def _decode_theory(self, obj):
rv = Theory()
if "method" in obj:
rv.method = obj["method"]
if "semi-empirical" in obj:
rv.method.is_semiempirical = obj["semi-empirical"]
if "grid" in obj:
rv.grid = obj["grid"]
if "solvent model" in obj and "solvent" in obj:
rv.solvent = ImplicitSolvent(obj["solvent model"], obj["solvent"])
if "disp" in obj:
rv.empirical_dispersion = obj["disp"]
if "nproc" in obj:
rv.processors = obj["nproc"]
if "mem" in obj:
rv.memory = obj["mem"]
if "jobs" in obj:
jobs = []
for job in obj["jobs"]:
if job == "OptimizationJob":
jobs.append(OptimizationJob(**obj["jobs"][job]))
elif job == "FrequencyJob":
jobs.append(FrequencyJob(**obj["jobs"][job]))
elif job == "SinglePointJob":
jobs.append(SinglePointJob(**obj["jobs"][job]))
elif job == "ForceJob":
jobs.append(ForceJob(**obj["jobs"][job]))
rv.job_type = jobs
if "basis" in obj or "ecp" in obj:
rv.basis = BasisSet([], [])
if "basis" in obj:
for name, aux_type, file, elements in zip(
obj["basis"]["name"],
obj["basis"]["auxiliary"],
obj["basis"]["file"],
obj["basis"]["elements"],
):
rv.basis.basis.append(
Basis(
name,
elements=elements,
aux_type=aux_type,
user_defined=file,
)
)
if "ecp" in obj:
for name, file, elements in zip(
obj["ecp"]["name"],
obj["ecp"]["file"],
obj["ecp"]["elements"],
):
rv.basis.ecp.append(
ECP(
name,
elements=elements,
user_defined=file,
)
)
if "other" in obj:
rv.kwargs = obj["other"]
return rv
def test_gaussian_tm_sp(self):
run(self.session, "open %s" % self.met_cat)
qm_input_tool = self.open_tool("Build QM Input")
self.assertTrue(bool(qm_input_tool))
ndx = qm_input_tool.file_type.findText("Gaussian", Qt.MatchExactly)
qm_input_tool.file_type.setCurrentIndex(ndx)
qm_input_tool.job_widget.do_geom_opt.setCheckState(Qt.Unchecked)
qm_input_tool.job_widget.do_freq.setCheckState(Qt.Unchecked)
qm_input_tool.job_widget.charge.setValue(0)
qm_input_tool.job_widget.multiplicity.setValue(1)
qm_input_tool.job_widget.nprocs.setValue(0)
qm_input_tool.job_widget.mem.setValue(0)
ndx = qm_input_tool.job_widget.solvent_option.findText(
"None", Qt.MatchExactly)
qm_input_tool.job_widget.solvent_option.setCurrentIndex(ndx)
qm_input_tool.method_widget.setMethod("B3LYP")
qm_input_tool.method_widget.setGrid("SuperFineGrid")
qm_input_tool.method_widget.setDispersion("None")
basis = BasisSet(basis=[
Basis(
"def2-TZVP",
elements=["H", "C", "N", "O", "P"],
),
Basis("SDD", elements=["Ru"])
],
ecp="Ru SDD")
qm_input_tool.basis_widget.setBasis(basis)
qm_input_tool.other_keywords_widget.setKeywords({})
contents, warnings = qm_input_tool.get_file_contents()
qm_input_tool.delete()
if warnings:
# there were warnings - I don't expect any
self.assertTrue(False)
ref_file = """#n B3LYP/genecp Integral=(grid=SuperFineGrid)
F:22-8;8-3;3-4
0 1
H -1.32054 -0.75890 -4.97019
C -0.83710 -0.67504 -3.98693
C -1.94818 -0.44720 -2.97055
O -2.60335 0.62340 -3.03491
H -2.15763 -1.15349 -2.24784
H -0.27898 -1.59632 -3.81264
H -0.14406 0.16910 -4.01642
Ru -0.62191 0.26814 0.06452
H -0.87528 -0.29689 -1.62782
H -0.64154 0.77071 1.63835
N -2.22027 1.67036 -0.35156
N -2.41708 -0.87753 0.60051
C -3.38272 1.38551 0.51399
H -1.96741 2.65271 -0.26188
H -2.47077 1.51040 -1.33734
C -3.67190 -0.11908 0.39143
H -2.48854 -1.76419 0.10163
H -2.32916 -1.12467 1.58359
H -4.23094 1.95099 0.18896
H -3.17970 1.65524 1.52934
H -4.05898 -0.33036 -0.58347
H -4.39170 -0.40689 1.12895
P 1.07205 1.71869 -0.34745
P 0.81151 -1.37184 0.70896
C 0.55526 3.14500 -1.41523
C 1.97994 2.59379 1.00651
C 2.49260 0.93221 -1.24347
C -0.11544 -2.48291 1.86409
C 1.60408 -2.58882 -0.43067
C 2.34100 -0.80590 1.59984
C 0.82744 4.48948 -1.13825
C -0.25736 2.85102 -2.51851
C 3.14155 3.31828 0.70808
C 1.54835 2.54133 2.33290
C 3.33578 0.04627 -0.58629
C 2.60045 1.09163 -2.65079
C -0.54933 -3.74618 1.44682
C -0.64383 -1.96605 3.05866
C 2.33984 -3.67519 0.06065
C 1.54474 -2.38323 -1.80618
C 3.33694 -0.12514 0.90812
C 2.46312 -0.97926 3.00323
C 0.32389 5.50137 -1.95561
H 1.42639 4.76771 -0.27860
C -0.75232 3.85682 -3.34145
H -0.53079 1.82144 -2.71815
C 3.85126 3.97307 1.70883
H 3.50559 3.36279 -0.31548
C 2.26924 3.17905 3.34133
H 0.65677 1.97347 2.57940
C 4.28462 -0.72389 -1.34298
C 3.51379 0.38421 -3.38194
H 1.94937 1.79380 -3.16019
C -1.46313 -4.47789 2.20565
H -0.19139 -4.16842 0.51384
C -1.54169 -2.70268 3.82536
H -0.38472 -0.96029 3.37605
C 2.97321 -4.55113 -0.81434
H 2.41820 -3.84020 1.13279
C 2.18627 -3.25197 -2.68724
H 1.01491 -1.51377 -2.18064
C 4.45682 0.42048 1.62607
C 3.50924 -0.44591 3.70435
H 1.71903 -1.55347 3.54106
C -0.46011 5.19061 -3.06285
H 0.54641 6.53809 -1.71862
H -1.37864 3.59473 -4.18971
C 3.42240 3.89544 3.03272
H 4.75240 4.52500 1.45765
H 1.92962 3.10901 4.37111
C 4.37499 -0.54687 -2.75091
C 5.13058 -1.69490 -0.73828
H 3.58576 0.52763 -4.45722
C -1.95775 -3.96357 3.39945
H -1.78959 -5.45264 1.85394
H -1.93165 -2.28048 4.74724
C 2.89822 -4.34014 -2.19222
H 3.53800 -5.39223 -0.42206
H 2.14147 -3.06592 -3.75679
C 4.52546 0.28009 3.03897
C 5.51015 1.12556 0.97778
H 3.57546 -0.58565 4.78041
H -0.85051 5.98165 -3.69692
H 3.98664 4.38925 3.81887
C 5.30218 -1.31658 -3.50131
C 6.01244 -2.43204 -1.48800
H 5.06355 -1.86999 0.32991
H -2.67024 -4.53306 3.98918
H 3.40448 -5.01737 -2.87435
C 5.61174 0.85060 3.75500
C 6.55752 1.65159 1.69023
H 5.47918 1.26388 -0.09684
C 6.10652 -2.24058 -2.88574
H 5.35443 -1.16301 -4.57638
H 6.63929 -3.17577 -1.00421
C 6.61007 1.52076 3.09726
H 5.63680 0.73814 4.83603
H 7.34699 2.18698 1.17049
H 6.81024 -2.83022 -3.46624
H 7.43996 1.95142 3.65012
C H N O P 0
def2TZVP
****
Ru 0
SDD
****
Ru 0
SDD
"""
content_lines = contents.splitlines()
ref_lines = ref_file.splitlines()
self.assertEqual(len(content_lines), len(ref_lines))
for ref, test in zip(ref_lines, content_lines):
self.assertEqual(ref, test)
def test_psi4_sp(self):
run(self.session, "open %s" % self.benzene)
qm_input_tool = self.open_tool("Build QM Input")
self.assertTrue(bool(qm_input_tool))
ndx = qm_input_tool.file_type.findText("Psi4", Qt.MatchExactly)
qm_input_tool.file_type.setCurrentIndex(ndx)
qm_input_tool.job_widget.do_geom_opt.setCheckState(Qt.Unchecked)
qm_input_tool.job_widget.do_freq.setCheckState(Qt.Unchecked)
qm_input_tool.job_widget.charge.setValue(0)
qm_input_tool.job_widget.multiplicity.setValue(1)
qm_input_tool.job_widget.nprocs.setValue(0)
qm_input_tool.job_widget.mem.setValue(0)
qm_input_tool.method_widget.setMethod("CCSD(T)")
qm_input_tool.method_widget.setGrid("Default")
qm_input_tool.method_widget.setDispersion("None")
basis = BasisSet("aug-cc-pVDZ")
qm_input_tool.basis_widget.setBasis(basis)
qm_input_tool.other_keywords_widget.setKeywords(
{"job": {
"energy": []
}})
contents, warnings = qm_input_tool.get_file_contents()
qm_input_tool.delete()
if warnings:
# there were warnings - I don't expect any
self.assertTrue(False)
ref_file = """#benzene_1-NO2_4-Cl.xyz 12,11=>H
basis {
assign aug-cc-pVDZ
}
molecule {
0 1
C -1.97696 -2.32718 0.00126
C -2.36814 -1.29554 0.85518
C -1.67136 -0.08735 0.85440
C -0.58210 0.08919 0.00026
C -0.19077 -0.94241 -0.85309
C -0.88848 -2.15056 -0.85289
H -3.22679 -1.43483 1.52790
H -1.98002 0.72606 1.52699
H 0.66766 -0.80358 -1.52636
H -0.57992 -2.96360 -1.52585
H -0.03766 1.03348 -0.00013
H -2.52191 -3.27117 0.00170
}
nrg = energy('CCSD(T)')
"""
content_lines = contents.splitlines()
ref_lines = ref_file.splitlines()
self.assertEqual(len(content_lines), len(ref_lines))
for ref, test in zip(ref_lines, content_lines):
self.assertEqual(ref, test)
def test_orca_numfreq(self):
run(self.session, "open %s" % self.benzene)
qm_input_tool = self.open_tool("Build QM Input")
self.assertTrue(bool(qm_input_tool))
ndx = qm_input_tool.file_type.findText("ORCA", Qt.MatchExactly)
qm_input_tool.file_type.setCurrentIndex(ndx)
qm_input_tool.job_widget.do_geom_opt.setCheckState(Qt.Unchecked)
qm_input_tool.job_widget.do_freq.setCheckState(Qt.Checked)
qm_input_tool.job_widget.raman.setCheckState(Qt.Unchecked)
qm_input_tool.job_widget.num_freq.setCheckState(Qt.Checked)
qm_input_tool.job_widget.temp.setValue(298.15)
qm_input_tool.job_widget.charge.setValue(0)
qm_input_tool.job_widget.multiplicity.setValue(1)
qm_input_tool.job_widget.nprocs.setValue(0)
qm_input_tool.job_widget.mem.setValue(0)
ndx = qm_input_tool.job_widget.solvent_option.findText(
"None", Qt.MatchExactly)
qm_input_tool.job_widget.solvent_option.setCurrentIndex(ndx)
qm_input_tool.method_widget.setMethod("M06-2X")
qm_input_tool.method_widget.setGrid("Grid7")
qm_input_tool.method_widget.setDispersion("None")
basis = BasisSet("def2-SVP")
qm_input_tool.basis_widget.setBasis(basis)
qm_input_tool.other_keywords_widget.setKeywords({})
contents, warnings = qm_input_tool.get_file_contents()
qm_input_tool.delete()
if warnings:
# there were warnings - I don't expect any
self.assertTrue(False)
ref_file = """#benzene_1-NO2_4-Cl.xyz 12,11=>H
! M062X Grid7 FinalGrid7 def2-SVP NumFreq
%freq
Temp 298.15
end
*xyz 0 1
C -1.976956 -2.327177 0.001258
C -2.368139 -1.295544 0.855179
C -1.671361 -0.087354 0.854401
C -0.582097 0.089190 0.000262
C -0.190773 -0.942409 -0.853088
C -0.888480 -2.150555 -0.852891
H -3.226790 -1.434829 1.527903
H -1.980024 0.726060 1.526994
H 0.667658 -0.803584 -1.526362
H -0.579922 -2.963602 -1.525852
H -0.037665 1.033485 -0.000129
H -2.521911 -3.271171 0.001704
*
"""
content_lines = contents.splitlines()
ref_lines = ref_file.splitlines()
self.assertEqual(len(content_lines), len(ref_lines))
for ref, test in zip(ref_lines, content_lines):
self.assertEqual(ref, test)
def test_gaussian_opt(self):
run(self.session, "open %s" % self.benzene)
qm_input_tool = self.open_tool("Build QM Input")
self.assertTrue(bool(qm_input_tool))
ndx = qm_input_tool.file_type.findText("Gaussian", Qt.MatchExactly)
qm_input_tool.file_type.setCurrentIndex(ndx)
qm_input_tool.job_widget.do_geom_opt.setCheckState(Qt.Checked)
qm_input_tool.job_widget.ts_opt.setCheckState(Qt.Unchecked)
qm_input_tool.job_widget.do_freq.setCheckState(Qt.Unchecked)
qm_input_tool.job_widget.charge.setValue(0)
qm_input_tool.job_widget.multiplicity.setValue(1)
qm_input_tool.job_widget.nprocs.setValue(0)
qm_input_tool.job_widget.mem.setValue(0)
ndx = qm_input_tool.job_widget.solvent_option.findText(
"None", Qt.MatchExactly)
qm_input_tool.job_widget.solvent_option.setCurrentIndex(ndx)
qm_input_tool.method_widget.setMethod("wB97X-D")
qm_input_tool.method_widget.setGrid("SuperFineGrid")
qm_input_tool.method_widget.setDispersion("None")
basis = BasisSet("def2-SVP")
qm_input_tool.basis_widget.setBasis(basis)
qm_input_tool.other_keywords_widget.setKeywords({})
contents, warnings = qm_input_tool.get_file_contents()
qm_input_tool.delete()
if warnings:
# there were warnings - I don't expect any
self.assertTrue(False)
ref_file = """#n wB97XD/def2SVP opt Integral=(grid=SuperFineGrid)
benzene_1-NO2_4-Cl.xyz 12,11=>H
0 1
C -1.97696 -2.32718 0.00126
C -2.36814 -1.29554 0.85518
C -1.67136 -0.08735 0.85440
C -0.58210 0.08919 0.00026
C -0.19077 -0.94241 -0.85309
C -0.88848 -2.15056 -0.85289
H -3.22679 -1.43483 1.52790
H -1.98002 0.72606 1.52699
H 0.66766 -0.80358 -1.52636
H -0.57992 -2.96360 -1.52585
H -0.03766 1.03348 -0.00013
H -2.52191 -3.27117 0.00170
"""
content_lines = contents.splitlines()
ref_lines = ref_file.splitlines()
self.assertEqual(len(content_lines), len(ref_lines))
for ref, test in zip(ref_lines, content_lines):
self.assertEqual(ref, test)
def test_qchem_opt(self):
run(self.session, "open %s" % self.benzene)
qm_input_tool = self.open_tool("Build QM Input")
self.assertTrue(bool(qm_input_tool))
ndx = qm_input_tool.file_type.findText("Q-Chem", Qt.MatchExactly)
qm_input_tool.file_type.setCurrentIndex(ndx)
qm_input_tool.job_widget.do_geom_opt.setCheckState(Qt.Checked)
qm_input_tool.job_widget.ts_opt.setCheckState(Qt.Unchecked)
qm_input_tool.job_widget.charge.setValue(0)
qm_input_tool.job_widget.multiplicity.setValue(1)
qm_input_tool.job_widget.nprocs.setValue(0)
qm_input_tool.job_widget.mem.setValue(0)
qm_input_tool.method_widget.setMethod("M06-2X")
qm_input_tool.method_widget.setGrid("SG-3")
qm_input_tool.method_widget.setDispersion("Zero-damped Grimme D3")
basis = BasisSet("def2-TZVP")
qm_input_tool.basis_widget.setBasis(basis)
qm_input_tool.other_keywords_widget.setKeywords({})
contents, warnings = qm_input_tool.get_file_contents()
qm_input_tool.delete()
if warnings:
# there were warnings - I don't expect any
self.assertTrue(False)
ref_file = """$rem
JOB_TYPE = OPT
DFT_D = D3_ZERO
XC_GRID = 3
BASIS = def2-TZVP
METHOD = M06-2X
$end
$comments
benzene_1-NO2_4-Cl.xyz 12,11=>H
$end
$molecule
0 1
C -1.97696 -2.32718 0.00126
C -2.36814 -1.29554 0.85518
C -1.67136 -0.08735 0.85440
C -0.58210 0.08919 0.00026
C -0.19077 -0.94241 -0.85309
C -0.88848 -2.15056 -0.85289
H -3.22679 -1.43483 1.52790
H -1.98002 0.72606 1.52699
H 0.66766 -0.80358 -1.52636
H -0.57992 -2.96360 -1.52585
H -0.03766 1.03348 -0.00013
H -2.52191 -3.27117 0.00170
$end
"""
content_lines = contents.splitlines()
ref_lines = ref_file.splitlines()
self.assertEqual(len(content_lines), len(ref_lines))
for ref, test in zip(ref_lines, content_lines):
self.assertEqual(ref, test)