def calc(self, **kwargs):
from ase.calculators.abinit import Abinit
legacy = kwargs.pop('v8_legacy_format', None)
if legacy is None:
legacy = self.is_legacy_version()
kw = self._base_kw(legacy)
kw.update(kwargs)
return Abinit(**kw)
def test_abinit_Si():
from ase.build import bulk
from ase.units import Ry
from ase.calculators.abinit import Abinit
atoms = bulk('Si')
calc = Abinit(label='Si',
nbands=8,
ecut=10 * Ry,
kpts=[4, 4, 4],
chksymbreak=0,
)
calc.set(toldfe=1.0e-2)
atoms.set_calculator(calc)
e = atoms.get_potential_energy()
print(e)
x=x)
if id is None:
continue
# perform EOS step
atoms.set_cell(cell * x, scale_atoms=True)
# set calculator
atoms.calc = Abinit(
pps='paw', # uses highest valence
label=name + '_' + code + '_' + str(n),
xc='PBE',
kpts=kpts,
ecut=ecut * Rydberg,
pawecutdg=pawecutdg * Rydberg,
occopt=3,
tsmear=width,
ecutsm=ecutsm,
toldfe=1.0e-6,
nstep=900,
pawovlp=-1, # bypass overlap check
fband=fband,
# http://forum.abinit.org/viewtopic.php?f=8&t=35
chksymbreak=0,
tolsym=tolsym,
prtwf=0,
prtden=0,
)
atoms.calc.set(**kwargs) # remaining calc keywords
t = time.time()
atoms.get_potential_energy()
c.write(atoms,
name=name,
ecut=ecut,
from ase import *
from ase.calculators.abinit import Abinit
a0 = 5.43
bulk = Atoms('Si2', [(0, 0, 0), (0.25, 0.25, 0.25)], pbc=True)
b = a0 / 2
bulk.set_cell([(0, b, b), (b, 0, b), (b, b, 0)], scale_atoms=True)
calc = Abinit(label='Si',
nbands=8,
xc='PBE',
ecut=50 * Ry,
mix=0.01,
kpts=[10, 10, 10])
bulk.set_calculator(calc)
e = bulk.get_potential_energy()
#
# https://wiki.fysik.dtu.dk/ase/ase/calculators/abinit.html
#
from ase.build import bulk
from ase.units import Ry
from ase.calculators.abinit import Abinit
atoms = bulk('Si')
calc = Abinit(label='Si',
nbands=8,
ecut=10 * Ry,
kpts=[4, 4, 4],
chksymbreak=0,
)
calc.set(toldfe=1.0e-2)
atoms.set_calculator(calc)
e = atoms.get_potential_energy()
print(e)
def calc(self, **kwargs):
from ase.calculators.abinit import Abinit
kw = self._base_kw()
kw.update(kwargs)
return Abinit(**kw)
atomstmp = atoms.copy()
if rmt:
kwargstmp.update({'rmt': rmt})
os.environ['ELK_SPECIES_PATH'] = ELK_SPECIES_PATH
atomstmp.calc = ELK(tasks=0, label=xlabel) # minimal calc
atomstmp.calc.set(**kwargstmp) # remaining calc keywords
atomstmp.get_potential_energy()
del atomstmp.calc
# hack ELK_SPECIES_PATH to use custom species
os.environ['ELK_SPECIES_PATH'] = os.path.abspath(xlabel) + '/'
# perform EOS step
atoms.set_cell(cell * x, scale_atoms=True)
# set calculator
if code == 'abinit':
p.update({'label': xlabel})
calc = Abinit(**p)
if code == 'aims':
p.update({'label': xlabel})
calc = Aims(**p)
if code == 'elk':
p.update({'label': xlabel})
calc = ELK(**p)
if code == 'exciting':
p.update({'dir': xlabel})
p.update({'vkloff': get_vkloff(kpts)}) # k-points shift
p.update({'speciespath': os.path.join(os.environ['EXCITING_SPECIES_PATH'])})
p.update({'bin': 'mpiexec ' + os.path.join(os.environ['EXCITINGROOT'], 'bin/excitingmpi')})
calc = Exciting(**p)
if code == 'espresso':
p.update({'outdir': xlabel})
if not structure.startswith('molecule'):
kptdensity=kptdensity,
width=width,
x=x)
if id is None:
continue
# perform EOS step
atoms.set_cell(cell * x, scale_atoms=True)
# set calculator
atoms.calc = Abinit(
label=name + '_' + code + '_' + str(n),
xc='PBE',
kpts=kpts,
ecut=ecut * Rydberg,
occopt=3,
tsmear=width,
toldfe=1.0e-6,
nstep=900,
diemix=0.1,
fband=0.95,
# http://forum.abinit.org/viewtopic.php?f=8&t=35
chksymbreak=0,
nsym=1, # various symmetry problems with various abinits ...
)
atoms.calc.set(**kwargs) # remaining calc keywords
t = time.time()
atoms.get_potential_energy()
c.write(atoms,
name=name,
ecut=ecut,
linspacestr=linspacestr,
kptdensity=kptdensity,
from ase import Atoms
from ase.units import Ry
from ase.calculators.abinit import Abinit
a0 = 5.43
bulk = Atoms('Si2', [(0, 0, 0),
(0.25, 0.25, 0.25)],
pbc=True)
b = a0 / 2
bulk.set_cell([(0, b, b),
(b, 0, b),
(b, b, 0)], scale_atoms=True)
calc = Abinit(label='Si',
nbands=8, # one can specify any abinit keywords
ecut=10 * Ry, # warning - used to speedup the test
kpts=[4, 4, 4], # warning - used to speedup the test
chksymbreak=0,
)
# one can specify abinit keywords also using set
calc.set(toldfe=1.0e-2) # warning - used to speedup the test
bulk.set_calculator(calc)
e = bulk.get_potential_energy()
def abinit(**kwargs):
kw = dict(ecut=150, chksymbreak=0, toldfe=1e-3)
kw.update(kwargs)
return Abinit(**kw)
def getCalculator(self):
"""Mangle the supplied settings and return an Abinit ASE Calculator object."""
if "tolsym" in self.settings["settings"].keys():
tolsym = self.settings["settings"]["tolsym"]
else:
tolsym = 1.0e-12
if "fband" in self.settings["settings"].keys():
fband = self.settings["settings"]["fband"]
else:
fband = 1.5
if "xc" in self.settings["settings"].keys():
xc = self.settings["settings"]["xc"]
else:
xc = 'PBE'
if "ecut" in self.settings["settings"].keys():
ecut = self.settings["settings"]["cutoff"]
else:
ecut = 100.
if "ecutsm" in self.settings["settings"].keys():
ecutsm = self.settings["settings"]["ecutsm"]
else:
ecutsm = 0.0
if "tsmear" in self.settings["settings"].keys():
tsmear = self.settings["settings"]["tsmear"]
else:
tsmear = 0.01
if "kpoints" in self.settings.keys():
kpts = list(self.settings["kpoints"])
else:
kpts = [12, 12, 12]
pseudopotential = self.settings["pseudopotential"]
if pseudopotential == "hgh.k.nlcc2015":
os.environ[
'ABINIT_PP_PATH'] = '/users/ralph/work/abinit/pseudos/HGH-NLCC2015'
pseudopotential = "hgh.k"
elif pseudopotential == "hgh.k.nlcc":
os.environ[
'ABINIT_PP_PATH'] = '/users/ralph/work/abinit/pseudos/HGH-NLCC'
pseudopotential = "hgh.k"
else:
os.environ[
'ABINIT_PP_PATH'] = '/users/ralph/work/abinit/pseudos/HGH'
if 'ABINIT_ASE_ABINIT_COMMAND' not in os.environ.keys():
os.environ[
'ASE_ABINIT_COMMAND'] = 'module load gcc-suite >/dev/null; nice -n 2 mpirun -np 4 /users/ralph/work/abinit/abinit-7.10.5/tmp9/abinit < PREFIX.files > PREFIX.out'
calc = Abinit(
label='test',
pps=pseudopotential, # uses highest valence hgh.k pps
xc='PBE',
kpts=kpts,
ecut=ecut,
occopt=3,
tsmear=tsmear,
ecutsm=ecutsm,
toldfe=1.0e-6,
nstep=900,
pawovlp=-1, # bypass overlap check
fband=fband,
# http://forum.abinit.org/viewtopic.php?f=8&t=35
chksymbreak=0,
tolsym=tolsym,
prtwf=0,
prtden=0,
)
return calc