import PsiMod
import os
import math
from molutil import *
from driver import *
from procutil import *
from util import *
# Scan from +1 electron to -1 electron
[docs]def frac_traverse(mol, **kwargs):
kwargs = kwargs_lower(kwargs)
# The molecule is required, and should be the neutral species
mol.update_geometry()
activate(mol)
charge0 = mol.molecular_charge()
mult0 = mol.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 = mult0 + 1
multm = mult0 + 1
if kwargs.has_key('cation_mult'):
multp = kwargs['cation_mult']
if kwargs.has_key('anion_mult'):
multm = kwargs['anion_mult']
# By default, we start the frac procedure on the 25th iteration
# when not reading a previous guess
frac_start = 25
if kwargs.has_key('frac_start'):
frac_start = kwargs['frac_start']
# By default, we occupy by tenths of electrons
LUMO_occs = [1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.0]
HOMO_occs = [1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.0]
if kwargs.has_key('HOMO_occs'):
HOMO_occs = kwargs['HOMO_occs']
if kwargs.has_key('LUMO_occs'):
LUMO_occs = kwargs['LUMO_occs']
# By default, HOMO and LUMO are both in alpha
Z = 0;
for A in range(mol.natom()):
Z += mol.Z(A)
Z -= charge0
if (Z%2):
HOMO = Z/2+1
else:
HOMO = Z/2
LUMO = HOMO+1
if kwargs.has_key('HOMO'):
HOMO = kwargs['HOMO']
if kwargs.has_key('LUMO'):
LUMO = kwargs['LUMO']
# By default, DIIS in FRAC (1.0 occupation is always DIIS'd)
frac_diis = True
if kwargs.has_key('frac_diis'):
frac_diis = kwargs['frac_diis']
# By default, use the neutral orbitals as a guess for the anion
neutral_guess = True
if kwargs.has_key('neutral_guess'):
neutral_guess = kwargs['neutral_guess']
# By default, burn-in with UHF first, if UKS
hf_guess = False
if PsiMod.get_global_option('REFERENCE') == 'UKS':
hf_guess = True
if kwargs.has_key('hf_guess'):
hf_guess = kwargs['hf_guess']
# By default, re-guess at each N
continuous_guess = False
if kwargs.has_key('continuous_guess'):
continuous_guess = kwargs['continuous_guess']
# By default, drop the files to the molecule's name
root = mol.name()
if kwargs.has_key('filename'):
root = kwargs['filename']
traverse_filename = root + '.traverse.dat'
# => Traverse <= #
occs = []
energies = []
potentials = []
convs = []
# => Run the neutral for its orbitals, if requested <= #
old_df_ints_io = PsiMod.get_global_option("DF_INTS_IO")
PsiMod.set_global_option("DF_INTS_IO", "SAVE")
old_guess = PsiMod.get_global_option("GUESS")
if (neutral_guess):
if (hf_guess):
PsiMod.set_global_option("REFERENCE","UHF")
energy('scf')
PsiMod.set_global_option("GUESS", "READ")
PsiMod.set_global_option("DF_INTS_IO", "LOAD")
# => Run the anion first <= #
mol.set_molecular_charge(chargem)
mol.set_multiplicity(multm)
# => Burn the anion in with hf, if requested <= #
if (hf_guess):
PsiMod.set_global_option("REFERENCE","UHF")
energy('scf')
PsiMod.set_global_option("REFERENCE","UKS")
PsiMod.set_global_option("GUESS", "READ")
PsiMod.set_global_option("DF_INTS_IO", "SAVE")
PsiMod.set_global_option("FRAC_START", frac_start)
PsiMod.set_global_option("FRAC_RENORMALIZE", True)
PsiMod.set_global_option("FRAC_LOAD", False)
for occ in LUMO_occs:
PsiMod.set_global_option("FRAC_OCC", [LUMO])
PsiMod.set_global_option("FRAC_VAL", [occ])
E = energy('scf')
C = 1
if (E == 0.0):
E = PsiMod.get_variable('SCF ITERATION ENERGY')
C = 0
if (LUMO > 0):
ref = PsiMod.wavefunction()
eps = ref.epsilon_a()
potentials.append(eps[int(LUMO)-1])
else:
ref = PsiMod.wavefunction()
eps = ref.epsilon_b()
potentials.append(eps[-int(LUMO)-1])
occs.append(occ)
energies.append(E)
convs.append(C)
PsiMod.set_global_option("FRAC_START", 2)
PsiMod.set_global_option("FRAC_LOAD", True)
PsiMod.set_global_option("GUESS", "READ")
PsiMod.set_global_option("FRAC_DIIS", frac_diis)
PsiMod.set_global_option("DF_INTS_IO", "LOAD")
# => Run the neutral next <= #
mol.set_molecular_charge(charge0)
mol.set_multiplicity(mult0)
# Burn the neutral in with hf, if requested <= #
if (not continuous_guess):
PsiMod.set_global_option("GUESS", old_guess)
if (hf_guess):
PsiMod.set_global_option("FRAC_START", 0)
PsiMod.set_global_option("REFERENCE","UHF")
energy('scf')
PsiMod.set_global_option("REFERENCE","UKS")
PsiMod.set_global_option("GUESS", "READ")
PsiMod.set_global_option("FRAC_LOAD", False)
PsiMod.set_global_option("FRAC_START", frac_start)
PsiMod.set_global_option("FRAC_RENORMALIZE", True)
for occ in HOMO_occs:
PsiMod.set_global_option("FRAC_OCC", [HOMO])
PsiMod.set_global_option("FRAC_VAL", [occ])
E = energy('scf')
C = 1
if (E == 0.0):
E = PsiMod.get_variable('SCF ITERATION ENERGY')
C = 0
if (LUMO > 0):
ref = PsiMod.wavefunction()
eps = ref.epsilon_a()
potentials.append(eps[int(HOMO)-1])
else:
ref = PsiMod.wavefunction()
eps = ref.epsilon_b()
potentials.append(eps[-int(HOMO)-1])
occs.append(occ - 1.0)
energies.append(E)
convs.append(C)
PsiMod.set_global_option("FRAC_START", 2)
PsiMod.set_global_option("FRAC_LOAD", True)
PsiMod.set_global_option("GUESS", "READ")
PsiMod.set_global_option("FRAC_DIIS", frac_diis)
PsiMod.set_global_option("DF_INTS_IO", "LOAD")
PsiMod.set_global_option("DF_INTS_IO", old_df_ints_io)
# => Print the results out <= #
E = {}
PsiMod.print_out('\n ==> Fractional Occupation Traverse Results <==\n\n')
PsiMod.print_out('\t%-11s %-24s %-24s %11s\n' %('N', 'Energy', 'HOMO Energy', 'Converged'))
for k in range(len(occs)):
PsiMod.print_out('\t%11.3E %24.16E %24.16E %11d\n' % (occs[k], energies[k], potentials[k], convs[k]))
E[occs[k]] = energies[k]
PsiMod.print_out('\n\t"You trying to be a hero Watkins?"\n')
PsiMod.print_out('\t"Just trying to kill some bugs sir!"\n')
PsiMod.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', 'HOMO 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()
return E
# Pull all the electrons out, one at a time
[docs]def frac_nuke(mol, **kwargs):
kwargs = kwargs_lower(kwargs)
# The molecule is required, and should be the neutral species
mol.update_geometry()
activate(mol)
charge0 = mol.molecular_charge()
mult0 = mol.multiplicity()
# By default, we start the frac procedure on the 25th iteration
# when not reading a previous guess
frac_start = 25
if kwargs.has_key('frac_start'):
frac_start = kwargs['frac_start']
# By default, we occupy by tenths of electrons
foccs = [1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.0]
if kwargs.has_key('foccs'):
foccs = kwargs['foccs']
# By default, HOMO and LUMO are both in alpha
N = 0;
for A in range(mol.natom()):
N += mol.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 (kwargs.has_key('nmax')):
Nmin = N - int(kwargs['nmax'])
# By default, DIIS in FRAC (1.0 occupation is always DIIS'd)
frac_diis = True
if kwargs.has_key('frac_diis'):
frac_diis = kwargs['frac_diis']
# By default, drop the files to the molecule's name
root = mol.name()
if kwargs.has_key('filename'):
root = kwargs['filename']
traverse_filename = root + '.traverse.dat'
stats_filename = root + '.stats.dat'
# => Traverse <= #
PsiMod.set_global_option("DF_INTS_IO", "SAVE")
Ns = []
energies = []
potentials = []
convs = []
stats = []
# Run one SCF to burn things in
energy('scf')
# Determine HOMO
ref = PsiMod.wavefunction()
eps_a = ref.epsilon_a()
eps_b = ref.epsilon_b()
if (Na == Nb):
HOMO = -Nb
elif (Nb == 0):
HOMO = Na
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if (E_a >= E_b):
HOMO = Na
else:
HOMO = -Nb
stats.append('\t%6d %6d %6d %6d %6d %6d\n' %(N, Na, Nb, charge, mult, HOMO))
if (HOMO > 0):
Na = Na - 1
else:
Nb = Nb - 1
charge = charge + 1
mult = Na - Nb + 1
PsiMod.set_global_option("DF_INTS_IO", "LOAD")
PsiMod.set_global_option("FRAC_START", frac_start)
PsiMod.set_global_option("FRAC_RENORMALIZE", True)
# Nuke 'em Rico!
for Nintegral in range(N,Nmin,-1):
# Nuke the current HOMO
for occ in foccs:
PsiMod.set_global_option("FRAC_OCC", [HOMO])
PsiMod.set_global_option("FRAC_VAL", [occ])
E = energy('scf')
C = 1
if (E == 0.0):
E = PsiMod.get_variable('SCF ITERATION ENERGY')
C = 0
if (HOMO > 0):
ref = PsiMod.wavefunction()
eps = ref.epsilon_a()
potentials.append(eps[HOMO-1])
else:
ref = PsiMod.wavefunction()
eps = ref.epsilon_b()
potentials.append(eps[-HOMO-1])
Ns.append(Nintegral + occ - 1.0)
energies.append(E)
convs.append(C)
PsiMod.set_global_option("FRAC_START", 2)
PsiMod.set_global_option("FRAC_LOAD", True)
PsiMod.set_global_option("FRAC_DIIS", frac_diis)
PsiMod.set_global_option("GUESS", "READ")
# Set the next charge/mult
mol.set_molecular_charge(charge)
mol.set_multiplicity(mult)
# Determine HOMO
ref = PsiMod.wavefunction()
eps_a = ref.epsilon_a()
eps_b = ref.epsilon_b()
if (Na == Nb):
HOMO = -Nb
elif (Nb == 0):
HOMO = Na
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if (E_a >= E_b):
HOMO = Na
else:
HOMO = -Nb
stats.append('\t%6d %6d %6d %6d %6d %6d\n' %(Nintegral-1, Na, Nb, charge, mult, HOMO))
if (HOMO > 0):
Na = Na - 1
else:
Nb = Nb - 1
charge = charge + 1
mult = Na - Nb + 1
PsiMod.set_global_option("DF_INTS_IO", "NONE")
# => Print the results out <= #
E = {}
PsiMod.print_out('\n ==> Fractional Occupation Nuke Results <==\n\n')
PsiMod.print_out('\t%-11s %-24s %-24s %11s\n' %('N', 'Energy', 'HOMO Energy', 'Converged'))
for k in range(len(Ns)):
PsiMod.print_out('\t%11.3E %24.16E %24.16E %11d\n' % (Ns[k], energies[k], potentials[k], convs[k]))
E[Ns[k]] = energies[k]
PsiMod.print_out('\n')
PsiMod.print_out('\t%6s %6s %6s %6s %6s %6s\n' %('N', 'Na', 'Nb', 'Charge', 'Mult', 'HOMO'))
for line in stats:
PsiMod.print_out(line)
PsiMod.print_out('\n\t"You shoot a nuke down a bug hole, you got a lot of dead bugs"\n')
PsiMod.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', 'HOMO 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', 'HOMO'))
for line in stats:
fh.write(line)
fh.close()
return E
[docs]def ip_fitting(mol, omega_l, omega_r, **kwargs):
kwargs = kwargs_lower(kwargs)
# By default, zero the omega to 3 digits
omega_tol = 1.0E-3;
if (kwargs.has_key('omega_tolerance')):
omega_tol = kwargs['omega_tolerance']
# By default, do up to twenty iterations
maxiter = 20;
if (kwargs.has_key('maxiter')):
maxiter = kwargs['maxiter']
# By default, do not read previous 180 orbitals file
read = False;
read180 = ''
if (kwargs.has_key('read')):
read = True;
read180 = kwargs['read']
# The molecule is required, and should be the neutral species
mol.update_geometry()
activate(mol)
charge0 = mol.molecular_charge()
mult0 = mol.multiplicity()
# How many electrons are there?
N = 0;
for A in range(mol.natom()):
N += mol.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
PsiMod.IO.set_default_namespace("ot")
# Burn in to determine orbital eigenvalues
if (read):
PsiMod.set_global_option("GUESS", "READ")
copy_file_to_scratch(read180, 'psi', 'ot', 180)
old_guess = PsiMod.get_global_option("GUESS")
PsiMod.set_global_option("DF_INTS_IO", "SAVE")
PsiMod.print_out('\n\t==> IP Fitting SCF: Burn-in <==\n')
energy('scf')
PsiMod.set_global_option("DF_INTS_IO", "LOAD")
# Determine HOMO, to determine mult1
ref = PsiMod.wavefunction()
eps_a = ref.epsilon_a()
eps_b = ref.epsilon_b()
if (Na == Nb):
HOMO = -Nb
elif (Nb == 0):
HOMO = Na
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if (E_a >= E_b):
HOMO = Na
else:
HOMO = -Nb
Na1 = Na;
Nb1 = Nb;
if (HOMO > 0):
Na1 = Na1-1;
else:
Nb1 = Nb1-1;
charge1 = charge0 + 1;
mult1 = Na1 - Nb1 + 1
omegas = [];
E0s = [];
E1s = [];
kIPs = [];
IPs = [];
types = [];
# Right endpoint
PsiMod.set_global_option('DFT_OMEGA',omega_r)
# Neutral
if (read):
PsiMod.set_global_option("GUESS", "READ")
copy_file_to_scratch(read180, 'psi', 'ot', 180)
mol.set_molecular_charge(charge0)
mol.set_multiplicity(mult0)
PsiMod.print_out('\n\t==> IP Fitting SCF: Neutral, Right Endpoint <==\n')
E0r = energy('scf')
ref = PsiMod.wavefunction()
eps_a = ref.epsilon_a()
eps_b = ref.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;
PsiMod.IO.change_file_namespace(180,"ot","neutral")
# Cation
if (read):
PsiMod.set_global_option("GUESS", "READ")
copy_file_to_scratch(read180, 'psi', 'ot', 180)
mol.set_molecular_charge(charge1)
mol.set_multiplicity(mult1)
PsiMod.print_out('\n\t==> IP Fitting SCF: Cation, Right Endpoint <==\n')
E1r = energy('scf')
PsiMod.IO.change_file_namespace(180,"ot","cation")
IPr = E1r - E0r;
kIPr = -E_HOMOr;
delta_r = IPr - kIPr;
if (IPr > kIPr):
PsiMod.print_out('\n***IP Fitting Error: Right Omega limit should have kIP > IP')
sys.exit(1)
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
PsiMod.set_global_option("GUESS","READ")
# Left endpoint
PsiMod.set_global_option('DFT_OMEGA',omega_l)
# Neutral
PsiMod.IO.change_file_namespace(180,"neutral","ot")
mol.set_molecular_charge(charge0)
mol.set_multiplicity(mult0)
PsiMod.print_out('\n\t==> IP Fitting SCF: Neutral, Left Endpoint <==\n')
E0l = energy('scf')
ref = PsiMod.wavefunction()
eps_a = ref.epsilon_a()
eps_b = ref.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;
PsiMod.IO.change_file_namespace(180,"ot","neutral")
# Cation
PsiMod.IO.change_file_namespace(180,"cation","ot")
mol.set_molecular_charge(charge1)
mol.set_multiplicity(mult1)
PsiMod.print_out('\n\t==> IP Fitting SCF: Cation, Left Endpoint <==\n')
E1l = energy('scf')
PsiMod.IO.change_file_namespace(180,"ot","cation")
IPl = E1l - E0l;
kIPl = -E_HOMOl;
delta_l = IPl - kIPl;
if (IPl < kIPl):
PsiMod.print_out('\n***IP Fitting Error: Left Omega limit should have kIP < IP')
sys.exit(1)
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;
PsiMod.set_global_option('DFT_OMEGA',omega)
# Neutral
PsiMod.IO.change_file_namespace(180,"neutral","ot")
mol.set_molecular_charge(charge0)
mol.set_multiplicity(mult0)
PsiMod.print_out('\n\t==> IP Fitting SCF: Neutral, Omega = %11.3E <==\n' % omega)
E0 = energy('scf')
ref = PsiMod.wavefunction()
eps_a = ref.epsilon_a()
eps_b = ref.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;
PsiMod.IO.change_file_namespace(180,"ot","neutral")
# Cation
PsiMod.IO.change_file_namespace(180,"cation","ot")
mol.set_molecular_charge(charge1)
mol.set_multiplicity(mult1)
PsiMod.print_out('\n\t==> IP Fitting SCF: Cation, Omega = %11.3E <==\n' % omega)
E1 = energy('scf')
PsiMod.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
PsiMod.IO.set_default_namespace("")
PsiMod.print_out('\n\t==> IP Fitting Results <==\n\n')
PsiMod.print_out('\t => Occupation Determination <= \n\n')
PsiMod.print_out('\t %6s %6s %6s %6s %6s %6s\n' %('N', 'Na', 'Nb', 'Charge', 'Mult', 'HOMO'))
PsiMod.print_out('\t Neutral: %6d %6d %6d %6d %6d %6d\n' %(N, Na, Nb, charge0, mult0, HOMO))
PsiMod.print_out('\t Cation: %6d %6d %6d %6d %6d\n\n' %(N-1, Na1, Nb1, charge1, mult1))
PsiMod.print_out('\t => Regula Falsi Iterations <=\n\n')
PsiMod.print_out('\t%3s %11s %14s %14s %14s %s\n' % ('N','Omega','IP','kIP','Delta','Type'))
for k in range(len(omegas)):
PsiMod.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):
PsiMod.print_out('\n\tIP Fitting Converged\n')
PsiMod.print_out('\tFinal omega = %14.6E\n' % ((omega_l + omega_r) / 2))
PsiMod.print_out('\n\t"M,I. does the dying. Fleet just does the flying."\n')
PsiMod.print_out('\t\t\t-Starship Troopers\n')
else:
PsiMod.print_out('\n\tIP Fitting did not converge!\n')
PsiMod.set_global_option("DF_INTS_IO", "NONE")
PsiMod.set_global_option("GUESS", old_guess)