def ip_fitting(molecule, omega_l, omega_r, **kwargs):
kwargs = p4util.kwargs_lower(kwargs)
# By default, zero the omega to 3 digits
omega_tol = kwargs.get('omega_tolerance', 1.0E-3)
# By default, do up to twenty iterations
maxiter = kwargs.get('maxiter', 20)
# By default, do not read previous 180 orbitals file
read = False
read180 = ''
if 'read' in kwargs:
read = True
read180 = kwargs['read']
# The molecule is required, and should be the neutral species
molecule.update_geometry()
charge0 = molecule.molecular_charge()
mult0 = molecule.multiplicity()
# How many electrons are there?
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)
# Work in the ot namespace for this procedure
core.IO.set_default_namespace("ot")
# Burn in to determine orbital eigenvalues
if read:
core.set_global_option("GUESS", "READ")
copy_file_to_scratch(read180, 'psi', 'ot', 180)
old_guess = core.get_global_option("GUESS")
core.set_global_option("DF_INTS_IO", "SAVE")
core.print_out("""\n\t==> IP Fitting SCF: Burn-in <==\n""")
E, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
core.set_global_option("DF_INTS_IO", "LOAD")
# Determine H**O, to determine mult1
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
Na1 = Na
Nb1 = Nb
if H**O > 0:
Na1 = Na1 - 1
else:
Nb1 = Nb1 - 1
charge1 = charge0 + 1
mult1 = Na1 - Nb1 + 1
omegas = []
E0s = []
E1s = []
kIPs = []
IPs = []
types = []
# Right endpoint
core.set_global_option('DFT_OMEGA', omega_r)
# Neutral
if read:
core.set_global_option("GUESS", "READ")
p4util.copy_file_to_scratch(read180, 'psi', 'ot', 180)
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
core.print_out("""\n\t==> IP Fitting SCF: Neutral, Right Endpoint <==\n""")
E0r, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
E_HOMO = 0.0
if Nb == 0:
E_HOMO = eps_a[int(Na - 1)]
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if E_a >= E_b:
E_HOMO = E_a
else:
E_HOMO = E_b
E_HOMOr = E_HOMO
core.IO.change_file_namespace(180, "ot", "neutral")
# Cation
if read:
core.set_global_option("GUESS", "READ")
p4util.copy_file_to_scratch(read180, 'psi', 'ot', 180)
molecule.set_molecular_charge(charge1)
molecule.set_multiplicity(mult1)
core.print_out("""\n\t==> IP Fitting SCF: Cation, Right Endpoint <==\n""")
E1r = energy('scf', molecule=molecule, **kwargs)
core.IO.change_file_namespace(180, "ot", "cation")
IPr = E1r - E0r
kIPr = -E_HOMOr
delta_r = IPr - kIPr
if IPr > kIPr:
message = (
"""\n***IP Fitting Error: Right Omega limit should have kIP > IP"""
)
raise ValidationError(message)
omegas.append(omega_r)
types.append('Right Limit')
E0s.append(E0r)
E1s.append(E1r)
IPs.append(IPr)
kIPs.append(kIPr)
# Use previous orbitals from here out
core.set_global_option("GUESS", "READ")
# Left endpoint
core.set_global_option('DFT_OMEGA', omega_l)
# Neutral
core.IO.change_file_namespace(180, "neutral", "ot")
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
core.print_out("""\n\t==> IP Fitting SCF: Neutral, Left Endpoint <==\n""")
E0l, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
E_HOMO = 0.0
if Nb == 0:
E_HOMO = eps_a[int(Na - 1)]
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if E_a >= E_b:
E_HOMO = E_a
else:
E_HOMO = E_b
E_HOMOl = E_HOMO
core.IO.change_file_namespace(180, "ot", "neutral")
# Cation
core.IO.change_file_namespace(180, "cation", "ot")
molecule.set_molecular_charge(charge1)
molecule.set_multiplicity(mult1)
core.print_out("""\n\t==> IP Fitting SCF: Cation, Left Endpoint <==\n""")
E1l = energy('scf', molecule=molecule, **kwargs)
core.IO.change_file_namespace(180, "ot", "cation")
IPl = E1l - E0l
kIPl = -E_HOMOl
delta_l = IPl - kIPl
if IPl < kIPl:
message = (
"""\n***IP Fitting Error: Left Omega limit should have kIP < IP""")
raise ValidationError(message)
omegas.append(omega_l)
types.append('Left Limit')
E0s.append(E0l)
E1s.append(E1l)
IPs.append(IPl)
kIPs.append(kIPl)
converged = False
repeat_l = 0
repeat_r = 0
step = 0
while True:
step = step + 1
# Regula Falsi (modified)
if repeat_l > 1:
delta_l = delta_l / 2.0
if repeat_r > 1:
delta_r = delta_r / 2.0
omega = -(omega_r - omega_l) / (delta_r - delta_l) * delta_l + omega_l
core.set_global_option('DFT_OMEGA', omega)
# Neutral
core.IO.change_file_namespace(180, "neutral", "ot")
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
core.print_out(
"""\n\t==> IP Fitting SCF: Neutral, Omega = %11.3E <==\n""" %
omega)
E0, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
E_HOMO = 0.0
if Nb == 0:
E_HOMO = eps_a[int(Na - 1)]
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if E_a >= E_b:
E_HOMO = E_a
else:
E_HOMO = E_b
core.IO.change_file_namespace(180, "ot", "neutral")
# Cation
core.IO.change_file_namespace(180, "cation", "ot")
molecule.set_molecular_charge(charge1)
molecule.set_multiplicity(mult1)
core.print_out(
"""\n\t==> IP Fitting SCF: Cation, Omega = %11.3E <==\n""" % omega)
E1 = energy('scf', molecule=molecule, **kwargs)
core.IO.change_file_namespace(180, "ot", "cation")
IP = E1 - E0
kIP = -E_HOMO
delta = IP - kIP
if kIP > IP:
omega_r = omega
E0r = E0
E1r = E1
IPr = IP
kIPr = kIP
delta_r = delta
repeat_r = 0
repeat_l = repeat_l + 1
else:
omega_l = omega
E0l = E0
E1l = E1
IPl = IP
kIPl = kIP
delta_l = delta
repeat_l = 0
repeat_r = repeat_r + 1
omegas.append(omega)
types.append('Regula-Falsi')
E0s.append(E0)
E1s.append(E1)
IPs.append(IP)
kIPs.append(kIP)
# Termination
if (abs(omega_l - omega_r) < omega_tol or step > maxiter):
converged = True
break
# Properly, should clone molecule but since not returned and easy to unblemish,
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
core.IO.set_default_namespace("")
core.print_out("""\n\t==> IP Fitting Results <==\n\n""")
core.print_out("""\t => Occupation Determination <= \n\n""")
core.print_out("""\t %6s %6s %6s %6s %6s %6s\n""" %
('N', 'Na', 'Nb', 'Charge', 'Mult', 'H**O'))
core.print_out("""\t Neutral: %6d %6d %6d %6d %6d %6d\n""" %
(N, Na, Nb, charge0, mult0, H**O))
core.print_out("""\t Cation: %6d %6d %6d %6d %6d\n\n""" %
(N - 1, Na1, Nb1, charge1, mult1))
core.print_out("""\t => Regula Falsi Iterations <=\n\n""")
core.print_out("""\t%3s %11s %14s %14s %14s %s\n""" %
('N', 'Omega', 'IP', 'kIP', 'Delta', 'Type'))
for k in range(len(omegas)):
core.print_out(
"""\t%3d %11.3E %14.6E %14.6E %14.6E %s\n""" %
(k + 1, omegas[k], IPs[k], kIPs[k], IPs[k] - kIPs[k], types[k]))
if converged:
core.print_out("""\n\tIP Fitting Converged\n""")
core.print_out("""\tFinal omega = %14.6E\n""" %
((omega_l + omega_r) / 2))
core.print_out(
"""\n\t"M,I. does the dying. Fleet just does the flying."\n""")
core.print_out("""\t\t\t-Starship Troopers\n""")
else:
core.print_out("""\n\tIP Fitting did not converge!\n""")
core.set_global_option("DF_INTS_IO", "NONE")
core.set_global_option("GUESS", old_guess)
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 ip_fitting(molecule, omega_l, omega_r, **kwargs):
kwargs = p4util.kwargs_lower(kwargs)
# By default, zero the omega to 3 digits
omega_tol = kwargs.get('omega_tolerance', 1.0E-3)
# By default, do up to twenty iterations
maxiter = kwargs.get('maxiter', 20)
# By default, do not read previous 180 orbitals file
read = False
read180 = ''
if 'read' in kwargs:
read = True
read180 = kwargs['read']
# The molecule is required, and should be the neutral species
molecule.update_geometry()
charge0 = molecule.molecular_charge()
mult0 = molecule.multiplicity()
# How many electrons are there?
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)
# Work in the ot namespace for this procedure
core.IO.set_default_namespace("ot")
# Burn in to determine orbital eigenvalues
if read:
core.set_global_option("GUESS", "READ")
copy_file_to_scratch(read180, 'psi', 'ot', 180)
old_guess = core.get_global_option("GUESS")
core.set_global_option("DF_INTS_IO", "SAVE")
core.print_out("""\n\t==> IP Fitting SCF: Burn-in <==\n""")
E, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
core.set_global_option("DF_INTS_IO", "LOAD")
# Determine H**O, to determine mult1
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
Na1 = Na;
Nb1 = Nb;
if H**O > 0:
Na1 = Na1 - 1;
else:
Nb1 = Nb1 - 1;
charge1 = charge0 + 1;
mult1 = Na1 - Nb1 + 1
omegas = []
E0s = []
E1s = []
kIPs = []
IPs = []
types = []
# Right endpoint
core.set_global_option('DFT_OMEGA', omega_r)
# Neutral
if read:
core.set_global_option("GUESS", "READ")
p4util.copy_file_to_scratch(read180, 'psi', 'ot', 180)
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
core.print_out("""\n\t==> IP Fitting SCF: Neutral, Right Endpoint <==\n""")
E0r, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
E_HOMO = 0.0;
if Nb == 0:
E_HOMO = eps_a[int(Na - 1)]
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if E_a >= E_b:
E_HOMO = E_a
else:
E_HOMO = E_b
E_HOMOr = E_HOMO
core.IO.change_file_namespace(180, "ot", "neutral")
# Cation
if read:
core.set_global_option("GUESS", "READ")
p4util.copy_file_to_scratch(read180, 'psi', 'ot', 180)
molecule.set_molecular_charge(charge1)
molecule.set_multiplicity(mult1)
core.print_out("""\n\t==> IP Fitting SCF: Cation, Right Endpoint <==\n""")
E1r = energy('scf', molecule=molecule, **kwargs)
core.IO.change_file_namespace(180, "ot", "cation")
IPr = E1r - E0r;
kIPr = -E_HOMOr;
delta_r = IPr - kIPr;
if IPr > kIPr:
message = ("""\n***IP Fitting Error: Right Omega limit should have kIP > IP""")
raise ValidationError(message)
omegas.append(omega_r)
types.append('Right Limit')
E0s.append(E0r)
E1s.append(E1r)
IPs.append(IPr)
kIPs.append(kIPr)
# Use previous orbitals from here out
core.set_global_option("GUESS", "READ")
# Left endpoint
core.set_global_option('DFT_OMEGA', omega_l)
# Neutral
core.IO.change_file_namespace(180, "neutral", "ot")
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
core.print_out("""\n\t==> IP Fitting SCF: Neutral, Left Endpoint <==\n""")
E0l, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
E_HOMO = 0.0
if Nb == 0:
E_HOMO = eps_a[int(Na - 1)]
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if E_a >= E_b:
E_HOMO = E_a
else:
E_HOMO = E_b
E_HOMOl = E_HOMO
core.IO.change_file_namespace(180, "ot", "neutral")
# Cation
core.IO.change_file_namespace(180, "cation", "ot")
molecule.set_molecular_charge(charge1)
molecule.set_multiplicity(mult1)
core.print_out("""\n\t==> IP Fitting SCF: Cation, Left Endpoint <==\n""")
E1l = energy('scf', molecule=molecule, **kwargs)
core.IO.change_file_namespace(180, "ot", "cation")
IPl = E1l - E0l
kIPl = -E_HOMOl
delta_l = IPl - kIPl
if IPl < kIPl:
message = ("""\n***IP Fitting Error: Left Omega limit should have kIP < IP""")
raise ValidationError(message)
omegas.append(omega_l)
types.append('Left Limit')
E0s.append(E0l)
E1s.append(E1l)
IPs.append(IPl)
kIPs.append(kIPl)
converged = False
repeat_l = 0
repeat_r = 0
step = 0
while True:
step = step + 1
# Regula Falsi (modified)
if repeat_l > 1:
delta_l = delta_l / 2.0
if repeat_r > 1:
delta_r = delta_r / 2.0
omega = - (omega_r - omega_l) / (delta_r - delta_l) * delta_l + omega_l
core.set_global_option('DFT_OMEGA', omega)
# Neutral
core.IO.change_file_namespace(180, "neutral", "ot")
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
core.print_out("""\n\t==> IP Fitting SCF: Neutral, Omega = %11.3E <==\n""" % omega)
E0, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
E_HOMO = 0.0
if Nb == 0:
E_HOMO = eps_a[int(Na - 1)]
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if E_a >= E_b:
E_HOMO = E_a
else:
E_HOMO = E_b
core.IO.change_file_namespace(180, "ot", "neutral")
# Cation
core.IO.change_file_namespace(180, "cation", "ot")
molecule.set_molecular_charge(charge1)
molecule.set_multiplicity(mult1)
core.print_out("""\n\t==> IP Fitting SCF: Cation, Omega = %11.3E <==\n""" % omega)
E1 = energy('scf', molecule=molecule, **kwargs)
core.IO.change_file_namespace(180, "ot", "cation")
IP = E1 - E0
kIP = -E_HOMO
delta = IP - kIP
if kIP > IP:
omega_r = omega
E0r = E0
E1r = E1
IPr = IP
kIPr = kIP
delta_r = delta
repeat_r = 0
repeat_l = repeat_l + 1
else:
omega_l = omega
E0l = E0
E1l = E1
IPl = IP
kIPl = kIP
delta_l = delta
repeat_l = 0;
repeat_r = repeat_r + 1
omegas.append(omega)
types.append('Regula-Falsi')
E0s.append(E0)
E1s.append(E1)
IPs.append(IP)
kIPs.append(kIP)
# Termination
if (abs(omega_l - omega_r) < omega_tol or step > maxiter):
converged = True
break
# Properly, should clone molecule but since not returned and easy to unblemish,
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
core.IO.set_default_namespace("")
core.print_out("""\n\t==> IP Fitting Results <==\n\n""")
core.print_out("""\t => Occupation Determination <= \n\n""")
core.print_out("""\t %6s %6s %6s %6s %6s %6s\n""" % ('N', 'Na', 'Nb', 'Charge', 'Mult', 'H**O'))
core.print_out("""\t Neutral: %6d %6d %6d %6d %6d %6d\n""" % (N, Na, Nb, charge0, mult0, H**O))
core.print_out("""\t Cation: %6d %6d %6d %6d %6d\n\n""" % (N - 1, Na1, Nb1, charge1, mult1))
core.print_out("""\t => Regula Falsi Iterations <=\n\n""")
core.print_out("""\t%3s %11s %14s %14s %14s %s\n""" % ('N','Omega','IP','kIP','Delta','Type'))
for k in range(len(omegas)):
core.print_out("""\t%3d %11.3E %14.6E %14.6E %14.6E %s\n""" %
(k + 1, omegas[k], IPs[k], kIPs[k], IPs[k] - kIPs[k], types[k]))
if converged:
core.print_out("""\n\tIP Fitting Converged\n""")
core.print_out("""\tFinal omega = %14.6E\n""" % ((omega_l + omega_r) / 2))
core.print_out("""\n\t"M,I. does the dying. Fleet just does the flying."\n""")
core.print_out("""\t\t\t-Starship Troopers\n""")
else:
core.print_out("""\n\tIP Fitting did not converge!\n""")
core.set_global_option("DF_INTS_IO", "NONE")
core.set_global_option("GUESS", old_guess)
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