Skip to content

Commit

Permalink
Update tests
Browse files Browse the repository at this point in the history
  • Loading branch information
@kavanase
kavanase committed Jun 24, 2024
1 parent ae5c9a5 commit b47f0c9
Show file tree
Hide file tree
Showing 2 changed files with 57 additions and 39 deletions.
35 changes: 25 additions & 10 deletions doped/chemical_potentials.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1349,21 +1349,13 @@ def from_vaspruns(self, path="competing_phases", folder="vasp_std", csv_path=Non
el = next(iter(vr.atomic_symbols)) # elemental, so first symbol is only (unique) element
if el not in self.elemental_energies:
self.elemental_energies[el] = energy_per_atom
if el not in self.elements: # new (extrinsic) element
if el not in self.elements + self.extrinsic_elements: # new (extrinsic) element
self.extrinsic_elements.append(el)

elif energy_per_atom < self.elemental_energies[el]:
# only include lowest energy elemental polymorph
self.elemental_energies[el] = energy_per_atom

# sort extrinsic elements and energies dict by atomic number (deterministically), and add to
# self.elements:
self.extrinsic_elements = sorted(self.extrinsic_elements, key=lambda x: Element(x).Z)
self.elemental_energies = dict(
sorted(self.elemental_energies.items(), key=lambda x: Element(x[0]).Z)
)
self.elements += self.extrinsic_elements

d = {
"Formula": comp.reduced_formula,
"k-points": kpoints,
Expand All @@ -1373,6 +1365,14 @@ def from_vaspruns(self, path="competing_phases", folder="vasp_std", csv_path=Non
}
data.append(d)

# sort extrinsic elements and energies dict by atomic number (deterministically), and add to
# self.elements:
self.extrinsic_elements = sorted(self.extrinsic_elements, key=lambda x: Element(x).Z)
self.elemental_energies = dict(
sorted(self.elemental_energies.items(), key=lambda x: Element(x[0]).Z)
)
self.elements += self.extrinsic_elements

formation_energy_df = _calculate_formation_energies(data, self.elemental_energies)
self.data = formation_energy_df.to_dict(orient="records")
self.formation_energy_df = pd.DataFrame(self._get_and_sort_formation_energy_data()) # sort data
Expand Down Expand Up @@ -1492,14 +1492,16 @@ def from_csv(self, csv_path):
for i in self.data:
c = Composition(i["Formula"])
if len(c.elements) == 1:
el = c.chemical_system
el = str(next(iter(c.elements))) # elemental, so first symbol is only (unique) element
if "DFT Energy (eV/atom)" in list(formation_energy_df.columns):
el_energy_per_atom = i["DFT Energy (eV/atom)"]
else:
el_energy_per_atom = i["DFT Energy (eV/fu)"] / c.num_atoms

if el not in self.elemental_energies or el_energy_per_atom < self.elemental_energies[el]:
self.elemental_energies[el] = el_energy_per_atom
if el not in self.elements + self.extrinsic_elements: # new (extrinsic) element
self.extrinsic_elements.append(el)

if "Formation Energy (eV/fu)" not in list(formation_energy_df.columns):
formation_energy_df = _calculate_formation_energies(self.data, self.elemental_energies)
Expand All @@ -1508,6 +1510,14 @@ def from_csv(self, csv_path):
self.formation_energy_df = pd.DataFrame(self._get_and_sort_formation_energy_data()) # sort data
self.formation_energy_df.set_index("Formula")

# sort extrinsic elements and energies dict by atomic number (deterministically), and add to
# self.elements:
self.extrinsic_elements = sorted(self.extrinsic_elements, key=lambda x: Element(x).Z)
self.elemental_energies = dict(
sorted(self.elemental_energies.items(), key=lambda x: Element(x[0]).Z)
)
self.elements += self.extrinsic_elements

def calculate_chempots(
self,
extrinsic_species: Optional[str] = None,
Expand Down Expand Up @@ -1759,6 +1769,11 @@ def _calculate_extrinsic_chempot_lims(
def chempots(self) -> dict:
"""
Returns the calculated chemical potential limits.
If this is used with ``ExtrinsicCompetingPhases``
before calling ``calculate_chempots`` with a specified
``extrinsic_species``, then the intrinsic chemical
potential limits will be returned.
"""
if not hasattr(self, "_chempots"):
self.calculate_chempots()
Expand Down
61 changes: 32 additions & 29 deletions tests/test_chemical_potentials.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -382,13 +382,11 @@ def tearDown(self) -> None:
def test_cpa_csv(self):
stable_cpa = chemical_potentials.CompetingPhasesAnalyzer(self.stable_system)
stable_cpa.from_csv(self.csv_path)
self.ext_cpa = chemical_potentials.CompetingPhasesAnalyzer(
self.stable_system, self.extrinsic_species
)
self.ext_cpa = chemical_potentials.CompetingPhasesAnalyzer(self.stable_system)
self.ext_cpa.from_csv(self.csv_path_ext)

assert len(stable_cpa.elemental) == 2
assert len(self.ext_cpa.elemental) == 3
assert len(stable_cpa.elements) == 2
assert len(self.ext_cpa.elements) == 3
assert any(entry["Formula"] == "O2" for entry in stable_cpa.data)
assert np.isclose(
next(
Expand All @@ -408,11 +406,9 @@ def test_cpa_chempots(self):
# check if it's no longer Element
assert isinstance(next(iter(stable_cpa.intrinsic_chempots["elemental_refs"].keys())), str)

self.ext_cpa = chemical_potentials.CompetingPhasesAnalyzer(
self.stable_system, self.extrinsic_species
)
self.ext_cpa = chemical_potentials.CompetingPhasesAnalyzer(self.stable_system)
self.ext_cpa.from_csv(self.csv_path_ext)
chempot_df = self.ext_cpa.calculate_chempots()
chempot_df = self.ext_cpa.calculate_chempots(extrinsic_species="La")
assert next(iter(chempot_df["La-Limiting Phase"])) == "La2Zr2O7"
assert np.isclose(next(iter(chempot_df["La"])), -9.46298748)

Expand Down Expand Up @@ -457,10 +453,16 @@ def test_ext_cpa_chempots(self):
stable_cpa.from_csv(self.csv_path)
_compare_chempot_dicts(stable_cpa.chempots, self.parsed_chempots)

self.ext_cpa = chemical_potentials.CompetingPhasesAnalyzer(
self.stable_system, self.extrinsic_species
)
# for ext_cpa, because we haven't yet specified the extrinsic species (with calculate_chempots),
# just returns the intrinsic chempots:
self.ext_cpa = chemical_potentials.CompetingPhasesAnalyzer(self.stable_system)
self.ext_cpa.from_csv(self.csv_path_ext)
for host_el, chempot in self.ext_cpa.chempots["elemental_refs"].items():
assert chempot == self.parsed_ext_chempots["elemental_refs"][host_el]

self.ext_cpa = chemical_potentials.CompetingPhasesAnalyzer(self.stable_system)
self.ext_cpa.from_csv(self.csv_path_ext)
self.ext_cpa.calculate_chempots(extrinsic_species="La")
assert self.ext_cpa.chempots["elemental_refs"] == self.parsed_ext_chempots["elemental_refs"]

def test_sort_by(self):
Expand All @@ -478,7 +480,7 @@ def test_vaspruns(self):
cpa = chemical_potentials.CompetingPhasesAnalyzer(self.stable_system)
path = self.path / "ZrO2"
cpa.from_vaspruns(path=path, folder="relax", csv_path=self.csv_path)
assert len(cpa.elemental) == 2
assert len(cpa.elements) == 2
assert cpa.data[0]["Formula"] == "O2"

cpa_no = chemical_potentials.CompetingPhasesAnalyzer(self.stable_system)
Expand All @@ -488,10 +490,11 @@ def test_vaspruns(self):
with pytest.raises(ValueError):
cpa_no.from_vaspruns(path=0)

ext_cpa = chemical_potentials.CompetingPhasesAnalyzer(self.stable_system, self.extrinsic_species)
ext_cpa = chemical_potentials.CompetingPhasesAnalyzer(self.stable_system)
path2 = self.path / "La_ZrO2"
ext_cpa.from_vaspruns(path=path2, folder="relax", csv_path=self.csv_path_ext)
assert len(ext_cpa.elemental) == 3
assert len(ext_cpa.elements) == 3
assert len(ext_cpa.extrinsic_elements) == 1
# sorted by num_species, then alphabetically, then by num_atoms_in_fu, then by
# formation_energy
assert [entry["Formula"] for entry in ext_cpa.data] == [
Expand Down Expand Up @@ -559,13 +562,13 @@ def test_vaspruns(self):
all_paths.append(ppgz)
lst_cpa = chemical_potentials.CompetingPhasesAnalyzer(self.stable_system)
lst_cpa.from_vaspruns(path=all_paths)
assert len(lst_cpa.elemental) == 2
assert len(lst_cpa.elements) == 2
assert len(lst_cpa.vasprun_paths) == 8

all_fols = [p / "relax" for p in path.iterdir() if not p.name.startswith(".")]
lst_fols_cpa = chemical_potentials.CompetingPhasesAnalyzer(self.stable_system)
lst_fols_cpa.from_vaspruns(path=all_fols)
assert len(lst_fols_cpa.elemental) == 2
assert len(lst_fols_cpa.elements) == 2

def test_vaspruns_hidden_files(self):
cpa = chemical_potentials.CompetingPhasesAnalyzer(self.stable_system)
Expand Down Expand Up @@ -693,14 +696,10 @@ def test_to_csv(self):
# check chem limits the same:
_compare_chempot_dicts(stable_cpa.chempots, reloaded_cpa.chempots)

self.ext_cpa = chemical_potentials.CompetingPhasesAnalyzer(
self.stable_system, self.extrinsic_species
)
self.ext_cpa = chemical_potentials.CompetingPhasesAnalyzer(self.stable_system)
self.ext_cpa.from_csv(self.csv_path_ext)
self.ext_cpa.to_csv("competing_phases.csv")
reloaded_ext_cpa = chemical_potentials.CompetingPhasesAnalyzer(
self.stable_system, self.extrinsic_species
)
reloaded_ext_cpa = chemical_potentials.CompetingPhasesAnalyzer(self.stable_system)
reloaded_ext_cpa.from_csv("competing_phases.csv")
reloaded_ext_cpa._get_and_sort_formation_energy_data()

Expand All @@ -723,17 +722,21 @@ def test_to_csv(self):
# check chem limits the same:
_compare_chempot_dicts(reloaded_cpa.chempots, stable_cpa.chempots)

self.ext_cpa = chemical_potentials.CompetingPhasesAnalyzer(
self.stable_system, self.extrinsic_species
)
# for ext_cpa, because we haven't yet specified the extrinsic species (with calculate_chempots),
# just returns the intrinsic chempots:
self.ext_cpa = chemical_potentials.CompetingPhasesAnalyzer(self.stable_system)
self.ext_cpa.from_csv(self.csv_path_ext)
for host_el, chempot in self.ext_cpa.chempots["elemental_refs"].items():
assert chempot == self.parsed_ext_chempots["elemental_refs"][host_el]

self.ext_cpa = chemical_potentials.CompetingPhasesAnalyzer(self.stable_system)
self.ext_cpa.from_csv(self.csv_path_ext)
self.ext_cpa.calculate_chempots(extrinsic_species="La")
assert self.ext_cpa.chempots["elemental_refs"] == self.parsed_ext_chempots["elemental_refs"]

# test correct sorting:
self.ext_cpa.to_csv("competing_phases.csv", prune_polymorphs=True, sort_by_energy=True)
reloaded_ext_cpa_energy_sorted = chemical_potentials.CompetingPhasesAnalyzer(
self.stable_system, self.extrinsic_species
)
reloaded_ext_cpa_energy_sorted = chemical_potentials.CompetingPhasesAnalyzer(self.stable_system)
reloaded_ext_cpa_energy_sorted.from_csv("competing_phases.csv")
assert len(reloaded_ext_cpa.data) == 8 # polymorphs pruned

Expand Down

0 comments on commit b47f0c9

Please sign in to comment.