def test_newton_rohf(self):
mf = solvent.PE(mol.ROHF(max_memory=0), potfile)
mf = mf.newton()
e = mf.kernel()
self.assertAlmostEqual(e, -112.35232445745123, 9)
mf = solvent.PE(mol.ROHF(max_memory=0), potfile)
e = mf.kernel()
self.assertAlmostEqual(e, -112.35232445745123, 9)
def test_rhf_tda(self):
# TDA with equilibrium_solvation
mf = solvent.PE(mol.RHF(), potfile).run()
td = solvent.PE(mf.TDA(), potfile).run(equilibrium_solvation=True)
ref = numpy.array([0.1506426609354755, 0.338251407831332, 0.4471267328974609])
self.assertAlmostEqual(abs(ref - td.e).max(), 0, 8)
# TDA without equilibrium_solvation
mf = solvent.PE(mol.RHF(), potfile).run()
td = solvent.PE(mf.TDA(), potfile).run()
ref = numpy.array([0.1506431269137912, 0.338254809044639, 0.4471487090255076])
self.assertAlmostEqual(abs(ref - td.e).max(), 0, 8)
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 test_as_scanner(self):
mf_scanner = solvent.PE(scf.RHF(mol), potfile).as_scanner()
mf_scanner(mol)
self.assertAlmostEqual(mf_scanner.with_solvent.e,
0.00020182314249546455, 9)
mf_scanner('H 0. 0. 0.; H 0. 0. .9')
self.assertAlmostEqual(mf_scanner.with_solvent.e,
5.2407234004672825e-05, 9)
def test_as_scanner(self):
mf = mol.RHF(chkfile=tempfile.NamedTemporaryFile().name)
mf_scanner = solvent.PE(mf, potfile).as_scanner()
mf_scanner(mol)
self.assertAlmostEqual(mf_scanner.with_solvent.e,
0.00020182314249546455, 9)
# Change solute. cppe may not support this
mf_scanner('H 0. 0. 0.; H 0. 0. .9')
self.assertAlmostEqual(mf_scanner.with_solvent.e,
5.2407234004672825e-05, 9)
def test_exec_cppe(self):
pe = solvent.PE(mol, os.path.join(dname, "pna_6w.potential"))
numpy.random.seed(2)
nao = mol.nao
dm = numpy.random.random((2,nao,nao))
dm = dm + dm.transpose(0,2,1)
eref, vref = _exec_cppe(pe, dm[1], elec_only=False)
e, v = pe._exec_cppe(dm, elec_only=False)
self.assertAlmostEqual(abs(vref - v[1]).max(), 0, 10)
eref, vref = _exec_cppe(pe, dm[0], elec_only=True)
e, v = pe._exec_cppe(dm, elec_only=True)
self.assertAlmostEqual(eref, e[0], 10)
self.assertAlmostEqual(abs(vref - v[0]).max(), 0, 10)
H 43.151000 37.062000 37.180000 H 40.929000 35.954000 37.704000 H 39.378000 37.062000 39.158000 H 40.246000 38.878000 40.859000 """ mol.basis = "6-31G*" mol.build() pe_options = cppe.PeOptions() pe_options.do_diis = True pe_options.potfile = "nilered_in_blg_1000WAT.pot" pe = pol_embed.PolEmbed(mol, pe_options) pe.verbose = 4 lib.num_threads(32) mf = solvent.PE(scf.RKS(mol), pe) mf.xc = "camb3lyp" mf._numint.libxc = xcfun mf.conv_tol = 1e-8 mf.verbose = 4 mf.kernel() print(mf._pol_embed.cppe_state.summary_string) td = TDA(mf) td.verbose = 5 td.conv_tol = 1e-7 td.triplet = False td.singlet = True td.nstates = 3 evals, xy = td.kernel()
def test_pe_scf(self):
pe = solvent.PE(mol, potfile)
mf = solvent.PE(mol.RHF(), pe).run(conv_tol=1e-10)
self.assertAlmostEqual(mf.e_tot, -112.35232445743728, 9)
self.assertAlmostEqual(mf.with_solvent.e, 0.00020182314249546455, 9)
def test_pe_scf_ecp(self):
pe = solvent.PE(mol2, {"potfile": potfile2, "ecp": True})
mf = solvent.PE(mol2.RHF(), pe).run(conv_tol=1e-10)
self.assertAlmostEqual(mf.e_tot, -168.147494986446, 8)
'''
A simple example of using polarizable embedding model in the mean-field
calculations. This example requires the cppe library
GitHub: https://github.com/maxscheurer/cppe
Code: 10.5281/zenodo.3345696
Publication: https://doi.org/10.1021/acs.jctc.9b00758
The CPPE library can be installed via:
pip install git+https://github.com/maxscheurer/cppe.git
The potfile required by this example can be generated with the script
04-pe_potfile_from_pyframe.py
'''
import pyscf
from pyscf import solvent
mol = pyscf.M(atom='''
C 0.000000 0.000000 -0.542500
O 0.000000 0.000000 0.677500
H 0.000000 0.9353074360871938 -1.082500
H 0.000000 -0.9353074360871938 -1.082500
''',
verbose = 4)
mf = mol.UKS()
mf.xc = 'b3lyp'
mf = solvent.PE(mf, '4NP_in_water/4NP_in_water.pot')
mf.run()
H 40.929000 35.954000 37.704000
H 39.378000 37.062000 39.158000
H 40.246000 38.878000 40.859000
""",
basis="cc-pvdz",
)
pe_options = cppe.PeOptions()
pe_options.do_diis = True
pe_options.potfile = "nilered_in_blg_1000WAT.pot"
pe = pol_embed.PolEmbed(mol, pe_options)
pe.verbose = 4
lib.num_threads(32)
scfres = solvent.PE(scf.RHF(mol), pe)
scfres.conv_tol = 1e-10
scfres.conv_tol_grad = 1e-8
scfres.verbose = 4
scfres.kernel()
print(adcc.banner())
# Run an adc2 calculation:
state = adcc.adc2(scfres, n_singlets=3, conv_tol=1e-5)
ptss_list = []
ptlr_list = []
# Print results
print()
print(" st ex.ene. (au) f transition dipole moment (au)"
