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()
from gpaw.analyse.vdwradii import vdWradii
# data from A. Bondi, J. Phys. Chem. 68 (1964) 441
data_Bondi = { # units Anstrom
'He': 1.40,
'Ne': 1.54,
'Ar': 1.88,
'Kr': 2.02,
'Xe': 2.16
}
# data from Felix Hanke (FHI-AIMS ?)
data_Hanke = { # units Anstrom
'H' : 1.640449351,
'C' : 1.8997461838999998,
'N' : 1.7674518813999998,
'O' : 1.6880752998999997,
'Cu': 1.9897063095999996,
}
for symbol in ['He', 'Ne', 'Ar', 'Kr', 'H', 'C', 'N', 'O', 'Cu']:
R = vdWradii([symbol], 'PBE')[0]
if symbol in data_Bondi:
Rref = data_Bondi[symbol]
else:
Rref = data_Hanke[symbol]
error = abs(R - Rref)
print("symbol, R, Rref, error:", symbol, R, Rref, error)
assert (error < 0.05)
from ase.units import Bohr
from gpaw.analyse.vdwradii import vdWradii
# data from A. Bondi, J. Phys. Chem. 68 (1964) 441
data_Bondi = {"He": 1.40, "Ne": 1.54, "Ar": 1.88, "Kr": 2.02, "Xe": 2.16} # units Anstrom
# data from Felix Hanke (FHI-AIMS ?)
data_Hanke = { # units Anstrom
"H": 1.640449351,
"C": 1.8997461838999998,
"N": 1.7674518813999998,
"O": 1.6880752998999997,
"Cu": 1.9897063095999996,
}
for symbol in ["He", "Ne", "Ar", "Kr", "H", "C", "N", "O", "Cu"]:
R = vdWradii([symbol], "PBE")[0]
if symbol in data_Bondi:
Rref = data_Bondi[symbol]
else:
Rref = data_Hanke[symbol]
error = abs(R - Rref)
print "symbol, R, Rref, error:", symbol, R, Rref, error
assert error < 0.05
# 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)