def compute_normal_modes(self, write_jmol=True):
"""
Use ase calculator to compute numerical frequencies for the molecule
Args:
write_jmol (bool): Write frequencies to input file for visualization in jmol (default=True)
"""
freq_file = os.path.join(self.working_dir, "normal_modes")
# Compute frequencies
frequencies = Vibrations(self.molecule, name=freq_file)
frequencies.run()
# Print a summary
frequencies.summary()
# Write jmol file if requested
if write_jmol:
frequencies.write_jmol()
def freq(atoms=None):
if atoms is None:
atoms = read('md.traj', index=0)
atoms.calc = IRFF(atoms=atoms,
libfile='ffield.json',
rcut=None,
nn=True,
massage=2)
# Compute frequencies
frequencies = Vibrations(atoms, name='freq')
frequencies.run()
# Print a summary
frequencies.summary()
frequencies.write_dos()
# Write jmol file if requested
# if write_jmol:
frequencies.write_jmol()
def run_task(self,fw_spec):
"""ONLY WORKS FOR QUANTUM ESPRESSO"""
from ase.vibrations import Vibrations
jobID = fw_spec['jobID']
job = db2object(jobID)
t0 = time.time()
atoms = job.atoms()
atoms.set_calculator(job.vibCalc())
vib = Vibrations(atoms,delta=job.delta(),indicies=job.vibids)
vib.run()
vib.summary(log='vibrations.txt')
vib.write_jmol()
vibs = vib.get_frequencies()
t = (time.time()-t0)/60.0 #min
return FWAction(stored_data= {'vibs':vibs,'avgtime':t},mod_spec=[{'_push': {'vibs':vibs,'time':t}}])
def test_vibration_on_surface(self, testdir):
from ase.build import fcc111, add_adsorbate
ag_slab = fcc111('Ag', (4, 4, 2), a=2)
n2 = Atoms('N2',
positions=[[0., 0., 0.], [0., np.sqrt(2),
np.sqrt(2)]])
add_adsorbate(ag_slab, n2, height=1, position='fcc')
# Add an interaction between the N atoms
hessian_bottom_corner = np.zeros((2, 3, 2, 3))
hessian_bottom_corner[-1, :, -2] = [1, 1, 1]
hessian_bottom_corner[-2, :, -1] = [1, 1, 1]
hessian = np.zeros((34, 3, 34, 3))
hessian[32:, :, 32:, :] = hessian_bottom_corner
ag_slab.calc = ForceConstantCalculator(hessian.reshape(
(34 * 3, 34 * 3)),
ref=ag_slab.copy(),
f0=np.zeros((34, 3)))
# Check that Vibrations with restricted indices returns correct Hessian
vibs = Vibrations(ag_slab, indices=[-2, -1])
vibs.run()
vibs.read()
assert_array_almost_equal(vibs.get_vibrations().get_hessian(),
hessian_bottom_corner)
# These should blow up if the vectors don't match number of atoms
vibs.summary()
vibs.write_jmol()
for i in range(6):
# Frozen atoms should have zero displacement
assert_array_almost_equal(vibs.get_mode(i)[0], [0., 0., 0.])
# The N atoms should have finite displacement
assert np.all(vibs.get_mode(i)[-2:, :])
def run_task(self,fw_spec):
"""ONLY WORKS FOR QUANTUM ESPRESSO"""
from ase.vibrations import Vibrations
job,params,atoms = initialize(fw_spec)
prev = g.glob('*.pckl') #delete incomplete pckls - facilitating restarted jobs
for p in prev:
if os.stat(p).st_size < 100: os.remove(p)
atoms.set_calculator(job.vibCalc())
vib = Vibrations(atoms,delta=job.delta(),indices=job.vibids())
vib.run(); vib.write_jmol()
vib.summary(log='vibrations.txt')
with open('vibrations.txt','r') as f: vibsummary = f.read()
vib_energies,vib_frequencies = vib.get_energies(),vib.get_frequencies()
resultDict = misc.mergeDicts([params, {'vibfreqs_pckl': pickle.dumps(vib_frequencies)
,'vibsummary':vibsummary
,'vibengs_pckl':pickle.dumps(vib_energies)}])
with open('result.json', 'w') as outfile: json.dumps(resultDict, outfile)
return fireworks.core.firework.FWAction(stored_data=resultDict)
def test_vibrations_on_surface(self, testdir):
atoms = self.n2_on_ag.copy()
atoms.calc = EMT()
vibs = Vibrations(atoms, indices=[-2, -1])
vibs.run()
freqs = vibs.get_frequencies()
assert len(freqs) == 6
vib_data = vibs.get_vibrations()
assert_array_almost_equal(freqs, vib_data.get_frequencies())
# These should blow up if the vectors don't match number of atoms
vibs.summary()
vibs.write_jmol()
for i in range(6):
# Frozen atoms should have zero displacement
assert_array_almost_equal(vibs.get_mode(i)[0], [0., 0., 0.])
# At least one of the N atoms should have finite displacement
# (It's a strange test system, the N aren't interacting.)
assert np.any(vibs.get_mode(i)[-2:, :])
def test_vibrations(self, testdir, n2_emt, n2_optimized):
atoms = n2_emt
vib = Vibrations(atoms)
vib.run()
freqs = vib.get_frequencies()
vib.write_mode(n=None, nimages=5)
vib.write_jmol()
vib_energies = vib.get_energies()
for image in vib.iterimages():
assert len(image) == 2
thermo = IdealGasThermo(vib_energies=vib_energies,
geometry='linear',
atoms=atoms,
symmetrynumber=2,
spin=0)
thermo.get_gibbs_energy(temperature=298.15,
pressure=2 * 101325.,
verbose=False)
vib.summary(log=self.logfile)
with open(self.logfile, 'rt') as f:
log_txt = f.read()
assert log_txt == vibrations_n2_log
mode1 = vib.get_mode(-1)
assert_array_almost_equal(mode1,
[[0., 0., -0.188935], [0., 0., 0.188935]])
assert_array_almost_equal(
vib.show_as_force(-1, show=False).get_forces(),
[[0., 0., -2.26722e-1], [0., 0., 2.26722e-1]])
for i in range(3):
assert not os.path.isfile('vib.{}.traj'.format(i))
mode_traj = ase.io.read('vib.3.traj', index=':')
assert len(mode_traj) == 5
assert_array_almost_equal(mode_traj[0].get_all_distances(),
atoms.get_all_distances())
with pytest.raises(AssertionError):
assert_array_almost_equal(mode_traj[4].get_all_distances(),
atoms.get_all_distances())
with open('vib.xyz', 'rt') as f:
jmol_txt = f.read()
assert jmol_txt == jmol_txt_ref
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, image in vib.iterdisplace(inplace=True):
assert d[name] == atoms
atoms2 = n2_emt
vib2 = Vibrations(atoms2)
vib2.run()
assert_array_almost_equal(freqs, vib.get_frequencies())
# write/read the data from another working directory
atoms3 = n2_optimized.copy() # No calculator needed!
workdir = os.path.abspath(os.path.curdir)
try:
os.mkdir('run_from_here')
os.chdir('run_from_here')
vib = Vibrations(atoms3, name=os.path.join(os.pardir, 'vib'))
assert_array_almost_equal(freqs, vib.get_frequencies())
assert vib.clean() == 13
finally:
os.chdir(workdir)
if os.path.isdir('run_from_here'):
os.rmdir('run_from_here')
print("***Without OPTIMIZITION***\n")
else:
print("choose only 1 or 0")
print('START FREQ CALCULATION:\n')
from ase.vibrations import Vibrations
vib = Vibrations(molecule)
vib.run()
vib.combine()
print('END OF FREQ CALCULATION\n')
print('VIBRATIONAL SUMMARY:\n')
vib.summary()
print('\nWRITING NORMAL MODE\n')
vib.write_jmol()
print('.')
print('.')
print('use JMOL for viewing of the modes')
print('.')
print('.')
print('DONE\n\n')
from ase.thermochemistry import IdealGasThermo
print("Thermochemistry DATA:\n'BY Ideal-gas limit'")
vib_energies = vib.get_energies()
potentialenergy = molecule.get_potential_energy()
thermo = IdealGasThermo(vib_energies=vib_energies,
potentialenergy=potentialenergy,
atoms=molecule,