def test_vib():
import os
from ase import Atoms
from ase.calculators.emt import EMT
from ase.optimize import QuasiNewton
from ase.vibrations import Vibrations
from ase.thermochemistry import IdealGasThermo
n2 = Atoms('N2', positions=[(0, 0, 0), (0, 0, 1.1)], calculator=EMT())
QuasiNewton(n2).run(fmax=0.01)
vib = Vibrations(n2)
vib.run()
freqs = vib.get_frequencies()
print(freqs)
vib.summary()
print(vib.get_mode(-1))
vib.write_mode(n=None, nimages=20)
vib_energies = vib.get_energies()
for image in vib.iterimages():
assert len(image) == 2
thermo = IdealGasThermo(vib_energies=vib_energies,
geometry='linear',
atoms=n2,
symmetrynumber=2,
spin=0)
thermo.get_gibbs_energy(temperature=298.15, pressure=2 * 101325.)
assert vib.clean(empty_files=True) == 0
assert vib.clean() == 13
assert len(list(vib.iterimages())) == 13
d = dict(vib.iterdisplace(inplace=False))
for name, atoms in vib.iterdisplace(inplace=True):
assert d[name] == atoms
vib = Vibrations(n2)
vib.run()
assert vib.combine() == 13
assert (freqs == vib.get_frequencies()).all()
vib = Vibrations(n2)
assert vib.split() == 1
assert (freqs == vib.get_frequencies()).all()
assert vib.combine() == 13
# Read the data from other working directory
dirname = os.path.basename(os.getcwd())
os.chdir('..') # Change working directory
vib = Vibrations(n2, name=os.path.join(dirname, 'vib'))
assert (freqs == vib.get_frequencies()).all()
assert vib.clean() == 1
def test_pickle_manipulation(self, n2_emt):
atoms = n2_emt
vib = Vibrations(atoms, name='interrupt')
vib.run()
disp_file = 'interrupt.1x-.pckl'
comb_file = 'interrupt.all.pckl'
assert os.path.isfile(disp_file)
assert not os.path.isfile(comb_file)
with pytest.raises(RuntimeError):
vib.split()
# Build a combined file
assert vib.combine() == 13
# Individual displacements should be gone, combination should exist
assert not os.path.isfile(disp_file)
assert os.path.isfile(comb_file)
# Not allowed to run after data has been combined
with pytest.raises(RuntimeError):
vib.run()
# But reading is allowed
vib.read()
# Splitting should fail if any split file already exists
with open(disp_file, 'w') as f:
f.write("hello")
with pytest.raises(RuntimeError):
vib.split()
os.remove(disp_file)
# Now split() for real: replace .all.pckl file with displacements
vib.split()
assert os.path.isfile(disp_file)
assert not os.path.isfile(comb_file)
# Not allowed to clobber existing combined file
with open(comb_file, 'w') as f:
f.write("Hello")
with pytest.raises(RuntimeError):
vib.combine()
os.remove(comb_file)
# Combining data also fails if some data is missing
os.remove('interrupt.1x-.pckl')
with pytest.raises(RuntimeError):
vib.combine()
vib.clean()
def test_json_manipulation(self, testdir, random_dimer):
vib = Vibrations(random_dimer, name='interrupt')
vib.run()
disp_file = Path('interrupt/cache.1x-.json')
comb_file = Path('interrupt/combined.json')
assert disp_file.is_file()
assert not comb_file.is_file()
# Should do nothing harmful as files are already split
# (It used to raise an error but this is no longer implemented.)
vib.split()
# Build a combined file
assert vib.combine() == 13
# Individual displacements should be gone, combination should exist
assert not disp_file.is_file()
assert comb_file.is_file()
# Not allowed to run after data has been combined
with pytest.raises(RuntimeError):
vib.run()
# But reading is allowed
vib.read()
# Splitting should fail if any split file already exists
with open(disp_file, 'w') as fd:
fd.write("hello")
with pytest.raises(AssertionError):
vib.split()
os.remove(disp_file)
# Now split() for real: replace .all.json file with displacements
vib.split()
assert disp_file.is_file()
assert not comb_file.is_file()
from ase.constraints import FixAtoms
from ase.units import *
from ase.vibrations import Vibrations
from flare import kernels
from flare.modules import gp_calculator
from mc_kernels import mc_simple
import pickle
# load TS
TS = read('dimer.traj')
# fix bottommost layer
fix = [atom.index for atom in TS if atom.position[2] < 9]
move = [atom.index for atom in TS if atom.position[2] > 9]
constraint = FixAtoms(mask=fix)
TS.set_constraint(constraint)
# 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
TS.set_calculator(gp_calculator.GPCalculator(gp_model))
# calculate Hessian
vib = Vibrations(TS, indices=move)
vib.run()
# clean up
vib.summary(log='gp_freq.txt')
vib.combine()
potential='../CourseGitRepo/HA5_al_potential.alloy') # Set up EAM
atoms.set_calculator(mishin)
# Relax structure
dyn = BFGS(atoms, trajectory=f'traj/Al{N}.traj')
dyn.run(fmax=0.05)
# Get vibrational spectrum
str1 = f'-------- N={N}'
str2 = ' ---------'
print(str1 + str2.ljust(40 - len(str1)))
##### Using Vibrations module
v = Vibrations(atoms, name=f'./vibs/vib_{N}')
if not p.isfile(f'./vibs/vib_{N}.all.pckl'):
print('Running vibration calculation')
v.run()
v.combine() # Combine pickle files
# Get frequencies and DOS - i.e # of states per frequency
all_freq = v.get_frequencies()
# if N==38:
# print(v.summary())
# print(all_freq)
(freq, counts) = np.unique(all_freq, return_counts=True)
fold_freq = v.fold(np.real(freq),
np.real(counts),
start=0,
end=np.real(freq.max()),
width=12,
normalize=False)
f_freq = np.array(fold_freq[0])
f_dos = np.array(fold_freq[1])
freq = np.array(freq)
for image in vib.iterimages():
assert len(image) == 2
thermo = IdealGasThermo(vib_energies=vib_energies,
geometry='linear',
atoms=n2,
symmetrynumber=2,
spin=0)
thermo.get_gibbs_energy(temperature=298.15, pressure=2 * 101325.)
assert vib.clean(empty_files=True) == 0
assert vib.clean() == 13
assert len(list(vib.iterimages())) == 13
d = dict(vib.iterdisplace(inplace=False))
for name, atoms in vib.iterdisplace(inplace=True):
assert d[name] == atoms
vib = Vibrations(n2)
vib.run()
assert vib.combine() == 13
assert (freqs == vib.get_frequencies()).all()
vib = Vibrations(n2)
assert vib.split() == 1
assert (freqs == vib.get_frequencies()).all()
assert vib.combine() == 13
assert vib.clean() == 1