def vib(struct, proj_path):
#struct.calc = Gaussian(label='calc/' + proj_name + '/freq',
# freq='')
print("\nBeginning calculation of IR frequencies...")
struct.calc = Gaussian(mem='4GB',
nprocshared='8',
label=proj_path + '/vib',
)
#struct.get_potential_energy()
ir = Infrared(struct)
ir.run()
ir.write_spectra('ir_spectra.dat')
spectrum = ir.get_spectrum()
ir.clean() # to get rid of disturbing .pckl files cluttering the directory
print("Calculation of vibrational frequencies completed!\nPrinting spectrum...")
return struct, spectrum
def test_folding(testdir):
"""Test that folding is consitent with intensities"""
atoms = molecule('C2H6')
atoms.calc = RandomCalculator()
ir = Infrared(atoms)
ir.run()
freqs = ir.get_frequencies().real
for folding in ['Gaussian', 'Lorentzian']:
x, y = ir.get_spectrum(start=freqs.min() - 100,
end=freqs.max() + 100,
type=folding,
normalize=True)
assert ir.intensities.sum() == pytest.approx(
y.sum() * (x[1] - x[0]), 1e-2)
def test_combine(testdir):
dirname = 'subdir'
vibname = 'ir'
with workdir(dirname, mkdir=True):
atoms = molecule('C2H6')
ir = Infrared(atoms)
assert ir.name == vibname
ir.calc = RandomCalculator()
ir.run()
freqs = ir.get_frequencies()
ints = ir.intensities
assert ir.combine() == 49
ir = Infrared(atoms)
assert (freqs == ir.get_frequencies()).all()
assert (ints == ir.intensities).all()
vib = Vibrations(atoms, name=vibname)
assert (freqs == vib.get_frequencies()).all()
# Read the data from other working directory
with workdir('..'):
ir = Infrared(atoms, name=f'{dirname}/{vibname}')
assert (freqs == ir.get_frequencies()).all()
ir = Infrared(atoms)
assert ir.split() == 1
assert (freqs == ir.get_frequencies()).all()
assert (ints == ir.intensities).all()
vib = Vibrations(atoms, name=vibname)
assert (freqs == vib.get_frequencies()).all()
assert ir.clean() == 49
alpha_back = 0.70
alpha_front = 1.0
for i, atoms in enumerate(ga_stru):
e = atoms.get_potential_energy()
Gs_slab[i] = e
colors[i] = color_lib[i]
# vibrational frequency calculations
calc = GPAW(mode=PW(500),
xc='PBE',
spinpol=True,
kpts=(2, 2, 1),
symmetry={'point_group': False},
basis='dzp')
O2.set_calculator(calc)
O2vib = Infrared(O2)
#print(O2vib)
#O2vib.run()
#O2vib.summary()
e_O2vib = O2vib.get_energies()
#print(e_O2vib)
thermo = IdealGasThermo(vib_energies=e_O2vib,
atoms=O2,
geometry='linear',
symmetrynumber=2,
spin=1)
#print(e_O2vib)
def get_mu(T, p):
class RandomCalculator():
"""Fake Calculator class.
"""
def __init__(self):
self.rng = RandomState(42)
def get_forces(self, atoms):
return self.rng.rand(len(atoms), 3)
def get_dipole_moment(self, atoms):
return self.rng.rand(3)
atoms = molecule('C2H6')
ir = Infrared(atoms)
ir.calc = RandomCalculator()
ir.run()
freqs = ir.get_frequencies()
ints = ir.intensities
assert ir.combine() == 49
ir = Infrared(atoms)
assert (freqs == ir.get_frequencies()).all()
assert (ints == ir.intensities).all()
vib = Vibrations(atoms, name='ir')
assert (freqs == vib.get_frequencies()).all()
# Read the data from other working directory
dirname = os.path.basename(os.getcwd())
def test_combine():
import os
from numpy.random import RandomState
from ase.build import molecule
from ase.vibrations import Vibrations
from ase.vibrations import Infrared
class RandomCalculator():
"""Fake Calculator class.
"""
def __init__(self):
self.rng = RandomState(42)
def get_forces(self, atoms):
return self.rng.rand(len(atoms), 3)
def get_dipole_moment(self, atoms):
return self.rng.rand(3)
atoms = molecule('C2H6')
ir = Infrared(atoms)
ir.calc = RandomCalculator()
ir.run()
freqs = ir.get_frequencies()
ints = ir.intensities
assert ir.combine() == 49
ir = Infrared(atoms)
assert (freqs == ir.get_frequencies()).all()
assert (ints == ir.intensities).all()
vib = Vibrations(atoms, name='ir')
assert (freqs == vib.get_frequencies()).all()
# Read the data from other working directory
dirname = os.path.basename(os.getcwd())
os.chdir('..') # Change working directory
ir = Infrared(atoms, name=os.path.join(dirname, 'ir'))
assert (freqs == ir.get_frequencies()).all()
os.chdir(dirname)
ir = Infrared(atoms)
assert ir.split() == 1
assert (freqs == ir.get_frequencies()).all()
assert (ints == ir.intensities).all()
vib = Vibrations(atoms, name='ir')
assert (freqs == vib.get_frequencies()).all()
assert ir.clean() == 49
class RandomCalculator():
"""Fake Calculator class.
"""
def __init__(self):
self.rng = RandomState(42)
def get_forces(self, atoms):
return self.rng.rand(len(atoms), 3)
def get_dipole_moment(self, atoms):
return self.rng.rand(3)
atoms = molecule('C2H6')
ir = Infrared(atoms)
ir.calc = RandomCalculator()
ir.run()
freqs = ir.get_frequencies()
ints = ir.intensities
assert ir.combine() == 49
ir = Infrared(atoms)
assert (freqs == ir.get_frequencies()).all()
assert (ints == ir.intensities).all()
vib = Vibrations(atoms, name='ir')
assert (freqs == vib.get_frequencies()).all()
ir = Infrared(atoms)
assert ir.split() == 1
from ase.db import connect
import os
for i in range(133885):
try:
print('-' * 100, i)
# os.system('ls | grep -v water.py | grep -v qm9*.db | xargs rm')
os.system('rm -rf *.pckl vasprun.xml')
a = read('qm9.db@' + str(i))
a.set_cell([10, 10, 10])
a.set_pbc([1, 1, 1])
calc = Vasp(prec='Accurate',
ediff=1E-8,
isym=0,
idipol=4, # calculate the total dipole moment
dipol=a.get_center_of_mass(scaled=True),
ldipol=True,
kpts=[1, 1, 1])
a.calc = calc
ir = Infrared(a)
ir.run()
ir.summary()
with connect('qm9_ir_spectrum.db') as db:
db.write(a, data={'ir_spectrum':ir.get_spectrum()})
# print(ir.get_spectrum()[0].shape)
except:
pass