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)
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)
# Calculate using EMT:
initial.calc = EMT()
# 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)
trajname = fname + '.traj'
print(trajname)
traj = Trajectory(trajname, 'w', runner)
traj.write()
# Making dimer mask list:
# d_mask = [atom.index == 69 for atom in initial]
d_mask = [False] * (N - 1) + [True] # [0, 0, 0, 0, 1]
# d_mask = initial.positions[:, 2] - min(initial.positions[:, 2]) < 1 * a
# Set up the dimer (gaus is for ramdom rotation std sets up the level):
d_control = DimerControl(
initial_eigenmode_method='gauss',
# initial_eigenmode_method='displacement',
displacement_method='gauss', # 'vector',
# displacement_method='vector',
gauss_std=0.1,
trial_angle=pi / 12.0,
logfile=fname + '.log',
mask=d_mask)
""" All the avaiable parameters are:
parameters = {'eigenmode_method': 'dimer',
'f_rot_min': 0.1,
'f_rot_max': 1.00,
'max_num_rot': 1,
'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,
# 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())
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
algo="N",
ismear=0,
sigma=0.1,
npar=8,
lreal="Auto",
lcharg=False,
lwave=True,
directory='calculator')
atoms.set_calculator(calc)
# Set up the dimer
d_control = DimerControl(initial_eigenmode_method='displacement',
displacement_method='vector',
logfile='dimer_control.log',
dimer_separation=0.008,
max_num_rot=2,
mask=mask,
eigenmode_logfile='dimer_eigenmodes.dat')
d_atoms = MinModeAtoms(atoms, d_control)
d_atoms.displace(displacement_vector=displacement_vector)
dim_rlx = MinModeTranslate(d_atoms,
trajectory="dimer_opt.traj",
logfile="dimer_opt.log")
dim_rlx.run(fmax=0.03)
# remember to add in the constraint
original_atoms = read("vasp_optimized.traj")
energy = atoms.get_potential_energy()
dimer.set_constraint(constraint)
d_mask = [False] * N_fix + [True] * (N_atom - N_fix)
# set gp calculator
gp_file = open('PdAg.gp', 'rb')
gp_model = pickle.load(gp_file)
gp_model.energy_force_kernel = mc_simple.two_plus_three_mc_force_en
dimer.set_calculator(gp_calculator.GPCalculator(gp_model))
# 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',