def test_dimer_method():
# Set up a small "slab" with an adatoms
atoms = fcc100('Pt', size=(2, 2, 1), vacuum=10.0)
add_adsorbate(atoms, 'Pt', 1.611, 'hollow')
# Freeze the "slab"
mask = [atom.tag > 0 for atom in atoms]
atoms.set_constraint(FixAtoms(mask=mask))
# Calculate using EMT
atoms.set_calculator(EMT())
atoms.get_potential_energy()
# Set up the dimer
d_control = DimerControl(initial_eigenmode_method = 'displacement', \
displacement_method = 'vector', logfile = None, \
mask = [0, 0, 0, 0, 1])
d_atoms = MinModeAtoms(atoms, d_control)
# Displace the atoms
displacement_vector = [[0.0] * 3] * 5
displacement_vector[-1][1] = -0.1
d_atoms.displace(displacement_vector=displacement_vector)
# Converge to a saddle point
dim_rlx = MinModeTranslate(d_atoms, trajectory = 'dimer_method.traj', \
logfile = None)
dim_rlx.run(fmax=0.001)
# Test the results
tolerance = 1e-3
assert (d_atoms.get_barrier_energy() - 1.03733136918 < tolerance)
assert (abs(d_atoms.get_curvature() + 0.900467048707) < tolerance)
assert (d_atoms.get_eigenmode()[-1][1] < -0.99)
assert (abs(d_atoms.get_positions()[-1][1]) < tolerance)
# Freeze the "slab"
mask = [atom.tag > 0 for atom in atoms]
atoms.set_constraint(FixAtoms(mask = mask))
# Calculate using EMT
atoms.set_calculator(EMT())
relaxed_energy = atoms.get_potential_energy()
# Set up the dimer
d_control = DimerControl(initial_eigenmode_method = 'displacement', \
displacement_method = 'vector', logfile = None, \
mask = [0, 0, 0, 0, 1])
d_atoms = MinModeAtoms(atoms, d_control)
# Dispalce the atoms
displacement_vector = [[0.0]*3]*5
displacement_vector[-1][1] = -0.1
d_atoms.displace(displacement_vector = displacement_vector)
# Converge to a saddle point
dim_rlx = MinModeTranslate(d_atoms, trajectory = 'dimer_method.traj', \
logfile = None)
dim_rlx.run(fmax = 0.001)
# Test the results
tolerance = 1e-3
assert(d_atoms.get_barrier_energy() - 1.03733136918 < tolerance)
assert(abs(d_atoms.get_curvature() + 0.889396) < tolerance)
assert(d_atoms.get_eigenmode()[-1][1] < -0.99)
assert(abs(d_atoms.get_positions()[-1][1]) < tolerance)
trial_angle=pi / 4,
max_num_rot=2,
logfile='%s_control.log' % prefix,
eigenmode_logfile='%s_eigenmode.log' % prefix)
dimer_atoms = MinModeAtoms(dimer, dimer_control, eigenmodes=[mode])
dimer_atoms.displace(displacement_vector=mode)
dimer_relax = MinModeTranslate(dimer_atoms,
trajectory='%s.traj' % prefix,
logfile='%s_relax.log' % prefix)
# also possible to use these:
#dimer_relax = FIRE(dimer_atoms, trajectory='dimer.traj',
# restart='restart_file',
# dt=0.1, # default 0.1
# maxmove=0.2, # default 0.2
# dtmax=1.0, # default 1.0
# Nmin=3, # default 5
# finc=1.1, # default 3
# fdec=0.71, # default 0.5
# astart=0.2, # default 0.1
# fa=0.99) # default 0.99
#dimer_relax = BFGS(dimer_atoms, trajectory='dimer.traj', restart='restart_file')
# run dimer
dimer_relax.run(fmax=force_tol)
# clean up
np.savetxt('%s.MODE' % prefix, dimer_atoms.get_eigenmode())
write('POSCAR.vasp', dimer_atoms.get_atoms(), format='vasp')
# Freeze the "slab"
mask = [atom.tag > 0 for atom in atoms]
atoms.set_constraint(FixAtoms(mask=mask))
# Calculate using EMT
atoms.set_calculator(EMT())
relaxed_energy = atoms.get_potential_energy()
# Set up the dimer
d_control = DimerControl(
initial_eigenmode_method="displacement", displacement_method="vector", logfile=None, mask=[0, 0, 0, 0, 1]
)
d_atoms = MinModeAtoms(atoms, d_control)
# Displace the atoms
displacement_vector = [[0.0] * 3] * 5
displacement_vector[-1][1] = -0.1
d_atoms.displace(displacement_vector=displacement_vector)
# Converge to a saddle point
dim_rlx = MinModeTranslate(d_atoms, trajectory="dimer_method.traj", logfile=None)
dim_rlx.run(fmax=0.001)
# Test the results
tolerance = 1e-3
assert d_atoms.get_barrier_energy() - 1.03733136918 < tolerance
assert abs(d_atoms.get_curvature() + 0.900467048707) < tolerance
assert d_atoms.get_eigenmode()[-1][1] < -0.99
assert abs(d_atoms.get_positions()[-1][1]) < tolerance
