def test_to_dict_from_dict(self):
k = Kpoints.monkhorst_automatic([2, 2, 2], [0, 0, 0])
d = k.to_dict
k2 = Kpoints.from_dict(d)
self.assertEqual(k.kpts, k2.kpts)
self.assertEqual(k.style, k2.style)
self.assertEqual(k.kpts_shift, k2.kpts_shift)
def test_to_dict_from_dict(self):
k = Kpoints.monkhorst_automatic([2, 2, 2], [0, 0, 0])
d = k.to_dict
k2 = Kpoints.from_dict(d)
self.assertEqual(k.kpts, k2.kpts)
self.assertEqual(k.style, k2.style)
self.assertEqual(k.kpts_shift, k2.kpts_shift)
def test_static_constructors(self):
kpoints = Kpoints.gamma_automatic([3, 3, 3], [0, 0, 0])
self.assertEqual(kpoints.style, "Gamma")
self.assertEqual(kpoints.kpts, [[3, 3, 3]])
kpoints = Kpoints.monkhorst_automatic([2, 2, 2], [0, 0, 0])
self.assertEqual(kpoints.style, "Monkhorst")
self.assertEqual(kpoints.kpts, [[2, 2, 2]])
kpoints = Kpoints.automatic(100)
self.assertEqual(kpoints.style, "Automatic")
self.assertEqual(kpoints.kpts, [[100]])
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
kpoints = Kpoints.automatic_density(poscar.structure, 500)
self.assertEqual(kpoints.kpts, [[2, 4, 4]])
self.assertEqual(kpoints.style, "Monkhorst")
kpoints = Kpoints.automatic_density(poscar.structure, 500, True)
self.assertEqual(kpoints.style, "Gamma")
kpoints = Kpoints.automatic_density_by_vol(poscar.structure, 1000)
self.assertEqual(kpoints.kpts, [[6, 11, 13]])
self.assertEqual(kpoints.style, "Gamma")
s = poscar.structure
s.make_supercell(3)
kpoints = Kpoints.automatic_density(s, 500)
self.assertEqual(kpoints.kpts, [[1, 1, 1]])
self.assertEqual(kpoints.style, "Gamma")
def test_static_constructors(self):
kpoints = Kpoints.gamma_automatic([3, 3, 3], [0, 0, 0])
self.assertEqual(kpoints.style, "Gamma")
self.assertEqual(kpoints.kpts, [[3, 3, 3]])
kpoints = Kpoints.monkhorst_automatic([2, 2, 2], [0, 0, 0])
self.assertEqual(kpoints.style, "Monkhorst")
self.assertEqual(kpoints.kpts, [[2, 2, 2]])
kpoints = Kpoints.automatic(100)
self.assertEqual(kpoints.style, "Automatic")
self.assertEqual(kpoints.kpts, [[100]])
filepath = os.path.join(test_dir, "POSCAR")
poscar = Poscar.from_file(filepath)
kpoints = Kpoints.automatic_density(poscar.structure, 500)
self.assertEqual(kpoints.kpts, [[2, 3, 4]])
def test_static_constructors(self):
kpoints = Kpoints.gamma_automatic([3, 3, 3], [0, 0, 0])
self.assertEqual(kpoints.style, "Gamma")
self.assertEqual(kpoints.kpts, [[3, 3, 3]])
kpoints = Kpoints.monkhorst_automatic([2, 2, 2], [0, 0, 0])
self.assertEqual(kpoints.style, "Monkhorst")
self.assertEqual(kpoints.kpts, [[2, 2, 2]])
kpoints = Kpoints.automatic(100)
self.assertEqual(kpoints.style, "Automatic")
self.assertEqual(kpoints.kpts, [[100]])
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
kpoints = Kpoints.automatic_density(poscar.structure, 500)
self.assertEqual(kpoints.kpts, [[2, 3, 4]])
def from_previous_vasp_run(previous_vasp_dir, output_dir='.',
user_incar_settings=None,
make_dir_if_not_present=True):
"""
Generate a set of Vasp input files for static calculations from a
directory of previous Vasp run.
Args:
previous_vasp_dir:
The directory contains the outputs(vasprun.xml and OUTCAR) of
previous vasp run.
output_dir:
The directory to write the VASP input files for the static
calculations. Default to write in the current directory.
make_dir_if_not_present:
Set to True if you want the directory (and the whole path) to
be created if it is not present.
"""
try:
vasp_run = Vasprun(os.path.join(previous_vasp_dir, "vasprun.xml"),
parse_dos=False, parse_eigen=None)
outcar = Outcar(os.path.join(previous_vasp_dir, "OUTCAR"))
previous_incar = vasp_run.incar
previous_kpoints = vasp_run.kpoints
previous_final_structure = vasp_run.final_structure
except:
traceback.format_exc()
raise RuntimeError("Can't get valid results from previous run")
structure = MPStaticVaspInputSet.get_structure(vasp_run, outcar)
mpsvip = MPStaticVaspInputSet()
mpsvip.write_input(structure, output_dir, make_dir_if_not_present)
#new_incar = Incar.from_file(os.path.join(output_dir, "INCAR"))
new_incar = mpsvip.get_incar(structure)
# Use previous run INCAR and override necessary parameters
previous_incar.update({"IBRION": -1, "ISMEAR": -5, "LAECHG": True,
"LCHARG": True, "LORBIT": 11, "LVHAR": True,
"LWAVE": False, "NSW": 0, "ICHARG": 0})
for incar_key in ["MAGMOM", "NUPDOWN"]:
if new_incar.get(incar_key, None):
previous_incar.update({incar_key: new_incar[incar_key]})
else:
previous_incar.pop(incar_key, None)
# use new LDAUU when possible b/c the Poscar might have changed
# representation
if previous_incar.get('LDAU'):
u = previous_incar.get('LDAUU', [])
j = previous_incar.get('LDAUJ', [])
if sum([u[x] - j[x] for x, y in enumerate(u)]) > 0:
for tag in ('LDAUU', 'LDAUL', 'LDAUJ'):
previous_incar.update({tag: new_incar[tag]})
# Compare ediff between previous and staticinputset values,
# choose the tighter ediff
previous_incar.update({"EDIFF": min(previous_incar.get("EDIFF", 1),
new_incar["EDIFF"])})
# add user settings
if user_incar_settings:
previous_incar.update(user_incar_settings)
previous_incar.write_file(os.path.join(output_dir, "INCAR"))
# Prefer to use k-point scheme from previous run
previous_kpoints_density = np.prod(previous_kpoints.kpts[0]) / \
previous_final_structure.lattice.reciprocal_lattice.volume
new_kpoints_density = max(previous_kpoints_density, 90)
new_kpoints = mpsvip.get_kpoints(structure,
kpoints_density=new_kpoints_density)
if previous_kpoints.style[0] != new_kpoints.style[0]:
if previous_kpoints.style[0] == "M" and \
SymmetryFinder(structure, 0.01).get_lattice_type() != \
"hexagonal":
k_div = (kp + 1 if kp % 2 == 1 else kp
for kp in new_kpoints.kpts[0])
Kpoints.monkhorst_automatic(k_div). \
write_file(os.path.join(output_dir, "KPOINTS"))
else:
Kpoints.gamma_automatic(new_kpoints.kpts[0]). \
write_file(os.path.join(output_dir, "KPOINTS"))
else:
new_kpoints.write_file(os.path.join(output_dir, "KPOINTS"))
slab_potcar.write_file("./Slab_with_vdw/POTCAR")
#set the common INCAR file and KPOINTS
incar_dict = {
'SYSTEM': 'ligand_PbS',
'ENCUT': 600,
'ISIF': 2,
'IBRION': 2,
'ALGO': 'Normal',
'ISMEAR': 1,
'ISPIN': 1,
'EDIFF': 1e-06,
'EDIFFG': -0.005,
'NPAR': 8,
'SIGMA': 0.1,
'PREC': 'Accurate',
'IVDW': 2,
'NSW': 1000
}
incar = Incar.from_dict(incar_dict)
kpoints = Kpoints.monkhorst_automatic(kpts= (8, 8, 1), shift= (0, 0, 0))
#write the files in appropriate directory
incar.write_file("./Interface_with_vdw/INCAR")
incar.write_file("./Slab_with_vdw/INCAR")
kpoints.write_file("./Interface_with_vdw/KPOINTS")
kpoints.write_file("./Slab_with_vdw/KPOINTS")
shu.copy("./submit_job", "./Interface_with_vdw/")
shu.copy("./submit_job", "./Slab_with_vdw")
def from_previous_vasp_run(previous_vasp_dir, output_dir='.',
user_incar_settings=None,
make_dir_if_not_present=True):
"""
Generate a set of Vasp input files for static calculations from a
directory of previous Vasp run.
Args:
previous_vasp_dir:
The directory contains the outputs(vasprun.xml and OUTCAR) of
previous vasp run.
output_dir:
The directory to write the VASP input files for the static
calculations. Default to write in the current directory.
make_dir_if_not_present:
Set to True if you want the directory (and the whole path) to
be created if it is not present.
"""
try:
vasp_run = Vasprun(os.path.join(previous_vasp_dir, "vasprun.xml"),
parse_dos=False, parse_eigen=None)
outcar = Outcar(os.path.join(previous_vasp_dir, "OUTCAR"))
previous_incar = Incar.from_file(os.path.join(previous_vasp_dir,
"INCAR"))
kpoints = Kpoints.from_file(os.path.join(previous_vasp_dir,
"KPOINTS"))
except:
traceback.format_exc()
raise RuntimeError("Can't get valid results from previous run")
structure = MPStaticVaspInputSet.get_structure(
vasp_run, outcar)
mpsvip = MPStaticVaspInputSet()
mpsvip.write_input(structure, output_dir, make_dir_if_not_present)
new_incar = Incar.from_file(os.path.join(output_dir, "INCAR"))
# Use previous run INCAR and override necessary parameters
previous_incar.update({"IBRION": -1, "ISMEAR": -5, "LAECHG": True,
"LCHARG": True, "LORBIT": 11, "LVHAR": True,
"LWAVE": False, "NSW": 0, "ICHARG": 0})
# Compare ediff between previous and staticinputset values,
# choose the tigher ediff
previous_incar.update({"EDIFF": min(previous_incar["EDIFF"],
new_incar["EDIFF"])})
# add user settings
if user_incar_settings:
previous_incar.update(user_incar_settings)
previous_incar.write_file(os.path.join(output_dir, "INCAR"))
# Prefer to use k-point scheme from previous run
kpoints_out = Kpoints.from_file(os.path.join(output_dir, "KPOINTS"))
if kpoints.style != kpoints_out.style and \
SymmetryFinder(structure, 0.01).get_lattice_type() != \
"hexagonal":
k_div = (kp + 1 if kp % 2 == 1 else kp
for kp in kpoints_out.kpts[0])
Kpoints.monkhorst_automatic(k_div).write_file(
os.path.join(output_dir, "KPOINTS"))
def get_calibration_task(structure, phase="CalibrateBulk", \
slab_interface_params={'hkl':[1,0,0], 'ligand': None},\
turn_knobs={}, incar_params={}, other_params={}):
"""
returns general calibration task for a structure
Args:
structure : pymatgen structure to be calibrated (can be a bulk, ligand, slab
or interface)
phase : calibration type, viz. CalibrateBulk, CalibrateMolecule,
CalibrateSlab, CalibrateInterface
hkl : in case of Slab and Interface miller indices of facet
turn_knobs : specifies the parameters to be calibrated
incar_params : dictionary of additional incar parameters, refer defined
incar_dict for defaults
other_params : other parameters for calibration, viz. job_dir, is_matrix, etc.
described in the calibrate module
"""
#structure definition
poscar = Poscar(structure)
incar_dict = { 'SYSTEM': 'slab',
'ENCUT': 500,
'ISIF': 2,
'IBRION': 2,
'ISMEAR': 1,
'EDIFF': 1e-05,
'NPAR': 4,
'SIGMA': 0.1,
'PREC': 'Accurate'
}
if incar_params:
incar_dict.update(incar_params)
incar = Incar.from_dict(incar_dict)
kpoints = Kpoints.monkhorst_automatic(kpts=(8, 8, 1))
que = { 'nnodes':1,
'nprocs':16,
'walltime':'48:00:00',
'job_bin': '/home/km468/Software/VASP/vaspsol_kappa.5.3.5/vasp'
}
# calibration task: relax hkl
calparams = {}
calparams['calibrate'] = phase
calparams['incar'] = incar.as_dict()
calparams['poscar'] = poscar.as_dict()
calparams['kpoints'] = kpoints.as_dict()
calparams['que_params'] = que
calparams['turn_knobs'] = turn_knobs
if phase == 'CalibrateSlab':
calparams['system'] = {'hkl':slab_interface_params['hkl'],
'ligand':slab_interface_params['ligand']
}
elif phase == 'CalibrateInterface':
calparams['system'] = {'hkl':hkl,
'ligand':structure.ligand.reduced_formula
}
calparams['other_params'] = {
'is_matrix':False,
'from_ase':True,
'Grid_type':'M'
}
if other_params:
calparams['other_params'].update(other_params)
return MPINTCalibrateTask(calparams)
def from_previous_vasp_run(previous_vasp_dir,
output_dir='.',
user_incar_settings=None,
make_dir_if_not_present=True):
"""
Generate a set of Vasp input files for static calculations from a
directory of previous Vasp run.
Args:
previous_vasp_dir:
The directory contains the outputs(vasprun.xml and OUTCAR) of
previous vasp run.
output_dir:
The directory to write the VASP input files for the static
calculations. Default to write in the current directory.
make_dir_if_not_present:
Set to True if you want the directory (and the whole path) to
be created if it is not present.
"""
try:
vasp_run = Vasprun(os.path.join(previous_vasp_dir, "vasprun.xml"),
parse_dos=False,
parse_eigen=None)
outcar = Outcar(os.path.join(previous_vasp_dir, "OUTCAR"))
previous_incar = vasp_run.incar
previous_kpoints = vasp_run.kpoints
previous_final_structure = vasp_run.final_structure
except:
traceback.format_exc()
raise RuntimeError("Can't get valid results from previous run")
structure = MPStaticVaspInputSet.get_structure(vasp_run, outcar)
mpsvip = MPStaticVaspInputSet()
mpsvip.write_input(structure, output_dir, make_dir_if_not_present)
#new_incar = Incar.from_file(os.path.join(output_dir, "INCAR"))
new_incar = mpsvip.get_incar(structure)
# Use previous run INCAR and override necessary parameters
previous_incar.update({
"IBRION": -1,
"ISMEAR": -5,
"LAECHG": True,
"LCHARG": True,
"LORBIT": 11,
"LVHAR": True,
"LWAVE": False,
"NSW": 0,
"ICHARG": 0
})
for incar_key in ["MAGMOM", "NUPDOWN"]:
if new_incar.get(incar_key, None):
previous_incar.update({incar_key: new_incar[incar_key]})
else:
previous_incar.pop(incar_key, None)
# use new LDAUU when possible b/c the Poscar might have changed
# representation
if previous_incar.get('LDAU'):
u = previous_incar.get('LDAUU', [])
j = previous_incar.get('LDAUJ', [])
if sum([u[x] - j[x] for x, y in enumerate(u)]) > 0:
for tag in ('LDAUU', 'LDAUL', 'LDAUJ'):
previous_incar.update({tag: new_incar[tag]})
# Compare ediff between previous and staticinputset values,
# choose the tighter ediff
previous_incar.update(
{"EDIFF": min(previous_incar.get("EDIFF", 1), new_incar["EDIFF"])})
# add user settings
if user_incar_settings:
previous_incar.update(user_incar_settings)
previous_incar.write_file(os.path.join(output_dir, "INCAR"))
# Prefer to use k-point scheme from previous run
previous_kpoints_density = np.prod(previous_kpoints.kpts[0]) / \
previous_final_structure.lattice.reciprocal_lattice.volume
new_kpoints_density = max(previous_kpoints_density, 90)
new_kpoints = mpsvip.get_kpoints(structure,
kpoints_density=new_kpoints_density)
if previous_kpoints.style[0] != new_kpoints.style[0]:
if previous_kpoints.style[0] == "M" and \
SymmetryFinder(structure, 0.01).get_lattice_type() != \
"hexagonal":
k_div = (kp + 1 if kp % 2 == 1 else kp
for kp in new_kpoints.kpts[0])
Kpoints.monkhorst_automatic(k_div). \
write_file(os.path.join(output_dir, "KPOINTS"))
else:
Kpoints.gamma_automatic(new_kpoints.kpts[0]). \
write_file(os.path.join(output_dir, "KPOINTS"))
else:
new_kpoints.write_file(os.path.join(output_dir, "KPOINTS"))
def from_previous_vasp_run(previous_vasp_dir, output_dir='.',
user_incar_settings=None,
make_dir_if_not_present=True,
kpoints_density=90, sym_prec=0.1):
"""
Generate a set of Vasp input files for static calculations from a
directory of previous Vasp run.
Args:
previous_vasp_dir (str): Directory containing the outputs(
vasprun.xml and OUTCAR) of previous vasp run.
output_dir (str): Directory to write the VASP input files for
the static calculations. Defaults to current directory.
make_dir_if_not_present (bool): Set to True if you want the
directory (and the whole path) to be created if it is not
present.
kpoints_density (int): kpoints density for the reciprocal cell
of structure. Might need to increase the default value when
calculating metallic materials.
sym_prec (float): Tolerance for symmetry finding
"""
# Read input and output from previous run
try:
vasp_run = Vasprun(os.path.join(previous_vasp_dir, "vasprun.xml"),
parse_dos=False, parse_eigen=None)
outcar = Outcar(os.path.join(previous_vasp_dir, "OUTCAR"))
previous_incar = vasp_run.incar
previous_kpoints = vasp_run.kpoints
except:
traceback.format_exc()
raise RuntimeError("Can't get valid results from previous run")
mpsvip = MPStaticVaspInputSet(kpoints_density=kpoints_density,
sym_prec=sym_prec)
structure = mpsvip.get_structure(vasp_run, outcar)
mpsvip.write_input(structure, output_dir, make_dir_if_not_present)
new_incar = mpsvip.get_incar(structure)
# Use previous run INCAR and override necessary parameters
previous_incar.update({"IBRION": -1, "ISMEAR": -5, "LAECHG": True,
"LCHARG": True, "LORBIT": 11, "LVHAR": True,
"LWAVE": False, "NSW": 0, "ICHARG": 0})
for incar_key in ["MAGMOM", "NUPDOWN"]:
if new_incar.get(incar_key, None):
previous_incar.update({incar_key: new_incar[incar_key]})
else:
previous_incar.pop(incar_key, None)
# use new LDAUU when possible b/c the Poscar might have changed
# representation
if previous_incar.get('LDAU'):
u = previous_incar.get('LDAUU', [])
j = previous_incar.get('LDAUJ', [])
if sum([u[x] - j[x] for x, y in enumerate(u)]) > 0:
for tag in ('LDAUU', 'LDAUL', 'LDAUJ'):
previous_incar.update({tag: new_incar[tag]})
# ensure to have LMAXMIX for GGA+U static run
if "LMAXMIX" not in previous_incar:
previous_incar.update({"LMAXMIX": new_incar["LMAXMIX"]})
# Compare ediff between previous and staticinputset values,
# choose the tighter ediff
previous_incar.update({"EDIFF": min(previous_incar.get("EDIFF", 1),
new_incar["EDIFF"])})
# add user settings
if user_incar_settings:
previous_incar.update(user_incar_settings)
previous_incar.write_file(os.path.join(output_dir, "INCAR"))
# Perform checking on INCAR parameters
if any([previous_incar.get("NSW", 0) != 0, previous_incar["IBRION"] != -1,
previous_incar["LCHARG"] != True,
any([sum(previous_incar["LDAUU"])<=0, previous_incar["LMAXMIX"]<4])
if previous_incar.get("LDAU") else False]):
raise ValueError("Incompatible INCAR parameters!")
# Prefer to use k-point scheme from previous run
new_kpoints = mpsvip.get_kpoints(structure)
if previous_kpoints.style[0] != new_kpoints.style[0]:
if previous_kpoints.style[0] == "M" and \
SymmetryFinder(structure, 0.1).get_lattice_type() != \
"hexagonal":
k_div = (kp + 1 if kp % 2 == 1 else kp
for kp in new_kpoints.kpts[0])
Kpoints.monkhorst_automatic(k_div). \
write_file(os.path.join(output_dir, "KPOINTS"))
else:
Kpoints.gamma_automatic(new_kpoints.kpts[0]). \
write_file(os.path.join(output_dir, "KPOINTS"))
else:
new_kpoints.write_file(os.path.join(output_dir, "KPOINTS"))
def get_calibration_task(structure, phase="CalibrateBulk", \
slab_interface_params={'hkl':[1,0,0], 'ligand': None},\
turn_knobs={}, incar_params={}, other_params={}):
"""
returns general calibration task for a structure
Args:
structure : pymatgen structure to be calibrated (can be a bulk, ligand, slab
or interface)
phase : calibration type, viz. CalibrateBulk, CalibrateMolecule,
CalibrateSlab, CalibrateInterface
hkl : in case of Slab and Interface miller indices of facet
turn_knobs : specifies the parameters to be calibrated
incar_params : dictionary of additional incar parameters, refer defined
incar_dict for defaults
other_params : other parameters for calibration, viz. job_dir, is_matrix, etc.
described in the calibrate module
"""
#structure definition
poscar = Poscar(structure)
incar_dict = {
'SYSTEM': 'slab',
'ENCUT': 500,
'ISIF': 2,
'IBRION': 2,
'ISMEAR': 1,
'EDIFF': 1e-05,
'NPAR': 4,
'SIGMA': 0.1,
'PREC': 'Accurate'
}
if incar_params:
incar_dict.update(incar_params)
incar = Incar.from_dict(incar_dict)
kpoints = Kpoints.monkhorst_automatic(kpts=(8, 8, 1))
que = {
'nnodes': 1,
'nprocs': 16,
'walltime': '48:00:00',
'job_bin': '/home/km468/Software/VASP/vaspsol_kappa.5.3.5/vasp'
}
# calibration task: relax hkl
calparams = {}
calparams['calibrate'] = phase
calparams['incar'] = incar.as_dict()
calparams['poscar'] = poscar.as_dict()
calparams['kpoints'] = kpoints.as_dict()
calparams['que_params'] = que
calparams['turn_knobs'] = turn_knobs
if phase == 'CalibrateSlab':
calparams['system'] = {
'hkl': slab_interface_params['hkl'],
'ligand': slab_interface_params['ligand']
}
elif phase == 'CalibrateInterface':
calparams['system'] = {
'hkl': hkl,
'ligand': structure.ligand.reduced_formula
}
calparams['other_params'] = {
'is_matrix': False,
'from_ase': True,
'Grid_type': 'M'
}
if other_params:
calparams['other_params'].update(other_params)
return MPINTCalibrateTask(calparams)
