def test_dimer_method(testdir):
# 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.calc = EMT()
atoms.get_potential_energy()
# Set up the dimer
with DimerControl(initial_eigenmode_method='displacement',
displacement_method='vector',
logfile=None,
mask=[0, 0, 0, 0, 1]) as d_control:
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
with MinModeTranslate(d_atoms,
trajectory='dimer_method.traj',
logfile="dimer_method.log") as dim_rlx:
dim_rlx.run(fmax=0.001)
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)
# Relax the initial state:
QuasiNewton(initial).run(fmax=0.05)
e0 = initial.get_potential_energy()
traj = Trajectory('dimer_along.traj', 'w', initial)
traj.write()
# Making dimer mask list:
d_mask = [False] * (N - 1) + [True]
# Set up the dimer:
d_control = DimerControl(initial_eigenmode_method='displacement',
displacement_method='vector',
logfile=None,
mask=d_mask)
d_atoms = MinModeAtoms(initial, d_control)
# Displacement settings:
displacement_vector = np.zeros((N, 3))
# Strength of displacement along y axis = along row:
displacement_vector[-1, 1] = 0.001
# The direction of the displacement is set by the a in
# displacement_vector[-1, a], where a can be 0 for x, 1 for y and 2 for z.
d_atoms.displace(displacement_vector=displacement_vector)
# Converge to a saddle point:
dim_rlx = MinModeTranslate(d_atoms, trajectory=traj, logfile=None)
dim_rlx.run(fmax=0.001)
diff = initial.get_potential_energy() - e0
print(('The energy barrier is %f eV.' % diff))
'trial_angle': pi / 4.0,
'trial_trans_step': 0.001,
'maximum_translation': 0.1,
'cg_translation': True,
'use_central_forces': True,
'dimer_separation': 0.0001,
'initial_eigenmode_method': 'gauss''displacement',
'extrapolate_forces': False,
'displacement_method': 'gauss''vector,
'gauss_std': 0.1,
'order': 1,
'mask': None, # NB mask should not be a "parameter"
'displacement_center': None,
'displacement_radius': None,
'number_of_displacement_atoms': None}"""
d_atoms = MinModeAtoms(runner, d_control)
"""# Enable with 'displacement' - 'vector'
# Displacement settings:
# initial vector:
displacement_vector = np.zeros((N, 3))
# Strength of displacement along y axis = along row:
displacement_vector[-1, 0] = 0.1
# The direction of the displacement needed if usint displacement vector method
# displacement_vector[-1, a], where a can be 0 for x, 1 for y and 2 for z.
d_atoms.displace(displacement_vector=displacement_vector)"""
# Converge to a saddle point:
dim_rlx = MinModeTranslate(d_atoms,
trajectory=traj) # , logfile=None)
dim_rlx.run(fmax=0.001)
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())
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)
# dimer setup
dimer_control = DimerControl(initial_eigenmode_method='displacement',
displacement_method='vector',
maximum_translation=0.2,
trial_trans_step=5.0e-3,
dimer_separation=dimer_dist,
mask=d_mask,
f_rot_min=0.01,
f_rot_max=0.2,
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
# Relax the initial state:
QuasiNewton(initial).run(fmax=0.05)
e0 = initial.get_potential_energy()
traj = Trajectory('dimer_along.traj', 'w', initial)
traj.write()
# Making dimer mask list:
d_mask = [False] * (N - 1) + [True]
# Set up the dimer:
d_control = DimerControl(initial_eigenmode_method='displacement',
displacement_method='vector',
logfile=None,
mask=d_mask)
d_atoms = MinModeAtoms(initial, d_control)
# Displacement settings:
displacement_vector = np.zeros((N, 3))
# Strength of displacement along y axis = along row:
displacement_vector[-1, 1] = 0.001
# The direction of the displacement is set by the a in
# displacement_vector[-1, a], where a can be 0 for x, 1 for y and 2 for z.
d_atoms.displace(displacement_vector=displacement_vector)
# Converge to a saddle point:
dim_rlx = MinModeTranslate(d_atoms,
trajectory=traj,
logfile=None)
dim_rlx.run(fmax=0.001)
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())
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
