def setUpModule():
global mol, mol1, mf_uhf, td_hf, mf_lda, mf_bp86, mf_b3lyp, mf_m06l
mol = gto.Mole()
mol.verbose = 5
mol.output = '/dev/null'
mol.atom = '''
O 0. 0. 0.
H 0. -0.757 0.587
H 0. 0.757 0.587'''
mol.spin = 2
mol.basis = '631g'
mol.build()
mol1 = gto.Mole()
mol1.verbose = 0
mol1.atom = '''
O 0. 0. 0.
H 0. -0.757 0.587
H 0. 0.757 0.587'''
mol1.basis = '631g'
mol1.build()
mf_uhf = scf.UHF(mol).run()
td_hf = tdscf.TDHF(mf_uhf).run(conv_tol=1e-12)
mf_lda = dft.UKS(mol).set(xc='lda', conv_tol=1e-12)
mf_lda.grids.prune = None
mf_lda = mf_lda.newton().run()
mf_bp86 = dft.UKS(mol).set(xc='b88,p86', conv_tol=1e-12)
mf_bp86.grids.prune = None
mf_bp86 = mf_bp86.newton().run()
mf_b3lyp = dft.UKS(mol).set(xc='b3lyp', conv_tol=1e-12)
mf_b3lyp.grids.prune = None
mf_b3lyp = mf_b3lyp.newton().run()
mf_m06l = dft.UKS(mol).run(xc='m06l')
def test_polarizability_with_freq_against_tdhf(self):
# modified based on https://github.com/pyscf/pyscf/issues/507
mol = gto.M(atom='''
O 0.0 0.0 0.0
O 0.0 0.0 1.5
H 1.0 0.0 0.0
H 0.0 0.7 1.0''')
nmo, nocc = mol.nao, mol.nelec[0]
nvir = nmo - nocc
mf = scf.RHF(mol).run()
mf_td = tdscf.TDHF(mf)
mf_td.nstates = nocc * nvir
mf_td.run()
td_transdip = mf_td.transition_dipole()
td_eig = mf_td.e
freq_to_res = lambda omega: numpy.einsum(
"nt, n, ns -> ts", td_transdip, 1 / (td_eig - omega), td_transdip)
freq_to_nonres = lambda omega: numpy.einsum(
"nt, n, ns -> ts", td_transdip, 1 / (td_eig + omega), td_transdip)
freq_to_alpha = lambda omega: freq_to_res(omega) + freq_to_nonres(omega
)
ref = freq_to_alpha(0.)
val = rhf.Polarizability(mf).polarizability_with_freq(freq=0.)
self.assertAlmostEqual(abs(ref - val).max(), 0, 8)
ref = freq_to_alpha(0.1)
val = rhf.Polarizability(mf).polarizability_with_freq(freq=0.1)
self.assertAlmostEqual(abs(ref - val).max(), 0, 8)
def setUpModule():
global mol, mf, td_hf, mf_lda, mf_bp86, mf_b3lyp, mf_m06l
mol = gto.Mole()
mol.verbose = 5
mol.output = '/dev/null'
mol.atom = [
['H' , (0. , 0. , .917)],
['F' , (0. , 0. , 0.)], ]
mol.basis = '631g'
mol.build()
mf = scf.RHF(mol).run()
td_hf = tdscf.TDHF(mf).run()
mf_lda = dft.RKS(mol)
mf_lda.xc = 'lda, vwn'
mf_lda.grids.prune = None
mf_lda.scf()
mf_bp86 = dft.RKS(mol)
mf_bp86.xc = 'b88,p86'
mf_bp86.grids.prune = None
mf_bp86.scf()
mf_b3lyp = dft.RKS(mol)
mf_b3lyp.xc = 'b3lyp'
mf_b3lyp.grids.prune = None
mf_b3lyp.scf()
mf_m06l = dft.RKS(mol).run(xc='m06l')
def test_analyze(self):
mf = scf.RHF(mol).run()
td = tdscf.TDHF(mf).run()
f = td.oscillator_strength(gauge='length')
self.assertAlmostEqual(lib.finger(f), -0.13908774016795605, 7)
f = td.oscillator_strength(gauge='velocity', order=2)
self.assertAlmostEqual(lib.finger(f), -0.096991134490587522, 7)
td.analyze()
def test_analyze(self):
mf = scf.UHF(mol).run()
td = tdscf.TDHF(mf).run()
f = td.oscillator_strength(gauge='length')
self.assertAlmostEqual(lib.finger(f), 0.16147450863004867, 7)
f = td.oscillator_strength(gauge='velocity', order=2)
self.assertAlmostEqual(lib.finger(f), 0.19750347627735745, 7)
td.analyze()
def seek_states(mf, nstates):
td = tdscf.TDHF(mf, nstates*2)
td.kernel()
n = int(nstates*1.5)
xy = td.xy[:n]
td_dm = td_density(td, xy[0])
for i in range(1,n):
dm = td_density(td, xy[i])
td_dm += dm
td_dm = td_dm * (1.0 / n)
no = get_no(td_dm)
return mf, no, nacto, (nacta, nactb)
def setUpModule():
global mol, mf, td_hf, mf_lda3, mf_lda, mf_bp86, mf_b3lyp, mf_b3lyp1#, mf_b3pw91g
mol = gto.Mole()
mol.verbose = 5
mol.output = '/dev/null'
mol.atom = [
['H' , (0. , 0. , .917)],
['F' , (0. , 0. , 0.)], ]
mol.basis = '631g'
mol.build()
mf = scf.RHF(mol).run()
td_hf = tdscf.TDHF(mf).run()
mf_lda3 = dft.RKS(mol)
mf_lda3.xc = 'lda, vwn_rpa'
mf_lda3.grids.prune = None
mf_lda3.scf()
mf_lda = dft.RKS(mol)
mf_lda.xc = 'lda, vwn'
mf_lda.grids.prune = None
mf_lda.scf()
mf_bp86 = dft.RKS(mol)
mf_bp86.xc = 'b88,p86'
mf_bp86.grids.prune = None
mf_bp86.scf()
mf_b3lyp = dft.RKS(mol)
mf_b3lyp.xc = 'b3lyp'
mf_b3lyp.grids.prune = None
mf_b3lyp.scf()
mf_b3lyp1 = dft.RKS(mol)
mf_b3lyp1.xc = 'b3lyp'
mf_b3lyp1.grids.prune = None
mf_b3lyp1._numint.libxc = dft.xcfun
mf_b3lyp1.scf()
from pyscf import lib, gto, scf, dft
from pyscf import tdscf
mol = gto.Mole()
mol.verbose = 5
mol.output = '/dev/null'
mol.atom = [
["O" , (0. , 0. , 0.)],
[1 , (0. , -0.757 , 0.587)],
[1 , (0. , 0.757 , 0.587)] ]
mol.spin = 2
mol.basis = '631g'
mol.build()
mf = scf.UHF(mol).run()
td_hf = tdscf.TDHF(mf).run(conv_tol=1e-12)
mf_lda = dft.UKS(mol).set(xc='lda', conv_tol=1e-12)
mf_lda.grids.prune = None
mf_lda = mf_lda.newton().run()
mf_bp86 = dft.UKS(mol).set(xc='b88,p86', conv_tol=1e-12)
mf_bp86.grids.prune = None
mf_bp86 = mf_bp86.newton().run()
mf_b3lyp = dft.UKS(mol).set(xc='b3lyp', conv_tol=1e-12)
mf_b3lyp.grids.prune = None
mf_b3lyp = mf_b3lyp.newton().run()
def diagonalize(a, b, nroots=4):
a_aa, a_ab, a_bb = a
b_aa, b_ab, b_bb = b
nocc_a, nvir_a, nocc_b, nvir_b = a_ab.shape
from pyscf.tdscf import rhf, rks
from pyscf import tdscf
from pyscf.data import nist
mol = gto.Mole()
mol.verbose = 5
mol.output = '/dev/null'
mol.atom = [
['H', (0., 0., .917)],
['F', (0., 0., 0.)],
]
mol.basis = '631g'
mol.build()
mf = scf.RHF(mol).run()
td_hf = tdscf.TDHF(mf).run()
mf_lda3 = dft.RKS(mol)
mf_lda3.xc = 'lda, vwn_rpa'
mf_lda3.grids.prune = None
mf_lda3.scf()
mf_lda = dft.RKS(mol)
mf_lda.xc = 'lda, vwn'
mf_lda.grids.prune = None
mf_lda.scf()
mf_bp86 = dft.RKS(mol)
mf_bp86.xc = 'b88,p86'
mf_bp86.grids.prune = None
mf_bp86.scf()
norm = lib.norm(x)**2 - lib.norm(y)**2
norm = numpy.sqrt(1.0 / norm)
return x * norm, y * norm
state = 0
lib.logger.info(mf, "Analyzing state : %s" % state)
xy = norm_xy(c[:, state])
coeff = mf.mo_coeff
occ = mf.mo_occ
orbo = coeff[:, occ == 2]
orbv = coeff[:, occ == 0]
x, y = xy
norm = x**2 - y**2
norm = numpy.sum(norm)
lib.logger.info(mf, "Norm X^2 - Y^2 = 1, value %s" % norm)
ab1 = a + b
ab2 = a - b
ab = numpy.dot(ab1, ab2)
e = numpy.linalg.eig(ab)[0]
e = numpy.sqrt(e)
e = numpy.sort(e[e > 0])[:nroots]
e = numpy.asarray(e) * nist.HARTREE2EV
lib.logger.info(mf, 'Alternative TD-HF: %s' % e.real)
from pyscf import tdscf
td = tdscf.TDHF(mf)
td.nstates = nov
td.kernel()
