def test_mrcc():
"""mrcc/ccsdt"""
#! CCSDT cc-pVDZ energy for the H2O molecule using MRCC
h2o = psi4.geometry("""
o
h 1 1.0
h 1 1.0 2 104.5
""")
psi4.set_options({'basis': 'cc-pvdz', 'freeze_core': 'true'})
psi4.energy('mrccsdt')
assert psi4.compare_values(8.801465529972,
psi4.variable("NUCLEAR REPULSION ENERGY"), 6,
'NRE')
assert psi4.compare_values(-76.021418445155,
psi4.variable("SCF TOTAL ENERGY"), 6, 'SCF')
assert psi4.compare_values(-0.204692406830,
psi4.variable("MP2 CORRELATION ENERGY"), 6,
'MP2 correlation')
assert psi4.compare_values(-0.217715210258,
psi4.variable("CCSDT CORRELATION ENERGY"), 6,
'CCSDT correlation')
assert psi4.compare_values(-76.239133655413,
psi4.variable("CURRENT ENERGY"), 6, 'CCSDT')
def test_psi4_cc():
"""cc1"""
#! RHF-CCSD 6-31G** all-electron optimization of the H2O molecule
jatin = """{"id": null, "schema_name": "qcschema_input", "schema_version": 1, "molecule": {"schema_name": "qcschema_molecule", "schema_version": 2, "validated": true, "symbols": ["O", "H", "H"], "geometry": [0.0, 0.0, -0.12770502190246294, 0.0, -1.4345476276003923, 1.013385685261514, 0.0, 1.4345476276003923, 1.013385685261514], "name": "H2O", "molecular_charge": 0.0, "molecular_multiplicity": 1, "masses": [15.99491461957, 1.00782503223, 1.00782503223], "real": [true, true, true], "atom_labels": ["", "", ""], "atomic_numbers": [8, 1, 1], "mass_numbers": [16, 1, 1], "fragments": [[0, 1, 2]], "fragment_charges": [0.0], "fragment_multiplicities": [1], "fix_com": false, "fix_orientation": false, "provenance": {"creator": "QCElemental", "version": "v0.17.0+7.gf55d5ac.dirty", "routine": "qcelemental.molparse.from_string"}}, "driver": "optimize", "model": {"method": "ccsd", "basis": "6-31G**"}, "keywords": {}, "protocols": {}, "extras": {"wfn_qcvars_only": true}, "provenance": {"creator": "Psi4", "version": "1.4a2.dev1087", "routine": "psi4.driver.p4util.procutil"}}"""
atres = psi4.schema_wrapper.run_qcschema(json.loads(jatin))
if "qcengine.exceptions.InputError" in atres.error.error_message:
pytest.xfail("no AtomicInput optimization")
# psi4.optimize('ccsd')
refnuc = 9.1654609427539
refscf = -76.0229427274435
refccsd = -0.20823570806196
reftotal = -76.2311784355056
assert psi4.compare_values(refnuc,
atres.properties.nuclear_repulsion_energy, 3,
"Nuclear repulsion energy")
assert psi4.compare_values(refscf,
atres.extras["qcvars"]["SCF total energy"], 5,
"SCF energy")
assert psi4.compare_values(refccsd,
psi4.variable("CCSD correlation energy"), 4,
"CCSD contribution")
assert psi4.compare_values(reftotal, psi4.variable("Current energy"), 7,
"Total energy")
def test_psi4_cc():
"""cc1"""
#! RHF-CCSD 6-31G** all-electron optimization of the H2O molecule
psi4.core.clean()
h2o = psi4.geometry("""
O
H 1 0.97
H 1 0.97 2 103.0
""")
psi4.set_options({"basis": '6-31G**'})
psi4.optimize('ccsd')
refnuc = 9.1654609427539
refscf = -76.0229427274435
refccsd = -0.20823570806196
reftotal = -76.2311784355056
assert psi4.compare_values(refnuc, h2o.nuclear_repulsion_energy(), 3,
"Nuclear repulsion energy")
assert psi4.compare_values(refscf, psi4.variable("SCF total energy"), 5,
"SCF energy")
assert psi4.compare_values(refccsd,
psi4.variable("CCSD correlation energy"), 4,
"CCSD contribution")
assert psi4.compare_values(reftotal, psi4.variable("Current energy"), 7,
"Total energy")
def test_psi4_sapt():
"""sapt1"""
#! SAPT0 cc-pVDZ computation of the ethene-ethyne interaction energy, using the cc-pVDZ-JKFIT RI basis for SCF
#! and cc-pVDZ-RI for SAPT. Monomer geometries are specified using Cartesian coordinates.
Eref = [
85.1890645313, -0.00359915058, 0.00362911158, -0.00083137117,
-0.00150542374, -0.00230683391
]
ethene_ethyne = psi4.geometry("""
0 1
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
--
0 1
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
units angstrom
""")
# this molecule will crash test if molecule passing broken
barrier = psi4.geometry("""
0 1
He
""")
psi4.set_options({
"basis": "cc-pvdz",
"df_basis_elst": "cc-pvdz-ri",
"guess": "sad",
"scf_type": "df",
"sad_print": 2,
"d_convergence": 11,
"puream": True,
"print": 1
})
psi4.energy('sapt0', molecule=ethene_ethyne)
Eelst = psi4.variable("SAPT ELST ENERGY")
Eexch = psi4.variable("SAPT EXCH ENERGY")
Eind = psi4.variable("SAPT IND ENERGY")
Edisp = psi4.variable("SAPT DISP ENERGY")
ET = psi4.variable("SAPT0 TOTAL ENERGY")
assert psi4.compare_values(Eref[0],
ethene_ethyne.nuclear_repulsion_energy(), 9,
"Nuclear Repulsion Energy")
assert psi4.compare_values(Eref[1], Eelst, 6, "SAPT0 Eelst")
assert psi4.compare_values(Eref[2], Eexch, 6, "SAPT0 Eexch")
assert psi4.compare_values(Eref[3], Eind, 6, "SAPT0 Eind")
assert psi4.compare_values(Eref[4], Edisp, 6, "SAPT0 Edisp")
assert psi4.compare_values(Eref[5], ET, 6, "SAPT0 Etotal")
def test_psi4_cc(datadir):
"""cc1"""
#! RHF-CCSD 6-31G** all-electron optimization of the H2O molecule
ref_file = datadir.join(f"jatin2.ref")
with open(ref_file) as f:
jatin = json.load(f)
atres = psi4.schema_wrapper.run_qcschema(jatin)
if "qcengine.exceptions.InputError" in atres.error.error_message:
pytest.xfail("no AtomicInput optimization")
# psi4.optimize('ccsd')
refnuc = 9.1654609427539
refscf = -76.0229427274435
refccsd = -0.20823570806196
reftotal = -76.2311784355056
assert psi4.compare_values(refnuc,
atres.properties.nuclear_repulsion_energy, 3,
"Nuclear repulsion energy")
assert psi4.compare_values(refscf,
atres.extras["qcvars"]["SCF total energy"], 5,
"SCF energy")
assert psi4.compare_values(refccsd,
psi4.variable("CCSD correlation energy"), 4,
"CCSD contribution")
assert psi4.compare_values(reftotal, psi4.variable("Current energy"), 7,
"Total energy")
def test_cancelled_qcvars():
err_substr = "no direct replacement"
with pytest.raises(psi4.UpgradeHelper) as e:
psi4.variable("scsn-mp2 same-spin correlation energy")
assert err_substr in str(e.value)
def disabled_test_forte():
"""aci-10: Perform aci on benzyne"""
import forte
refscf = -229.20378006852584
refaci = -229.359450812283
refacipt2 = -229.360444943286
mbenzyne = psi4.geometry("""
0 1
C 0.0000000000 -2.5451795941 0.0000000000
C 0.0000000000 2.5451795941 0.0000000000
C -2.2828001669 -1.3508352528 0.0000000000
C 2.2828001669 -1.3508352528 0.0000000000
C 2.2828001669 1.3508352528 0.0000000000
C -2.2828001669 1.3508352528 0.0000000000
H -4.0782187459 -2.3208602146 0.0000000000
H 4.0782187459 -2.3208602146 0.0000000000
H 4.0782187459 2.3208602146 0.0000000000
H -4.0782187459 2.3208602146 0.0000000000
units bohr
""")
psi4.set_options({
'basis': 'DZ',
'df_basis_mp2': 'cc-pvdz-ri',
'reference': 'uhf',
'scf_type': 'pk',
'd_convergence': 10,
'e_convergence': 12,
'guess': 'gwh',
})
psi4.set_module_options("FORTE", {
'root_sym': 0,
'frozen_docc': [2,1,0,0,0,0,2,1],
'restricted_docc': [3,2,0,0,0,0,2,3],
'active': [1,0,1,2,1,2,1,0],
'multiplicity': 1,
'aci_nroot': 1,
'job_type': 'aci',
'sigma': 0.001,
'aci_select_type': 'aimed_energy',
'aci_spin_projection': 1,
'aci_enforce_spin_complete': True,
'aci_add_aimed_degenerate': False,
'aci_project_out_spin_contaminants': False,
'diag_algorithm': 'full',
'aci_quiet_mode': True,
})
scf = psi4.energy('scf')
assert psi4.compare_values(refscf, scf,10,"SCF Energy")
psi4.energy('forte')
assert psi4.compare_values(refaci, psi4.variable("ACI ENERGY"),10,"ACI energy")
assert psi4.compare_values(refacipt2, psi4.variable("ACI+PT2 ENERGY"),8,"ACI+PT2 energy")
def test_psi4_sapt():
"""sapt1"""
#! SAPT0 cc-pVDZ computation of the ethene-ethyne interaction energy, using the cc-pVDZ-JKFIT RI basis for SCF
#! and cc-pVDZ-RI for SAPT. Monomer geometries are specified using Cartesian coordinates.
Eref = [ 85.1890645313, -0.00359915058, 0.00362911158,
-0.00083137117, -0.00150542374, -0.00230683391 ]
ethene_ethyne = psi4.geometry("""
0 1
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
--
0 1
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
units angstrom
""")
# this molecule will crash test if molecule passing broken
barrier = psi4.geometry("""
0 1
He
""")
psi4.set_options({
"basis": "cc-pvdz",
"guess": "sad",
"scf_type": "df",
"sad_print": 2,
"d_convergence": 11,
"puream": True,
"print": 1})
psi4.energy('sapt0', molecule=ethene_ethyne)
Eelst = psi4.variable("SAPT ELST ENERGY")
Eexch = psi4.variable("SAPT EXCH ENERGY")
Eind = psi4.variable("SAPT IND ENERGY")
Edisp = psi4.variable("SAPT DISP ENERGY")
ET = psi4.variable("SAPT0 TOTAL ENERGY")
assert psi4.compare_values(Eref[0], ethene_ethyne.nuclear_repulsion_energy(), 9, "Nuclear Repulsion Energy")
assert psi4.compare_values(Eref[1], Eelst, 6, "SAPT0 Eelst")
assert psi4.compare_values(Eref[2], Eexch, 6, "SAPT0 Eexch")
assert psi4.compare_values(Eref[3], Eind, 6, "SAPT0 Eind")
assert psi4.compare_values(Eref[4], Edisp, 6, "SAPT0 Edisp")
assert psi4.compare_values(Eref[5], ET, 6, "SAPT0 Etotal")
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', {
'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_renamed_qcvars():
psi4.set_variable("SCS(N)-MP2 TOTAL ENERGY", 3.3)
with pytest.warns(FutureWarning) as e:
ans = psi4.variable("SCSN-MP2 TOTAL ENERGY")
assert ans == 3.3
def test_dft_block_scheme_distantpoints():
"""Test removal of distant grid points. all DFT_BLOCK_SCHEME should give same results and number
of grid points."""
mol = psi4.geometry(
"""
0 1
O -1.551007 -0.114520 0.000000
H -1.934259 0.762503 0.000000
H -0.599677 0.040712 0.000000
no_com
no_reorient
symmetry c1
"""
)
psi4.set_options(
{
"BASIS": "sto-3g",
"maxiter": 1,
"FAIL_ON_MAXITER": False,
"DFT_PRUNING_SCHEME": "ROBUST",
"DFT_WEIGHTS_TOLERANCE": -1.0,
}
)
ref = {"True": 45929, "False": 46890}
YESNO = [True,False]
SCHEMES = ["OCTREE", "NAIVE", "ATOMIC"]
for YN in YESNO:
psi4.set_options({"DFT_REMOVE_DISTANT_POINTS":YN})
for S in SCHEMES:
psi4.set_options({"DFT_BLOCK_SCHEME": S})
e, wfn = psi4.energy("pbe", return_wfn=True)
P = psi4.variable("XC GRID TOTAL POINTS")
XC = wfn.variable("DFT XC ENERGY")
assert psi4.compare_integers(ref[f"{YN}"], P, f" scheme={S}; distant points={YN} ")
def test_dft_block_schemes(scheme):
"""all DFT_BLOCK_SCHEME should give same results and number
of grid points. Water dimer with ghost atoms"""
mol = psi4.geometry(
"""
0 1
O -1.490196515110 -0.043256842172 0.000000000000
H -1.845932568294 0.844902886698 0.000000000000
H -0.533258283804 0.073267064698 0.000000000000
@O 1.416663724802 0.038738966977 0.000000000000
@H 1.773104797767 -0.423233996755 0.760023878024
@H 1.773104797767 -0.423233996755 -0.760023878024
no_com
no_reorient
symmetry c1
"""
)
psi4.set_options(
{
"BASIS": "def2-SVPD",
"DFT_SPHERICAL_POINTS": 590,
"DFT_RADIAL_POINTS": 85,
"D_convergence": 1e-8,
"DFT_WEIGHTS_TOLERANCE": -1.0,
}
)
ref = {"XC GRID TOTAL POINTS": 300900, "DFT XC ENERGY": -9.218561399189895}
psi4.set_options({"DFT_BLOCK_SCHEME": scheme})
e, wfn = psi4.energy("pbe/def2-SVPD", return_wfn=True)
P = psi4.variable("XC GRID TOTAL POINTS")
XC = wfn.variable("DFT XC ENERGY")
assert psi4.compare_integers(ref["XC GRID TOTAL POINTS"], P, f" {scheme} GRID POINTS:")
assert psi4.compare_values(ref["DFT XC ENERGY"], XC, f" {scheme} XC 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_deprecated_component_dipole():
#with pytest.warns(FutureWarning) as e:
psi4.set_variable("current dipole x", 5)
with pytest.warns(FutureWarning) as e:
ans = psi4.variable("current dipole x")
assert ans == 5
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 test_mrcc():
"""mrcc/ccsdt"""
#! CCSDT cc-pVDZ energy for the H2O molecule using MRCC
h2o = psi4.geometry("""
o
h 1 1.0
h 1 1.0 2 104.5
""")
psi4.set_options({
'basis': 'cc-pvdz',
'freeze_core': 'true'})
psi4.energy('mrccsdt')
assert psi4.compare_values( 8.801465529972, psi4.variable("NUCLEAR REPULSION ENERGY"), 6, 'NRE')
assert psi4.compare_values(-76.021418445155, psi4.variable("SCF TOTAL ENERGY"), 6, 'SCF')
assert psi4.compare_values( -0.204692406830, psi4.variable("MP2 CORRELATION ENERGY") , 6, 'MP2 correlation')
assert psi4.compare_values( -0.217715210258, psi4.variable("CCSDT CORRELATION ENERGY"), 6, 'CCSDT correlation')
assert psi4.compare_values(-76.239133655413, psi4.variable("CURRENT ENERGY"), 6, 'CCSDT')
def test_cfour():
"""cfour/sp-rhf-ccsd_t_"""
#! single-point CCSD(T)/qz2p on water
print(' <<< Translation of ZMAT to Psi4 format to Cfour >>>')
psi4.geometry("""
O
H 1 R
H 1 R 2 A
R=0.958
A=104.5
""")
psi4.set_options({
'cfour_CALC_level': 'CCSD(T)',
'cfour_BASIS': 'qz2p',
'cfour_SCF_CONV': 12,
'cfour_CC_CONV': 12,
})
psi4.energy('cfour')
assert psi4.compare_values(-76.062748460117, psi4.variable('scf total energy'), 6, 'SCF')
assert psi4.compare_values(-76.332940127333, psi4.variable('mp2 total energy'), 6, 'MP2')
assert psi4.compare_values(-76.338453951890, psi4.variable('ccsd total energy'), 6, 'CCSD')
assert psi4.compare_values(-0.275705491773, psi4.variable('ccsd correlation energy'), 6, 'CCSD corl')
assert psi4.compare_values(-76.345717549886, psi4.variable('ccsd(t) total energy'), 6, 'CCSD(T)')
assert psi4.compare_values(-0.282969089769, psi4.variable('ccsd(t) correlation energy'), 6, 'CCSD(T) corl')
def test_snsmp2():
"""snsmp2/he-he"""
HeHe = psi4.geometry("""
0 1
He 0 0 0
--
He 2 0 0
""")
e = psi4.energy('sns-mp2')
assert psi4.compare_values(0.00176708227, psi4.variable('SNS-MP2 TOTAL ENERGY'), 5, "SNS-MP2 IE [Eh]")
def test_allen_focal_point():
be = psi4.geometry("Be")
psi4.energy("allen_focal_point", scf_basis="cc-pV[TQ5]Z", corl_basis="cc-pV[Q5]Z", delta_basis="cc-pV[Q5]Z", delta2_basis="cc-pV[Q5]Z")
psi4.core.print_variables()
assert compare_values(-14.57305004, psi4.variable("CBS REFERENCE ENERGY"), 7, "scf tq5")
#ADD VAR assert compare_values(-0.06148737, psi4.variable("CBS CORL ENERGY"), 7, "corl mp2 q5")
assert compare_values(-0.01767880, psi4.variable("CBS DELTA1 TOTAL ENERGY"), 7, "delta1 ccsd q5")
assert compare_values(-0.00063008, psi4.variable("CBS DELTA2 TOTAL ENERGY"), 7, "delta2 (t) q5")
assert compare_values(-0.00001090, psi4.variable("CBS DELTA3 TOTAL ENERGY"), 7, "delta3 t 3")
assert compare_values(-0.00000205, psi4.variable("CBS DELTA4 TOTAL ENERGY"), 7, "delta4 (q) 2")
assert compare_values(-14.65285924, psi4.variable("CBS TOTAL ENERGY"), 7, "cbs")
assert compare_values(-14.65285924, psi4.variable("CURRENT ENERGY"), 7, "current")
assert compare(5, psi4.variable("CBS NUMBER"), "cbs no")
def test_spacious_option():
"""tu1-h2o-energy"""
#! Sample HF/cc-pVDZ H2O computation
h2o = psi4.geometry("""
O
H 1 0.96
H 1 0.96 2 104.5
""")
psi4.set_options({' basis ': "cc-pVDZ"})
psi4.energy('scf')
assert psi4.compare_values(-76.0266327341067125, psi4.variable('SCF TOTAL ENERGY'), 6, 'SCF energy')
def test_psi4_basic():
"""tu1-h2o-energy"""
#! Sample HF/cc-pVDZ H2O computation
h2o = psi4.geometry("""
O
H 1 0.96
H 1 0.96 2 104.5
""")
psi4.set_options({'basis': "cc-pVDZ"})
psi4.energy('scf')
assert psi4.compare_values(-76.0266327341067125, psi4.variable('SCF TOTAL ENERGY'), 6, 'SCF energy')
def test_restart_scf_orbital_file():
"""wfn serialization"""
h2o = psi4.geometry("""
O
H 1 0.96
H 1 0.96 2 104.5
""")
psi4.set_options({'basis': "cc-pVDZ"})
_, scf_wfn = psi4.energy('scf', return_wfn=True, write_orbitals='my_mos')
psi4.core.clean()
psi4.set_options({'maxiter': 1})
scf_wfn = psi4.energy('scf', restart_file='my_mos')
assert psi4.compare_values(-76.0266327341067125, psi4.variable('SCF TOTAL ENERGY'), 6, 'SCF energy')
def test_psi4_cc():
"""cc1"""
#! RHF-CCSD 6-31G** all-electron optimization of the H2O molecule
psi4.core.clean()
h2o = psi4.geometry("""
O
H 1 0.97
H 1 0.97 2 103.0
""")
psi4.set_options({"basis": '6-31G**'})
psi4.optimize('ccsd')
refnuc = 9.1654609427539
refscf = -76.0229427274435
refccsd = -0.20823570806196
reftotal = -76.2311784355056
assert psi4.compare_values(refnuc, h2o.nuclear_repulsion_energy(), 3, "Nuclear repulsion energy")
assert psi4.compare_values(refscf, psi4.variable("SCF total energy"), 5, "SCF energy")
assert psi4.compare_values(refccsd, psi4.variable("CCSD correlation energy"), 4, "CCSD contribution")
assert psi4.compare_values(reftotal, psi4.variable("Current energy"), 7, "Total energy")
def callback(self, pos, **kwargs):
"""Initialize psi with new positions and calculate force.
Arguments:
- pos: positions of the atoms as array.
"""
self.initial_molecule.set_geometry(psi4.core.Matrix.from_array(pos))
self.calculate_gradient(self.LOT, pos=pos, **kwargs)
self._potential = psi4.variable('CURRENT ENERGY')
self._force = -np.array(self.grd)
self._vir = np.array([[0.0,0.0,0.0],[0.0,0.0,0.0],[0.0,0.0,0.0]])
return self._force, np.float64(self._potential)
def test_restart_scf_serial_wfn():
"""scf restart from wfn file"""
h2o = psi4.geometry("""
O
H 1 0.96
H 1 0.96 2 104.5
""")
psi4.set_options({'basis': "cc-pVDZ"})
_, scf_wfn = psi4.energy('scf', return_wfn=True)
scf_wfn.to_file('pytest_wfn')
psi4.core.clean()
psi4.set_options({'maxiter': 1})
psi4.energy('scf', restart_file='pytest_wfn')
psi4.core.clean()
assert psi4.compare_values(-76.0266327341067125, psi4.variable('SCF TOTAL ENERGY'), 6, 'SCF energy')
def test_chemps2():
"""chemps2/scf-n2"""
#! dmrg-scf on N2
N2 = psi4.geometry("""
N 0.0000 0.0000 0.0000
N 0.0000 0.0000 2.1180
units au
""")
psi4.set_options({
'basis': 'cc-pVDZ',
'reference': 'rhf',
'e_convergence': 1e-12,
'd_convergence': 1e-12,
'dmrg_irrep': 0,
'dmrg_multiplicity': 1,
'restricted_docc': [ 1 , 0 , 0 , 0 , 0 , 1 , 0 , 0 ],
'active': [ 2 , 0 , 1 , 1 , 0 , 2 , 1 , 1 ],
'dmrg_sweep_states': [ 500, 1000, 1000 ],
'dmrg_sweep_energy_conv': [ 1e-10, 1e-10, 1e-10 ],
'dmrg_sweep_dvdson_rtol': [ 1e-4, 1e-6, 1e-8 ],
'dmrg_sweep_max_sweeps': [ 5, 5, 10 ],
'dmrg_sweep_noise_prefac': [ 0.05, 0.05, 0.0 ],
'dmrg_print_corr': True,
'dmrg_mps_write': False,
'dmrg_unitary_write': True,
'dmrg_diis': True,
'dmrg_scf_diis_thr': 1e-2,
'dmrg_diis_write': True,
'dmrg_excitation': 0, # Ground state
'dmrg_scf_state_avg': False,
'dmrg_scf_active_space': 'NO', # INPUT; NO; LOC
'dmrg_local_init': False,
})
psi4.energy("dmrg-scf")
ref_energy = -109.1035023353
assert psi4.compare_values(ref_energy, psi4.variable("CURRENT ENERGY"), 6, "DMRG Energy")
def get_grad(self, mol):
self.update_coor(mol)
g, wfn = psi4.gradient(self.met, return_wfn=True)
mol.func += psi4.variable('CURRENT ENERGY') * self._ce
g = sum(g.to_array().tolist(), [])
qm3.engines.LA_gradient(self.vla, g)
for i in range(len(self.sel)):
i3 = i * 3
for j in [0, 1, 2]:
mol.grad[3 * self.sel[i] + j] += g[i3 + j] * self._cg
if (len(self.nbn) > 0):
ef = psi4.core.OEProp(wfn)
ef.add("GRID_FIELD")
ef.compute()
efx = ef.Exvals()
efy = ef.Eyvals()
efz = ef.Ezvals()
for i in range(len(self.nbn)):
mol.grad[3 * self.nbn[i]] -= self._cg * mol.chrg[
self.nbn[i]] * efx[i]
mol.grad[3 * self.nbn[i] +
1] -= self._cg * mol.chrg[self.nbn[i]] * efy[i]
mol.grad[3 * self.nbn[i] +
2] -= self._cg * mol.chrg[self.nbn[i]] * efz[i]
_, wfn = psi4.energy('ccsd', return_wfn=True, molecule=Ne)
amps = wfn.get_amplitudes()
TIjAb = amps['tIjAb'].to_array()
TIA = amps['tIA'].to_array()
tau_IjAb = TIjAb + np.einsum("ia,jb->ijab", TIA, TIA)
mints = psi4.core.MintsHelper(wfn.basisset())
D = mints.mo_eri(
wfn.Ca_subset("AO", "OCC"), wfn.Ca_subset("AO", "VIR"), wfn.Ca_subset("AO", "OCC"),
wfn.Ca_subset("AO", "VIR")).to_array()
D = D.swapaxes(1, 2)
RHF_ccsd_corr_e = 2 * np.einsum("ijab,ijab->", tau_IjAb, D) - np.einsum("ijab,ijba->", tau_IjAb, D)
psi4.compare_values(RHF_ccsd_corr_e, psi4.variable('CCSD CORRELATION ENERGY'), 8, "RHF CCSD CORRELATION ENERGY")
# END RHF
psi4.core.clean()
# UHF
psi4.set_options({
'basis': 'cc-pvdz',
'freeze_core': 'false',
'reference': 'UHF',
})
_, wfn = psi4.energy('ccsd', return_wfn=True, molecule=Ne)
amps = wfn.get_amplitudes()
def test_deprecated_component_dipole():
with pytest.raises(psi4.UpgradeHelper) as e:
psi4.variable("current dipole x")
R["vv"],
t2,
optimize=True)
r2 += temp + temp.transpose((1, 0, 3, 2)) - temp.transpose(
(0, 1, 3, 2)) - temp.transpose((1, 0, 2, 3))
### One Electron Terms. For canonical orbitals, this will reduce to -t2, after dividing by D
temp = -np.einsum("Ii, iJAB -> IJAB", F["oo"], t2, optimize=True)
r2 += temp - temp.transpose((1, 0, 2, 3))
temp = +np.einsum("aA, IJaB -> IJAB", F["vv"], t2, optimize=True)
r2 += temp - temp.transpose((0, 1, 3, 2))
### Step
t2 += r2 / D
t2 = dsd.diis(r2, t2)
r_norm = np.linalg.norm(r2)
Elccd = 0.5 * np.einsum(
"iaq, jbq, ijab", R["ov"], R["ov"], t2, optimize=True)
print(f"{i:3d} E={Elccd:3.10f} R = {r_norm:0.8f}")
if r_norm < float(f"1e-{target_convergence}"):
break
else:
raise Exception("Equations did not converge.")
if compare_psi4:
wfn = psi4.energy("lccd", return_wfn=True)[1]
# Change to wfn.variable when DFOCC variables are available on the wfn.
psi4.compare_values(psi4.variable("CURRENT CORRELATION ENERGY"), Elccd,
target_convergence, "LCCD Energy")
AllChem.EmbedMolecule(mol, AllChem.ETKDGv2())
AllChem.UFFOptimizeMolecule(mol)
conf = mol.GetConformer(-1)
xyz = '0 1'
for atom, (x, y, z) in zip(mol.GetAtoms(), conf.GetPositions()):
xyz += '\n'
xyz += '{}\t{}\t{}\t{}'.format(atom.GetSymbol(), x, y, z)
return xyz
# 入力する分子（thiacloprid）
smiles = 'C1CSC(=NC#N)N1CC2=CN=C(C=C2)Cl'
psi4.set_output_file('04_thiacloprid.txt')
dinotefuran = psi4.geometry(smi2xyz(smiles))
_, wfn_dtf = psi4.optimize('B3LYP/6-31G*',
molecule=dinotefuran,
return_wfn=True)
rdkit_dinotefuran = Chem.AddHs(Chem.MolFromSmiles(smiles))
## 双極子モーメントの計算
psi4.oeprop(wfn_dtf, 'DIPOLE', titile='dipole')
dipole_x, dipole_y, dipole_z = psi4.variable('SCF DIPOLE X'), psi4.variable(
'SCF DIPOLE Y'), psi4.variable('SCF DIPOLE Z')
dipole_moment = np.sqrt(dipole_x**2 + dipole_y**2 + dipole_z**2)
#print(round(dipole_moment,3),'D')
def test_psi4_scfproperty():
"""scf-property"""
#! UFH and B3LYP cc-pVQZ properties for the CH2 molecule.
ref_hf_di_au = np.array([0.0, 0.0, 0.22531665104559076])
ref_hf_quad_au = np.array([[-5.69804565317, 0.0, 0.0],
[0.0, -4.53353128969, 0.0],
[0.0, 0.0, -5.25978856037]])
ref_b3lyp_di_au = np.array([0.0, 0.0, 0.252480541747])
ref_b3lyp_quad_au = np.array([[-5.66266837697, 0.0, 0.0],
[0.0, -4.46523692003, 0.0],
[0.0, 0.0, -5.22054902407]])
with open('grid.dat', 'w') as handle:
handle.write("""\
0.0 0.0 0.0
1.1 1.3 1.4
""")
ch2 = psi4.geometry("""
0 3
c
h 1 b1
h 1 b1 2 a1
b1 = 1.0
a1 = 125.0
""")
# Get a reasonable guess, to save some iterations
psi4.set_options({
"scf_type": "pk",
"basis": "6-31G**",
"e_convergence": 8,
"docc": [2, 0, 0, 1],
"socc": [1, 0, 1, 0],
"reference": "uhf"
})
ch2.update_geometry()
assert psi4.compare_values(6.6484189450, ch2.nuclear_repulsion_energy(), 9,
"Nuclear repulsion energy")
props = [
'DIPOLE', 'QUADRUPOLE', 'MULLIKEN_CHARGES', 'LOWDIN_CHARGES',
'WIBERG_LOWDIN_INDICES', 'MAYER_INDICES', 'MAYER_INDICES',
'MO_EXTENTS', 'GRID_FIELD', 'GRID_ESP', 'ESP_AT_NUCLEI',
'MULTIPOLE(5)', 'NO_OCCUPATIONS'
]
psi4.properties('scf', properties=props)
assert psi4.compare_values(-38.91591819679808,
psi4.variable("CURRENT ENERGY"), 6,
"SCF energy")
assert psi4.compare_values(ref_hf_di_au, psi4.variable('SCF DIPOLE'), 4,
"SCF DIPOLE")
assert psi4.compare_values(ref_hf_quad_au, psi4.variable('SCF QUADRUPOLE'),
4, "SCF QUADRUPOLE")
psi4.properties('B3LYP', properties=props)
assert psi4.compare_values(psi4.variable('CURRENT ENERGY'),
-39.14134740550916, 6, "B3LYP energy")
assert psi4.compare_values(ref_b3lyp_di_au, psi4.variable('B3LYP DIPOLE'),
4, "B3LYP DIPOLE")
assert psi4.compare_values(ref_b3lyp_quad_au,
psi4.variable('B3LYP QUADRUPOLE'), 4,
"B3LYP QUADRUPOLE")
1.0042710000 1.0000000000
S 1 1.00
0.3006860000 1.0000000000
S 1 1.00
0.0900300000 1.0000000000
P 4 1.00
34.8564630000 0.0156480000
7.8431310000 0.0981970000
2.3062490000 0.3077680000
0.7231640000 0.4924700000
P 1 1.00
0.2148820000 1.0000000000
P 1 1.00
0.0638500000 1.0000000000
D 2 1.00
2.3062000000 0.2027000000
0.7232000000 0.5791000000
D 2 1.00
0.2149000000 0.7854500000
0.0639000000 0.5338700000
****
""")
ccsd_e, wfn = psi4.properties('ccsd', properties=['dipole'], return_wfn=True)
psi4.oeprop(wfn, "DIPOLE", "QUADRUPOLE", title="(OEPROP)CC")
psi4.compare_values(ref_di_au, psi4.variable('(OEPROP)CC DIPOLE'), 4,
"CC DIPOLE") #TEST
psi4.compare_values(ref_quad_au, psi4.variable('(OEPROP)CC QUADRUPOLE'), 4,
"CC QUADRUPOLE") #TEST
def test_psi4_scfproperty():
"""scf-property"""
#! UFH and B3LYP cc-pVQZ properties for the CH2 molecule.
with open('grid.dat', 'w') as handle:
handle.write("""\
0.0 0.0 0.0
1.1 1.3 1.4
""")
ch2 = psi4.geometry("""
0 3
c
h 1 b1
h 1 b1 2 a1
b1 = 1.0
a1 = 125.0
""")
# Get a reasonable guess, to save some iterations
psi4.set_options({
"scf_type": "pk",
"basis": "6-31G**",
"e_convergence": 8,
"docc": [2, 0, 0, 1],
"socc": [1, 0, 1, 0],
"reference": "uhf"})
ch2.update_geometry()
assert psi4.compare_values(6.6484189450, ch2.nuclear_repulsion_energy(), 9, "Nuclear repulsion energy")
props = ['DIPOLE', 'QUADRUPOLE', 'MULLIKEN_CHARGES', 'LOWDIN_CHARGES',
'WIBERG_LOWDIN_INDICES', 'MAYER_INDICES', 'MAYER_INDICES',
'MO_EXTENTS', 'GRID_FIELD', 'GRID_ESP', 'ESP_AT_NUCLEI',
'MULTIPOLE(5)', 'NO_OCCUPATIONS']
psi4.properties('scf', properties=props)
assert psi4.compare_values(psi4.variable("CURRENT ENERGY"), -38.91591819679808, 6, "SCF energy")
assert psi4.compare_values(psi4.variable('SCF DIPOLE X'), 0.000000000000, 4, "SCF DIPOLE X")
assert psi4.compare_values(psi4.variable('SCF DIPOLE Y'), 0.000000000000, 4, "SCF DIPOLE Y")
assert psi4.compare_values(psi4.variable('SCF DIPOLE Z'), 0.572697798348, 4, "SCF DIPOLE Z")
assert psi4.compare_values(psi4.variable('SCF QUADRUPOLE XX'), -7.664066833060, 4, "SCF QUADRUPOLE XX")
assert psi4.compare_values(psi4.variable('SCF QUADRUPOLE YY'), -6.097755074075, 4, "SCF QUADRUPOLE YY")
assert psi4.compare_values(psi4.variable('SCF QUADRUPOLE ZZ'), -7.074596012050, 4, "SCF QUADRUPOLE ZZ")
assert psi4.compare_values(psi4.variable('SCF QUADRUPOLE XY'), 0.000000000000, 4, "SCF QUADRUPOLE XY")
assert psi4.compare_values(psi4.variable('SCF QUADRUPOLE XZ'), 0.000000000000, 4, "SCF QUADRUPOLE XZ")
assert psi4.compare_values(psi4.variable('SCF QUADRUPOLE YZ'), 0.000000000000, 4, "SCF QUADRUPOLE YZ")
psi4.properties('B3LYP', properties=props)
assert psi4.compare_values(psi4.variable('CURRENT ENERGY'), -39.14134740550916, 6, "B3LYP energy")
assert psi4.compare_values(psi4.variable('B3LYP DIPOLE X'), 0.000000000000, 4, "B3LYP DIPOLE X")
assert psi4.compare_values(psi4.variable('B3LYP DIPOLE Y'), -0.000000000000, 4, "B3LYP DIPOLE Y")
assert psi4.compare_values(psi4.variable('B3LYP DIPOLE Z'), 0.641741521158, 4, "B3LYP DIPOLE Z")
assert psi4.compare_values(psi4.variable('B3LYP QUADRUPOLE XX'), -7.616483183211, 4, "B3LYP QUADRUPOLE XX")
assert psi4.compare_values(psi4.variable('B3LYP QUADRUPOLE YY'), -6.005896804551, 4, "B3LYP QUADRUPOLE YY")
assert psi4.compare_values(psi4.variable('B3LYP QUADRUPOLE ZZ'), -7.021817489904, 4, "B3LYP QUADRUPOLE ZZ")
assert psi4.compare_values(psi4.variable('B3LYP QUADRUPOLE XY'), 0.000000000000, 4, "B3LYP QUADRUPOLE XY")
assert psi4.compare_values(psi4.variable('B3LYP QUADRUPOLE XZ'), 0.000000000000, 4, "B3LYP QUADRUPOLE XZ")
assert psi4.compare_values(psi4.variable('B3LYP QUADRUPOLE YZ'), -0.000000000000, 4, "B3LYP QUADRUPOLE YZ")
def test_pcmsolver():
"""pcmsolver/scf"""
#! pcm
nucenergy = 12.0367196636183458
polenergy = -0.0053060443528559
totalenergy = -55.4559426361734040
NH3 = psi4.geometry("""
symmetry c1
N -0.0000000001 -0.1040380466 0.0000000000
H -0.9015844116 0.4818470201 -1.5615900098
H -0.9015844116 0.4818470201 1.5615900098
H 1.8031688251 0.4818470204 0.0000000000
units bohr
no_reorient
no_com
""")
psi4.set_options({
'basis': 'STO-3G',
'scf_type': 'pk',
'pcm': True,
'pcm_scf_type': 'total',
})
psi4.pcm_helper("""
Units = Angstrom
Medium {
SolverType = IEFPCM
Solvent = Water
}
Cavity {
RadiiSet = UFF
Type = GePol
Scaling = False
Area = 0.3
Mode = Implicit
}
""")
print('RHF-PCM, total algorithm')
energy_scf1, wfn1 = psi4.energy('scf', return_wfn=True)
assert psi4.compare_values(
nucenergy, NH3.nuclear_repulsion_energy(), 10,
"Nuclear repulsion energy (PCM, total algorithm)") #TEST
assert psi4.compare_values(totalenergy, energy_scf1, 10,
"Total energy (PCM, total algorithm)") #TEST
assert psi4.compare_values(
polenergy, wfn1.variable("PCM POLARIZATION ENERGY"), 6,
"Polarization energy (PCM, total algorithm)") #TEST
psi4.set_options({'pcm_scf_type': 'separate'})
print('RHF-PCM, separate algorithm')
energy_scf2 = psi4.energy('scf')
assert psi4.compare_values(totalenergy, energy_scf2, 10,
"Total energy (PCM, separate algorithm)")
assert psi4.compare_values(
polenergy, psi4.variable("PCM POLARIZATION ENERGY"), 6,
"Polarization energy (PCM, separate algorithm)")
# Now force use of UHF on NH3 to check sanity of the algorithm with PCM
psi4.set_options({'pcm_scf_type': 'total', 'reference': 'uhf'})
print('UHF-PCM, total algorithm')
energy_scf3 = psi4.energy('scf')
assert psi4.compare_values(totalenergy, energy_scf3, 10,
"Total energy (PCM, separate algorithm)")
assert psi4.compare_values(
polenergy, psi4.variable("PCM POLARIZATION ENERGY"), 6,
"Polarization energy (PCM, separate algorithm)")
psi4.set_options({'pcm_scf_type': 'total', 'reference': 'rohf'})
print('ROHF-PCM, total algorithm')
energy_scf4 = psi4.energy('scf')
assert psi4.compare_values(totalenergy, energy_scf4, 10,
"Total energy (PCM, separate algorithm)") #TEST
assert psi4.compare_values(
polenergy, psi4.variable("PCM POLARIZATION ENERGY"), 6,
"Polarization energy (PCM, separate algorithm)") #TEST
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_libefp():
"""libefp/qchem-qmefp-sp"""
#! EFP on mixed QM (water) and EFP (water + 2 * ammonia) system.
#! An EFP-only calc performed first to test vales against q-chem.
qmefp = psi4.geometry("""
# QM fragment
0 1
units bohr
O1 0.000000000000 0.000000000000 0.224348285559
H2 -1.423528800232 0.000000000000 -0.897393142237
H3 1.423528800232 0.000000000000 -0.897393142237
# EFP as EFP fragments
--
efp h2o -4.014110144291 2.316749370493 -1.801514729931 -2.902133 1.734999 -1.953647
--
efp NH3,1.972094713645,,3.599497221584 , 5.447701074734 -1.105309 2.033306 -1.488582
--
efp NH3 -7.876296399270 -1.854372164887 -2.414804197762 2.526442 1.658262 -2.742084
""")
# <<< EFP calc >>>
psi4.set_options({
'basis': '6-31g*',
'scf_type': 'pk',
'guess': 'core',
'df_scf_guess': False})
psi4.energy('efp')
assert psi4.compare_values( 9.1793879214, qmefp.nuclear_repulsion_energy(), 6, 'QM NRE')
assert psi4.compare_values(-0.0004901368, psi4.variable('efp elst energy'), 6, 'EFP-EFP Elst') # from q-chem
assert psi4.compare_values(-0.0003168768, psi4.variable('efp ind energy'), 6, 'EFP-EFP Indc')
assert psi4.compare_values(-0.0021985285, psi4.variable('efp disp energy'), 6, 'EFP-EFP Disp') # from q-chem
assert psi4.compare_values( 0.0056859871, psi4.variable('efp exch energy'), 6, 'EFP-EFP Exch') # from q-chem
assert psi4.compare_values( 0.0026804450, psi4.variable('efp total energy'), 6, 'EFP-EFP Totl')
assert psi4.compare_values( 0.0026804450, psi4.variable('current energy'), 6, 'Current')
psi4.core.print_variables()
psi4.core.clean()
psi4.core.clean_variables()
# <<< QM + EFP calc >>>
psi4.set_options({
'e_convergence': 12,
'd_convergence': 12})
psi4.energy('scf')
assert psi4.compare_values( 9.1793879214, qmefp.nuclear_repulsion_energy(), 6, 'QM NRE')
assert psi4.compare_values( 0.2622598847, psi4.variable('efp total energy') - psi4.variable('efp ind energy'), 6, 'EFP corr to SCF') # from q-chem
assert psi4.compare_values(-0.0117694790, psi4.variable('efp ind energy'), 6, 'QM-EFP Indc') # from q-chem
assert psi4.compare_values(-0.0021985285, psi4.variable('efp disp energy'), 6, 'EFP-EFP Disp') # from q-chem
assert psi4.compare_values( 0.0056859871, psi4.variable('efp exch energy'), 6, 'EFP-EFP Exch') # from q-chem
assert psi4.compare_values( 0.2504904057, psi4.variable('efp total energy'), 6, 'EFP-EFP Totl') # from q-chem
assert psi4.compare_values(-76.0139362744, psi4.variable('scf total energy'), 6, 'SCF') # from q-chem
psi4.core.print_variables()
def test_pcmsolver():
"""pcmsolver/scf"""
#! pcm
nucenergy = 12.0367196636183458
polenergy = -0.0053060443528559
totalenergy = -55.4559426361734040
NH3 = psi4.geometry("""
symmetry c1
N -0.0000000001 -0.1040380466 0.0000000000
H -0.9015844116 0.4818470201 -1.5615900098
H -0.9015844116 0.4818470201 1.5615900098
H 1.8031688251 0.4818470204 0.0000000000
units bohr
no_reorient
no_com
""")
psi4.set_options({
'basis': 'STO-3G',
'scf_type': 'pk',
'pcm': True,
'pcm_scf_type': 'total',
})
psi4.pcm_helper("""
Units = Angstrom
Medium {
SolverType = IEFPCM
Solvent = Water
}
Cavity {
RadiiSet = UFF
Type = GePol
Scaling = False
Area = 0.3
Mode = Implicit
}
""")
print('RHF-PCM, total algorithm')
energy_scf1, wfn1 = psi4.energy('scf', return_wfn=True)
assert psi4.compare_values(nucenergy, NH3.nuclear_repulsion_energy(), 10, "Nuclear repulsion energy (PCM, total algorithm)") #TEST
assert psi4.compare_values(totalenergy, energy_scf1, 10, "Total energy (PCM, total algorithm)") #TEST
assert psi4.compare_values(polenergy, wfn1.variable("PCM POLARIZATION ENERGY"), 6, "Polarization energy (PCM, total algorithm)") #TEST
psi4.set_options({'pcm_scf_type': 'separate'})
print('RHF-PCM, separate algorithm')
energy_scf2 = psi4.energy('scf')
assert psi4.compare_values(totalenergy, energy_scf2, 10, "Total energy (PCM, separate algorithm)")
assert psi4.compare_values(polenergy, psi4.variable("PCM POLARIZATION ENERGY"), 6, "Polarization energy (PCM, separate algorithm)")
# Now force use of UHF on NH3 to check sanity of the algorithm with PCM
psi4.set_options({'pcm_scf_type': 'total', 'reference': 'uhf'})
print('UHF-PCM, total algorithm')
energy_scf3 = psi4.energy('scf')
assert psi4.compare_values(totalenergy, energy_scf3, 10, "Total energy (PCM, separate algorithm)")
assert psi4.compare_values(polenergy, psi4.variable("PCM POLARIZATION ENERGY"), 6, "Polarization energy (PCM, separate algorithm)")
psi4.set_options({'pcm_scf_type': 'total', 'reference': 'rohf'})
print('ROHF-PCM, total algorithm')
energy_scf4 = psi4.energy('scf')
assert psi4.compare_values(totalenergy, energy_scf4, 10, "Total energy (PCM, separate algorithm)") #TEST
assert psi4.compare_values(polenergy, psi4.variable("PCM POLARIZATION ENERGY"), 6, "Polarization energy (PCM, separate algorithm)") #TEST
P 4 1.00
34.8564630000 0.0156480000
7.8431310000 0.0981970000
2.3062490000 0.3077680000
0.7231640000 0.4924700000
P 1 1.00
0.2148820000 1.0000000000
P 1 1.00
0.0638500000 1.0000000000
D 2 1.00
2.3062000000 0.2027000000
0.7232000000 0.5791000000
D 2 1.00
0.2149000000 0.7854500000
0.0639000000 0.5338700000
****
""")
ccsd_e, wfn = psi4.properties('ccsd',properties=['dipole'],return_wfn=True)
psi4.oeprop(wfn,"DIPOLE", "QUADRUPOLE", title="(OEPROP)CC")
psi4.compare_values(psi4.variable("(OEPROP)CC DIPOLE X"), 0.000000000000,6,"CC DIPOLE X") #TEST
psi4.compare_values(psi4.variable("(OEPROP)CC DIPOLE Y"), 0.000000000000,6,"CC DIPOLE Y") #TEST
psi4.compare_values(psi4.variable("(OEPROP)CC DIPOLE Z"),-1.840334899884,6,"CC DIPOLE Z") #TEST
psi4.compare_values(psi4.variable("(OEPROP)CC QUADRUPOLE XX"),-7.864006962064,6,"CC QUADRUPOLE XX") #TEST
psi4.compare_values(psi4.variable("(OEPROP)CC QUADRUPOLE XY"), 0.000000000000,6,"CC QUADRUPOLE XY") #TEST
psi4.compare_values(psi4.variable("(OEPROP)CC QUADRUPOLE XZ"), 0.000000000000,6,"CC QUADRUPOLE XZ") #TEST
psi4.compare_values(psi4.variable("(OEPROP)CC QUADRUPOLE YY"),-4.537386915305,6,"CC QUADRUPOLE YY") #TEST
psi4.compare_values(psi4.variable("(OEPROP)CC QUADRUPOLE YZ"), 0.000000000000,6,"CC QUADRUPOLE YZ") #TEST
psi4.compare_values(psi4.variable("(OEPROP)CC QUADRUPOLE ZZ"),-6.325836255265,6,"CC QUADRUPOLE ZZ") #TEST
psi4.core.print_variables()
