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
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
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_vibrations_restart_dir(self, testdir, random_dimer):
vib = Vibrations(random_dimer)
vib.run()
freqs = vib.get_frequencies()
assert freqs is not None
# write/read the data from another working directory
atoms = random_dimer.copy() # This copy() removes the Calculator
with ase.utils.workdir('run_from_here', mkdir=True):
vib = Vibrations(atoms, name=str(Path.cwd().parent / 'vib'))
assert_array_almost_equal(freqs, vib.get_frequencies())
assert vib.clean() == 13
def characteriseTSinternal(self, mol):
os.chdir((self.workingDir + '/Raw/' + self.procNum))
if (self.lowMeth == 'nwchem'):
mol = tl.setCalc(mol, self.lowString, 'nwchem2', self.lowLev)
self.Reac.get_forces()
else:
mol = tl.setCalc(mol, self.lowString, self.lowMeth, self.lowLev)
vib = Vibrations(mol)
vib.clean()
vib.run()
viblist = vib.get_frequencies()
print("getting vibs")
TSFreqs, zpe = tl.getVibString(viblist, False, True)
print("vibs done " + str(zpe))
imaginaryFreq = tl.getImageFreq(viblist)
vib.clean()
os.chdir((self.workingDir))
# Finally get single point energy
mol = tl.setCalc(mol, self.singleString, self.singleMeth,
self.singleLev)
print("Getting single point energy for TS = " +
str(mol.get_potential_energy()) + "zpe = " + str(zpe) +
"reactant energy = " + str(self.reactantEnergy))
energy = mol.get_potential_energy() + zpe
return TSFreqs, imaginaryFreq, zpe, energy
def test_Ag_Cu100():
from math import sqrt
from ase import Atom, Atoms
from ase.neb import NEB
from ase.constraints import FixAtoms
from ase.vibrations import Vibrations
from ase.calculators.emt import EMT
from ase.optimize import QuasiNewton, BFGS
# Distance between Cu atoms on a (100) surface:
d = 3.6 / sqrt(2)
initial = Atoms('Cu',
positions=[(0, 0, 0)],
cell=(d, d, 1.0),
pbc=(True, True, False))
initial *= (2, 2, 1) # 2x2 (100) surface-cell
# Approximate height of Ag atom on Cu(100) surfece:
h0 = 2.0
initial += Atom('Ag', (d / 2, d / 2, h0))
# Make band:
images = [initial.copy() for i in range(6)]
neb = NEB(images, climb=True)
# Set constraints and calculator:
constraint = FixAtoms(range(len(initial) - 1))
for image in images:
image.calc = EMT()
image.set_constraint(constraint)
# Displace last image:
images[-1].positions[-1] += (d, 0, 0)
# Relax height of Ag atom for initial and final states:
dyn1 = QuasiNewton(images[0])
dyn1.run(fmax=0.01)
dyn2 = QuasiNewton(images[-1])
dyn2.run(fmax=0.01)
# Interpolate positions between initial and final states:
neb.interpolate()
for image in images:
print(image.positions[-1], image.get_potential_energy())
dyn = BFGS(neb, trajectory='mep.traj')
dyn.run(fmax=0.05)
for image in images:
print(image.positions[-1], image.get_potential_energy())
a = images[0]
vib = Vibrations(a, [4])
vib.run()
print(vib.get_frequencies())
vib.summary()
print(vib.get_mode(-1))
vib.write_mode(-1, nimages=20)
def characteriseFreqInternal(self, mol):
os.chdir((self.workingDir + '/' + '/Raw/' + self.procNum))
vib = Vibrations(mol)
vib.clean()
vib.run()
viblist = vib.get_frequencies()
freqs, zpe = tl.getVibString(viblist, False, False)
vib.clean()
os.chdir((self.workingDir))
return freqs, zpe
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()
vib_data = vibs.get_vibrations()
assert_array_almost_equal(freqs, vib_data.get_frequencies())
def test_gs_minimum():
"""Test ground state minimum distance, energy and
vibrational frequency"""
atoms = H2Morse()
assert atoms.get_distance(0, 1) == pytest.approx(Re[0], 1.e-12)
assert atoms.get_potential_energy() == -De[0]
# check ground state vibrations
vib = Vibrations(atoms)
vib.run()
assert (vib.get_frequencies().real[-1] == pytest.approx(ome[0], 1e-2))
def VibScript():
from ase.vibrations import Vibrations
import glob, json, cPickle, ase, os
#######################
print "Initializing..."
#----------------------
params, atoms = initialize(
) # Remove old .out/.err files, load from fw_spec, and write 'init.traj'
prev = glob.glob(
'*.pckl') #delete incomplete pckls - facilitating restarted jobs
if rank() == 0:
for p in prev:
if os.stat(p).st_size < 100: os.remove(p)
atoms.set_calculator(makeCalc(params))
vib = Vibrations(atoms,
delta=params['delta'],
indices=json.loads(params['vibids_json']))
vib.run()
vib.write_jmol()
##########################
print "Storing Results..."
#-------------------------
vib.summary(log='vibrations.txt')
with open('vibrations.txt', 'r') as f:
vibsummary = f.read()
ase.io.write('final.traj', atoms)
optAtoms = ase.io.read('final.traj')
vib_energies, vib_frequencies = vib.get_energies(), vib.get_frequencies()
resultDict = mergeDicts([
params,
trajDetails(optAtoms), {
'vibfreqs_pckl': cPickle.dumps(vib_frequencies),
'vibsummary': vibsummary,
'vibengs_pckl': cPickle.dumps(vib_energies)
}
])
with open('result.json', 'w') as outfile:
outfile.write(json.dumps(resultDict))
with open('result.json', 'r') as outfile:
json.loads(outfile.read()) #test that dictionary isn't 'corrupted'
if rank() == 0: log(params, optAtoms)
return 0
def get_modes(self,atm,freqname="vib."):
for f in [f for f in os.listdir(".") if freqname in f and '.pckl' in f]:
os.remove(f)
new_target = open(os.devnull, "w")
old_target, sys.stdout = sys.stdout, new_target
atm.set_calculator(ANIENS(self.ens))
vib = Vibrations(atm, nfree=2, name=freqname)
vib.run()
freq = vib.get_frequencies()
modes = np.stack(vib.get_mode(i) for i in range(freq.size))
vib.clean()
sys.stdout = old_target
return modes
def __init__(self, atoms, vibname, minfreq=None, maxfreq=None):
"""Input is a atoms object and the corresponding vibrations.
With minfreq and maxfreq frequencies can
be excluded from the calculation"""
self.atoms = atoms
# V = a * v is the combined atom and xyz-index
self.mm05_V = np.repeat(1.0 / np.sqrt(atoms.get_masses()), 3)
self.minfreq = minfreq
self.maxfreq = maxfreq
self.shape = (len(self.atoms), 3)
vib = Vibrations(atoms, name=vibname)
self.energies = np.real(vib.get_energies(method="frederiksen")) # [eV]
self.frequencies = np.real(vib.get_frequencies(method="frederiksen")) # [cm^-1]
self.modes = vib.modes
self.H = vib.H
def __init__(self, atoms, vibname, minfreq=-np.inf, maxfreq=np.inf):
"""Input is a atoms object and the corresponding vibrations.
With minfreq and maxfreq frequencies can
be excluded from the calculation"""
self.atoms = atoms
# V = a * v is the combined atom and xyz-index
self.mm05_V = np.repeat(1. / np.sqrt(atoms.get_masses()), 3)
self.minfreq = minfreq
self.maxfreq = maxfreq
self.shape = (len(self.atoms), 3)
vib = Vibrations(atoms, name=vibname)
self.energies = np.real(vib.get_energies(method='frederiksen')) # [eV]
self.frequencies = np.real(
vib.get_frequencies(method='frederiksen')) # [cm^-1]
self.modes = vib.modes
self.H = vib.H
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_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 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 characteriseMinInternal(self, mol):
os.chdir((self.workingDir + '/' + '/Raw/' + self.procNum))
if (self.lowMeth == 'nwchem'):
mol = tl.setCalc(mol, self.lowString, 'nwchem2', self.lowLev)
self.Reac.get_forces()
else:
mol = tl.setCalc(mol, self.lowString, self.lowMeth, self.lowLev)
min = BFGS(mol)
min.run(fmax=0.05, steps=50)
vib = Vibrations(mol)
vib.clean()
vib.run()
viblist = vib.get_frequencies()
Freqs, zpe = tl.getVibString(viblist, False, False)
vib.clean()
os.chdir((self.workingDir))
# Finally get single point energy
mol = tl.setCalc(mol, self.singleString, self.singleMeth,
self.singleLev)
print("Getting single point energy for TS = " +
str(mol.get_potential_energy()) + "zpe = " + str(zpe) +
"reactant energy = " + str(self.reactantEnergy))
energy = mol.get_potential_energy() + zpe
return Freqs, energy, mol
from __future__ import print_function
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
def calculate(element, ref_data, p):
values_dict = {}
values_dict[p['xc']] = {}
for XY, data in ref_data[p['xc']].items():
X = XY.split('-')[0]
Y = XY.split('-')[1]
if (X == Y and X == element) or (X != Y and (X == element or Y == element)):
# compound contains the requested element
re_ref = data['re']
we_ref = data['we']
m0_ref = data.get('m0', 0.0)
#
compound = Atoms(X+Y,
[
(0, 0, 0.5 ),
(0, 0, 0.5+re_ref/a),
],
pbc=0)
compound.set_cell([a, b, c], scale_atoms=1)
compound.center()
# calculation on the reference geometry
calc = Calculator(**p)
compound.set_calculator(calc)
e_compound = compound.get_potential_energy()
finegd = calc.density.finegd
dip = finegd.calculate_dipole_moment(calc.density.rhot_g)*calc.a0
vib = Vibrations(compound)
vib.run()
vib_compound = vib.get_frequencies(method='frederiksen').real[-1]
world.barrier()
vib_pckl = glob('vib.*.pckl')
if rank == 0:
for file in vib_pckl: remove(file)
# calculation on the relaxed geometry
qn = QuasiNewton(compound)
#qn.attach(PickleTrajectory('compound.traj', 'w', compound).write)
qn.run(fmax=0.05)
e_compound_r = compound.get_potential_energy()
dist_compound_r = compound.get_distance(0,1)
dip_r = finegd.calculate_dipole_moment(calc.density.rhot_g)*calc.a0
vib = Vibrations(compound)
vib.run()
vib_compound_r = vib.get_frequencies(method='frederiksen').real[-1]
world.barrier()
vib_pckl = glob('vib.*.pckl')
if rank == 0:
for file in vib_pckl: remove(file)
del compound
e = e_compound
we = vib_compound
m0 = dip
e_r = e_compound_r
we_r = vib_compound_r
re_r = dist_compound_r
m0_r = dip_r
#
values_dict[p['xc']][XY] = {'re': re_r, 'we': (we_r, we), 'm0': (m0_r, m0)}
#
return values_dict
maxiter=777,
convergence={'lshift': 0.0},
basis=basis,
basispar='spherical',
direct='noio',
raw='set int:txs:limxmem 134217728\nmemory total 8000 Mb noverify\n',
label=label)
atoms.set_calculator(calc)
t = time.time()
if len(atoms) > 1:
# need a copy of atoms for calculation of vibrations
vibatoms = atoms.copy()
vibatoms.set_calculator(calc)
vib = Vibrations(vibatoms, name=label + '_fixed')
vib.run()
f = vib.get_frequencies()[-1].real
# clean nwchem restart
if os.path.exists(name + '_' + code + '.db'):
os.remove(name + '_' + code + '.db')
atoms.get_potential_energy()
c.write(atoms, name=name, relaxed=False, basis=basis,
frequency=f,
time=time.time()-t)
else:
atoms.get_potential_energy()
c.write(atoms, name=name, relaxed=False, basis=basis,
time=time.time()-t)
if len(atoms) > 1:
opt = BFGS(atoms,
logfile=name + '_' + code + '.log',
trajectory=name + '_' + code + '.traj')
Analysis_CalculateForces = 'Yes')
# Mixing calculators
QMMMcalc = ase.calculators.mixing.SumCalculator([DFTBcalc,SchNetcalc], atoms)
atoms.set_calculator(QMMMcalc)
# Optmizing geometry
qn = BFGS(atoms, trajectory='mol.traj')
qn.run(fmax=0.0001)
write('final.xyz', atoms)
# Computing vibrational modes
vib = Vibrations(atoms, delta=0.01,nfree=4)
vib.run()
vib.summary()
vb_ev = vib.get_energies()
vb_cm = vib.get_frequencies()
ENE = float(atoms.get_total_energy())
o1 = open('info-modes.dat', 'w')
o1.write("# Potential energy: " + "{: >24}".format(ENE) + "\n")
for i in range(0, len(vb_ev)):
o1.write("{: >24}".format(vb_ev.real[i]) + "{: >24}".format(vb_ev.imag[i]) + "{: >24}".format(vb_cm.real[i]) + "{: >24}".format(vb_cm.imag[i]) + "\n")
vib.write_jmol()
o1.close()
chdir(odir)
# 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)
dos = np.array(counts)
def calculate(element, ref_data, p):
values_dict = {}
values_dict[p['xc']] = {}
for XY, data in ref_data[p['xc']].items():
X = XY.split('-')[0]
Y = XY.split('-')[1]
if (X == Y and X == element) or (X != Y and
(X == element or Y == element)):
# compound contains the requested element
re_ref = data['re']
we_ref = data['we']
m0_ref = data.get('m0', 0.0)
#
compound = Atoms(X + Y, [
(0, 0, 0.5),
(0, 0, 0.5 + re_ref / a),
],
pbc=0)
compound.set_cell([a, b, c], scale_atoms=1)
compound.center()
# calculation on the reference geometry
calc = Calculator(**p)
compound.set_calculator(calc)
e_compound = compound.get_potential_energy()
finegd = calc.density.finegd
dip = finegd.calculate_dipole_moment(calc.density.rhot_g) * calc.a0
vib = Vibrations(compound)
vib.run()
vib_compound = vib.get_frequencies(method='frederiksen').real[-1]
world.barrier()
vib_pckl = glob('vib.*.pckl')
if rank == 0:
for file in vib_pckl:
remove(file)
# calculation on the relaxed geometry
qn = QuasiNewton(compound)
#qn.attach(PickleTrajectory('compound.traj', 'w', compound).write)
qn.run(fmax=0.05)
e_compound_r = compound.get_potential_energy()
dist_compound_r = compound.get_distance(0, 1)
dip_r = finegd.calculate_dipole_moment(
calc.density.rhot_g) * calc.a0
vib = Vibrations(compound)
vib.run()
vib_compound_r = vib.get_frequencies(method='frederiksen').real[-1]
world.barrier()
vib_pckl = glob('vib.*.pckl')
if rank == 0:
for file in vib_pckl:
remove(file)
del compound
e = e_compound
we = vib_compound
m0 = dip
e_r = e_compound_r
we_r = vib_compound_r
re_r = dist_compound_r
m0_r = dip_r
#
values_dict[p['xc']][XY] = {
're': re_r,
'we': (we_r, we),
'm0': (m0_r, m0)
}
#
return values_dict
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')
dw=8000, # density cutoff
nbands=-10, # number of bands
kpts=(8, 8, 8), # k points
xc='rpbe', # exchange correlation method
sigma=0.2, # Fermi temperature
dipole={'status': False},
spinpol=False,
convergence={
'energy': 0.0005,
'mixing': 0.1,
'nmix': 10,
'maxsteps': 500,
'diag': 'david'
},
outdirprefix='vibdir')
atoms.set_calculator(calc)
vib = Vibrations(atoms, delta=0.04, indices=vib_atoms)
vib.run()
vib.summary(log='vibrations.txt')
vib.write_jmol()
realFreq = [
x * 0.00012 for x in vib.get_frequencies() if not isinstance(x, complex)
] #eV
S = HarmonicThermo(realFreq).get_entropy(300)
with open('vibrations.txt', 'a') as f:
f.write('\nTS at 300K: ' + str(S))
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()
print vib.get_frequencies()
vib.summary()
print vib.get_mode(-1)
vib.write_mode(-1, nimages=20)
vib_energies = vib.get_energies()
thermo = IdealGasThermo(vib_energies=vib_energies, geometry='linear',
atoms=n2, symmetrynumber=2, spin=0)
thermo.get_free_energy(temperature=298.15, pressure=2*101325.)
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()
print(vib.get_frequencies())
vib.summary()
print(vib.get_mode(-1))
vib.write_mode(n=None, nimages=20)
vib_energies = vib.get_energies()
thermo = IdealGasThermo(vib_energies=vib_energies, geometry='linear',
atoms=n2, symmetrynumber=2, spin=0)
thermo.get_gibbs_energy(temperature=298.15, pressure=2 * 101325.)
from __future__ import print_function
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()
print(vib.get_frequencies())
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))
from ase import *
from ase.vibrations import Vibrations
n2 = Atoms('N2',
positions=[(0, 0, 0), (0, 0, 1.1)],
calculator=EMT())
QuasiNewton(n2).run(fmax=0.01)
vib = Vibrations(n2)
vib.run()
print vib.get_frequencies()
vib.summary()
print vib.get_mode(-1)
vib.write_mode(-1, nimages=20)
# Using optimal lattice parameter from task 2
a = 4.043 # A
atoms = bulk('Al', 'fcc', a)
# view(atoms) # DEBUG
#### Calculate vibrational spectrum
# Attach EAM calculator to atoms
mishin = EAM(potential='../CourseGitRepo/HA5_al_potential.alloy') # Set up EAM
atoms.set_calculator(mishin)
# Get vibrational spectrum
v = Vibrations(atoms, name='./vibs/vib_bulk')
v.run()
v.summary()
# Get frequencies and DOS - i.e # of states per frequency
(freq, counts) = np.unique(v.get_frequencies(), return_counts=True)
freq = np.array(freq)
dos = np.array(counts)
# Save to db
vibDB.write(atoms, data={'frequency': freq, 'DOS': dos})
#### Calculate band structure
N = 7 # Use a supercell of size 7x7x7
ph = Phonons(atoms,
mishin,
name='./phonons/ph_bulk',
supercell=(N, N, N),
delta=0.05)
ph.run()
# Read the results from the run and obtain the bandpath and DOS
ph.read(acoustic=True)
# Calc minimized energies
e = geometry.get_potential_energy()
print('Total energy', e, 'eV')
# Get the forces again
print('Forces:')
print(geometry.get_forces())
# Run the vibrational analysis
vib = Vibrations(geometry, nfree=2)
vib.run()
print(vib.summary())
print(vib.get_zero_point_energy())
# Get freqs
f = vib.get_frequencies()
# Print modes + freq
for i in range(0, len(f)):
print('Mode(' + str(i) + ') Freq: ' + "{:.7e}".format(f[i]))
print(vib.get_mode(i))
'''
# We will alse need to use these functions to get thermo-chem data
thermo = IdealGasThermo(vib_energies=vib_energies,
potentialenergy=potentialenergy,
atoms=atoms,
geometry='linear',
symmetrynumber=2, spin=0)
G = thermo.get_gibbs_energy(temperature=298.15, pressure=101325.)
'''
