def run(lastres=[]):
results = []
# Hirshfeld ----------------------------------------
if 1:
hd = HirshfeldDensity(calc)
# check for the number of electrons
expected = [
[None, 10],
[[0, 1, 2], 10],
[[1, 2], 2],
[[0], 8],
]
#expected = [[[0, 2], 9], ]
#expected = [[None, 10], ]
for gridrefinement in [1, 2, 4]:
#Test for all gridrefinements for get_all_electron_density
parprint('grid refinement', gridrefinement)
for result in expected:
indicees, result = result
full, gd = hd.get_density(indicees, gridrefinement)
parprint('indicees', indicees, end=': ')
parprint('result, expected:', gd.integrate(full), result)
if gridrefinement < 4:
#The highest level of gridrefinement gets wrong electron numbers
equal(gd.integrate(full), result, 1.e-8)
else:
equal(gd.integrate(full), result, 1.e-4)
hp = HirshfeldPartitioning(calc)
vr = hp.get_effective_volume_ratios()
parprint('Hirshfeld:', vr)
if len(lastres):
equal(vr, lastres.pop(0), 1.e-10)
results.append(vr)
# Wigner-Seitz ----------------------------------------
if 1:
ws = WignerSeitz(calc.density.finegd, mol, calc)
vr = ws.get_effective_volume_ratios()
parprint('Wigner-Seitz:', vr)
if len(lastres):
equal(vr, lastres.pop(0), 1.e-10)
results.append(vr)
return results
def run(lastres=[]):
results = []
# Hirshfeld ----------------------------------------
if 1:
hd = HirshfeldDensity(calc)
# check for the number of electrons
expected = [[None, 10],
[[0, 1, 2], 10],
[[1, 2], 2],
[[0], 8],
]
#expected = [[[0, 2], 9], ]
#expected = [[None, 10], ]
for gridrefinement in [1, 2, 4]:
#Test for all gridrefinements for get_all_electron_density
parprint('grid refinement', gridrefinement)
for result in expected:
indicees, result = result
full, gd = hd.get_density(indicees, gridrefinement)
parprint('indicees', indicees, end=': ')
parprint('result, expected:', gd.integrate(full), result)
if gridrefinement < 4:
#The highest level of gridrefinement gets wrong electron numbers
equal(gd.integrate(full), result, 1.e-8)
else:
equal(gd.integrate(full), result, 1.e-5)
hp = HirshfeldPartitioning(calc)
vr = hp.get_effective_volume_ratios()
parprint('Hirshfeld:', vr)
if len(lastres):
equal(vr, lastres.pop(0), 1.e-10)
results.append(vr)
# Wigner-Seitz ----------------------------------------
if 1:
ws = WignerSeitz(calc.density.finegd, mol, calc)
vr = ws.get_effective_volume_ratios()
parprint('Wigner-Seitz:', vr)
if len(lastres):
equal(vr, lastres.pop(0), 1.e-10)
results.append(vr)
return results
# split the structures
s1 = ss.find_connected(0)
s2 = ss.find_connected(-1)
assert len(ss) == len(s1) + len(s2)
c = GPAW(xc='PBE', h=h, nbands=-6,
occupations=FermiDirac(width=0.1), txt=None)
cdf = GPAW(xc='vdW-DF', h=h, nbands=-6, occupations=FermiDirac(width=0.1),
txt=None)
for s in [s1, s2, ss]:
s.set_calculator(c)
s.minimal_box(box, h=h)
Energy['PBE'].append(s.get_potential_energy())
cc = vdWTkatchenko09prl(HirshfeldPartitioning(c),
vdWradii(s.get_chemical_symbols(), 'PBE'))
s.set_calculator(cc)
Energy['TS09'].append(s.get_potential_energy())
s.set_calculator(cdf)
Energy['vdW-DF'].append(s.get_potential_energy())
parprint('Coupled cluster binding energy',
-data[molecule]['interaction energy CC'] * 1000, 'meV')
for xc in ['PBE', 'vdW-DF', 'TS09']:
ene = Energy[xc]
# print xc, 'energies', ene
parprint(xc, 'binding energy',
(ene[0] + ene[1] - ene[2]) * 1000, 'meV')
"""Test Hirshfeld for spin/no spin consitency"""
from ase import Atom
from gpaw import GPAW
from ase.parallel import parprint
from gpaw.analyse.hirshfeld import HirshfeldPartitioning
from gpaw import FermiDirac
from gpaw.cluster import Cluster
from gpaw.test import equal
h = 0.25
box = 3
atoms = Cluster()
atoms.append(Atom('H'))
atoms.minimal_box(box)
volumes = []
for spinpol in [False, True]:
calc = GPAW(h=h,
occupations=FermiDirac(0.1, fixmagmom=True),
experimental={'niter_fixdensity': 2},
spinpol=spinpol)
calc.calculate(atoms)
volumes.append(HirshfeldPartitioning(calc).get_effective_volume_ratios())
parprint(volumes)
equal(volumes[0][0], volumes[1][0], 4e-9)
hd = HirshfeldDensity(calc)
# check for the number of electrons
expected = [
[None, 10],
[[0, 1, 2], 10],
[[1, 2], 2],
[[0], 8],
]
#expected = [[[0, 2], 9], ]
#expected = [[None, 10], ]
for result in expected:
indicees, result = result
full, gd = hd.get_density(indicees)
parprint('indicees', indicees, end=': ')
parprint('result, expected:', gd.integrate(full), result)
equal(gd.integrate(full), result, 1.e-8)
hp = HirshfeldPartitioning(calc)
vr = hp.get_effective_volume_ratios()
parprint('Hirshfeld:', vr)
# equal(vr[1], vr[2], 1.e-3)
# Wigner-Seitz ----------------------------------------
if 1:
ws = WignerSeitz(calc.density.finegd, mol, calc)
vr = ws.get_effective_volume_ratios()
parprint('Wigner-Seitz:', vr)
equal(q_a.sum(), q, 0.03)
return q_a
# spin unpolarized
if 1:
out_traj = 'LiH.traj'
out_txt = 'LiH.txt'
cc = GPAW(h=h, xc='PBE', txt=out_txt)
# this is needed to initialize txt output
cc.initialize(s)
hp = HirshfeldPartitioning(cc)
c = vdWTkatchenko09prl(hp, vdWradii(s.get_chemical_symbols(), 'PBE'))
s.set_calculator(c)
E = s.get_potential_energy()
F_ac = s.get_forces()
s.write(out_traj)
q_a = print_charge_and_check(hp)
barrier()
# test I/O, accuracy due to text output
accuracy = 1.e-5
for fname in [out_traj, out_txt]:
print(fname)
s_out = ase.io.read(fname)
print(s_out.calc)
hd = HirshfeldDensity(calc)
# check for the number of electrons
expected = [[None, 10],
[[0, 1, 2], 10],
[[1, 2], 2],
[[0], 8],
]
#expected = [[[0, 2], 9], ]
#expected = [[None, 10], ]
for result in expected:
indicees, result = result
full, gd = hd.get_density(indicees)
parprint('indicees', indicees, end=': ')
parprint('result, expected:', gd.integrate(full), result)
equal(gd.integrate(full), result, 1.e-8)
hp = HirshfeldPartitioning(calc)
vr = hp.get_effective_volume_ratios()
parprint('Hirshfeld:', vr)
# equal(vr[1], vr[2], 1.e-3)
# Wigner-Seitz ----------------------------------------
if 1:
ws = WignerSeitz(calc.density.finegd, mol, calc)
vr = ws.get_effective_volume_ratios()
parprint('Wigner-Seitz:', vr)
