def test_rohf(self):
pmol = mol.copy()
pmol.charge = 1
pmol.spin = 1
pmol.build(False, False)
mf = scf.density_fit(scf.ROHF(pmol))
self.assertAlmostEqual(mf.scf(), -75.626515724371814, 9)
def test_rohf(self):
pmol = mol.copy()
pmol.charge = 1
pmol.spin = 1
pmol.build(False, False)
mf = scf.density_fit(scf.ROHF(pmol), auxbasis='weigend')
self.assertAlmostEqual(mf.scf(), -75.626515724371814, 9)
def test_uhf_veff(self):
mf = scf.density_fit(scf.UHF(mol), auxbasis='weigend')
nao = mol.nao_nr()
numpy.random.seed(1)
dm = numpy.random.random((2,4,nao,nao))
vhf = mf.get_veff(mol, dm, hermi=0)
self.assertAlmostEqual(numpy.linalg.norm(vhf), 413.82341595365853, 9)
def test_cc(): # pragma: nocover
from pyscf import gto
from pyscf import scf
mol = gto.Mole()
mol.atom = [[8, (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]]
mol.basis = {
'H': '3-21g',
'O': '3-21g',
}
mol.build()
rhf = scf.RHF(mol)
rhf = scf.density_fit(scf.RHF(mol))
rhf.scf() # -76.0267656731
from tcc.rccsd_mul import RCCSD_MUL_RI
from tcc.rccsd_cpd import RCCSD_CPD_LS_T
from tcc.cc_solvers import (residual_diis_solver, classic_solver,
root_solver)
cc1 = RCCSD_CPD_LS_T(rhf, rankt={'t2': 20})
cc2 = RCCSD_MUL_RI(rhf)
converged1, energy1, amps1 = classic_solver(cc1, max_cycle=150)
converged2, energy2, amps2 = classic_solver(cc2, max_cycle=150)
def test_uhf_veff(self):
mf = scf.density_fit(scf.UHF(mol))
nao = mol.nao_nr()
numpy.random.seed(1)
dm = numpy.random.random((4,nao,nao))
vhf = mf.get_veff(mol, dm, hermi=0)
self.assertAlmostEqual(numpy.linalg.norm(vhf), 188.34081056589872, 9)
def test_cc_unit(): # pragma: nocover
from pyscf import gto
from pyscf import scf
mol = gto.Mole()
mol.atom = [[8, (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]]
mol.basis = {
'H': '3-21g',
'O': '3-21g',
}
mol.build()
rhf = scf.RHF(mol)
rhf = scf.density_fit(scf.RHF(mol))
rhf.scf()
from tcc.rccsdt_ri import RCCSDT_UNIT_RI
from tcc.cc_solvers import (classic_solver, update_diis_solver)
cc = RCCSDT_UNIT_RI(rhf)
converged, energy, amps = classic_solver(cc,
conv_tol_energy=1e-8,
max_cycle=100)
cc._converged = False
converged, energy, amps = update_diis_solver(cc,
conv_tol_energy=1e-8,
max_cycle=100)
print('dE: {}'.format(energy - -1.304738e-01))
def test_uhf_veff(self):
mf = scf.density_fit(scf.UHF(mol), auxbasis='weigend')
nao = mol.nao_nr()
numpy.random.seed(1)
dm = numpy.random.random((2, 4, nao, nao))
vhf = mf.get_veff(mol, dm, hermi=0)
self.assertAlmostEqual(numpy.linalg.norm(vhf), 413.82341595365853, 9)
def test_uhf_veff(self):
mf = scf.density_fit(scf.UHF(mol))
nao = mol.nao_nr()
numpy.random.seed(1)
dm = numpy.random.random((4, nao, nao))
vhf = mf.get_veff(mol, dm, hermi=0)
self.assertAlmostEqual(numpy.linalg.norm(vhf), 199.20550115531233, 9)
def test_cc_t2f(): # pragma: nocover
from pyscf import gto
from pyscf import scf
mol = gto.Mole()
mol.atom = [
[8, (0., 0., 0.)],
[1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]]
mol.basis = {'H': '3-21g',
'O': '3-21g', }
mol.build()
rhf = scf.RHF(mol)
rhf.scf()
rhfri = scf.density_fit(scf.RHF(mol))
rhfri.scf()
from tcc.rccsdt import RCCSDT, RCCSDT_UNIT
from tcc.rccsdt_cpd import (RCCSDT_UNIT_nCPD_LS_T,
RCCSDT_UNIT_nCPD_T_LS_T)
from tcc.cc_solvers import (classic_solver, step_solver)
cc1 = RCCSDT_UNIT(rhf)
cc2 = RCCSDT_UNIT_nCPD_T_LS_T(rhfri, rankt={'t3': 40})
converged1, energy1, amps1 = classic_solver(
cc1, conv_tol_energy=1e-7, lam=3,
max_cycle=100)
converged2, energy2, amps2 = step_solver(
cc2, conv_tol_energy=1e-7, beta=1 - 1 / 5,
max_cycle=100)
print('E(full) - E(T2 CPD): {}'.format(energy2 - energy1))
def test_rccsd_mul_ri(self):
from pyscf import gto
from pyscf import scf
mol = gto.Mole()
mol.atom = [[8, (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]]
mol.basis = {
'H': 'sto-3g',
'O': 'sto-3g',
}
mol.build(parse_arg=False)
rhfri = scf.density_fit(scf.RHF(mol))
rhfri.scf() # -74.961181409648674
from tcc.cc_solvers import classic_solver
from tcc.rccsd_mul import RCCSD_MUL_RI
cc = RCCSD_MUL_RI(rhfri)
converged, energy, _ = classic_solver(cc,
conv_tol_amps=1e-8,
conv_tol_energy=1e-8)
self.assertEqual(np.allclose(energy, -0.049399404240317468, 1e-6),
True)
def test_rccsd_cpd_true():
from pyscf import gto
from pyscf import scf
mol = gto.Mole()
mol.atom = [[8, (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]]
mol.basis = '3-21g'
mol.build()
rhf_ri = scf.density_fit(scf.RHF(mol))
rhf_ri.scf()
from tcc.rccsd_cpd import (RCCSD_CPD_LS_T, RCCSD_CPD_LS_T_TRUE)
cc1 = RCCSD_CPD_LS_T(rhf_ri, rankt={'t2': 30})
cc2 = RCCSD_CPD_LS_T_TRUE(rhf_ri, rankt={'t2': 30})
from tcc.cc_solvers import (update_diis_solver, classic_solver)
converged1, energy1, amps1 = update_diis_solver(cc1,
conv_tol_energy=1e-8,
conv_tol_res=1e-8,
beta=0.666,
max_cycle=140)
converged2, energy2, amps2 = update_diis_solver(cc2,
conv_tol_energy=1e-8,
conv_tol_res=1e-8,
beta=0.666,
max_cycle=140)
def test_assign_cderi(self):
nao = mol.nao_nr()
w, u = scipy.linalg.eigh(mol.intor('int2e_sph', aosym='s4'))
idx = w > 1e-9
mf = scf.density_fit(scf.UHF(mol), auxbasis='weigend')
mf._cderi = (u[:, idx] * numpy.sqrt(w[idx])).T.copy()
self.assertAlmostEqual(mf.kernel(), -76.026765673110447, 9)
def test_rohf_symm(self):
pmol = mol.copy()
pmol.charge = 1
pmol.spin = 1
pmol.symmetry = 1
pmol.build(False, False)
mf = scf.density_fit(scf.ROHF(pmol), auxbasis='weigend')
self.assertAlmostEqual(mf.scf(), -75.626515724371814, 9)
def test_assign_cderi(self):
nao = mol.nao_nr()
w, u = scipy.linalg.eigh(mol.intor('int2e_sph', aosym='s4'))
idx = w > 1e-9
mf = scf.density_fit(scf.UHF(mol), auxbasis='weigend')
mf._cderi = (u[:,idx] * numpy.sqrt(w[idx])).T.copy()
self.assertAlmostEqual(mf.kernel(), -76.026765673110447, 9)
def test_rohf_symm(self):
pmol = mol.copy()
pmol.charge = 1
pmol.spin = 1
pmol.symmetry = 1
pmol.build(False, False)
mf = scf.density_fit(scf.ROHF(pmol))
self.assertAlmostEqual(mf.scf(), -75.626515724371814, 9)
def run_ccsd():
basis = BASIS
dists = DISTS_REFERENCE.copy()
lambdas = LAMBDAS_REFERENCE.copy()
def make_mol(dist):
from pyscf import gto
mol = gto.Mole()
mol.atom = [[7, (0., 0., 0.)], [7, (0., 0., dist)]]
mol.basis = {'N': basis}
mol.build()
return mol
mols = [make_mol(dist) for dist in dists]
# Run all scfs here so we will have same starting points for CC
run_scfs(mols, 'reference/{}/scfs_different_dist.p'.format(basis))
with open('reference/{}/scfs_different_dist.p'.format(basis), 'rb') as fp:
ref_scfs = pickle.load(fp)
from tcc.rccsd_mul import RCCSD_MUL_RI
energies = []
amps = None
for idxd, (dist, curr_scf) in enumerate(zip(dists, ref_scfs)):
tim = time.process_time()
rhf = scf.density_fit(scf.RHF(mols[idxd]))
rhf.max_cycle = 1
rhf.scf()
e_scf, mo_coeff, mo_energy = curr_scf
cc = RCCSD_MUL_RI(rhf, mo_coeff=mo_coeff, mo_energy=mo_energy)
converged, energy, amps = residual_diis_solver(cc,
conv_tol_energy=1e-9,
conv_tol_res=1e-8,
max_cycle=500,
verbose=logger.NOTE,
amps=amps)
energies.append(energy + e_scf)
elapsed = time.process_time() - tim
print('Step {} out of {}, dist = {}, time: {}\n'.format(
idxd + 1, len(dists), dist, elapsed))
np.savetxt('reference/{}/RCCSD.txt'.format(basis),
np.column_stack((dists, energies)),
header='U E_total')
# Plot
from matplotlib import pyplot as plt
fig, ax = plt.subplots()
plt.plot(dists, energies)
plt.xlabel('$D, \AA$')
plt.ylabel('$E$, H')
plt.title('Energy in RCCSD (RI)')
fig.show()
def test_gto2sv_df(self):
from pyscf import scf
""" Test import of density-fitting Gaussian functions ... hm """
mf = scf.density_fit(scf.RHF(mol))
self.assertAlmostEqual(mf.scf(), -76.025936299702536, 2)
sv = system_vars_c().init_pyscf_gto(mol)
prod_log = prod_log_c().init_prod_log_df(mf.with_df.auxmol, sv)
self.assertEqual(prod_log.rr[0], sv.ao_log.rr[0])
self.assertEqual(prod_log.pp[0], sv.ao_log.pp[0])
self.assertEqual(prod_log.nspecies, sv.ao_log.nspecies)
self.assertEqual(prod_log.sp2charge, sv.ao_log.sp2charge)
def test_gto2sv_df(self): from pyscf import scf """ Test import of density-fitting Gaussian functions ... hm """ mf = scf.density_fit(scf.RHF(mol)) self.assertAlmostEqual(mf.scf(), -76.025936299702536, 2) sv = nao(gto=mol) prod_log = prod_log_c().init_prod_log_df(mf.with_df.auxmol, sv) self.assertEqual(prod_log.rr[0], sv.ao_log.rr[0]) self.assertEqual(prod_log.pp[0], sv.ao_log.pp[0]) self.assertEqual(prod_log.nspecies, sv.ao_log.nspecies) self.assertEqual(prod_log.sp2charge, sv.ao_log.sp2charge)
def test_gto2sv_df(self):
from pyscf import scf
""" Test import of density-fitting Gaussian functions ... hm """
mf = scf.density_fit(scf.RHF(mol))
self.assertAlmostEqual(mf.scf(), -76.025936299702536, 2)
sv = nao(gto=mol)
prod_log = prod_log_c(auxmol=mf.with_df.auxmol, nao=sv)
self.assertEqual(prod_log.rr[0], sv.ao_log.rr[0])
self.assertEqual(prod_log.pp[0], sv.ao_log.pp[0])
self.assertEqual(prod_log.nspecies, sv.ao_log.nspecies)
for a, b in zip(prod_log.sp2charge, sv.ao_log.sp2charge):
self.assertEqual(a, b)
def test_assign_cderi(self):
nao = molsym.nao_nr()
w, u = scipy.linalg.eigh(mol.intor('cint2e_sph', aosym='s4'))
idx = w > 1e-9
mf = scf.density_fit(scf.RHF(molsym))
mf._cderi = (u[:,idx] * numpy.sqrt(w[idx])).T.copy()
mf.kernel()
mc = mcscf.DFCASSCF(mf, 6, 6)
mc.kernel()
self.assertAlmostEqual(mc.e_tot, -108.98010545803884, 7)
def test_assign_cderi(self):
nao = molsym.nao_nr()
w, u = scipy.linalg.eigh(mol.intor('int2e_sph', aosym='s4'))
idx = w > 1e-9
mf = scf.density_fit(scf.RHF(molsym))
mf._cderi = (u[:, idx] * numpy.sqrt(w[idx])).T.copy()
mf.kernel()
mc = mcscf.DFCASSCF(mf, 6, 6)
mc.kernel()
self.assertAlmostEqual(mc.e_tot, -108.98010545803884, 7)
def test_df_ao2mo(self):
mf = scf.density_fit(msym)
mf.max_memory = 100
mf.kernel()
mc = mcscf.DFCASSCF(mf, 4, 4)
eri0 = numpy.dot(mf._cderi.T, mf._cderi)
nmo = mc.mo_coeff.shape[1]
ncore = mc.ncore
nocc = ncore + mc.ncas
eri0 = ao2mo.restore(1, ao2mo.kernel(eri0, mc.mo_coeff), nmo)
eris = mc.ao2mo(mc.mo_coeff)
self.assertTrue(numpy.allclose(eri0[:,:,ncore:nocc,ncore:nocc], eris.ppaa))
self.assertTrue(numpy.allclose(eri0[:,ncore:nocc,:,ncore:nocc], eris.papa))
def test_nr_df_rohf(self):
mol = gto.Mole()
mol.build(
verbose=0,
atom=[["O", (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]],
basis='cc-pvdz',
charge=1,
spin=1,
)
mf = scf.density_fit(scf.ROHF(mol))
mf.conv_tol = 1e-11
self.assertAlmostEqual(mf.scf(), -75.626515724371899, 9)
def run_cc_ref(workdir):
from pyscf.lib import logger
print('Running CC')
# Restore RHF object
with open(workdir + 'rhf_results.p', 'rb') as fp:
rhf_results = pickle.load(fp)
e_tot, mo_coeff, mo_energy, atom = rhf_results
mol = gto.Mole()
mol.atom = atom
mol.basis = BASIS
mol.build()
rhf = scf.density_fit(scf.RHF(mol))
rhf.max_cycle = 1
rhf.scf()
# Run RCCSD_RI
from tcc.rccsd import RCCSD_DIR_RI
from tcc.cc_solvers import residual_diis_solver
tim = time.process_time()
if (not isfile(workdir + 'ccsd_results.p')
or not isfile(workdir + 'RCCSD.txt')):
cc = RCCSD_DIR_RI(rhf,
mo_coeff=mo_coeff,
mo_energy=mo_energy)
converged, energy, amps = residual_diis_solver(
cc, conv_tol_energy=1e-9, conv_tol_res=1e-8,
max_cycle=500,
verbose=logger.INFO)
ccsd_results = [energy, amps]
with open(workdir + 'ccsd_results.p', 'wb') as fp:
pickle.dump(ccsd_results, fp)
np.savetxt(
workdir + 'RCCSD.txt',
np.array([energy, ]),
header='Energy'
)
elapsed = time.process_time() - tim
print('Done reference RCCSD, time: {}'.format(elapsed))
def test_nr_df_rohf(self):
mol = gto.Mole()
mol.build(
verbose = 0,
atom = [
["O" , (0. , 0. , 0.)],
[1 , (0. , -0.757 , 0.587)],
[1 , (0. , 0.757 , 0.587)] ],
basis = 'cc-pvdz',
charge = 1,
spin = 1,
)
mf = scf.density_fit(scf.ROHF(mol))
mf.conv_tol = 1e-11
self.assertAlmostEqual(mf.scf(), -75.626515724371899, 9)
def test_df_ao2mo(self):
mf = scf.density_fit(msym)
mf.max_memory = 100
mf.kernel()
mc = mcscf.DFCASSCF(mf, 4, 4)
with df.load(mf._cderi) as feri:
cderi = numpy.asarray(feri)
eri0 = numpy.dot(cderi.T, cderi)
nmo = mc.mo_coeff.shape[1]
ncore = mc.ncore
nocc = ncore + mc.ncas
eri0 = ao2mo.restore(1, ao2mo.kernel(eri0, mc.mo_coeff), nmo)
eris = mc.ao2mo(mc.mo_coeff)
self.assertTrue(numpy.allclose(eri0[:,:,ncore:nocc,ncore:nocc], eris.ppaa))
self.assertTrue(numpy.allclose(eri0[:,ncore:nocc,:,ncore:nocc], eris.papa))
def test_nr_df_rohf(self):
mol = gto.Mole()
mol.build(
verbose = 0,
atom = [
["O" , (0. , 0. , 0.)],
[1 , (0. , -0.757 , 0.587)],
[1 , (0. , 0.757 , 0.587)] ],
basis = {"H": '6-31g',
"O": '6-31g',},
charge = 1,
spin = 1,
)
mf = scf.density_fit(scf.ROHF(mol))
mf.conv_tol = 1e-11
self.assertAlmostEqual(mf.scf(), -75.5775921401438, 9)
def test_nr_df_rohf(self):
mol = gto.Mole()
mol.build(
verbose=0,
atom=[["O", (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]],
basis={
"H": '6-31g',
"O": '6-31g',
},
charge=1,
spin=1,
)
mf = scf.density_fit(scf.ROHF(mol), 'weigend')
mf.conv_tol = 1e-11
self.assertAlmostEqual(mf.scf(), -75.5775921401438, 9)
def __init__(self, mf):
self.mol = mf.mol
self.verbose = self.mol.verbose
self.stdout = self.mol.stdout
self.max_memory = mf.max_memory
self.nmo = len(mf.mo_energy)
self.nocc = self.mol.nelectron // 2
if hasattr(mf, 'with_df') and mf.with_df:
self._scf = mf
else:
self._scf = scf.density_fit(mf)
logger.warn(self, 'The input "mf" object is not DF object. '
'DF-MP2 converts it to DF object with %s basis',
self._scf.auxbasis)
self.emp2 = None
self.t2 = None
def run_scfs(mols, filename):
scf_energies = []
scf_mos = []
scf_mo_energies = []
for idm, mol in enumerate(mols):
rhf = scf.density_fit(scf.RHF(mol))
rhf.scf()
scf_energies.append(rhf.e_tot)
scf_mos.append(rhf.mo_coeff)
scf_mo_energies.append(rhf.mo_energy)
results = tuple(
tuple([e_tot, mo_coeff, mo_energy]) for e_tot, mo_coeff, mo_energy in
zip(scf_energies, scf_mos, scf_mo_energies))
with open(filename, 'wb') as fp:
pickle.dump(results, fp)
def test_cpd_unf():
from pyscf import gto
from pyscf import scf
mol = gto.Mole()
mol.atom = [[8, (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]]
mol.basis = {
'H': '3-21g',
'O': '3-21g',
}
mol.build()
rhf_ri = scf.density_fit(scf.RHF(mol))
rhf_ri.scf() # -76.0267656731
from tcc.rccsd import RCCSD, RCCSD_DIR_RI
from tcc.rccsd_cpd import (RCCSD_nCPD_LS_T, RCCSD_CPD_LS_T)
from tcc.cc_solvers import (classic_solver, step_solver)
cc1 = RCCSD_DIR_RI(rhf_ri)
cc2 = RCCSD_nCPD_LS_T(rhf_ri, rankt={'t2': 30})
cc3 = RCCSD_CPD_LS_T(rhf_ri, rankt={'t2': 30})
converged1, energy1, amps1 = classic_solver(
cc1,
conv_tol_energy=1e-8,
)
converged2, energy2, amps2 = classic_solver(cc2,
conv_tol_energy=1e-8,
max_cycle=50)
converged2, energy2, amps2 = step_solver(cc2,
conv_tol_energy=1e-8,
beta=0,
max_cycle=150)
converged3, energy3, amps3 = classic_solver(cc3,
conv_tol_energy=1e-8,
max_cycle=50)
converged3, energy3, amps3 = step_solver(cc3,
conv_tol_energy=1e-8,
beta=0,
max_cycle=150)
def test_cc(): # pragma: nocover
from pyscf import gto
from pyscf import scf
mol = gto.Mole()
mol.atom = [[8, (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]]
mol.basis = {
'H': '3-21g',
'O': '3-21g',
}
mol.build()
rhf = scf.RHF(mol)
rhf = scf.density_fit(scf.RHF(mol))
rhf.scf()
from tcc.rccsdt_ri import RCCSDT_RI
from tcc.rccsdt_cpd import RCCSDT_nCPD_LS_T
from tcc.rccsdt_cpd import RCCSDT_CPD_LS_T
from tcc.cc_solvers import (classic_solver, step_solver)
cc1 = RCCSDT_RI(rhf)
cc2 = RCCSDT_nCPD_LS_T(rhf, rankt={'t2': 20, 't3': 40})
cc3 = RCCSDT_CPD_LS_T(rhf, rankt={'t2': 20, 't3': 40})
converged1, energy1, amps1 = classic_solver(cc1,
conv_tol_energy=1e-9,
conv_tol_res=1e-8,
max_cycle=100)
print('dE: {}'.format(energy1 - -1.304876e-01))
import numpy as np
np.seterr(all='raise')
import warnings
warnings.filterwarnings("error")
converged2, energy2, amps2 = step_solver(cc2,
conv_tol_energy=1e-8,
max_cycle=100)
converged3, energy3, amps3 = step_solver(cc3,
conv_tol_energy=1e-8,
max_cycle=100)
print('dE: {}'.format(energy2 - -0.12621546190311517))
print('E(CPD)-E(nCPD): {}'.format(energy3 - energy2))
def test_mp2_energy(): # pragma: nocover
from pyscf import gto
from pyscf import scf
mol = gto.Mole()
mol.atom = [[8, (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]]
mol.basis = {
'H': 'cc-pvdz',
'O': 'cc-pvdz',
}
mol.build()
rhf = scf.RHF(mol)
rhf = scf.density_fit(scf.RHF(mol))
rhf.scf() # -76.0267656731
cc = RCCSD_MUL_RI(rhf)
h = cc.create_ham()
a = cc.init_amplitudes(h)
energy = cc.calculate_energy(h, a)
print('E_mp2 - E_cc,init = {:18.12g}'.format(energy - -0.204019967288338))
def test_cc(): # pragma: nocover
from pyscf import gto
from pyscf import scf
mol = gto.Mole()
mol.atom = [[8, (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]]
mol.basis = {
'H': 'cc-pvdz',
'O': 'cc-pvdz',
}
mol.build()
rhf = scf.RHF(mol)
rhf = scf.density_fit(scf.RHF(mol))
rhf.scf() # -76.0267656731
from tcc.cc_solvers import classic_solver
from tcc.rccsd_mul import RCCSD_MUL_RI
cc = RCCSD_MUL_RI(rhf)
converged, energy, _ = classic_solver(cc)
def test_rhf_veff(self):
nao = mol.nao_nr()
numpy.random.seed(1)
dm = numpy.random.random((2,nao,nao))
mf = scf.density_fit(scf.RHF(mol))
vhf1 = mf.get_veff(mol, dm, hermi=0)
naux = mf._cderi.shape[0]
cderi = numpy.empty((naux,nao,nao))
for i in range(naux):
cderi[i] = lib.unpack_tril(mf._cderi[i])
vj0 = []
vk0 = []
for dmi in dm:
v1 = numpy.einsum('kij,ij->k', cderi, dmi)
vj0.append(numpy.einsum('kij,k->ij', cderi, v1))
v1 = numpy.einsum('pij,jk->pki', cderi, dmi.T)
vk0.append(numpy.einsum('pki,pkj->ij', cderi, v1))
vj1, vk1 = scf.dfhf.get_jk_(mf, mol, dm, 0)
self.assertTrue(numpy.allclose(vj0, vj1))
self.assertTrue(numpy.allclose(numpy.array(vk0), vk1))
vhf0 = vj1 - vk1 * .5
self.assertTrue(numpy.allclose(vhf0, vhf1))
def test_rhf_veff(self):
nao = mol.nao_nr()
numpy.random.seed(1)
dm = numpy.random.random((2, nao, nao))
mf = scf.density_fit(scf.RHF(mol), auxbasis='weigend')
vhf1 = mf.get_veff(mol, dm, hermi=0)
naux = mf._cderi.shape[0]
cderi = numpy.empty((naux, nao, nao))
for i in range(naux):
cderi[i] = lib.unpack_tril(mf._cderi[i])
vj0 = []
vk0 = []
for dmi in dm:
v1 = numpy.einsum('kij,ij->k', cderi, dmi)
vj0.append(numpy.einsum('kij,k->ij', cderi, v1))
v1 = numpy.einsum('pij,jk->pki', cderi, dmi.T)
vk0.append(numpy.einsum('pki,pkj->ij', cderi, v1))
vj1, vk1 = df_jk.get_jk(mf.with_df, dm, 0)
self.assertTrue(numpy.allclose(vj0, vj1))
self.assertTrue(numpy.allclose(numpy.array(vk0), vk1))
vhf0 = vj1 - vk1 * .5
self.assertTrue(numpy.allclose(vhf0, vhf1))
def build_rhf(workdir):
print('Running SCF')
if (not isfile(workdir + 'rhf_results.p')
or not isfile(workdir + 'rhf_results.p')):
mol = gto.Mole()
mol.atom = load_geom(workdir)
mol.basis = BASIS
mol.build()
rhf = scf.RHF(mol)
rhf = scf.density_fit(scf.RHF(mol))
rhf.scf()
rhf_results = tuple([rhf.e_tot, rhf.mo_coeff, rhf.mo_energy, mol.atom])
with open(workdir + 'rhf_results.p', 'wb') as fp:
pickle.dump(rhf_results, fp)
np.savetxt(
workdir + 'RHF.txt',
np.array([rhf.e_tot, ]),
header='Energy'
)
def test_cc_ri(): # pragma: nocover
from pyscf import gto
from pyscf import scf
mol = gto.Mole()
mol.atom = [['O', (0., 0., 0.)], ['H', (0., -0.757, 0.587)],
['H', (0., 0.757, 0.587)]]
mol.basis = 'sto-3g'
mol.build()
rhf = scf.RHF(mol)
rhf.scf() # -76.0267656731
rhf_ri = scf.density_fit(scf.RHF(mol))
rhf_ri.scf()
from tcc.cc_solvers import residual_diis_solver
from tcc.cc_solvers import classic_solver
from tcc.rccsd import RCCSD_DIR_RI, RCCSD
cc1 = RCCSD_DIR_RI(rhf_ri)
cc2 = RCCSD(rhf)
converged1, energy2, _ = classic_solver(cc1, conv_tol_energy=-1)
converged2, energy2, _ = classic_solver(cc2, conv_tol_energy=-1)
def test_nr_df_rhf(self):
rhf = scf.density_fit(scf.RHF(mol))
rhf.conv_tol = 1e-11
self.assertAlmostEqual(rhf.scf(), -76.025936299701982, 9)
def test_uhf_symm(self):
mf = scf.density_fit(scf.UHF(symol))
self.assertAlmostEqual(mf.scf(), -76.025936299702536, 9)
def test_nr_df_rhf(self):
rhf = scf.density_fit(scf.RHF(mol), 'weigend')
rhf.conv_tol = 1e-11
self.assertAlmostEqual(rhf.scf(), -75.983210886950, 9)
def test_dhf(self):
pmol = mol.copy()
pmol.build(False, False)
mf = scf.density_fit(scf.DHF(pmol), auxbasis='weigend')
mf.conv_tol = 1e-10
self.assertAlmostEqual(mf.scf(), -76.080738677021458, 8)
def test_dhf(self):
pmol = mol.copy()
pmol.build(False, False)
mf = scf.density_fit(scf.DHF(pmol))
self.assertAlmostEqual(mf.scf(), -76.080738685142961, 9)
the Hessian for the large-basis-density-fitted-scf scheme.
"""
mol = gto.Mole()
mol.build(
verbose=0,
atom="""8 0 0. 0
1 0 -0.757 0.587
1 0 0.757 0.587""",
basis="ccpvdz",
)
#
# 1. spin-free X2C-HF with density fitting approximation on 2E integrals
#
mf = scf.density_fit(scf.sfx2c(scf.RHF(mol)))
energy = mf.kernel()
print("E = %.12f, ref = -76.075115837941" % energy)
#
# 2. spin-free X2C correction for density-fitting HF. Since X2C correction is
# commutable with density fitting operation, it is fully equivalent to case 1.
#
mf = scf.sfx2c(scf.density_fit(scf.RHF(mol)))
energy = mf.kernel()
print("E = %.12f, ref = -76.075115837941" % energy)
#
# 3. Newton method for non-relativistic HF
#
mo_init = mf.eig(mf.get_hcore(), mf.get_ovlp())[1]
def test_rhf(self):
mf = scf.density_fit(scf.RHF(mol))
self.assertAlmostEqual(mf.scf(), -76.025936299702536, 9)
def test_rhf_symm(self):
mf = scf.density_fit(scf.RHF(symol), auxbasis='weigend')
self.assertAlmostEqual(mf.scf(), -76.025936299702536, 9)
the Hessian for the large-basis-density-fitted-scf scheme.
'''
mol = gto.Mole()
mol.build(
verbose = 0,
atom = '''8 0 0. 0
1 0 -0.757 0.587
1 0 0.757 0.587''',
basis = 'ccpvdz',
)
#
# 1. spin-free X2C-HF with density fitting approximation on 2E integrals
#
mf = scf.density_fit(scf.sfx2c1e(scf.RHF(mol)))
mf = scf.RHF(mol).x2c().density_fit() # Stream style
energy = mf.kernel()
print('E = %.12f, ref = -76.075408156180' % energy)
#
# 2. spin-free X2C correction for density-fitting HF. Since X2C correction is
# commutable with density fitting operation, it is fully equivalent to case 1.
#
mf = scf.sfx2c1e(scf.density_fit(scf.RHF(mol)))
mf = scf.RHF(mol).density_fit().x2c() # Stream style
energy = mf.kernel()
print('E = %.12f, ref = -76.075408156180' % energy)
#
# 3. The order to apply X2C or newton method matters. If relativistic effects
int3c = df.incore.cholesky_eri(mol, auxbasis='ccpvdz-fit')
# Integrals on disk
ftmp = tempfile.NamedTemporaryFile()
df.outcore.cholesky_eri(mol, ftmp.name, auxbasis='ccpvdz-fit')
fake_mol = gto.M()
fake_mol.nelectron = 10 # Note: you need define the problem size
#
# Redefine the 2-electron integrals by overwriting mf._cderi with the given
# 3-center intagrals. You need create density-fitting SCF object. The
# regulare SCF object cannot hold the 3-center integrals.
#
mf = scf.density_fit(scf.RHF(fake_mol))
mf.get_hcore = lambda *args: (mol.intor('cint1e_kin_sph') +
mol.intor('cint1e_nuc_sph'))
mf.get_ovlp = lambda *args: mol.intor('cint1e_ovlp_sph')
mf._cderi = int3c
mf.init_guess = '1e' # Initial guess from Hcore
mf.kernel()
#
# Assuming the 3-center integrals happens too huge to be held in memory, there
# is a hacky way to input the integrals. The h5py dataset can be accessed in
# the same way as the numpy ndarray.
#
with h5py.File(ftmp.name, 'r') as file1:
mf = scf.density_fit(scf.RHF(fake_mol))
def test_nr_df_rhf(self):
rhf = scf.density_fit(scf.RHF(mol), 'weigend')
rhf.conv_tol = 1e-11
self.assertAlmostEqual(rhf.scf(), -75.983210886950, 9)
[8 , (0. , 0. , 0.)],
[1 , (0. , -0.757 , 0.587)],
[1 , (0. , 0.757 , 0.587)]]
mol.basis = 'cc-pvdz'
mol.build()
mf = scf.RHF(mol).run()
pt = DFMP2(mf)
emp2, t2 = pt.kernel()
print(emp2 - -0.204004830285)
pt.with_df = df.DF(mol)
pt.with_df.auxbasis = 'weigend'
emp2, t2 = pt.kernel()
print(emp2 - -0.204254500453)
mf = scf.density_fit(scf.RHF(mol), 'weigend')
mf.kernel()
pt = DFMP2(mf)
emp2, t2 = pt.kernel()
print(emp2 - -0.203986171133)
pt.with_df = df.DF(mol)
pt.with_df.auxbasis = df.make_auxbasis(mol, mp2fit=True)
emp2, t2 = pt.kernel()
print(emp2 - -0.203738031827)
pt.frozen = 2
emp2, t2 = pt.kernel()
print(emp2 - -0.14433975122418313)
def test_init(self):
from pyscf import dft
from pyscf import x2c
mol_r = mol
mol_u = gto.M(atom='Li', spin=1, verbose=0)
mol_r1 = gto.M(atom='H', spin=1, verbose=0)
sym_mol_r = molsym
sym_mol_u = gto.M(atom='Li', spin=1, symmetry=1, verbose=0)
sym_mol_r1 = gto.M(atom='H', spin=1, symmetry=1, verbose=0)
self.assertTrue(isinstance(scf.RKS(mol_r), dft.rks.RKS))
self.assertTrue(isinstance(scf.RKS(mol_u), dft.roks.ROKS))
self.assertTrue(isinstance(scf.UKS(mol_r), dft.uks.UKS))
self.assertTrue(isinstance(scf.ROKS(mol_r), dft.roks.ROKS))
self.assertTrue(isinstance(scf.GKS(mol_r), dft.gks.GKS))
self.assertTrue(isinstance(scf.KS(mol_r), dft.rks.RKS))
self.assertTrue(isinstance(scf.KS(mol_u), dft.uks.UKS))
self.assertTrue(isinstance(scf.RHF(mol_r), scf.hf.RHF))
self.assertTrue(isinstance(scf.RHF(mol_u), scf.rohf.ROHF))
self.assertTrue(isinstance(scf.RHF(mol_r1), scf.rohf.ROHF))
self.assertTrue(isinstance(scf.UHF(mol_r), scf.uhf.UHF))
self.assertTrue(isinstance(scf.UHF(mol_u), scf.uhf.UHF))
self.assertTrue(isinstance(scf.UHF(mol_r1), scf.uhf.UHF))
self.assertTrue(isinstance(scf.ROHF(mol_r), scf.rohf.ROHF))
self.assertTrue(isinstance(scf.ROHF(mol_u), scf.rohf.ROHF))
self.assertTrue(isinstance(scf.ROHF(mol_r1), scf.rohf.ROHF))
self.assertTrue(isinstance(scf.HF(mol_r), scf.hf.RHF))
self.assertTrue(isinstance(scf.HF(mol_u), scf.uhf.UHF))
self.assertTrue(isinstance(scf.HF(mol_r1), scf.rohf.ROHF))
self.assertTrue(isinstance(scf.GHF(mol_r), scf.ghf.GHF))
self.assertTrue(isinstance(scf.GHF(mol_u), scf.ghf.GHF))
self.assertTrue(isinstance(scf.GHF(mol_r1), scf.ghf.GHF))
self.assertTrue(not isinstance(scf.DHF(mol_r), scf.dhf.RHF))
self.assertTrue(isinstance(scf.DHF(mol_u), scf.dhf.UHF))
self.assertTrue(isinstance(scf.DHF(mol_r1), scf.dhf.HF1e))
self.assertTrue(isinstance(scf.RHF(sym_mol_r), scf.hf_symm.RHF))
self.assertTrue(isinstance(scf.RHF(sym_mol_u), scf.hf_symm.ROHF))
self.assertTrue(isinstance(scf.RHF(sym_mol_r1), scf.hf_symm.ROHF))
self.assertTrue(isinstance(scf.UHF(sym_mol_r), scf.uhf_symm.UHF))
self.assertTrue(isinstance(scf.UHF(sym_mol_u), scf.uhf_symm.UHF))
self.assertTrue(isinstance(scf.UHF(sym_mol_r1), scf.uhf_symm.UHF))
self.assertTrue(isinstance(scf.ROHF(sym_mol_r), scf.hf_symm.ROHF))
self.assertTrue(isinstance(scf.ROHF(sym_mol_u), scf.hf_symm.ROHF))
self.assertTrue(isinstance(scf.ROHF(sym_mol_r1), scf.hf_symm.ROHF))
self.assertTrue(isinstance(scf.HF(sym_mol_r), scf.hf_symm.RHF))
self.assertTrue(isinstance(scf.HF(sym_mol_u), scf.uhf_symm.UHF))
self.assertTrue(isinstance(scf.HF(sym_mol_r1), scf.hf_symm.ROHF))
self.assertTrue(isinstance(scf.GHF(sym_mol_r), scf.ghf_symm.GHF))
self.assertTrue(isinstance(scf.GHF(sym_mol_u), scf.ghf_symm.GHF))
self.assertTrue(isinstance(scf.GHF(sym_mol_r1), scf.ghf_symm.GHF))
self.assertTrue(isinstance(scf.X2C(mol_r), x2c.x2c.UHF))
self.assertTrue(isinstance(scf.sfx2c1e(scf.HF(mol_r)), scf.rhf.RHF))
self.assertTrue(isinstance(scf.sfx2c1e(scf.HF(mol_u)), scf.uhf.UHF))
self.assertTrue(isinstance(scf.sfx2c1e(scf.HF(mol_r1)), scf.rohf.ROHF))
self.assertTrue(isinstance(scf.sfx2c1e(scf.HF(sym_mol_r)), scf.rhf_symm.RHF))
self.assertTrue(isinstance(scf.sfx2c1e(scf.HF(sym_mol_u)), scf.uhf_symm.UHF))
self.assertTrue(isinstance(scf.sfx2c1e(scf.HF(sym_mol_r1)), scf.hf_symm.ROHF))
self.assertTrue(isinstance(scf.density_fit(scf.HF(mol_r)), scf.rhf.RHF))
self.assertTrue(isinstance(scf.density_fit(scf.HF(mol_u)), scf.uhf.UHF))
self.assertTrue(isinstance(scf.density_fit(scf.HF(mol_r1)), scf.rohf.ROHF))
self.assertTrue(isinstance(scf.density_fit(scf.HF(sym_mol_r)), scf.rhf_symm.RHF))
self.assertTrue(isinstance(scf.density_fit(scf.HF(sym_mol_u)), scf.uhf_symm.UHF))
self.assertTrue(isinstance(scf.density_fit(scf.HF(sym_mol_r1)), scf.hf_symm.ROHF))
self.assertTrue(isinstance(scf.newton(scf.HF(mol_r)), scf.rhf.RHF))
self.assertTrue(isinstance(scf.newton(scf.HF(mol_u)), scf.uhf.UHF))
self.assertTrue(isinstance(scf.newton(scf.HF(mol_r1)), scf.rohf.ROHF))
self.assertTrue(isinstance(scf.newton(scf.HF(sym_mol_r)), scf.rhf_symm.RHF))
self.assertTrue(isinstance(scf.newton(scf.HF(sym_mol_u)), scf.uhf_symm.UHF))
self.assertTrue(isinstance(scf.newton(scf.HF(sym_mol_r1)), scf.hf_symm.ROHF))
m = scf.RHF(mol)
ehf = m.scf()
mc = density_fit(mcscf.CASSCF(m, 6, 4))
mc.verbose = 4
mo = addons.sort_mo(mc, m.mo_coeff, (3,4,6,7,8,9), 1)
emc = mc.kernel(mo)[0]
print(ehf, emc, emc-ehf)
#-76.0267656731 -76.0873922924 -0.0606266193028
print(emc - -76.0873923174, emc - -76.0926176464)
mc = density_fit(mcscf.CASSCF(m, 6, (3,1)))
mc.verbose = 4
emc = mc.mc2step(mo)[0]
print(emc - -75.7155632535814)
mf = scf.density_fit(m)
mf.kernel()
#mc = density_fit(mcscf.CASSCF(mf, 6, 4))
#mc = mcscf.CASSCF(mf, 6, 4)
mc = mcscf.DFCASSCF(mf, 6, 4)
mc.verbose = 4
mo = addons.sort_mo(mc, mc.mo_coeff, (3,4,6,7,8,9), 1)
emc = mc.kernel(mo)[0]
print(emc, 'ref = -76.0917567904955', emc - -76.0917567904955)
#mc = density_fit(mcscf.CASCI(mf, 6, 4))
#mc = mcscf.CASCI(mf, 6, 4)
mc = mcscf.DFCASCI(mf, 6, 4)
mo = addons.sort_mo(mc, mc.mo_coeff, (3,4,6,7,8,9), 1)
emc = mc.kernel(mo)[0]
print(emc, 'ref = -76.0476686258461', emc - -76.0476686258461)
nocc = mol.nelectron // 2
nmo = mf.mo_energy.size
nvir = nmo - nocc
co = mf.mo_coeff[:, :nocc]
cv = mf.mo_coeff[:, nocc:]
g = ao2mo.incore.general(mf._eri, (co, cv, co, cv)).ravel()
eia = mf.mo_energy[:nocc, None] - mf.mo_energy[nocc:]
t2ref0 = g / (eia.reshape(-1, 1) + eia.reshape(-1)).ravel()
t2ref0 = t2ref0.reshape(nocc, nvir, nocc, nvir).transpose(0, 2, 1, 3)
pt = MP2(mf)
emp2, t2 = pt.kernel()
print(emp2 - -0.204019967288338)
print("incore", numpy.allclose(t2, t2ref0))
pt.max_memory = 1
print("direct", numpy.allclose(pt.kernel()[1], t2ref0))
rdm1 = make_rdm1_ao(pt, mf.mo_energy, mf.mo_coeff)
print(numpy.allclose(reduce(numpy.dot, (mf.mo_coeff, pt.make_rdm1(), mf.mo_coeff.T)), rdm1))
eri = ao2mo.restore(1, ao2mo.kernel(mf._eri, mf.mo_coeff), nmo)
rdm2 = pt.make_rdm2()
e1 = numpy.einsum("ij,ij", mf.make_rdm1(), mf.get_hcore())
e2 = 0.5 * numpy.dot(eri.flatten(), rdm2.flatten())
print(e1 + e2 + mf.energy_nuc() - mf.e_tot - -0.204019976381)
pt = MP2(scf.density_fit(mf))
print(pt.kernel()[0] - -0.204254500454)
for i in range(start, end, step):
yield i, min(i+step, end)
if __name__ == '__main__':
from pyscf import scf
from pyscf import gto
mol = gto.Mole()
mol.verbose = 0
mol.atom = [
[8 , (0. , 0. , 0.)],
[1 , (0. , -0.757 , 0.587)],
[1 , (0. , 0.757 , 0.587)]]
mol.basis = 'cc-pvdz'
mol.build()
mf = scf.RHF(mol)
mf.scf()
pt = MP2(mf)
pt.max_memory = .05
emp2, t2 = pt.kernel()
print(emp2 - -0.204254491987)
mf = scf.density_fit(scf.RHF(mol))
mf.scf()
pt = MP2(mf)
pt.max_memory = .05
pt.ioblk = .05
pt.verbose = 5
emp2, t2 = pt.kernel()
print(emp2 - -0.203986171133)
def test_nr_df_uhf(self):
uhf = scf.density_fit(scf.UHF(mol))
uhf.conv_tol = 1e-11
self.assertAlmostEqual(uhf.scf(), -76.025936299702096, 9)
from pyscf import gto, df, scf, mcscf ''' Input Cholesky decomposed integrals for CASSCF See also examples/df/40-precompute_df_ints.py ''' mol = gto.M(atom='H 0 0 0; F 0 0 1', basis='ccpvdz') # # Integrals in memory. The size of the integral array is (M,N*(N+1)/2), where # the last two AO indices are compressed due to the symmetry # int3c = df.incore.cholesky_eri(mol, auxbasis='ccpvdz-fit') mf = scf.density_fit(scf.RHF(mol)) mf.with_df._cderi = int3c mf.kernel() # 3-cetner DF or Cholesky decomposed integrals need to be initialized once in # mf.with_df._cderi. DFCASSCF method automatically use the approximate integrals mc = mcscf.DFCASSCF(mf, 8, 8) mc.kernel() # # Integrals on disk # ftmp = tempfile.NamedTemporaryFile() df.outcore.cholesky_eri(mol, ftmp.name, auxbasis='ccpvdz-fit')
m.max_cycle = 1
#m.verbose = 5
m.scf()
e1 = kernel(newton(m), m.mo_coeff, m.mo_occ, max_cycle=50, verbose=5)[1]
m = scf.UHF(mol)
m.max_cycle = 1
#m.verbose = 5
m.scf()
e2 = kernel(newton(m), m.mo_coeff, m.mo_occ, max_cycle=50, verbose=5)[1]
m = scf.UHF(mol)
m.max_cycle = 1
#m.verbose = 5
m.scf()
nrmf = scf.density_fit(newton(m))
nrmf.max_cycle = 50
nrmf.conv_tol = 1e-8
nrmf.conv_tol_grad = 1e-5
#nrmf.verbose = 5
e4 = nrmf.kernel()
m = scf.density_fit(scf.UHF(mol))
m.max_cycle = 1
#m.verbose = 5
m.scf()
nrmf = scf.density_fit(newton(m))
nrmf.max_cycle = 50
nrmf.conv_tol_grad = 1e-5
e5 = nrmf.kernel()
time0 = log.timer('mp2 ao2mo_ovov pass2', *time0)
return h5dat
del(WITH_T2)
if __name__ == '__main__':
from pyscf import scf
from pyscf import gto
mol = gto.Mole()
mol.atom = [
[8 , (0. , 0. , 0.)],
[1 , (0. , -0.757 , 0.587)],
[1 , (0. , 0.757 , 0.587)]]
mol.basis = 'cc-pvdz'
mol.build()
mf = scf.RHF(mol).run()
mp = MP2(mf)
mp.verbose = 5
pt = MP2(mf)
emp2, t2 = pt.kernel()
print(emp2 - -0.204019967288338)
pt.max_memory = 1
emp2, t2 = pt.kernel()
print(emp2 - -0.204019967288338)
pt = MP2(scf.density_fit(mf, 'weigend'))
print(pt.kernel()[0] - -0.204254500454)
*time1)
time0 = log.timer('mp2 ao2mo_ovov pass2', *time0)
return h5dat
del (WITH_T2)
if __name__ == '__main__':
from pyscf import scf
from pyscf import gto
mol = gto.Mole()
mol.atom = [[8, (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]]
mol.basis = 'cc-pvdz'
mol.build()
mf = scf.RHF(mol).run()
mp = MP2(mf)
mp.verbose = 5
pt = MP2(mf)
emp2, t2 = pt.kernel()
print(emp2 - -0.204019967288338)
pt.max_memory = 1
emp2, t2 = pt.kernel()
print(emp2 - -0.204019967288338)
pt = MP2(scf.density_fit(mf, 'weigend'))
print(pt.kernel()[0] - -0.204254500454)
def test_nr_df_uhf(self):
uhf = scf.density_fit(scf.UHF(mol))
uhf.conv_tol = 1e-11
self.assertAlmostEqual(uhf.scf(), -75.983210886950, 9)
