def compute_charges(charge_method, charge_type, molecule):
"""
Compute charges for nbody fragments
"""
from psi4.driver.driver import energy
from psi4.driver.p4util.util import oeprop
charges = {}
molecule = molecule.clone()
for i in range(1, molecule.nfragments() + 1):
molecule.set_name('charges%i' %i)
e, wfn = energy(charge_method, molecule=molecule.extract_subsets([i]), return_wfn=True)
oeprop(wfn, charge_type)
charges[i] = wfn.atomic_point_charges().np
return charges
def compute_charges(charge_method, charge_type, molecule):
"""
Compute charges for nbody fragments
"""
from psi4.driver.driver import energy
from psi4.driver.p4util.util import oeprop
charges = {}
molecule = molecule.clone()
for i in range(1, molecule.nfragments() + 1):
molecule.set_name('charges%i' % i)
e, wfn = energy(charge_method, molecule=molecule.extract_subsets([i]), return_wfn=True)
oeprop(wfn, charge_type)
charges[i] = wfn.atomic_point_charges().np
return charges
def ip_fitting(name,
omega_l=0.05,
omega_r=2.5,
omega_convergence=1.0e-3,
maxiter=20,
**kwargs):
"""Optimize DFT omega parameter for molecular system.
Parameters
----------
name : string or function
DFT functional string name or function defining functional
whose omega is to be optimized.
omega_l : float, optional
Minimum omega to be considered during fitting.
omega_r : float, optional
Maximum omega to be considered during fitting.
molecule : :ref:`molecule <op_py_molecule>`, optional
Target molecule (neutral) for which omega is to be tuned, if not last defined.
omega_convergence : float, optional
Threshold below which to consider omega converged. (formerly omega_tolerance)
maxiter : int, optional
Maximum number of iterations towards omega convergence.
Returns
-------
float
Optimal omega parameter.
"""
optstash = p4util.OptionsState(['SCF', 'REFERENCE'], ['SCF', 'GUESS'],
['SCF', 'DF_INTS_IO'], ['SCF', 'DFT_OMEGA'],
['DOCC'], ['SOCC'])
kwargs = p4util.kwargs_lower(kwargs)
# By default, do not read previous 180 orbitals file
read = False
read180 = ''
if 'read' in kwargs:
read = True
read180 = kwargs['read']
if core.get_option('SCF', 'REFERENCE') != 'UKS':
core.print_out(
""" Requested procedure `ip_fitting` runs further calculations with UKS reference.\n"""
)
core.set_local_option('SCF', 'REFERENCE', 'UKS')
# Make sure the molecule the user provided is the active one, and neutral
molecule = kwargs.pop('molecule', core.get_active_molecule())
molecule.update_geometry()
if molecule.molecular_charge() != 0:
raise ValidationError(
"""IP Fitting requires neutral molecule to start.""")
if molecule.schoenflies_symbol() != 'c1':
core.print_out(
""" Requested procedure `ip_fitting` does not make use of molecular symmetry: """
"""further calculations in C1 point group.\n""")
molecule = molecule.clone()
molecule.reset_point_group('c1')
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_local_option("SCF", "GUESS", "READ")
copy_file_to_scratch(read180, 'psi', 'ot', 180)
core.set_local_option("SCF", "DF_INTS_IO", "SAVE")
E, wfn = driver.energy('scf',
dft_functional=name,
return_wfn=True,
molecule=molecule,
banner='IP Fitting SCF: Burn-in',
**kwargs)
core.set_local_option("SCF", "DF_INTS_IO", "LOAD")
if not wfn.functional().is_x_lrc():
raise ValidationError(
"""Not sensible to optimize omega for non-long-range-correction functional."""
)
# 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.np[int(Na - 1)]
E_b = eps_b.np[int(Nb - 1)]
if E_a >= E_b:
H**O = Na
else:
H**O = -Nb
Na1 = Na
Nb1 = Nb
if H**O > 0:
Na1 -= 1
else:
Nb1 -= 1
charge1 = charge0 + 1
mult1 = Na1 - Nb1 + 1
omegas = []
E0s = []
E1s = []
kIPs = []
IPs = []
types = []
# Right endpoint
core.set_local_option('SCF', 'DFT_OMEGA', omega_r)
# Neutral
if read:
core.set_local_option("SCF", "GUESS", "READ")
p4util.copy_file_to_scratch(read180, 'psi', 'ot', 180)
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
E0r, wfn = driver.energy('scf',
dft_functional=name,
return_wfn=True,
molecule=molecule,
banner='IP Fitting SCF: Neutral, Right Endpoint',
**kwargs)
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
if Nb == 0:
E_HOMO = eps_a.np[int(Na - 1)]
else:
E_a = eps_a.np[int(Na - 1)]
E_b = eps_b.np[int(Nb - 1)]
E_HOMO = max(E_a, E_b)
E_HOMOr = E_HOMO
core.IO.change_file_namespace(180, "ot", "neutral")
# Cation
if read:
core.set_local_option("SCF", "GUESS", "READ")
p4util.copy_file_to_scratch(read180, 'psi', 'ot', 180)
molecule.set_molecular_charge(charge1)
molecule.set_multiplicity(mult1)
E1r = driver.energy('scf',
dft_functional=name,
molecule=molecule,
banner='IP Fitting SCF: Cation, Right Endpoint',
**kwargs)
core.IO.change_file_namespace(180, "ot", "cation")
IPr = E1r - E0r
kIPr = -E_HOMOr
delta_r = IPr - kIPr
if IPr > kIPr:
raise ValidationError(
"""\n***IP Fitting Error: Right Omega limit should have kIP > IP: {} !> {}"""
.format(kIPr, IPr))
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_local_option("SCF", "GUESS", "READ")
# Left endpoint
core.set_local_option('SCF', 'DFT_OMEGA', omega_l)
# Neutral
core.IO.change_file_namespace(180, "neutral", "ot")
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
core.set_global_option("DOCC", [Nb])
core.set_global_option("SOCC", [Na - Nb])
E0l, wfn = driver.energy('scf',
dft_functional=name,
return_wfn=True,
molecule=molecule,
banner='IP Fitting SCF: Neutral, Left Endpoint',
**kwargs)
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
if Nb == 0:
E_HOMO = eps_a.np[int(Na - 1)]
else:
E_a = eps_a.np[int(Na - 1)]
E_b = eps_b.np[int(Nb - 1)]
E_HOMO = max(E_a, 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.set_global_option("DOCC", [Nb1])
core.set_global_option("SOCC", [Na1 - Nb1])
E1l = driver.energy('scf',
dft_functional=name,
molecule=molecule,
banner='IP Fitting SCF: Cation, Left Endpoint',
**kwargs)
core.IO.change_file_namespace(180, "ot", "cation")
IPl = E1l - E0l
kIPl = -E_HOMOl
delta_l = IPl - kIPl
if IPl < kIPl:
raise ValidationError(
"""\n***IP Fitting Error: Left Omega limit should have kIP < IP: {} !< {}"""
.format(kIPl, IPl))
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
for step in range(maxiter):
# Regula Falsi (modified)
if repeat_l > 1:
delta_l /= 2.0
if repeat_r > 1:
delta_r /= 2.0
omega = -(omega_r - omega_l) / (delta_r - delta_l) * delta_l + omega_l
core.set_local_option('SCF', 'DFT_OMEGA', omega)
# Neutral
core.IO.change_file_namespace(180, "neutral", "ot")
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
core.set_global_option("DOCC", [Nb])
core.set_global_option("SOCC", [Na - Nb])
E0, wfn = driver.energy(
'scf',
dft_functional=name,
return_wfn=True,
molecule=molecule,
banner='IP Fitting SCF: Neutral, Omega = {:11.3E}'.format(omega),
**kwargs)
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
if Nb == 0:
E_HOMO = eps_a.np[int(Na - 1)]
else:
E_a = eps_a.np[int(Na - 1)]
E_b = eps_b.np[int(Nb - 1)]
E_HOMO = max(E_a, 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.set_global_option("DOCC", [Nb1])
core.set_global_option("SOCC", [Na1 - Nb1])
E1 = driver.energy(
'scf',
dft_functional=name,
molecule=molecule,
banner='IP Fitting SCF: Cation, Omega = {:11.3E}'.format(omega),
**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 += 1
else:
omega_l = omega
E0l = E0
E1l = E1
IPl = IP
kIPl = kIP
delta_l = delta
repeat_l = 0
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_convergence:
converged = True
break
core.IO.set_default_namespace("")
core.print_out("""\n ==> IP Fitting Results <==\n\n""")
core.print_out(""" => Occupation Determination <= \n\n""")
core.print_out(""" %6s %6s %6s %6s %6s %6s\n""" %
('N', 'Na', 'Nb', 'Charge', 'Mult', 'H**O'))
core.print_out(""" Neutral: %6d %6d %6d %6d %6d %6d\n""" %
(N, Na, Nb, charge0, mult0, H**O))
core.print_out(""" Cation: %6d %6d %6d %6d %6d\n\n""" %
(N - 1, Na1, Nb1, charge1, mult1))
core.print_out(""" => Regula Falsi Iterations <=\n\n""")
core.print_out(""" %3s %11s %14s %14s %14s %s\n""" %
('N', 'Omega', 'IP', 'kIP', 'Delta', 'Type'))
for k in range(len(omegas)):
core.print_out(
""" %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]))
optstash.restore()
if converged:
core.print_out("""\n IP Fitting Converged\n""")
core.print_out(""" Final omega = %14.6E\n""" %
((omega_l + omega_r) / 2))
core.print_out(
"""\n "M,I. does the dying. Fleet just does the flying."\n""")
core.print_out(""" -Starship Troopers\n""")
else:
raise ConvergenceError("""IP Fitting """, step + 1)
return ((omega_l + omega_r) / 2)
def frac_traverse(name, **kwargs):
"""Scan electron occupancy from +1 electron to -1.
Parameters
----------
name : string or function
DFT functional string name or function defining functional
whose omega is to be optimized.
molecule : :ref:`molecule <op_py_molecule>`, optional
Target molecule (neutral) for which omega is to be tuned, if not last defined.
cation_mult : int, optional
Multiplicity of cation, if not neutral multiplicity + 1.
anion_mult : int, optional
Multiplicity of anion, if not neutral multiplicity + 1.
frac_start : int, optional
Iteration at which to start frac procedure when not reading previous
guess. Defaults to 25.
HOMO_occs : list, optional
Occupations to step through for cation, by default `[1 - 0.1 * x for x in range(11)]`.
LUMO_occs : list, optional
Occupations to step through for anion, by default `[1 - 0.1 * x for x in range(11)]`.
H**O : int, optional
Index of H**O.
LUMO : int, optional
Index of LUMO.
frac_diis : bool, optional
Do use DIIS for non-1.0-occupied points?
neutral_guess : bool, optional
Do use neutral orbitals as guess for the anion?
hf_guess: bool, optional
Do use UHF guess before UKS?
continuous_guess : bool, optional
Do carry along guess rather than reguessing at each occupation?
filename : str, optional
Result filename, if not name of molecule.
Returns
-------
dict
Dictionary associating SCF energies with occupations.
"""
optstash = p4util.OptionsState(
['SCF', 'GUESS'],
['SCF', 'DF_INTS_IO'],
['SCF', 'REFERENCE'],
["SCF", "FRAC_START"],
["SCF", "FRAC_RENORMALIZE"],
#["SCF", "FRAC_LOAD"],
["SCF", "FRAC_OCC"],
["SCF", "FRAC_VAL"],
["SCF", "FRAC_DIIS"])
kwargs = p4util.kwargs_lower(kwargs)
# Make sure the molecule the user provided is the active one, and neutral
molecule = kwargs.pop('molecule', core.get_active_molecule())
molecule.update_geometry()
if molecule.molecular_charge() != 0:
raise ValidationError(
"""frac_traverse requires neutral molecule to start.""")
if molecule.schoenflies_symbol() != 'c1':
core.print_out(
""" Requested procedure `frac_traverse` does not make use of molecular symmetry: """
"""further calculations in C1 point group.\n""")
molecule = molecule.clone()
molecule.reset_point_group('c1')
molecule.update_geometry()
charge0 = molecule.molecular_charge()
mult0 = molecule.multiplicity()
chargep = charge0 + 1
chargem = charge0 - 1
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_local_option('SCF', '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 <= #
core.set_local_option("SCF", "DF_INTS_IO", "SAVE")
old_guess = core.get_local_option("SCF", "GUESS")
if (neutral_guess):
if (hf_guess):
core.set_local_option("SCF", "REFERENCE", "UHF")
driver.energy('scf', dft_functional=name, molecule=molecule, **kwargs)
core.set_local_option("SCF", "GUESS", "READ")
core.set_local_option("SCF", "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_local_option("SCF", "REFERENCE", "UHF")
driver.energy('scf', dft_functional=name, molecule=molecule, **kwargs)
core.set_local_option("SCF", "REFERENCE", "UKS")
core.set_local_option("SCF", "GUESS", "READ")
core.set_local_option("SCF", "DF_INTS_IO", "SAVE")
core.set_local_option("SCF", "FRAC_START", frac_start)
core.set_local_option("SCF", "FRAC_RENORMALIZE", True)
# NYI core.set_local_option("SCF", "FRAC_LOAD", False)
for occ in LUMO_occs:
core.set_local_option("SCF", "FRAC_OCC", [LUMO])
core.set_local_option("SCF", "FRAC_VAL", [occ])
E, wfn = driver.energy('scf',
dft_functional=name,
return_wfn=True,
molecule=molecule,
**kwargs)
C = 1
if E == 0.0:
E = core.variable('SCF ITERATION ENERGY')
C = 0
if LUMO > 0:
eps = wfn.epsilon_a()
potentials.append(eps.get(int(LUMO) - 1))
else:
eps = wfn.epsilon_b()
potentials.append(eps.get(-int(LUMO) - 1))
occs.append(occ)
energies.append(E)
convs.append(C)
core.set_local_option("SCF", "FRAC_START", 2)
#core.set_local_option("SCF", "FRAC_LOAD", True)
core.set_local_option("SCF", "GUESS", "READ")
core.set_local_option("SCF", "FRAC_DIIS", frac_diis)
core.set_local_option("SCF", "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_local_option("SCF", "GUESS", old_guess)
if hf_guess:
core.set_local_option("SCF", "FRAC_START", 0)
core.set_local_option("SCF", "REFERENCE", "UHF")
driver.energy('scf',
dft_functional=name,
molecule=molecule,
**kwargs)
core.set_local_option("SCF", "REFERENCE", "UKS")
core.set_local_option("SCF", "GUESS", "READ")
# NYI core.set_local_option("SCF", "FRAC_LOAD", False)
core.set_local_option("SCF", "FRAC_START", frac_start)
core.set_local_option("SCF", "FRAC_RENORMALIZE", True)
for occ in HOMO_occs:
core.set_local_option("SCF", "FRAC_OCC", [H**O])
core.set_local_option("SCF", "FRAC_VAL", [occ])
E, wfn = driver.energy('scf',
dft_functional=name,
return_wfn=True,
molecule=molecule,
**kwargs)
C = 1
if E == 0.0:
E = core.variable('SCF ITERATION ENERGY')
C = 0
if LUMO > 0:
eps = wfn.epsilon_a()
potentials.append(eps.get(int(H**O) - 1))
else:
eps = wfn.epsilon_b()
potentials.append(eps.get(-int(H**O) - 1))
occs.append(occ - 1.0)
energies.append(E)
convs.append(C)
core.set_local_option("SCF", "FRAC_START", 2)
# NYI core.set_local_option("SCF", "FRAC_LOAD", True)
core.set_local_option("SCF", "GUESS", "READ")
core.set_local_option("SCF", "FRAC_DIIS", frac_diis)
core.set_local_option("SCF", "DF_INTS_IO", "LOAD")
# => Print the results out <= #
E = {}
core.print_out(
"""\n ==> Fractional Occupation Traverse Results <==\n\n""")
core.print_out(""" %-11s %-24s %-24s %11s\n""" %
('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(occs)):
core.print_out(""" %11.3E %24.16E %24.16E %11d\n""" %
(occs[k], energies[k], potentials[k], convs[k]))
E[occs[k]] = energies[k]
core.print_out("""
You trying to be a hero Watkins?
Just trying to kill some bugs sir!
-Starship Troopers""")
# Drop the files out
with open(traverse_filename, 'w') as fh:
fh.write(""" %-11s %-24s %-24s %11s\n""" %
('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(occs)):
fh.write(""" %11.3E %24.16E %24.16E %11d\n""" %
(occs[k], energies[k], potentials[k], convs[k]))
optstash.restore()
return E
def frac_nuke(name, **kwargs):
"""Pull all the electrons out, one at a time"""
optstash = p4util.OptionsState(
['SCF', 'GUESS'],
['SCF', 'DF_INTS_IO'],
["SCF", "FRAC_START"],
["SCF", "FRAC_RENORMALIZE"],
# NYI ["SCF", "FRAC_LOAD"],
["SCF", "FRAC_OCC"],
["SCF", "FRAC_VAL"],
["SCF", "FRAC_DIIS"])
kwargs = p4util.kwargs_lower(kwargs)
# Make sure the molecule the user provided is the active one, and neutral
molecule = kwargs.pop('molecule', core.get_active_molecule())
molecule.update_geometry()
if molecule.molecular_charge() != 0:
raise ValidationError(
"""frac_nuke requires neutral molecule to start.""")
if molecule.schoenflies_symbol() != 'c1':
core.print_out(
""" Requested procedure `frac_nuke` does not make use of molecular symmetry: """
"""further calculations in C1 point group.\n""")
molecule = molecule.clone()
molecule.reset_point_group('c1')
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_local_option("SCF", "DF_INTS_IO", "SAVE")
Ns = []
energies = []
potentials = []
convs = []
stats = []
# Run one SCF to burn things in
E, wfn = driver.energy('scf',
dft_functional=name,
return_wfn=True,
molecule=molecule,
**kwargs)
# Determine H**O
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
eps_a.print_out()
if Na == Nb:
H**O = -Nb
elif Nb == 0:
H**O = Na
else:
E_a = eps_a.get(int(Na - 1))
E_b = eps_b.get(int(Nb - 1))
if E_a >= E_b:
H**O = Na
else:
H**O = -Nb
stats.append(""" %6d %6d %6d %6d %6d %6d\n""" %
(N, Na, Nb, charge, mult, H**O))
if H**O > 0:
Na -= 1
else:
Nb -= 1
charge += 1
mult = Na - Nb + 1
core.set_local_option("SCF", "DF_INTS_IO", "LOAD")
core.set_local_option("SCF", "FRAC_START", frac_start)
core.set_local_option("SCF", "FRAC_RENORMALIZE", True)
# Nuke 'em Rico!
for Nintegral in range(N, Nmin, -1):
# Nuke the current H**O
for occ in foccs:
core.set_local_option("SCF", "FRAC_OCC", [H**O])
core.set_local_option("SCF", "FRAC_VAL", [occ])
E, wfn = driver.energy('scf',
dft_functional=name,
return_wfn=True,
molecule=molecule,
**kwargs)
C = 1
if E == 0.0:
E = core.variable('SCF ITERATION ENERGY')
C = 0
if H**O > 0:
eps = wfn.epsilon_a()
potentials.append(eps.np[H**O - 1])
else:
eps = wfn.epsilon_b()
potentials.append(eps.np[-H**O - 1])
Ns.append(Nintegral + occ - 1.0)
energies.append(E)
convs.append(C)
core.set_local_option("SCF", "FRAC_START", 2)
# NYI core.set_local_option("SCF", "FRAC_LOAD", True)
core.set_local_option("SCF", "FRAC_DIIS", frac_diis)
core.set_local_option("SCF", "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.np[int(Na - 1)]
E_b = eps_b.np[int(Nb - 1)]
if E_a >= E_b:
H**O = Na
else:
H**O = -Nb
stats.append(""" %6d %6d %6d %6d %6d %6d\n""" %
(Nintegral - 1, Na, Nb, charge, mult, H**O))
if H**O > 0:
Na -= 1
else:
Nb -= 1
charge += 1
mult = Na - Nb + 1
core.set_local_option("SCF", "DF_INTS_IO", "NONE")
# => Print the results out <= #
E = {}
core.print_out("""\n ==> Fractional Occupation Nuke Results <==\n\n""")
core.print_out(""" %-11s %-24s %-24s %11s\n""" %
('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(Ns)):
core.print_out(""" %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(""" %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 "You shoot a nuke down a bug hole, you got a lot of dead bugs"\n'
)
core.print_out(' -Starship Troopers\n')
# Drop the files out
with open(traverse_filename, 'w') as fh:
fh.write(""" %-11s %-24s %-24s %11s\n""" %
('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(Ns)):
fh.write(""" %11.3E %24.16E %24.16E %11d\n""" %
(Ns[k], energies[k], potentials[k], convs[k]))
with open(stats_filename, 'w') as fh:
fh.write(""" %6s %6s %6s %6s %6s %6s\n""" %
('N', 'Na', 'Nb', 'Charge', 'Mult', 'H**O'))
for line in stats:
fh.write(line)
optstash.restore()
return E
def run_gaussian_2(name, **kwargs):
# throw an exception for open-shells
if (core.get_option('SCF','REFERENCE') != 'RHF' ):
raise ValidationError("""g2 computations require "reference rhf".""")
# stash user options:
optstash = p4util.OptionsState(
['FNOCC','COMPUTE_TRIPLES'],
['FNOCC','COMPUTE_MP4_TRIPLES'],
['FREEZE_CORE'],
['MP2_TYPE'],
['SCF','SCF_TYPE'])
# override default scf_type
core.set_local_option('SCF','SCF_TYPE','PK')
# optimize geometry at scf level
core.clean()
core.set_global_option('BASIS',"6-31G(D)")
driver.optimize('scf')
core.clean()
# scf frequencies for zpe
# NOTE This line should not be needed, but without it there's a seg fault
scf_e, ref = driver.frequency('scf', return_wfn=True)
# thermodynamic properties
du = core.get_variable('INTERNAL ENERGY CORRECTION')
dh = core.get_variable('ENTHALPY CORRECTION')
dg = core.get_variable('GIBBS FREE ENERGY CORRECTION')
freqs = ref.frequencies()
nfreq = freqs.dim(0)
freqsum = 0.0
for i in range(0, nfreq):
freqsum += freqs.get(i)
zpe = freqsum / p4const.psi_hartree2wavenumbers * 0.8929 * 0.5
core.clean()
# optimize geometry at mp2 (no frozen core) level
# note: freeze_core isn't an option in MP2
core.set_global_option('FREEZE_CORE',"FALSE")
core.set_global_option('MP2_TYPE', 'CONV')
driver.optimize('mp2')
core.clean()
# qcisd(t)
core.set_local_option('FNOCC','COMPUTE_MP4_TRIPLES',"TRUE")
core.set_global_option('FREEZE_CORE',"TRUE")
core.set_global_option('BASIS',"6-311G(D_P)")
ref = driver.proc.run_fnocc('qcisd(t)', return_wfn=True, **kwargs)
# HLC: high-level correction based on number of valence electrons
nirrep = ref.nirrep()
frzcpi = ref.frzcpi()
nfzc = 0
for i in range (0,nirrep):
nfzc += frzcpi[i]
nalpha = ref.nalpha() - nfzc
nbeta = ref.nbeta() - nfzc
# hlc of gaussian-2
hlc = -0.00481 * nalpha -0.00019 * nbeta
# hlc of gaussian-1
hlc1 = -0.00614 * nalpha
eqci_6311gdp = core.get_variable("QCISD(T) TOTAL ENERGY")
emp4_6311gd = core.get_variable("MP4 TOTAL ENERGY")
emp2_6311gd = core.get_variable("MP2 TOTAL ENERGY")
core.clean()
# correction for diffuse functions
core.set_global_option('BASIS',"6-311+G(D_P)")
driver.energy('mp4')
emp4_6311pg_dp = core.get_variable("MP4 TOTAL ENERGY")
emp2_6311pg_dp = core.get_variable("MP2 TOTAL ENERGY")
core.clean()
# correction for polarization functions
core.set_global_option('BASIS',"6-311G(2DF_P)")
driver.energy('mp4')
emp4_6311g2dfp = core.get_variable("MP4 TOTAL ENERGY")
emp2_6311g2dfp = core.get_variable("MP2 TOTAL ENERGY")
core.clean()
# big basis mp2
core.set_global_option('BASIS',"6-311+G(3DF_2P)")
#run_fnocc('_mp2',**kwargs)
driver.energy('mp2')
emp2_big = core.get_variable("MP2 TOTAL ENERGY")
core.clean()
eqci = eqci_6311gdp
e_delta_g2 = emp2_big + emp2_6311gd - emp2_6311g2dfp - emp2_6311pg_dp
e_plus = emp4_6311pg_dp - emp4_6311gd
e_2df = emp4_6311g2dfp - emp4_6311gd
eg2 = eqci + e_delta_g2 + e_plus + e_2df
eg2_mp2_0k = eqci + (emp2_big - emp2_6311gd) + hlc + zpe
core.print_out('\n')
core.print_out(' ==> G1/G2 Energy Components <==\n')
core.print_out('\n')
core.print_out(' QCISD(T): %20.12lf\n' % eqci)
core.print_out(' E(Delta): %20.12lf\n' % e_delta_g2)
core.print_out(' E(2DF): %20.12lf\n' % e_2df)
core.print_out(' E(+): %20.12lf\n' % e_plus)
core.print_out(' E(G1 HLC): %20.12lf\n' % hlc1)
core.print_out(' E(G2 HLC): %20.12lf\n' % hlc)
core.print_out(' E(ZPE): %20.12lf\n' % zpe)
core.print_out('\n')
core.print_out(' ==> 0 Kelvin Results <==\n')
core.print_out('\n')
eg2_0k = eg2 + zpe + hlc
core.print_out(' G1: %20.12lf\n' % (eqci + e_plus + e_2df + hlc1 + zpe))
core.print_out(' G2(MP2): %20.12lf\n' % eg2_mp2_0k)
core.print_out(' G2: %20.12lf\n' % eg2_0k)
core.set_variable("G1 TOTAL ENERGY",eqci + e_plus + e_2df + hlc1 + zpe)
core.set_variable("G2 TOTAL ENERGY",eg2_0k)
core.set_variable("G2(MP2) TOTAL ENERGY",eg2_mp2_0k)
core.print_out('\n')
T = core.get_global_option('T')
core.print_out(' ==> %3.0lf Kelvin Results <==\n'% T)
core.print_out('\n')
internal_energy = eg2_mp2_0k + du - zpe / 0.8929
enthalpy = eg2_mp2_0k + dh - zpe / 0.8929
gibbs = eg2_mp2_0k + dg - zpe / 0.8929
core.print_out(' G2(MP2) energy: %20.12lf\n' % internal_energy )
core.print_out(' G2(MP2) enthalpy: %20.12lf\n' % enthalpy)
core.print_out(' G2(MP2) free energy: %20.12lf\n' % gibbs)
core.print_out('\n')
core.set_variable("G2(MP2) INTERNAL ENERGY",internal_energy)
core.set_variable("G2(MP2) ENTHALPY",enthalpy)
core.set_variable("G2(MP2) FREE ENERGY",gibbs)
internal_energy = eg2_0k + du - zpe / 0.8929
enthalpy = eg2_0k + dh - zpe / 0.8929
gibbs = eg2_0k + dg - zpe / 0.8929
core.print_out(' G2 energy: %20.12lf\n' % internal_energy )
core.print_out(' G2 enthalpy: %20.12lf\n' % enthalpy)
core.print_out(' G2 free energy: %20.12lf\n' % gibbs)
core.set_variable("CURRENT ENERGY",eg2_0k)
core.set_variable("G2 INTERNAL ENERGY",internal_energy)
core.set_variable("G2 ENTHALPY",enthalpy)
core.set_variable("G2 FREE ENERGY",gibbs)
core.clean()
optstash.restore()
# return 0K g2 results
return eg2_0k
def run_gaussian_2(name, **kwargs):
# throw an exception for open-shells
if (core.get_option('SCF', 'REFERENCE') != 'RHF'):
raise ValidationError("""g2 computations require "reference rhf".""")
# stash user options:
optstash = p4util.OptionsState(['FNOCC', 'COMPUTE_TRIPLES'],
['FNOCC', 'COMPUTE_MP4_TRIPLES'], ['BASIS'],
['FREEZE_CORE'], ['MP2_TYPE'], ['SCF_TYPE'])
# override default scf_type
core.set_global_option('SCF_TYPE', 'PK')
# optimize geometry at scf level
core.clean()
core.set_global_option('BASIS', "6-31G(D)")
driver.optimize('scf')
core.clean()
# scf frequencies for zpe
# NOTE This line should not be needed, but without it there's a seg fault
scf_e, ref = driver.frequency('scf', return_wfn=True)
# thermodynamic properties
du = core.variable('THERMAL ENERGY CORRECTION')
dh = core.variable('ENTHALPY CORRECTION')
dg = core.variable('GIBBS FREE ENERGY CORRECTION')
freqs = ref.frequencies()
nfreq = freqs.dim(0)
freqsum = 0.0
for i in range(0, nfreq):
freqsum += freqs.get(i)
zpe = freqsum / constants.hartree2wavenumbers * 0.8929 * 0.5
core.clean()
# optimize geometry at mp2 (no frozen core) level
# note: freeze_core isn't an option in MP2
core.set_global_option('FREEZE_CORE', "FALSE")
core.set_global_option('MP2_TYPE', 'CONV')
driver.optimize('mp2')
core.clean()
# qcisd(t)
core.set_local_option('FNOCC', 'COMPUTE_MP4_TRIPLES', "TRUE")
core.set_global_option('FREEZE_CORE', "TRUE")
core.set_global_option('BASIS', "6-311G(D_P)")
ref = driver.proc.run_fnocc('qcisd(t)', return_wfn=True, **kwargs)
# HLC: high-level correction based on number of valence electrons
nirrep = ref.nirrep()
frzcpi = ref.frzcpi()
nfzc = 0
for i in range(0, nirrep):
nfzc += frzcpi[i]
nalpha = ref.nalpha() - nfzc
nbeta = ref.nbeta() - nfzc
# hlc of gaussian-2
hlc = -0.00481 * nalpha - 0.00019 * nbeta
# hlc of gaussian-1
hlc1 = -0.00614 * nalpha
eqci_6311gdp = core.variable("QCISD(T) TOTAL ENERGY")
emp4_6311gd = core.variable("MP4 TOTAL ENERGY")
emp2_6311gd = core.variable("MP2 TOTAL ENERGY")
core.clean()
# correction for diffuse functions
core.set_global_option('BASIS', "6-311+G(D_P)")
driver.energy('mp4')
emp4_6311pg_dp = core.variable("MP4 TOTAL ENERGY")
emp2_6311pg_dp = core.variable("MP2 TOTAL ENERGY")
core.clean()
# correction for polarization functions
core.set_global_option('BASIS', "6-311G(2DF_P)")
driver.energy('mp4')
emp4_6311g2dfp = core.variable("MP4 TOTAL ENERGY")
emp2_6311g2dfp = core.variable("MP2 TOTAL ENERGY")
core.clean()
# big basis mp2
core.set_global_option('BASIS', "6-311+G(3DF_2P)")
#run_fnocc('_mp2',**kwargs)
driver.energy('mp2')
emp2_big = core.variable("MP2 TOTAL ENERGY")
core.clean()
eqci = eqci_6311gdp
e_delta_g2 = emp2_big + emp2_6311gd - emp2_6311g2dfp - emp2_6311pg_dp
e_plus = emp4_6311pg_dp - emp4_6311gd
e_2df = emp4_6311g2dfp - emp4_6311gd
eg2 = eqci + e_delta_g2 + e_plus + e_2df
eg2_mp2_0k = eqci + (emp2_big - emp2_6311gd) + hlc + zpe
core.print_out('\n')
core.print_out(' ==> G1/G2 Energy Components <==\n')
core.print_out('\n')
core.print_out(' QCISD(T): %20.12lf\n' % eqci)
core.print_out(' E(Delta): %20.12lf\n' % e_delta_g2)
core.print_out(' E(2DF): %20.12lf\n' % e_2df)
core.print_out(' E(+): %20.12lf\n' % e_plus)
core.print_out(' E(G1 HLC): %20.12lf\n' % hlc1)
core.print_out(' E(G2 HLC): %20.12lf\n' % hlc)
core.print_out(' E(ZPE): %20.12lf\n' % zpe)
core.print_out('\n')
core.print_out(' ==> 0 Kelvin Results <==\n')
core.print_out('\n')
eg2_0k = eg2 + zpe + hlc
core.print_out(' G1: %20.12lf\n' %
(eqci + e_plus + e_2df + hlc1 + zpe))
core.print_out(' G2(MP2): %20.12lf\n' % eg2_mp2_0k)
core.print_out(' G2: %20.12lf\n' % eg2_0k)
core.set_variable("G1 TOTAL ENERGY", eqci + e_plus + e_2df + hlc1 + zpe)
core.set_variable("G2 TOTAL ENERGY", eg2_0k)
core.set_variable("G2(MP2) TOTAL ENERGY", eg2_mp2_0k)
core.print_out('\n')
T = core.get_global_option('T')
core.print_out(' ==> %3.0lf Kelvin Results <==\n' % T)
core.print_out('\n')
internal_energy = eg2_mp2_0k + du - zpe / 0.8929
enthalpy = eg2_mp2_0k + dh - zpe / 0.8929
gibbs = eg2_mp2_0k + dg - zpe / 0.8929
core.print_out(' G2(MP2) energy: %20.12lf\n' % internal_energy)
core.print_out(' G2(MP2) enthalpy: %20.12lf\n' % enthalpy)
core.print_out(' G2(MP2) free energy: %20.12lf\n' % gibbs)
core.print_out('\n')
core.set_variable("G2(MP2) INTERNAL ENERGY", internal_energy)
core.set_variable("G2(MP2) ENTHALPY", enthalpy)
core.set_variable("G2(MP2) FREE ENERGY", gibbs)
internal_energy = eg2_0k + du - zpe / 0.8929
enthalpy = eg2_0k + dh - zpe / 0.8929
gibbs = eg2_0k + dg - zpe / 0.8929
core.print_out(' G2 energy: %20.12lf\n' % internal_energy)
core.print_out(' G2 enthalpy: %20.12lf\n' % enthalpy)
core.print_out(' G2 free energy: %20.12lf\n' % gibbs)
core.set_variable("CURRENT ENERGY", eg2_0k)
core.set_variable("G2 INTERNAL ENERGY", internal_energy)
core.set_variable("G2 ENTHALPY", enthalpy)
core.set_variable("G2 FREE ENERGY", gibbs)
core.clean()
optstash.restore()
# return 0K g2 results
return eg2_0k
def ip_fitting(name, omega_l=0.05, omega_r=2.5, omega_convergence=1.0e-3, maxiter=20, **kwargs):
"""Optimize DFT omega parameter for molecular system.
Parameters
----------
name : string or function
DFT functional string name or function defining functional
whose omega is to be optimized.
omega_l : float, optional
Minimum omega to be considered during fitting.
omega_r : float, optional
Maximum omega to be considered during fitting.
molecule : :ref:`molecule <op_py_molecule>`, optional
Target molecule (neutral) for which omega is to be tuned, if not last defined.
omega_convergence : float, optional
Threshold below which to consider omega converged. (formerly omega_tolerance)
maxiter : int, optional
Maximum number of iterations towards omega convergence.
Returns
-------
float
Optimal omega parameter.
"""
optstash = p4util.OptionsState(
['SCF', 'REFERENCE'],
['SCF', 'GUESS'],
['SCF', 'DF_INTS_IO'],
['SCF', 'DFT_OMEGA'],
['DOCC'],
['SOCC'])
kwargs = p4util.kwargs_lower(kwargs)
# By default, do not read previous 180 orbitals file
read = False
read180 = ''
if 'read' in kwargs:
read = True
read180 = kwargs['read']
if core.get_option('SCF', 'REFERENCE') != 'UKS':
core.print_out(""" Requested procedure `ip_fitting` runs further calculations with UKS reference.\n""")
core.set_local_option('SCF', 'REFERENCE', 'UKS')
# Make sure the molecule the user provided is the active one, and neutral
molecule = kwargs.pop('molecule', core.get_active_molecule())
molecule.update_geometry()
if molecule.molecular_charge() != 0:
raise ValidationError("""IP Fitting requires neutral molecule to start.""")
if molecule.schoenflies_symbol() != 'c1':
core.print_out(""" Requested procedure `ip_fitting` does not make use of molecular symmetry: """
"""further calculations in C1 point group.\n""")
molecule = molecule.clone()
molecule.reset_point_group('c1')
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_local_option("SCF", "GUESS", "READ")
copy_file_to_scratch(read180, 'psi', 'ot', 180)
core.set_local_option("SCF", "DF_INTS_IO", "SAVE")
E, wfn = driver.energy('scf', dft_functional=name, return_wfn=True, molecule=molecule,
banner='IP Fitting SCF: Burn-in', **kwargs)
core.set_local_option("SCF", "DF_INTS_IO", "LOAD")
if not wfn.functional().is_x_lrc():
raise ValidationError("""Not sensible to optimize omega for non-long-range-correction functional.""")
# 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.np[int(Na - 1)]
E_b = eps_b.np[int(Nb - 1)]
if E_a >= E_b:
H**O = Na
else:
H**O = -Nb
Na1 = Na
Nb1 = Nb
if H**O > 0:
Na1 -= 1
else:
Nb1 -= 1
charge1 = charge0 + 1
mult1 = Na1 - Nb1 + 1
omegas = []
E0s = []
E1s = []
kIPs = []
IPs = []
types = []
# Right endpoint
core.set_local_option('SCF', 'DFT_OMEGA', omega_r)
# Neutral
if read:
core.set_local_option("SCF", "GUESS", "READ")
p4util.copy_file_to_scratch(read180, 'psi', 'ot', 180)
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
E0r, wfn = driver.energy('scf', dft_functional=name, return_wfn=True, molecule=molecule,
banner='IP Fitting SCF: Neutral, Right Endpoint', **kwargs)
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
if Nb == 0:
E_HOMO = eps_a.np[int(Na - 1)]
else:
E_a = eps_a.np[int(Na - 1)]
E_b = eps_b.np[int(Nb - 1)]
E_HOMO = max(E_a, E_b)
E_HOMOr = E_HOMO
core.IO.change_file_namespace(180, "ot", "neutral")
# Cation
if read:
core.set_local_option("SCF", "GUESS", "READ")
p4util.copy_file_to_scratch(read180, 'psi', 'ot', 180)
molecule.set_molecular_charge(charge1)
molecule.set_multiplicity(mult1)
E1r = driver.energy('scf', dft_functional=name, molecule=molecule,
banner='IP Fitting SCF: Cation, Right Endpoint', **kwargs)
core.IO.change_file_namespace(180, "ot", "cation")
IPr = E1r - E0r
kIPr = -E_HOMOr
delta_r = IPr - kIPr
if IPr > kIPr:
raise ValidationError("""\n***IP Fitting Error: Right Omega limit should have kIP > IP: {} !> {}""".format(kIPr, IPr))
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_local_option("SCF", "GUESS", "READ")
# Left endpoint
core.set_local_option('SCF', 'DFT_OMEGA', omega_l)
# Neutral
core.IO.change_file_namespace(180, "neutral", "ot")
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
core.set_global_option("DOCC", [Nb])
core.set_global_option("SOCC", [Na - Nb])
E0l, wfn = driver.energy('scf', dft_functional=name, return_wfn=True, molecule=molecule,
banner='IP Fitting SCF: Neutral, Left Endpoint', **kwargs)
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
if Nb == 0:
E_HOMO = eps_a.np[int(Na - 1)]
else:
E_a = eps_a.np[int(Na - 1)]
E_b = eps_b.np[int(Nb - 1)]
E_HOMO = max(E_a, 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.set_global_option("DOCC", [Nb1])
core.set_global_option("SOCC", [Na1 - Nb1])
E1l = driver.energy('scf', dft_functional=name, molecule=molecule,
banner='IP Fitting SCF: Cation, Left Endpoint', **kwargs)
core.IO.change_file_namespace(180, "ot", "cation")
IPl = E1l - E0l
kIPl = -E_HOMOl
delta_l = IPl - kIPl
if IPl < kIPl:
raise ValidationError("""\n***IP Fitting Error: Left Omega limit should have kIP < IP: {} !< {}""".format(kIPl, IPl))
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
for step in range(maxiter):
# Regula Falsi (modified)
if repeat_l > 1:
delta_l /= 2.0
if repeat_r > 1:
delta_r /= 2.0
omega = - (omega_r - omega_l) / (delta_r - delta_l) * delta_l + omega_l
core.set_local_option('SCF', 'DFT_OMEGA', omega)
# Neutral
core.IO.change_file_namespace(180, "neutral", "ot")
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
core.set_global_option("DOCC", [Nb])
core.set_global_option("SOCC", [Na - Nb])
E0, wfn = driver.energy('scf', dft_functional=name, return_wfn=True, molecule=molecule,
banner='IP Fitting SCF: Neutral, Omega = {:11.3E}'.format(omega), **kwargs)
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
if Nb == 0:
E_HOMO = eps_a.np[int(Na - 1)]
else:
E_a = eps_a.np[int(Na - 1)]
E_b = eps_b.np[int(Nb - 1)]
E_HOMO = max(E_a, 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.set_global_option("DOCC", [Nb1])
core.set_global_option("SOCC", [Na1 - Nb1])
E1 = driver.energy('scf', dft_functional=name, molecule=molecule,
banner='IP Fitting SCF: Cation, Omega = {:11.3E}'.format(omega), **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 += 1
else:
omega_l = omega
E0l = E0
E1l = E1
IPl = IP
kIPl = kIP
delta_l = delta
repeat_l = 0
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_convergence:
converged = True
break
core.IO.set_default_namespace("")
core.print_out("""\n ==> IP Fitting Results <==\n\n""")
core.print_out(""" => Occupation Determination <= \n\n""")
core.print_out(""" %6s %6s %6s %6s %6s %6s\n""" % ('N', 'Na', 'Nb', 'Charge', 'Mult', 'H**O'))
core.print_out(""" Neutral: %6d %6d %6d %6d %6d %6d\n""" % (N, Na, Nb, charge0, mult0, H**O))
core.print_out(""" Cation: %6d %6d %6d %6d %6d\n\n""" % (N - 1, Na1, Nb1, charge1, mult1))
core.print_out(""" => Regula Falsi Iterations <=\n\n""")
core.print_out(""" %3s %11s %14s %14s %14s %s\n""" % ('N','Omega','IP','kIP','Delta','Type'))
for k in range(len(omegas)):
core.print_out(""" %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]))
optstash.restore()
if converged:
core.print_out("""\n IP Fitting Converged\n""")
core.print_out(""" Final omega = %14.6E\n""" % ((omega_l + omega_r) / 2))
core.print_out("""\n "M,I. does the dying. Fleet just does the flying."\n""")
core.print_out(""" -Starship Troopers\n""")
else:
raise ConvergenceError("""IP Fitting """, step + 1)
return ((omega_l + omega_r) / 2)
def frac_traverse(name, **kwargs):
"""Scan electron occupancy from +1 electron to -1.
Parameters
----------
name : string or function
DFT functional string name or function defining functional
whose omega is to be optimized.
molecule : :ref:`molecule <op_py_molecule>`, optional
Target molecule (neutral) for which omega is to be tuned, if not last defined.
cation_mult : int, optional
Multiplicity of cation, if not neutral multiplicity + 1.
anion_mult : int, optional
Multiplicity of anion, if not neutral multiplicity + 1.
frac_start : int, optional
Iteration at which to start frac procedure when not reading previous
guess. Defaults to 25.
HOMO_occs : list, optional
Occupations to step through for cation, by default `[1 - 0.1 * x for x in range(11)]`.
LUMO_occs : list, optional
Occupations to step through for anion, by default `[1 - 0.1 * x for x in range(11)]`.
H**O : int, optional
Index of H**O.
LUMO : int, optional
Index of LUMO.
frac_diis : bool, optional
Do use DIIS for non-1.0-occupied points?
neutral_guess : bool, optional
Do use neutral orbitals as guess for the anion?
hf_guess: bool, optional
Do use UHF guess before UKS?
continuous_guess : bool, optional
Do carry along guess rather than reguessing at each occupation?
filename : str, optional
Result filename, if not name of molecule.
Returns
-------
dict
Dictionary associating SCF energies with occupations.
"""
optstash = p4util.OptionsState(
['SCF', 'GUESS'],
['SCF', 'DF_INTS_IO'],
['SCF', 'REFERENCE'],
["SCF", "FRAC_START"],
["SCF", "FRAC_RENORMALIZE"],
#["SCF", "FRAC_LOAD"],
["SCF", "FRAC_OCC"],
["SCF", "FRAC_VAL"],
["SCF", "FRAC_DIIS"])
kwargs = p4util.kwargs_lower(kwargs)
# Make sure the molecule the user provided is the active one, and neutral
molecule = kwargs.pop('molecule', core.get_active_molecule())
molecule.update_geometry()
if molecule.molecular_charge() != 0:
raise ValidationError("""frac_traverse requires neutral molecule to start.""")
if molecule.schoenflies_symbol() != 'c1':
core.print_out(""" Requested procedure `frac_traverse` does not make use of molecular symmetry: """
"""further calculations in C1 point group.\n""")
molecule = molecule.clone()
molecule.reset_point_group('c1')
molecule.update_geometry()
charge0 = molecule.molecular_charge()
mult0 = molecule.multiplicity()
chargep = charge0 + 1
chargem = charge0 - 1
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_local_option('SCF', '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 <= #
core.set_local_option("SCF", "DF_INTS_IO", "SAVE")
old_guess = core.get_local_option("SCF", "GUESS")
if (neutral_guess):
if (hf_guess):
core.set_local_option("SCF", "REFERENCE", "UHF")
driver.energy('scf', dft_functional=name, molecule=molecule, **kwargs)
core.set_local_option("SCF", "GUESS", "READ")
core.set_local_option("SCF", "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_local_option("SCF", "REFERENCE","UHF")
driver.energy('scf', dft_functional=name, molecule=molecule, **kwargs)
core.set_local_option("SCF", "REFERENCE", "UKS")
core.set_local_option("SCF", "GUESS", "READ")
core.set_local_option("SCF", "DF_INTS_IO", "SAVE")
core.set_local_option("SCF", "FRAC_START", frac_start)
core.set_local_option("SCF", "FRAC_RENORMALIZE", True)
# NYI core.set_local_option("SCF", "FRAC_LOAD", False)
for occ in LUMO_occs:
core.set_local_option("SCF", "FRAC_OCC", [LUMO])
core.set_local_option("SCF", "FRAC_VAL", [occ])
E, wfn = driver.energy('scf', dft_functional=name, return_wfn=True, molecule=molecule, **kwargs)
C = 1
if E == 0.0:
E = core.variable('SCF ITERATION ENERGY')
C = 0
if LUMO > 0:
eps = wfn.epsilon_a()
potentials.append(eps.get(int(LUMO) - 1))
else:
eps = wfn.epsilon_b()
potentials.append(eps.get(-int(LUMO) - 1))
occs.append(occ)
energies.append(E)
convs.append(C)
core.set_local_option("SCF", "FRAC_START", 2)
#core.set_local_option("SCF", "FRAC_LOAD", True)
core.set_local_option("SCF", "GUESS", "READ")
core.set_local_option("SCF", "FRAC_DIIS", frac_diis)
core.set_local_option("SCF", "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_local_option("SCF", "GUESS", old_guess)
if hf_guess:
core.set_local_option("SCF", "FRAC_START", 0)
core.set_local_option("SCF", "REFERENCE", "UHF")
driver.energy('scf', dft_functional=name, molecule=molecule, **kwargs)
core.set_local_option("SCF", "REFERENCE", "UKS")
core.set_local_option("SCF", "GUESS", "READ")
# NYI core.set_local_option("SCF", "FRAC_LOAD", False)
core.set_local_option("SCF", "FRAC_START", frac_start)
core.set_local_option("SCF", "FRAC_RENORMALIZE", True)
for occ in HOMO_occs:
core.set_local_option("SCF", "FRAC_OCC", [H**O])
core.set_local_option("SCF", "FRAC_VAL", [occ])
E, wfn = driver.energy('scf', dft_functional=name, return_wfn=True, molecule=molecule, **kwargs)
C = 1
if E == 0.0:
E = core.variable('SCF ITERATION ENERGY')
C = 0
if LUMO > 0:
eps = wfn.epsilon_a()
potentials.append(eps.get(int(H**O) - 1))
else:
eps = wfn.epsilon_b()
potentials.append(eps.get(-int(H**O) - 1))
occs.append(occ - 1.0)
energies.append(E)
convs.append(C)
core.set_local_option("SCF", "FRAC_START", 2)
# NYI core.set_local_option("SCF", "FRAC_LOAD", True)
core.set_local_option("SCF", "GUESS", "READ")
core.set_local_option("SCF", "FRAC_DIIS", frac_diis)
core.set_local_option("SCF", "DF_INTS_IO", "LOAD")
# => Print the results out <= #
E = {}
core.print_out("""\n ==> Fractional Occupation Traverse Results <==\n\n""")
core.print_out(""" %-11s %-24s %-24s %11s\n""" % ('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(occs)):
core.print_out(""" %11.3E %24.16E %24.16E %11d\n""" % (occs[k], energies[k], potentials[k], convs[k]))
E[occs[k]] = energies[k]
core.print_out("""
You trying to be a hero Watkins?
Just trying to kill some bugs sir!
-Starship Troopers""")
# Drop the files out
with open(traverse_filename, 'w') as fh:
fh.write(""" %-11s %-24s %-24s %11s\n""" % ('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(occs)):
fh.write(""" %11.3E %24.16E %24.16E %11d\n""" % (occs[k], energies[k], potentials[k], convs[k]))
optstash.restore()
return E
def frac_nuke(name, **kwargs):
"""Pull all the electrons out, one at a time"""
optstash = p4util.OptionsState(
['SCF', 'GUESS'],
['SCF', 'DF_INTS_IO'],
["SCF", "FRAC_START"],
["SCF", "FRAC_RENORMALIZE"],
# NYI ["SCF", "FRAC_LOAD"],
["SCF", "FRAC_OCC"],
["SCF", "FRAC_VAL"],
["SCF", "FRAC_DIIS"])
kwargs = p4util.kwargs_lower(kwargs)
# Make sure the molecule the user provided is the active one, and neutral
molecule = kwargs.pop('molecule', core.get_active_molecule())
molecule.update_geometry()
if molecule.molecular_charge() != 0:
raise ValidationError("""frac_nuke requires neutral molecule to start.""")
if molecule.schoenflies_symbol() != 'c1':
core.print_out(""" Requested procedure `frac_nuke` does not make use of molecular symmetry: """
"""further calculations in C1 point group.\n""")
molecule = molecule.clone()
molecule.reset_point_group('c1')
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_local_option("SCF", "DF_INTS_IO", "SAVE")
Ns = []
energies = []
potentials = []
convs = []
stats = []
# Run one SCF to burn things in
E, wfn = driver.energy('scf', dft_functional=name, return_wfn=True, molecule=molecule, **kwargs)
# Determine H**O
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
eps_a.print_out()
if Na == Nb:
H**O = -Nb
elif Nb == 0:
H**O = Na
else:
E_a = eps_a.get(int(Na - 1))
E_b = eps_b.get(int(Nb - 1))
if E_a >= E_b:
H**O = Na
else:
H**O = -Nb
stats.append(""" %6d %6d %6d %6d %6d %6d\n""" % (N, Na, Nb, charge, mult, H**O))
if H**O > 0:
Na -= 1
else:
Nb -= 1
charge += 1
mult = Na - Nb + 1
core.set_local_option("SCF", "DF_INTS_IO", "LOAD")
core.set_local_option("SCF", "FRAC_START", frac_start)
core.set_local_option("SCF", "FRAC_RENORMALIZE", True)
# Nuke 'em Rico!
for Nintegral in range(N, Nmin, -1):
# Nuke the current H**O
for occ in foccs:
core.set_local_option("SCF", "FRAC_OCC", [H**O])
core.set_local_option("SCF", "FRAC_VAL", [occ])
E, wfn = driver.energy('scf', dft_functional=name, return_wfn=True, molecule=molecule, **kwargs)
C = 1
if E == 0.0:
E = core.variable('SCF ITERATION ENERGY')
C = 0
if H**O > 0:
eps = wfn.epsilon_a()
potentials.append(eps.np[H**O - 1])
else:
eps = wfn.epsilon_b()
potentials.append(eps.np[-H**O - 1])
Ns.append(Nintegral + occ - 1.0)
energies.append(E)
convs.append(C)
core.set_local_option("SCF", "FRAC_START", 2)
# NYI core.set_local_option("SCF", "FRAC_LOAD", True)
core.set_local_option("SCF", "FRAC_DIIS", frac_diis)
core.set_local_option("SCF", "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.np[int(Na - 1)]
E_b = eps_b.np[int(Nb - 1)]
if E_a >= E_b:
H**O = Na
else:
H**O = -Nb
stats.append(""" %6d %6d %6d %6d %6d %6d\n""" % (Nintegral-1, Na, Nb, charge, mult, H**O))
if H**O > 0:
Na -= 1
else:
Nb -= 1
charge += 1
mult = Na - Nb + 1
core.set_local_option("SCF", "DF_INTS_IO", "NONE")
# => Print the results out <= #
E = {}
core.print_out("""\n ==> Fractional Occupation Nuke Results <==\n\n""")
core.print_out(""" %-11s %-24s %-24s %11s\n""" % ('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(Ns)):
core.print_out(""" %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(""" %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 "You shoot a nuke down a bug hole, you got a lot of dead bugs"\n')
core.print_out(' -Starship Troopers\n')
# Drop the files out
with open(traverse_filename, 'w') as fh:
fh.write(""" %-11s %-24s %-24s %11s\n""" % ('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(Ns)):
fh.write(""" %11.3E %24.16E %24.16E %11d\n""" % (Ns[k], energies[k], potentials[k], convs[k]))
with open(stats_filename, 'w') as fh:
fh.write(""" %6s %6s %6s %6s %6s %6s\n""" % ('N', 'Na', 'Nb', 'Charge', 'Mult', 'H**O'))
for line in stats:
fh.write(line)
optstash.restore()
return E
def run_psi4(para: dict):
try:
if (not para.__contains__("multiplicity")):
para["multiplicity"] = 1
if (not para.__contains__("charge")):
para["charge"] = 0
if (not para.__contains__("basis")):
para["basis"] = 0
if (not para.__contains__("EQ_TOLERANCE")):
para["EQ_TOLERANCE"] = 1e-8
str_mol = para["mol"]
str_mol = str_mol + "\n symmetry c1"
mol = geometry(str_mol, "mol")
core.IO.set_default_namespace("mol")
mol.set_multiplicity(para["multiplicity"])
mol.set_molecular_charge(para["charge"])
core.set_global_option("BASIS", para["basis"])
core.set_global_option("SCF_TYPE", "pk")
core.set_global_option("SOSCF", "false")
core.set_global_option("FREEZE_CORE", "false")
core.set_global_option("DF_SCF_GUESS", "false")
core.set_global_option("OPDM", "true")
core.set_global_option("TPDM", "true")
core.set_global_option("MAXITER", 1e6)
core.set_global_option("NUM_AMPS_PRINT", 1e6)
core.set_global_option("R_CONVERGENCE", 1e-6)
core.set_global_option("D_CONVERGENCE", 1e-6)
core.set_global_option("E_CONVERGENCE", 1e-6)
core.set_global_option("DAMPING_PERCENTAGE", 0)
if mol.multiplicity == 1:
core.set_global_option("REFERENCE", "rhf")
core.set_global_option("GUESS", "sad")
else:
core.set_global_option("REFERENCE", "rohf")
core.set_global_option("GUESS", "gwh")
hf_energy, hf_wavefunction = energy('scf', return_wfn=True)
except Exception as exception:
return (-1, traceback.format_exc())
else:
nuclear_repulsion = mol.nuclear_repulsion_energy()
canonical_orbitals = numpy.asarray(hf_wavefunction.Ca())
mints = core.MintsHelper(hf_wavefunction.basisset())
fermion_str = get_molecular_hamiltonian(mints, canonical_orbitals,
nuclear_repulsion,
para["EQ_TOLERANCE"])
return (0, fermion_str)
