Source code for frac

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.reference_wavefunction() eps = ref.epsilon_a() potentials.append(eps[int(LUMO)-1]) else: ref = PsiMod.reference_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.reference_wavefunction() eps = ref.epsilon_a() potentials.append(eps[int(HOMO)-1]) else: ref = PsiMod.reference_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.reference_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.reference_wavefunction() eps = ref.epsilon_a() potentials.append(eps[HOMO-1]) else: ref = PsiMod.reference_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.reference_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.reference_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.reference_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.reference_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.reference_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)