Clean up test files: VASP outputs

pymatgen/io/vasp/sets.py

@@ -2746,7 +2746,7 @@ def get_vasprun_outcar(path: str | Path, parse_dos: bool = True, parse_eigen: bo
  if len(vruns) == 0 or len(outcars) == 0:
  raise ValueError(f"Unable to get vasprun.xml/OUTCAR from prev calculation in {path}")
  vsfile_fullpath = str(path / "vasprun.xml")
- outcarfile_fullpath = str(path / "OUTCAR")
+ outcarfile_fullpath = str(path / "OUTCAR.gz")
  vsfile = vsfile_fullpath if vsfile_fullpath in vruns else sorted(vruns)[-1]
  outcarfile = outcarfile_fullpath if outcarfile_fullpath in outcars else sorted(outcars)[-1]
  return (

pymatgen/util/testing/__init__.py

@@ -26,6 +26,7 @@
 MODULE_DIR = Path(__file__).absolute().parent
 STRUCTURES_DIR = MODULE_DIR / ".." / "structures"
 TEST_FILES_DIR = Path(SETTINGS.get("PMG_TEST_FILES_DIR", f"{ROOT}/tests/files"))
+VASP_OUT_DIR = f"{TEST_FILES_DIR}/vasp/outputs"
 # fake POTCARs have original header information, meaning properties like number of electrons,
 # nuclear charge, core radii, etc. are unchanged (important for testing) while values of the and
 # pseudopotential kinetic energy corrections are scrambled to avoid VASP copyright infringement

tests/analysis/test_structure_analyzer.py

@@ -18,12 +18,12 @@
 )
 from pymatgen.core import Element, Lattice, Structure
 from pymatgen.io.vasp.outputs import Xdatcar
-from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pymatgen.util.testing import TEST_FILES_DIR, VASP_OUT_DIR, PymatgenTest
 
 
 class TestVoronoiAnalyzer(PymatgenTest):
  def setUp(self):
- self.ss = Xdatcar(f"{TEST_FILES_DIR}/XDATCAR.MD").structures
+ self.ss = Xdatcar(f"{VASP_OUT_DIR}/XDATCAR.MD").structures
  self.s = self.ss[1]
  self.va = VoronoiAnalyzer(cutoff=4)
 
@@ -40,7 +40,7 @@ def test_analyze(self):
 class TestRelaxationAnalyzer(unittest.TestCase):
  def setUp(self):
  s1 = Structure.from_file(f"{TEST_FILES_DIR}/POSCAR.Li2O")
- s2 = Structure.from_file(f"{TEST_FILES_DIR}/CONTCAR.Li2O")
+ s2 = Structure.from_file(f"{VASP_OUT_DIR}/CONTCAR.Li2O")
  self.analyzer = RelaxationAnalyzer(s1, s2)
 
  def test_vol_and_para_changes(self):
@@ -77,7 +77,7 @@ def test_connectivity_array(self):
 
 class TestMiscFunction(PymatgenTest):
  def test_average_coordination_number(self):
- xdatcar = Xdatcar(f"{TEST_FILES_DIR}/XDATCAR.MD")
+ xdatcar = Xdatcar(f"{VASP_OUT_DIR}/XDATCAR.MD")
  coordination_numbers = average_coordination_number(xdatcar.structures, freq=1)
  assert coordination_numbers["Fe"] == approx(
  4.771903318390836, 5

tests/analysis/test_xps.py

@@ -2,12 +2,12 @@
 
 from pymatgen.analysis.xps import XPS
 from pymatgen.io.vasp import Vasprun
-from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pymatgen.util.testing import VASP_OUT_DIR, PymatgenTest
 
 
 class XPSTestCase(PymatgenTest):
  def test_from_dos(self):
- vasp_run = Vasprun(f"{TEST_FILES_DIR}/vasprun.xml.LiF.gz")
+ vasp_run = Vasprun(f"{VASP_OUT_DIR}/vasprun.LiF.xml.gz")
  dos = vasp_run.complete_dos
  xps = XPS.from_dos(dos)
  assert len(xps) == 301

tests/apps/borg/test_hive.py

@@ -3,6 +3,7 @@
 import os
 import unittest
 
+from monty.tempfile import ScratchDir
 from pytest import approx
 
 from pymatgen.apps.borg.hive import (
@@ -11,7 +12,7 @@
  VaspToComputedEntryDrone,
 )
 from pymatgen.entries.computed_entries import ComputedStructureEntry
-from pymatgen.util.testing import TEST_FILES_DIR
+from pymatgen.util.testing import TEST_FILES_DIR, VASP_OUT_DIR
 
 
 class TestVaspToComputedEntryDrone(unittest.TestCase):
@@ -20,23 +21,30 @@ def setUp(self):
  self.structure_drone = VaspToComputedEntryDrone(inc_structure=True)
 
  def test_get_valid_paths(self):
- for path in os.walk(TEST_FILES_DIR):
- if path[0] == TEST_FILES_DIR:
+ for path in os.walk(VASP_OUT_DIR):
+ if path[0] == VASP_OUT_DIR:
  assert len(self.drone.get_valid_paths(path)) > 0
 
  def test_assimilate(self):
- entry = self.drone.assimilate(TEST_FILES_DIR)
- for param in ("hubbards", "is_hubbard", "potcar_spec", "run_type"):
- assert param in entry.parameters
- assert entry.data["efermi"] == approx(-6.62148548)
- assert entry.reduced_formula == "Xe"
- assert entry.energy == approx(0.5559329)
- entry = self.structure_drone.assimilate(TEST_FILES_DIR)
- assert entry.reduced_formula == "Xe"
- assert entry.energy == approx(0.5559329)
- assert isinstance(entry, ComputedStructureEntry)
- assert entry.structure is not None
- # assert len(entry.parameters["history"]) == 2
+ """Test assimilate data from "vasprun.xe.xml.gz" file."""
+
+ with ScratchDir("."):
+ # Need to rename the test file to "vasprun.xml.xe.gz" as
+ # hive is looking for pattern "vasprun.xml*"
+ os.symlink(f"{VASP_OUT_DIR}/vasprun.xe.xml.gz", "vasprun.xml.xe.gz")
+ entry = self.drone.assimilate(".")
+
+ for param in ("hubbards", "is_hubbard", "potcar_spec", "run_type"):
+ assert param in entry.parameters
+ assert entry.data["efermi"] == approx(-6.62148548)
+ assert entry.reduced_formula == "Xe"
+ assert entry.energy == approx(0.5559329)
+
+ entry = self.structure_drone.assimilate(".")
+ assert entry.reduced_formula == "Xe"
+ assert entry.energy == approx(0.5559329)
+ assert isinstance(entry, ComputedStructureEntry)
+ assert entry.structure is not None
 
  def test_as_from_dict(self):
  dct = self.structure_drone.as_dict()
@@ -50,8 +58,8 @@ def setUp(self):
  self.structure_drone = SimpleVaspToComputedEntryDrone(inc_structure=True)
 
  def test_get_valid_paths(self):
- for path in os.walk(TEST_FILES_DIR):
- if path[0] == TEST_FILES_DIR:
+ for path in os.walk(VASP_OUT_DIR):
+ if path[0] == VASP_OUT_DIR:
  assert len(self.drone.get_valid_paths(path)) > 0
 
  def test_as_from_dict(self):

tests/command_line/test_bader_caller.py

@@ -12,7 +12,7 @@
 from pytest import approx
 
 from pymatgen.command_line.bader_caller import BaderAnalysis, bader_analysis_from_path
-from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pymatgen.util.testing import TEST_FILES_DIR, VASP_OUT_DIR, PymatgenTest
 
 
 @unittest.skipIf(not which("bader"), "bader executable not present")
@@ -23,9 +23,9 @@ def setUp(self):
  def test_init(self):
  # test with reference file
  analysis = BaderAnalysis(
- chgcar_filename=f"{TEST_FILES_DIR}/CHGCAR.Fe3O4",
+ chgcar_filename=f"{VASP_OUT_DIR}/CHGCAR.Fe3O4.gz",
  potcar_filename=f"{TEST_FILES_DIR}/POTCAR.Fe3O4",
- chgref_filename=f"{TEST_FILES_DIR}/CHGCAR.Fe3O4_ref",
+ chgref_filename=f"{VASP_OUT_DIR}/CHGCAR.Fe3O4_ref.gz",
  )
  assert len(analysis.data) == 14
  assert analysis.data[0]["charge"] == approx(6.6136782, abs=1e-3)
@@ -55,7 +55,7 @@ def test_init(self):
  assert struct[0].specie.oxi_state == approx(1.3863218, abs=1e-3)
 
  # make sure bader still runs without reference file
- analysis = BaderAnalysis(chgcar_filename=f"{TEST_FILES_DIR}/CHGCAR.Fe3O4")
+ analysis = BaderAnalysis(chgcar_filename=f"{VASP_OUT_DIR}/CHGCAR.Fe3O4.gz")
  assert len(analysis.data) == 14
 
  # Test Cube file format parsing
@@ -118,9 +118,9 @@ def test_bader_analysis_from_path(self):
  def test_atom_parsing(self):
  # test with reference file
  analysis = BaderAnalysis(
- chgcar_filename=f"{TEST_FILES_DIR}/CHGCAR.Fe3O4",
+ chgcar_filename=f"{VASP_OUT_DIR}/CHGCAR.Fe3O4.gz",
  potcar_filename=f"{TEST_FILES_DIR}/POTCAR.Fe3O4",
- chgref_filename=f"{TEST_FILES_DIR}/CHGCAR.Fe3O4_ref",
+ chgref_filename=f"{VASP_OUT_DIR}/CHGCAR.Fe3O4_ref.gz",
  parse_atomic_densities=True,
  )
 
@@ -139,4 +139,4 @@ def test_missing_file_bader_exe_path(self):
  RuntimeError, match="BaderAnalysis requires the executable bader be in the PATH or the full path "
  ),
  ):
- BaderAnalysis(chgcar_filename=f"{TEST_FILES_DIR}/CHGCAR.Fe3O4", bader_path="")
+ BaderAnalysis(chgcar_filename=f"{VASP_OUT_DIR}/CHGCAR.Fe3O4.gz", bader_exe_path="")

tests/core/test_trajectory.py

@@ -10,13 +10,13 @@
 from pymatgen.core.trajectory import Trajectory
 from pymatgen.io.qchem.outputs import QCOutput
 from pymatgen.io.vasp.outputs import Xdatcar
-from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pymatgen.util.testing import TEST_FILES_DIR, VASP_OUT_DIR, PymatgenTest
 
 
 class TestTrajectory(PymatgenTest):
  def setUp(self):
- xdatcar = Xdatcar(f"{TEST_FILES_DIR}/Traj_XDATCAR")
- self.traj = Trajectory.from_file(f"{TEST_FILES_DIR}/Traj_XDATCAR")
+ xdatcar = Xdatcar(f"{VASP_OUT_DIR}/XDATCAR_traj")
+ self.traj = Trajectory.from_file(f"{VASP_OUT_DIR}/XDATCAR_traj")
  self.structures = xdatcar.structures
 
  out = QCOutput(f"{TEST_FILES_DIR}/molecules/new_qchem_files/ts.out")
@@ -221,15 +221,15 @@ def test_extend(self):
  traj = copy.deepcopy(self.traj)
 
  # Case of compatible trajectories
- compatible_traj = Trajectory.from_file(f"{TEST_FILES_DIR}/Traj_Combine_Test_XDATCAR_1")
+ compatible_traj = Trajectory.from_file(f"{VASP_OUT_DIR}/XDATCAR_traj_combine_test_1")
  traj.extend(compatible_traj)
 
- full_traj = Trajectory.from_file(f"{TEST_FILES_DIR}/Traj_Combine_Test_XDATCAR_Full")
+ full_traj = Trajectory.from_file(f"{VASP_OUT_DIR}/XDATCAR_traj_combine_test_full")
  compatible_success = self._check_traj_equality(self.traj, full_traj)
 
  # Case of incompatible trajectories
  traj = copy.deepcopy(self.traj)
- incompatible_traj = Trajectory.from_file(f"{TEST_FILES_DIR}/Traj_Combine_Test_XDATCAR_2")
+ incompatible_traj = Trajectory.from_file(f"{VASP_OUT_DIR}/XDATCAR_traj_combine_test_2")
  incompatible_test_success = False
  try:
  traj.extend(incompatible_traj)

tests/electronic_structure/test_bandstructure.py

@@ -20,7 +20,7 @@
 from pymatgen.electronic_structure.core import Orbital, Spin
 from pymatgen.electronic_structure.plotter import BSPlotterProjected
 from pymatgen.io.vasp import BSVasprun
-from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pymatgen.util.testing import TEST_FILES_DIR, VASP_OUT_DIR, PymatgenTest
 
 
 class TestKpoint(unittest.TestCase):
@@ -264,7 +264,7 @@ def test_reconstruct_band_structure(self):
 
  def test_vasprun_bs(self):
  bsv = BSVasprun(
- f"{TEST_FILES_DIR}/vasprun.xml.gz",
+ f"{VASP_OUT_DIR}/vasprun.xml.gz",
  parse_projected_eigen=True,
  parse_potcar_file=True,
  )

tests/electronic_structure/test_plotter.py

@@ -30,7 +30,7 @@
  plot_ellipsoid,
 )
 from pymatgen.io.vasp import Vasprun
-from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pymatgen.util.testing import TEST_FILES_DIR, VASP_OUT_DIR, PymatgenTest
 
 rc("text", usetex=False) # Disabling latex is needed for this test to work.
 
@@ -212,7 +212,7 @@ class TestBSDOSPlotter(unittest.TestCase):
  # Minimal baseline testing for get_plot. not a true test. Just checks that
  # it can actually execute.
  def test_methods(self):
- vasp_run = Vasprun(f"{TEST_FILES_DIR}/vasprun_Si_bands.xml.gz")
+ vasp_run = Vasprun(f"{VASP_OUT_DIR}/vasprun_Si_bands.xml.gz")
  plotter = BSDOSPlotter()
  band_struct = vasp_run.get_band_structure(kpoints_filename=f"{TEST_FILES_DIR}/KPOINTS_Si_bands")
  ax = plotter.get_plot(band_struct)

tests/entries/test_computed_entries.py

@@ -22,10 +22,9 @@
  TemperatureEnergyAdjustment,
 )
 from pymatgen.io.vasp.outputs import Vasprun
-from pymatgen.util.testing import TEST_FILES_DIR
+from pymatgen.util.testing import TEST_FILES_DIR, VASP_OUT_DIR
 
-filepath = f"{TEST_FILES_DIR}/vasprun.xml.gz"
-vasp_run = Vasprun(filepath)
+vasp_run = Vasprun(f"{VASP_OUT_DIR}/vasprun.xml.gz")
 
 
 def test_energy_adjustment():