def fire(frames=files.read_xyz("CNH_HCN.xyz"), maxiter=1000):
new_opt_params = {'dt': 0.1, 'euler': False, 'maxiter': maxiter}
return neb.NEB("neb_test",
frames,
"! HF-3c",
opt="FIRE",
new_opt_params=new_opt_params)
def quick_min(frames=files.read_xyz("CNH_HCN.xyz"), maxiter=1000):
new_opt_params = {
'dt': 0.1,
'verbose': False,
'euler': False,
'maxiter': maxiter
}
return neb.NEB("neb_test",
frames,
"! HF-3c",
opt="QM",
new_opt_params=new_opt_params)
def sd(frames=files.read_xyz("CNH_HCN.xyz"), maxiter=1000):
new_opt_params = {
'step_size': 0.1,
'step_size_adjustment': 0.5,
'max_step': 0.2,
'linesearch': 'backtrack',
'accelerate': True,
'maxiter': maxiter
}
return neb.NEB("neb_test",
frames,
"! HF-3c",
opt="SD",
new_opt_params=new_opt_params)
def scipy(method="slsqp", frames=files.read_xyz("CNH_HCN.xyz"), maxiter=1000):
new_opt_params = {
'disp': False,
'gtol': units.convert_energy("Ha", "eV", 1e-3),
'eps': 1.4901161193847656e-08,
'return_all': False,
'maxiter': maxiter,
'norm': 2.0,
'ftol': 0.0
}
return neb.NEB("scipy",
frames,
"! HF-3c",
opt="scipy_" + method,
new_opt_params=new_opt_params)
def conjugate_gradient(frames=files.read_xyz("CNH_HCN.xyz"), maxiter=1000):
new_opt_params = {
'step_size': 0.1,
'step_size_adjustment': 0.5,
'max_step': 0.2,
'linesearch': 'backtrack',
'accelerate': True,
'maxiter': maxiter,
'method': 'FR',
'linesearch': 'backtrack'
}
return neb.NEB("squid_cg",
frames,
"! HF-3c",
opt="CG",
new_opt_params=new_opt_params)
def lbfgs(frames=files.read_xyz("CNH_HCN.xyz"), maxiter=1000):
new_opt_params = {
'step_size': 1.0,
'step_size_adjustment': 0.5,
'max_step': 0.04,
'linesearch': None,
'accelerate': True,
'reset_step_size': 20,
'maxiter': maxiter
}
return neb.NEB("neb_test",
frames,
"! HF-3c",
opt="LBFGS",
queue=None,
procs=1,
new_opt_params=new_opt_params,
ci_neb=True,
no_energy=False)
atom.fz = units.convert("kcal/ang", "Ha/ang", float(atom.extras['fz']))
energy = open("lammps/solv_box-%d-%d/energy.profile" % (step_to_use, i),
'r').read().strip().split("\n")[-1]
new_energy = float(energy.strip().split()[-1].strip())
# Add the forces onto our state
for a, b in zip(state, new_atoms):
a.fx, a.fy, a.fz = b.fx, b.fy, b.fz
return units.convert_energy("kcal/mol", "Ha", new_energy), new_atoms
frames = generate_frames()
files.write_xyz(frames, "neb_initial_configuration.xyz")
sim = neb.NEB(
'benzene',
frames,
('water.cml', 1.0),
#('CH3OH.cml', 0.8),
DFT="None",
opt="LBFGS",
queue="short",
procs=4,
start_job=run_simulation,
get_results=read_simulation,
no_energy=False)
sim.optimize()