Merge branch 'dopey_fermi' into master

SMTG-Bham · Oct 31, 2023 · 9cb2c6f · 9cb2c6f
2 parents 4052cb6 + 9ee645e
commit 9cb2c6f
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Showing 4 changed files with 42 additions and 29 deletions.
diff --git a/docs/Tutorials.rst b/docs/Tutorials.rst
@@ -12,4 +12,5 @@ tutorials:
    YT_defects_tutorial
    dope_workflow_example
    dope_parsing_example
-   dope_chemical_potentials
+   dope_chemical_potentials
+   interface_py_sc_fermi
diff --git a/docs/interface_py_sc_fermi.ipynb b/docs/interface_py_sc_fermi.ipynb
@@ -0,0 +1 @@
+../examples/interface_py_sc_fermi.ipynb
diff --git a/doped/interface/py_sc_fermi.py b/doped/interface/py_sc_fermi.py
@@ -1,24 +1,27 @@
-from dataclasses import dataclass, field
-from doped.utils.legacy_pmg.thermodynamics import DefectPhaseDiagram
 from copy import deepcopy
-from typing import List, Dict, Union, Tuple, Optional
-from scipy.spatial import Delaunay, ConvexHull
-from tqdm import tqdm
-import pandas as pd
+from dataclasses import dataclass, field
+from typing import Dict, List, Optional
+
 import numpy as np
+import pandas as pd
+from scipy.spatial import ConvexHull, Delaunay
+from tqdm import tqdm
+
+from doped.utils.legacy_pmg.thermodynamics import DefectPhaseDiagram
 
 try:
-    from py_sc_fermi.dos import DOS
-    from py_sc_fermi.defect_system import DefectSystem
     from py_sc_fermi.defect_species import DefectSpecies
+    from py_sc_fermi.defect_system import DefectSystem
+    from py_sc_fermi.dos import DOS
 except ImportError:
     raise ImportError(
         "Please install py-sc-fermi via `pip install py-sc-fermi` to use this functionality."
     )
 
 
 def _get_label_and_charge(name: str) -> tuple:
-    """Extracts the label and charge from a defect name string.
+    """
+    Extracts the label and charge from a defect name string.
 
     Args:
         name (str): Name of the defect.
@@ -58,7 +61,9 @@ def _defect_picker(self, name: str):  # Type hint should represent the actual ty
         return defect
 
     def _generate_defect_system(self, temperature: float, chemical_potentials: dict) -> DefectSystem:
-        """Generates a DefectSystem object from the DefectPhaseDiagram and a set of chemical potentials.
+        """
+        Generates a DefectSystem object from the DefectPhaseDiagram and a set
+        of chemical potentials.
 
         Args:
             temperature (float): Temperature in K.
@@ -97,8 +102,10 @@ def _generate_defect_system(self, temperature: float, chemical_potentials: dict)
     def defect_system_from_chemical_potentials(
         self, chemical_potentials: dict, temperature: float = 300.0
     ) -> DefectSystem:
-        """Updates the energies of the DefectSystem with a new set of chemical potentials."""
-
+        """
+        Updates the energies of the DefectSystem with a new set of chemical
+        potentials.
+        """
         defect_system = self._generate_defect_system(
             temperature=temperature, chemical_potentials=chemical_potentials
         )
@@ -121,7 +128,8 @@ def scan_temperature(
         file_name: str = None,
     ) -> pd.DataFrame:
         """
-        Scans a range of temperatures and saves the concentration_dict() to a DataFrame.
+        Scans a range of temperatures and returns the concentration_dict() as a
+        DataFrame.
 
         Args:
             temp_range (List[float]): List of temperatures to scan.
@@ -175,15 +183,15 @@ def scan_temperature(
         return all_data
 
     def _get_concentrations(self, defect_system: DefectSystem):
-        """_summary_
+        """
+        _summary_.
 
         Args:
             defect_system (DefectSystem): _description_
 
         Returns:
             _type_: _description_
         """
-
         conc_dict = defect_system.concentration_dict()
 
         concentration_data = []
@@ -267,6 +275,9 @@ def interpolate_chemical_potentials(
                     annealing_temperature=anneal_temperature,
                     target_temperature=temperature,
                     fix_defect_species=fix_defect_species,
+                    annealing_temperature=anneal_temp,
+                    target_temperature=temp,
+                    level=level,
                     exceptions=exceptions,
                 )
 
@@ -349,14 +360,15 @@ def generate_annealed_defect_system(
             elif fix_defect_species == False:
                 for k, v in defect_species.charge_states.items():
                     key = f"{defect_species.name}_{int(k)}"
-                    if key in [k for k in fixed_concs.keys()]:
+                    if key in list(fixed_concs.keys()):
                         v.fix_concentration(fixed_concs[key] / 1e24 * self.volume)
 
         target_system = self.update_defect_system_temperature(initial_system, target_temperature)
         return target_system
 
     def chempot_grid(self, chemical_potentials, num_points=10, num_points_along_edge=5):
-        """generate a grid of chemical potentials.
+        """
+        Generate a grid of chemical potentials.
 
         Args:
             chemical_potenials ([type]): [description]
@@ -401,8 +413,8 @@ def grid_solve(
         """
         all_concentration_data = []
         all_fermi_level_data = []
-        for i, row in tqdm(chempot_grid.iterrows()):
-            row.drop(["is_vertex", "facet"], inplace=True)
+        for _i, row in tqdm(chempot_grid.iterrows()):
+            row = row.drop(["is_vertex", "facet"])
             chemical_potentials = row.to_dict()
 
             if anneal_temperature:
@@ -431,15 +443,14 @@ def grid_solve(
         all_data = pd.merge(
             concentration_df,
             fermi_level_df,
-            on=["Temperature"] + list(chemical_potentials.keys()),
+            on=["Temperature", *list(chemical_potentials.keys())],
         )
 
         if file_name is not None:
             all_data.to_csv(file_name)
 
         return all_data
 
-
 @dataclass
 class ChemicalPotentialGrid:
     chemical_potentials: dict
@@ -535,7 +546,7 @@ def get_grid(self) -> pd.DataFrame:
 
         df = pd.concat([grid_df, internal_grid_df, vertices_df], ignore_index=True)
         grid_df = df.drop_duplicates(
-            subset=list(list(self.chemical_potentials["facets"].values())[0].keys()) + ["is_vertex"]
+            subset=[*list(list(self.chemical_potentials["facets"].values())[0].keys()), "is_vertex"]
         )
 
         return grid_df
diff --git a/examples/interface_py_sc_fermi.ipynb b/examples/interface_py_sc_fermi.ipynb
@@ -424,7 +424,7 @@
     "# define a range of chemical potentials to scan over\n",
     "chem_pot_df = fs.interpolate_chemical_potentials_and_save(chem_pot_start=chemical_potentials[\"facets\"][\"Cu2SiSe3-Cu2Se-Cu\"],\n",
     "                                                chem_pot_end=chemical_potentials[\"facets\"][\"Cu2SiSe3-SiSe2-Se\"],\n",
-    "                                                n_points=100, temp=300, anneal_temp=1000)\n",
+    "                                                n_points=100, temp=300)\n",
     "\n",
     "# Create a unique list of defects\n",
     "unique_defects = chem_pot_df['Defect'].unique()\n",
@@ -1679,23 +1679,23 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [
     {
      "ename": "NameError",
-     "evalue": "name 'sliced_df' is not defined",
+     "evalue": "name 'concs' is not defined",
      "output_type": "error",
      "traceback": [
       "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
       "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
-      "\u001b[1;32m/Users/alex/work/doped/examples/interface_py_sc_fermi.ipynb Cell 20\u001b[0m line \u001b[0;36m1\n\u001b[0;32m----> <a href='vscode-notebook-cell:/Users/alex/work/doped/examples/interface_py_sc_fermi.ipynb#X25sZmlsZQ%3D%3D?line=0'>1</a>\u001b[0m \u001b[39mprint\u001b[39m(sliced_df)\n",
-      "\u001b[0;31mNameError\u001b[0m: name 'sliced_df' is not defined"
+      "\u001b[1;32m/Users/alex/work/doped/examples/interface_py_sc_fermi.ipynb Cell 20\u001b[0m line \u001b[0;36m1\n\u001b[0;32m----> <a href='vscode-notebook-cell:/Users/alex/work/doped/examples/interface_py_sc_fermi.ipynb#X25sZmlsZQ%3D%3D?line=0'>1</a>\u001b[0m \u001b[39mprint\u001b[39m(concs)\n",
+      "\u001b[0;31mNameError\u001b[0m: name 'concs' is not defined"
      ]
     }
    ],
    "source": [
-    "print(sliced_df)"
+    "print(concs)"
    ]
   },
   {