def frac_traverse(molecule, **kwargs):
kwargs = p4util.kwargs_lower(kwargs)
# The molecule is required, and should be the neutral species
molecule.update_geometry()
charge0 = molecule.molecular_charge()
mult0 = molecule.multiplicity()
chargep = charge0 + 1
chargem = charge0 - 1
# By default, the multiplicity of the cation/anion are mult0 + 1
# These are overridden with the cation_mult and anion_mult kwargs
multp = kwargs.get('cation_mult', mult0 + 1)
multm = kwargs.get('anion_mult', mult0 + 1)
# By default, we start the frac procedure on the 25th iteration
# when not reading a previous guess
frac_start = kwargs.get('frac_start', 25)
# By default, we occupy by tenths of electrons
HOMO_occs = kwargs.get(
'HOMO_occs', [1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.0])
LUMO_occs = kwargs.get(
'LUMO_occs', [1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.0])
# By default, H**O and LUMO are both in alpha
Z = 0
for A in range(molecule.natom()):
Z += molecule.Z(A)
Z -= charge0
H**O = kwargs.get('H**O', (Z / 2 + 1 if (Z % 2) else Z / 2))
LUMO = kwargs.get('LUMO', H**O + 1)
# By default, DIIS in FRAC (1.0 occupation is always DIIS'd)
frac_diis = kwargs.get('frac_diis', True)
# By default, use the neutral orbitals as a guess for the anion
neutral_guess = kwargs.get('neutral_guess', True)
# By default, burn-in with UHF first, if UKS
hf_guess = False
if core.get_global_option('REFERENCE') == 'UKS':
hf_guess = kwargs.get('hf_guess', True)
# By default, re-guess at each N
continuous_guess = kwargs.get('continuous_guess', False)
# By default, drop the files to the molecule's name
root = kwargs.get('filename', molecule.name())
traverse_filename = root + '.traverse.dat'
# => Traverse <= #
occs = []
energies = []
potentials = []
convs = []
# => Run the neutral for its orbitals, if requested <= #
old_df_ints_io = core.get_global_option("DF_INTS_IO")
core.set_global_option("DF_INTS_IO", "SAVE")
old_guess = core.get_global_option("GUESS")
if (neutral_guess):
if (hf_guess):
core.set_global_option("REFERENCE", "UHF")
energy('scf')
core.set_global_option("GUESS", "READ")
core.set_global_option("DF_INTS_IO", "LOAD")
# => Run the anion first <= #
molecule.set_molecular_charge(chargem)
molecule.set_multiplicity(multm)
# => Burn the anion in with hf, if requested <= #
if hf_guess:
core.set_global_option("REFERENCE", "UHF")
energy('scf', molecule=molecule, **kwargs)
core.set_global_option("REFERENCE", "UKS")
core.set_global_option("GUESS", "READ")
core.set_global_option("DF_INTS_IO", "SAVE")
core.set_global_option("FRAC_START", frac_start)
core.set_global_option("FRAC_RENORMALIZE", True)
core.set_global_option("FRAC_LOAD", False)
for occ in LUMO_occs:
core.set_global_option("FRAC_OCC", [LUMO])
core.set_global_option("FRAC_VAL", [occ])
E, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
C = 1
if E == 0.0:
E = core.get_variable('SCF ITERATION ENERGY')
C = 0
if LUMO > 0:
eps = wfn.epsilon_a()
potentials.append(eps[int(LUMO) - 1])
else:
eps = wfn.epsilon_b()
potentials.append(eps[-int(LUMO) - 1])
occs.append(occ)
energies.append(E)
convs.append(C)
core.set_global_option("FRAC_START", 2)
core.set_global_option("FRAC_LOAD", True)
core.set_global_option("GUESS", "READ")
core.set_global_option("FRAC_DIIS", frac_diis)
core.set_global_option("DF_INTS_IO", "LOAD")
# => Run the neutral next <= #
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
# Burn the neutral in with hf, if requested <= #
if not continuous_guess:
core.set_global_option("GUESS", old_guess)
if hf_guess:
core.set_global_option("FRAC_START", 0)
core.set_global_option("REFERENCE", "UHF")
energy('scf', molecule=molecule, **kwargs)
core.set_global_option("REFERENCE", "UKS")
core.set_global_option("GUESS", "READ")
core.set_global_option("FRAC_LOAD", False)
core.set_global_option("FRAC_START", frac_start)
core.set_global_option("FRAC_RENORMALIZE", True)
for occ in HOMO_occs:
core.set_global_option("FRAC_OCC", [H**O])
core.set_global_option("FRAC_VAL", [occ])
E, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
C = 1
if E == 0.0:
E = core.get_variable('SCF ITERATION ENERGY')
C = 0
if LUMO > 0:
eps = wfn.epsilon_a()
potentials.append(eps[int(H**O) - 1])
else:
eps = wfn.epsilon_b()
potentials.append(eps[-int(H**O) - 1])
occs.append(occ - 1.0)
energies.append(E)
convs.append(C)
core.set_global_option("FRAC_START", 2)
core.set_global_option("FRAC_LOAD", True)
core.set_global_option("GUESS", "READ")
core.set_global_option("FRAC_DIIS", frac_diis)
core.set_global_option("DF_INTS_IO", "LOAD")
core.set_global_option("DF_INTS_IO", old_df_ints_io)
# => Print the results out <= #
E = {}
core.print_out(
"""\n ==> Fractional Occupation Traverse Results <==\n\n""")
core.print_out("""\t%-11s %-24s %-24s %11s\n""" %
('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(occs)):
core.print_out("""\t%11.3E %24.16E %24.16E %11d\n""" %
(occs[k], energies[k], potentials[k], convs[k]))
E[occs[k]] = energies[k]
core.print_out('\n\t"You trying to be a hero Watkins?"\n')
core.print_out('\t"Just trying to kill some bugs sir!"\n')
core.print_out('\t\t\t-Starship Troopers\n')
# Drop the files out
fh = open(traverse_filename, 'w')
fh.write("""\t%-11s %-24s %-24s %11s\n""" %
('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(occs)):
fh.write("""\t%11.3E %24.16E %24.16E %11d\n""" %
(occs[k], energies[k], potentials[k], convs[k]))
fh.close()
# Properly, should clone molecule but since not returned and easy to unblemish,
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
return E
def frac_traverse(molecule, **kwargs):
kwargs = p4util.kwargs_lower(kwargs)
# The molecule is required, and should be the neutral species
molecule.update_geometry()
charge0 = molecule.molecular_charge()
mult0 = molecule.multiplicity()
chargep = charge0 + 1
chargem = charge0 - 1
# By default, the multiplicity of the cation/anion are mult0 + 1
# These are overridden with the cation_mult and anion_mult kwargs
multp = kwargs.get('cation_mult', mult0 + 1)
multm = kwargs.get('anion_mult', mult0 + 1)
# By default, we start the frac procedure on the 25th iteration
# when not reading a previous guess
frac_start = kwargs.get('frac_start', 25)
# By default, we occupy by tenths of electrons
HOMO_occs = kwargs.get('HOMO_occs', [1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.0])
LUMO_occs = kwargs.get('LUMO_occs', [1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.0])
# By default, H**O and LUMO are both in alpha
Z = 0;
for A in range(molecule.natom()):
Z += molecule.Z(A)
Z -= charge0
H**O = kwargs.get('H**O', (Z / 2 + 1 if (Z % 2) else Z / 2))
LUMO = kwargs.get('LUMO', H**O + 1)
# By default, DIIS in FRAC (1.0 occupation is always DIIS'd)
frac_diis = kwargs.get('frac_diis', True)
# By default, use the neutral orbitals as a guess for the anion
neutral_guess = kwargs.get('neutral_guess', True)
# By default, burn-in with UHF first, if UKS
hf_guess = False
if core.get_global_option('REFERENCE') == 'UKS':
hf_guess = kwargs.get('hf_guess', True)
# By default, re-guess at each N
continuous_guess = kwargs.get('continuous_guess', False)
# By default, drop the files to the molecule's name
root = kwargs.get('filename', molecule.name())
traverse_filename = root + '.traverse.dat'
# => Traverse <= #
occs = []
energies = []
potentials = []
convs = []
# => Run the neutral for its orbitals, if requested <= #
old_df_ints_io = core.get_global_option("DF_INTS_IO")
core.set_global_option("DF_INTS_IO", "SAVE")
old_guess = core.get_global_option("GUESS")
if (neutral_guess):
if (hf_guess):
core.set_global_option("REFERENCE","UHF")
energy('scf')
core.set_global_option("GUESS", "READ")
core.set_global_option("DF_INTS_IO", "LOAD")
# => Run the anion first <= #
molecule.set_molecular_charge(chargem)
molecule.set_multiplicity(multm)
# => Burn the anion in with hf, if requested <= #
if hf_guess:
core.set_global_option("REFERENCE","UHF")
energy('scf', molecule=molecule, **kwargs)
core.set_global_option("REFERENCE","UKS")
core.set_global_option("GUESS", "READ")
core.set_global_option("DF_INTS_IO", "SAVE")
core.set_global_option("FRAC_START", frac_start)
core.set_global_option("FRAC_RENORMALIZE", True)
core.set_global_option("FRAC_LOAD", False)
for occ in LUMO_occs:
core.set_global_option("FRAC_OCC", [LUMO])
core.set_global_option("FRAC_VAL", [occ])
E, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
C = 1
if E == 0.0:
E = core.get_variable('SCF ITERATION ENERGY')
C = 0
if LUMO > 0:
eps = wfn.epsilon_a()
potentials.append(eps[int(LUMO) - 1])
else:
eps = wfn.epsilon_b()
potentials.append(eps[-int(LUMO) - 1])
occs.append(occ)
energies.append(E)
convs.append(C)
core.set_global_option("FRAC_START", 2)
core.set_global_option("FRAC_LOAD", True)
core.set_global_option("GUESS", "READ")
core.set_global_option("FRAC_DIIS", frac_diis)
core.set_global_option("DF_INTS_IO", "LOAD")
# => Run the neutral next <= #
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
# Burn the neutral in with hf, if requested <= #
if not continuous_guess:
core.set_global_option("GUESS", old_guess)
if hf_guess:
core.set_global_option("FRAC_START", 0)
core.set_global_option("REFERENCE", "UHF")
energy('scf', molecule=molecule, **kwargs)
core.set_global_option("REFERENCE", "UKS")
core.set_global_option("GUESS", "READ")
core.set_global_option("FRAC_LOAD", False)
core.set_global_option("FRAC_START", frac_start)
core.set_global_option("FRAC_RENORMALIZE", True)
for occ in HOMO_occs:
core.set_global_option("FRAC_OCC", [H**O])
core.set_global_option("FRAC_VAL", [occ])
E, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
C = 1
if E == 0.0:
E = core.get_variable('SCF ITERATION ENERGY')
C = 0
if LUMO > 0:
eps = wfn.epsilon_a()
potentials.append(eps[int(H**O) - 1])
else:
eps = wfn.epsilon_b()
potentials.append(eps[-int(H**O) - 1])
occs.append(occ - 1.0)
energies.append(E)
convs.append(C)
core.set_global_option("FRAC_START", 2)
core.set_global_option("FRAC_LOAD", True)
core.set_global_option("GUESS", "READ")
core.set_global_option("FRAC_DIIS", frac_diis)
core.set_global_option("DF_INTS_IO", "LOAD")
core.set_global_option("DF_INTS_IO", old_df_ints_io)
# => Print the results out <= #
E = {}
core.print_out("""\n ==> Fractional Occupation Traverse Results <==\n\n""")
core.print_out("""\t%-11s %-24s %-24s %11s\n""" % ('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(occs)):
core.print_out("""\t%11.3E %24.16E %24.16E %11d\n""" % (occs[k], energies[k], potentials[k], convs[k]))
E[occs[k]] = energies[k]
core.print_out('\n\t"You trying to be a hero Watkins?"\n')
core.print_out('\t"Just trying to kill some bugs sir!"\n')
core.print_out('\t\t\t-Starship Troopers\n')
# Drop the files out
fh = open(traverse_filename, 'w')
fh.write("""\t%-11s %-24s %-24s %11s\n""" % ('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(occs)):
fh.write("""\t%11.3E %24.16E %24.16E %11d\n""" % (occs[k], energies[k], potentials[k], convs[k]))
fh.close()
# Properly, should clone molecule but since not returned and easy to unblemish,
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
return E
def frac_nuke(molecule, **kwargs):
kwargs = p4util.kwargs_lower(kwargs)
# The molecule is required, and should be the neutral species
molecule.update_geometry()
charge0 = molecule.molecular_charge()
mult0 = molecule.multiplicity()
# By default, we start the frac procedure on the 25th iteration
# when not reading a previous guess
frac_start = kwargs.get('frac_start', 25)
# By default, we occupy by tenths of electrons
foccs = kwargs.get('foccs',
[1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.0])
# By default, H**O and LUMO are both in alpha
N = 0
for A in range(molecule.natom()):
N += molecule.Z(A)
N -= charge0
N = int(N)
Nb = int((N - mult0 + 1) / 2)
Na = int(N - Nb)
charge = charge0
mult = mult0
# By default, nuke all the electrons
Nmin = 0
if ('nmax' in kwargs):
Nmin = N - int(kwargs['nmax'])
# By default, DIIS in FRAC (1.0 occupation is always DIIS'd)
frac_diis = kwargs.get('frac_diis', True)
# By default, drop the files to the molecule's name
root = kwargs.get('filename', molecule.name())
traverse_filename = root + '.traverse.dat'
stats_filename = root + '.stats.dat'
# => Traverse <= #
core.set_global_option("DF_INTS_IO", "SAVE")
Ns = []
energies = []
potentials = []
convs = []
stats = []
# Run one SCF to burn things in
E, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
# Determine H**O
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
if Na == Nb:
H**O = -Nb
elif Nb == 0:
H**O = Na
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if E_a >= E_b:
H**O = Na
else:
H**O = -Nb
stats.append("""\t%6d %6d %6d %6d %6d %6d\n""" %
(N, Na, Nb, charge, mult, H**O))
if H**O > 0:
Na = Na - 1
else:
Nb = Nb - 1
charge = charge + 1
mult = Na - Nb + 1
core.set_global_option("DF_INTS_IO", "LOAD")
core.set_global_option("FRAC_START", frac_start)
core.set_global_option("FRAC_RENORMALIZE", True)
# Nuke 'em Rico!
for Nintegral in range(N, Nmin, -1):
# Nuke the current H**O
for occ in foccs:
core.set_global_option("FRAC_OCC", [H**O])
core.set_global_option("FRAC_VAL", [occ])
E, wfn = energy('scf',
return_wfn=True,
molecule=molecule,
**kwargs)
C = 1
if E == 0.0:
E = core.get_variable('SCF ITERATION ENERGY')
C = 0
if H**O > 0:
eps = wfn.epsilon_a()
potentials.append(eps[H**O - 1])
else:
eps = wfn.epsilon_b()
potentials.append(eps[-H**O - 1])
Ns.append(Nintegral + occ - 1.0)
energies.append(E)
convs.append(C)
core.set_global_option("FRAC_START", 2)
core.set_global_option("FRAC_LOAD", True)
core.set_global_option("FRAC_DIIS", frac_diis)
core.set_global_option("GUESS", "READ")
# Set the next charge/mult
molecule.set_molecular_charge(charge)
molecule.set_multiplicity(mult)
# Determine H**O
print('DGAS: What ref should this point to?')
#ref = core.legacy_wavefunction()
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
if Na == Nb:
H**O = -Nb
elif Nb == 0:
H**O = Na
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if E_a >= E_b:
H**O = Na
else:
H**O = -Nb
stats.append("""\t%6d %6d %6d %6d %6d %6d\n""" %
(Nintegral - 1, Na, Nb, charge, mult, H**O))
if H**O > 0:
Na = Na - 1
else:
Nb = Nb - 1
charge = charge + 1
mult = Na - Nb + 1
core.set_global_option("DF_INTS_IO", "NONE")
# => Print the results out <= #
E = {}
core.print_out("""\n ==> Fractional Occupation Nuke Results <==\n\n""")
core.print_out("""\t%-11s %-24s %-24s %11s\n""" %
('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(Ns)):
core.print_out("""\t%11.3E %24.16E %24.16E %11d\n""" %
(Ns[k], energies[k], potentials[k], convs[k]))
E[Ns[k]] = energies[k]
core.print_out('\n')
core.print_out("""\t%6s %6s %6s %6s %6s %6s\n""" %
('N', 'Na', 'Nb', 'Charge', 'Mult', 'H**O'))
for line in stats:
core.print_out(line)
core.print_out(
'\n\t"You shoot a nuke down a bug hole, you got a lot of dead bugs"\n')
core.print_out('\t\t\t-Starship Troopers\n')
# Drop the files out
fh = open(traverse_filename, 'w')
fh.write("""\t%-11s %-24s %-24s %11s\n""" %
('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(Ns)):
fh.write("""\t%11.3E %24.16E %24.16E %11d\n""" %
(Ns[k], energies[k], potentials[k], convs[k]))
fh.close()
fh = open(stats_filename, 'w')
fh.write("""\t%6s %6s %6s %6s %6s %6s\n""" %
('N', 'Na', 'Nb', 'Charge', 'Mult', 'H**O'))
for line in stats:
fh.write(line)
fh.close()
# Properly, should clone molecule but since not returned and easy to unblemish,
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
return E
def frac_nuke(molecule, **kwargs):
kwargs = p4util.kwargs_lower(kwargs)
# The molecule is required, and should be the neutral species
molecule.update_geometry()
charge0 = molecule.molecular_charge()
mult0 = molecule.multiplicity()
# By default, we start the frac procedure on the 25th iteration
# when not reading a previous guess
frac_start = kwargs.get('frac_start', 25)
# By default, we occupy by tenths of electrons
foccs = kwargs.get('foccs', [1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.0])
# By default, H**O and LUMO are both in alpha
N = 0;
for A in range(molecule.natom()):
N += molecule.Z(A)
N -= charge0
N = int(N)
Nb = int((N - mult0 + 1) / 2)
Na = int(N - Nb)
charge = charge0
mult = mult0
# By default, nuke all the electrons
Nmin = 0;
if ('nmax' in kwargs):
Nmin = N - int(kwargs['nmax'])
# By default, DIIS in FRAC (1.0 occupation is always DIIS'd)
frac_diis = kwargs.get('frac_diis', True)
# By default, drop the files to the molecule's name
root = kwargs.get('filename', molecule.name())
traverse_filename = root + '.traverse.dat'
stats_filename = root + '.stats.dat'
# => Traverse <= #
core.set_global_option("DF_INTS_IO", "SAVE")
Ns = []
energies = []
potentials = []
convs = []
stats = []
# Run one SCF to burn things in
E, wfn= energy('scf', return_wfn=True, molecule=molecule, **kwargs)
# Determine H**O
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
if Na == Nb:
H**O = -Nb
elif Nb == 0:
H**O = Na
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if E_a >= E_b:
H**O = Na
else:
H**O = -Nb
stats.append("""\t%6d %6d %6d %6d %6d %6d\n""" % (N, Na, Nb, charge, mult, H**O))
if H**O > 0:
Na = Na - 1
else:
Nb = Nb - 1
charge = charge + 1
mult = Na - Nb + 1
core.set_global_option("DF_INTS_IO", "LOAD")
core.set_global_option("FRAC_START", frac_start)
core.set_global_option("FRAC_RENORMALIZE", True)
# Nuke 'em Rico!
for Nintegral in range(N, Nmin, -1):
# Nuke the current H**O
for occ in foccs:
core.set_global_option("FRAC_OCC", [H**O])
core.set_global_option("FRAC_VAL", [occ])
E, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
C = 1
if E == 0.0:
E = core.get_variable('SCF ITERATION ENERGY')
C = 0
if H**O > 0:
eps = wfn.epsilon_a()
potentials.append(eps[H**O - 1])
else:
eps = wfn.epsilon_b()
potentials.append(eps[-H**O - 1])
Ns.append(Nintegral + occ - 1.0)
energies.append(E)
convs.append(C)
core.set_global_option("FRAC_START", 2)
core.set_global_option("FRAC_LOAD", True)
core.set_global_option("FRAC_DIIS", frac_diis)
core.set_global_option("GUESS", "READ")
# Set the next charge/mult
molecule.set_molecular_charge(charge)
molecule.set_multiplicity(mult)
# Determine H**O
print('DGAS: What ref should this point to?')
#ref = core.legacy_wavefunction()
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
if Na == Nb:
H**O = -Nb
elif Nb == 0:
H**O = Na
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if E_a >= E_b:
H**O = Na
else:
H**O = -Nb
stats.append("""\t%6d %6d %6d %6d %6d %6d\n""" % (Nintegral-1, Na, Nb, charge, mult, H**O))
if H**O > 0:
Na = Na - 1
else:
Nb = Nb - 1
charge = charge + 1
mult = Na - Nb + 1
core.set_global_option("DF_INTS_IO", "NONE")
# => Print the results out <= #
E = {}
core.print_out("""\n ==> Fractional Occupation Nuke Results <==\n\n""")
core.print_out("""\t%-11s %-24s %-24s %11s\n""" % ('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(Ns)):
core.print_out("""\t%11.3E %24.16E %24.16E %11d\n""" % (Ns[k], energies[k], potentials[k], convs[k]))
E[Ns[k]] = energies[k]
core.print_out('\n')
core.print_out("""\t%6s %6s %6s %6s %6s %6s\n""" % ('N', 'Na', 'Nb', 'Charge', 'Mult', 'H**O'))
for line in stats:
core.print_out(line)
core.print_out('\n\t"You shoot a nuke down a bug hole, you got a lot of dead bugs"\n')
core.print_out('\t\t\t-Starship Troopers\n')
# Drop the files out
fh = open(traverse_filename, 'w')
fh.write("""\t%-11s %-24s %-24s %11s\n""" % ('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(Ns)):
fh.write("""\t%11.3E %24.16E %24.16E %11d\n""" % (Ns[k], energies[k], potentials[k], convs[k]))
fh.close()
fh = open(stats_filename, 'w')
fh.write("""\t%6s %6s %6s %6s %6s %6s\n""" % ('N', 'Na', 'Nb', 'Charge', 'Mult', 'H**O'))
for line in stats:
fh.write(line)
fh.close()
# Properly, should clone molecule but since not returned and easy to unblemish,
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
return E