def setUp(self):
with path("saddle.test.data", "rct.xyz") as rct_path:
with path("saddle.test.data", "prd.xyz") as prd_path:
mol = TSConstruct.from_file(rct_path, prd_path)
mol.auto_generate_ts(dihed_special=True)
self.ts = mol.ts
self.dir_vec = mol.rct.ic_values - mol.prd.ic_values
self.r_p1 = ReactPoint(self.ts, self.dir_vec)
def test_update_rct_prd_structure(self):
with path("saddle.test.data", "rct.xyz") as rct_path:
with path("saddle.test.data", "prd.xyz") as prd_path:
ts_mol = TSConstruct.from_file(rct_path, prd_path)
ts_mol.auto_generate_ts(task="path")
assert len(ts_mol.ts.ic) == 9
ts_mol.ts.auto_select_ic(keep_bond=True)
assert len(ts_mol.ts.ic) == 12
ts_mol.update_rct_and_prd_with_ts()
assert len(ts_mol.rct.ic) == 12
assert len(ts_mol.prd.ic) == 12
for i in range(12):
assert ts_mol.rct.ic[i].atoms == ts_mol.prd.ic[i].atoms
def setUp(self):
with path("saddle.optimizer.test.data", "HNCS.xyz") as rct_f:
with path("saddle.optimizer.test.data", "HSCN.xyz") as prd_f:
ts_cons = TSConstruct.from_file(rct_f, prd_f)
ts_cons.auto_generate_ts(dihed_special=True)
self.ts = ts_cons.ts
self.dir_vec = ts_cons.prd.ic_values - ts_cons.rct.ic_values
with path("saddle.optimizer.test.data",
"pathloop_hscn.fchk") as fchk_f:
self.ts.energy_from_fchk(fchk_f)
self.opt_ob = PathLoop(self.ts,
self.dir_vec,
quasi_nt="bfgs",
trust_rad="trim",
upd_size="energy")
def setup_class(self):
with path("saddle.test.data", "rct.xyz") as rct_path:
with path("saddle.test.data", "prd.xyz") as prd_path:
self.ts_mol = TSConstruct.from_file(rct_path, prd_path)
self.ts_mol.auto_generate_ts(task="path")
self.path_mol = self.ts_mol.ts
def test_dihed_special_structure(self):
with path("saddle.test.data", "rct.xyz") as rct_path:
with path("saddle.test.data", "prd.xyz") as prd_path:
ts_mol = TSConstruct.from_file(rct_path, prd_path)
ts_mol.auto_generate_ts(dihed_special=True)
assert len(ts_mol.ts.ic) == 11
def test_from_file_to_path(self):
with path("saddle.test.data", "rct.xyz") as rct_path:
with path("saddle.test.data", "prd.xyz") as prd_path:
ts_mol = TSConstruct.from_file(rct_path, prd_path)
ts_mol.auto_generate_ts(task="path")
assert isinstance(ts_mol.ts, PathRI)