if __name__ == '__main__':
from qchem import QChem
from pes import PES
from molecule import Molecule
from _linesearch import NoLineSearch
from slots import Distance
basis = "6-31G*"
nproc = 8
filepath = "examples/tests/bent_benzene.xyz"
lot = QChem.from_options(states=[(1, 0)],
charge=0,
basis=basis,
functional='HF',
nproc=nproc,
fnm=filepath)
pes = PES.from_options(lot=lot, ad_idx=0, multiplicity=1)
M = Molecule.from_options(fnm=filepath, PES=pes, coordinate_type="DLC")
distance = Distance(5, 8) #Not 1 based!!
print(distance)
ef = eigenvector_follow.from_options() #Linesearch=NoLineSearch)
geoms = ef.optimize(molecule=M, refE=M.energy, opt_steps=5)
#geoms = ef.optimize(molecule=M,refE=M.energy,opt_steps=1)
print(M.primitive_internal_coordinates)
manage_xyz.write_xyzs('opt.xyz', geoms, scale=1.)
#functional='HF'
functional = 'B3LYP'
filepath1 = "examples/tests/butadiene_ethene.xyz"
filepath2 = "examples/tests/cyclohexene.xyz"
#filepath1='reactant.xyz'
#filepath2='product.xyz'
lot1 = QChem.from_options(states=[(1, 0)],
charge=0,
basis=basis,
functional=functional,
nproc=nproc,
fnm=filepath1)
lot2 = QChem(lot1.options.copy().set_values({'fnm': filepath2}))
pes1 = PES.from_options(lot=lot1, ad_idx=0, multiplicity=1)
pes2 = PES(pes1.options.copy().set_values({'lot': lot2}))
M1 = Molecule.from_options(fnm=filepath1, PES=pes1, coordinate_type="DLC")
M2 = Molecule.from_options(fnm=filepath2, PES=pes2, coordinate_type="DLC")
optimizer = eigenvector_follow.from_options(
print_level=1
) #default parameters fine here/opt_type will get set by GSM
gsm = GSM.from_options(reactant=M1,
product=M2,
nnodes=9,
optimizer=optimizer,
print_level=1)
gsm.go_gsm(rtype=2, opt_steps=3)