def _verify_inputs(self):
"""Validation of input files under user NEB directory."""
user_incar = Incar.from_file(os.path.join(self.user_dir, "INCAR"))
ref_incar = Incar.from_file(os.path.join(self.ref_dir_input, "INCAR"))
# Check INCAR
params_to_check = self.get("params_to_check", [])
defaults = {"ICHAIN": 0, "LCLIMB": True}
for p in params_to_check:
if user_incar.get(p, defaults.get(p)) != ref_incar.get(p, defaults.get(p)):
raise ValueError("INCAR value of {} is inconsistent!".format(p))
# Check KPOINTS
user_kpoints = Kpoints.from_file(os.path.join(self.user_dir, "KPOINTS"))
ref_kpoints = Kpoints.from_file(os.path.join(self.ref_dir_input, "KPOINTS"))
if user_kpoints.style != ref_kpoints.style or user_kpoints.num_kpts != ref_kpoints.num_kpts:
raise ValueError("KPOINT files are inconsistent! "
"Paths are:\n{}\n{} with kpts = {} {}".format(
self.user_dir, self.ref_dir_input, user_kpoints, ref_kpoints))
# Check POTCAR
user_potcar = Potcar.from_file(os.path.join(self.user_dir, "POTCAR"))
ref_potcar = Potcar.from_file(os.path.join(self.ref_dir_input, "POTCAR"))
if user_potcar.symbols != ref_potcar.symbols:
raise ValueError("POTCAR files are inconsistent! "
"Paths are:\n{}\n{}".format(self.user_dir, self.ref_dir_input))
# Check POSCARs
for u, r in zip(self.user_sdir, self.ref_sdir_input):
user_poscar = Poscar.from_file(os.path.join(u, "POSCAR"))
ref_poscar = Poscar.from_file(os.path.join(r, "POSCAR"))
if user_poscar.natoms != ref_poscar.natoms or \
user_poscar.site_symbols != ref_poscar.site_symbols:
raise ValueError("POSCAR files are inconsistent! Paths are:\n{}\n{}".format(u, r))
def test_setup(self):
if "VASP_PSP_DIR" not in os.environ:
os.environ["VASP_PSP_DIR"] = test_dir
os.chdir(os.path.join(test_dir, 'setup_neb'))
v = VaspNEBJob("hello", half_kpts=True)
v.setup()
incar = Incar.from_file("INCAR")
count = multiprocessing.cpu_count()
if count > 1:
self.assertGreater(incar["NPAR"], 1)
kpt = Kpoints.from_file("KPOINTS")
kpt_pre = Kpoints.from_file("KPOINTS.orig")
self.assertEqual(kpt_pre.style.name, "Monkhorst")
self.assertEqual(kpt.style.name, "Gamma")
shutil.copy("KPOINTS.orig", "KPOINTS")
os.remove("INCAR.orig")
os.remove("KPOINTS.orig")
os.remove("POTCAR.orig")
poscars = glob.glob("[0-9][0-9]/POSCAR.orig")
for p in poscars:
os.remove(p)
def test_setup(self):
if "VASP_PSP_DIR" not in os.environ:
os.environ["VASP_PSP_DIR"] = test_dir
os.chdir(os.path.join(test_dir, 'setup_neb'))
v = VaspNEBJob("hello", half_kpts=True)
v.setup()
incar = Incar.from_file("INCAR")
count = multiprocessing.cpu_count()
if count > 1:
self.assertGreater(incar["NPAR"], 1)
kpt = Kpoints.from_file("KPOINTS")
kpt_pre = Kpoints.from_file("KPOINTS.orig")
self.assertEqual(kpt_pre.style.name, "Monkhorst")
self.assertEqual(kpt.style.name, "Gamma")
shutil.copy("KPOINTS.orig", "KPOINTS")
os.remove("INCAR.orig")
os.remove("KPOINTS.orig")
os.remove("POTCAR.orig")
poscars = glob.glob("[0-9][0-9]/POSCAR.orig")
for p in poscars:
os.remove(p)
def _verify_inputs(self):
user_incar = Incar.from_file(os.path.join(os.getcwd(), "INCAR"))
ref_incar = Incar.from_file(os.path.join(self["ref_dir"], "inputs", "INCAR"))
# perform some BASIC tests
# check INCAR
params_to_check = self.get("params_to_check", [])
defaults = {"ISPIN": 1, "ISMEAR": 1, "SIGMA": 0.2}
for p in params_to_check:
if user_incar.get(p, defaults.get(p)) != ref_incar.get(p, defaults.get(p)):
raise ValueError("INCAR value of {} is inconsistent!".format(p))
# check KPOINTS
user_kpoints = Kpoints.from_file(os.path.join(os.getcwd(), "KPOINTS"))
ref_kpoints = Kpoints.from_file(os.path.join(self["ref_dir"], "inputs", "KPOINTS"))
if user_kpoints.style != ref_kpoints.style or user_kpoints.num_kpts != ref_kpoints.num_kpts:
raise ValueError("KPOINT files are inconsistent! Paths are:\n{}\n{}".format(
os.getcwd(), os.path.join(self["ref_dir"], "inputs")))
# check POSCAR
user_poscar = Poscar.from_file(os.path.join(os.getcwd(), "POSCAR"))
ref_poscar = Poscar.from_file(os.path.join(self["ref_dir"], "inputs", "POSCAR"))
if user_poscar.natoms != ref_poscar.natoms or user_poscar.site_symbols != ref_poscar.site_symbols:
raise ValueError("POSCAR files are inconsistent! Paths are:\n{}\n{}".format(
os.getcwd(), os.path.join(self["ref_dir"], "inputs")))
# check POTCAR
user_potcar = Potcar.from_file(os.path.join(os.getcwd(), "POTCAR"))
ref_potcar = Potcar.from_file(os.path.join(self["ref_dir"], "inputs", "POTCAR"))
if user_potcar.symbols != ref_potcar.symbols:
raise ValueError("POTCAR files are inconsistent! Paths are:\n{}\n{}".format(
os.getcwd(), os.path.join(self["ref_dir"], "inputs")))
logger.info("RunVaspFake: verified inputs successfully")
def _verify_inputs(self):
"""Validation of input files under user NEB directory."""
user_incar = Incar.from_file(os.path.join(self.user_dir, "INCAR"))
ref_incar = Incar.from_file(os.path.join(self.ref_dir_input, "INCAR"))
# Check INCAR
params_to_check = self.get("params_to_check", [])
defaults = {"ICHAIN": 0, "LCLIMB": True}
for p in params_to_check:
if user_incar.get(p, defaults.get(p)) != ref_incar.get(p, defaults.get(p)):
raise ValueError("INCAR value of {} is inconsistent!".format(p))
# Check KPOINTS
user_kpoints = Kpoints.from_file(os.path.join(self.user_dir, "KPOINTS"))
ref_kpoints = Kpoints.from_file(os.path.join(self.ref_dir_input, "KPOINTS"))
if user_kpoints.style != ref_kpoints.style or user_kpoints.num_kpts != ref_kpoints.num_kpts:
raise ValueError("KPOINT files are inconsistent! "
"Paths are:\n{}\n{} with kpts = {} {}".format(
self.user_dir, self.ref_dir_input, user_kpoints, ref_kpoints))
# Check POTCAR
user_potcar = Potcar.from_file(os.path.join(self.user_dir, "POTCAR"))
ref_potcar = Potcar.from_file(os.path.join(self.ref_dir_input, "POTCAR"))
if user_potcar.symbols != ref_potcar.symbols:
raise ValueError("POTCAR files are inconsistent! "
"Paths are:\n{}\n{}".format(self.user_dir, self.ref_dir_input))
# Check POSCARs
for u, r in zip(self.user_sdir, self.ref_sdir_input):
user_poscar = Poscar.from_file(os.path.join(u, "POSCAR"))
ref_poscar = Poscar.from_file(os.path.join(r, "POSCAR"))
if user_poscar.natoms != ref_poscar.natoms or \
user_poscar.site_symbols != ref_poscar.site_symbols:
raise ValueError("POSCAR files are inconsistent! Paths are:\n{}\n{}".format(u, r))
def setup(self):
"""
Performs initial setup for VaspNEBJob, including overriding any settings
and backing up.
"""
neb_dirs = self.neb_dirs
if self.backup:
# Back up KPOINTS, INCAR, POTCAR
for f in VASP_NEB_INPUT_FILES:
shutil.copy(f, "{}.orig".format(f))
# Back up POSCARs
for path in neb_dirs:
poscar = os.path.join(path, "POSCAR")
shutil.copy(poscar, "{}.orig".format(poscar))
if self.half_kpts and os.path.exists("KPOINTS"):
kpts = Kpoints.from_file("KPOINTS")
kpts.kpts = np.maximum(np.array(kpts.kpts) / 2, 1)
kpts.kpts = kpts.kpts.astype(int).tolist()
if tuple(kpts.kpts[0]) == (1, 1, 1):
kpt_dic = kpts.as_dict()
kpt_dic["generation_style"] = 'Gamma'
kpts = Kpoints.from_dict(kpt_dic)
kpts.write_file("KPOINTS")
if self.auto_npar:
try:
incar = Incar.from_file("INCAR")
import multiprocessing
# Try sge environment variable first
# (since multiprocessing counts cores on the current
# machine only)
ncores = os.environ.get(
'NSLOTS') or multiprocessing.cpu_count()
ncores = int(ncores)
for npar in range(int(math.sqrt(ncores)), ncores):
if ncores % npar == 0:
incar["NPAR"] = npar
break
incar.write_file("INCAR")
except:
pass
if self.auto_continue and \
os.path.exists("STOPCAR") and \
not os.access("STOPCAR", os.W_OK):
# Remove STOPCAR
os.chmod("STOPCAR", 0o644)
os.remove("STOPCAR")
# Copy CONTCAR to POSCAR
for path in self.neb_sub:
contcar = os.path.join(path, "CONTCAR")
poscar = os.path.join(path, "POSCAR")
shutil.copy(contcar, poscar)
if self.settings_override is not None:
VaspModder().apply_actions(self.settings_override)
def setup(self):
"""
Performs initial setup for VaspNEBJob, including overriding any settings
and backing up.
"""
neb_dirs = self.neb_dirs
if self.backup:
# Back up KPOINTS, INCAR, POTCAR
for f in VASP_NEB_INPUT_FILES:
shutil.copy(f, "{}.orig".format(f))
# Back up POSCARs
for path in neb_dirs:
poscar = os.path.join(path, "POSCAR")
shutil.copy(poscar, "{}.orig".format(poscar))
if self.half_kpts and os.path.exists("KPOINTS"):
kpts = Kpoints.from_file("KPOINTS")
kpts.kpts = np.maximum(np.array(kpts.kpts) / 2, 1)
kpts.kpts = kpts.kpts.astype(int).tolist()
if tuple(kpts.kpts[0]) == (1, 1, 1):
kpt_dic = kpts.as_dict()
kpt_dic["generation_style"] = 'Gamma'
kpts = Kpoints.from_dict(kpt_dic)
kpts.write_file("KPOINTS")
if self.auto_npar:
try:
incar = Incar.from_file("INCAR")
import multiprocessing
# Try sge environment variable first
# (since multiprocessing counts cores on the current
# machine only)
ncores = os.environ.get('NSLOTS') or multiprocessing.cpu_count()
ncores = int(ncores)
for npar in range(int(math.sqrt(ncores)),
ncores):
if ncores % npar == 0:
incar["NPAR"] = npar
break
incar.write_file("INCAR")
except:
pass
if self.auto_continue and \
os.path.exists("STOPCAR") and \
not os.access("STOPCAR", os.W_OK):
# Remove STOPCAR
os.chmod("STOPCAR", 0o644)
os.remove("STOPCAR")
# Copy CONTCAR to POSCAR
for path in self.neb_sub:
contcar = os.path.join(path, "CONTCAR")
poscar = os.path.join(path, "POSCAR")
shutil.copy(contcar, poscar)
if self.settings_override is not None:
VaspModder().apply_actions(self.settings_override)
def _verify_inputs(self):
user_incar = Incar.from_file(os.path.join(os.getcwd(), "INCAR"))
# Carry out some BASIC tests.
# Check INCAR
if self.get("check_incar", True):
ref_incar = Incar.from_file(
os.path.join(self["ref_dir"], "inputs", "INCAR"))
params_to_check = self.get("params_to_check", [])
defaults = {"ISPIN": 1, "ISMEAR": 1, "SIGMA": 0.2}
for p in params_to_check:
if user_incar.get(p, defaults.get(p)) != ref_incar.get(
p, defaults.get(p)):
raise ValueError(
"INCAR value of {} is inconsistent!".format(p))
# Check KPOINTS
if self.get("check_kpoints", True):
user_kpoints = Kpoints.from_file(
os.path.join(os.getcwd(), "KPOINTS"))
ref_kpoints = Kpoints.from_file(
os.path.join(self["ref_dir"], "inputs", "KPOINTS"))
if user_kpoints.style != ref_kpoints.style or \
user_kpoints.num_kpts != ref_kpoints.num_kpts:
raise ValueError(
"KPOINT files are inconsistent! Paths are:\n{}\n{} with kpoints {} and {}"
.format(os.getcwd(), os.path.join(self["ref_dir"],
"inputs"), user_kpoints,
ref_kpoints))
# Check POSCAR
if self.get("check_poscar", True):
user_poscar = Poscar.from_file(os.path.join(os.getcwd(), "POSCAR"))
ref_poscar = Poscar.from_file(
os.path.join(self["ref_dir"], "inputs", "POSCAR"))
if user_poscar.natoms != ref_poscar.natoms or user_poscar.site_symbols != \
ref_poscar.site_symbols:
raise ValueError(
"POSCAR files are inconsistent! Paths are:\n{}\n{}".format(
os.getcwd(), os.path.join(self["ref_dir"], "inputs")))
# Check POTCAR
if self.get("check_potcar", True):
user_potcar = Potcar.from_file(os.path.join(os.getcwd(), "POTCAR"))
ref_potcar = Potcar.from_file(
os.path.join(self["ref_dir"], "inputs", "POTCAR"))
if user_potcar.symbols != ref_potcar.symbols:
raise ValueError(
"POTCAR files are inconsistent! Paths are:\n{}\n{}".format(
os.getcwd(), os.path.join(self["ref_dir"], "inputs")))
logger.info("RunVaspFake: verified inputs successfully")
def test_setup(self):
with cd(os.path.join(test_dir, 'setup_neb')):
with ScratchDir('.', copy_from_current_on_enter=True) as d:
v = VaspNEBJob("hello", half_kpts=True)
v.setup()
incar = Incar.from_file("INCAR")
count = multiprocessing.cpu_count()
if count > 3:
self.assertGreater(incar["NPAR"], 1)
kpt = Kpoints.from_file("KPOINTS")
kpt_pre = Kpoints.from_file("KPOINTS.orig")
self.assertEqual(kpt_pre.style.name, "Monkhorst")
self.assertEqual(kpt.style.name, "Gamma")
def test_setup(self):
with cd(os.path.join(test_dir, 'setup_neb')):
with ScratchDir('.', copy_from_current_on_enter=True) as d:
v = VaspNEBJob("hello", half_kpts=True)
v.setup()
incar = Incar.from_file("INCAR")
count = multiprocessing.cpu_count()
if count > 3:
self.assertGreater(incar["NPAR"], 1)
kpt = Kpoints.from_file("KPOINTS")
kpt_pre = Kpoints.from_file("KPOINTS.orig")
self.assertEqual(kpt_pre.style.name, "Monkhorst")
self.assertEqual(kpt.style.name, "Gamma")
def band_path(line_density):
"""
for band calculation
"""
poscar = Poscar.from_file('POSCAR', check_for_POTCAR=False)
highsymmkp = MyHighSymmKpath(poscar.structure)
kpts = highsymmkp.get_kpoints(line_density)
args = {'comment': "Kpoints for band calc",
'kpts': kpts[0],
'num_kpts': len(kpts[0]),
'labels': kpts[1],
'style': 'Reciprocal',
'kpts_weights': [1]*len(kpts[0])}
kpoints = Kpoints(**args)
kpoints.write_file('KPOINTS_band')
def post_process(self, task_list):
cwd = os.getcwd()
poscar_start = os.path.abspath(
os.path.join(task_list[0], '..', 'POSCAR'))
os.chdir(os.path.join(task_list[0], '..'))
if os.path.isfile(os.path.join(task_list[0], 'INCAR')):
incar = incar_upper(
Incar.from_file(os.path.join(task_list[0], 'INCAR')))
kspacing = incar.get('KSPACING')
kgamma = incar.get('KGAMMA', False)
ret = vasp.make_kspacing_kpoints(poscar_start, kspacing, kgamma)
kp = Kpoints.from_string(ret)
if os.path.isfile('KPOINTS'):
os.remove('KPOINTS')
kp.write_file("KPOINTS")
os.chdir(cwd)
kpoints_universal = os.path.abspath(
os.path.join(task_list[0], '..', 'KPOINTS'))
for ii in task_list:
if os.path.isfile(os.path.join(ii, 'KPOINTS')):
os.remove(os.path.join(ii, 'KPOINTS'))
if os.path.islink(os.path.join(ii, 'KPOINTS')):
os.remove(os.path.join(ii, 'KPOINTS'))
os.chdir(ii)
os.symlink(os.path.relpath(kpoints_universal), 'KPOINTS')
os.chdir(cwd)
def setUpClass(cls):
if not os.environ.get("VASP_PSP_DIR"):
os.environ["VASP_PSP_DIR"] = os.path.join(module_dir,
"reference_files")
print(
'Note: This system is not set up to run VASP jobs. '
'Please set your VASP_PSP_DIR environment variable.')
cls.struct_si = PymatgenTest.get_structure("Si")
cls.ref_incar = Incar.from_file(
os.path.join(module_dir, "reference_files", "setup_test", "INCAR"))
cls.ref_poscar = Poscar.from_file(
os.path.join(module_dir, "reference_files", "setup_test",
"POSCAR"))
cls.ref_potcar = Potcar.from_file(
os.path.join(module_dir, "reference_files", "setup_test",
"POTCAR"))
cls.ref_kpoints = Kpoints.from_file(
os.path.join(module_dir, "reference_files", "setup_test",
"KPOINTS"))
cls.ref_incar_preserve = Incar.from_file(os.path.join(module_dir,
"reference_files",
"preserve_incar",
"INCAR"))
def make_atom_mp_relax_set():
for element, potcar in PotcarSet.mp_relax_set.potcar_dict().items():
if potcar is None:
continue
if is_target_element(element) is False:
continue
structure = Structure(Lattice.cubic(10),
coords=[[0.5] * 3],
species=[element])
mp_set = MPRelaxSet(structure,
user_kpoints_settings=Kpoints(kpts=((1, 1, 1), )),
user_incar_settings={
"ALGO": "D",
"ISIF": 2,
"ISMEAR": 0,
"MAGMOM": {
"H": 1.0
},
"NELM": 300
})
Path(element).mkdir()
mp_set.write_input(element)
def run_task(self, fw_spec):
from pymatgen.io.vasp import Kpoints
modify_kpoints_params = self.get('modify_kpoints_params')
kpoint = Kpoints.from_file('KPOINTS')
if 'kpts' in modify_kpoints_params.keys():
kpoint.kpts = modify_kpoints_params['kpts']
kpoint.write_file('KPOINTS')
def make_vasp_kpoints_from_incar(work_dir, jdata):
cwd = os.getcwd()
fp_aniso_kspacing = jdata.get('fp_aniso_kspacing')
os.chdir(work_dir)
# get kspacing and kgamma from incar
assert (os.path.exists('INCAR'))
with open('INCAR') as fp:
incar = fp.read()
standard_incar = incar_upper(Incar.from_string(incar))
if fp_aniso_kspacing is None:
try:
kspacing = standard_incar['KSPACING']
except KeyError:
raise RuntimeError("KSPACING must be given in INCAR")
else:
kspacing = fp_aniso_kspacing
try:
gamma = standard_incar['KGAMMA']
if isinstance(gamma, bool):
pass
else:
if gamma[0].upper() == "T":
gamma = True
else:
gamma = False
except KeyError:
raise RuntimeError("KGAMMA must be given in INCAR")
# check poscar
assert (os.path.exists('POSCAR'))
# make kpoints
ret = make_kspacing_kpoints('POSCAR', kspacing, gamma)
kp = Kpoints.from_string(ret)
kp.write_file("KPOINTS")
os.chdir(cwd)
def testEntry(self):
entries = []
for i, f in enumerate(self.iter_path):
vi = VaspInput.from_directory(f)
ls = LabeledSystem(os.path.join(f, 'OUTCAR'))
attrib = loadfn(os.path.join(f, 'job.json'))
comp = vi['POSCAR'].structure.composition
entry = Entry(comp,
'vasp',
vi.as_dict(),
ls.as_dict(),
entry_id='pku-' + str(i),
attribute=attrib)
entries.append(entry)
self.assertEqual(len(entries), len(self.ref_entries))
ret0 = entries[0]
r0 = self.ref_entries[0]
self.assertEqual(Incar.from_dict(ret0.inputs['INCAR']),
Incar.from_dict(r0.inputs['INCAR']))
self.assertEqual(str(r0.inputs['KPOINTS']),
str(Kpoints.from_dict(ret0.inputs['KPOINTS'])))
self.assertEqual(ret0.inputs['POTCAR'], r0.inputs['POTCAR'].as_dict())
self.assertEqual(
Poscar.from_dict(ret0.inputs['POSCAR']).structure,
r0.inputs['POSCAR'].structure)
self.assertEqual(ret0.entry_id, 'pku-0')
def setUpClass(cls):
cls.struct_si = PymatgenTest.get_structure("Si")
cls.ref_incar = Incar.from_file(p_setup_test / "INCAR")
cls.ref_poscar = Poscar.from_file(p_setup_test / "POSCAR")
cls.ref_potcar = Potcar.from_file(p_setup_test / "POTCAR")
cls.ref_kpoints = Kpoints.from_file(p_setup_test / "KPOINTS")
cls.ref_incar_preserve = Incar.from_file(p_preserve_incar / "INCAR")
def _verify_files(self):
self.assertEqual(Incar.from_file(os.path.join(module_dir, "INCAR")), self.ref_incar)
self.assertEqual(str(Poscar.from_file(os.path.join(module_dir, "POSCAR"))),
str(self.ref_poscar))
self.assertEqual(Potcar.from_file(os.path.join(module_dir, "POTCAR")).symbols,
self.ref_potcar.symbols)
self.assertEqual(str(Kpoints.from_file(os.path.join(module_dir, "KPOINTS"))),
str(self.ref_kpoints))
def _get_kpoints(kpoint_mesh: Union[float, int, List[int]],
structure: Structure,
symprec: float = 0.01,
return_full_kpoints: bool = False
) -> Tuple[np.ndarray, ...]:
"""Gets the symmetry inequivalent k-points from a k-point mesh.
Follows the same process as SpacegroupAnalyzer.get_ir_reciprocal_mesh
but is faster and allows returning of the full k-point mesh and mapping.
Args:
kpoint_mesh: The k-point mesh as a 1x3 array. E.g.,``[6, 6, 6]``.
Alternatively, if a single value is provided this will be
treated as a reciprocal density and the k-point mesh dimensions
generated automatically.
structure: A structure.
symprec: Symmetry tolerance used when determining the symmetry
inequivalent k-points on which to interpolate.
return_full_kpoints: Whether to return the full list of k-points
covering the entire Brillouin zone and the indices of
inequivalent k-points.
Returns:
The irreducible k-points and their weights as tuple, formatted as::
(ir_kpoints, weights)
If return_full_kpoints, the data will be returned as::
(ir_kpoints, weights, full_kpoints, ir_kpoints_idx, ir_to_full_idx)
Where ``ir_kpoints_idx`` is the index of the unique irreducible k-points
in ``full_kpoints``. ``ir_to_full_idx`` is a list of indices that can be
used to construct the full Brillouin zone from the ir_mesh. Note the
ir -> full conversion will only work with calculated scalar properties
such as energy (not vector properties such as velocity).
"""
if isinstance(kpoint_mesh, (int, float)):
# TODO: Update this to use reciprocal length as in kgrid
kpoint_mesh = Kpoints.automatic_density_by_vol(structure, kpoint_mesh)
atoms = AseAtomsAdaptor().get_atoms(structure)
if not symprec:
symprec = 0.1
mapping, grid = spglib.get_ir_reciprocal_mesh(
kpoint_mesh, atoms, symprec=symprec)
full_kpoints = grid / kpoint_mesh
ir_kpoints_idx, ir_to_full_idx, weights = np.unique(
mapping, return_inverse=True, return_counts=True)
ir_kpoints = full_kpoints[ir_kpoints_idx]
if return_full_kpoints:
return ir_kpoints, weights, full_kpoints, ir_kpoints_idx, ir_to_full_idx
else:
return ir_kpoints, weights
def setUp(self):
lattice = [[10, 0, 0], [-5, 8.660254, 0], [0, 0, 5]]
self.hexagonal = Structure(lattice=lattice,
species=["H"],
coords=[[0, 0, 0]])
self.kpoints_g = Kpoints.gamma_automatic(kpts=(2, 2, 2))
lattice2 = [[1, 0, 0], [0, 2, 0], [0, 0, 3]]
self.ortho = Structure(lattice=lattice2,
species=["H"],
coords=[[0, 0, 0]])
self.kpoints_mp = Kpoints.monkhorst_automatic(kpts=(2, 2, 2))
self.kpoints_reciprocal = \
Kpoints(style=Kpoints.supported_modes.Reciprocal,
num_kpts=2,
kpts=((0, 0, 0), (0.5, 0.5, 0.5)),
kpts_weights=[1, 1])
def _check_kpoints(testCase, idx) :
fp_path = os.path.join('iter.%06d' % idx, '02.fp')
tasks = glob.glob(os.path.join(fp_path, 'task.*'))
for ii in tasks :
kpoints=Kpoints.from_file(os.path.join(os.path.join(ii, 'KPOINTS')))
incar=Incar.from_file(os.path.join(os.path.join(ii, 'INCAR')))
kspacing = incar['KSPACING']
gamma = incar['KGAMMA']
if isinstance(gamma,bool):
pass
else:
if gamma[0].upper()=="T":
gamma=True
else:
gamma=False
ret=make_kspacing_kpoints(os.path.join(os.path.join(ii, 'POSCAR')), kspacing, gamma)
kpoints_ref=Kpoints.from_string(ret)
testCase.assertEqual(repr(kpoints), repr(kpoints_ref))
def _verify_files(self, skip_kpoints=False, preserve_incar=False):
if not preserve_incar:
self.assertEqual(Incar.from_file(os.path.join(module_dir, "INCAR")), self.ref_incar)
self.assertEqual(str(Poscar.from_file(os.path.join(module_dir, "POSCAR"))), str(self.ref_poscar))
self.assertEqual((Potcar.from_file(os.path.join(module_dir, "POTCAR"))).symbols, self.ref_potcar.symbols)
if not skip_kpoints:
self.assertEqual(str(Kpoints.from_file(os.path.join(module_dir, "KPOINTS"))), str(self.ref_kpoints))
else:
self.assertEqual(Incar.from_file(os.path.join(module_dir, "INCAR")), self.ref_incar_preserve)
def double_relaxation_run(cls, vasp_cmd, auto_npar=True, ediffg=-0.05,
half_kpts_first_relax=False, auto_continue=False):
"""
Returns a list of two jobs corresponding to an AFLOW style double
relaxation run.
Args:
vasp_cmd (str): Command to run vasp as a list of args. For example,
if you are using mpirun, it can be something like
["mpirun", "pvasp.5.2.11"]
auto_npar (bool): Whether to automatically tune NPAR to be sqrt(
number of cores) as recommended by VASP for DFT calculations.
Generally, this results in significant speedups. Defaults to
True. Set to False for HF, GW and RPA calculations.
ediffg (float): Force convergence criteria for subsequent runs (
ignored for the initial run.)
half_kpts_first_relax (bool): Whether to halve the kpoint grid
for the first relaxation. Speeds up difficult convergence
considerably. Defaults to False.
Returns:
List of two jobs corresponding to an AFLOW style run.
"""
incar_update = {"ISTART": 1}
if ediffg:
incar_update["EDIFFG"] = ediffg
settings_overide_1 = None
settings_overide_2 = [
{"dict": "INCAR",
"action": {"_set": incar_update}},
{"file": "CONTCAR",
"action": {"_file_copy": {"dest": "POSCAR"}}}]
if half_kpts_first_relax and os.path.exists("KPOINTS") and \
os.path.exists("POSCAR"):
kpts = Kpoints.from_file("KPOINTS")
orig_kpts_dict = kpts.as_dict()
# lattice vectors with length < 8 will get >1 KPOINT
kpts.kpts = np.round(np.maximum(np.array(kpts.kpts) / 2,
1)).astype(int).tolist()
low_kpts_dict = kpts.as_dict()
settings_overide_1 = [
{"dict": "KPOINTS",
"action": {"_set": low_kpts_dict}}
]
settings_overide_2.append(
{"dict": "KPOINTS",
"action": {"_set": orig_kpts_dict}}
)
return [VaspJob(vasp_cmd, final=False, suffix=".relax1",
auto_npar=auto_npar, auto_continue=auto_continue,
settings_override=settings_overide_1),
VaspJob(vasp_cmd, final=True, backup=False, suffix=".relax2",
auto_npar=auto_npar, auto_continue=auto_continue,
settings_override=settings_overide_2)]
def double_relaxation_run(cls, vasp_cmd, auto_npar=True, ediffg=-0.05,
half_kpts_first_relax=False, auto_continue=False):
"""
Returns a list of two jobs corresponding to an AFLOW style double
relaxation run.
Args:
vasp_cmd (str): Command to run vasp as a list of args. For example,
if you are using mpirun, it can be something like
["mpirun", "pvasp.5.2.11"]
auto_npar (bool): Whether to automatically tune NPAR to be sqrt(
number of cores) as recommended by VASP for DFT calculations.
Generally, this results in significant speedups. Defaults to
True. Set to False for HF, GW and RPA calculations.
ediffg (float): Force convergence criteria for subsequent runs (
ignored for the initial run.)
half_kpts_first_relax (bool): Whether to halve the kpoint grid
for the first relaxation. Speeds up difficult convergence
considerably. Defaults to False.
Returns:
List of two jobs corresponding to an AFLOW style run.
"""
incar_update = {"ISTART": 1}
if ediffg:
incar_update["EDIFFG"] = ediffg
settings_overide_1 = None
settings_overide_2 = [
{"dict": "INCAR",
"action": {"_set": incar_update}},
{"file": "CONTCAR",
"action": {"_file_copy": {"dest": "POSCAR"}}}]
if half_kpts_first_relax and os.path.exists("KPOINTS") and \
os.path.exists("POSCAR"):
kpts = Kpoints.from_file("KPOINTS")
orig_kpts_dict = kpts.as_dict()
# lattice vectors with length < 8 will get >1 KPOINT
kpts.kpts = np.round(np.maximum(np.array(kpts.kpts) / 2,
1)).astype(int).tolist()
low_kpts_dict = kpts.as_dict()
settings_overide_1 = [
{"dict": "KPOINTS",
"action": {"_set": low_kpts_dict}}
]
settings_overide_2.append(
{"dict": "KPOINTS",
"action": {"_set": orig_kpts_dict}}
)
return [VaspJob(vasp_cmd, final=False, suffix=".relax1",
auto_npar=auto_npar, auto_continue=auto_continue,
settings_override=settings_overide_1),
VaspJob(vasp_cmd, final=True, backup=False, suffix=".relax2",
auto_npar=auto_npar, auto_continue=auto_continue,
settings_override=settings_overide_2)]
def _get_dos_calc(self, phonon, structure, kpoint_density):
tempfilename = tempfile.gettempprefix() + '.yaml'
kpoint = Kpoints.automatic_density(structure=structure,
kppa=kpoint_density,
force_gamma=True)
phonon.run_mesh(kpoint.kpts[0])
phonon.run_total_dos()
phonon.write_total_dos(filename=tempfilename)
dos = get_ph_dos(tempfilename)
os.remove(tempfilename)
return dos
def _verify_files(self, skip_kpoints=False, preserve_incar=False):
if not preserve_incar:
self.assertEqual(Incar.from_file("INCAR"), self.ref_incar)
self.assertEqual(str(Poscar.from_file("POSCAR")), str(self.ref_poscar))
self.assertEqual(Potcar.from_file("POTCAR").symbols,
self.ref_potcar.symbols)
if not skip_kpoints:
self.assertEqual(str(Kpoints.from_file("KPOINTS")),
str(self.ref_kpoints))
else:
self.assertEqual(Incar.from_file("INCAR"),
self.ref_incar_preserve)
def test_modify_kpoints(self):
# create an KPOINTS
kpoints = self.ref_kpoints
kpoints.write_file("KPOINTS")
# modify and test
ft = ModifyKpoints(kpoints_update={"kpts": [[3, 4, 5]]}, )
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
kpoints_mod = Kpoints.from_file("KPOINTS")
self.assertEqual(kpoints_mod.kpts, [[3, 4, 5]])
def run_task(self, fw_spec):
kpoints_name = self.get("input_filename", "KPOINTS")
kpoints = Kpoints.from_file(kpoints_name)
kpoints_update = env_chk(self.get("kpoints_update"), fw_spec)
if kpoints_update:
for key, value in kpoints_update.items():
setattr(kpoints, key, value)
kpoints.write_file(self.get("output_filename", "KPOINTS"))
def _get_phono3pyobject_phono3py(self, structure, potential,
kpoint_density,
displacementdistancephono3py,
max_distance_third_order):
cell = get_phonopy_structure(structure)
kpoint = Kpoints.automatic_density(structure=structure,
kppa=kpoint_density,
force_gamma=True)
mesh = kpoint.kpts[0]
phono3py = Phono3py(cell,
self.smat,
primitive_matrix=[[1, 0., 0.], [0., 1, 0.],
[0., 0., 1]],
mesh=mesh,
log_level=1)
phono3py.generate_displacements(
distance=displacementdistancephono3py,
cutoff_pair_distance=max_distance_third_order)
scells_with_disps = phono3py.get_supercells_with_displacements()
disp_dataset = phono3py.get_displacement_dataset()
numatoms = len(scells_with_disps[0].get_scaled_positions())
dummy_force = np.zeros((numatoms, 3))
set_of_forces = []
for scell in scells_with_disps:
if scell is not None:
# this part is adapted from: https://web.archive.org/web/20200610084959/https://github.com/phonopy/phonopy/blob/develop/example/ase/8Si-phonon.py
# Copyright by Atsushi Togo
cell = Atoms(symbols=scell.get_chemical_symbols(),
scaled_positions=scell.get_scaled_positions(),
cell=scell.get_cell(),
pbc=True)
cell.set_calculator(potential)
forces = cell.get_forces()
drift_force = forces.sum(axis=0)
print(("[Phonopy] Drift force:" + "%11.5f" * 3) %
tuple(drift_force))
for force in forces:
force -= drift_force / forces.shape[0]
set_of_forces.append(forces)
else:
set_of_forces.append(dummy_force)
phono3py.produce_fc3(set_of_forces,
displacement_dataset=disp_dataset,
symmetrize_fc3r=True)
fc3 = phono3py.get_fc3()
show_drift_fc3(fc3)
return phono3py
def _verify_files(self):
self.assertEqual(Incar.from_file(os.path.join(module_dir, "INCAR")),
self.ref_incar)
self.assertEqual(
str(Poscar.from_file(os.path.join(module_dir, "POSCAR"))),
str(self.ref_poscar))
self.assertEqual(
Potcar.from_file(os.path.join(module_dir, "POTCAR")).symbols,
self.ref_potcar.symbols)
self.assertEqual(
str(Kpoints.from_file(os.path.join(module_dir, "KPOINTS"))),
str(self.ref_kpoints))
def test_run(self):
with ScratchDir(".") as d:
for f in ["INCAR", "POSCAR", "POTCAR", "KPOINTS"]:
shutil.copy(os.path.join(test_dir, f), f)
oldincar = Incar.from_file("INCAR")
v = GenerateVaspInputJob("pymatgen.io.vasp.sets.MPNonSCFSet",
contcar_only=False)
v.run()
incar = Incar.from_file("INCAR")
self.assertEqual(incar["ICHARG"], 11)
self.assertEqual(oldincar["ICHARG"], 1)
kpoints = Kpoints.from_file("KPOINTS")
self.assertEqual(str(kpoints.style), "Reciprocal")
def test_run(self):
with ScratchDir(".") as d:
for f in ["INCAR", "POSCAR", "POTCAR", "KPOINTS"]:
shutil.copy(os.path.join('..', test_dir, f), f)
oldincar = Incar.from_file("INCAR")
v = GenerateVaspInputJob("pymatgen.io.vasp.sets.MPNonSCFSet",
contcar_only=False)
v.run()
incar = Incar.from_file("INCAR")
self.assertEqual(incar["ICHARG"], 11)
self.assertEqual(oldincar["ICHARG"], 1)
kpoints = Kpoints.from_file("KPOINTS")
self.assertEqual(str(kpoints.style), "Reciprocal")
def setUpClass(cls):
coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
lattice = Lattice([[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]])
cls.struct_si = IStructure(lattice, ["Si"] * 2, coords)
cls.ref_incar = Incar.from_file(
os.path.join(module_dir, "..", "test_files", "setup_test", "INCAR"))
cls.ref_poscar = Poscar.from_file(
os.path.join(module_dir, "..", "test_files", "setup_test", "POSCAR"))
cls.ref_potcar = Potcar.from_file(
os.path.join(module_dir, "..", "test_files", "setup_test", "POTCAR"))
cls.ref_kpoints = Kpoints.from_file(
os.path.join(module_dir, "..", "test_files", "setup_test", "KPOINTS"))
def setUpClass(cls):
if not SETTINGS.get("VASP_PSP_DIR"):
SETTINGS["VASP_PSP_DIR"] = os.path.join(module_dir, "reference_files")
print(
"This system is not set up to run VASP jobs. "
"Please set VASP_PSP_DIR variable in your ~/.pmgrc.yaml file."
)
cls.struct_si = PymatgenTest.get_structure("Si")
cls.ref_incar = Incar.from_file(os.path.join(module_dir, "reference_files", "setup_test", "INCAR"))
cls.ref_poscar = Poscar.from_file(os.path.join(module_dir, "reference_files", "setup_test", "POSCAR"))
cls.ref_potcar = Potcar.from_file(os.path.join(module_dir, "reference_files", "setup_test", "POTCAR"))
cls.ref_kpoints = Kpoints.from_file(os.path.join(module_dir, "reference_files", "setup_test", "KPOINTS"))
cls.ref_incar_preserve = Incar.from_file(os.path.join(module_dir, "reference_files", "preserve_incar", "INCAR"))
def setUpClass(cls):
cls.struct_si = PymatgenTest.get_structure("Si")
cls.ref_incar = Incar.from_file(
os.path.join(module_dir, "..", "..", "test_files", "setup_test", "INCAR"))
cls.ref_poscar = Poscar.from_file(
os.path.join(module_dir, "..", "..", "test_files", "setup_test",
"POSCAR"))
cls.ref_potcar = Potcar.from_file(
os.path.join(module_dir, "..", "..", "test_files", "setup_test",
"POTCAR"))
cls.ref_kpoints = Kpoints.from_file(
os.path.join(module_dir, "..", "..", "test_files", "setup_test",
"KPOINTS"))
cls.ref_incar_preserve = Incar.from_file(os.path.join(module_dir,
"..", "..", "test_files",
"preserve_incar", "INCAR"))
def setUpClass(cls):
cls.struct_si = PymatgenTest.get_structure("Si")
cls.ref_incar = Incar.from_file(
os.path.join(module_dir, "..", "..", "test_files", "setup_test", "INCAR"))
cls.ref_poscar = Poscar.from_file(
os.path.join(module_dir, "..", "..", "test_files", "setup_test",
"POSCAR"))
cls.ref_potcar = Potcar.from_file(
os.path.join(module_dir, "..", "..", "test_files", "setup_test",
"POTCAR"))
cls.ref_kpoints = Kpoints.from_file(
os.path.join(module_dir, "..", "..", "test_files", "setup_test",
"KPOINTS"))
cls.ref_incar_preserve = Incar.from_file(os.path.join(module_dir,
"..", "..", "test_files",
"preserve_incar", "INCAR"))
def setUpClass(cls):
if not SETTINGS.get("VASP_PSP_DIR"):
raise unittest.SkipTest(
"This system is not set up to run VASP jobs. "
"Please set VASP_PSP_DIR variable in your ~/.pmgrc.yaml file."
)
coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
lattice = Lattice(
[[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]
)
cls.struct_si = IStructure(lattice, ["Si"] * 2, coords)
cls.ref_incar = Incar.from_file(os.path.join(module_dir, "reference_files", "setup_test", "INCAR"))
cls.ref_poscar = Poscar.from_file(os.path.join(module_dir, "reference_files", "setup_test", "POSCAR"))
cls.ref_potcar = Potcar.from_file(os.path.join(module_dir, "reference_files", "setup_test", "POTCAR"))
cls.ref_kpoints = Kpoints.from_file(os.path.join(module_dir, "reference_files", "setup_test", "KPOINTS"))
def make_atom_mp_relax_set():
for element, potcar in PotcarSet.mp_relax_set.potcar_dict().items():
if potcar is None:
continue
Path(element).mkdir()
structure = Structure(Lattice.cubic(10),
coords=[[0.5] * 3],
species=[element])
mp_set = MPRelaxSet(structure,
user_kpoints_settings=Kpoints(kpts=((1, 1, 1), )),
user_incar_settings={
"ISIF": 2,
"ISMEAR": 0,
"NUPDOWN": nupdown[element],
"NELM": 300
})
mp_set.write_input(element)
def setUpClass(cls):
coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
lattice = Lattice([[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]])
cls.struct_si = IStructure(lattice, ["Si"] * 2, coords)
cls.ref_incar = Incar.from_file(
os.path.join(module_dir, "..", "test_files", "setup_test",
"INCAR"))
cls.ref_poscar = Poscar.from_file(
os.path.join(module_dir, "..", "test_files", "setup_test",
"POSCAR"))
cls.ref_potcar = Potcar.from_file(
os.path.join(module_dir, "..", "test_files", "setup_test",
"POTCAR"))
cls.ref_kpoints = Kpoints.from_file(
os.path.join(module_dir, "..", "test_files", "setup_test",
"KPOINTS"))
def from_structure(cls,
structure: Structure,
reciprocal_density: Optional[int] = 50000,
**kwargs):
"""
Get a ShengBTE control object from a structure.
Args:
structure: A structure object.
reciprocal_density: If not None, the q-point grid ("ngrid") will be
set using this density.
kwargs: Additional options to be passed to the Control constructor.
See the docstring of the __init__ method for more details
Returns:
A ShengBTE control object.
"""
elements = list(map(str, structure.composition.elements))
unique_nums = np.unique(structure.atomic_numbers)
types_dict = dict(zip(unique_nums, range(len(unique_nums))))
types = [types_dict[i] + 1 for i in structure.atomic_numbers]
control_dict = {
"nelements": structure.ntypesp,
"natoms": structure.num_sites,
"norientations": 0,
"lfactor": 0.1,
"lattvec": structure.lattice.matrix.tolist(),
"elements": elements,
"types": types,
"positions": structure.frac_coords.tolist(),
}
if reciprocal_density:
kpoints = Kpoints.automatic_density(structure, reciprocal_density)
control_dict["ngrid"] = kpoints.kpts[0]
control_dict.update(**kwargs)
return Control(**control_dict)
def _verify_files(self,
skip_kpoints=False,
preserve_incar=False,
potcar_spec=False):
if not preserve_incar:
self.assertEqual(Incar.from_file("INCAR"), self.ref_incar)
poscar = Poscar.from_file("POSCAR")
self.assertEqual(str(poscar), str(self.ref_poscar))
if potcar_spec:
symbols = Path("POTCAR.spec").read_text().split()
self.assertEqual(symbols, self.ref_potcar.symbols)
else:
potcar = Potcar.from_file("POTCAR")
self.assertEqual(potcar.symbols, self.ref_potcar.symbols)
if not skip_kpoints:
kpoints = Kpoints.from_file("KPOINTS")
self.assertEqual(str(kpoints), str(self.ref_kpoints))
else:
self.assertEqual(Incar.from_file("INCAR"), self.ref_incar_preserve)
def setUpClass(cls):
if not SETTINGS.get("VASP_PSP_DIR"):
raise unittest.SkipTest(
'This system is not set up to run VASP jobs. '
'Please set VASP_PSP_DIR variable in your ~/.pmgrc.yaml file.')
coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
lattice = Lattice([[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]])
cls.struct_si = IStructure(lattice, ["Si"] * 2, coords)
cls.ref_incar = Incar.from_file(
os.path.join(module_dir, "reference_files", "setup_test", "INCAR"))
cls.ref_poscar = Poscar.from_file(
os.path.join(module_dir, "reference_files", "setup_test",
"POSCAR"))
cls.ref_potcar = Potcar.from_file(
os.path.join(module_dir, "reference_files", "setup_test",
"POTCAR"))
cls.ref_kpoints = Kpoints.from_file(
os.path.join(module_dir, "reference_files", "setup_test",
"KPOINTS"))
def setUpClass(cls):
if not SETTINGS.get("VASP_PSP_DIR"):
SETTINGS["VASP_PSP_DIR"] = os.path.join(module_dir,
"reference_files")
print(
'This system is not set up to run VASP jobs. '
'Please set VASP_PSP_DIR variable in your ~/.pmgrc.yaml file.')
cls.struct_si = PymatgenTest.get_structure("Si")
cls.ref_incar = Incar.from_file(
os.path.join(module_dir, "reference_files", "setup_test", "INCAR"))
cls.ref_poscar = Poscar.from_file(
os.path.join(module_dir, "reference_files", "setup_test",
"POSCAR"))
cls.ref_potcar = Potcar.from_file(
os.path.join(module_dir, "reference_files", "setup_test",
"POTCAR"))
cls.ref_kpoints = Kpoints.from_file(
os.path.join(module_dir, "reference_files", "setup_test",
"KPOINTS"))
cls.ref_incar_preserve = Incar.from_file(
os.path.join(module_dir, "reference_files", "preserve_incar",
"INCAR"))
def run(self):
"""
Perform the actual VASP run.
Returns:
(subprocess.Popen) Used for monitoring.
"""
cmd = list(self.vasp_cmd)
if self.auto_gamma:
kpts = Kpoints.from_file("KPOINTS")
if kpts.style == Kpoints.supported_modes.Gamma \
and tuple(kpts.kpts[0]) == (1, 1, 1):
if self.gamma_vasp_cmd is not None and which(
self.gamma_vasp_cmd[-1]):
cmd = self.gamma_vasp_cmd
elif which(cmd[-1] + ".gamma"):
cmd[-1] += ".gamma"
logger.info("Running {}".format(" ".join(cmd)))
with open(self.output_file, 'w') as f_std, \
open(self.stderr_file, "w", buffering=1) as f_err:
# Use line buffering for stderr
p = subprocess.Popen(cmd, stdout=f_std, stderr=f_err)
return p
def run(self):
"""
Perform the actual VASP run.
Returns:
(subprocess.Popen) Used for monitoring.
"""
cmd = list(self.vasp_cmd)
if self.auto_gamma:
kpts = Kpoints.from_file("KPOINTS")
if kpts.style == Kpoints.supported_modes.Gamma \
and tuple(kpts.kpts[0]) == (1, 1, 1):
if self.gamma_vasp_cmd is not None and which(
self.gamma_vasp_cmd[-1]):
cmd = self.gamma_vasp_cmd
elif which(cmd[-1] + ".gamma"):
cmd[-1] += ".gamma"
logger.info("Running {}".format(" ".join(cmd)))
with open(self.output_file, 'w') as f_std, \
open(self.stderr_file, "w", buffering=1) as f_err:
# Use line buffering for stderr
p = subprocess.Popen(cmd, stdout=f_std, stderr=f_err)
return p
def full_opt_run(cls, vasp_cmd, vol_change_tol=0.02,
max_steps=10, ediffg=-0.05, half_kpts_first_relax=False,
**vasp_job_kwargs):
"""
Returns a generator of jobs for a full optimization run. Basically,
this runs an infinite series of geometry optimization jobs until the
% vol change in a particular optimization is less than vol_change_tol.
Args:
vasp_cmd (str): Command to run vasp as a list of args. For example,
if you are using mpirun, it can be something like
["mpirun", "pvasp.5.2.11"]
vol_change_tol (float): The tolerance at which to stop a run.
Defaults to 0.05, i.e., 5%.
max_steps (int): The maximum number of runs. Defaults to 10 (
highly unlikely that this limit is ever reached).
ediffg (float): Force convergence criteria for subsequent runs (
ignored for the initial run.)
half_kpts_first_relax (bool): Whether to halve the kpoint grid
for the first relaxation. Speeds up difficult convergence
considerably. Defaults to False.
\*\*vasp_job_kwargs: Passthrough kwargs to VaspJob. See
:class:`custodian.vasp.jobs.VaspJob`.
Returns:
Generator of jobs.
"""
for i in range(max_steps):
if i == 0:
settings = None
backup = True
if half_kpts_first_relax and os.path.exists("KPOINTS") and \
os.path.exists("POSCAR"):
kpts = Kpoints.from_file("KPOINTS")
orig_kpts_dict = kpts.as_dict()
kpts.kpts = np.maximum(np.array(kpts.kpts) / 2, 1).tolist()
low_kpts_dict = kpts.as_dict()
settings = [
{"dict": "KPOINTS",
"action": {"_set": low_kpts_dict}}
]
else:
backup = False
initial = Poscar.from_file("POSCAR").structure
final = Poscar.from_file("CONTCAR").structure
vol_change = (final.volume - initial.volume) / initial.volume
logger.info("Vol change = %.1f %%!" % (vol_change * 100))
if abs(vol_change) < vol_change_tol:
logger.info("Stopping optimization!")
break
else:
incar_update = {"ISTART": 1}
if ediffg:
incar_update["EDIFFG"] = ediffg
settings = [
{"dict": "INCAR",
"action": {"_set": incar_update}},
{"file": "CONTCAR",
"action": {"_file_copy": {"dest": "POSCAR"}}}]
if i == 1 and half_kpts_first_relax:
settings.append({"dict": "KPOINTS",
"action": {"_set": orig_kpts_dict}})
logger.info("Generating job = %d!" % (i+1))
yield VaspJob(vasp_cmd, final=False, backup=backup,
suffix=".relax%d" % (i+1), settings_override=settings,
**vasp_job_kwargs)
def vac_antisite_def_struct_gen(args):
mpid = args.mpid
mapi_key = args.mapi_key
cellmax = args.cellmax
if not mpid:
print ("============\nERROR: Provide an mpid\n============")
return
if not mapi_key:
with MPRester() as mp:
struct = mp.get_structure_by_material_id(mpid)
else:
with MPRester(mapi_key) as mp:
struct = mp.get_structure_by_material_id(mpid)
prim_struct_sites = len(struct.sites)
struct = SpacegroupAnalyzer(struct).get_conventional_standard_structure()
conv_struct_sites = len(struct.sites)
conv_prim_rat = int(conv_struct_sites/prim_struct_sites)
sc_scale = get_sc_scale(struct,cellmax)
mpvis = MPRelaxSet(struct, user_incar_settings={"LDAU": False})
# Begin defaults: All default settings.
blk_vasp_incar_param = {'IBRION':-1,'EDIFF':1e-4,'EDIFFG':0.001,'NSW':0,}
def_vasp_incar_param = {'ISIF':2,'NELM':99,'IBRION':2,'EDIFF':1e-6,
'EDIFFG':0.001,'NSW':40,}
kpoint_den = 6000
# End defaults
ptcr_flag = True
try:
potcar = mpvis.potcar
except:
print ("VASP POTCAR folder not detected.\n" \
"Only INCAR, POSCAR, KPOINTS are generated.\n" \
"If you have VASP installed on this system, \n" \
"refer to pymatgen documentation for configuring the settings.")
ptcr_flag = False
vac = Vacancy(struct, {}, {})
scs = vac.make_supercells_with_defects(sc_scale)
site_no = scs[0].num_sites
if site_no > cellmax:
max_sc_dim = max(sc_scale)
i = sc_scale.index(max_sc_dim)
sc_scale[i] -= 1
scs = vac.make_supercells_with_defects(sc_scale)
for i in range(len(scs)):
sc = scs[i]
mpvis = MPRelaxSet(sc, user_incar_settings={"LDAU": False})
poscar = mpvis.poscar
kpoints = Kpoints.automatic_density(sc,kpoint_den)
incar = mpvis.incar
if ptcr_flag:
potcar = mpvis.potcar
interdir = mpid
if not i:
fin_dir = os.path.join(interdir,'bulk')
try:
os.makedirs(fin_dir)
except:
pass
incar.update(blk_vasp_incar_param)
incar.write_file(os.path.join(fin_dir,'INCAR'))
poscar.write_file(os.path.join(fin_dir,'POSCAR'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir,'POTCAR'))
kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))
else:
blk_str_sites = set(scs[0].sites)
vac_str_sites = set(sc.sites)
vac_sites = blk_str_sites - vac_str_sites
vac_site = list(vac_sites)[0]
site_mult = int(vac.get_defectsite_multiplicity(i-1)/conv_prim_rat)
vac_site_specie = vac_site.specie
vac_symbol = vac_site.specie.symbol
vac_dir ='vacancy_{}_mult-{}_sitespecie-{}'.format(str(i),
site_mult, vac_symbol)
fin_dir = os.path.join(interdir,vac_dir)
try:
os.makedirs(fin_dir)
except:
pass
incar.update(def_vasp_incar_param)
poscar.write_file(os.path.join(fin_dir,'POSCAR'))
incar.write_file(os.path.join(fin_dir,'INCAR'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir,'POTCAR'))
kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))
# Antisite generation at all vacancy sites
struct_species = scs[0].types_of_specie
for specie in set(struct_species)-set([vac_site_specie]):
subspecie_symbol = specie.symbol
anti_struct = sc.copy()
anti_struct.append(specie, vac_site.frac_coords)
mpvis = MPRelaxSet(anti_struct, user_incar_settings={"LDAU": False})
poscar = mpvis.poscar
incar = mpvis.incar
incar.update(def_vasp_incar_param)
as_dir ='antisite_{}_mult-{}_sitespecie-{}_subspecie-{}'.format(
str(i), site_mult, vac_symbol, subspecie_symbol)
fin_dir = os.path.join(interdir,as_dir)
try:
os.makedirs(fin_dir)
except:
pass
poscar.write_file(os.path.join(fin_dir,'POSCAR'))
incar.write_file(os.path.join(fin_dir,'INCAR'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir,'POTCAR'))
kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))
def get_jobs(args):
# Returns a generator of jobs. Allows of "infinite" jobs.
vasp_command = args.command.split()
# save initial INCAR for rampU runs
n_ramp_u = args.jobs.count('rampU')
ramps = 0
if n_ramp_u:
incar = Incar.from_file('INCAR')
ldauu = incar['LDAUU']
ldauj = incar['LDAUJ']
njobs = len(args.jobs)
post_settings = [] # append to this list to have settings applied on next job
for i, job in enumerate(args.jobs):
final = False if i != njobs - 1 else True
if any(c.isdigit() for c in job):
suffix = "." + job
else:
suffix = ".{}{}".format(job, i + 1)
settings = post_settings
post_settings = []
backup = True if i == 0 else False
copy_magmom = False
vinput = VaspInput.from_directory(".")
if i > 0:
settings.append(
{"file": "CONTCAR",
"action": {"_file_copy": {"dest": "POSCAR"}}})
job_type = job.lower()
auto_npar = True
if args.no_auto_npar:
auto_npar = False
if job_type.startswith("static_derived"):
from pymatgen.io.vasp.sets import MPStaticSet
vis = MPStaticSet.from_prev_calc(
".", user_incar_settings={"LWAVE": True, "EDIFF": 1e-6},
ediff_per_atom=False)
settings.extend([
{"dict" : "INCAR",
"action": {"_set": dict(vis.incar)}},
{'dict': 'KPOINTS',
'action': {'_set': vis.kpoints.as_dict()}}])
if job_type.startswith("static_dielectric_derived"):
from pymatgen.io.vasp.sets import MPStaticSet, MPStaticDielectricDFPTVaspInputSet
# vis = MPStaticSet.from_prev_calc(
# ".", user_incar_settings={"EDIFF": 1e-6, "IBRION": 8,
# "LEPSILON": True, 'LREAL':False,
# "LPEAD": True, "ISMEAR": 0,
# "SIGMA": 0.01},
# ediff_per_atom=False)
vis = MPStaticDielectricDFPTVaspInputSet()
incar = vis.get_incar(vinput["POSCAR"].structure)
unset = {}
for k in ["NPAR", "KPOINT_BSE", "LAECHG", "LCHARG", "LVHAR",
"NSW"]:
incar.pop(k, None)
if k in vinput["INCAR"]:
unset[k] = 1
kpoints = vis.get_kpoints(vinput["POSCAR"].structure)
settings.extend([
{"dict": "INCAR",
"action": {"_set": dict(incar),
"_unset": unset}},
{'dict': 'KPOINTS',
'action': {'_set': kpoints.as_dict()}}])
auto_npar = False
elif job_type.startswith("static"):
m = [i * args.static_kpoint for i in vinput["KPOINTS"].kpts[0]]
settings.extend([
{"dict": "INCAR",
"action": {"_set": {"NSW": 0}}},
{'dict': 'KPOINTS',
'action': {'_set': {'kpoints': [m]}}}])
elif job_type.startswith("nonscf_derived"):
from pymatgen.io.vasp.sets import MPNonSCFSet
vis = MPNonSCFSet.from_prev_calc(".", copy_chgcar=False,
user_incar_settings={"LWAVE": True})
settings.extend([
{"dict": "INCAR",
"action": {"_set": dict(vis.incar)}},
{'dict': 'KPOINTS',
'action': {'_set': vis.kpoints.as_dict()}}])
elif job_type.startswith("optics_derived"):
from pymatgen.io.vasp.sets import MPNonSCFSet
vis = MPNonSCFSet.from_prev_calc(
".", optics=True, copy_chgcar=False,
nedos=2001, mode="uniform", nbands_factor=5,
user_incar_settings={"LWAVE": True, "ALGO": "Exact", "SIGMA": 0.01, "EDIFF": 1e-6},
ediff_per_atom=False)
settings.extend([
{"dict": "INCAR",
"action": {"_set": dict(vis.incar)}},
{'dict': 'KPOINTS',
'action': {'_set': vis.kpoints.as_dict()}}])
elif job_type.startswith("rampu"):
f = ramps / (n_ramp_u - 1)
settings.append(
{"dict": "INCAR",
"action": {"_set": {"LDAUJ": [j * f for j in ldauj],
"LDAUU": [u * f for u in ldauu]}}})
copy_magmom = True
ramps += 1
elif job_type.startswith("quick_relax") or job_type.startswith(\
"quickrelax"):
kpoints = vinput["KPOINTS"]
incar = vinput["INCAR"]
structure = vinput["POSCAR"].structure
if "ISMEAR" in incar:
post_settings.append(
{"dict": "INCAR",
"action": {"_set": {"ISMEAR": incar["ISMEAR"]}}})
else:
post_settings.append(
{"dict": "INCAR",
"action": {"_unset": {"ISMEAR": 1}}})
post_settings.append({"dict": "KPOINTS",
"action": {"_set": kpoints.as_dict()}})
# lattice vectors with length < 9 will get >1 KPOINT
low_kpoints = Kpoints.gamma_automatic(
[max(int(18/l), 1) for l in structure.lattice.abc])
settings.extend([
{"dict": "INCAR",
"action": {"_set": {"ISMEAR": 0}}},
{'dict': 'KPOINTS',
'action': {'_set': low_kpoints.as_dict()}}])
# let vasp determine encut (will be lower than
# needed for compatibility with other runs)
if "ENCUT" in incar:
post_settings.append(
{"dict": "INCAR",
"action": {"_set": {"ENCUT": incar["ENCUT"]}}})
settings.append(
{"dict": "INCAR",
"action": {"_unset": {"ENCUT": 1}}})
elif job_type.startswith("relax"):
pass
elif job_type.startswith("full_relax"):
for j in VaspJob.full_opt_run(
vasp_command):
yield j
else:
print("Unsupported job type: {}".format(job))
sys.exit(-1)
if not job_type.startswith("full_relax"):
yield VaspJob(vasp_command, final=final, suffix=suffix,
backup=backup, settings_override=settings,
copy_magmom=copy_magmom, auto_npar=auto_npar)
def process_killed_run(self, dir_name):
"""
Process a killed vasp run.
"""
fullpath = os.path.abspath(dir_name)
logger.info("Processing Killed run " + fullpath)
d = {"dir_name": fullpath, "state": "killed", "oszicar": {}}
for f in os.listdir(dir_name):
filename = os.path.join(dir_name, f)
if fnmatch(f, "INCAR*"):
try:
incar = Incar.from_file(filename)
d["incar"] = incar.as_dict()
d["is_hubbard"] = incar.get("LDAU", False)
if d["is_hubbard"]:
us = np.array(incar.get("LDAUU", []))
js = np.array(incar.get("LDAUJ", []))
if sum(us - js) == 0:
d["is_hubbard"] = False
d["hubbards"] = {}
else:
d["hubbards"] = {}
if d["is_hubbard"]:
d["run_type"] = "GGA+U"
elif incar.get("LHFCALC", False):
d["run_type"] = "HF"
else:
d["run_type"] = "GGA"
except Exception as ex:
print(str(ex))
logger.error("Unable to parse INCAR for killed run {}."
.format(dir_name))
elif fnmatch(f, "KPOINTS*"):
try:
kpoints = Kpoints.from_file(filename)
d["kpoints"] = kpoints.as_dict()
except:
logger.error("Unable to parse KPOINTS for killed run {}."
.format(dir_name))
elif fnmatch(f, "POSCAR*"):
try:
s = Poscar.from_file(filename).structure
comp = s.composition
el_amt = s.composition.get_el_amt_dict()
d.update({"unit_cell_formula": comp.as_dict(),
"reduced_cell_formula": comp.to_reduced_dict,
"elements": list(el_amt.keys()),
"nelements": len(el_amt),
"pretty_formula": comp.reduced_formula,
"anonymous_formula": comp.anonymized_formula,
"nsites": comp.num_atoms,
"chemsys": "-".join(sorted(el_amt.keys()))})
d["poscar"] = s.as_dict()
except:
logger.error("Unable to parse POSCAR for killed run {}."
.format(dir_name))
elif fnmatch(f, "POTCAR*"):
try:
potcar = Potcar.from_file(filename)
d["pseudo_potential"] = {
"functional": potcar.functional.lower(),
"pot_type": "paw",
"labels": potcar.symbols}
except:
logger.error("Unable to parse POTCAR for killed run in {}."
.format(dir_name))
elif fnmatch(f, "OSZICAR"):
try:
d["oszicar"]["root"] = \
Oszicar(os.path.join(dir_name, f)).as_dict()
except:
logger.error("Unable to parse OSZICAR for killed run in {}."
.format(dir_name))
elif re.match("relax\d", f):
if os.path.exists(os.path.join(dir_name, f, "OSZICAR")):
try:
d["oszicar"][f] = Oszicar(
os.path.join(dir_name, f, "OSZICAR")).as_dict()
except:
logger.error("Unable to parse OSZICAR for killed "
"run in {}.".format(dir_name))
return d