def test_ts09():
from ase import io
from ase.calculators.vdwcorrection import vdWTkatchenko09prl
from ase.calculators.emt import EMT
from ase.build import bulk
# fake objects for the test
class FakeHirshfeldPartitioning:
def __init__(self, calculator):
self.calculator = calculator
def initialize(self):
pass
def get_effective_volume_ratios(self):
return [1]
def get_calculator(self):
return self.calculator
class FakeDFTcalculator(EMT):
def get_xc_functional(self):
return 'PBE'
a = 4.05 # Angstrom lattice spacing
al = bulk('Al', 'fcc', a=a)
cc = FakeDFTcalculator()
hp = FakeHirshfeldPartitioning(cc)
c = vdWTkatchenko09prl(hp, [3])
al.set_calculator(c)
al.get_potential_energy()
fname = 'out.traj'
al.write(fname)
# check that the output exists
io.read(fname)
# maybe assert something about what we just read?
p = io.read(fname).get_calculator().parameters
p['calculator']
p['xc']
p['uncorrected_energy']
print >> f, molecule,
ss = Cluster(Atoms(data[molecule]['symbols'],
data[molecule]['positions']))
# split the structures
s1 = ss.find_connected(0)
s2 = ss.find_connected(-1)
assert(len(ss) == len(s1) + len(s2))
if xc == 'TS09' or xc == 'TPSS' or xc == 'M06L':
c = GPAW(xc='PBE', h=h, nbands=-6, occupations=FermiDirac(width=0.1))
else:
c = GPAW(xc=xc, h=h, nbands=-6, occupations=FermiDirac(width=0.1))
E = []
for s in [s1, s2, ss]:
s.set_calculator(c)
s.minimal_box(box, h=h)
if xc == 'TS09':
s.get_potential_energy()
cc = vdWTkatchenko09prl(HirshfeldPartitioning(c),
vdWradii(s.get_chemical_symbols(), 'PBE'))
s.set_calculator(cc)
if xc == 'TPSS' or xc == 'M06L':
ene = s.get_potential_energy()
ene += c.get_xc_difference(xc)
E.append(ene)
else:
E.append(s.get_potential_energy())
print >> f, E[0], E[1], E[2],
print >> f, E[0] + E[1] - E[2]
f.flush()
f.close()
# 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')
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)
equal(s_out.get_potential_energy(), E, accuracy)