Fix (most) failing tests, formatting, match other test preferences (`…

…np.isclose` over `assertAlmostEqual` etc), pull chempots from DefectThermodynamics if present and not supplied...

doped/interface/fermi_solver.py

@@ -12,7 +12,7 @@
 from copy import deepcopy
 from itertools import product
 from typing import TYPE_CHECKING, Any, Optional, Union
-from warnings import warn, filterwarnings
+from warnings import filterwarnings, warn
 
 import numpy as np
 import pandas as pd
@@ -68,14 +68,22 @@ class FermiSolver(MSONable):
  """
 
  def __init__(
- self, defect_thermodynamics: "DefectThermodynamics", bulk_dos_vr_path: str, chemical_potentials: dict
+ self,
+ defect_thermodynamics: "DefectThermodynamics",
+ bulk_dos_vr_path: str,
+ chemical_potentials: Optional[dict] = None,
  ):
  """
  Initialize the FermiSolver object.
  """
  self.defect_thermodynamics = defect_thermodynamics
  self.bulk_dos = bulk_dos_vr_path
  self.chemical_potentials = chemical_potentials
+
+ if self.chemical_potentials is None and self.defect_thermodynamics.chempots is not None:
+ # if chempots not supplied, but present in DefectThermodynamics, then use them
+ self.chemical_potentials = self.defect_thermodynamics.chempots
+
  self._not_implemented_message = (
  "This method is implemented in the derived class, "
  "use FermiSolverDoped or FermiSolverPyScFermi instead."
@@ -778,7 +786,7 @@ def pseudo_equilibrium_solve(
  for column, value in new_columns.items():
  concentrations[column] = value
 
- # trimmed_concentrations = 
+ # trimmed_concentrations =
  trimmed_concentrations_sub_duplicates = concentrations.drop_duplicates()
  excluded_columns = ["Defect"]
  for column in concentrations.columns.difference(excluded_columns):
@@ -971,7 +979,6 @@ def equilibrium_solve(
  pd.DataFrame: DataFrame containing defect and carrier concentrations
  and the self consistent Fermi energy
  """
-
  if self.supress_warnings:
  filterwarnings("ignore", category=RuntimeWarning)
 
@@ -1021,7 +1028,6 @@ def pseudo_equilibrium_solve(
  pd.DataFrame: DataFrame containing defect and carrier concentrations
  and the self consistent Fermi energy
  """
-
  if self.supress_warnings:
  filterwarnings("ignore", category=RuntimeWarning)
 

tests/test_interface_fermi_solver.py

@@ -1,10 +1,17 @@
-from doped.interface.fermi_solver import FermiSolver, FermiSolverDoped, FermiSolverPyScFermi
-from monty.serialization import loadfn
+"""
+Tests for doped.interface.fermi_solver module.
+"""
+
 import unittest
 from unittest.mock import patch
-import pandas as pd
+
+import numpy as np
+import pytest
+from monty.serialization import loadfn
 from pymatgen.electronic_structure.dos import FermiDos
 
+from doped.interface.fermi_solver import FermiSolver, FermiSolverDoped, FermiSolverPyScFermi
+
 
 class FermiSolverTestCase(unittest.TestCase):
  def setUp(self):
@@ -19,41 +26,56 @@ def test_init(self):
 
  def test_equilibrium_solve(self):
  # test that equilibrium solve raises not implemented error
- with self.assertRaises(NotImplementedError):
+ with pytest.raises(NotImplementedError) as exc:
  self.fs.equilibrium_solve()
 
+ print(exc.value) # for debugging
+ assert (
+ "This method is implemented in the derived class, use FermiSolverDoped or "
+ "FermiSolverPyScFermi instead."
+ ) in str(exc.value)
+
  def test_pseudoequilibrium_solve(self):
  # test that pseudoequilibrium solve raises not implemented error
- with self.assertRaises(NotImplementedError):
+ with pytest.raises(NotImplementedError) as exc:
  self.fs.pseudo_equilibrium_solve()
 
+ print(exc.value) # for debugging
+ assert (
+ "This method is implemented in the derived class, use FermiSolverDoped or "
+ "FermiSolverPyScFermi instead."
+ ) in str(exc.value)
+
  def test_assert_scan_temperature_raises(self):
 
- with self.assertRaises(ValueError):
+ with pytest.raises(ValueError) as exc:
  self.fs.scan_temperature(
  {},
  temperature_range=[1, 2, 3],
  annealing_temperature_range=[1, 2, 3],
  quenching_temperature_range=None,
  )
+ print(exc.value) # for debugging
 
- with self.assertRaises(ValueError):
+ with pytest.raises(ValueError) as exc:
  self.fs.scan_temperature(
  {},
  temperature_range=[1, 2, 3],
  annealing_temperature_range=None,
  quenching_temperature_range=[1, 2, 3],
  )
+ print(exc.value) # for debugging
 
- with self.assertRaises(ValueError):
+ with pytest.raises(ValueError) as exc:
  self.fs.scan_temperature(
  {},
  temperature_range=[],
  annealing_temperature_range=None,
  quenching_temperature_range=None,
  )
+ print(exc.value) # for debugging
 
- def test__get_interpolated_chempots(self):
+ def test_get_interpolated_chempots(self):
 
  int_chempots = self.fs._get_interpolated_chempots({"a": -1, "b": -1}, {"a": 1, "b": 1}, 11)
  assert len(int_chempots) == 11
@@ -75,13 +97,25 @@ def setUp(self):
  def test__init__(self):
  assert self.fs.defect_thermodynamics == self.thermo
  assert isinstance(self.fs.bulk_dos, FermiDos)
- self.assertEqual(self.fs.bulk_dos.nelecs, 18.0)
+ assert self.fs.bulk_dos.nelecs == 18.0
 
  def test_assert_scan_dopant_concentration_raises(self):
- with self.assertRaises(NotImplementedError):
+ with pytest.raises(TypeError) as exc: # missing arguments
  self.fs.scan_dopant_concentration()
 
- def test__get_fermi_level_and_carriers(self):
+ print(exc.value) # for debugging
+
+ # TODO: This doesn't raise a NotImplementedError because it's a method for the parent
+ # `FermiSolver` class. Is this not also possible with `FermiSolverDoped`? As it's just fixing
+ # the dopant concentrations? Thought we could do it with both backends without issue
+ with pytest.raises(NotImplementedError) as exc:
+ self.fs.scan_dopant_concentration(
+ chempots=None, effective_dopant_concentration_range=[1, 2, 3]
+ )
+
+ print(exc.value) # for debugging
+
+ def test_get_fermi_level_and_carriers(self):
  # set return value for the thermodynamics method `get_equilibrium_fermi_level`,
  # does it need to be a mock?
  with patch(
@@ -96,26 +130,24 @@ def test__get_fermi_level_and_carriers(self):
  def test_equilibrium_solve(self):
 
  equilibrium_results = self.fs.equilibrium_solve({"Cd": -2, "Te": -2}, 300)
- self.assertAlmostEqual(equilibrium_results["Fermi Level"][0], 0.798379, places=6)
- self.assertAlmostEqual(equilibrium_results["Electrons (cm^-3)"][0], 57861.403451, places=6)
- self.assertAlmostEqual(equilibrium_results["Holes (cm^-3)"][0], 390268.197798, places=6)
- self.assertAlmostEqual(equilibrium_results["Temperature"][0], 300, places=6)
- self.assertAlmostEqual(equilibrium_results["Concentration (cm^-3)"][0], 1.423000e-24, places=6)
+ assert np.isclose(equilibrium_results["Fermi Level"][0], 0.798379, rtol=1e-4)
+ assert np.isclose(equilibrium_results["Electrons (cm^-3)"][0], 57861.403451, rtol=1e-4)
+ assert np.isclose(equilibrium_results["Holes (cm^-3)"][0], 390268.197798, rtol=1e-4)
+ assert np.isclose(equilibrium_results["Temperature"][0], 300, rtol=1e-4)
+ assert np.isclose(equilibrium_results["Concentration (cm^-3)"][0], 1.423000e-24, rtol=1e-4)
 
  def test_pseudo_equilibrium_solve(self):
  pseudo_equilibrium_results = self.fs.pseudo_equilibrium_solve(
  {"Cd": -2, "Te": -2}, annealing_temperature=900, quenched_temperature=300
  )
 
- self.assertAlmostEqual(pseudo_equilibrium_results["Fermi Level"][0], 0.456269, places=6)
- self.assertAlmostEqual(pseudo_equilibrium_results["Electrons (cm^-3)"][0], 0.10356, places=6)
- self.assertAlmostEqual(
- pseudo_equilibrium_results["Holes (cm^-3)"][0], 218051006211.37335, places=6
- )
- self.assertAlmostEqual(pseudo_equilibrium_results["Annealing Temperature"][0], 900.0, places=6)
- self.assertAlmostEqual(pseudo_equilibrium_results["Quenched Temperature"][0], 300.0, places=6)
- self.assertAlmostEqual(
- pseudo_equilibrium_results["Concentration (cm^-3)"][0], 5.426998900437918e20, places=6
+ assert np.isclose(pseudo_equilibrium_results["Fermi Level"][0], 0.456269, rtol=1e-4)
+ assert np.isclose(pseudo_equilibrium_results["Electrons (cm^-3)"][0], 0.10356, rtol=1e-4)
+ assert np.isclose(pseudo_equilibrium_results["Holes (cm^-3)"][0], 218051006212.72186, rtol=1e-4)
+ assert np.isclose(pseudo_equilibrium_results["Annealing Temperature"][0], 900.0, rtol=1e-4)
+ assert np.isclose(pseudo_equilibrium_results["Quenched Temperature"][0], 300.0, rtol=1e-4)
+ assert np.isclose(
+ pseudo_equilibrium_results["Concentration (cm^-3)"][0], 5.426998900437918e20, rtol=1e-4
  )
 
 
@@ -132,23 +164,18 @@ def test__init__(self):
  def test_equilibrium_solve(self):
 
  equilibrium_results = self.fs.equilibrium_solve({"Cd": -2, "Te": -2}, 300)
- self.assertAlmostEqual(equilibrium_results["Fermi Level"][0], 0.8878258982206311, places=6)
- self.assertAlmostEqual(equilibrium_results["Electrons (cm^-3)"][0], 4490462.40649167, places=6)
- self.assertAlmostEqual(equilibrium_results["Holes (cm^-3)"][0], 12219.64626151177, places=6)
- self.assertAlmostEqual(equilibrium_results["Temperature"][0], 300, places=6)
+ assert np.isclose(equilibrium_results["Fermi Level"][0], 0.8878258982206311, rtol=1e-4)
+ assert np.isclose(equilibrium_results["Electrons (cm^-3)"][0], 4490462.40649167, rtol=1e-4)
+ assert np.isclose(equilibrium_results["Holes (cm^-3)"][0], 12219.64626151177, rtol=1e-4)
+ assert np.isclose(equilibrium_results["Temperature"][0], 300, rtol=1e-4)
 
  def test_pseudo_equilibrium_solve(self):
  pseudo_equilibrium_results = self.fs.pseudo_equilibrium_solve(
  {"Cd": -2, "Te": -2}, annealing_temperature=900, quenched_temperature=300
  )
 
- self.assertAlmostEqual(pseudo_equilibrium_results["Fermi Level"][0], 0.8900579775197812, places=6)
- self.assertAlmostEqual(
- pseudo_equilibrium_results["Electrons (cm^-3)"][0], 4895401.840081683, places=6
- )
- self.assertAlmostEqual(pseudo_equilibrium_results["Holes (cm^-3)"][0], 11208.85760769246, places=6)
- self.assertAlmostEqual(pseudo_equilibrium_results["Annealing Temperature"][0], 900.0, places=6)
- self.assertAlmostEqual(pseudo_equilibrium_results["Quenched Temperature"][0], 300.0, places=6)
-
-if __name__ == "__main__":
- unittest.main()
+ assert np.isclose(pseudo_equilibrium_results["Fermi Level"][0], 0.8900579775197812, rtol=1e-4)
+ assert np.isclose(pseudo_equilibrium_results["Electrons (cm^-3)"][0], 4895401.840081683, rtol=1e-4)
+ assert np.isclose(pseudo_equilibrium_results["Holes (cm^-3)"][0], 11208.85760769246, rtol=1e-4)
+ assert np.isclose(pseudo_equilibrium_results["Annealing Temperature"][0], 900.0, rtol=1e-4)
+ assert np.isclose(pseudo_equilibrium_results["Quenched Temperature"][0], 300.0, rtol=1e-4)