def test_base(self):
monkhorst = KSampling.monkhorst((3, 3, 3), (0.5, 0.5, 0.5), 0, False, False)
gamma_centered = KSampling.gamma_centered((3, 3, 3), False, False)
monkhorst.to_abivars()
# Test dict methods
self.assertMSONable(monkhorst)
self.assertMSONable(gamma_centered)
def __init__(self, a_guess, struct_type, pseudo, ecut_list=None, pawecutdg=None, ngkpt=(8, 8, 8),
spin_mode="unpolarized", include_soc=False, tolvrs=1.e-10, smearing="fermi_dirac:0.001 Ha",
ecutsm=0.05, chksymbreak=0, workdir=None, manager=None):
"""
Build a :class:`Work` for the computation of the relaxed lattice parameter.
Args:
structure_type: fcc, bcc
pseudo: :class:`Pseudo` object.
ecut_list: Cutoff energy in Hartree
ngkpt: MP divisions.
spin_mode: Spin polarization mode.
toldfe: Tolerance on the energy (Ha)
smearing: Smearing technique.
workdir: String specifing the working directory.
manager: :class:`TaskManager` responsible for the submission of the tasks.
"""
super(RelaxWithGbrvParamsWork, self).__init__(workdir=workdir, manager=manager)
self_pseudo = pseudo
self.include_soc = include_soc
self.struct_type = struct_type
if struct_type == "bcc":
structure = Structure.bcc(a_guess, species=[pseudo.symbol])
elif struct_type == "fcc":
structure = Structure.fcc(a_guess, species=[pseudo.symbol])
# Set extra_abivars.
extra_abivars = dict(
pawecutdg=pawecutdg,
tolvrs=tolvrs,
prtwf=-1,
fband=3.0,
nstep=100,
ntime=50,
ecutsm=ecutsm,
dilatmx=1.1,
)
self.ecut_list = ecut_list
smearing = Smearing.as_smearing(smearing)
# Kpoint sampling: shiftk depends on struct_type
shiftk = {"fcc": [0, 0, 0], "bcc": [0.5, 0.5, 0.5]}.get(struct_type)
spin_mode = SpinMode.as_spinmode(spin_mode)
ksampling = KSampling.monkhorst(ngkpt, chksymbreak=chksymbreak, shiftk=shiftk,
use_time_reversal=spin_mode.nspinor==1)
relax_algo = RelaxationMethod.atoms_and_cell()
inp = abilab.AbinitInput(structure, pseudo)
inp.add_abiobjects(ksampling, relax_algo, spin_mode, smearing)
inp.set_vars(extra_abivars)
# Register structure relaxation task.
for ecut in self.ecut_list:
self.relax_task = self.register_relax_task(inp.new_with_vars(ecut=ecut))
def __init__(self, structure, struct_type, pseudo, ecut=None, pawecutdg=None, ngkpt=(8, 8, 8),
spin_mode="unpolarized", include_soc=False, toldfe=1.e-9, smearing="fermi_dirac:0.001 Ha",
ecutsm=0.05, chksymbreak=0,
workdir=None, manager=None, **kwargs):
"""
Build a :class:`Work` for the computation of the relaxed lattice parameter.
Args:
structure: :class:`Structure` object
structure_type: fcc, bcc
pseudo: :class:`Pseudo` object.
ecut: Cutoff energy in Hartree
ngkpt: MP divisions.
spin_mode: Spin polarization mode.
toldfe: Tolerance on the energy (Ha)
smearing: Smearing technique.
workdir: String specifing the working directory.
manager: :class:`TaskManager` responsible for the submission of the tasks.
"""
super(GbrvRelaxAndEosWork, self).__init__(workdir=workdir, manager=manager)
self.struct_type = struct_type
# nband must be large enough to accomodate fractional occupancies.
self._pseudo = pseudo
self.include_soc = include_soc
def gbrv_nband(pseudo):
# nband/fband are usually too small for the GBRV calculations.
# FIXME this is not optimal
nband = pseudo.Z_val
nband += 0.5 * nband
nband = int(nband)
nband = max(nband, 8)
# Use even numer of bands. Needed when nspinor == 2
if nband % 2 != 0: nband += 1
return nband
nband = gbrv_nband(self.dojo_pseudo)
# Set extra_abivars.
self.extra_abivars = dict(
ecut=ecut,
pawecutdg=pawecutdg,
toldfe=toldfe,
prtwf=-1,
nband=nband,
#ecutsm=0.5,
#paral_kgb=paral_kgb
)
self.extra_abivars.update(**kwargs)
self.ecut = ecut
self.smearing = Smearing.as_smearing(smearing)
# Kpoint sampling: shiftk depends on struct_type
shiftk = {"fcc": [0, 0, 0], "bcc": [0.5, 0.5, 0.5]}.get(struct_type)
self.spin_mode = SpinMode.as_spinmode(spin_mode)
self.ksampling = KSampling.monkhorst(ngkpt, chksymbreak=chksymbreak, shiftk=shiftk,
use_time_reversal=self.spin_mode.nspinor==1)
relax_algo = RelaxationMethod.atoms_and_cell()
inp = abilab.AbinitInput(structure, pseudo)
inp.add_abiobjects(self.ksampling, relax_algo, self.spin_mode, self.smearing)
inp.set_vars(self.extra_abivars)
# Register structure relaxation task.
self.relax_task = self.register_relax_task(inp)
def __init__(self, structure, formula, struct_type, pseudos, xc, accuracy,
ecut=None, pawecutdg=None, ngkpt=(8, 8, 8), fband=2.0,
spin_mode="unpolarized", smearing="fermi_dirac:0.001 Ha",
chksymbreak=0, workdir=None, manager=None):
"""
Build a :class:`Work` for the computation of the relaxed lattice parameter.
Args:
structure: :class:`Structure` object.
struct_type: fcc, bcc
pseudos: Pseudopotentials
xc: Exchange-correlation type.
accuracy:
ecut: Cutoff energy in Hartree
ngkpt: Divisions for k-mesh.
fband: Input variable, used to compute the number of bands.
spin_mode: Spin polarization mode.
smearing: Smearing technique.
chksymbreak: Input variable.
workdir: String specifing the working directory.
manager: :class:`TaskManager` responsible for the submission of the tasks.
"""
super(GbrvCompoundRelaxAndEosWork, self).__init__(workdir=workdir, manager=manager)
self.pseudos = pseudos
self.xc = xc
if (any(xc != p.xc for p in pseudos)):
raise ValueError("Input XC does not agree with XC from pseudos.")
self.formula = formula
self.struct_type = struct_type
self.accuracy = accuracy
self.ecut, self.pawecutdg = ecut, pawecutdg
# Set extra_abivars.
# Use tolvrs for the relaxation, toldfe for the EOS
self.extra_abivars = dict(
ecut=ecut,
pawecutdg=pawecutdg,
tolvrs=1e-10,
ecutsm=0.5,
mem_test=0,
fband=fband,
# nband must be large enough to accomodate fractional occupancies.
#paral_kgb=kwargs.pop("paral_kgb", 0),
#nband=nband,
)
self.smearing = Smearing.as_smearing(smearing)
# Kpoint sampling: shiftk depends on struct_type
#shiftk = {"fcc": [0, 0, 0], "bcc": [0.5, 0.5, 0.5]}.get(struct_type)
shiftk = [0, 0, 0]
self.ksampling = KSampling.monkhorst(ngkpt, chksymbreak=chksymbreak, shiftk=shiftk)
self.spin_mode = SpinMode.as_spinmode(spin_mode)
relax_algo = RelaxationMethod.atoms_and_cell()
inp = abilab.AbinitInput(structure, pseudos)
inp.add_abiobjects(self.ksampling, relax_algo, self.spin_mode, self.smearing)
inp.set_vars(self.extra_abivars)
# Register structure relaxation task.
self.relax_task = self.register_relax_task(inp)
def __init__(self,
structure,
formula,
struct_type,
pseudos,
xc,
accuracy,
ecut=None,
pawecutdg=None,
ngkpt=(8, 8, 8),
fband=2.0,
spin_mode="unpolarized",
smearing="fermi_dirac:0.001 Ha",
chksymbreak=0,
workdir=None,
manager=None):
"""
Build a :class:`Work` for the computation of the relaxed lattice parameter.
Args:
structure: :class:`Structure` object.
struct_type: fcc, bcc
pseudos: Pseudopotentials
xc: Exchange-correlation type.
accuracy:
ecut: Cutoff energy in Hartree
ngkpt: Divisions for k-mesh.
fband: Input variable, used to compute the number of bands.
spin_mode: Spin polarization mode.
smearing: Smearing technique.
chksymbreak: Input variable.
workdir: String specifing the working directory.
manager: :class:`TaskManager` responsible for the submission of the tasks.
"""
super(GbrvCompoundRelaxAndEosWork, self).__init__(workdir=workdir,
manager=manager)
self.pseudos = pseudos
self.xc = xc
if (any(xc != p.xc for p in pseudos)):
raise ValueError("Input XC does not agree with XC from pseudos.")
self.formula = formula
self.struct_type = struct_type
self.accuracy = accuracy
self.ecut, self.pawecutdg = ecut, pawecutdg
# Set extra_abivars.
# Use tolvrs for the relaxation, toldfe for the EOS
self.extra_abivars = dict(
ecut=ecut,
pawecutdg=pawecutdg,
tolvrs=1e-10,
ecutsm=0.5,
mem_test=0,
fband=fband,
# nband must be large enough to accomodate fractional occupancies.
#paral_kgb=kwargs.pop("paral_kgb", 0),
#nband=nband,
)
self.smearing = Smearing.as_smearing(smearing)
# Kpoint sampling: shiftk depends on struct_type
#shiftk = {"fcc": [0, 0, 0], "bcc": [0.5, 0.5, 0.5]}.get(struct_type)
shiftk = [0, 0, 0]
self.ksampling = KSampling.monkhorst(ngkpt,
chksymbreak=chksymbreak,
shiftk=shiftk)
self.spin_mode = SpinMode.as_spinmode(spin_mode)
relax_algo = RelaxationMethod.atoms_and_cell()
inp = abilab.AbinitInput(structure, pseudos)
inp.add_abiobjects(self.ksampling, relax_algo, self.spin_mode,
self.smearing)
inp.set_vars(self.extra_abivars)
# Register structure relaxation task.
self.relax_task = self.register_relax_task(inp)