def write_vasp_input(structure: IStructure,
kpath_division: int,
write_dir: str = "."):
vasp_input = VaspInput(
Incar.from_file("INCAR"),
Kpoints.automatic_linemode(kpath_division, HighSymmKpath(structure)),
Poscar(structure), Potcar.from_file("POTCAR"))
vasp_input.write_input(write_dir)
class VaspInputTest(PymatgenTest):
def setUp(self):
filepath = self.TEST_FILES_DIR / "INCAR"
incar = Incar.from_file(filepath)
filepath = self.TEST_FILES_DIR / "POSCAR"
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(self.TEST_FILES_DIR)
filepath = self.TEST_FILES_DIR / "POTCAR"
potcar = Potcar.from_file(filepath)
filepath = self.TEST_FILES_DIR / "KPOINTS.auto"
kpoints = Kpoints.from_file(filepath)
self.vinput = VaspInput(incar, kpoints, poscar, potcar)
def test_to_from_dict(self):
d = self.vinput.as_dict()
vinput = VaspInput.from_dict(d)
comp = vinput["POSCAR"].structure.composition
self.assertEqual(comp, Composition("Fe4P4O16"))
def test_write(self):
tmp_dir = Path("VaspInput.testing")
self.vinput.write_input(tmp_dir)
filepath = tmp_dir / "INCAR"
incar = Incar.from_file(filepath)
self.assertEqual(incar["NSW"], 99)
for name in ("INCAR", "POSCAR", "POTCAR", "KPOINTS"):
(tmp_dir / name).unlink()
tmp_dir.rmdir()
def test_run_vasp(self):
# To add some test.
with ScratchDir(".") as d:
self.vinput.run_vasp(d, vasp_cmd=["cat", "INCAR"])
with open(os.path.join(d, "vasp.out"), "r") as f:
output = f.read()
self.assertEqual(output.split("\n")[0], "ALGO = Damped")
def test_from_directory(self):
vi = VaspInput.from_directory(
self.TEST_FILES_DIR, optional_files={"CONTCAR.Li2O": Poscar}
)
self.assertEqual(vi["INCAR"]["ALGO"], "Damped")
self.assertIn("CONTCAR.Li2O", vi)
d = vi.as_dict()
vinput = VaspInput.from_dict(d)
self.assertIn("CONTCAR.Li2O", vinput)
class VaspInputTest(PymatgenTest):
def setUp(self):
filepath = self.TEST_FILES_DIR / 'INCAR'
incar = Incar.from_file(filepath)
filepath = self.TEST_FILES_DIR / 'POSCAR'
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(self.TEST_FILES_DIR)
filepath = self.TEST_FILES_DIR / 'POTCAR'
potcar = Potcar.from_file(filepath)
filepath = self.TEST_FILES_DIR / 'KPOINTS.auto'
kpoints = Kpoints.from_file(filepath)
self.vinput = VaspInput(incar, kpoints, poscar, potcar)
def test_to_from_dict(self):
d = self.vinput.as_dict()
vinput = VaspInput.from_dict(d)
comp = vinput["POSCAR"].structure.composition
self.assertEqual(comp, Composition("Fe4P4O16"))
def test_write(self):
tmp_dir = Path("VaspInput.testing")
self.vinput.write_input(tmp_dir)
filepath = tmp_dir / "INCAR"
incar = Incar.from_file(filepath)
self.assertEqual(incar["NSW"], 99)
for name in ("INCAR", "POSCAR", "POTCAR", "KPOINTS"):
(tmp_dir / name).unlink()
tmp_dir.rmdir()
def test_run_vasp(self):
# To add some test.
with ScratchDir(".") as d:
self.vinput.run_vasp(d, vasp_cmd=["cat", "INCAR"])
with open(os.path.join(d, "vasp.out"), "r") as f:
output = f.read()
self.assertEqual(output.split("\n")[0], "ALGO = Damped")
def test_from_directory(self):
vi = VaspInput.from_directory(self.TEST_FILES_DIR,
optional_files={"CONTCAR.Li2O": Poscar})
self.assertEqual(vi["INCAR"]["ALGO"], "Damped")
self.assertIn("CONTCAR.Li2O", vi)
d = vi.as_dict()
vinput = VaspInput.from_dict(d)
self.assertIn("CONTCAR.Li2O", vinput)
class VaspInputTest(unittest.TestCase):
def setUp(self):
filepath = os.path.join(test_dir, 'INCAR')
incar = Incar.from_file(filepath)
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
if "VASP_PSP_DIR" not in os.environ:
test_potcar_dir = os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "..", "..", "..",
"test_files"))
os.environ["VASP_PSP_DIR"] = test_potcar_dir
filepath = os.path.join(test_dir, 'POTCAR')
potcar = Potcar.from_file(filepath)
filepath = os.path.join(test_dir, 'KPOINTS.auto')
kpoints = Kpoints.from_file(filepath)
self.vinput = VaspInput(incar, kpoints, poscar, potcar)
def test_to_from_dict(self):
d = self.vinput.as_dict()
vinput = VaspInput.from_dict(d)
comp = vinput["POSCAR"].structure.composition
self.assertEqual(comp, Composition("Fe4P4O16"))
def test_write(self):
tmp_dir = "VaspInput.testing"
self.vinput.write_input(tmp_dir)
filepath = os.path.join(tmp_dir, "INCAR")
incar = Incar.from_file(filepath)
self.assertEqual(incar["NSW"], 99)
for name in ("INCAR", "POSCAR", "POTCAR", "KPOINTS"):
os.remove(os.path.join(tmp_dir, name))
os.rmdir(tmp_dir)
def test_from_directory(self):
vi = VaspInput.from_directory(test_dir,
optional_files={"CONTCAR.Li2O": Poscar})
self.assertEqual(vi["INCAR"]["ALGO"], "Damped")
self.assertIn("CONTCAR.Li2O", vi)
d = vi.as_dict()
vinput = VaspInput.from_dict(d)
self.assertIn("CONTCAR.Li2O", vinput)
class VaspInputTest(unittest.TestCase):
def setUp(self):
filepath = os.path.join(test_dir, 'INCAR')
incar = Incar.from_file(filepath)
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
if "VASP_PSP_DIR" not in os.environ:
test_potcar_dir = os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "..", "..", "..",
"test_files"))
os.environ["VASP_PSP_DIR"] = test_potcar_dir
filepath = os.path.join(test_dir, 'POTCAR')
potcar = Potcar.from_file(filepath)
filepath = os.path.join(test_dir, 'KPOINTS.auto')
kpoints = Kpoints.from_file(filepath)
self.vinput = VaspInput(incar, kpoints, poscar, potcar)
def test_to_from_dict(self):
d = self.vinput.as_dict()
vinput = VaspInput.from_dict(d)
comp = vinput["POSCAR"].structure.composition
self.assertEqual(comp, Composition("Fe4P4O16"))
def test_write(self):
tmp_dir = "VaspInput.testing"
self.vinput.write_input(tmp_dir)
filepath = os.path.join(tmp_dir, "INCAR")
incar = Incar.from_file(filepath)
self.assertEqual(incar["NSW"], 99)
for name in ("INCAR", "POSCAR", "POTCAR", "KPOINTS"):
os.remove(os.path.join(tmp_dir, name))
os.rmdir(tmp_dir)
def test_from_directory(self):
vi = VaspInput.from_directory(test_dir,
optional_files={"CONTCAR.Li2O": Poscar})
self.assertEqual(vi["INCAR"]["ALGO"], "Damped")
self.assertIn("CONTCAR.Li2O", vi)
d = vi.as_dict()
vinput = VaspInput.from_dict(d)
self.assertIn("CONTCAR.Li2O", vinput)
# POSCAR
poscar = Poscar(struct)
poscar_dict = poscar.as_dict()
# KPOINTS
k = 7
kpoints = Kpoints.gamma_automatic(kpts=(k, k, k), shift=(0.0, 0.0, 0.0))
# get POTCAR with right order from POSCAR
# check for prevoius element - if it's the same don't write it twice
prevoius_el = None
# initializing potcar_symbols
potcar_symbols = []
#getting sites list
sites = poscar_dict['structure']['sites']
# getting label for element on site
for site_index in range(0, len(sites)):
el = sites[site_index]['label']
# write only if it is different from the prevoious one
if prevoius_el != el:
potcar_symbols.append(potcar_choices[el])
prevoius_el = el
# set Potcar object
potcar = Potcar(symbols=potcar_symbols,
functional='PBE',
sym_potcar_map=None)
VASP_input = VaspInput(incar, kpoints, poscar, potcar)
VASP_input.write_input(file_dir, make_dir_if_not_present=True)
