def test_si_scf_cg():
si = bulk('Si', 'fcc', 10.2 * Bohr)
kpts = np.asarray([[0.1250000, 0.1250000, 0.1250000, 1.00],
[0.1250000, 0.1250000, 0.3750000, 3.00],
[0.1250000, 0.1250000, 0.6250000, 3.00],
[0.1250000, 0.1250000, 0.8750000, 3.00],
[0.1250000, 0.3750000, 0.3750000, 3.00],
[0.1250000, 0.3750000, 0.6250000, 6.00],
[0.1250000, 0.3750000, 0.8750000, 6.00],
[0.1250000, 0.6250000, 0.6250000, 3.00],
[0.3750000, 0.3750000, 0.3750000, 1.00],
[0.3750000, 0.3750000, 0.6250000, 3.00]])
calc = Espresso(pw=18.0 * Rydberg, calculation='scf', kpts=kpts,
tprnfor=True, tstress=True, occupations='smearing',
smearing='marzari-vanderbilt', degauss=0.05,
convergence={'energy': 1e-6, 'mixing': 0.7,
'maxsteps': 100, 'diag': 'cg'},
outdir='si_scf')
si.set_calculator(calc)
calc.calculate(si)
assert np.allclose(si.get_potential_energy(), -152.90087195020132)
def getCalculator(self):
"""Mangle the supplied settings and return an Abinit ASE Calculator object.
The pseudopotential path is semi-hardcoded. Because crap.
"""
ecut = self.settings["settings"]["cutoff_pw"]
xc = self.settings["settings"]["xc"]
sigma = self.settings["settings"]["sigma"]
smearing = str(self.settings["settings"]["smearing"])
kpts = list(self.settings["kpoints"])
pseudopotential = self.settings["pseudopotential"]
from espresso import Espresso
calc = Espresso(
mode="scf",
pw=ecut, # density cutoff automatically 4*ecut ?
kpts=kpts,
xc=xc,
outdir='./',
smearing=smearing,
sigma=sigma,
psppath=pseudopotential,
output={
'removewf': True,
'removesave': True
},
parflags='-npool 4',
)
return calc
def test_relax_co_ase_bfgs(tmpdir):
tmpdir.chdir()
co = Atoms('CO', [[2.256 * Bohr, 0.0, 0.0], [0.0, 0.0, 0.0]])
co.set_cell(np.ones(3) * 12.0 * Bohr)
calc = Espresso(pw=24.0 * Rydberg,
dw=144.0 * Rydberg,
kpts='gamma',
xc='PBE',
calculation='scf',
ion_dynamics=None,
spinpol=False,
outdir='qe_ase_bfgs')
co.set_calculator(calc)
minimizer = BFGS(co, logfile='minimizer.log', trajectory='relaxed.traj')
minimizer.run(fmax=0.01)
print('ase(scf) bfgs:')
print('energy: ', co.get_potential_energy())
print('positions: ', co.positions)
print('forces: ', co.get_forces())
def runcalc(self, atoms):
if not self.ready:
self.arg['outdir'] = self.outdirprefix + '_%04d' % self.counter
self.counter += 1
if self.firststep:
self.esp = Espresso(**self.arg)
self.esp.set_atoms(atoms)
self.esp.get_potential_energy(atoms)
self.esp.save_chg(self.equilibriumdensity)
self.firststep = False
self.esp.close()
else:
self.arg['startingpot'] = 'file'
self.esp = Espresso(**self.arg)
self.esp.set_atoms(atoms)
self.esp.initialize(atoms)
self.esp.load_chg(self.equilibriumdensity)
self.esp.get_potential_energy(atoms)
self.esp.close()
self.ready = True
def class_instance():
temp_service_config_path = os.path.join("/tmp", SERVICE_CONFIG_NAME)
try:
# Placing the service_manifest.yml in the tmp directory
shutil.copyfile(SERVICE_CONFIG_PATH, temp_service_config_path)
from espresso import Espresso
yield Espresso()
finally:
# Delete the service_manifest.yml
os.remove(temp_service_config_path)
def test_relax_co_qe_bfgs():
co = Atoms('CO', [[2.256 * Bohr, 0.0, 0.0], [0.0, 0.0, 0.0]])
co.set_cell(np.ones(3) * 12.0 * Bohr)
calc = Espresso(pw=24.0 * Rydberg,
dw=144.0 * Rydberg,
kpts='gamma',
xc='PBE',
calculation='relax',
ion_dynamics='bfgs',
spinpol=False,
outdir='qe_bfgs')
co.set_calculator(calc)
calc.calculate(co)
print('qe bfgs:')
print('energy: ', co.get_potential_energy())
print('positions: ', co.positions)
print('forces: ', co.get_forces())
def test_starbuzz_coffee(self):
beverage_1 = Espresso()
self.simulate(beverage_1)
beverage_2 = DarkRoast()
beverage_2 = Mocha(beverage_2)
beverage_2 = Mocha(beverage_2)
beverage_2 = Whip(beverage_2)
self.simulate(beverage_2)
beverage_3 = HouseBlend()
beverage_3 = Soy(beverage_3)
beverage_3 = Mocha(beverage_3)
beverage_3 = Whip(beverage_3)
self.simulate(beverage_3)
def test_co_espresso_vibrations(tmpdir):
tmpdir.chdir()
co = Atoms('CO', positions=[[1.19382389081, 0.0, 0.0], [0.0, 0.0, 0.0]])
co.set_cell(np.ones(3) * 12.0 * Bohr)
calc = Espresso(pw=34.0 * Rydberg,
dw=144.0 * Rydberg,
kpts='gamma',
xc='PBE',
calculation='scf',
ion_dynamics='None',
spinpol=False,
outdir='vibs')
co.set_calculator(calc)
# calculate the vibrations
vib = Vibrations(co, indices=range(len(co)), delta=0.01, nfree=2)
vib.run()
assert np.allclose(vib.get_energies(), REF_ENE)
calc = Espresso(
pw=500, # IMP | (ev)
nbands=-50,
# #########################################################################
# kpts=3 * (1, ),
kpts=(6, 6, 6),
kptshift=(0, 0, 0),
calculation='relax',
ion_dynamics='bfgs',
fmax=0.05,
xc='PBE', # IMP
# #########################################################################
outdir="calcdir",
U_projection_type='atomic',
site=site_config,
tot_magnetization=-1,
occupations='smearing',
dipole={'status': False},
field={'status': False},
output={
'disk_io': 'default',
'avoidio': True,
'removewf': True,
'removesave': True,
'wf_collect': False,
},
convergence={
'energy': 1e-4,
'mixing': 0.1,
'maxsteps': 300,
'diag': 'david',
},
smearing='fd',
sigma=0.1,
# #########################################################################
# parflags=pflags,
alwayscreatenewarrayforforces=True,
verbose='low',
)
def test_al_scf_david():
al = bulk('Al', 'fcc', 7.5 * Bohr)
kpts = np.asarray([[0.0625000, 0.0625000, 0.0625000, 1.00],
[0.0625000, 0.0625000, 0.1875000, 3.00],
[0.0625000, 0.0625000, 0.3125000, 3.00],
[0.0625000, 0.0625000, 0.4375000, 3.00],
[0.0625000, 0.0625000, 0.5625000, 3.00],
[0.0625000, 0.0625000, 0.6875000, 3.00],
[0.0625000, 0.0625000, 0.8125000, 3.00],
[0.0625000, 0.0625000, 0.9375000, 3.00],
[0.0625000, 0.1875000, 0.1875000, 3.00],
[0.0625000, 0.1875000, 0.3125000, 6.00],
[0.0625000, 0.1875000, 0.4375000, 6.00],
[0.0625000, 0.1875000, 0.5625000, 6.00],
[0.0625000, 0.1875000, 0.6875000, 6.00],
[0.0625000, 0.1875000, 0.8125000, 6.00],
[0.0625000, 0.1875000, 0.9375000, 6.00],
[0.0625000, 0.3125000, 0.3125000, 3.00],
[0.0625000, 0.3125000, 0.4375000, 6.00],
[0.0625000, 0.3125000, 0.5625000, 6.00],
[0.0625000, 0.3125000, 0.6875000, 6.00],
[0.0625000, 0.3125000, 0.8125000, 6.00],
[0.0625000, 0.3125000, 0.9375000, 6.00],
[0.0625000, 0.4375000, 0.4375000, 3.00],
[0.0625000, 0.4375000, 0.5625000, 6.00],
[0.0625000, 0.4375000, 0.6875000, 6.00],
[0.0625000, 0.4375000, 0.8125000, 6.00],
[0.0625000, 0.4375000, 0.9375000, 6.00],
[0.0625000, 0.5625000, 0.5625000, 3.00],
[0.0625000, 0.5625000, 0.6875000, 6.00],
[0.0625000, 0.5625000, 0.8125000, 6.00],
[0.0625000, 0.6875000, 0.6875000, 3.00],
[0.0625000, 0.6875000, 0.8125000, 6.00],
[0.0625000, 0.8125000, 0.8125000, 3.00],
[0.1875000, 0.1875000, 0.1875000, 1.00],
[0.1875000, 0.1875000, 0.3125000, 3.00],
[0.1875000, 0.1875000, 0.4375000, 3.00],
[0.1875000, 0.1875000, 0.5625000, 3.00],
[0.1875000, 0.1875000, 0.6875000, 3.00],
[0.1875000, 0.1875000, 0.8125000, 3.00],
[0.1875000, 0.3125000, 0.3125000, 3.00],
[0.1875000, 0.3125000, 0.4375000, 6.00],
[0.1875000, 0.3125000, 0.5625000, 6.00],
[0.1875000, 0.3125000, 0.6875000, 6.00],
[0.1875000, 0.3125000, 0.8125000, 6.00],
[0.1875000, 0.4375000, 0.4375000, 3.00],
[0.1875000, 0.4375000, 0.5625000, 6.00],
[0.1875000, 0.4375000, 0.6875000, 6.00],
[0.1875000, 0.4375000, 0.8125000, 6.00],
[0.1875000, 0.5625000, 0.5625000, 3.00],
[0.1875000, 0.5625000, 0.6875000, 6.00],
[0.1875000, 0.6875000, 0.6875000, 3.00],
[0.3125000, 0.3125000, 0.3125000, 1.00],
[0.3125000, 0.3125000, 0.4375000, 3.00],
[0.3125000, 0.3125000, 0.5625000, 3.00],
[0.3125000, 0.3125000, 0.6875000, 3.00],
[0.3125000, 0.4375000, 0.4375000, 3.00],
[0.3125000, 0.4375000, 0.5625000, 6.00],
[0.3125000, 0.4375000, 0.6875000, 6.00],
[0.3125000, 0.5625000, 0.5625000, 3.00],
[0.4375000, 0.4375000, 0.4375000, 1.00],
[0.4375000, 0.4375000, 0.5625000, 3.00]])
calc = Espresso(pw=15.0 * Rydberg, calculation='scf', kpts=kpts,
tprnfor=True, tstress=True, occupations='smearing',
smearing='marzari-vanderbilt', degauss=0.05,
outdir='al_scf')
al.set_calculator(calc)
calc.calculate(al)
assert np.allclose(al.get_potential_energy(), -74.44991079398747)
assert np.allclose(al.get_forces(), np.zeros(3))
assert np.allclose(al.get_stress(), np.array([-0.02784864, -0.02784864,
-0.02784864, -0.0, -0.0, -0.0]))
def main():
beverage = Espresso()
print(beverage.get_description(), '$', beverage.cost())
beverage = HouseBlend()
print(beverage.get_description(), '$', beverage.cost())
beverage = Mocha(beverage)
print(beverage.get_description(), '$', beverage.cost())
beverage = Whip(beverage)
print(beverage.get_description(), '$', beverage.cost())
calc = Espresso(
# atoms=None,
pw=350.0,
dw=None,
fw=None,
nbands=-10,
# #########################################################################
kpts=3 * (1, ),
kptshift=(0, 0, 0),
fft_grid=None,
calculation='relax',
ion_dynamics='bfgs',
nstep=None,
constr_tol=None,
fmax=0.05,
cell_dynamics=None,
press=None,
dpress=None,
cell_factor=None,
cell_dofree=None,
dontcalcforces=False,
nosym=False,
noinv=False,
nosym_evc=False,
no_t_rev=False,
xc='PBE',
beefensemble=False,
printensemble=False,
psppath=None,
spinpol=False,
noncollinear=False,
spinorbit=False,
# #########################################################################
outdir="calcdir",
txt=None,
calcstress=False,
smearing='fd',
sigma=0.1,
fix_magmom=False,
isolated=None,
U=None,
J=None,
U_alpha=None,
U_projection_type='atomic',
nqx1=None,
nqx2=None,
nqx3=None,
exx_fraction=None,
screening_parameter=None,
exxdiv_treatment=None,
ecutvcut=None,
tot_charge=None,
charge=None,
tot_magnetization=-1,
occupations='smearing',
dipole={'status': False},
field={'status': False},
output={
# Default
# 'disk_io': 'default',
# 'avoidio': False,
# 'removewf': True,
# 'removesave': False,
# 'wf_collect': False,
'disk_io': 'default',
'avoidio': True,
'removewf': True,
'removesave': True,
'wf_collect': False,
},
convergence={
# Default
# 'energy': 1e-6,
# 'mixing': 0.7,
# 'maxsteps': 100,
# 'diag': 'david',
'energy': 1e-3,
'mixing': 0.1,
'maxsteps': 300,
'diag': 'david',
},
startingpot=None,
startingwfc=None,
ion_positions=None,
# #########################################################################
# parflags=None,
# parflags=pflags,
alwayscreatenewarrayforforces=True,
verbose='low',
# automatically generated list of parameters
# some coincide with ase-style names
iprint=None,
tstress=None,
tprnfor=None,
dt=None,
lkpoint_dir=None,
max_seconds=None,
etot_conv_thr=None,
forc_conv_thr=None,
tefield=None,
dipfield=None,
lelfield=None,
nberrycyc=None,
lorbm=None,
lberry=None,
gdir=None,
nppstr=None,
nbnd=None,
ecutwfc=None,
ecutrho=None,
ecutfock=None,
force_symmorphic=None,
use_all_frac=None,
one_atom_occupations=None,
starting_spin_angle=None,
degauss=None,
nspin=None,
ecfixed=None,
qcutz=None,
q2sigma=None,
x_gamma_extrapolation=None,
lda_plus_u=None,
lda_plus_u_kind=None,
edir=None,
emaxpos=None,
eopreg=None,
eamp=None,
clambda=None,
report=None,
lspinorb=None,
esm_w=None,
esm_efield=None,
esm_nfit=None,
london=None,
london_s6=None,
london_rcut=None,
xdm=None,
xdm_a1=None,
xdm_a2=None,
electron_maxstep=None,
scf_must_converge=None,
conv_thr=None,
adaptive_thr=None,
conv_thr_init=None,
conv_thr_multi=None,
mixing_beta=None,
mixing_ndim=None,
mixing_fixed_ns=None,
ortho_para=None,
diago_thr_init=None,
diago_cg_maxiter=None,
diago_david_ndim=None,
diago_full_acc=None,
efield=None,
tqr=None,
remove_rigid_rot=None,
tempw=None,
tolp=None,
delta_t=None,
nraise=None,
refold_pos=None,
upscale=None,
bfgs_ndim=None,
trust_radius_max=None,
trust_radius_min=None,
trust_radius_ini=None,
w_1=None,
w_2=None,
wmass=None,
press_conv_thr=None,
# site=None,
site=site_config,
)
def test_Espresso(self):
espresso = Espresso()
self.simulate(espresso)