def test_nr_uks_fast_newton(self):
mf = dft.UKS(h4_z1_s)
mf.xc = 'b3lyp'
mf1 = scf.fast_newton(mf)
self.assertAlmostEqual(mf1.e_tot, -39.696083841107587, 9)
mf1 = scf.fast_newton(dft.UKS(h4_z1_s))
self.assertAlmostEqual(mf1.e_tot, -39.330377813428001, 9)
def test_nr_uks_fast_newton(self):
mf = dft.UKS(h4_z1_s)
mf.xc = 'b3lyp'
mf1 = scf.fast_newton(mf)
self.assertAlmostEqual(mf1.e_tot, -39.696083841107587, 8)
mf1 = scf.fast_newton(dft.UKS(h4_z1_s))
self.assertAlmostEqual(mf1.e_tot, -39.330377813428001, 8)
def test_scanner(self):
from pyscf import dft
mol1 = molsym.copy()
mol1.set_geom_('''
O 0. 0. .1
H 0. -0.757 0.587
H 0. 0.757 0.587''')
mf_scanner = scf.UHF(molsym).density_fit('weigend').as_scanner()
self.assertAlmostEqual(mf_scanner(molsym), -75.98321088694874, 8)
self.assertAlmostEqual(mf_scanner(mol1), -75.97901175977492, 8)
mf_scanner = scf.fast_newton(scf.ROHF(molsym)).as_scanner()
self.assertAlmostEqual(mf_scanner(molsym), -75.983948498066198, 8)
self.assertAlmostEqual(mf_scanner(mol1), -75.97974371226907, 8)
mf_scanner = dft.RKS(molsym).set(xc='bp86').as_scanner()
self.assertAlmostEqual(mf_scanner(molsym), -76.385043416002361, 8)
eref = dft.RKS(mol1).set(xc='bp86').kernel()
e1 = mf_scanner(mol1)
self.assertAlmostEqual(e1, -76.372784697245777, 8)
self.assertAlmostEqual(e1, eref, 8)
# Test init_guess_by_chkfile for stretched geometry and different basis set
mol1.atom = '''
O 0. 0. -.5
H 0. -0.957 0.587
H 0. 0.957 0.587'''
mol1.basis = 'ccpvdz'
mol1.build(0, 0)
self.assertAlmostEqual(mf_scanner(mol1), -76.273052274103648, 7)
def test_scanner(self):
from pyscf import dft
mol1 = molsym.copy()
mol1.set_geom_('''
O 0. 0. .1
H 0. -0.757 0.587
H 0. 0.757 0.587''')
mf_scanner = scf.UHF(molsym).density_fit('weigend').as_scanner()
self.assertAlmostEqual(mf_scanner(molsym), -75.98321088694874, 8)
self.assertAlmostEqual(mf_scanner(mol1), -75.97901175977492, 8)
mf_scanner = scf.fast_newton(scf.ROHF(molsym)).as_scanner()
self.assertAlmostEqual(mf_scanner(molsym), -75.983948498066198, 8)
self.assertAlmostEqual(mf_scanner(mol1), -75.97974371226907, 8)
mf_scanner = dft.RKS(molsym).set(xc='bp86').as_scanner()
self.assertAlmostEqual(mf_scanner(molsym), -76.385043416002361, 8)
self.assertAlmostEqual(mf_scanner(mol1), -76.372784697245777, 8)
# Test init_guess_by_chkfile for stretched geometry and different basis set
mol1.atom = '''
O 0. 0. -.5
H 0. -0.957 0.587
H 0. 0.957 0.587'''
mol1.basis = 'ccpvdz'
mol1.build(0,0)
self.assertAlmostEqual(mf_scanner(mol1), -76.273052274103648, 8)
def test_fast_newton(self):
nao = mol.nao_nr()
dm0 = numpy.zeros((nao, nao))
mf = scf.fast_newton(scf.RHF(mol),
dm0=dm0,
dual_basis=True,
kf_trust_region=3.)
self.assertAlmostEqual(mf.e_tot, -75.983948497843272, 9)
def solve_scf(mol, **scfargs):
HFmethod = scf.HF if not _MUST_UNRES else scf.UHF
mf = HFmethod(mol).set(init_guess_breaksym=True)
init_dm = mf.get_init_guess()
# if _MUST_UNRES:
# init_dm[1][:2,:2] = 0
mf.kernel(init_dm)
if _USE_NEWTON:
mf = scf.fast_newton(mf)
return mf
def test_nr_uks_fast_newton(self):
mol = gto.M(
verbose = 5,
output = '/dev/null',
atom = '''C 0 0 0
H 1 1 1
H -1 -1 1
H -1 1 -1
H 1 -1 -1''',
basis = '6-31g',
charge = 1,
spin = 1,
symmetry = 1,
)
mf = dft.UKS(mol)
mf.xc = 'b3lyp'
mf1 = scf.fast_newton(mf)
self.assertAlmostEqual(mf1.e_tot, -39.69608384046235, 9)
mf1 = scf.fast_newton(dft.UKS(mol))
self.assertAlmostEqual(mf1.e_tot, -39.330377813428001, 9)
def test_nr_uks_fast_newton(self):
mol = gto.M(
verbose=5,
output='/dev/null',
atom='''C 0 0 0
H 1 1 1
H -1 -1 1
H -1 1 -1
H 1 -1 -1''',
basis='6-31g',
charge=1,
spin=1,
symmetry=1,
)
mf = dft.UKS(mol)
mf.xc = 'b3lyp'
mf1 = scf.fast_newton(mf)
self.assertAlmostEqual(mf1.e_tot, -39.696083841107587, 9)
mf1 = scf.fast_newton(dft.UKS(mol))
self.assertAlmostEqual(mf1.e_tot, -39.330377813428001, 9)
def test_nr_rks_fast_newton(self):
mol = gto.M(
verbose = 5,
output = '/dev/null',
atom = '''C 0 0 0
H 1 1 1
H -1 -1 1
H -1 1 -1
H 1 -1 -1''',
basis = '6-31g',
symmetry = 1,
)
mf = dft.RKS(mol)
mf.xc = 'b3lyp'
mf1 = scf.fast_newton(mf)
self.assertAlmostEqual(mf1.e_tot, -40.10277421254213, 9)
def test_nr_rks_fast_newton(self):
mol = gto.M(
verbose=5,
output='/dev/null',
atom='''C 0 0 0
H 1 1 1
H -1 -1 1
H -1 1 -1
H 1 -1 -1''',
basis='6-31g',
symmetry=1,
)
mf = dft.RKS(mol)
mf.xc = 'b3lyp'
mf1 = scf.fast_newton(mf)
self.assertAlmostEqual(mf1.e_tot, -40.10277421254213, 9)
def test_nr_rohf_fast_newton(self):
mol = gto.M(
verbose=5,
output='/dev/null',
atom='''C 0 0 0
H 1 1 1
H -1 -1 1
H -1 1 -1
H 1 -1 -1''',
basis='6-31g',
charge=1,
spin=1,
symmetry=1,
)
mf = scf.ROHF(mol)
mf1 = scf.fast_newton(mf)
self.assertAlmostEqual(mf1.e_tot, -39.365972147397649, 9)
def test_nr_rohf_fast_newton(self):
mol = gto.M(
verbose = 5,
output = '/dev/null',
atom = '''C 0 0 0
H 1 1 1
H -1 -1 1
H -1 1 -1
H 1 -1 -1''',
basis = '6-31g',
charge = 1,
spin = 1,
symmetry = 1,
)
mf = scf.ROHF(mol)
mf1 = scf.fast_newton(mf)
self.assertAlmostEqual(mf1.e_tot, -39.365972147397649, 9)
def test_scanner(self):
from pyscf import dft
mol1 = molsym.copy()
mol1.set_geom_('''
O 0. 0. .1
H 0. -0.757 0.587
H 0. 0.757 0.587''')
mf_scanner = scf.UHF(molsym).density_fit('weigend').as_scanner()
self.assertAlmostEqual(mf_scanner(molsym), -75.98321088694874, 9)
self.assertAlmostEqual(mf_scanner(mol1), -75.97901175977492, 9)
mf_scanner = scf.fast_newton(scf.ROHF(molsym)).as_scanner()
self.assertAlmostEqual(mf_scanner(molsym), -75.983948498066198, 9)
self.assertAlmostEqual(mf_scanner(mol1), -75.97974371226907, 9)
mf_scanner = dft.RKS(molsym).set(xc='bp86').as_scanner()
self.assertAlmostEqual(mf_scanner(molsym), -76.385043416002361, 9)
self.assertAlmostEqual(mf_scanner(mol1), -76.372784697245777, 9)
def test_nr_rohf_fast_newton(self):
mf = scf.ROHF(h4_z1_s)
mf1 = scf.fast_newton(mf)
self.assertAlmostEqual(mf1.e_tot, -39.365972147397649, 9)
def test_nr_rks_fast_newton(self):
mf = dft.RKS(h4_z0_s)
mf.xc = 'b3lyp'
mf1 = scf.fast_newton(mf)
self.assertAlmostEqual(mf1.e_tot, -40.10277421254213, 9)
def test_nr_rohf_fast_newton(self):
mf = scf.ROHF(h4_z1_s)
mf1 = scf.fast_newton(mf)
self.assertAlmostEqual(mf1.e_tot, -39.365972147397649, 9)
H 6.771983 5.230175 -0.172724
H 7.325546 6.456228 -1.103449
H 8.153994 6.005554 0.233135
H 3.372639 5.237613 5.430001
H 2.420871 5.752619 4.203299
H 2.631033 4.150531 4.458321
H 6.225091 2.641675 2.914287
H 5.612530 2.721618 4.428971
H 4.651591 2.282146 3.180231
H 4.947415 4.665452 0.537824
H 3.725531 3.767789 1.151899
H 3.515369 5.369877 0.896878
H 9.224480 4.780740 3.228456
H 10.002053 5.784964 4.259380
H 9.010897 4.621544 4.842435
H 7.210886 6.878915 6.599377
H 8.578203 7.641391 6.125073
H 7.135300 8.403680 6.011782
H 8.308553 8.287098 2.094287
H 7.797036 9.254716 3.309999
H 9.239940 8.492427 3.423290
''',
basis = 'ccpvdz',
charge = 3,
spin = 3,
verbose = 5,
output = 'cu3.out')
mf = scf.fast_newton(scf.RHF(mol))
mf.kernel()
['C' , (-2.4150 , -2.4083 , 0.0000)],
['C' , (2.4150 , -2.4083 , 0.0000)],
['H' , (3.1855 , 3.1752 , 0.0000)],
['H' , (-3.1855 , 3.1752 , 0.0000)],
['H' , (-3.1855 , -3.1752 , 0.0000)],
['H' , (3.1855 , -3.1752 , 0.0000)],
]
mol.basis = 'ccpvdz'
mol.verbose = 4
mol.output = 'fepor.out'
mol.spin = 4
mol.symmetry = True
mol.build()
mf = scf.ROHF(mol)
mf = scf.fast_newton(mf)
#
# CAS(8e, 11o)
#
# mcscf.density_fit approximates the orbital hessian. It does not affect
# CASSCF results.
#
mc = mcscf.density_fit(mcscf.CASSCF(mf, 11, 8))
idx = [i for i,s in enumerate(mol.spheric_labels(1)) if 'Fe 3d' in s or 'Fe 4d' in s]
mo = dmet_cas(mc, mf.make_rdm1(), idx)
mc.fcisolver.wfnsym = 'Ag'
mc.kernel(mo)
#mc.analyze()
e_q = mc.e_tot # -2244.82910509839
['C' , (-2.4150 , -2.4083 , 0.0000)],
['C' , (2.4150 , -2.4083 , 0.0000)],
['H' , (3.1855 , 3.1752 , 0.0000)],
['H' , (-3.1855 , 3.1752 , 0.0000)],
['H' , (-3.1855 , -3.1752 , 0.0000)],
['H' , (3.1855 , -3.1752 , 0.0000)],
]
mol.basis = 'ccpvdz'
mol.verbose = 4
mol.output = 'fepor.out'
mol.spin = 4
mol.symmetry = True
mol.build()
mf = scf.ROHF(mol)
mf = scf.fast_newton(mf)
# ao_labels are keyword(s) to match the AOs generated by mol.ao_labels()
# function. ao_labels can be a string, or a pattern of regular expression
# or a list of strings/patterns. The code can detect the format and find
# the AOs to be taken into the active space.
# See also function gto.mole.search_ao_label for the rules of ao_pattern
ao_pattern = ['Fe 3d', 'Fe 4d']
ncas, nelecas, mo = dmet_cas.guess_cas(mf, mf.make_rdm1(), ao_pattern)
mc = mcscf.approx_hessian(mcscf.CASSCF(mf, ncas, nelecas))
mc.kernel(mo)
e_q = mc.e_tot # -2244.82910509839
def test_fast_newton(self):
nao = mol.nao_nr()
dm0 = numpy.zeros((nao,nao))
mf = scf.fast_newton(scf.RHF(mol), dm0=dm0, dual_basis=True,
kf_trust_region=3.)
self.assertAlmostEqual(mf.e_tot, -75.983948497843272, 9)
['H' , (-1.3558 , -5.0416 , 0.0000)],
['H' , (1.3558 , -5.0416 , 0.0000)],
['C' , (2.4150 , 2.4083 , 0.0000)],
['C' , (-2.4150 , 2.4083 , 0.0000)],
['C' , (-2.4150 , -2.4083 , 0.0000)],
['C' , (2.4150 , -2.4083 , 0.0000)],
['H' , (3.1855 , 3.1752 , 0.0000)],
['H' , (-3.1855 , 3.1752 , 0.0000)],
['H' , (-3.1855 , -3.1752 , 0.0000)],
['H' , (3.1855 , -3.1752 , 0.0000)],
]
mol.basis = 'ccpvdz'
mol.verbose = 5
mol.output = 'fepor3.out'
mol.spin = 2
mol.symmetry = True
mol.build()
m = scf.ROHF(mol)
m.level_shift_factor = 1.5
scf.fast_newton(m)
mc = mcscf.CASSCF(m, 10, 10)
idx3d = [i for i,s in enumerate(mol.spheric_labels(1)) if 'Fe 3d' in s]
mo = dmet_cas.dmet_cas(mc, m.make_rdm1(), idx3d, base=0)
fci.addons.fix_spin_(mc.fcisolver, ss_value=2) # Triplet, ss_value = S*(S+1)
mc.fcisolver.wfnsym = 'B1g'
mc.kernel(mo)
def test_nr_rks_fast_newton(self):
mf = dft.RKS(h4_z0_s)
mf.xc = 'b3lyp'
mf1 = scf.fast_newton(mf)
self.assertAlmostEqual(mf1.e_tot, -40.10277421254213, 9)
H 10.002053 5.784964 4.259380
H 9.010897 4.621544 4.842435
H 7.210886 6.878915 6.599377
H 8.578203 7.641391 6.125073
H 7.135300 8.403680 6.011782
H 8.308553 8.287098 2.094287
H 7.797036 9.254716 3.309999
H 9.239940 8.492427 3.423290
''',
basis='ccpvdz',
charge=3,
spin=3,
verbose=4,
output='cu3.out')
mf = scf.fast_newton(scf.RHF(mol))
print('E(tot) %.15g ref = -5668.38221757799' % mf.e_tot)
#
# scf.fast_newton function can be used for specific initial guess.
#
# We first create an initial guess with DIIS iterations. The DIIS results are
# saved in a checkpoint file which can be load in another calculation.
#
mf = scf.RHF(mol)
mf.chkfile = 'cu3-diis.chk'
mf.max_cycle = 2
mf.kernel()
#
# Load the DIIS results then use it as initial guess for function
#!/usr/bin/env python
#
# Author: Qiming Sun <*****@*****.**>
#
from pyscf import gto
from pyscf import scf, dft
'''
As a Python script, you can use any Python trick to create your calculation.
In this example, we read the molecule geometry from another file.
'''
mol = gto.Mole()
mol.verbose = 5
mol.atom = open('glycine.xyz').read()
mol.basis = '6-31g*'
mol.build()
mf = scf.RHF(mol)
scf.fast_newton(mf)
mf = dft.RKS(mol)
scf.fast_newton(mf)