def test_keep_ccre():
path = Path("../../tests_staging/test_turbo_butadien_td_opt/butadiene")
calc = Turbomole(path)
ccre_pattern = "__ccre*"
pat, multi, key = calc.prepare_pattern(ccre_pattern)
assert pat == "ccre*"
assert multi
assert key == "ccres"
def test_benzene_wfoverlap():
control_path = THIS_DIR / "benzene_3states"
td_vec_fn = str(control_path / "ciss_a")
mos_fn = str(control_path / "mos")
turbo = Turbomole(control_path)
geom = geom_from_library("benzene_bp86sto3g_opt.xyz")
geom.set_calculator(turbo)
turbo.td_vec_fn = td_vec_fn
turbo.mos = mos_fn
def test_wfo_compare_butadiene_cc2_sto3g():
in_path = THIS_DIR / "butadiene_cc2_sto3g"
geom = geom_from_xyz_file(in_path / "buta.xyz")
turbo = Turbomole(in_path, track=True, wfo_basis="sto3g")
geom.set_calculator(turbo)
# opt_kwargs = {
# "max_cycles": 1,
# "dump": True,
# }
# opt = SteepestDescent(geom, **opt_kwargs)
# opt.run()
turbo.run_calculation(geom.atoms, geom.coords)
wfow = turbo.wfow
wfow.compare(wfow)
def turbo_comp():
calc_kwargs = {
"xc": "pbe",
"method": "tddft",
"basis": "def2-SVP",
"pal": 4,
"nstates": 2,
"root": 1,
"track": True,
}
pyscf_ = PySCF(**calc_kwargs)
geom = geom_from_xyz_file("cytosin.xyz")
geom.set_calculator(pyscf_)
f = geom.forces.reshape(-1, 3)
print("pyscf")
print(f.reshape(-1, 3))
ref_geom = geom.copy()
turbo_kwargs = {
"control_path": "/scratch/turbontos/control_pbe_clean",
"track": True,
"ovlp_type": "wf",
"ovlp_with": "first",
"pal": 4,
}
turbo = Turbomole(**turbo_kwargs)
ref_geom.set_calculator(turbo)
f_ref = ref_geom.forces
print("Turbo")
print(f_ref.reshape(-1, 3))
def test_forces():
geom = geom_from_xyz_file(THIS_DIR / "h2o.xyz")
control_path = THIS_DIR / "h2o_forces"
turbo = Turbomole(control_path)
geom.set_calculator(turbo)
forces = geom.forces
ref_forces = -np.loadtxt("h2o_gradient.ref")
np.testing.assert_allclose(forces, ref_forces, atol=1e-8)
def test_wfo_ref():
in_path = THIS_DIR / "butadiene_twist"
geom = geom_from_xyz_file(in_path / "02_buta_twist.xyz")
turbo = Turbomole(in_path, track=True, wfo_basis="def2-svp")
geom.set_calculator(turbo)
opt_kwargs = {
"max_cycles": 2,
"dump": True,
}
opt = SteepestDescent(geom, **opt_kwargs)
opt.run()
def test_wfo_compare_sto3g():
in_path = THIS_DIR / "butadiene_twist_sto3g"
geom = geom_from_xyz_file(in_path / "02_buta_twist.xyz")
turbo = Turbomole(in_path, track=True, wfo_basis="sto-3g")
geom.set_calculator(turbo)
opt_kwargs = {
"max_cycles": 1,
"dump": True,
}
opt = SteepestDescent(geom, **opt_kwargs)
opt.run()
wfow = turbo.wfow
wfow.compare(wfow)
def test_wfo_compare_neon():
in_path = THIS_DIR / "neon"
geom = geom_from_xyz_file(in_path / "neon.xyz")
turbo = Turbomole(in_path, track=True, wfo_basis="def2-svp")
geom.set_calculator(turbo)
opt_kwargs = {
"max_cycles": 1,
"dump": True,
}
opt = SteepestDescent(geom, **opt_kwargs)
opt.run()
wfow = turbo.wfow
wfow.compare(wfow)
def get_calc(ovlp_type, ovlp_with):
calc_kwargs = {
"control_path": THIS_DIR / "control_pbe0_clean",
"track": True,
"ovlp_type": ovlp_type,
"ovlp_with": ovlp_with,
# "cdds": "render",
# "orient": "reset;center {-3.5575373 2.2096293 1.4794437E-5}; " \
# "rotate z -112.54; rotate y 41.57; rotate z 99.02;",
"adapt_args": [0.5, 0.3, 0.6],
"pal": 4,
}
calc = Turbomole(**calc_kwargs)
return calc
def test_wfo_compare_neon_dimer():
in_path = THIS_DIR / "neon_dimer"
geom = geom_from_xyz_file(in_path / "neon_dimer.xyz")
turbo = Turbomole(in_path, track=True, wfo_basis="def2-svp")
geom.set_calculator(turbo)
opt_kwargs = {
"max_cycles": 5,
"dump": True,
"track": True,
# "convergence": {
# "max_force_thresh": 2.5e-8,
# }
}
opt = SteepestDescent(geom, **opt_kwargs)
#import pdb; pdb.set_trace()
opt.run()
def test_diabatize():
geoms = geoms_from_trj(THIS_DIR / "ma_proton_transfer/interpolated.trj")
in_path = THIS_DIR / "ma_turbo"
calc_kwargs = {
"track": True,
"wfo_basis": "sto-3g",
}
turbos = list()
wfos = list()
for i, geom in enumerate(geoms):
pickle_fn = f"wfo_pickle_{i}"
turbo = Turbomole(in_path, calc_number=i, **calc_kwargs)
geom.set_calculator(turbo)
forces = geom.forces
print(f"cycle {i}")
turbos.append(turbo)
wfos.append(turbo.wfow)
with open(pickle_fn, "wb") as handle:
cloudpickle.dump(turbo.wfow, handle)
def test_diabatize():
geoms = geoms_from_trj(THIS_DIR /
"ma_proton_transfer/interpolated.trj")[:4]
#in_path = THIS_DIR / "ma_turbo"
in_path = THIS_DIR / "ma_turbo_no_exopt"
calc_kwargs = {
"track": True,
"wfo_basis": "sto-3g",
}
#geoms = geoms_from_trj(THIS_DIR / "biaryl_trj/biaryl_first_13.trj")[:4]
#in_path = THIS_DIR / "biaryl"
#calc_kwargs = {
# "track": True,
# "wfo_basis": "def2-svp",
#}
turbos = list()
wfos = list()
mos = None
np.set_printoptions(precision=2, suppress=True)
# for i, geom in enumerate(geoms):
# pickle_fn = f"wfo_pickle_{i}"
# turbo = Turbomole(in_path, calc_number=i, **calc_kwargs)
# if i > 0:
# turbo.mos = mos
# none_ = turbo.get_tddft(geom.atoms, geom.coords)
# mos = turbo.mos
# print(f"cycle {i}")
# turbos.append(turbo)
# wfos.append(turbo.wfow)
# with open(pickle_fn, "wb") as handle:
# cloudpickle.dump(turbo.wfow, handle)
# if i > 0:
# wfo1 = wfos[i-1]
# inds = wfo1.compare(turbo.wfow)
# print(inds)
mos = natsorted(THIS_DIR.glob("*.mos"))
td_vecs = natsorted(THIS_DIR.glob("*.ciss_a"))
for i, (geom, mos, td_vec) in enumerate(zip(geoms, mos, td_vecs)):
print("cycle", i, geom, mos, td_vec)
turbo = Turbomole(in_path, calc_number=i, **calc_kwargs)
turbo.mos = mos
turbo.td_vec_fn = td_vec
turbo.check_for_root_flip(geom.atoms, geom.coords)
wfos.append(turbo.wfow)
if i > 0:
wfo1 = wfos[i - 1]
inds = wfo1.compare(turbo.wfow)
def test_h2o_wfoverlap():
path1 = THIS_DIR / "h2o1_wfoverlap"
path2 = THIS_DIR / "h2o2_wfoverlap"
geom1 = geom_from_xyz_file(path1 / "h2o1.xyz")
geom2 = geom_from_xyz_file(path2 / "h2o2.xyz")
turbo = Turbomole(path1)
get_mos_ciss = lambda path: (str(path / "mos"), str(path / "ciss_a"))
mos1, ciss1 = get_mos_ciss(path1)
mos2, ciss2 = get_mos_ciss(path2)
turbo.td_vec_fn = ciss1
turbo.mos = mos1
turbo.td_vec_fn = ciss2
turbo.mos = mos2
def test_butadiene_track_opt():
in_path = THIS_DIR / "butadiene"
geom = geom_from_xyz_file(in_path / "butadiene_hf_sto3g.xyz")
turbo = Turbomole(in_path, track=True, wfo_basis="def2-svp")
geom.set_calculator(turbo)
#fn = "/scratch/programme/pysisyphus/tests/test_turbo_butadien_td_opt/wfo_backup.out"
#with open(fn) as handle:
# stdout = handle.read()
#wfo = turbo.wfow
#a = wfo.parse_wfoverlap_out(stdout)
#print(a)
#print(a.reshape(-1, 6))
opt_kwargs = {
"max_cycles": 10,
"dump": True,
}
opt = ConjugateGradient(geom, **opt_kwargs)
opt = SteepestDescent(geom, **opt_kwargs)
opt.run()