def __init__(self, mol, options_or_potfile):
self.mol = mol
self.stdout = mol.stdout
self.verbose = mol.verbose
self.max_memory = mol.max_memory
self.frozen = False
# FIXME: Should the solvent in PE model by default has the character
# of rapid process?
self.equilibrium_solvation = False
##################################################
# don't modify the following attributes, they are not input options
if isinstance(options_or_potfile, str):
options = cppe.PeOptions()
options.potfile = options_or_potfile
else:
options = options_or_potfile
if not isinstance(options, cppe.PeOptions):
raise TypeError("Invalid type for options.")
self.options = options
self.cppe_state = self._create_cppe_state(mol)
self.potentials = self.cppe_state.potentials
self.V_es = None
# e (the dielectric correction) and v (the additional potential) are
# updated during the SCF iterations
self.e = None
self.v = None
self._dm = None
self._keys = set(self.__dict__.keys())
def test_pol_embed_scf(self):
mol = gto.Mole()
mol.atom = '''
C 8.64800 1.07500 -1.71100
C 9.48200 0.43000 -0.80800
C 9.39600 0.75000 0.53800
C 8.48200 1.71200 0.99500
C 7.65300 2.34500 0.05500
C 7.73200 2.03100 -1.29200
H 10.18300 -0.30900 -1.16400
H 10.04400 0.25200 1.24700
H 6.94200 3.08900 0.38900
H 7.09700 2.51500 -2.01800
N 8.40100 2.02500 2.32500
N 8.73400 0.74100 -3.12900
O 7.98000 1.33100 -3.90100
O 9.55600 -0.11000 -3.46600
H 7.74900 2.71100 2.65200
H 8.99100 1.57500 2.99500
'''
mol.basis = "STO-3G"
mol.build()
pe_options = cppe.PeOptions()
pe_options.potfile = os.path.join(dname, "pna_6w.potential")
print(pe_options.potfile)
pe = pol_embed.PolEmbed(mol, pe_options)
mf = solvent.PE(scf.RHF(mol), pe)
mf.conv_tol = 1e-10
mf.kernel()
ref_pe_energy = -0.03424830892844
ref_scf_energy = -482.9411084900
assert_allclose(ref_pe_energy, mf.with_solvent.e, atol=1e-6)
assert_allclose(ref_scf_energy, mf.e_tot, atol=1e-6)
def get_pe_options():
if core.get_option('SCF', 'PCM'):
raise ValidationError("""Error: 3-layer QM/PE/PCM not implemented.\n""")
potfile_name = core.get_option('PE', 'POTFILE')
pol_embed_options = cppe.PeOptions()
pol_embed_options.potfile = potfile_name
pol_embed_options.induced_thresh = core.get_option('PE', 'INDUCED_CONVERGENCE')
pol_embed_options.iso_pol = core.get_option('PE', 'ISOTROPIC_POL')
pol_embed_options.do_diis = core.get_option('PE', 'DIIS')
pol_embed_options.maxiter = core.get_option('PE', 'MAXITER')
pol_embed_options.pe_border = core.get_option('PE', 'BORDER')
if pol_embed_options.pe_border:
pol_embed_border_options = cppe.PeBorderOptions()
pe_btype = core.get_option('PE', 'BORDER_TYPE').upper()
if pe_btype == "REMOVE":
pol_embed_border_options.border_type = core.PeBorderOptions.BorderType.rem
elif pe_btype == "REDIST":
pol_embed_border_options.border_type = core.PeBorderOptions.BorderType.redist
pol_embed_border_options.rmin = core.get_option('PE', 'BORDER_RMIN')
if core.get_option('PE', 'BORDER_RMIN_UNIT').upper() == "AA":
pol_embed_border_options.rmin *= 1.0 / constants.bohr2angstroms
pol_embed_border_options.redist_order = core.get_option('PE', 'BORDER_REDIST_ORDER')
pol_embed_border_options.nredist = core.get_option('PE', 'BORDER_N_REDIST')
pol_embed_border_options.redist_pol = core.get_option('PE', 'BORDER_REDIST_POL')
pol_embed_options.border_options = pol_embed_border_options
return pol_embed_options
3
AA
O 3.53300000 2.99600000 0.88700000 1
H 4.11100000 3.13200000 1.63800000 2
H 4.10500000 2.64200000 0.20600000 3
@MULTIPOLES
ORDER 0
3
1 -0.67444000
2 0.33722000
3 0.33722000
@POLARIZABILITIES
ORDER 1 1
3
1 5.73935000 0.00000000 0.00000000 5.73935000 0.00000000 5.73935000
2 2.30839000 0.00000000 0.00000000 2.30839000 0.00000000 2.30839000
3 2.30839000 0.00000000 0.00000000 2.30839000 0.00000000 2.30839000
EXCLISTS
3 3
1 2 3
2 1 3
3 1 2''')
f.flush()
pe_options = cppe.PeOptions()
pe_options.potfile = f.name
#pe = pol_embed.PolEmbed(mol, pe_options)
#mf = PE(mf, pe).run()
mf = PE(mf, pe_options).run()
print(mf.e_tot - -112.35232445743728)
print(mf.with_solvent.e - 0.00020182314249546455)