,
             k_voigt=k_voigt,
             k_reuss=k_reuss,
             k_vrh=k_vrh,
@@ -590,13 +600,14 @@ def query(
             poisson_ratio=poisson_ratio,
             e_total=e_total,
             e_ionic=e_ionic,
-            e_static=e_static,
+            e_electronic=e_electronic,
             n=n,
             piezoelectric_modulus=piezoelectric_modulus,
             weighted_surface_energy=weighted_surface_energy,
             weighted_work_function=weighted_work_function,
-            surface_anisotropy=surface_anisotropy,
+            surface_energy_anisotropy=surface_energy_anisotropy,
             shape_factor=shape_factor,
+            has_reconstructed=has_reconstructed,
             has_props=has_props,
             theoretical=theoretical,
             sort_field=sort_field,

src/mp_api/routes/__init__.py

@@ -15,7 +15,7 @@
 from mp_api.routes.dois.client import DOIRester
 from mp_api.routes.piezo.client import PiezoRester
 from mp_api.routes.magnetism.client import MagnetismRester
-from mp_api.routes.search.client import SearchRester
+from mp_api.routes.summary.client import SummaryRester
 from mp_api.routes.robocrys.client import RobocrysRester
 from mp_api.routes.molecules.client import MoleculesRester
 from mp_api.routes.synthesis.client import SynthesisRester

src/mp_api/routes/dielectric/client.py

@@ -15,7 +15,7 @@ def search_dielectric_docs(
         self,
         e_total: Optional[Tuple[float, float]] = None,
         e_ionic: Optional[Tuple[float, float]] = None,
-        e_static: Optional[Tuple[float, float]] = None,
+        e_electronic: Optional[Tuple[float, float]] = None,
         n: Optional[Tuple[float, float]] = None,
         sort_field: Optional[str] = None,
         ascending: Optional[bool] = None,
@@ -30,7 +30,7 @@ def search_dielectric_docs(
         Arguments:
             e_total (Tuple[float,float]): Minimum and maximum total dielectric constant to consider.
             e_ionic (Tuple[float,float]): Minimum and maximum ionic dielectric constant to consider.
-            e_static (Tuple[float,float]): Minimum and maximum electronic dielectric constant to consider.
+            e_electronic (Tuple[float,float]): Minimum and maximum electronic dielectric constant to consider.
             n (Tuple[float,float]): Minimum and maximum refractive index to consider.
             sort_field (str): Field used to sort results.
             ascending (bool): Whether sorting should be in ascending order.
@@ -52,8 +52,13 @@ def search_dielectric_docs(
         if e_ionic:
             query_params.update({"e_ionic_min": e_ionic[0], "e_ionic_max": e_ionic[1]})
 
-        if e_static:
-            query_params.update({"e_static_min": e_static[0], "e_static_max": e_static[1]})
+        if e_electronic:
+            query_params.update(
+                {
+                    "e_electronic_min": e_electronic[0],
+                    "e_electronic_max": e_electronic[1],
+                }
+            )
 
         if n:
             query_params.update({"n_min": n[0], "n_max": n[1]})
@@ -64,8 +69,16 @@ def search_dielectric_docs(
         if ascending is not None:
             query_params.update({"ascending": ascending})
 
-        query_params = {entry: query_params[entry] for entry in query_params if query_params[entry] is not None}
+        query_params = {
+            entry: query_params[entry]
+            for entry in query_params
+            if query_params[entry] is not None
+        }
 
         return super().search(
-            num_chunks=num_chunks, chunk_size=chunk_size, all_fields=all_fields, fields=fields, **query_params
+            num_chunks=num_chunks,
+            chunk_size=chunk_size,
+            all_fields=all_fields,
+            fields=fields,
+            **query_params
         )

src/mp_api/routes/dielectric/query_operators.py

@@ -25,11 +25,11 @@ def query(
         e_ionic_min: Optional[float] = Query(
             None, description="Minimum value for the ionic dielectric constant.",
         ),
-        e_static_max: Optional[float] = Query(
-            None, description="Maximum value for the static dielectric constant.",
+        e_electronic_max: Optional[float] = Query(
+            None, description="Maximum value for the electronic dielectric constant.",
         ),
-        e_static_min: Optional[float] = Query(
-            None, description="Minimum value for the static dielectric constant.",
+        e_electronic_min: Optional[float] = Query(
+            None, description="Minimum value for the electronic dielectric constant.",
         ),
         n_max: Optional[float] = Query(
             None, description="Maximum value for the refractive index.",
@@ -44,7 +44,7 @@ def query(
         d = {
             "dielectric.e_total": [e_total_min, e_total_max],
             "dielectric.e_ionic": [e_ionic_min, e_ionic_max],
-            "dielectric.e_static": [e_static_min, e_static_max],
+            "dielectric.e_electronic": [e_electronic_min, e_electronic_max],
             "dielectric.n": [n_min, n_max],
         }
 
@@ -61,7 +61,7 @@ def ensure_indexes(self):  # pragma: no cover
         keys = [
             "dielectric.e_total",
             "dielectric.e_ionic",
-            "dielectric.e_static",
+            "dielectric.e_electronic",
             "dielectric.n",
         ]
         return [(key, False) for key in keys]

src/mp_api/routes/electrodes/client.py

@@ -15,10 +15,8 @@ class ElectrodeRester(BaseRester):
     def search_electrode_docs(  # pragma: ignore
         self,
         working_ion: Optional[Element] = None,
-        delta_volume: Optional[Tuple[float, float]] = None,
+        max_delta_volume: Optional[Tuple[float, float]] = None,
         average_voltage: Optional[Tuple[float, float]] = None,
-        max_voltage: Optional[Tuple[float, float]] = None,
-        min_voltage: Optional[Tuple[float, float]] = None,
         capacity_grav: Optional[Tuple[float, float]] = None,
         capacity_vol: Optional[Tuple[float, float]] = None,
         energy_grav: Optional[Tuple[float, float]] = None,
@@ -27,7 +25,7 @@ def search_electrode_docs(  # pragma: ignore
         fracA_discharge: Optional[Tuple[float, float]] = None,
         stability_charge: Optional[Tuple[float, float]] = None,
         stability_discharge: Optional[Tuple[float, float]] = None,
-        num_steps: Optional[Tuple[float, float]] = None,
+        num_steps: Optional[Tuple[int, int]] = None,
         max_voltage_step: Optional[Tuple[float, float]] = None,
         sort_field: Optional[str] = None,
         ascending: Optional[bool] = None,
@@ -41,13 +39,11 @@ def search_electrode_docs(  # pragma: ignore
 
         Arguments:
             working_ion (Element): Element of the working ion.
-            delta_volume (Tuple[float,float]): Minimum and maximum value of the max volume change in percent for a
+            max_delta_volume (Tuple[float,float]): Minimum and maximum value of the max volume change in percent for a
                 particular voltage step.
             average_voltage (Tuple[float,float]): Minimum and maximum value of the average voltage for a particular
                 voltage step in V.
-            max_voltage (Tuple[float,float]): Minimum and maximum value of the maximum voltage for a particular
-                voltage step in V.
-            min_voltage (Tuple[float,float]): Minimum and maximum value of the minimum voltage for a particular
+            max_voltage_step (Tuple[float,float]): Minimum and maximum value of the maximum voltage for a particular
                 voltage step in V.
             capacity_grav (Tuple[float,float]): Minimum and maximum value of the gravimetric capacity in maH/g.
             capacity_vol (Tuple[float,float]): Minimum and maximum value of the volumetric capacity in maH/cc.