def get_gsinput_si(usepaw=0, as_task=False):
# Build GS input file.
pseudos = abidata.pseudos("14si.pspnc") if usepaw == 0 else data.pseudos("Si.GGA_PBE-JTH-paw.xml")
#silicon = abilab.Structure.zincblende(5.431, ["Si", "Si"], units="ang")
silicon = abidata.cif_file("si.cif")
from abipy.abio.inputs import AbinitInput
scf_input = AbinitInput(silicon, pseudos)
ecut = 6
scf_input.set_vars(
ecut=ecut,
pawecutdg=40,
nband=6,
paral_kgb=0,
iomode=3,
toldfe=1e-9,
)
if usepaw:
scf_input.set_vars(pawecutdg=4 * ecut)
# K-point sampling (shifted)
scf_input.set_autokmesh(nksmall=4)
if not as_task:
return scf_input
else:
from abipy.flowtk.tasks import ScfTask
return ScfTask(scf_input)
def get_gsinput_alas_ngkpt(ngkpt, usepaw=0, as_task=False):
"""
Build and return a GS input file for AlAs or a Task if `as_task`
"""
if usepaw != 0: raise NotImplementedError("PAW")
pseudos = abidata.pseudos("13al.981214.fhi", "33as.pspnc")
structure = abidata.structure_from_ucell("AlAs")
from abipy.abio.inputs import AbinitInput
scf_input = AbinitInput(structure, pseudos=pseudos)
scf_input.set_vars(
nband=5,
ecut=8.0,
ngkpt=ngkpt,
nshiftk=1,
shiftk=[0, 0, 0],
tolvrs=1.0e-6,
diemac=12.0,
)
if not as_task:
return scf_input
else:
from abipy.flowtk.tasks import ScfTask
return ScfTask(scf_input)
def get_gsinput_si(usepaw=0, as_task=False):
"""
Build and return a GS input file for silicon or a Task if `as_task`
"""
pseudos = abidata.pseudos(
"14si.pspnc") if usepaw == 0 else abidata.pseudos(
"Si.GGA_PBE-JTH-paw.xml")
silicon = abidata.cif_file("si.cif")
from abipy.abio.inputs import AbinitInput
scf_input = AbinitInput(silicon, pseudos)
ecut = 6
scf_input.set_vars(
ecut=ecut,
nband=6,
paral_kgb=0,
iomode=3,
toldfe=1e-9,
)
if usepaw:
scf_input.set_vars(pawecutdg=4 * ecut)
# K-point sampling (shifted)
scf_input.set_autokmesh(nksmall=4)
if not as_task:
return scf_input
else:
from abipy.flowtk.tasks import ScfTask
return ScfTask(scf_input)
def scf_input(structure, pseudos, kppa=None, ecut=None, pawecutdg=None, nband=None, accuracy="normal",
spin_mode="polarized", smearing="fermi_dirac:0.1 eV", charge=0.0, scf_algorithm=None,
shift_mode="Monkhorst-Pack"):
structure = Structure.as_structure(structure)
abinit_input = AbinitInput(structure, pseudos)
# Set the cutoff energies.
abinit_input.set_vars(_find_ecut_pawecutdg(ecut, pawecutdg, abinit_input.pseudos))
# SCF calculation.
kppa = _DEFAULTS.get("kppa") if kppa is None else kppa
shifts = (0.5, 0.5, 0.5) if shift_mode[0].lower() == "m" else (0.0, 0.0, 0.0)
scf_ksampling = aobj.KSampling.automatic_density(structure, kppa, chksymbreak=0, shifts=shifts)
scf_electrons = aobj.Electrons(spin_mode=spin_mode, smearing=smearing, algorithm=scf_algorithm,
charge=charge, nband=nband, fband=None)
if spin_mode=="polarized":
abinit_input.set_autospinat()
if scf_electrons.nband is None:
scf_electrons.nband = _find_scf_nband(structure, abinit_input.pseudos, scf_electrons,abinit_input.get('spinat', None))
abinit_input.set_vars(scf_ksampling.to_abivars())
abinit_input.set_vars(scf_electrons.to_abivars())
abinit_input.set_vars(_stopping_criterion("scf", accuracy))
return abinit_input
def scf_piezo_elastic_inputs(structure, pseudos, kppa, ecut=None, pawecutdg=None, scf_nband=None,
accuracy="normal", spin_mode="polarized",
smearing="fermi_dirac:0.1 eV", charge=0.0, scf_algorithm=None, ddk_tol=None, rf_tol=None):
"""
Returns a :class:`AbinitInput` for performing elastic and piezoelectric constants calculations.
GS input + the input files for the elastic and piezoelectric constants calculation.
Args:
structure: :class:`Structure` object.
pseudos: List of filenames or list of :class:`Pseudo` objects or :class:`PseudoTable` object.
kppa: Defines the sampling used for the SCF run.
ecut: cutoff energy in Ha (if None, ecut is initialized from the pseudos according to accuracy)
pawecutdg: cutoff energy in Ha for PAW double-grid (if None, pawecutdg is initialized from the
pseudos according to accuracy)
scf_nband: Number of bands for SCF run. If scf_nband is None, nband is automatically initialized
from the list of pseudos, the structure and the smearing option.
accuracy: Accuracy of the calculation.
spin_mode: Spin polarization.
smearing: Smearing technique.
charge: Electronic charge added to the unit cell.
scf_algorithm: Algorithm used for solving of the SCF cycle.
ddk_tol
"""
# Build the input file for the GS run.
gs_inp = AbinitInput(structure=structure, pseudos=pseudos)
# Set the cutoff energies.
gs_inp.set_vars(_find_ecut_pawecutdg(ecut, pawecutdg, gs_inp.pseudos))
ksampling = aobj.KSampling.automatic_density(gs_inp.structure, kppa, chksymbreak=0, shifts=(0.0, 0.0, 0.0))
gs_inp.set_vars(ksampling.to_abivars())
gs_inp.set_vars(tolvrs=1.0e-18)
scf_electrons = aobj.Electrons(spin_mode=spin_mode, smearing=smearing, algorithm=scf_algorithm,
charge=charge, nband=None, fband=None)
if scf_electrons.nband is None:
scf_electrons.nband = _find_scf_nband(structure, gs_inp.pseudos, scf_electrons)
gs_inp.set_vars(scf_electrons.to_abivars())
all_inps = [gs_inp]
# Add the ddk input
ddk_inp = gs_inp.deepcopy()
ddk_inp.set_vars(
rfelfd=2, # Activate the calculation of the d/dk perturbation
rfdir=(1,1,1), # All directions
nqpt=1, # One wavevector is to be considered
qpt=(0, 0, 0), # q-wavevector.
kptopt=2, # Take into account time-reversal symmetry.
iscf=-3, # The d/dk perturbation must be treated in a non-self-consistent way
)
if ddk_tol is None:
ddk_tol = {"tolwfr": 1.0e-20}
if len(ddk_tol) != 1 or any(k not in _tolerances for k in ddk_tol):
raise ValueError("Invalid tolerance: {}".format(ddk_tol))
ddk_inp.pop_tolerances()
ddk_inp.set_vars(ddk_tol)
ddk_inp.add_tags(DDK)
all_inps.append(ddk_inp)
# Add the Response Function calculation
rf_inp = gs_inp.deepcopy()
rf_inp.set_vars(rfphon=1, # Atomic displacement perturbation
rfatpol=(1,len(gs_inp.structure)), # Perturbation of all atoms
rfstrs=3, # Do the strain perturbations
rfdir=(1,1,1), # All directions
nqpt=1, # One wavevector is to be considered
qpt=(0, 0, 0), # q-wavevector.
kptopt=2, # Take into account time-reversal symmetry.
iscf=7, # The d/dk perturbation must be treated in a non-self-consistent way
)
if rf_tol is None:
rf_tol = {"tolvrs": 1.0e-12}
if len(rf_tol) != 1 or any(k not in _tolerances for k in rf_tol):
raise ValueError("Invalid tolerance: {}".format(rf_tol))
rf_inp.pop_tolerances()
rf_inp.set_vars(rf_tol)
rf_inp.add_tags([DFPT, STRAIN])
all_inps.append(rf_inp)
return MultiDataset.from_inputs(all_inps)
def scf_phonons_inputs(structure, pseudos, kppa,
ecut=None, pawecutdg=None, scf_nband=None, accuracy="normal", spin_mode="polarized",
smearing="fermi_dirac:0.1 eV", charge=0.0, scf_algorithm=None):
"""
Returns a :class:`AbinitInput` for performing phonon calculations.
GS input + the input files for the phonon calculation.
Args:
structure: :class:`Structure` object.
pseudos: List of filenames or list of :class:`Pseudo` objects or :class:`PseudoTable` object.
kppa: Defines the sampling used for the SCF run.
ecut: cutoff energy in Ha (if None, ecut is initialized from the pseudos according to accuracy)
pawecutdg: cutoff energy in Ha for PAW double-grid (if None, pawecutdg is initialized from the
pseudos according to accuracy)
scf_nband: Number of bands for SCF run. If scf_nband is None, nband is automatically initialized from the list of
pseudos, the structure and the smearing option.
accuracy: Accuracy of the calculation.
spin_mode: Spin polarization.
smearing: Smearing technique.
charge: Electronic charge added to the unit cell.
scf_algorithm: Algorithm used for solving of the SCF cycle.
"""
# Build the input file for the GS run.
gs_inp = AbinitInput(structure=structure, pseudos=pseudos)
# Set the cutoff energies.
gs_inp.set_vars(_find_ecut_pawecutdg(ecut, pawecutdg, gs_inp.pseudos))
ksampling = aobj.KSampling.automatic_density(gs_inp.structure, kppa, chksymbreak=0)
gs_inp.set_vars(ksampling.to_abivars())
gs_inp.set_vars(tolvrs=1.0e-18)
# Get the qpoints in the IBZ. Note that here we use a q-mesh with ngkpt=(4,4,4) and shiftk=(0,0,0)
# i.e. the same parameters used for the k-mesh in gs_inp.
qpoints = gs_inp.abiget_ibz(ngkpt=(4,4,4), shiftk=(0,0,0), kptopt=1).points
#print("get_ibz qpoints:", qpoints)
# Build the input files for the q-points in the IBZ.
ph_inputs = MultiDataset(gs_inp.structure, pseudos=gs_inp.pseudos, ndtset=len(qpoints))
for ph_inp, qpt in zip(ph_inputs, qpoints):
# Response-function calculation for phonons.
ph_inp.set_vars(
rfphon=1, # Will consider phonon-type perturbation
nqpt=1, # One wavevector is to be considered
qpt=qpt, # This wavevector is q=0 (Gamma)
tolwfr=1.0e-20,
kptopt=3, # One could used symmetries for Gamma.
)
#rfatpol 1 1 # Only the first atom is displaced
#rfdir 1 0 0 # Along the first reduced coordinate axis
#kptopt 2 # Automatic generation of k points, taking
irred_perts = ph_inp.abiget_irred_phperts()
#for pert in irred_perts:
# #print(pert)
# # TODO this will work for phonons, but not for the other types of perturbations.
# ph_inp = q_inp.deepcopy()
# rfdir = 3 * [0]
# rfdir[pert.idir -1] = 1
# ph_inp.set_vars(
# rfdir=rfdir,
# rfatpol=[pert.ipert, pert.ipert]
# )
# ph_inputs.append(ph_inp)
# Split input into gs_inp and ph_inputs
all_inps = [gs_inp]
all_inps.extend(ph_inputs.split_datasets())
return all_inps
def scf_phonons_inputs(structure,
pseudos,
kppa,
ecut=None,
pawecutdg=None,
scf_nband=None,
accuracy="normal",
spin_mode="polarized",
smearing="fermi_dirac:0.1 eV",
charge=0.0,
scf_algorithm=None):
"""
Returns a :class:`AbinitInput` for performing phonon calculations.
GS input + the input files for the phonon calculation.
Args:
structure: :class:`Structure` object.
pseudos: List of filenames or list of :class:`Pseudo` objects or :class:`PseudoTable` object.
kppa: Defines the sampling used for the SCF run.
ecut: cutoff energy in Ha (if None, ecut is initialized from the pseudos according to accuracy)
pawecutdg: cutoff energy in Ha for PAW double-grid (if None, pawecutdg is initialized from the
pseudos according to accuracy)
scf_nband: Number of bands for SCF run. If scf_nband is None, nband is automatically initialized from the list of
pseudos, the structure and the smearing option.
accuracy: Accuracy of the calculation.
spin_mode: Spin polarization.
smearing: Smearing technique.
charge: Electronic charge added to the unit cell.
scf_algorithm: Algorithm used for solving of the SCF cycle.
"""
# Build the input file for the GS run.
gs_inp = AbinitInput(structure=structure, pseudos=pseudos)
# Set the cutoff energies.
gs_inp.set_vars(_find_ecut_pawecutdg(ecut, pawecutdg, gs_inp.pseudos))
ksampling = aobj.KSampling.automatic_density(gs_inp.structure,
kppa,
chksymbreak=0)
gs_inp.set_vars(ksampling.to_abivars())
gs_inp.set_vars(tolvrs=1.0e-18)
# Get the qpoints in the IBZ. Note that here we use a q-mesh with ngkpt=(4,4,4) and shiftk=(0,0,0)
# i.e. the same parameters used for the k-mesh in gs_inp.
qpoints = gs_inp.abiget_ibz(ngkpt=(4, 4, 4), shiftk=(0, 0, 0),
kptopt=1).points
#print("get_ibz qpoints:", qpoints)
# Build the input files for the q-points in the IBZ.
ph_inputs = MultiDataset(gs_inp.structure,
pseudos=gs_inp.pseudos,
ndtset=len(qpoints))
for ph_inp, qpt in zip(ph_inputs, qpoints):
# Response-function calculation for phonons.
ph_inp.set_vars(
rfphon=1, # Will consider phonon-type perturbation
nqpt=1, # One wavevector is to be considered
qpt=qpt, # This wavevector is q=0 (Gamma)
tolwfr=1.0e-20,
kptopt=3, # One could used symmetries for Gamma.
)
#rfatpol 1 1 # Only the first atom is displaced
#rfdir 1 0 0 # Along the first reduced coordinate axis
#kptopt 2 # Automatic generation of k points, taking
irred_perts = ph_inp.abiget_irred_phperts()
#for pert in irred_perts:
# #print(pert)
# # TODO this will work for phonons, but not for the other types of perturbations.
# ph_inp = q_inp.deepcopy()
# rfdir = 3 * [0]
# rfdir[pert.idir -1] = 1
# ph_inp.set_vars(
# rfdir=rfdir,
# rfatpol=[pert.ipert, pert.ipert]
# )
# ph_inputs.append(ph_inp)
# Split input into gs_inp and ph_inputs
all_inps = [gs_inp]
all_inps.extend(ph_inputs.split_datasets())
return all_inps
