def run(job, atoms):
kwargs = {'mode': 0,
'label': 'vib-{0}'.format(job, job),
'xc': 'PBE',
'scf_guess': 'atomic',
'max_scf': 500,
'EPS_SCF': 5.0E-7,
'added_mos': 500,
'sme/method': 'fermi_dirac',
'ELECTRONIC_TEMPERATURE': 300,
'DIA/ALGORITHM': 'STANDARD',
'mix/METHOD': 'BROYDEN_MIXING',
'ALPHA': 0.1,
'BETA': 1.5,
'NBUFFER': 8,
'cpu': 36,
'cutoff': 300,
'run_type': 'ENERGY_FORCE', # ENERGY_FORCE, GEO_OPT, CELL_OPT, MD
'atoms': atoms,
}
calc = CP2K(**kwargs)
atoms.set_calculator(calc)
vib = Vibrations(atoms, indices = [65, 69])
vib.run()
vib.summary()
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 neural_hessian_ase(ase_atoms):
print("Calculating Numerical Hessian using ASE")
vib = Vibrations(ase_atoms, delta=0.05)
vib.run()
vib.summary()
hessian = np.array(vib.H) * (kcal/mol) * Bohr**2
vib.clean()
return hessian
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 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_methods(self, testdir, random_dimer):
vib = Vibrations(random_dimer)
vib.run()
vib_energies = vib.get_energies()
for image in vib.iterimages():
assert len(image) == 2
thermo = IdealGasThermo(vib_energies=vib_energies,
geometry='linear',
atoms=vib.atoms,
symmetrynumber=2,
spin=0)
thermo.get_gibbs_energy(temperature=298.15,
pressure=2 * 101325.,
verbose=False)
with open(self.logfile, 'w') as fd:
vib.summary(log=fd)
with open(self.logfile, 'rt') as fd:
log_txt = fd.read()
assert log_txt == '\n'.join(
VibrationsData._tabulate_from_energies(vib_energies)) + '\n'
last_mode = vib.get_mode(-1)
scale = 0.5
assert_array_almost_equal(
vib.show_as_force(-1, scale=scale, show=False).get_forces(),
last_mode * 3 * len(vib.atoms) * scale)
vib.write_mode(n=3, nimages=5)
for i in range(3):
assert not Path('vib.{}.traj'.format(i)).is_file()
mode_traj = ase.io.read('vib.3.traj', index=':')
assert len(mode_traj) == 5
assert_array_almost_equal(mode_traj[0].get_all_distances(),
random_dimer.get_all_distances())
with pytest.raises(AssertionError):
assert_array_almost_equal(mode_traj[4].get_all_distances(),
random_dimer.get_all_distances())
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] == random_dimer
def test_vibrations_example(testdir):
"""Test the example from the Vibrations.__init__() docstring"""
n2 = Atoms('N2', [(0, 0, 0), (0, 0, 1.1)], calculator=EMT())
BFGS(n2).run(fmax=0.01)
vib = Vibrations(n2)
vib.run()
with io.StringIO() as f:
vib.summary(log=f)
f.seek(0)
summary = f.read()
assert len(summary.split()) == len(expected_summary.split())
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 test_harmonic_thermo():
atoms = fcc100('Cu', (2, 2, 2), vacuum=10.)
atoms.calc = EMT()
add_adsorbate(atoms, 'Pt', 1.5, 'hollow')
atoms.set_constraint(FixAtoms(indices=[atom.index for atom in atoms
if atom.symbol == 'Cu']))
QuasiNewton(atoms).run(fmax=0.01)
vib = Vibrations(atoms, name='harmonicthermo-vib',
indices=[atom.index for atom in atoms
if atom.symbol != 'Cu'])
vib.run()
vib.summary()
vib_energies = vib.get_energies()
thermo = HarmonicThermo(vib_energies=vib_energies,
potentialenergy=atoms.get_potential_energy())
thermo.get_helmholtz_energy(temperature=298.15)
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 run(label, atoms):
#calc.mode = 1
calc.directory = 'vib/pt/{0}'.format(label)
calc.prefix = 'al2o3-pt-{0}'.format(label)
calc.results = {}
calc.CP2K_INPUT.FORCE_EVAL_list[0].DFT.Wfn_restart_file_name = 'al2o3-pt-{0}-RESTART.wfn'.format(label)
calc.CP2K_INPUT.MOTION.CONSTRAINT.FIXED_ATOMS_list = []
#===============================================================================
atoms.set_calculator(calc)
###calc.write_input_file()
#e = atoms.get_potential_energy()
#t = calc.get_time()
print(' {0} '.format(label))
vib = Vibrations(atoms, indices = [120])
vib.run()
vib.summary()
import os, shutil
for file in os.listdir('.'):
if "pckl" in file:
shutil.move(file,calc.directory)
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
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 test_thermochemistry():
"""Tests of the major methods (HarmonicThermo, IdealGasThermo,
CrystalThermo) from the thermochemistry module."""
# Ideal gas thermo.
atoms = Atoms('N2', positions=[(0, 0, 0), (0, 0, 1.1)], calculator=EMT())
QuasiNewton(atoms).run(fmax=0.01)
energy = atoms.get_potential_energy()
vib = Vibrations(atoms, name='idealgasthermo-vib')
vib.run()
vib_energies = vib.get_energies()
thermo = IdealGasThermo(vib_energies=vib_energies,
geometry='linear',
atoms=atoms,
symmetrynumber=2,
spin=0,
potentialenergy=energy)
thermo.get_gibbs_energy(temperature=298.15, pressure=2 * 101325.)
# Harmonic thermo.
atoms = fcc100('Cu', (2, 2, 2), vacuum=10.)
atoms.set_calculator(EMT())
add_adsorbate(atoms, 'Pt', 1.5, 'hollow')
atoms.set_constraint(
FixAtoms(indices=[atom.index for atom in atoms
if atom.symbol == 'Cu']))
QuasiNewton(atoms).run(fmax=0.01)
vib = Vibrations(
atoms,
name='harmonicthermo-vib',
indices=[atom.index for atom in atoms if atom.symbol != 'Cu'])
vib.run()
vib.summary()
vib_energies = vib.get_energies()
thermo = HarmonicThermo(vib_energies=vib_energies,
potentialenergy=atoms.get_potential_energy())
thermo.get_helmholtz_energy(temperature=298.15)
# Crystal thermo.
atoms = bulk('Al', 'fcc', a=4.05)
calc = EMT()
atoms.set_calculator(calc)
energy = atoms.get_potential_energy()
# Phonon calculator
N = 7
ph = Phonons(atoms, calc, supercell=(N, N, N), delta=0.05)
ph.run()
ph.read(acoustic=True)
phonon_energies, phonon_DOS = ph.dos(kpts=(4, 4, 4), npts=30, delta=5e-4)
thermo = CrystalThermo(phonon_energies=phonon_energies,
phonon_DOS=phonon_DOS,
potentialenergy=energy,
formula_units=4)
thermo.get_helmholtz_energy(temperature=298.15)
# Hindered translator / rotor.
# (Taken directly from the example given in the documentation.)
vibs = np.array([
3049.060670, 3040.796863, 3001.661338, 2997.961647, 2866.153162,
2750.855460, 1436.792655, 1431.413595, 1415.952186, 1395.726300,
1358.412432, 1335.922737, 1167.009954, 1142.126116, 1013.918680,
803.400098, 783.026031, 310.448278, 136.112935, 112.939853, 103.926392,
77.262869, 60.278004, 25.825447
])
vib_energies = vibs / 8065.54429 # Convert to eV from cm^-1.
trans_barrier_energy = 0.049313 # eV
rot_barrier_energy = 0.017675 # eV
sitedensity = 1.5e15 # cm^-2
rotationalminima = 6
symmetrynumber = 1
mass = 30.07 # amu
inertia = 73.149 # amu Ang^-2
thermo = HinderedThermo(vib_energies=vib_energies,
trans_barrier_energy=trans_barrier_energy,
rot_barrier_energy=rot_barrier_energy,
sitedensity=sitedensity,
rotationalminima=rotationalminima,
symmetrynumber=symmetrynumber,
mass=mass,
inertia=inertia)
helmholtz = thermo.get_helmholtz_energy(temperature=298.15)
target = 1.593 # Taken from documentation example.
assert (helmholtz - target) < 0.001
from __init__ import AnharmonicModes
slab = fcc111('Al', size=(2, 2, 2), vacuum=3.0)
CH3 = molecule('CH3')
add_adsorbate(slab, CH3, 2.5, 'ontop')
constraint = FixAtoms(mask=[a.symbol == 'Al' for a in slab])
slab.set_constraint(constraint)
slab.set_calculator(EMT())
dyn = QuasiNewton(slab, logfile='/dev/null')
dyn.run(fmax=0.05)
vib = Vibrations(slab, indices=[8, 9, 10, 11])
vib.run()
vib.summary(log='/dev/null')
vib.clean()
AM = AnharmonicModes(vibrations_object=vib)
rot_mode = AM.define_rotation(
basepos=[0., 0., -1.],
branch=[9, 10, 11],
symnumber=3)
AM.run()
AM.summary(log='/dev/null')
AM.clean()
# print(AM.get_ZPE(), AM.get_entropic_energy())
assert abs(AM.get_ZPE() - 0.388) < 1e-3, AM.get_ZPE()
assert abs(AM.get_entropic_energy() - (0.091)) < 1e-3, (
from __init__ import AnharmonicModes
slab = fcc111('Au', size=(2, 2, 2), vacuum=4.0)
H = molecule('H')
add_adsorbate(slab, H, 3.0, 'ontop')
constraint = FixAtoms(mask=[a.symbol == 'Au' for a in slab])
slab.set_constraint(constraint)
slab.set_calculator(EMT())
QuasiNewton(slab).run(fmax=0.001)
vib = Vibrations(slab, indices=[8])
vib.run()
vib.summary()
vib.clean()
AM = AnharmonicModes(vibrations_object=vib, settings={
'plot_mode': True,
})
for i in range(len(vib.hnu)):
AM.define_vibration(mode_number=-1)
AM.inspect_anmodes()
AM.run()
AM.summary()
AM.clean()
print(AM.get_ZPE(), AM.get_entropic_energy())
#!/usr/bin/env python
from ase.db import connect
from ase.calculators.aims import Aims
from ase.lattice.surface import fcc111, add_adsorbate
from ase.constraints import FixAtoms
from ase import Atoms, Atom
from ase.io.aims import read_aims
from ase.optimize import BFGS
from ase.vibrations import Vibrations
mydb = connect("mydb.db")
atoms = mydb.get_atoms(name='pt-co-relax')
calc = Aims(label='cluster/pt-co-vib-cons',
xc='pbe',
spin='none',
relativistic = 'atomic_zora scalar',
sc_accuracy_etot=1e-7,
sc_accuracy_eev=1e-3,
sc_accuracy_rho=1e-4,
sc_accuracy_forces=1e-3)
atoms.set_calculator(calc)
vib = Vibrations(atoms, indices=[1, 2], name='cluster/pt-co-vib-cons/vib')
vib.run()
vib.summary()
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Jun 15 00:45:20 2020
@author: macenrola
"""
from ase import Atoms, io, calculators
import ase.calculators.cp2k
from gpaw import GPAW, PW
from ase.optimize import BFGS
from ase.vibrations import Vibrations
mol = io.read(
"/home/macenrola/Documents/cb8_MV_electrochemistry_JIA/apbs_ref/benzene.pdb"
)
mol.center(vacuum=3.5)
print(mol.cell)
print(mol.positions)
c = ase.calculators.cp2k.CP2K()
CP2K.command = "env OMP_NUM_THREADS=2 mpirun -np 4 cp2k"
print(mol.set_calculator(c))
BFGS(mol).run(fmax=0.01)
vib = Vibrations(mol)
vib.run()
print(vib.summary())
from ase.build import molecule
from ase.optimize import QuasiNewton
from ase.calculators.emt import EMT
from ase.vibrations import Vibrations
from __init__ import AnharmonicModes
H2 = molecule('H2')
H2.set_calculator(EMT())
dyn = QuasiNewton(H2, logfile='/dev/null')
dyn.run(fmax=0.05)
vib = Vibrations(H2, indices=[0, 1])
vib.run()
vib.summary(log='/dev/null')
vib.clean()
AM = AnharmonicModes(vib, settings={
'temperature': 1000,
})
vib_mode = AM.define_vibration(mode_number=-1)
AM.run()
AM.summary(log='/dev/null')
AM.clean()
assert abs(AM.get_ZPE() - 0.497) < 1e-3, AM.get_ZPE()
assert abs(AM.get_entropic_energy()) < 1e-3, AM.get_entropic_energy()
AM = AnharmonicModes(vib,
settings={
calc = espresso(outdir = 'calcdir', **params) # regular espresso calculator
calcvib = vibespresso(outdirprefix = 'vibdir', **params) # special calculator for the vibration calculations
atoms.set_calculator(calc) # attach calculator to the atoms
energy = atoms.get_potential_energy() # caclulate the energy, to be used to determine G
# vibrate N and H atoms
vibrateatoms = [atom.index for atom in atoms if atom.symbol in ['H','N']] # calculate the vibrational modes for all N and H atoms
atoms.set_calculator(calcvib) # attach vibrations calculator to the atoms
# Calculate vibrations
vib = Vibrations(atoms,indices=vibrateatoms,delta=0.03) # define a vibration calculation
vib.run() # run the vibration calculation
vib.summary(method='standard') # summarize the calculated results
for mode in range(len(vibrateatoms)*3): # Make trajectory files to visualize the modes.
vib.write_mode(mode)
### UNCOMMENT TO CALCULATE FREE get_energies
### YOU CAN ALSO USER get_ads_free_energy.py and get_gas_free_energy.py
### Calculate free energy
# vibenergies=vib.get_energies()
# vibenergies=[vib for vib in vibenergies if not isinstance(vib,complex)] # only take the real modes
# gibbs = HarmonicThermo(vib_energies = vibenergies, electronicenergy = energy)
### At 300K and 101325 Pa
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()
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))
def vibrate(self, atoms: Atoms, indices: list, read_only=False):
'''
This method uses ase.vibrations module, see more for info.
User provides the FHI-aims parameters, the Atoms object and list
of indices of atoms to be vibrated. Variables related to FHI-aims are governed by the React object.
Calculation folders are generated automatically and a sockets calculator is used for efficiency.
Work in progress
Args:
atoms: Atoms object
indices: list
List of indices of atoms that require vibrations
read_only: bool
Flag for postprocessing - if True, the method only extracts information from existing files,
no calculations are performed
Returns:
Zero-Point Energy: float
'''
'''Retrieve common properties'''
basis_set = self.basis_set
hpc = self.hpc
params = self.params
parent_dir = os.getcwd()
dimensions = sum(atoms.pbc)
if not self.filename:
'''develop a naming scheme based on chemical formula'''
self.filename = atoms.get_chemical_formula()
vib_dir = parent_dir + "/VibData_" + self.filename + "/Vibs"
print(vib_dir)
vib = Vibrations(atoms, indices=indices, name=vib_dir)
'''If a calculation was terminated prematurely (e.g. time limit) empty .json files remain and the calculation
of the corresponding stretch modes would be skipped on restart. The line below prevents this'''
vib.clean(empty_files=True)
'''Extract vibration data from existing files'''
if read_only:
vib.read()
else:
'''Calculate required vibration modes'''
required_cache = [
os.path.join(vib_dir, "cache." + str(x) + y + ".json")
for x in indices
for y in ["x+", "x-", "y+", "y-", "y-", "z+", "z-"]
]
check_required_modes_files = np.array(
[os.path.exists(file) for file in required_cache])
if np.all(check_required_modes_files == True):
vib.read()
else:
'''Set the environment variables for geometry optimisation'''
set_aims_command(hpc=hpc,
basis_set=basis_set,
defaults=2020,
nodes_per_instance=self.nodes_per_instance)
'''Generate a unique folder for aims calculation'''
counter, subdirectory_name = self._restart_setup(
"Vib",
filename=self.filename,
restart=False,
verbose=False)
os.makedirs(subdirectory_name, exist_ok=True)
os.chdir(subdirectory_name)
'''Name the aims output file'''
out = str(counter) + "_" + str(self.filename) + ".out"
'''Calculate vibrations and write the in a separate directory'''
with _calc_generator(params, out_fn=out,
dimensions=dimensions)[0] as calculator:
if not self.dry_run:
atoms.calc = calculator
else:
atoms.calc = EMT()
vib = Vibrations(atoms, indices=indices, name=vib_dir)
vib.run()
vib.summary()
'''Generate a unique folder for aims calculation'''
if not read_only:
os.chdir(vib_dir)
vib.write_mode()
os.chdir(parent_dir)
return vib.get_zero_point_energy()
"""Calculate the vibrational modes of a H2O molecule."""
from ase.vibrations import Vibrations
from gpaw import GPAW
h2o = GPAW('h2o.gpw', txt=None).get_atoms()
# Create vibration calculator
vib = Vibrations(h2o)
vib.run()
vib.summary(method='frederiksen')
# Make trajectory files to visualize normal modes:
for mode in range(9):
vib.write_mode(mode)
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')
vibDB = connect('./vib.db', append=False) # DB for vibration spectrum
phonDB = connect('./ph.db', append=False) # DB for phonon structure and DOS
# 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()
# | - TEMP *********************************************************************
from ase.vibrations import Vibrations
from ase_modules.ase_methods import thermochem_IG_corr
vib = Vibrations(
atoms,
indices=None,
)
vib.run()
# print("an_ads_vib | Getting vibrational energies")
vib_e_list = vib.get_energies()
vib.summary(log="vib_summ.out")
thermochem_IG_corr(
vib_e_list,
Temperature=300.0,
Pressure=100000.0,
potentialenergy=0.,
symmetrynumber=2,
spin=1,
atoms=atoms,
linear=True,
)
# # H2O, H2, O2: 2,
# symmetrynumber=symmetrynumber, # symmetry numbers from point group
# spin=spin, # 1 for O2, 0 for H2O and H2
psppath='/home/vossj/suncat/psp/gbrv1.5pbe', # pseudopotential
convergence={
'energy': 1e-5,
'mixing': 0.1,
'nmix': 10,
'mix': 4,
'maxsteps': 500,
'diag': 'david'
}, # convergence parameters
outdirprefix='calcdirv') # output directory for Quantum Espresso files
atoms.set_calculator(calcvib)
vib = Vibrations(atoms, indices=vibrateatoms, delta=0.03)
vib.run()
vib.summary(method='standard')
# Make trajectory files to visualize the modes.
for mode in range(len(vibrateatoms) * 3):
vib.write_mode(mode)
# Calculate free energy
vib_energies = vib.get_energies()
thermo = IdealGasThermo(vib_energies=vib_energies,
electronicenergy=energy,
atoms=atoms,
geometry='linear',
symmetrynumber=2,
spin=0)
# At 300K and 101325 Pa
psppath='/home/vossj/suncat/psp/gbrv1.5pbe', # pseudopotential
convergence={'energy': 1e-5,
'mixing': 0.1,
'nmix': 10,
'mix': 4,
'maxsteps': 500,
'diag': 'david'
}, # convergence parameters
outdirprefix='calcdirv') # output directory for Quantum Espresso files
atoms.set_calculator(calcvib)
vib = Vibrations(atoms, indices=vibrateatoms, delta=0.03)
vib.run()
vib.summary(method='standard')
# Make trajectory files to visualize the modes.
for mode in range(len(vibrateatoms) * 3):
vib.write_mode(mode)
# Calculate free energy
vib_energies = vib.get_energies()
thermo = IdealGasThermo(vib_energies=vib_energies,
electronicenergy=energy,
atoms=atoms,
geometry='linear',
symmetrynumber=2, spin=0)
# At 300K and 101325 Pa
# change for your operating conditions
def calc(primitive,
cachedir=None,
supercell=(1, 1, 1),
delta=0.01,
quick=True):
"""Calculates the Hessian for a given atoms object (which *must* have an
attached calculator).
.. note:: We choose to use the Hessian as the fundamental quantity in
vibrational analysis in `matdb`.
.. note:: `atoms` will be relaxed before calculating the Hessian.
Args:
primitive (matdb.atoms.Atoms): atomic structure of the *primitive*.
cachedir (str): path to the directory where phonon calculations are
cached. If not specified, a temporary directory will be used.
supercell (tuple): number of times to duplicate the cell when
forming the supercell.
delta (float): displacement in Angstroms of each atom when computing the
phonons.
quick (bool): when True, use symmetry to speed up the Hessian
calculation. See :func:`_calc_quick`.
Returns:
numpy.ndarray: Hessian matrix that has dimension `(natoms*3, natoms*3)`,
where `natoms` is the number of atoms in the *supercell*.
"""
if quick:
return _calc_quick(primitive, supercell, delta)
else:
atoms = primitive.make_supercell(supercell)
atoms.set_calculator(primitive.get_calculator())
from ase.vibrations import Vibrations
#The phonon calculator caches the displacements and force sets for each
#atomic displacement using pickle. This generates three files for each
#atomic degree of freedom (one for each cartesian direction). We want to
#save these in a special directory.
tempcache = False
if cachedir is None:
cachedir = mkdtemp()
tempcache = True
else:
cachedir = path.abspath(path.expanduser(cachedir))
if not path.isdir(cachedir):
mkdir(cachedir)
result = None
precon = Exp(A=3)
aphash = None
#Calculate a hash of the calculator and atoms object that we are calculating
#for. If the potential doesn't have a `to_dict` method, then we ignore the
#hashing.
if not tempcache and hasattr(atoms, "to_dict") and hasattr(
atoms._calc, "to_dict"):
atoms_pot = {"atoms": atoms.to_dict(), "pot": atoms._calc.to_dict()}
#This UUID will probably be different, even if the positions and species
#are identical.
del atoms_pot["atoms"]["uuid"]
hash_str = convert_dict_to_str(atoms_pot)
aphash = str(sha1(hash_str).hexdigest())
if not tempcache:
#Check whether we should clobber the cache or not.
extras = ["vibsummary.log", "vib.log", "phonons.log"]
with chdir(cachedir):
hash_match = False
if path.isfile("atomspot.hash"):
with open("atomspot.hash") as f:
xhash = f.read()
hash_match = xhash == aphash
hascache = False
if not hash_match:
for vibfile in glob("vib.*.pckl"):
remove(vibfile)
hascache = True
for xfile in extras:
if path.isfile(xfile):
remove(xfile)
hascache = True
if hascache:
msg.warn(
"Using hard-coded cache directory. We were unable to "
"verify that the atoms-potential combination matches "
"the one for which existing cache files exist. So, we "
"clobbered the existing files to get the science "
"right. You can fix this by using `matdb.atoms.Atoms` "
"and `matdb.calculators.*Calculator` objects.")
with chdir(cachedir):
#Relax the cell before we calculate the Hessian; this gets the forces
#close to zero before we make harmonic approximation.
try:
with open("phonons.log") as f:
with redirect_stdout(f):
minim = PreconLBFGS(atoms, precon=precon, use_armijo=True)
minim.run(fmax=1e-5)
except:
#The potential is unstable probably. Issue a warning.
msg.warn(
"Couldn't optimize the atoms object. Potential may be unstable."
)
vib = Vibrations(atoms, delta=delta)
with open("vib.log", 'a') as f:
with redirect_stdout(f):
vib.run()
vib.summary(log="vibsummary.log")
result = vib.H
#Cache the hash of the atoms object and potential that we were using so
#that we can check next time whether we should clobber the cache or not.
if aphash is not None and not tempcache:
with open(path.join(cachedir, "atomspot.hash"), 'w') as f:
f.write(aphash)
return result
from ase.optimize import QuasiNewton
from ase.vibrations import Vibrations
from gpaw import GPAW
# Water molecule:
d = 0.9575
t = pi / 180 * 104.51
H2O = Atoms("H2O", positions=[(0, 0, 0), (d, 0, 0), (d * cos(t), d * sin(t), 0)])
H2O.center(vacuum=3.5)
calc = GPAW(h=0.2, txt="h2o.txt", mode="lcao", basis="dzp")
H2O.set_calculator(calc)
QuasiNewton(H2O).run(fmax=0.05)
"""Calculate the vibrational modes of a H2O molecule."""
# Create vibration calculator
vib = Vibrations(H2O)
vib.run()
vib.summary(method="frederiksen")
# Make trajectory files to visualize normal modes:
for mode in range(9):
vib.write_mode(mode)
# name of output file for free energies
output_name = 'out.energy'
### At 300K and 101325 Pa
### change for your operating conditions
T = 300 # K
P = 101325 # Pa
#########################################################################################################
##### END #####
#########################################################################################################
energy = atoms.get_potential_energy() # caclulate the energy, to be used to determine G
vibrateatoms = [atom.index for atom in atoms if atom.symbol in ['H','N']] # calculate the vibrational modes for all N and H atoms
# Calculate vibrations
vib = Vibrations(atoms,indices=vibrateatoms,delta=0.03) # define a vibration calculation
vib.run() # run the vibration calculation
vib.summary(method='standard') # summarize the calculated results
for mode in range(len(vibrateatoms)*3): # Make trajectory files to visualize the modes.
vib.write_mode(mode)
vibenergies=vib.get_energies()
vibenergies=[vib for vib in vibenergies if not isinstance(vib,complex)] # only take the real modes
gibbs = HarmonicThermo(vib_energies = vibenergies, electronicenergy = energy)
freeenergy = gibbs.get_gibbs_energy(T,P)
f=open(output_name,'w')
f.write('Potential energy: '+str(energy)+'\n'+'Free energy: '+str(freeenergy)+'\n')
f.close
