def template_adc2_r2methyloxirane(self, basis):
results = {}
for b in backends:
scfres = cached_backend_hf(b,
"r2methyloxirane",
basis,
conv_tol=1e-10)
results[b] = adcc.adc2(scfres, n_singlets=3, conv_tol=1e-9)
compare_adc_results(results, 5e-8)
def base_test(self, system, **args):
hf = DataHfProvider(cache.hfdata[system])
refdata = cache.reference_data[system]
res = adcc.adc2(hf, n_singlets=9, **args)
assert isinstance(res, ExcitedStates)
ref = refdata["adc2"]["singlet"]["eigenvalues"]
assert res.converged
assert res.excitation_energy == approx(ref)
def template_adc2_uhf_ch2nh2(self, basis):
results = {}
# UHF not supported for VeloxChem
if "veloxchem" in backends:
backends.remove("veloxchem")
if not len(backends):
pytest.skip("Not enough backends that support UHF available.")
for b in backends:
scfres = cached_backend_hf(b, "ch2nh2", basis, multiplicity=2)
results[b] = adcc.adc2(scfres, n_states=5, conv_tol=1e-10)
compare_adc_results(results, 5e-9)
def run_spin_flip(distance):
# Run SCF in pyscf
mol = gto.M(
atom='H 0 0 0;'
'F 0 0 {}'.format(distance),
basis='6-31G',
unit="Bohr",
spin=2 # =2S, ergo triplet
)
scfres = scf.UHF(mol)
scfres.conv_tol = 1e-12
scfres.conv_tol_grad = 1e-8
scfres.kernel()
# Run ADC and compute total energy
states = adcc.adc2(scfres, n_spin_flip=1)
ene = scfres.energy_tot() + states.ground_state.energy_correction(2)
return ene + states.excitation_energy[0]
#!/usr/bin/env python3 ## vi: tabstop=4 shiftwidth=4 softtabstop=4 expandtab import adcc from import_data import import_data # Gather precomputed data data = import_data() # Run an adc2 calculation: singlets = adcc.adc2(data, n_singlets=5, conv_tol=1e-8) triplets = adcc.adc2(singlets.matrix, n_triplets=5, conv_tol=1e-8) print(singlets.describe()) print(triplets.describe())
def template_adc2_h2o(self, basis):
results = {}
for b in backends:
scfres = cached_backend_hf(b, "h2o", basis)
results[b] = adcc.adc2(scfres, n_singlets=5, conv_tol=1e-10)
compare_adc_results(results, 5e-9)
# Make a core hole
mo0 = copy.deepcopy(mf.mo_coeff)
occ0 = copy.deepcopy(mf.mo_occ)
occ0[1][0] = 0.0 # beta core hole
dm = mf.make_rdm1(mo0, occ0)
mf_core = scf.UHF(mol)
mf_core.conv_tol = 1e-13
mf_core.conv_tol_grad = 1e-8
scf.addons.mom_occ(mf_core, mo0, occ0)
mf_core.kernel(dm)
del dm
print("Water core hole energy", mf_core.energy_tot())
# Run an adc2 calculation:
state = adcc.adc2(mf_core, n_states=4)
# Print results in a nice way
print()
print(" st ex.ene. (au) f transition dipole moment (au)"
" state dip (au)")
for i, val in enumerate(state.excitation_energies):
fmt = "{0:2d} {1:12.8g} {2:9.3g} [{3:9.3g}, {4:9.3g}, {5:9.3g}]"
fmt += " [{6:9.3g}, {7:9.3g}, {8:9.3g}]"
print(
state.kind[0],
fmt.format(i, val, state.oscillator_strengths[i],
*state.transition_dipole_moments[i],
*state.state_dipole_moments[i]))
state.plot_spectrum()
#!/usr/bin/env python3
## vi: tabstop=4 shiftwidth=4 softtabstop=4 expandtab
import adcc
import psi4
# Run SCF in psi4
mol = psi4.geometry("""
0 3
H 0 0 0
F 0 0 2.5
symmetry c1
units au
no_reorient
no_com
""")
psi4.set_num_threads(adcc.thread_pool.n_cores)
psi4.core.be_quiet()
psi4.set_options({
'basis': "6-31g",
'e_convergence': 1e-14,
'd_convergence': 1e-9,
'reference': 'uhf'
})
scf_e, wfn = psi4.energy('SCF', return_wfn=True)
# Run solver and print results
states = adcc.adc2(wfn, n_spin_flip=5, conv_tol=1e-8)
print(states.describe())
print(states.describe_amplitudes())
with open(infile, "w") as fp:
fp.write("""
@jobs
task: hf
@end
@method settings
basis: sto-3g
@end
@molecule
charge: 0
multiplicity: 1
units: bohr
xyz:
O 0 0 0
H 0 0 1.795239827225189
H 1.693194615993441 0 -0.599043184453037
@end
""")
task = MpiTask([infile, outfile], MPI.COMM_WORLD)
scfdrv = vlx.ScfRestrictedDriver(task.mpi_comm, task.ostream)
scfdrv.conv_thresh = 1e-8
scfdrv.compute(task.molecule, task.ao_basis, task.min_basis)
scfdrv.task = task
# Run an adc2 calculation:
state = adcc.adc2(scfdrv, n_singlets=5)
print(state.describe())
xyz:
O 0 0 0
H 0 0 1.795239827225189
H 1.693194615993441 0 -0.599043184453037
@end
""")
task = MpiTask([infile, outfile], MPI.COMM_WORLD)
scfdrv = vlx.ScfRestrictedDriver(task.mpi_comm, task.ostream)
scfdrv.conv_thresh = 1e-9
scfdrv.compute(task.molecule, task.ao_basis, task.min_basis)
scfdrv.task = task
print(adcc.banner())
# Run an adc2 calculation:
state = adcc.adc2(scfdrv, n_singlets=7, conv_tol=1e-8)
print()
print(" st ex.ene. (au) f transition dipole moment (au)"
" state dip (au)")
for i, val in enumerate(state.excitation_energy):
fmt = "{0:2d} {1:12.8g} {2:9.3g} [{3:9.3g}, {4:9.3g}, {5:9.3g}]"
fmt += " [{6:9.3g}, {7:9.3g}, {8:9.3g}]"
print(state.kind[0], fmt.format(i, val, state.oscillator_strength[i],
*state.transition_dipole_moment[i],
*state.state_dipole_moment[i]))
# Plot a spectrum
state.plot_spectrum()
plt.savefig("veloxchem_ccpvdz_adc2_spectrum.pdf")
plt.show()
## vi: tabstop=4 shiftwidth=4 softtabstop=4 expandtab
import adcc
import psi4
mol = psi4.geometry("""
0 3
O 0 0 0
H 0 0 1.795239827225189
H 1.693194615993441 0 -0.599043184453037
symmetry c1
units au
""")
# set the number of cores equal to the auto-determined value from
# the adcc ThreadPool
psi4.set_num_threads(adcc.get_n_threads())
psi4.core.be_quiet()
psi4.set_options({
'basis': "sto-3g",
'scf_type': 'pk',
'e_convergence': 1e-12,
'reference': 'uhf',
'd_convergence': 1e-8
})
scf_e, wfn = psi4.energy('SCF', return_wfn=True)
# Run an adc2 calculation:
state = adcc.adc2(wfn, n_states=5)
print(state.describe())
#!/usr/bin/env python3
## vi: tabstop=4 shiftwidth=4 softtabstop=4 expandtab
import adcc
from pyscf import gto, scf
# Run SCF in pyscf
mol = gto.M(
atom='H 0 0 0;'
'F 0 0 2.5',
basis='6-31G',
unit="Bohr",
spin=2 # =2S, ergo triplet
)
scfres = scf.UHF(mol)
scfres.conv_tol = 1e-14
scfres.conv_tol_grad = 1e-10
scfres.kernel()
# Run solver and print results
states = adcc.adc2(scfres, n_spin_flip=5, conv_tol=1e-8)
print(states.describe())
#!/usr/bin/env python3 ## vi: tabstop=4 shiftwidth=4 softtabstop=4 expandtab import adcc from import_data import import_data # Gather precomputed data data = import_data() # Make it unrestricted data["restricted"] = False # Run an unrestricted adc2 calculation: states = adcc.adc2(data, n_states=10, conv_tol=1e-8) print(states.describe())
#!/usr/bin/env python3
## vi: tabstop=4 shiftwidth=4 softtabstop=4 expandtab
import adcc
import psi4
mol = psi4.geometry("""
O 0 0 0
H 0 0 1.795239827225189
H 1.693194615993441 0 -0.599043184453037
symmetry c1
units au
""")
# set the number of cores equal to the auto-determined value from
# the adcc ThreadPool
psi4.set_num_threads(adcc.get_n_threads())
psi4.core.be_quiet()
psi4.set_options({
'basis': "sto-3g",
'scf_type': 'pk',
'e_convergence': 1e-12,
'd_convergence': 1e-8
})
scf_e, wfn = psi4.energy('SCF', return_wfn=True)
# Run an adc2 calculation:
state = adcc.adc2(wfn, n_singlets=5)
print(state.describe())
S_mat = np.asarray(mints.ao_overlap())
molden_dict = {"basis_file": "n2.molden", "molecule": "molden"}
s = pyopencap.System(molden_dict)
s.check_overlap_mat(S_mat, "psi4")
print('', end='', flush=True)
cap_dict = {
"cap_type": "box",
"cap_x": "2.76",
"cap_y": "2.76",
"cap_z": "4.88",
}
nstates = 30
pc = pyopencap.CAP(s, cap_dict, nstates)
# ground state energy
state = adcc.adc2(wfn, n_singlets=1)
E_0 = E + state.ground_state.energy_correction(2)
print("MP2 energy of neutral:" + str(E_0))
# now starting anion calculation, starting from UHF reference
mol = psi4.geometry("""
-1 2
N 0.0000000000 0.0000000000 0.548756750
N 0.0000000000 0.0000000000 -0.548756750
Gh(He) 0.0000000000 0.0000000000 0.000
Symmetry C1
""")
psi4.qcdb.libmintsbasisset.basishorde[
'ANONYMOUS03952CBD'] = basisspec_psi4_yo__anonymous03952cbd
psi4.core.set_global_option("BASIS", "anonymous03952cbd")
psi4.core.set_global_option("REFERENCE", "uhf")
#!/usr/bin/env python3
## vi: tabstop=4 shiftwidth=4 softtabstop=4 expandtab
import adcc
from pyscf import gto, scf
# Run SCF in pyscf
mol = gto.M(atom='O 0 0 0;'
'H 0 0 1.795239827225189;'
'H 1.693194615993441 0 -0.599043184453037',
basis='sto-3g',
spin=2,
unit="Bohr")
scfres = scf.UHF(mol)
scfres.conv_tol = 1e-8
scfres.conv_tol_grad = 1e-8
scfres.max_cycle = 100
scfres.verbose = 4
scfres.kernel()
# Run an adc2 calculation:
singlets = adcc.adc2(scfres, n_states=5)
print(singlets.describe())
N_bas = gto.basis.load('n2.nw', 'N')
mol = gto.M(
atom = ' N 0.0000000000 0.0000000000 0.548756750;\
N 0.0000000000 0.0000000000 -0.548756750;\
ghost 0.0 0.0 0.0',
basis = {'N': N_bas, 'ghost': ghost_bas} )
mol.build()
scfres = scf.RHF(mol)
scfres.kernel()
# check overlap matrix
pyscf_smat = scf.hf.get_ovlp(mol)
s.check_overlap_mat(pyscf_smat,"pyscf")
# run scf and mp2 on neutral
state = adcc.adc2(scfres, n_singlets=1)
E_0 = scfres.energy_tot() + state.ground_state.energy_correction(2)
print("MP2 energy of neutral:" + str(E_0))
# run scf and mp2 on anion
mol.charge = -1
mol.spin = 1
mol.build()
scfres = scf.UHF(mol)
scfres.kernel()
# now run adc
state = adcc.adc2(scfres, n_states=nstates)
print(state.describe())
E_0 = scfres.energy_tot() + state.ground_state.energy_correction(2)
print("MP2 energy of anion:" + str(E_0))
#!/usr/bin/env python3 ## vi: tabstop=4 shiftwidth=4 softtabstop=4 expandtab import adcc from import_data import import_data # Gather precomputed data data = import_data() # Run an adc2 calculation: singlets = adcc.adc2(data, frozen_core=1, n_singlets=5, conv_tol=1e-8) triplets = adcc.adc2(singlets.matrix, frozen_core=1, n_triplets=5, conv_tol=1e-8) print(singlets.describe()) print(triplets.describe())
#!/usr/bin/env python3
## vi: tabstop=4 shiftwidth=4 softtabstop=4 expandtab
import adcc
import molsturm
# Run SCF in molsturm
atoms = ["O", "H", "H"]
coords = [[0, 0, 0],
[0, 0, 1.795239827225189],
[1.693194615993441, 0, -0.599043184453037]]
system = molsturm.System(atoms, coords)
hfres = molsturm.hartree_fock(system, basis_type="gaussian",
basis_set_name="sto-3g",
conv_tol=1e-12, print_iterations=True)
# Run an adc2 calculation:
singlets = adcc.adc2(hfres, n_singlets=5, conv_tol=1e-9)
triplets = adcc.adc2(singlets.matrix, n_triplets=3, conv_tol=1e-9)
print(singlets.describe())
print(triplets.describe())
# set the number of cores equal to the auto-determined value from
# the adcc ThreadPool
psi4.set_num_threads(adcc.thread_pool.n_cores)
psi4.core.be_quiet()
psi4.set_options({
'basis': "cc-pvdz",
'scf_type': 'pk',
'e_convergence': 1e-14,
'd_convergence': 1e-9
})
scf_e, wfn = psi4.energy('SCF', return_wfn=True)
print(adcc.banner())
# Run an adc2 calculation:
state = adcc.adc2(wfn, n_singlets=7, conv_tol=1e-8)
# Print results
print()
print(" st ex.ene. (au) f transition dipole moment (au)"
" state dip (au)")
for i, val in enumerate(state.excitation_energies):
fmt = "{0:2d} {1:12.8g} {2:9.3g} [{3:9.3g}, {4:9.3g}, {5:9.3g}]"
fmt += " [{6:9.3g}, {7:9.3g}, {8:9.3g}]"
print(
state.kind[0],
fmt.format(i, val, state.oscillator_strengths[i],
*state.transition_dipole_moments[i],
*state.state_dipole_moments[i]))
state.plot_spectrum()
#!/usr/bin/env python3
## vi: tabstop=4 shiftwidth=4 softtabstop=4 expandtab
from pyscf import gto, scf
from matplotlib import pyplot as plt
import adcc
# pyscf-H2O Hartree-Fock calculation
mol = gto.M(atom='O 0 0 0;'
'H 0 0 1.795239827225189;'
'H 1.693194615993441 0 -0.599043184453037',
basis='cc-pvtz',
unit="Bohr")
scfres = scf.RHF(mol)
scfres.conv_tol = 1e-13
scfres.kernel()
plt.figure(figsize=(7, 5))
state = adcc.adc2(scfres, n_singlets=10)
state.plot_spectrum()
plt.savefig("plot_spectrum_water.png", bbox="tight")
plt.close()
# Run SCF in pyscf
mol = gto.M(
atom='O 0 0 0;'
'H 0 0 1.795239827225189;'
'H 1.693194615993441 0 -0.599043184453037',
basis='aug-cc-pvdz',
unit="Bohr"
)
scfres = scf.RHF(mol)
scfres.conv_tol = 1e-12
scfres.conv_tol_grad = 1e-9
scfres.kernel()
# solve for Eigenvalues
state = adcc.adc2(scfres, n_singlets=1, conv_tol=1e-8)
# setup modified transition moments
dips = state.reference_state.operators.electric_dipole
rhss = [
compute_modified_transition_moments(state.matrix, dip, "adc2")
for dip in dips
]
S = np.zeros((len(state.excitation_energies), 3, 3))
for f, ee in enumerate(state.excitation_energies):
freq = ee / 2.0
matrix = ShiftedMat("adc2", state.ground_state, freq)
preconditioner = JacobiPreconditioner(matrix)
explicit_symmetrisation = IndexSymmetrisation(matrix)
preconditioner.update_shifts(freq)
#!/usr/bin/env python3
## vi: tabstop=4 shiftwidth=4 softtabstop=4 expandtab
import adcc
from pyscf import gto, scf
# Run SCF in pyscf
mol = gto.M(atom='O 0 0 0;'
'H 0 0 1.795239827225189;'
'H 1.693194615993441 0 -0.599043184453037',
basis='sto-3g',
unit="Bohr")
scfres = scf.RHF(mol)
scfres.conv_tol = 1e-14
scfres.conv_tol_grad = 1e-10
scfres.kernel()
# Run an adc2 calculation:
singlets = adcc.adc2(scfres, n_singlets=5)
triplets = adcc.adc2(singlets.matrix, n_triplets=3)
print(singlets.describe())
print()
print(triplets.describe())
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
symmetry c1
no_reorient
no_com
""")
psi4.core.set_num_threads(4)
psi4.set_options({
'basis': "sto-3g",
'scf_type': 'pk',
'pe': 'true',
'e_convergence': 1e-10,
'd_convergence': 1e-10
})
psi4.set_module_options("pe", {"potfile": "pna_6w.pot"})
scf_e, wfn = psi4.energy('SCF', return_wfn=True)
# Run an adc2 calculation:
state = adcc.adc2(wfn, n_singlets=5, conv_tol=1e-8, environment=True)
print(state.describe())
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
""",
basis='sto-3g',
)
scfres = PE(scf.RHF(mol), {"potfile": "pna_6w.pot"})
scfres.conv_tol = 1e-8
scfres.conv_tol_grad = 1e-6
scfres.max_cycle = 250
scfres.kernel()
# model the solvent through perturbative corrections
state_pt = adcc.adc2(scfres,
n_singlets=5,
conv_tol=1e-5,
environment=['ptss', 'ptlr'])
# now model the solvent through linear-response coupling
# in the ADC matrix, re-using the matrix from previous run.
# This will modify state_pt.matrix
state_lr = adcc.run_adc(state_pt.matrix,
n_singlets=5,
conv_tol=1e-5,
environment='linear_response')
print(state_pt.describe())
print(state_lr.describe())
