def _run_psi4(self, options: dict, method=None, return_wfn=True, point_group=None, filename: str = None,
guess_wfn=None, ref_wfn=None, *args, **kwargs):
psi4.core.clean()
if self.active_space and not self.active_space.psi4_representable:
print("Warning: Active space is not Psi4 representable")
if "threads" in kwargs:
psi4.set_num_threads(nthread=kwargs["threads"])
if filename is None:
filename = "{}_{}.out".format(self.parameters.filename, method)
psi4.core.set_output_file(filename)
# easier guess read in
if guess_wfn is not None:
if isinstance(guess_wfn, QuantumChemistryPsi4):
guess_wfn = guess_wfn.logs["hf"].wfn
if isinstance(guess_wfn, str):
guess_wfn = psi4.core.Wavefunction.from_file(guess_wfn)
guess_wfn.to_file(guess_wfn.get_scratch_filename(180)) # this is necessary
options["guess"] = "read"
# prevent known flaws
if "guess" in options and options["guess"].lower() == "read":
options["basis_guess"] = False
# additionally the outputfile needs to be the same
# as in the previous guess
# this can not be determined here
# better pass down a guess_wfn
mol = psi4.geometry(self.parameters.get_geometry_string())
mol.set_multiplicity(self.parameters.multiplicity)
if self.parameters.multiplicity != 1:
raise TequilaPsi4Exception("Multiplicity != 1 no yet supported")
mol.set_molecular_charge(self.parameters.charge)
if point_group is not None:
mol.reset_point_group(point_group.lower())
if ref_wfn is None and hasattr(self, "ref_wfn"):
ref_wfn = self.ref_wfn
if point_group is not None and point_group.lower() == "c1":
ref_wfn = None # ref_wfn.c1_deep_copy(ref_wfn.basisset()) # CC will not converge otherwise
guess_wfn = None
psi4.activate(mol)
psi4.set_options(options)
if ref_wfn is None or method.lower() == "hf":
energy, wfn = psi4.energy(name=method.lower(), return_wfn=return_wfn, molecule=mol)
else:
energy, wfn = psi4.energy(name=method.lower(), ref_wfn=ref_wfn, return_wfn=return_wfn, molecule=mol,
guess_wfn=guess_wfn)
self.energies[method.lower()] = energy
self.logs[method.lower()] = Psi4Results(filename=filename, variables=copy.deepcopy(psi4.core.variables()),
wfn=wfn, mol=mol)
return energy, wfn
def v2rdm_psi4():
mol = psi4.geometry("""
0 1
b
h 1 1.1
""")
psi4.set_options({
'basis': 'sto-3g',
'scf_type': 'out_of_core',
'd_convergence': 1e-10,
'maxiter': 500,
})
psi4.set_module_options('hilbert', {
#'sdp_solver': 'rrsdp',
'positivity': 'dqg',
'r_convergence': 1e-5,
'e_convergence': 1e-4,
'maxiter': 20000,
})
psi4.activate(mol)
# get scf wfn
scf_energy,ref_wfn = psi4.energy('scf',return_wfn=True)
# grab options object
options = psi4.core.get_options()
options.set_current_module('HILBERT')
v2rdm_psi4 = hilbert.v2RDMHelper(ref_wfn,options)
current_energy = v2rdm_psi4.compute_energy()
return current_energy, mol.nuclear_repulsion_energy()
def __init__(self, parameters: ParametersQC,
transformation: typing.Union[str, typing.Callable] = None,
active_orbitals=None,
reference=None,
*args,
**kwargs):
"""
Parameters
----------
parameters
transformation
active_orbitals: dictionary :
dictionary with irreps as keys and a list of integers as values
i.e. occ = {"A1":[0,1], "A2":[0]}
means the occupied active space is made up of spatial orbitals
0A1, 1A1 and 0A2
as list: Give a list of spatial orbital indices
i.e. occ = [0,1,3] means that spatial orbital 0, 1 and 3 are used
reference: (Default value=None)
List of orbitals which form the reference
Can be given in the same format as active_orbitals
If given as None then the first N_electron/2 orbitals are taken
and the corresponding active orbitals are removed
args
kwargs
"""
self.psi4_mol = psi4.geometry(parameters.get_geometry_string())
psi4.activate(self.psi4_mol)
self.energies = {} # history to avoid recomputation
self.logs = {} # store full psi4 output
self.active_space = None # will be assigned in super
# active space will be formed later
super().__init__(parameters=parameters, transformation=transformation, active_orbitals=None, reference=None, *args, **kwargs)
self.ref_energy = self.molecule.hf_energy
self.ref_wfn = self.logs['hf'].wfn
self.irreps = [self.psi4_mol.point_group().char_table().gamma(i).symbol().upper() for i in range(self.nirrep)]
oenergies = []
for i in self.irreps:
oenergies += [(i, j, x) for j, x in enumerate(self.orbital_energies(irrep=i))]
oenergies = sorted(oenergies, key=lambda x: x[2])
self.orbitals = [self.OrbitalData(irrep=data[0], idx_irrep=data[1], idx_total=i, energy=data[2]) for i, data in
enumerate(oenergies)]
orbitals_by_irrep = {o.irrep: [] for o in self.orbitals}
for o in self.orbitals:
orbitals_by_irrep[o.irrep] += [o]
self.orbitals_by_irrep = orbitals_by_irrep
if active_orbitals is not None:
self.active_space = self._make_psi4_active_space_data(active_orbitals=active_orbitals, reference=reference)
# need to recompute
# (psi4 won't take over active space information otherwise)
self.compute_energy(method="hf", recompute=True)
self.ref_wfn = self.logs["hf"].wfn
def test_v2rdm_casscf():
"""v2rdm_casscf/tests/v2rdm1"""
#! cc-pvdz N2 (6,6) active space Test DQG
print(
' N2 / cc-pVDZ / DQG(6,6), scf_type = CD / 1e-12, rNN = 0.5 A')
import v2rdm_casscf
n2 = psi4.geometry("""
0 1
n
n 1 r
""")
interloper = psi4.geometry("""
0 1
O
H 1 1.0
H 1 1.0 2 90.0
""")
psi4.set_options({
'basis': 'cc-pvdz',
'scf_type': 'cd',
'cholesky_tolerance': 1e-12,
'd_convergence': 1e-10,
'maxiter': 500,
'restricted_docc': [2, 0, 0, 0, 0, 2, 0, 0],
'active': [1, 0, 1, 1, 0, 1, 1, 1],
})
psi4.set_module_options(
'v2rdm_casscf',
{
'positivity': 'dqg',
'r_convergence': 1e-5,
'e_convergence': 1e-6,
'maxiter': 20000,
#'orbopt_frequency': 1000,
#'mu_update_frequency': 1000,
})
psi4.activate(n2)
n2.r = 0.5 * 0.52917721067 / 0.52917720859
refscf = -103.04337420425350
refv2rdm = -103.086205379481
psi4.energy('v2rdm-casscf', molecule=n2)
assert psi4.compare_values(refscf, psi4.variable("SCF TOTAL ENERGY"), 8,
"SCF total energy")
assert psi4.compare_values(refv2rdm, psi4.variable("CURRENT ENERGY"), 5,
"v2RDM-CASSCF total energy")
def test_v2rdm_casscf():
"""v2rdm_casscf/tests/v2rdm1"""
#! cc-pvdz N2 (6,6) active space Test DQG
print(' N2 / cc-pVDZ / DQG(6,6), scf_type = CD / 1e-12, rNN = 0.5 A')
import v2rdm_casscf
n2 = psi4.geometry("""
0 1
n
n 1 r
""")
interloper = psi4.geometry("""
0 1
O
H 1 1.0
H 1 1.0 2 90.0
""")
psi4.set_options({
'basis': 'cc-pvdz',
'scf_type': 'cd',
'cholesky_tolerance': 1e-12,
'd_convergence': 1e-10,
'maxiter': 500,
'restricted_docc': [ 2, 0, 0, 0, 0, 2, 0, 0 ],
'active': [ 1, 0, 1, 1, 0, 1, 1, 1 ],
})
##psi4.set_module_options('v2rdm_casscf', {
psi4.set_options({
# 'positivity': 'dqg',
'r_convergence': 1e-5,
'e_convergence': 1e-6,
'maxiter': 20000,
# #'orbopt_frequency': 1000,
# #'mu_update_frequency': 1000,
})
psi4.activate(n2)
n2.r = 0.5
refscf = -103.04337420425350
refv2rdm = -103.086205379481
psi4.energy('v2rdm-casscf', molecule=n2)
assert psi4.compare_values(refscf, psi4.get_variable("SCF TOTAL ENERGY"), 8, "SCF total energy")
assert psi4.compare_values(refv2rdm, psi4.get_variable("CURRENT ENERGY"), 5, "v2RDM-CASSCF total energy")
def test_v2rdm6():
#! cc-pvdz N2 (6,6) active space Test DQG
print(' N2 / cc-pVDZ / DQG(6,6), geometry optimization')
import psi4
n2 = psi4.geometry("""
0 1
n
n 1 1.1
""")
psi4.set_options({
'basis': 'cc-pvdz',
'scf_type': 'pk',
'd_convergence': 1e-10,
'maxiter': 500,
'restricted_docc': [2, 0, 0, 0, 0, 2, 0, 0],
'active': [1, 0, 1, 1, 0, 1, 1, 1],
})
psi4.set_module_options(
'v2rdm_casscf',
{
'positivity': 'dqg',
#'r_convergence': 1e-7,
'r_convergence': 1e-6,
'e_convergence': 1e-5,
'orbopt_gradient_convergence': 1e-8,
'maxiter': 20000,
})
psi4.activate(n2)
psi4.optimize('v2rdm-casscf')
refnuc = 23.1968666562054260
refscf = -108.95016246035139
refv2rdm = -109.095505119442
assert psi4.compare_values(refnuc, n2.nuclear_repulsion_energy(), 4,
"Nuclear repulsion energy")
assert psi4.compare_values(refscf, psi4.variable("SCF TOTAL ENERGY"), 5,
"SCF total energy")
assert psi4.compare_values(refv2rdm, psi4.variable("CURRENT ENERGY"), 4,
"v2RDM-CASSCF total energy")
def test_v2rdm():
#! cc-pvdz N2 (6,6) active space Test DQG
print(' N2 / cc-pVDZ / DQG(6,6), scf_type = DF, rNN = 1.1 A')
import psi4
import sys
sys.path.insert(0, '../..')
import hilbert
n2 = psi4.geometry("""
0 1
n
n 1 r
""")
psi4.set_options({
'basis': 'cc-pvdz',
'scf_type': 'df',
'd_convergence': 1e-10,
'maxiter': 500,
'restricted_docc': [2, 0, 0, 0, 0, 2, 0, 0],
'active': [1, 0, 1, 1, 0, 1, 1, 1],
})
psi4.set_module_options(
'hilbert', {
'positivity': 'dqg',
'r_convergence': 1e-5,
'e_convergence': 1e-6,
'maxiter': 20000,
})
psi4.activate(n2)
n2.r = 1.1
refscf = -108.95348837831371
refv2rdm = -109.094404909477
psi4.energy('v2rdm-casscf')
assert psi4.compare_values(refscf, psi4.variable("SCF TOTAL ENERGY"), 8,
"SCF total energy")
assert psi4.compare_values(refv2rdm, psi4.variable("CURRENT ENERGY"), 5,
"v2RDM-CASSCF total energy")
def test_v2rdm8():
# H2 / cc-pVDZ / D(2,2), scf_type = DF, rHH = 1.0 A
print(' H2 / cc-pVDZ / D(2,2), scf_type = DF, rHH = 1.0 A')
import v2rdm_casscf
import psi4
h2 = psi4.geometry("""
0 1
h
h 1 r
symmetry c1
""")
psi4.set_options({
"basis": "cc-pvdz",
"mcscf_type": "df",
"scf_type": "df",
"d_convergence": 1e-10,
"maxiter": 500,
"restricted_docc": [0],
"restricted_uocc": [8],
"active": [2],
})
psi4.set_module_options(
'v2rdm_casscf', {
"positivity": "d",
"r_convergence": 1e-6,
"e_convergence": 1e-8,
"maxiter": 20000,
})
psi4.activate(h2)
h2.r = 1.0
psi4.set_options({"df_ints_io": "save"})
en, wfn = psi4.energy('scf', return_wfn=True)
en1 = v2rdm_casscf.v2rdm_scf_solver(wfn)
en2 = psi4.energy('casscf')
assert psi4.compare_values(en1, en2, 6, "v2RDM-CASSCF total energy")
def test_v2rdm5():
#! cc-pvdz N2 (6,6) active space Test DQG
print(' N2 / cc-pVDZ / DQG+T2(6,6), scf_type = PK, rNN = 1.1 A')
import psi4
n2 = psi4.geometry("""
0 1
n
n 1 r
""")
psi4.set_options({
'basis': 'cc-pvdz',
'scf_type': 'pk',
'd_convergence': 1e-10,
'maxiter': 500,
'restricted_docc': [2, 0, 0, 0, 0, 2, 0, 0],
'active': [1, 0, 1, 1, 0, 1, 1, 1],
})
psi4.set_module_options(
'v2rdm_casscf', {
'positivity': 'dqgt2',
'r_convergence': 1e-4,
'e_convergence': 5e-4,
'maxiter': 20000,
})
psi4.activate(n2)
n2.r = 1.1
refscf = -108.95379624015767
refv2rdm = -109.091487394061
psi4.energy('v2rdm-casscf')
assert psi4.compare_values(refscf, psi4.variable("SCF TOTAL ENERGY"), 8,
"SCF total energy")
assert psi4.compare_values(refv2rdm, psi4.variable("CURRENT ENERGY"), 4,
"v2RDM-CASSCF total energy")
def energy(geom, confId, method='HF-3C', **kwargs):
"""
Finds the energy of a given molecule
:param geom: an RDKit.Mol or a string
:param confId: the ID of the conformer to optimize
:param method: the PSI4 method to calculate the H**O and LUMO
:return: wavefunction (energy is available under wavefunction.energy)
"""
try:
geom = make_psi4_geometry(geom, confId)
psi4.activate(geom)
psi4.core.IO.set_default_namespace(str(id(geom)))
psi4.core.set_global_option("MAXITER", 1000)
return psi4.energy(method, return_wfn=True, **kwargs)[1]
except Exception as e:
print(e)
return np.nan
def optimize(geom, confId=None, method='HF-3C', **kwargs):
"""
Optimizes the given conformation.
:param mol: an RDKit.Mol or a string
:param confId: the ID of the conformer to optimize, if needed
:param method: the PSI4 method to use
:return: wavefunction (energy is available under wavefunction.energy)
"""
try:
geom = make_psi4_geometry(geom, confId)
psi4.activate(geom)
psi4.core.IO.set_default_namespace(str(id(geom)))
psi4.core.set_global_option("MAXITER", 1000)
return psi4.optimize(method, return_wfn=True, **kwargs)[1]
except Exception as e:
pass
return np.nan
def test_v2rdm3():
#! H3 / cc-pvdz / D+D3 vs full CI, scf_type = PK
print(' H3 / cc-pvdz / D+D3 vs full CI, scf_type = PK')
import psi4
h3 = psi4.geometry("""
0 2
H
H 1 1.0
H 1 2.0 2 90.0
""")
psi4.set_options({
'basis': 'sto-3g',
'scf_type': 'pk',
'reference': 'rohf',
'guess': 'sad',
'd_convergence': 1e-10,
'maxiter': 500,
})
psi4.set_module_options(
'v2rdm_casscf', {
'positivity': 'd',
'constrain_d3': True,
'r_convergence': 1e-5,
'e_convergence': 1e-6,
'maxiter': 20000,
'optimize_orbitals': False,
'semicanonicalize_orbitals': False,
})
psi4.activate(h3)
v2rdm = psi4.energy('v2rdm-casscf')
fci = psi4.energy('fci')
assert psi4.compare_values(v2rdm, fci, 5, "v2RDM vs full CI")
def __init__(self, mol, opts, sele, nbnd=[], link=[]):
"""
opts = { "reference": "rks", "basis": "6-31g*", "d_convergence": 6, "scf_type": "direct", "guess": "read",
"output": False, "charge": 0, "method": "b3lyp", "ncpus": 1, "memory": "1024 MB" }
"""
self._ce = qm3.constants.H2J
self._cg = self._ce / qm3.constants.A0
self.sel = sele[:]
self.lnk = link[:]
t = [j for i, j in self.lnk]
self.nbn = [i for i in nbnd if not i in t]
self.smb = mol.guess_symbols(sele)
buf = "\n%d 1\n" % (opts.pop("charge"))
j = 0
for i in sele:
i3 = i * 3
buf += "%-2s%20.10lf%20.10lf%20.10lf\n" % (
self.smb[j], mol.coor[i3] - mol.boxl[0] *
round(mol.coor[i3] / mol.boxl[0], 0), mol.coor[i3 + 1] -
mol.boxl[1] * round(mol.coor[i3 + 1] / mol.boxl[1], 0),
mol.coor[i3 + 2] -
mol.boxl[2] * round(mol.coor[i3 + 2] / mol.boxl[2], 0))
j += 1
self.vla = []
if (len(self.lnk) > 0):
k = len(self.sel)
for i, j in self.lnk:
c, v = qm3.engines.LA_coordinates(i, j, mol)
buf += "%-2s%20.10lf%20.10lf%20.10lf\n" % ("H", c[0], c[1],
c[2])
self.vla.append((self.sel.index(i), k, v[:]))
k += 1
# -- psi4 --
if (opts.pop("output")):
psi4.core.set_output_file("psi4.out", False)
else:
psi4.core.be_quiet()
psi4.set_memory(opts.pop("memory"))
psi4.set_num_threads(opts.pop("ncpus"))
buf += "symmetry c1\nno_reorient\nno_com\n"
self.QMatm = psi4.geometry(buf)
psi4.activate(self.QMatm)
if (len(self.nbn) > 0):
self.MMatm = psi4.QMMM()
self.MMatm.charges = []
for i in self.nbn:
i3 = i * 3
self.MMatm.charges.append([
mol.chrg[i], mol.coor[i3] -
mol.boxl[0] * round(mol.coor[i3] / mol.boxl[0], 0),
mol.coor[i3 + 1] -
mol.boxl[1] * round(mol.coor[i3 + 1] / mol.boxl[1], 0),
mol.coor[i3 + 2] -
mol.boxl[2] * round(mol.coor[i3 + 2] / mol.boxl[2], 0)
])
self.MMatm.populateExtern()
psi4.core.set_global_option_python("EXTERN", self.MMatm.extern)
self.met = opts.pop("method")
psi4.set_options(opts)
def test_dftd3():
"""dftd3/energy"""
#! Exercises the various DFT-D corrections, both through python directly and through c++
ref_d2 = [-0.00390110, -0.00165271, -0.00058118]
ref_d3zero = [-0.00285088, -0.00084340, -0.00031923]
ref_d3bj = [-0.00784595, -0.00394347, -0.00226683]
ref_pbe_d2 = [-0.00278650, -0.00118051, -0.00041513]
ref_pbe_d3zero = [-0.00175474, -0.00045421, -0.00016839]
ref_pbe_d3bj = [-0.00475937, -0.00235265, -0.00131239]
eneyne = psi4.geometry("""
C 0.000000 -0.667578 -2.124659
C 0.000000 0.667578 -2.124659
H 0.923621 -1.232253 -2.126185
H -0.923621 -1.232253 -2.126185
H -0.923621 1.232253 -2.126185
H 0.923621 1.232253 -2.126185
--
C 0.000000 0.000000 2.900503
C 0.000000 0.000000 1.693240
H 0.000000 0.000000 0.627352
H 0.000000 0.000000 3.963929
""")
print(' -D correction from Py-side')
eneyne.update_geometry()
E, G = eneyne.run_dftd3('b3lyp', 'd2')
assert psi4.compare_values(ref_d2[0], E, 7, 'Ethene-Ethyne -D2')
mA = eneyne.extract_subsets(1)
E, G = mA.run_dftd3('b3lyp', 'd2')
assert psi4.compare_values(ref_d2[1], E, 7, 'Ethene -D2')
mB = eneyne.extract_subsets(2)
E, G = mB.run_dftd3('b3lyp', 'd2')
assert psi4.compare_values(ref_d2[2], E, 7, 'Ethyne -D2')
#mBcp = eneyne.extract_subsets(2,1)
#E, G = mBcp.run_dftd3('b3lyp', 'd2')
#compare_values(ref_d2[2], E, 7, 'Ethyne(CP) -D2')
E, G = eneyne.run_dftd3('b3lyp', 'd3zero')
assert psi4.compare_values(ref_d3zero[0], E, 7, 'Ethene-Ethyne -D3 (zero)')
mA = eneyne.extract_subsets(1)
E, G = mA.run_dftd3('b3lyp', 'd3zero')
assert psi4.compare_values(ref_d3zero[1], E, 7, 'Ethene -D3 (zero)')
mB = eneyne.extract_subsets(2)
E, G = mB.run_dftd3('b3lyp', 'd3zero')
assert psi4.compare_values(ref_d3zero[2], E, 7, 'Ethyne -D3 (zero)')
E, G = eneyne.run_dftd3('b3lyp', 'd3bj')
assert psi4.compare_values(ref_d3bj[0], E, 7, 'Ethene-Ethyne -D3 (bj)')
mA = eneyne.extract_subsets(1)
E, G = mA.run_dftd3('b3lyp', 'd3bj')
assert psi4.compare_values(ref_d3bj[1], E, 7, 'Ethene -D3 (bj)')
mB = eneyne.extract_subsets(2)
E, G = mB.run_dftd3('b3lyp', 'd3bj')
assert psi4.compare_values(ref_d3bj[2], E, 7, 'Ethyne -D3 (bj)')
E, G = eneyne.run_dftd3('b3lyp', 'd3')
assert psi4.compare_values(ref_d3zero[0], E, 7,
'Ethene-Ethyne -D3 (alias)')
E, G = eneyne.run_dftd3('b3lyp', 'd')
assert psi4.compare_values(ref_d2[0], E, 7, 'Ethene-Ethyne -D (alias)')
E, G = eneyne.run_dftd3('b3lyp', 'd2')
assert psi4.compare_values(ref_d2[0], E, 7, 'Ethene-Ethyne -D2 (alias)')
psi4.set_options({
'basis': 'sto-3g',
'scf_type': 'df',
'dft_radial_points':
50, # use really bad grid for speed since all we want is the -D value
'dft_spherical_points': 110,
#'scf print': 3, # will print dftd3 program output to psi4 output file
})
print(' -D correction from C-side')
psi4.activate(mA)
#psi4.energy('b3lyp-d2', engine='libdisp')
#assert psi4.compare_values(ref_d2[1], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D2 (calling psi4 Disp class)')
#psi4.energy('b3lyp-d2')
#assert psi4.compare_values(ref_d2[1], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D2 (calling dftd3 -old)')
#psi4.energy('b3lyp-d3zero')
#assert psi4.compare_values(ref_d3zero[1], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D3 (calling dftd3 -zero)')
psi4.energy('b3lyp-d3bj')
assert psi4.compare_values(ref_d3bj[1],
psi4.variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethene -D3 (calling dftd3 -bj)')
psi4.energy('b3lyp-d2', engine='libdisp')
assert psi4.compare_values(ref_d2[1],
psi4.variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethene -D2 (alias)')
#psi4.energy('b3lyp-d3')
#assert psi4.compare_values(ref_d3zero[1], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D3 (alias)')
#psi4.energy('b3lyp-d')
#assert psi4.compare_values(ref_d2[1], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D (alias)')
psi4.energy('wb97x-d')
assert psi4.compare_values(-0.000834247063,
psi4.variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethene wb97x-d (chg)')
print(' non-default -D correction from C-side')
psi4.activate(mB)
#psi4.set_options({'dft_dispersion_parameters': [0.75]})
#psi4.energy('b3lyp-d2', engine='libdisp')
#assert psi4.compare_values(ref_pbe_d2[2], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D2 (calling psi4 Disp class)')
#psi4.set_options({'dft_dispersion_parameters': [0.75, 20.0]})
#psi4.energy('b3lyp-d2')
#assert psi4.compare_values(ref_pbe_d2[2], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D2 (calling dftd3 -old)')
#psi4.set_options({'dft_dispersion_parameters': [1.0, 0.722, 1.217, 14.0]})
#psi4.energy('b3lyp-d3zero')
#assert psi4.compare_values(ref_pbe_d3zero[2], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D3 (calling dftd3 -zero)')
psi4.set_options(
{'dft_dispersion_parameters': [1.000, 0.7875, 0.4289, 4.4407]})
psi4.energy('b3lyp-d3bj')
assert psi4.compare_values(ref_pbe_d3bj[2],
psi4.variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethene -D3 (calling dftd3 -bj)')
psi4.set_options({'dft_dispersion_parameters': [0.75]})
psi4.energy('b3lyp-d2', engine='dftd3')
assert psi4.compare_values(ref_pbe_d2[2],
psi4.variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethene -D2 (alias)')
psi4.set_options({'dft_dispersion_parameters': [1.0, 0.722, 1.217, 14.0]})
psi4.energy('b3lyp-d3')
assert psi4.compare_values(ref_pbe_d3zero[2],
psi4.variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethene -D3 (alias)')
psi4.set_options({'dft_dispersion_parameters': [0.75]})
psi4.energy('b3lyp-d')
assert psi4.compare_values(ref_pbe_d2[2],
psi4.variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethene -D (alias)')
psi4.activate(mA)
psi4.set_options({'dft_dispersion_parameters': [1.0]})
psi4.energy('wb97x-d')
assert psi4.compare_values(-0.000834247063,
psi4.variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethene wb97x-d (chg)')
print(' non-default -D correction from Py-side')
eneyne.update_geometry()
eneyne.run_dftd3('b3lyp', 'd2', {'s6': 0.75})
assert psi4.compare_values(ref_pbe_d2[0],
psi4.variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethene-Ethyne -D2')
mA = eneyne.extract_subsets(1)
mA.run_dftd3('b3lyp', 'd2', {'s6': 0.75})
assert psi4.compare_values(ref_pbe_d2[1],
psi4.variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethene -D2')
mB = eneyne.extract_subsets(2)
mB.run_dftd3('b3lyp', 'd2', {'s6': 0.75})
assert psi4.compare_values(ref_pbe_d2[2],
psi4.variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethyne -D2')
eneyne.run_dftd3('b3lyp', 'd3zero', {
's6': 1.0,
's8': 0.722,
'sr6': 1.217,
'alpha6': 14.0
})
assert psi4.compare_values(ref_pbe_d3zero[0],
psi4.variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethene-Ethyne -D3 (zero)')
mA = eneyne.extract_subsets(1)
mA.run_dftd3('b3lyp', 'd3zero', {
's6': 1.0,
's8': 0.722,
'sr6': 1.217,
'alpha6': 14.0
})
assert psi4.compare_values(ref_pbe_d3zero[1],
psi4.variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethene -D3 (zero)')
mB = eneyne.extract_subsets(2)
mB.run_dftd3('b3lyp', 'd3zero', {
's6': 1.0,
's8': 0.722,
'sr6': 1.217,
'alpha6': 14.0
})
assert psi4.compare_values(ref_pbe_d3zero[2],
psi4.variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethyne -D3 (zero)')
eneyne.run_dftd3('b3lyp', 'd3bj', {
's6': 1.000,
's8': 0.7875,
'a1': 0.4289,
'a2': 4.4407
})
assert psi4.compare_values(ref_pbe_d3bj[0],
psi4.variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethene-Ethyne -D3 (bj)')
mA = eneyne.extract_subsets(1)
mA.run_dftd3('b3lyp', 'd3bj', {
's6': 1.000,
's8': 0.7875,
'a1': 0.4289,
'a2': 4.4407
})
assert psi4.compare_values(ref_pbe_d3bj[1],
psi4.variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethene -D3 (bj)')
mB = eneyne.extract_subsets(2)
mB.run_dftd3('b3lyp', 'd3bj', {
's6': 1.000,
's8': 0.7875,
'a1': 0.4289,
'a2': 4.4407
})
assert psi4.compare_values(ref_pbe_d3bj[2],
psi4.variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethyne -D3 (bj)')
eneyne.run_dftd3('b3lyp', 'd3', {
's6': 1.0,
's8': 0.722,
'sr6': 1.217,
'alpha6': 14.0
})
assert psi4.compare_values(ref_pbe_d3zero[0],
psi4.variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethene-Ethyne -D3 (alias)')
eneyne.run_dftd3('b3lyp', 'd', {'s6': 0.75})
assert psi4.compare_values(ref_pbe_d2[0],
psi4.variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethene-Ethyne -D (alias)')
eneyne.run_dftd3('b3lyp', 'd2', {'s6': 0.75})
assert psi4.compare_values(ref_pbe_d2[0],
psi4.variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethene-Ethyne -D2 (alias)')
def test_pp2rdm():
"""hilbert/tests/pp2rdm"""
#! 6-31g H2O pp2RDM Test
import psi4
import sys
sys.path.insert(0, '../..')
import hilbert
h2o = psi4.geometry("""
0 1
o
h 1 1.0
h 1 1.0 2 104.5
symmetry c1
""")
interloper = psi4.geometry("""
0 1
O
H 1 1.0
H 1 1.0 2 90.0
""")
psi4.set_options({
'basis': '6-31g',
'scf_type': 'df',
'e_convergence': 1e-10,
'r_convergence': 1e-8,
'orbopt_gradient_convergence': 1e-6,
'orbopt_energy_convergence': 1e-8,
'maxiter': 500,
})
psi4.set_module_options(
'hilbert', {
'orbopt_maxiter': 1,
'localize_orbitals': True,
'noisy_orbitals': True,
'optimize_orbitals': True,
'p2rdm_type': 'k',
})
psi4.activate(h2o)
ref_scf = -75.98014193580194
ref_pp2rdm = -76.052804542359
# be sure to save three-index integrals after scf
psi4.core.set_local_option('SCF', 'DF_INTS_IO', 'SAVE')
# get scf wfn
scf_energy, ref_wfn = psi4.energy('scf', return_wfn=True)
# grab options object
options = psi4.core.get_options()
options.set_current_module('HILBERT')
# evaluate pp2RDM energy
pp2rdm = hilbert.pp2RDMHelper(ref_wfn, options)
current_energy = pp2rdm.compute_energy()
assert psi4.compare_values(ref_scf, scf_energy, 8, "SCF total energy")
assert psi4.compare_values(ref_pp2rdm, current_energy, 5,
"pp2RDM total energy")
def test_v2rdm7():
# STO-3g benzene (6,6) guess orbital rotation test DQG
print(' benzene (6,6), scf_type = PK')
import psi4
# orbital rotation needed before MCSCF calculation
benzene_c1 = psi4.geometry("""
0 1
symmetry c1
C 0.00000000 1.38980400 0.00000000
C 1.20360500 0.69490200 0.00000000
C 1.20360500 -0.69490200 0.00000000
C 0.00000000 -1.38980400 0.00000000
C -1.20360500 -0.69490200 0.00000000
C -1.20360500 0.69490200 0.00000000
H 0.00000000 2.47523400 0.00000000
H 2.14361600 1.23761700 0.00000000
H 2.14361600 -1.23761700 0.00000000
H 0.00000000 -2.47523400 0.00000000
H -2.14361600 -1.23761700 0.00000000
H -2.14361600 1.23761700 0.00000000
""")
psi4.set_options({
'basis': 'sto-3g',
'scf_type': 'pk',
'd_convergence': 1e-10,
'maxiter': 500,
'restricted_docc': [18],
'active': [6],
})
psi4.energy('hf')
psi4.set_module_options(
'v2rdm_casscf',
{
# Switch the 17th (index 16) and the 19th (index 18) orbitals of the 1st irrep (index 0)
# If more than one set of orbitals need to be rotated, use the following syntex
# mcscf_rotate [[irrep_1, orb1_1, orb2_1, theta_1], [irrep_2, orb1_2, orb2_2, theta2],...]
# Setting theta to 90 would switch the orbitals, setting it to 0 does nothing.
'mcscf_rotate': [[0, 16, 18, 90]],
'positivity': 'dq',
'r_convergence': 1e-5,
'e_convergence': 1e-6,
'maxiter': 20000,
'guess_orbitals_write': False,
'molden_write': False,
})
psi4.activate(benzene_c1)
E_c1 = psi4.energy('v2rdm-casscf')
psi4.core.clean()
# reference calculation, no need to rotate orbitals for MCSCF
benzene_d2h = psi4.geometry("""
0 1
symmetry d2h
C 0.00000000 1.38980400 0.00000000
C 1.20360500 0.69490200 0.00000000
C 1.20360500 -0.69490200 0.00000000
C 0.00000000 -1.38980400 0.00000000
C -1.20360500 -0.69490200 0.00000000
C -1.20360500 0.69490200 0.00000000
H 0.00000000 2.47523400 0.00000000
H 2.14361600 1.23761700 0.00000000
H 2.14361600 -1.23761700 0.00000000
H 0.00000000 -2.47523400 0.00000000
H -2.14361600 -1.23761700 0.00000000
H -2.14361600 1.23761700 0.00000000
""")
psi4.set_options({
'basis': 'sto-3g',
'scf_type': 'pk',
'd_convergence': 1e-10,
'maxiter': 500,
'restricted_docc': [6, 3, 0, 0, 0, 0, 5, 4],
'active': [0, 0, 1, 2, 1, 2, 0, 0],
})
psi4.energy('hf')
psi4.set_module_options(
'v2rdm_casscf',
{
# Note that when mcscf_rotate is set for the previous molecule, the calculations afterwards
# also use this input, unless you overwrite it. A safe way to unset it is to overwrite it
# with mcscf_rotate [[0, 0, 0, 0]], which should work as long as your molecule has at
# least 1 orbital in the 1st irrep. This problem can also be simply avoided by calculating
# the molecules that do not require orbital rotations first.
'mcscf_rotate': [[0, 0, 0, 0]],
'positivity': 'dq',
'r_convergence': 1e-5,
'e_convergence': 1e-6,
'maxiter': 20000,
'guess_orbitals_write': False,
'molden_write': False,
})
psi4.activate(benzene_d2h)
E_d2h = psi4.energy('v2rdm-casscf')
assert psi4.compare_values(E_c1, E_d2h, 4, "v2RDM-CASSCF total energy")
def run_n_body(name, **kwargs):
r"""Function encoding sequence of PSI module and plugin calls so that
n_body can be called via :py:func:`~driver.energy`. For post-scf plugins.
>>> energy('n_body')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
# print("START run_n_body()")
# Your plugin's psi4 run sequence goes here
psi4.core.set_local_option('MYPLUGIN', 'PRINT', 1)
##### BEGIN TAYLOR'S run_n_body() FUNCTION #####
# Only energy and properties are implemented for now, not sure others even
# make sense anyways.
db = shelve.open('database', writeback=True)
# print(db)
# Initialize database
if not 'initialized' in db:
n_body.initialize_database(db, kwargs)
db['initialized'] = True
elif not db['initialized']:
n_body.initialize_database(db, kwargs)
db['initialized'] = True
# Remove n_body_func, it's being tracked in the database and we don't want to propagate it
if 'n_body_func' in kwargs:
kwargs.pop('n_body_func')
# Process user requested options
n_body_options = n_body.process_options(name, db, kwargs.pop('n_body'))
# Compare database options to n_body_options
if 'distributed' in n_body_options:
db['distributed'] = n_body_options['distributed']
if not db['distributed']:
raise Exception(
"Currently n_body jobs must be run in distributed mode"
" use the n_body wrapper instead.\n")
if 'cutoff' in n_body_options:
db['cutoff'] = n_body_options['cutoff']
if 'num_threads' in n_body_options:
db['num_threads'] = n_body_options['num_threads']
if 'bsse' in n_body_options:
db['bsse'] = n_body_options['bsse']
if 'pcm' in n_body_options:
db['pcm'] = n_body_options['pcm']
if 'solute' in n_body_options:
db['solute'] = n_body_options['solute']
if 'timing' in n_body_options:
db['timing'] = n_body_options['timing']
if 'harvest' in n_body_options:
db['harvest'] = n_body_options['harvest']
if 'cook' in n_body_options:
db['cook'] = n_body_options['cook']
# methods consistency check
if 'methods' in n_body_options:
for key, val in n_body_options['methods'].items():
if key in db['methods'].keys():
# requested n_body_max smaller than previously requested
if val < db['methods'][key]:
raise Exception('n_body_max for {} has '
'decreased.'.format(key))
# requested n_body_max has increased
elif val > db['methods'][key]:
# save requested n_body_max
db['methods'][key] = val
# update database entries
n_body.extend_database(db, kwargs)
# set flag to regenerate inputs
db['inputs_generated'] = False
else: # method not already in database
# add method and n_body_max to database
db['methods'][key] = val
# update database entries
n_body.extend_database(db, kwargs)
# set flag to regenerate inputs
db['inputs_generated'] = False
# Get complete system
molecule = psi4.core.get_active_molecule()
# Determine interacting fragments
if db['cutoff']:
i_pairs = n_body.interacting_pairs(db['cutoff'])
i_clusters = []
if not db['inputs_generated']:
# Create method directories
for method, n_body_max in db['methods'].items():
try:
os.makedirs(method)
except:
if os.path.isdir(method):
print(method)
pass
else:
raise Exception('Attempt to create {} directory '
'failed.'.format(method))
# Create n_body_level directories
for n in range(1, n_body_max + 1):
directory = '{}/{}'.format(method, n_body.n_body_dir(n))
try:
os.makedirs(directory)
except:
if os.path.isdir(directory):
print(directory)
pass
else:
raise Exception('Attempt to create {} directory '
'failed.'.format(directory))
# Create job input files
# Grab all ghost functions if SSFC
# Else, get all possible clusters without ghost atoms
if db['bsse'] == 'ssfc':
clusters = psi4.extract_clusters(molecule, True, n)
else:
clusters = psi4.extract_clusters(molecule, False, n)
# Flip distance-dropoff off for now
#if db['bsse'] == 'radius'
#clusters = extract_clusters(molecule, False, n)
#clusters = n_body.expand_basis(clusters, db['basis_cutoff'])
# Get list of fragments involved in clusters
indexes = psi4.extract_cluster_indexing(molecule, n)
print('Length of index array = {}'.format(len(indexes)))
# Testing for extension to inclusion of nearby atoms (ghosted)
#cluster_string = clusters[0].save_string_xyz_g09()
#print(cluster_string)
#cluster_string += molecule.extract_subsets(2).save_string_xyz_g09()
#print(molecule.extract_subsets(2).save_string_xyz_g09())
#print(clusters[0].save_string_xyz_g09())
#print(cluster_string)
#cluster_string = ''
# Get interacting clusters
if db['cutoff']:
if n == 1:
# Generate all inputs
pass
elif n == 2:
# generate inputs for i_pairs only
for k in range(len(clusters) - 1, -1, -1):
clus = indexes[k]
if clus in i_pairs:
i_clusters.append(clus)
else:
# Remove non-interacting clusters from lists
clusters.pop(k)
indexes.pop(k)
elif n > 2:
prev_clusters = copy.deepcopy(i_clusters)
i_clusters = []
for k in range(len(clusters) - 1, -1, -1):
# Check if interacting cluster
clus = indexes[k]
for p_clus in prev_clusters:
# previous cluster is contained within current cluster
if set(p_clus).issubset(set(clus)):
# Get remaining frag number
if len(set(clus).difference(
set(p_clus))) == 1:
l = set(clus).difference(
set(p_clus)).pop()
else:
raise Exception(
'Length of difference '
'set is greater than 1')
for m in p_clus:
# Is this an interacting pair?
if sorted([l, m],
reverse=True) in i_pairs:
i_clusters.append(clus)
# Don't check anymore pairs
break
if clus in i_clusters:
break
else:
# Remove non-interacting clusters from lists
clusters.pop(k)
indexes.pop(k)
# Create input files
db[method][n]['total_num_jobs'] = len(clusters)
print('n = {}'.format(n))
print('Number of jobs created = {}'.format(len(clusters)))
for k in range(len(clusters)):
psi4.activate(clusters[k])
cluster = psi4.core.get_active_molecule()
# db[method][n]['MW'][job] = value
### Set-up things for input generation
# Get list of combinations to ghost
# MBCP
if db['bsse'] == 'mbcp' and n > 1:
mbcp = list(itertools.combinations(indexes[k], n - 1))
for ghost in mbcp:
directory = '{}/{}/{}'.format(
method, n_body.n_body_dir(n),
n_body.ghost_dir(indexes[k], ghost))
cluster.set_ghost_fragments(list(ghost))
cluster.update_geometry()
cluster.set_name('{}_{}'.format(
molecule.name(),
n_body.ghost_dir(indexes[k], ghost)))
n_body.plant(cluster, db, kwargs, method,
directory)
# Update job_status dict
n_basis = n
n_real = n - len(ghost)
ghost_jobs = '{}-{}r'.format(n_basis, n_real)
# db[method][ghost_jobs]['total_num_jobs'] = len(mbcp) * len(clusters)
# db[method][ghost_jobs]['job_status'].update({n_body.ghost_dir(indexes[k],ghost):
# 'not_started'})
db[method][n]['total_num_jobs'] = len(mbcp) * len(
clusters)
db[method][n]['job_status'].update({
n_body.ghost_dir(indexes[k], ghost):
'not_started'
})
# Calculate molecular weight
totalmass = sum(
mol2.mass(i) for i in range(mol2.natom())
if mol2.Z(i))
totmass = sum(
cluster.mass(i) for i in range(cluster.natom())
if cluster.Z(i))
db[method][n]['MW'].update(
{n_body.ghost_dir(indexes[k], ghost): totmass})
# Reactivate fragments for next round
cluster.set_active_fragments(list(ghost))
cluster.update_geometry()
# VMFC
elif db['bsse'] == 'vmfc':
vmfc = []
for n_ghost in range(n - 1, 0, -1):
vmfc.extend(
list(
itertools.combinations(
indexes[k], n_ghost)))
for ghost in vmfc:
directory = '{}/{}/{}'.format(
method, n_body.n_body_dir(n),
n_body.ghost_dir(indexes[k], ghost))
cluster.set_ghost_fragments(list(ghost))
cluster.update_geometry()
cluster.set_name('{}_{}'.format(
molecule.name(),
n_body.ghost_dir(indexes[k], ghost)))
n_body.plant(cluster, db, kwargs, method,
directory)
# Update job_status dict
n_basis = n
n_real = n - len(ghost)
ghost_jobs = '{}-{}r'.format(n_basis, n_real)
#db[method][ghost_jobs]['total_num_jobs'] = len(vmfc) * len(clusters)
# db[method][ghost_jobs]['total_num_jobs'] = len(list(itertools.combinations(range(0,n),n_real))) * len(clusters)
# db[method][ghost_jobs]['job_status'].update({n_body.ghost_dir(indexes[k],ghost):
# 'not_started'})
db[method][n]['total_num_jobs'] = len(
list(
itertools.combinations(
range(0, n), n_real))) * len(clusters)
db[method][n]['job_status'].update({
n_body.ghost_dir(indexes[k], ghost):
'not_started'
})
# Calculate molecular weight
totmass = sum(
cluster.mass(i) for i in range(cluster.natom())
if cluster.Z(i))
db[method][n]['MW'].update(
{n_body.ghost_dir(indexes[k], ghost): totmass})
# Reactivate fragments for next round
cluster.set_active_fragments(list(ghost))
cluster.update_geometry()
# SSFC or no BSSE
else:
cluster.set_name('{}_{}'.format(
molecule.name(), n_body.cluster_dir(indexes[k])))
#molecule.set_name('{}_{}'.format(molecule.name(),cluster_dir(indexes[k])))
directory = '{}/{}/{}'.format(
method, n_body.n_body_dir(n),
n_body.cluster_dir(indexes[k]))
n_body.plant(cluster, db, kwargs, method, directory)
# Update database job_status dict
db[method][n]['job_status'].update(
{n_body.cluster_dir(indexes[k]): 'not_started'})
# Calculate molecular weight
totmass = sum(
cluster.mass(i) for i in range(cluster.natom())
if cluster.Z(i))
db[method][n]['MW'].update(
{n_body.cluster_dir(indexes[k]): totmass})
# Check for zero jobs (happens occasionally due to cutoff)
for method in db['methods']:
for n in range(1, db[method]['n_body_max'] + 1):
if db[method][n]['total_num_jobs'] == 0:
db[method]['n_body_max'] = n - 1
break
# Inputs successfully generated
db['inputs_generated'] = True
# For now open and close database frequently, until I figure out atexit
db.close()
db = shelve.open('database', writeback=True)
# Check status of jobs
if not db['jobs_complete']:
n_incomplete = 0
# Check all methods
for method in db['methods'].keys():
#### NOTE: dft_methods is defunct #####
# if method in n_body.dft_methods:
# outname = 'input.log'
# complete_message = 'Normal termination of Gaussian'
# if (method == 'b3lyp'):
if method in n_body.dft_methods:
outname = 'input.log'
complete_message = 'Normal termination of Gaussian'
error_message = 'Error termination'
else:
outname = 'output.dat'
complete_message = 'Psi4 exiting successfully'
error_message = 'Psi4 encountered an error'
# Check all n_body_levels
print('Before job checking:')
for field in db[method]['farm']:
num_fin = db[method][field]['num_jobs_complete']
tot_num = db[method][field]['total_num_jobs']
print('{}/{} {}-body jobs finished'.format(
num_fin, tot_num, field))
n_complete = num_fin
if num_fin != tot_num:
db_stat = db[method][field]['job_status']
n_complete = 0
for job, status in db_stat.items():
if status == 'complete':
n_complete += 1
elif status in ('not_started', 'running', 'error'):
try:
outfile = open('{}/{}/{}/{}'.format(
method, n_body.n_body_dir(field), job,
outname))
for line in outfile:
if complete_message in line:
# This actually marks the job complete as soon as
# the first route section is complete in the case
# of g09, not when the job is totally finished.
db_stat[job] = 'complete'
n_complete += 1
break
elif error_message in line:
db_stat[job] = 'error'
break
else:
db_stat[job] = 'running'
n_incomplete += 1
except:
# this print statement is super annoying, muting it for now
# print('Exception: probably could not open file for {}'.format(job))
n_incomplete += 1
db[method][field]['num_jobs_complete'] = n_complete
if n_incomplete == 0:
db['jobs_complete'] = True
db.close()
db = shelve.open('database', writeback=True)
# Gather results
if not db['results_computed']:
for method in db['methods'].keys():
print('\nAfter job checking:')
for field in db[method]['farm']:
num_fin = db[method][field]['num_jobs_complete']
tot_num = db[method][field]['total_num_jobs']
print('{}/{} {}-body jobs finished'.format(
num_fin, tot_num, field))
if (db[method][field]['num_jobs_complete'] == db[method][field]
['total_num_jobs']):
if db['harvest']:
if method in n_body.dft_methods:
n_body.harvest_g09(db, method, field)
else:
n_body.harvest_data(db, method, field)
if not db['harvest']:
print("Data harvesting has been disabled.")
elif not db['cook']:
print("Data cooking has been disabled.")
else:
for field in db[method]['farm']:
if (db[method][field]['num_jobs_complete'] == db[method]
[field]['total_num_jobs']):
n_body.cook_data(db, method, field)
# #if db['bsse'] == 'vmfc' and field > 1:
# # n_body.vmfc_cook(db, method, field)
# # n_body.mbcp_cook(db, method, field)
# if db['bsse'] == 'vmfc':
# n_body.vmfc_cook(db, method, field)
# if field > 1:
# n_body.mbcp_cook(db, method, field)
# elif db['bsse'] == 'mbcp' and field > 1:
# n_body.mbcp_cook(db,method,field)
# # Future location of an if check for mass adjust or not
# if 'rotation' in db[method]['results']:
# n_body.mass_adjust_rotations(db,method,field)
db.close()
db = shelve.open('database', writeback=True)
# Print banner to output file including user options
n_body.banner(db)
db.close()
pass
def test_v2rdm_doci():
"""hilbert/tests/v2rdm_doci"""
#! 6-31g H2O v2RDM-DOCI Test
import psi4
import sys
sys.path.insert(0, '../..')
import hilbert
h2o = psi4.geometry("""
0 1
o
h 1 1.0
h 1 1.0 2 104.5
symmetry c1
""")
interloper = psi4.geometry("""
0 1
O
H 1 1.0
H 1 1.0 2 90.0
""")
psi4.set_options({
'basis': '6-31g',
'scf_type': 'df',
'e_convergence': 1e-4,
'r_convergence': 1e-6,
'maxiter': 100000,
})
psi4.set_module_options(
'hilbert', {
'orbopt_maxiter': 20,
'localize_orbitals': True,
'noisy_orbitals': True,
'optimize_orbitals': True,
'orbopt_gradient_convergence': 1e-6,
'orbopt_energy_convergence': 1e-8,
'orbopt_frequency': 1000,
})
psi4.activate(h2o)
ref_scf = -75.98014193580194
ref_v2rdm_doci = -76.053681341564
# be sure to save three-index integrals after scf
psi4.core.set_local_option('SCF', 'DF_INTS_IO', 'SAVE')
# get scf wfn
scf_energy, ref_wfn = psi4.energy('scf', return_wfn=True)
# grab options object
options = psi4.core.get_options()
options.set_current_module('HILBERT')
# evaluate v2RDM-DOCI energy
v2rdm_doci = hilbert.v2RDM_DOCIHelper(ref_wfn, options)
current_energy = v2rdm_doci.compute_energy()
assert psi4.compare_values(ref_scf, scf_energy, 8, "SCF total energy")
assert psi4.compare_values(ref_v2rdm_doci, current_energy, 4,
"v2RDM-DOCI total energy")
def test_v2rdm4():
print(' 1,4-phenylenedinitrene/(10,10)/cc-pVDZ')
import psi4
singlet = psi4.geometry("""
0 1
C 0.00000000 -1.43825841 0.00000000
C 1.26321637 -0.67149862 0.00000000
C 1.26321637 0.67149862 0.00000000
C 0.00000000 1.43825841 0.00000000
C -1.26321637 0.67149862 0.00000000
C -1.26321637 -0.67149862 0.00000000
H 2.18678709 -1.24095300 0.00000000
H 2.18678709 1.24095300 0.00000000
H -2.18678709 1.24095300 0.00000000
H -2.18678709 -1.24095300 0.00000000
N 0.00000000 2.71003942 0.00000000
N 0.00000000 -2.71003942 0.00000000
""")
triplet = psi4.geometry("""
0 3
C 0.00000000 -1.43825841 0.00000000
C 1.26321637 -0.67149862 0.00000000
C 1.26321637 0.67149862 0.00000000
C 0.00000000 1.43825841 0.00000000
C -1.26321637 0.67149862 0.00000000
C -1.26321637 -0.67149862 0.00000000
H 2.18678709 -1.24095300 0.00000000
H 2.18678709 1.24095300 0.00000000
H -2.18678709 1.24095300 0.00000000
H -2.18678709 -1.24095300 0.00000000
N 0.00000000 2.71003942 0.00000000
N 0.00000000 -2.71003942 0.00000000
""")
psi4.set_options({
'basis': 'cc-pvdz',
'scf_type': 'df',
'd_convergence': 1e-8,
'maxiter': 500,
'reference': 'rohf',
'restricted_docc': [8, 3, 0, 0, 0, 0, 7, 4],
'active': [0, 1, 1, 3, 1, 3, 0, 1],
})
psi4.set_module_options(
'v2rdm_casscf', {
'positivity': 'dqg',
'constrain_spin': True,
'r_convergence': 1e-4,
'e_convergence': 1e-4,
'cg_convergence': 1e-8,
'mu_update_frequency': 250,
'orbopt_frequency': 500,
'maxiter': 100000,
})
# singlet
# from JCTC, with r_convergence = e_convergence = 1e-5
# * v2RDM total energy: -338.502362198038
psi4.activate(singlet)
ref_singlet = -338.502342367694
e_singlet = psi4.energy('v2rdm-casscf')
assert psi4.compare_values(e_singlet, ref_singlet, 4, "singlet")
# triplet
# from JCTC, with r_convergence = e_convergence = 1e-5
# * v2RDM total energy: -338.495146818081
psi4.activate(triplet)
ref_triplet = -338.495170913420
e_triplet = psi4.energy('v2rdm-casscf')
assert psi4.compare_values(e_triplet, ref_triplet, 4, "triplet")
def test_dftd3():
"""dftd3/energy"""
#! Exercises the various DFT-D corrections, both through python directly and through c++
ref_d2 = [-0.00390110, -0.00165271, -0.00058118]
ref_d3zero = [-0.00285088, -0.00084340, -0.00031923]
ref_d3bj = [-0.00784595, -0.00394347, -0.00226683]
ref_pbe_d2 = [-0.00278650, -0.00118051, -0.00041513]
ref_pbe_d3zero = [-0.00175474, -0.00045421, -0.00016839]
ref_pbe_d3bj = [-0.00475937, -0.00235265, -0.00131239]
eneyne = psi4.geometry("""
C 0.000000 -0.667578 -2.124659
C 0.000000 0.667578 -2.124659
H 0.923621 -1.232253 -2.126185
H -0.923621 -1.232253 -2.126185
H -0.923621 1.232253 -2.126185
H 0.923621 1.232253 -2.126185
--
C 0.000000 0.000000 2.900503
C 0.000000 0.000000 1.693240
H 0.000000 0.000000 0.627352
H 0.000000 0.000000 3.963929
""")
print(' -D correction from Py-side')
eneyne.update_geometry()
E, G = eneyne.run_dftd3('b3lyp', 'd2')
assert psi4.compare_values(ref_d2[0], E, 7, 'Ethene-Ethyne -D2')
mA = eneyne.extract_subsets(1)
E, G = mA.run_dftd3('b3lyp', 'd2')
assert psi4.compare_values(ref_d2[1], E, 7, 'Ethene -D2')
mB = eneyne.extract_subsets(2)
E, G = mB.run_dftd3('b3lyp', 'd2')
assert psi4.compare_values(ref_d2[2], E, 7, 'Ethyne -D2')
#mBcp = eneyne.extract_subsets(2,1)
#E, G = mBcp.run_dftd3('b3lyp', 'd2')
#compare_values(ref_d2[2], E, 7, 'Ethyne(CP) -D2')
E, G = eneyne.run_dftd3('b3lyp', 'd3zero')
assert psi4.compare_values(ref_d3zero[0], E, 7, 'Ethene-Ethyne -D3 (zero)')
mA = eneyne.extract_subsets(1)
E, G = mA.run_dftd3('b3lyp', 'd3zero')
assert psi4.compare_values(ref_d3zero[1], E, 7, 'Ethene -D3 (zero)')
mB = eneyne.extract_subsets(2)
E, G = mB.run_dftd3('b3lyp', 'd3zero')
assert psi4.compare_values(ref_d3zero[2], E, 7, 'Ethyne -D3 (zero)')
E, G = eneyne.run_dftd3('b3lyp', 'd3bj')
assert psi4.compare_values(ref_d3bj[0], E, 7, 'Ethene-Ethyne -D3 (bj)')
mA = eneyne.extract_subsets(1)
E, G = mA.run_dftd3('b3lyp', 'd3bj')
assert psi4.compare_values(ref_d3bj[1], E, 7, 'Ethene -D3 (bj)')
mB = eneyne.extract_subsets(2)
E, G = mB.run_dftd3('b3lyp', 'd3bj')
assert psi4.compare_values(ref_d3bj[2], E, 7, 'Ethyne -D3 (bj)')
E, G = eneyne.run_dftd3('b3lyp', 'd3')
assert psi4.compare_values(ref_d3zero[0], E, 7, 'Ethene-Ethyne -D3 (alias)')
E, G = eneyne.run_dftd3('b3lyp', 'd')
assert psi4.compare_values(ref_d2[0], E, 7, 'Ethene-Ethyne -D (alias)')
E, G = eneyne.run_dftd3('b3lyp', 'd2')
assert psi4.compare_values(ref_d2[0], E, 7, 'Ethene-Ethyne -D2 (alias)')
psi4.set_options({'basis': 'sto-3g',
'scf_type': 'df',
'dft_radial_points': 50, # use really bad grid for speed since all we want is the -D value
'dft_spherical_points': 110,
#'scf print': 3, # will print dftd3 program output to psi4 output file
})
print(' -D correction from C-side')
psi4.activate(mA)
#psi4.energy('b3lyp-d2', engine='libdisp')
#assert psi4.compare_values(ref_d2[1], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D2 (calling psi4 Disp class)')
#psi4.energy('b3lyp-d2')
#assert psi4.compare_values(ref_d2[1], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D2 (calling dftd3 -old)')
#psi4.energy('b3lyp-d3zero')
#assert psi4.compare_values(ref_d3zero[1], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D3 (calling dftd3 -zero)')
psi4.energy('b3lyp-d3bj')
assert psi4.compare_values(ref_d3bj[1], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D3 (calling dftd3 -bj)')
psi4.energy('b3lyp-d2', engine='libdisp')
assert psi4.compare_values(ref_d2[1], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D2 (alias)')
#psi4.energy('b3lyp-d3')
#assert psi4.compare_values(ref_d3zero[1], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D3 (alias)')
#psi4.energy('b3lyp-d')
#assert psi4.compare_values(ref_d2[1], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D (alias)')
psi4.energy('wb97x-d')
assert psi4.compare_values(-0.000834247063, psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene wb97x-d (chg)')
print(' non-default -D correction from C-side')
psi4.activate(mB)
#psi4.set_options({'dft_dispersion_parameters': [0.75]})
#psi4.energy('b3lyp-d2', engine='libdisp')
#assert psi4.compare_values(ref_pbe_d2[2], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D2 (calling psi4 Disp class)')
#psi4.set_options({'dft_dispersion_parameters': [0.75, 20.0]})
#psi4.energy('b3lyp-d2')
#assert psi4.compare_values(ref_pbe_d2[2], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D2 (calling dftd3 -old)')
#psi4.set_options({'dft_dispersion_parameters': [1.0, 0.722, 1.217, 14.0]})
#psi4.energy('b3lyp-d3zero')
#assert psi4.compare_values(ref_pbe_d3zero[2], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D3 (calling dftd3 -zero)')
psi4.set_options({'dft_dispersion_parameters': [1.000, 0.7875, 0.4289, 4.4407]})
psi4.energy('b3lyp-d3bj')
assert psi4.compare_values(ref_pbe_d3bj[2], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D3 (calling dftd3 -bj)')
psi4.set_options({'dft_dispersion_parameters': [0.75]})
psi4.energy('b3lyp-d2', engine='dftd3')
assert psi4.compare_values(ref_pbe_d2[2], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D2 (alias)')
psi4.set_options({'dft_dispersion_parameters': [1.0, 0.722, 1.217, 14.0]})
psi4.energy('b3lyp-d3')
assert psi4.compare_values(ref_pbe_d3zero[2], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D3 (alias)')
psi4.set_options({'dft_dispersion_parameters': [0.75]})
psi4.energy('b3lyp-d')
assert psi4.compare_values(ref_pbe_d2[2], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D (alias)')
psi4.activate(mA)
psi4.set_options({'dft_dispersion_parameters': [1.0]})
psi4.energy('wb97x-d')
assert psi4.compare_values(-0.000834247063, psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene wb97x-d (chg)')
print(' non-default -D correction from Py-side')
eneyne.update_geometry()
eneyne.run_dftd3('b3lyp', 'd2', {'s6': 0.75})
assert psi4.compare_values(ref_pbe_d2[0], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene-Ethyne -D2')
mA = eneyne.extract_subsets(1)
mA.run_dftd3('b3lyp', 'd2', {'s6': 0.75})
assert psi4.compare_values(ref_pbe_d2[1], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D2')
mB = eneyne.extract_subsets(2)
mB.run_dftd3('b3lyp', 'd2', {'s6': 0.75})
assert psi4.compare_values(ref_pbe_d2[2], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethyne -D2')
eneyne.run_dftd3('b3lyp', 'd3zero', {'s6': 1.0, 's8': 0.722, 'sr6': 1.217, 'alpha6': 14.0})
assert psi4.compare_values(ref_pbe_d3zero[0], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene-Ethyne -D3 (zero)')
mA = eneyne.extract_subsets(1)
mA.run_dftd3('b3lyp', 'd3zero', {'s6': 1.0, 's8': 0.722, 'sr6': 1.217, 'alpha6': 14.0})
assert psi4.compare_values(ref_pbe_d3zero[1], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D3 (zero)')
mB = eneyne.extract_subsets(2)
mB.run_dftd3('b3lyp', 'd3zero', {'s6': 1.0, 's8': 0.722, 'sr6': 1.217, 'alpha6': 14.0})
assert psi4.compare_values(ref_pbe_d3zero[2], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethyne -D3 (zero)')
eneyne.run_dftd3('b3lyp', 'd3bj', {'s6': 1.000, 's8': 0.7875, 'a1': 0.4289, 'a2': 4.4407})
assert psi4.compare_values(ref_pbe_d3bj[0], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene-Ethyne -D3 (bj)')
mA = eneyne.extract_subsets(1)
mA.run_dftd3('b3lyp', 'd3bj', {'s6': 1.000, 's8': 0.7875, 'a1': 0.4289, 'a2': 4.4407})
assert psi4.compare_values(ref_pbe_d3bj[1], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D3 (bj)')
mB = eneyne.extract_subsets(2)
mB.run_dftd3('b3lyp', 'd3bj', {'s6': 1.000, 's8': 0.7875, 'a1': 0.4289, 'a2': 4.4407})
assert psi4.compare_values(ref_pbe_d3bj[2], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethyne -D3 (bj)')
eneyne.run_dftd3('b3lyp', 'd3', {'s6': 1.0, 's8': 0.722, 'sr6': 1.217, 'alpha6': 14.0})
assert psi4.compare_values(ref_pbe_d3zero[0], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene-Ethyne -D3 (alias)')
eneyne.run_dftd3('b3lyp', 'd', {'s6': 0.75})
assert psi4.compare_values(ref_pbe_d2[0], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene-Ethyne -D (alias)')
eneyne.run_dftd3('b3lyp', 'd2', {'s6': 0.75})
assert psi4.compare_values(ref_pbe_d2[0], psi4.variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene-Ethyne -D2 (alias)')