def vibCalc(self):
from espresso.vibespresso import vibespresso
spinpol = any([x > 0 for x in self.magmomsinit()])
dipole = True if self.kind() == 'surface' else False
return vibespresso(
pw=self.pw # planewave cutoff
,
dw=self.pw * self.dwratio() # density cutoff
,
xc=self.xc,
kpts=self.kpt(),
spinpol=spinpol,
convergence={
'energy': self.econv(),
'mixing': self.mixing(),
'nmix': self.nmix(),
'maxsteps': self.maxstep(),
'diag': 'david'
},
nbands=self.nbands(),
sigma=self.sigma(),
dipole={'status': dipole},
outdirprefix='vibdir',
output={'removesave': True},
psppath=psppath)
def makeQEvibcalc(p):
from espresso.vibespresso import vibespresso
pspDict = {
'sherlock': {
'gbrv15pbe': '/home/vossj/suncat/psp/gbrv1.5pbe'
},
'suncat': {
'gbrv15pbe':
'/nfs/slac/g/suncatfs/sw/external/esp-psp/gbrv1.5pbe'
}
}
pspPath = pspDict[getCluster()][p['psp']]
return vibespresso(pw=p['pw'],
dw=p['pw'] * p['dwrat'],
xc=p['xc'],
kpts=kpt,
spinpol=spinpol,
convergence={
'energy': p['econv'],
'mixing': p['mixing'],
'nmix': p['nmix'],
'maxsteps': p['maxstep'],
'diag': 'david'
},
nbands=p['nbands'],
sigma=p['sigma'],
dipole={'status': p['kind'] == 'surface'},
outdir='calcdir',
startingwfc='atomic+random',
psppath=pspPath,
output={'removesave': True})
def makeQEvibcalc(params):
from espresso.vibespresso import vibespresso
return vibespresso(pw=p['pw'],
dw=p['pw'] * p['dwrat'],
xc=p['xc'],
kpts=kpt,
spinpol=spinpol,
convergence={
'energy': p['econv'],
'mixing': p['mixing'],
'nmix': p['nmix'],
'maxsteps': p['maxstep'],
'diag': 'david'
},
nbands=p['nbands'],
sigma=p['sigma'],
dipole={'status': p['kind'] == 'surface'},
outdir='calcdir',
startingwfc='atomic+random',
psppath=pspPath,
output={'removesave': True})
def vibCalc(self):
from espresso.vibespresso import vibespresso
return vibespresso(
pw=self.pw(),
dw=self.pw() * self.dwrat(),
xc=self.xc(),
kpts=self.kpt(),
spinpol=self.spinpol(),
convergence={
'energy': self.econv(),
'mixing': self.mixing(),
'nmix': self.nmix(),
'maxsteps': self.maxstep(),
'diag': 'david'
},
nbands=self.nbands(),
sigma=self.sigma(),
dipole={'status': self.dipole()},
outdir='calcdir' # output directory
,
startingwfc='atomic+random' #alternatively, 'file' for restart
,
psppath=self.psppath(),
output={'removesave': True})
dyn.run(fmax=0.05)
energy = atoms.get_potential_energy()
calc.stop()
# Calculate vibrations
calcvib = vibespresso(
pw=500, # plane-wave cutoff
dw=5000, # density cutoff
xc='BEEF-vdW', # exchange-correlation functional
kpts='gamma', # k-point sampling
nbands=-10, # 10 extra bands besides the bands needed to hold
# the valence electrons
sigma=0.1,
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')
else:
print "Wrong number of metal atoms! Check your input trajectory!"
exit()
params = {'pw':500,
'dw':5000,
'kpts':kpts,
'nbands':-20,
'xc':'BEEF-vdW',
'psppath':'/home/vossj/suncat/psp/gbrv1.5pbe',
'convergence':{'energy':1e-5, 'mixing':0.1, 'nmix':10, 'maxsteps':500, 'diag':'david'},
'spinpol':False}
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.
atoms = io.read('qn.traj') # optimized
atoms.set_masses()
from espresso import espresso
calc = vibespresso(
pw=800, # planewave cutoff
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()
dyn = QuasiNewton(atoms, logfile=name + '.log', trajectory=name + '.traj')
dyn.run(fmax=0.05)
energy = atoms.get_potential_energy()
calc.stop()
# Calculate vibrations
calcvib = vibespresso(pw=500, # plane-wave cutoff
dw=5000, # density cutoff
xc='BEEF-vdW', # exchange-correlation functional
kpts='gamma', # k-point sampling
nbands=-10, # 10 extra bands besides the bands needed to hold
# the valence electrons
sigma=0.1,
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')
atoms.rattle()
atoms.set_masses()
calc = vibespresso(
pw=pw, # planewave cutoff
dw=dw, # density cutoff
nbands=-10, # number of bands
kpts=kpts, # k points
xc=xc, # exchange correlation method
sigma=sigma, # Fermi temperature
dipole= dipole,
spinpol = spinpol,
convergence={
'energy': 0.0005,
'mixing': mixing,
'nmix':10,
'maxsteps': maxsteps,
'diag': 'david'},
#mode = 'scf',
output = {'avoidio':False,
'removewf':True,
'wf_collect':False},
outdirprefix='vibdir'
)
atoms.set_calculator(calc)
vib = Vibrations(atoms, delta=0.04, indices=vib_atoms)
vib.run()
