Merge branch 'master' of github.com:materialsproject/pymatgen

pymatgen/io/vasp/inputs.py

@@ -209,18 +209,18 @@ def __setattr__(self, name, value):
         super().__setattr__(name, value)
 
     @staticmethod
-    def from_file(filename, check_for_POTCAR=True, read_velocities=True) -> Poscar:
+    def from_file(filename, check_for_potcar=True, read_velocities=True, **kwargs) -> Poscar:
         """
         Reads a Poscar from a file.
 
         The code will try its best to determine the elements in the POSCAR in
         the following order:
 
-        1. If check_for_POTCAR is True, the code will try to check if a POTCAR
+        1. If check_for_potcar is True, the code will try to check if a POTCAR
         is in the same directory as the POSCAR and use elements from that by
         default. (This is the VASP default sequence of priority).
         2. If the input file is VASP5-like and contains element symbols in the
-        6th line, the code will use that if check_for_POTCAR is False or there
+        6th line, the code will use that if check_for_potcar is False or there
         is no POTCAR found.
         3. Failing (2), the code will check if a symbol is provided at the end
         of each coordinate.
@@ -233,17 +233,21 @@ def from_file(filename, check_for_POTCAR=True, read_velocities=True) -> Poscar:
 
         Args:
             filename (str): File name containing Poscar data.
-            check_for_POTCAR (bool): Whether to check if a POTCAR is present
+            check_for_potcar (bool): Whether to check if a POTCAR is present
                 in the same directory as the POSCAR. Defaults to True.
             read_velocities (bool): Whether to read or not velocities if they
                 are present in the POSCAR. Default is True.
 
         Returns:
             Poscar object.
         """
+        if "check_for_POTCAR" in kwargs:
+            warnings.warn("check_for_POTCAR is deprecated. Use check_for_potcar instead.", DeprecationWarning)
+            check_for_potcar = kwargs.pop("check_for_POTCAR")
+
         dirname = os.path.dirname(os.path.abspath(filename))
         names = None
-        if check_for_POTCAR and SETTINGS.get("PMG_POTCAR_CHECKS") is not False:
+        if check_for_potcar and SETTINGS.get("PMG_POTCAR_CHECKS") is not False:
             potcars = glob(f"{dirname}/*POTCAR*")
             if potcars:
                 try:

tests/io/vasp/test_inputs.py

@@ -90,7 +90,7 @@ def test_init(self):
 
     def test_from_file(self):
         filepath = f"{TEST_FILES_DIR}/POSCAR.symbols_natoms_multilines"
-        poscar = Poscar.from_file(filepath, check_for_POTCAR=False, read_velocities=False)
+        poscar = Poscar.from_file(filepath, check_for_potcar=False, read_velocities=False)
         ordered_expected_elements = [
             "Fe",
             "Cr",
@@ -264,15 +264,15 @@ def test_str(self):
 
     def test_from_md_run(self):
         # Parsing from an MD type run with velocities and predictor corrector data
-        poscar = Poscar.from_file(f"{TEST_FILES_DIR}/CONTCAR.MD", check_for_POTCAR=False)
+        poscar = Poscar.from_file(f"{TEST_FILES_DIR}/CONTCAR.MD", check_for_potcar=False)
         assert np.sum(np.array(poscar.velocities)) == approx(0.0065417961324)
         assert poscar.predictor_corrector[0][0][0] == 0.33387820e00
         assert poscar.predictor_corrector[0][1][1] == -0.10583589e-02
 
     def test_write_md_poscar(self):
         # Parsing from an MD type run with velocities and predictor corrector data
         # And writing a new POSCAR from the new structure
-        poscar = Poscar.from_file(f"{TEST_FILES_DIR}/CONTCAR.MD", check_for_POTCAR=False)
+        poscar = Poscar.from_file(f"{TEST_FILES_DIR}/CONTCAR.MD", check_for_potcar=False)
 
         path = Path("POSCAR.testing.md")
         poscar.write_file(path)
@@ -286,7 +286,7 @@ def test_write_md_poscar(self):
 
     def test_setattr(self):
         filepath = f"{TEST_FILES_DIR}/POSCAR"
-        poscar = Poscar.from_file(filepath, check_for_POTCAR=False)
+        poscar = Poscar.from_file(filepath, check_for_potcar=False)
         with pytest.raises(ValueError, match="velocities array must be same length as the structure"):
             poscar.velocities = [[0, 0, 0]]
         poscar.selective_dynamics = np.array([[True, False, False]] * 24)
@@ -1187,7 +1187,7 @@ def setUp(self):
         filepath = f"{TEST_FILES_DIR}/INCAR"
         incar = Incar.from_file(filepath)
         filepath = f"{TEST_FILES_DIR}/POSCAR"
-        poscar = Poscar.from_file(filepath, check_for_POTCAR=False)
+        poscar = Poscar.from_file(filepath, check_for_potcar=False)
         if "PMG_VASP_PSP_DIR" not in os.environ:
             os.environ["PMG_VASP_PSP_DIR"] = str(TEST_FILES_DIR)
         filepath = f"{TEST_FILES_DIR}/POTCAR"