def test_sp_mp2_rohf_fc_error(mtd, opts, errmsg, nh2):
"""cfour/???/input.dat
#! single point MP2/qz2p on water
"""
nh2 = qcdb.set_molecule(nh2)
qcdb.set_options(opts)
with pytest.raises(qcng.exceptions.InputError) as e:
qcdb.gradient(mtd, molecule=nh2)
assert errmsg in str(e.value)
def test_4b():
system1()
scf_dtz, jrec = qcdb.gradient('c4-HF/cc-pV[23]Z', return_wfn=True)
assert compare_arrays(ref_scf_dtz, scf_dtz, 6,
"[4] SCF/cc-pV[DT]Z Gradient, dertype=1")
pp.pprint(jrec)
def test_grad():
h2o = qcdb.set_molecule(
"""
O 0.00000000 0.00000000 0.00000000
H 0.00000000 1.93042809 -1.10715266
H 0.00000000 -1.93042809 -1.10715266
units au"""
)
qcdb.set_options(
{
"basis": "sto-3g",
"scf__e_convergence": 1e-6,
#'nwchem_driver__tight': True
}
)
val = qcdb.gradient("nwc-scf")
scf = -74.888142460799
grads = np.array(
[[0.000000, 0.000000, 0.058550], [0.000000, 0.140065, -0.029275], [0.000000, -0.140065, -0.029275]]
)
assert compare_values(scf, qcdb.variable("HF TOTAL ENERGY"), 5, "scf")
assert compare_arrays(grads, qcdb.variable("CURRENT GRADIENT"), 5, "scf grad")
def test_1_eom_ccsd_grad():
h2o = qcdb.set_molecule("""
O 0.000000000000 0.000000000000 -0.123909374404
H 0.000000000000 1.429936611037 0.983265845431
H 0.000000000000 -1.429936611037 0.983265845431
symmetry c1
units au
""")
qcdb.set_options({
"basis": "sto-3g",
"memory": "1500 mb",
"nwchem_scf__rhf": True,
"scf__e_convergence": 1.0e-10,
"nwchem_scf__tol2e": 1.0e-10,
"nwchem_scf__thresh": 1.0e-10,
"nwchem_scf__singlet": True,
"qc_module": "TCE",
"nwchem_tce__ccsd": True,
"nwchem_tce__nroots": 1,
})
print("Testing EOM-CCSD grad...")
val = qcdb.gradient("nwc-eom-ccsd")
check_eom_ccsd_grad(val)
def test_1e():
system2()
scf_dz, jrec = qcdb.gradient("c4-SCF/cc-pVDZ", return_wfn=True)
assert compare_arrays(ref_scf_dz_y, scf_dz, 6, "[1e] SCF/cc-pVDZ Gradient")
assert compare_arrays(ref_scf_dz_y, jrec["qcvars"]["CURRENT GRADIENT"].data, 6, "[1e] SCF/cc-pVDZ Gradient")
assert compare_arrays(ref_scf_dz_y, qcdb.variable("CURRENT GRADIENT"), 6, "[1e] SCF/cc-pVDZ Gradient")
# assert compare_arrays(ref_scf_dz_y, jrec['qcvars']['HF/CC-PVDZ TOTAL GRADIENT'].data, 6, "[1e] SCF/cc-pVDZ Gradient")
assert "CFOUR" == jrec["provenance"]["creator"], "[1e] prov"
def test_1i():
system3()
scf_dz, jrec = qcdb.gradient("gms-SCF/cc-pVDZ", return_wfn=True)
assert compare_arrays(ref2_scf_dz, scf_dz, 6, "[1i] SCF/cc-pVDZ Gradient")
assert compare_arrays(ref2_scf_dz, jrec["qcvars"]["CURRENT GRADIENT"].data, 6, "[1i] SCF/cc-pVDZ Gradient")
assert compare_arrays(ref2_scf_dz, qcdb.variable("CURRENT GRADIENT"), 6, "[1i] SCF/cc-pVDZ Gradient")
##assert compare_arrays(ref_scf_dz, jrec['qcvars']['HF/CC-PVDZ TOTAL GRADIENT'].data, 6, "[1i] SCF/cc-pVDZ Gradient")
assert "GAMESS" == jrec["provenance"]["creator"], "[1i] prov"
def test_1g():
system3()
scf_dz, jrec = qcdb.gradient("SCF/cc-pVDZ", return_wfn=True)
assert compare_arrays(ref2_scf_dz, scf_dz, 6, "[1g] SCF/cc-pVDZ Gradient")
assert compare_arrays(ref2_scf_dz, jrec["qcvars"]["CURRENT GRADIENT"].data, 6, "[1g] SCF/cc-pVDZ Gradient")
assert compare_arrays(ref2_scf_dz, qcdb.variable("CURRENT GRADIENT"), 6, "[1g] SCF/cc-pVDZ Gradient")
# assert compare_arrays(ref_scf_dz, jrec['qcvars']['HF/CC-PVDZ TOTAL GRADIENT'].data, 6, "[1g] SCF/cc-pVDZ Gradient")
# assert ['QCDB', 'Psi4'] == [d['creator'] for d in jrec['provenance']], "[1g] prov"
assert "Psi4" == jrec["provenance"]["creator"], "[1g] prov"
def test_1b():
system1()
scf_dz, jrec = qcdb.gradient('c4-SCF/cc-pVDZ', return_wfn=True)
assert compare_arrays(ref_scf_dz, scf_dz, 6, "[1b] SCF/cc-pVDZ Gradient")
assert compare_arrays(ref_scf_dz, jrec['qcvars']['CURRENT GRADIENT'].data,
6, "[1b] SCF/cc-pVDZ Hessian")
assert compare_arrays(ref_scf_dz, qcdb.get_variable('CURRENT GRADIENT'), 6,
"[1b] SCF/cc-pVDZ Hessian")
#assert compare_arrays(ref_scf_dz, jrec['qcvars']['HF/CC-PVDZ TOTAL GRADIENT'].data, 6, "[1b] SCF/cc-pVDZ Hessian")
assert 'CFOUR' == jrec['provenance']['creator'], "[1b] prov"
def test_sp_mp2_rhf_fc(mtd, opts, h2o):
"""cfour/???/input.dat
#! single point MP2/qz2p on water
"""
h2o = qcdb.set_molecule(h2o)
qcdb.set_options(opts)
g, jrec = qcdb.gradient(mtd, return_wfn=True, molecule=h2o)
print(g)
assert compare_arrays(rhf_mp2_fc, g, atol=1.0e-5)
def test_sp_mp2_rohf_ae(mtd, opts, nh2):
"""cfour/???/input.dat
#! single point MP2/qz2p on water
"""
nh2 = qcdb.set_molecule(nh2)
qcdb.set_options(opts)
g, jrec = qcdb.gradient(mtd, return_wfn=True, molecule=nh2)
print(g)
assert compare_arrays(rohf_mp2_ae, g, atol=1.0e-5)
def test_sp_hf_uhf(mtd, opts, nh2):
"""cfour/???/input.dat
#! single-point HF/qz2p on NH2
"""
nh2 = qcdb.set_molecule(nh2)
qcdb.set_options(opts)
g, jrec = qcdb.gradient(mtd, return_wfn=True, molecule=nh2)
print(g)
assert compare_arrays(uhf_scf, g, atol=1.0e-5)
def test_1_hf():
qcdb.set_options({
'basis': 'cc-pvdz',
'memory': '400 mb',
'nwchem_scf__rhf': True,
'scf__e_convergence': 1.0e-8,
'nwchem_scf__nopen': 0,
#'nwchem_task_hf' : 'gradient'
})
print('Testing hf...')
val = qcdb.gradient('nwc-hf')
check_hf(val)
pprint.pprint(val)
def test_2_hf():
qcdb.set_options({
'basis': 'cc-pvdz',
'memory': '400 mb',
'scf__e_convergence': 1.0e-4,
'nwchem_scf__rhf': True,
#'nwchem_scf__thresh': 1.0e-4,
'nwchem_scf__nopen': 0,
'nwchem_mp2__tight': True,
})
print('Testing hf...')
val = qcdb.gradient('nwc-mp2')
check_mp2(val, is_df=True, is5050=False)
def test_1_mp2():
qcdb.set_options({
'basis': 'cc-pvdz',
'memory': '400 mb',
'nwchem_scf': 'rhf',
'nwchem_scf_thresh': 1.0e-4,
'nwchem_scf_nopen': 0,
'nwchem_mp2_tight': True,
'nwchem_task_mp2': 'gradient'
})
print('Testing mp2 ...')
val = qcdb.gradient('nwc-mp2')
check_mp2_tot(val, is_df=True)
def test_sp_mp2_rhf_ae(mtd, opts, h2o):
"""cfour/???/input.dat
#! single point MP2/qz2p on water
"""
h2o = qcdb.set_molecule(h2o)
qcdb.set_options(opts)
g, jrec = qcdb.gradient(mtd, return_wfn=True, molecule=h2o)
#print(h2o.geometry())
#print(jrec['stdout'])
#print(h2o.geometry())
print(g)
assert compare_arrays(rhf_mp2_ae, g, atol=1.0e-3)
def test_1a():
system1()
scf_dz, jrec = qcdb.gradient('SCF/cc-pVDZ', return_wfn=True)
assert compare_arrays(ref_scf_dz, scf_dz, 6, "[1a] SCF/cc-pVDZ Gradient")
assert compare_arrays(ref_scf_dz, jrec['qcvars']['CURRENT GRADIENT'].data,
6, "[1a] SCF/cc-pVDZ Hessian")
assert compare_arrays(ref_scf_dz, qcdb.get_variable('CURRENT GRADIENT'), 6,
"[1a] SCF/cc-pVDZ Hessian")
#assert compare_arrays(ref_scf_dz, jrec['qcvars']['HF/CC-PVDZ TOTAL GRADIENT'].data, 6, "[1a] SCF/cc-pVDZ Hessian")
# TODO provenance kill list
assert ['QCDB',
'Psi4'] == [d['creator'] for d in jrec['provenance']], "[1a] prov"
print(jrec['provenance'])
def test_1_ccsd_df():
qcdb.set_options({
'basis': 'sto-3g',
'memory': '1500 mb',
'qc_module': 'tce',
#'scf__e_convergence': 1.0e-10,
'nwchem_dft__rdft': True,
#'nwchem_scf__thresh' : 1.0e-10,
#'nwchem_scf__tol2e' : 1.0e-10,
'nwchem_tce__dft': True,
'nwchem_tce__ccsd': True,
'nwchem_tce__nroots': 1
})
print('Testing ccsd(dft)...')
val = qcdb.gradient('nwc-ccsd')
check_ccsd(val, is_df=True)
def test_2_ccsd_hf():
qcdb.set_options({
'basis': 'sto-3g',
'memory': '1500 mb',
'qc_module': 'tce',
#'scf__e_convergence': 1.0e-10,
'nwchem_scf__rhf': True,
'nwchem_scf__singlet': True,
'nwchem_scf__thresh': 1.0e-10,
'nwchem_scf__tol2e': 1.0e-10,
'nwchem_tce__scf': True,
'nwchem_tce__nroots': 1,
'nwchem_tce__ccsd': True
})
print('Testing ccsd(hf)...')
val = qcdb.gradient('nwc-ccsd')
check_ccsd(val, is_df=False)
def test_2_hf():
h2o = qcdb.set_molecule("""
O 0.000000000000 0.000000000000 -0.065638538099
H 0.757480611647 0.000000000000 0.520865616174
H -0.757480611647 0.000000000000 0.520865616174
""")
qcdb.set_options({
"basis": "cc-pvdz",
"scf__e_convergence": 1.0e-4,
"nwchem_scf__rhf": True,
#'nwchem_scf__thresh': 1.0e-4,
"nwchem_scf__nopen": 0,
"nwchem_mp2__tight": True,
})
print("Testing hf...")
val = qcdb.gradient("nwc-mp2")
check_mp2(val, is_df=True, is5050=False)
def test_1_hf():
h2o = qcdb.set_molecule("""
O 0.000000000000 0.000000000000 -0.065638538099
H 0.000000000000 -0.757480611647 0.520865616174
H 0.000000000000 0.757480611647 0.520865616174
""")
qcdb.set_options({
"basis": "cc-pvdz",
"nwchem_scf__rhf": True,
"scf__e_convergence": 1.0e-8,
"nwchem_scf__nopen": 0,
#'nwchem_task_hf' : 'gradient'
})
print("Testing hf...")
val = qcdb.gradient("nwc-hf")
check_hf(val)
pprint.pprint(val)
def test_sp_rhf_ccsd(h2o):
"""cfour/sp-rhf-ccsd/input.dat
#! single point CCSD/qz2p on water
"""
h2o = qcdb.set_molecule(h2o)
qcdb.set_options({
#'cfour_CALC_level': 'CCSD',
'BASIS': 'cc-pvtz',
'nwchem_scf__thresh': 12,
'nwchem_ccsd__thresh': 12
})
e, jrec = qcdb.energy('nwc-ccsd', return_wfn=True, molecule=h2o)
scftot = -76.057112730196 #qz2p -76.062748460117
mp2tot = -76.332242848821 #qz2p -76.332940127333
ccsdcorl = -0.280877944529 #qz2p -0.275705491773
ccsdtot = -76.337990674725 #qz2p-76.338453951890
tnm = sys._getframe().f_code.co_name
assert compare_values(scftot, qcdb.get_variable('hf total energy'), 6,
tnm + ' SCF')
assert compare_values(mp2tot, qcdb.get_variable('mp2 total energy'), 6,
tnm + ' MP2')
assert compare_values(ccsdcorl,
qcdb.get_variable('ccsd correlation energy'), 6,
tnm + ' CCSD corl')
assert compare_values(ccsdtot, qcdb.get_variable('ccsd total energy'), 6,
tnm + ' CCSD')
# gradient gives every appearence of working but array should be tested and reorientation to input tested
e, jrec = qcdb.gradient('nwc-ccsd', return_wfn=True, molecule=h2o)
assert compare_values(scftot, qcdb.get_variable('hf total energy'), 6,
tnm + ' SCF')
assert compare_values(mp2tot, qcdb.get_variable('mp2 total energy'), 6,
tnm + ' MP2')
assert compare_values(ccsdcorl,
qcdb.get_variable('ccsd correlation energy'), 6,
tnm + ' CCSD corl')
assert compare_values(ccsdtot, qcdb.get_variable('ccsd total energy'), 6,
tnm + ' CCSD')
def test_molsymm_calc(subject, qcprog):
from .data_mints5 import mints5
ref_block = mints5[subject]
expected = data[subject]
abbr = {"cfour": "c4", "gamess": "gms", "nwchem": "nwc", "psi4": "p4"}
symmol = qcdb.Molecule(data[subject]["mol"].format(
isoA="")) # since no iso subjects yet. later: expected["A"]
symmol.update_geometry()
assert compare(expected["pg"], symmol.get_full_point_group(),
"point group")
assert compare(expected["rsn"], symmol.rotational_symmetry_number(),
"sigma")
units = "bohr" if expected.get("au", False) else "angstrom"
refau = np.array(data[subject]["ref"]) * qcel.constants.conversion_factor(
units, "bohr")
assert compare_values(refau, symmol.full_geometry(), atol=1.0e-6)
if subject == "Ih":
if qcprog in ["cfour", "gamess"]:
pytest.xfail("weird hang, probably atom permutations")
elif qcprog == "nwchem":
pytest.xfail("weird gradient rotation")
elif subject == "SF6" and qcprog == "nwchem":
pytest.xfail(
"TODO new bug 'autosym bug : too many atoms:Received an Error in Communication' after fixed basis set for ghosts"
)
extra_keywords = {
"cfour": {
"HOOH_dimer": {
"cfour_scf_damping": 900
},
"TFCOT": {
"cfour_scf_damping": 800
},
},
"gamess": {
"HOOH_dimer": {
"gamess_contrl__maxit": 60,
"gamess_scf__conv": 1.0e-7
},
},
"nwchem": {
"CN": {
"nwchem_scf__thresh": 1.0e-8
},
"HOOH_dimer": {
"nwchem_scf__nr": 0.0,
"nwchem_scf__maxiter": 100,
"nwchem_scf__thresh": 1.0e-6
},
},
"psi4": {
"HOOH_dimer": {
"psi4_soscf": True
},
"Ih": {
"psi4_guess": "gwh"
},
},
}
qcdb.set_options({
"scf_type":
"conv", # longstanding "pk"
"e_convergence":
9,
"d_convergence":
9,
"reference":
"r{}hf".format("" if symmol.multiplicity() == 1 else "o"),
})
qcdb.set_options(extra_keywords[qcprog].get(subject, {}))
model = f"{abbr[qcprog]}-hf/cc-pvdz"
grad, wfn = qcdb.gradient(model,
return_wfn=True,
molecule=symmol,
local_options={"ncores": 2})
pprint.pprint(wfn, width=200)
with np.printoptions(precision=3, suppress=True):
# DEBUG
pprint.pprint(ref_block)
print("refau")
print(refau)
print("full_geometry")
print(symmol.full_geometry(np_out=True))
print("wfn mol")
print(wfn["molecule"]["geometry"])
print("frad")
print(grad)
dgrad = np.array2string(grad, separator=", ")
print(dgrad)
for i, item in enumerate([
symmol.nuclear_repulsion_energy(),
wfn["qcvars"]["NUCLEAR REPULSION ENERGY"].data,
wfn["extras"]["qcvars"]["NUCLEAR REPULSION ENERGY"],
wfn["properties"]["nuclear_repulsion_energy"],
]):
assert compare_values(
ref_block["nre"], item, atol=1.0e-6,
label="NRE"), f"NRE {i}: {item} != (ref) {ref_block['nre']}"
for i, item in enumerate([
wfn["qcvars"]["HF TOTAL ENERGY"].data,
wfn["qcvars"]["CURRENT ENERGY"].data,
wfn["extras"]["qcvars"]["HF TOTAL ENERGY"],
wfn["extras"]["qcvars"]["CURRENT ENERGY"],
wfn["properties"]["return_energy"],
wfn["properties"]["scf_total_energy"],
]):
assert compare_values(
ref_block["hf_total_energy"], item, atol=1.0e-6, label="ene"
), f"Energy {i}: {item} != (ref) {ref_block['hf_total_energy']}"
assert compare(ref_block["elez"],
wfn["molecule"]["atomic_numbers"],
label="elez"), "elez"
assert compare(ref_block["elea"],
wfn["molecule"]["mass_numbers"],
label="elea"), "elea"
assert compare(False, wfn["molecule"]["fix_orientation"],
label="frame"), "frame"
for i, item in enumerate([
symmol.geometry(),
wfn["molecule"]["geometry"],
# qcdb.driver.driver_helpers.get_active_molecule().geometry(),
]):
assert compare_values(np.array(ref_block["geom"]).reshape((-1, 3)),
item,
atol=1.0e-6,
label="geom"), f"Geometry {i}"
for i, item in enumerate([
grad,
wfn["qcvars"]["HF TOTAL GRADIENT"].data,
wfn["qcvars"]["CURRENT GRADIENT"].data,
wfn["extras"]["qcvars"]["HF TOTAL GRADIENT"],
wfn["extras"]["qcvars"]["CURRENT GRADIENT"],
# wfn["properties"]["return_gradient"],
np.array(wfn["properties"]["scf_total_gradient"]).reshape(
(-1, 3)), # TODO shouldn't need to reshape
]):
assert compare_values(np.array(ref_block["hf_total_gradient"]).reshape(
(-1, 3)),
item,
atol=1.0e-6,
label="grad"), f"Gradient {i}"
def test_6d():
system2()
mp2_dtz = qcdb.gradient("c4-MP2/cc-pV[DT]Z")
assert compare_arrays(ref_mp2_dtz_y, mp2_dtz, 6, "[6] MP2/cc-pV[DT]Z Gradient")
def test_6c():
system1()
mp2_dtz = qcdb.gradient("gms-MP2/cc-pV[DT]Z")
assert compare_arrays(ref_mp2_dtz, mp2_dtz, 6, "[6] MP2/cc-pV[DT]Z Gradient")
def test_5c():
system1()
scf_dtqz = qcdb.gradient("gms-HF/cc-pV[DTQ]Z")
assert compare_arrays(ref_scf_dtqz, scf_dtqz, 6, "[5] SCF/cc-pV[DTQ]Z Gradient")
