simplify Poscar.from_file().structure to Structure.from_file()

pymatgen/analysis/surface_analysis.py

@@ -38,25 +38,22 @@
 import itertools
 import random
 import warnings
-from typing import TYPE_CHECKING
 
 import matplotlib.pyplot as plt
 import numpy as np
 from sympy import Symbol
 from sympy.solvers import linsolve, solve
 
 from pymatgen.analysis.wulff import WulffShape
+from pymatgen.core import Structure
 from pymatgen.core.composition import Composition
 from pymatgen.core.surface import get_slab_regions
 from pymatgen.entries.computed_entries import ComputedStructureEntry
-from pymatgen.io.vasp.outputs import Locpot, Outcar, Poscar
+from pymatgen.io.vasp.outputs import Locpot, Outcar
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.util.due import Doi, due
 from pymatgen.util.plotting import pretty_plot
 
-if TYPE_CHECKING:
-    from pymatgen.core import Structure
-
 EV_PER_ANG2_TO_JOULES_PER_M2 = 16.0217656
 
 __author__ = "Richard Tran"
@@ -1578,11 +1575,10 @@ def from_files(cls, poscar_filename, locpot_filename, outcar_filename, shift=0,
         Returns:
             WorkFunctionAnalyzer: A WorkFunctionAnalyzer instance.
         """
-        poscar = Poscar.from_file(poscar_filename)
         locpot = Locpot.from_file(locpot_filename)
         outcar = Outcar(outcar_filename)
         return cls(
-            poscar.structure,
+            Structure.from_file(poscar_filename),
             locpot.get_average_along_axis(2),
             outcar.efermi,
             shift=shift,

pymatgen/analysis/transition_state.py

@@ -17,7 +17,8 @@
 from scipy.interpolate import CubicSpline
 
 from pymatgen.analysis.structure_matcher import StructureMatcher
-from pymatgen.io.vasp import Outcar, Poscar
+from pymatgen.core import Structure
+from pymatgen.io.vasp import Outcar
 from pymatgen.util.plotting import pretty_plot
 
 
@@ -267,10 +268,10 @@ def from_dir(cls, root_dir, relaxation_dirs=None, **kwargs):
                         break
                 else:
                     raise ValueError(f"OUTCAR cannot be found for terminal point {d}")
-                structures.append(Poscar.from_file(poscar[0]).structure)
+                structures.append(Structure.from_file(poscar[0]))
             else:
                 outcars.append(Outcar(outcar[0]))
-                structures.append(Poscar.from_file(contcar[0]).structure)
+                structures.append(Structure.from_file(contcar[0]))
         return NEBAnalysis.from_outcars(outcars, structures, **kwargs)
 
     def as_dict(self):

tests/analysis/test_ewald.py

@@ -7,15 +7,14 @@
 from pytest import approx
 
 from pymatgen.analysis.ewald import EwaldMinimizer, EwaldSummation
-from pymatgen.io.vasp.inputs import Poscar
+from pymatgen.core.structure import Structure
 from pymatgen.util.testing import TEST_FILES_DIR
 
 
 class TestEwaldSummation(unittest.TestCase):
     def setUp(self):
         filepath = f"{TEST_FILES_DIR}/POSCAR"
-        poscar = Poscar.from_file(filepath, check_for_POTCAR=False)
-        self.original_struct = poscar.structure
+        self.original_struct = Structure.from_file(filepath)
         self.struct = self.original_struct.copy()
         self.struct.add_oxidation_state_by_element({"Li": 1, "Fe": 2, "P": 5, "O": -2})
 
@@ -109,9 +108,8 @@ def test_init(self):
     def test_site(self):
         """Test that uses an uncharged structure."""
         filepath = f"{TEST_FILES_DIR}/POSCAR"
-        p = Poscar.from_file(filepath, check_for_POTCAR=False)
-        original_s = p.structure
-        s = original_s.copy()
+        struct = Structure.from_file(filepath)
+        s = struct.copy()
         s.add_oxidation_state_by_element({"Li": 1, "Fe": 3, "P": 5, "O": -2})
 
         # Comparison to LAMMPS result

tests/analysis/test_structure_analyzer.py

@@ -19,7 +19,6 @@
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.periodic_table import Element
 from pymatgen.core.structure import Structure
-from pymatgen.io.vasp.inputs import Poscar
 from pymatgen.io.vasp.outputs import Xdatcar
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
 
@@ -42,16 +41,14 @@ def test_analyze(self):
 
 class TestRelaxationAnalyzer(unittest.TestCase):
     def setUp(self):
-        p = Poscar.from_file(f"{TEST_FILES_DIR}/POSCAR.Li2O", check_for_POTCAR=False)
-        s1 = p.structure
-        p = Poscar.from_file(f"{TEST_FILES_DIR}/CONTCAR.Li2O", check_for_POTCAR=False)
-        s2 = p.structure
+        s1 = Structure.from_file(f"{TEST_FILES_DIR}/POSCAR.Li2O")
+        s2 = Structure.from_file(f"{TEST_FILES_DIR}/CONTCAR.Li2O")
         self.analyzer = RelaxationAnalyzer(s1, s2)
 
     def test_vol_and_para_changes(self):
-        for v in self.analyzer.get_percentage_lattice_parameter_changes().values():
-            assert approx(v) == -0.0092040921155279731
-            latt_change = v
+        for val in self.analyzer.get_percentage_lattice_parameter_changes().values():
+            assert approx(val) == -0.0092040921155279731
+            latt_change = val
         vol_change = self.analyzer.get_percentage_volume_change()
         assert approx(vol_change) == -0.0273589101391
         # This is a simple cubic cell, so the latt and vol change are simply

tests/command_line/test_gulp_caller.py

@@ -24,7 +24,6 @@
     get_energy_tersoff,
 )
 from pymatgen.core.structure import Structure
-from pymatgen.io.vasp.inputs import Poscar
 from pymatgen.util.testing import TEST_FILES_DIR
 
 gulp_present = which("gulp") and os.getenv("GULP_LIB") and ("win" not in sys.platform)
@@ -100,8 +99,7 @@ def test_decimal(self):
 @unittest.skipIf(not gulp_present, "gulp not present.")
 class TestGulpIO(unittest.TestCase):
     def setUp(self):
-        p = Poscar.from_file(f"{TEST_FILES_DIR}/POSCAR.Al12O18", check_for_POTCAR=False)
-        self.structure = p.structure
+        self.structure = Structure.from_file(f"{TEST_FILES_DIR}/POSCAR.Al12O18")
         self.gio = GulpIO()
 
     def test_keyword_line_with_correct_keywords(self):
@@ -282,8 +280,7 @@ def setUp(self):
         self.val_dict = dict(zip(el, val))
 
     def test_get_energy_tersoff(self):
-        p = Poscar.from_file(f"{TEST_FILES_DIR}/POSCAR.Al12O18", check_for_POTCAR=False)
-        structure = p.structure
+        structure = Structure.from_file(f"{TEST_FILES_DIR}/POSCAR.Al12O18")
         energy = get_energy_tersoff(structure)
         assert isinstance(energy, float)
 

tests/core/test_trajectory.py

@@ -10,7 +10,6 @@
 from pymatgen.core.structure import Molecule, Structure
 from pymatgen.core.trajectory import Trajectory
 from pymatgen.io.qchem.outputs import QCOutput
-from pymatgen.io.vasp.inputs import Poscar
 from pymatgen.io.vasp.outputs import Xdatcar
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
 
@@ -418,8 +417,7 @@ def test_length(self):
         assert len(self.traj_mols) == len(self.molecules)
 
     def test_displacements(self):
-        poscar = Poscar.from_file(f"{TEST_FILES_DIR}/POSCAR")
-        structures = [poscar.structure]
+        structures = [Structure.from_file(f"{TEST_FILES_DIR}/POSCAR")]
         displacements = np.zeros((11, *np.shape(structures[-1].frac_coords)))
 
         for i in range(10):

tests/io/test_ase.py

@@ -9,15 +9,13 @@
 from pymatgen.core import Composition, Lattice, Molecule, Structure
 from pymatgen.core.structure import StructureError
 from pymatgen.io.ase import AseAtomsAdaptor
-from pymatgen.io.vasp.inputs import Poscar
 from pymatgen.util.testing import TEST_FILES_DIR
 
-poscar = Poscar.from_file(TEST_FILES_DIR / "POSCAR")
+structure = Structure.from_file(TEST_FILES_DIR / "POSCAR")
 ase = pytest.importorskip("ase")
 
 
 def test_get_atoms_from_structure():
-    structure = poscar.structure
     atoms = AseAtomsAdaptor.get_atoms(structure)
     ase_composition = Composition(atoms.get_chemical_formula())
     assert ase_composition == structure.composition
@@ -30,28 +28,24 @@ def test_get_atoms_from_structure():
     assert not atoms.has("initial_charges")
     assert atoms.calc is None
 
-    structure = poscar.structure
     prop = [3.14] * len(structure)
     structure.add_site_property("prop", prop)
     atoms = AseAtomsAdaptor.get_atoms(structure)
     assert atoms.get_array("prop").tolist() == prop
 
 
 def test_get_atoms_from_structure_mags():
-    structure = poscar.structure
     mags = [1.0] * len(structure)
     structure.add_site_property("final_magmom", mags)
     atoms = AseAtomsAdaptor.get_atoms(structure)
     assert not atoms.has("initial_magmoms")
     assert atoms.get_magnetic_moments().tolist() == mags
 
-    structure = poscar.structure
     initial_mags = [0.5] * len(structure)
     structure.add_site_property("magmom", initial_mags)
     atoms = AseAtomsAdaptor.get_atoms(structure)
     assert atoms.get_initial_magnetic_moments().tolist() == initial_mags
 
-    structure = poscar.structure
     mags = [1.0] * len(structure)
     structure.add_site_property("final_magmom", mags)
     initial_mags = [2.0] * len(structure)
@@ -62,20 +56,17 @@ def test_get_atoms_from_structure_mags():
 
 
 def test_get_atoms_from_structure_charge():
-    structure = poscar.structure
     charges = [1.0] * len(structure)
     structure.add_site_property("final_charge", charges)
     atoms = AseAtomsAdaptor.get_atoms(structure)
     assert not atoms.has("initial_charges")
     assert atoms.get_charges().tolist() == charges
 
-    structure = poscar.structure
     charges = [0.5] * len(structure)
     structure.add_site_property("charge", charges)
     atoms = AseAtomsAdaptor.get_atoms(structure)
     assert atoms.get_initial_charges().tolist() == charges
 
-    structure = poscar.structure
     charges = [1.0] * len(structure)
     structure.add_site_property("final_charge", charges)
     initial_charges = [2.0] * len(structure)
@@ -86,15 +77,13 @@ def test_get_atoms_from_structure_charge():
 
 
 def test_get_atoms_from_structure_oxi_states():
-    structure = poscar.structure
     oxi_states = [1.0] * len(structure)
     structure.add_oxidation_state_by_site(oxi_states)
     atoms = AseAtomsAdaptor.get_atoms(structure)
     assert atoms.get_array("oxi_states").tolist() == oxi_states
 
 
 def test_get_atoms_from_structure_dyn():
-    structure = poscar.structure
     structure.add_site_property("selective_dynamics", [[False] * 3] * len(structure))
     atoms = AseAtomsAdaptor.get_atoms(structure)
     assert atoms.constraints[0].get_indices().tolist() == [atom.index for atom in atoms]

tests/io/test_cif.py

@@ -13,7 +13,6 @@
 from pymatgen.core.structure import Structure
 from pymatgen.electronic_structure.core import Magmom
 from pymatgen.io.cif import CifBlock, CifParser, CifWriter
-from pymatgen.io.vasp.inputs import Poscar
 from pymatgen.symmetry.structure import SymmetrizedStructure
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
 
@@ -421,8 +420,8 @@ def test_parse_symbol(self):
 
     def test_cif_writer(self):
         filepath = f"{TEST_FILES_DIR}/POSCAR"
-        poscar = Poscar.from_file(filepath)
-        writer = CifWriter(poscar.structure, symprec=0.01)
+        struct = Structure.from_file(filepath)
+        writer = CifWriter(struct, symprec=0.01)
         answer = """# generated using pymatgen
 data_FePO4
 _symmetry_space_group_name_H-M   Pnma
@@ -466,13 +465,13 @@ def test_cif_writer(self):
 
     def test_symmetrized(self):
         filepath = f"{TEST_FILES_DIR}/POSCAR"
-        poscar = Poscar.from_file(filepath, check_for_POTCAR=False)
-        writer = CifWriter(poscar.structure, symprec=0.1)
+        struct = Structure.from_file(filepath)
+        writer = CifWriter(struct, symprec=0.1)
 
         cif = CifParser.from_str(str(writer))
         m = StructureMatcher()
 
-        assert m.fit(cif.get_structures()[0], poscar.structure)
+        assert m.fit(cif.get_structures()[0], struct)
 
         # for l1, l2 in zip(str(writer).split("\n"), answer.split("\n")):
         #     assert l1.strip() == l2.strip()
@@ -716,11 +715,10 @@ def test_get_lattice_from_lattice_type(self):
         parser = CifParser.from_str(cif_structure)
         s_test = parser.get_structures(primitive=False)[0]
         filepath = f"{TEST_FILES_DIR}/POSCAR"
-        poscar = Poscar.from_file(filepath)
-        s_ref = poscar.structure
+        struct = Structure.from_file(filepath)
 
         sm = StructureMatcher(stol=0.05, ltol=0.01, angle_tol=0.1)
-        assert sm.fit(s_ref, s_test)
+        assert sm.fit(struct, s_test)
 
     def test_empty(self):
         # single line

tests/io/test_cssr.py

@@ -6,7 +6,6 @@
 
 from pymatgen.core.structure import Structure
 from pymatgen.io.cssr import Cssr
-from pymatgen.io.vasp.inputs import Poscar
 from pymatgen.util.testing import TEST_FILES_DIR
 
 __author__ = "Shyue Ping Ong"
@@ -20,8 +19,7 @@
 class TestCssr(unittest.TestCase):
     def setUp(self):
         filepath = f"{TEST_FILES_DIR}/POSCAR"
-        p = Poscar.from_file(filepath)
-        self.cssr = Cssr(p.structure)
+        self.cssr = Cssr(Structure.from_file(filepath))
 
     def test_str(self):
         expected_string = """10.4118 6.0672 4.7595

tests/io/test_jarvis.py

@@ -2,23 +2,24 @@
 
 import unittest
 
-import pymatgen.io.jarvis as jio
-from pymatgen.io.vasp.inputs import Poscar
+from pymatgen.core import Structure
+from pymatgen.io.jarvis import Atoms, JarvisAtomsAdaptor
 from pymatgen.util.testing import TEST_FILES_DIR
 
 
+@unittest.skipIf(not Atoms, "JARVIS-tools not loaded.")
 class TestJarvisAtomsAdaptor(unittest.TestCase):
-    @unittest.skipIf(not jio.Atoms, "JARVIS-tools not loaded.")
     def test_get_atoms_from_structure(self):
-        structure = Poscar.from_file(f"{TEST_FILES_DIR}/POSCAR").structure
-        atoms = jio.JarvisAtomsAdaptor.get_atoms(structure)
+        struct = Structure.from_file(f"{TEST_FILES_DIR}/POSCAR")
+        atoms = JarvisAtomsAdaptor.get_atoms(struct)
         jarvis_composition = atoms.composition.reduced_formula
-        assert jarvis_composition == structure.composition.reduced_formula
+        assert jarvis_composition == struct.composition.reduced_formula
         assert atoms.lattice_mat is not None
         assert atoms.lattice_mat.any()
 
-    @unittest.skipIf(not jio.Atoms, "JARVIS-tools not loaded.")
     def test_get_structure(self):
-        structure = Poscar.from_file(f"{TEST_FILES_DIR}/POSCAR").structure
-        atoms = jio.JarvisAtomsAdaptor.get_atoms(structure)
-        assert jio.JarvisAtomsAdaptor.get_structure(atoms).composition.reduced_formula == "FePO4"
+        struct = Structure.from_file(f"{TEST_FILES_DIR}/POSCAR")
+        atoms = JarvisAtomsAdaptor.get_atoms(struct)
+        assert len(atoms.frac_coords) == len(struct) == 24
+        round_trip = JarvisAtomsAdaptor.get_structure(atoms)
+        assert round_trip.formula == struct.formula == "Fe4 P4 O16"

tests/io/test_xr.py

@@ -3,7 +3,6 @@
 import unittest
 
 from pymatgen.core.structure import Structure
-from pymatgen.io.vasp.inputs import Poscar
 from pymatgen.io.xr import Xr
 from pymatgen.util.testing import TEST_FILES_DIR
 
@@ -17,8 +16,8 @@
 
 class TestXr(unittest.TestCase):
     def setUp(self):
-        p = Poscar.from_file(TEST_FILES_DIR / "POSCAR")
-        self.xr = Xr(p.structure)
+        struct = Structure.from_file(TEST_FILES_DIR / "POSCAR")
+        self.xr = Xr(struct)
 
     def test_str(self):
         expected_string = """pymatgen   10.4118 6.0672 4.7595

tests/io/test_xyz.py

@@ -7,8 +7,8 @@
 import pytest
 from pytest import approx
 
+from pymatgen.core import Structure
 from pymatgen.core.structure import Molecule
-from pymatgen.io.vasp.inputs import Poscar
 from pymatgen.io.xyz import XYZ
 from pymatgen.util.testing import TEST_FILES_DIR
 
@@ -136,8 +136,7 @@ def test_from_file(self):
 
     def test_init_from_structure(self):
         filepath = f"{TEST_FILES_DIR}/POSCAR"
-        poscar = Poscar.from_file(filepath)
-        struct = poscar.structure
+        struct = Structure.from_file(filepath)
         xyz = XYZ(struct)
         expected = """24
 Fe4 P4 O16