def build_db(update='.', prefix='datas'):
user = os.getenv('USER')
print('Reading.....')
dbfile = '%s.db' % prefix
with connect(dbfile) as db:
calc = Espresso()
cwd = os.getcwd()
for dire, j, y in os.walk(update):
prefix = is_espresso(dire)
if prefix:
calc.prefix = prefix
else:
continue
print(dire)
label = dire
inputfile = dire + '/%s.pwi' % calc.prefix
calc.directory = os.path.join(cwd, dire)
calc.prefix = prefix
print(inputfile)
atoms, input_data, pseudopotentials, kpts = read_espresso_input(
inputfile)
newcalc = Espresso(label=dire,
prefix=prefix,
pseudopotentials=pseudopotentials,
input_data=input_data,
kpts=kpts)
converged, fromfile, meg0 = calc.read_convergence()
calc.results = {}
try:
calc.read_results()
atoms = calc.results['atoms']
except Exception as e:
print('=' * 30, '\n', dire, e)
# atoms.calc = newcalc
print('dire: ', dire, converged)
nid = 0
for row in db.select(label=label):
dbid = row.id
nid += 1
if nid > 0:
db.write(atoms, id=dbid, label=label, converged=meg0)
else:
db.write(atoms, label=label)
print('Finished')
def run_atoms(self, job, atoms):
self.log('-'*60)
self.log('Submit job {0}'.format(job))
self.log.print_atoms(atoms)
calc = Espresso(
label = os.path.join(self.label, job),
**self.calculator,
)
calc.parameters['input_data']['prefix'] = job
# self.log(' Commnad: {0}'.format(calc.command))
atoms.calc = calc
# atoms.get_potential_energy()
calc.run(atoms = atoms, restart = 1)
calc.read_results()
self.results[job] = deepcopy(calc.results)
calc.clean()
return job, self.results[job]['energy']
def __init__(self,
calc=None,
label=None,
prefix=None,
debug=False,
colors=None):
"""Electronic Density Of States object.
calc: quantum espresso calculator object
label: the directory and prefix
dos_energies
print(pdos_info) to see the detail
pdos_kinds[species][channel][ncomponents]
"""
if not calc and not label:
raise ValueError('Please give one of them: calc or label')
if label:
calc = Espresso(label=label, prefix=prefix, debug=True)
calc.read_results()
self.debug = debug
if self.debug:
print(calc.results)
self.directory = calc.directory
self.label = calc.label
self.prefix = calc.prefix
self.efermi = calc.get_fermi_level()
self.atoms = calc.results['atoms']
self.nspins = calc.get_number_of_spins()
if self.nspins == 0: self.nspins = 1
def __init__(self,
label='xespresso',
prefix=None,
images=[Atoms('')],
package='neb',
parallel='',
queue=None,
debug=False,
**kwargs):
"""
"""
atoms = images[0]
Espresso.__init__(self,
label=label,
prefix=prefix,
atoms=atoms,
package=package,
parallel=parallel,
queue=queue,
debug=debug,
**kwargs)
self.images = images
def vib_zpe(self, job, atoms):
from ase.vibrations import Vibrations
self.log('-' * 60)
self.log('Run ZEP calculation: {0}'.format(job))
label = os.path.join(self.label, job)
label = os.path.join(label, 'vib')
# copy file
calculator = deepcopy(self.calculator)
dip = dipole_correction(atoms, edir=3)
calculator.update(dip)
calculator.update({
'calculation': 'scf',
'tstress': True,
'tprnfor': True,
'outdir': '../',
'prefix': '%s' % job,
'startingpot': 'file',
'startingwfc': 'file',
'etot_conv_thr': 1e-6,
'disk_io': 'none',
})
# better to restart from previous geo_relax calculation
calc = Espresso(
label=label,
**calculator,
)
atoms.calc = calc
if job[-1] == 'O':
indices = [-1]
elif job[-2:] == 'OH' and job[-3:] != 'OOH':
indices = [-1, -2]
elif job[-3:] == 'OOH':
indices = [-1, -2, -3]
elif job[-2:] == 'O2':
indices = [-1, -2]
else:
indices = []
# print('%!!!')
return job, 0
vib = Vibrations(atoms, name=os.path.join(label, job), indices=indices)
vib.run()
vib_energies = np.real(vib.get_energies())
zpe = 0.
for energy in vib_energies:
zpe += 0.5 * energy
self.zpes[job] = zpe
return job, zpe
def summary(updates=[], prefix='datas'):
import pandas as pd
columns = [
'label', 'atoms', 'cell', 'positions', 'energy', 'forces', 'stress'
]
file = '%s.pickle' % prefix
db = '%s.db' % prefix
if os.path.exists(file):
with open(file, 'rb') as f:
datas, df = pickle.load(f)
else:
datas = {}
df = pd.DataFrame(columns=columns)
calc = Espresso()
print('Reading.....')
for update in updates:
cwd = os.getcwd()
for i, j, y in os.walk(update):
output = is_espresso(i)
if output:
os.chdir(i)
print('dire:', i)
calc.directory = cwd + '/' + i
calc.prefix = output[0:-4]
try:
calc.results = {}
calc.read_results()
# gap, p1, p2 = bandgap(calc)
# calc.results['gap'] = gap
# t = calc.get_time()
# calc.results['time'] = t
datas[i] = calc.results
atoms = calc.results['atoms']
atoms.write(
os.path.join(calc.directory, '%s.cif' % calc.prefix))
# results = ana(i, calc)
# df.loc[len(df)] = results
except Exception as e:
print('=' * 30, '\n', i, e)
os.chdir(cwd)
with open(file, 'wb') as f:
pickle.dump([datas, df], f)
print('Finished')
def __init__(self, calc = None, label = None,
):
"""Electronic Density Of States object.
calc: quantum espresso calculator object
label: the directory and prefix
"""
if not calc and not label:
raise ValueError('Please give one of them: calc or label')
if label:
calc = Espresso(label = label)
calc.read_results()
self.directory = calc.directory
self.label = calc.label
self.prefix = calc.prefix
self.efermi = calc.get_fermi_level()
self.atoms = calc.atoms
self.nspins = calc.get_number_of_spins()
if self.nspins == 0: self.nspins = 1
def cell_relax_espresso(self, job, atoms):
"""
"""
self.log('-' * 60)
self.log('Submit job {0}'.format(job))
self.log.print_atoms(atoms)
calculator = deepcopy(self.calculator)
calculator.update({
'calculation': 'vc-relax',
'prefix': job,
})
calc = Espresso(
label=os.path.join(self.label, job),
**calculator,
)
atoms.calc = calc
calc.run(atoms=atoms)
calc.read_results()
self.results[job] = deepcopy(calc.results)
return job, self.results[job]['energy']
def geo_relax_espresso(self, job, atoms):
"""
"""
self.log('-' * 60)
self.log('Run geometry relaxtion: {0}'.format(job))
self.log.print_atoms(atoms)
calculator = deepcopy(self.calculator)
calculator.update({
'calculation': 'relax',
'prefix': job,
})
dip = dipole_correction(atoms, edir=3)
calculator.update(dip)
calc = Espresso(
label=os.path.join(self.label, job),
**calculator,
)
atoms.calc = calc
calc.run(atoms=atoms)
calc.read_results()
energy = calc.results['energy']
self.results[job] = deepcopy(calc.results)
self.calcs[job] = calc
return job, energy
'Hubbard_U': {
'Fe': 4.3,
'Fe1': 4.3
},
}
input_data = {
'ecutwfc': 30.0,
'occupations': 'smearing',
'degauss': 0.03,
'nspin': 2,
'lda_plus_u': True,
'input_ntyp': input_ntyp,
#
'mixing_beta': 0.3,
'conv_thr': 1.0e-8,
}
pseudopotentials = {
'Fe': 'Fe.pbe-spn-rrkjus_psl.1.0.0.UPF',
'Fe1': 'Fe.pbe-spn-rrkjus_psl.1.0.0.UPF',
}
calc = Espresso(pseudopotentials=pseudopotentials,
label='scf/fe+u',
input_data=input_data,
kpts=(4, 4, 4))
atoms.calc = calc
e = atoms.get_potential_energy()
print('Energy {0:1.3f}'.format(e))
'''
Energy -10451.104
'''
from xespresso.cohp import COHP
# build CO molecule
atoms = molecule('CO')
atoms.center(5)
atoms.pbc = [True, True, True]
pseudopotentials = {'O': 'O.pbe-n-kjpaw_psl.0.1.UPF',
'C': 'C.pbe-n-kjpaw_psl.1.0.0.UPF'}
queue = None
# start scf calculation
calc = Espresso(label='scf/co',
pseudopotentials=pseudopotentials,
wf_collect=True, # for lobster run, make sure adding this
outdir='.', # for lobster run, make sure adding this
ecutwfc=30,
occupations='smearing',
degauss=0.03,
kpts=(1, 1, 1),
debug=True,
)
atoms.calc = calc
e = atoms.get_potential_energy()
print('Energy = {0:1.3f} eV'.format(e))
# start COHP analysis
cohp = COHP(
directory='scf/co', # same as label in scf calculation
prefix='co', # same as scf calculation
index=[[1, 2]], # the bond of interest, multiple bond can be set as [[1,2],[3,5]]
command='your lobster path' # path of lobster program
# other arguments can also be parsed, such as follows
'occupations': 'smearing',
'smearing': 'gaussian',
'degauss': 0.03,
'nspin': 2,
'input_ntyp': input_ntyp,
#
'mixing_beta': 0.3,
'conv_thr': 1.0e-8,
}
pseudopotentials = {
'Fe': 'Fe.pbe-spn-rrkjus_psl.1.0.0.UPF',
'Fe1': 'Fe.pbe-spn-rrkjus_psl.1.0.0.UPF',
}
calc = Espresso(pseudopotentials=pseudopotentials,
label='scf/fe-afm',
input_data=input_data,
kpts=(6, 6, 6))
atoms.calc = calc
e = atoms.get_potential_energy()
calc.read_results()
e = calc.results['energy']
print('Energy {0:1.3f}'.format(e))
parameters_hp = {
'nq1': 1,
'nq2': 1,
'nq3': 1,
'equiv_type': 0,
'conv_thr_chi': 1e-5,
'perturb_only_atom': {
'1': True
'queue': queue,
'debug': True,
'parallel': '-nk 4',
}
# Build the Pt (001) surface
atoms = bulk('Pt')
atoms = surface(atoms, (0, 0, 1), 2, vacuum=1)
atoms.pbc = [True, True, True]
atoms = atoms * [2, 2, 1]
atoms.positions[:, 2] -= min(atoms.positions[:, 2]) - 0.01
atoms.cell[2][2] = max(atoms.positions[:, 2]) + 10
atoms = fix_layers(atoms, (0, 0, 1), 1.0, [0, 2])
#
calc = Espresso(
label='relax/001-221-Pt',
**parameters,
)
atoms.calc = calc
calc.run(atoms=atoms)
calc.read_results()
atoms_opt = calc.results['atoms']
del atoms_opt.info['species']
#==========================================================================
# parameter for QE
parameters = {
'pseudopotentials': mypseudo,
'calculation': 'relax',
'ecutwfc': 40.0,
'ecutrho': 320.0,
'ecutrho': 302.0,
'occupations': 'smearing',
'smearing': 'gaussian',
'degauss': 0.03,
#
'mixing_beta': 0.3,
'conv_thr': 1.0e-8,
}
pseudopotentials = {
'Fe': 'Fe.pbe-spn-rrkjus_psl.1.0.0.UPF',
}
queue = {
'nodes': 1,
'ntasks-per-node': 4,
'account': 'dcb',
'partition': 'all',
'time': '0:10:00'
}
calc = Espresso(
pseudopotentials=pseudopotentials,
queue=queue,
label='scf/fe', # 'scf/fe' is the directory, 'fe' is the prefix
input_data=input_data,
kpts=(6, 6, 6))
atoms.calc = calc
e = atoms.get_potential_energy()
print('Energy: {0:1.3f}'.format(e))
'''
Energy: -3368.435
'''
from ase.build import bulk, fcc111
from ase.visualize import view
from xespresso import Espresso
from xespresso.dos import DOS
from xespresso.tools import get_nbnd
import matplotlib.pyplot as plt
atoms = fcc111('Al', size=(1, 1, 2), vacuum=4.0)
view(atoms)
print(atoms)
pseudopotentials = {
'Al': 'Al.pbe-n-rrkjus_psl.1.0.0.UPF',
}
calc = Espresso(pseudopotentials=pseudopotentials,
label='scf/al',
ecutwfc=40,
occupations='smearing',
degauss=0.01,
kpts=(4, 4, 1))
atoms.calc = calc
e = atoms.get_potential_energy()
calc.read_results()
e = calc.results['energy']
fermi = calc.get_fermi_level()
print('Energy: {0:1.3f}'.format(e))
#===============================================================
# post calculation
calc.post(package='pp',
plot_num=5,
sample_bias=0.0735,
iflag=3,
output_format=6,
from ase.build import bulk
from xespresso import Espresso
atoms = bulk('Fe')
pseudopotentials = {'Fe': 'Fe.pbe-spn-rrkjus_psl.1.0.0.UPF'}
input_data = {'smearing': 'gaussian'}
calc = Espresso(pseudopotentials = pseudopotentials,
label = 'scf/fe', # 'scf/fe' is the directory, 'fe' is the prefix
ecutwfc = 40,
occupations = 'smearing',
degauss = 0.02,
input_data = input_data,
kpts=(6, 6, 6),
debug = True,
)
atoms.calc = calc
calc.run(atoms = atoms)
e = calc.results['energy']
print('Energy: {0:1.3f}'.format(e))
'''
Energy: -3368.401
'''
from ase.build import molecule
from xespresso import Espresso
atoms = molecule('H2')
atoms.center(5)
atoms.pbc = [True, True, True]
pseudopotentials = {'H': 'H.pbe-rrkjus_psl.1.0.0.UPF'}
calc = Espresso(
label='relax/h2',
pseudopotentials=pseudopotentials,
calculation='relax',
ecutwfc=20,
kpts=(1, 1, 1),
debug=True,
)
atoms.calc = calc
e = atoms.get_potential_energy()
print('Energy = {0:1.3f} eV'.format(e))
from ase.build import bulk
from xespresso import Espresso
atoms = bulk('Fe')
pseudopotentials = {'Fe': 'Fe.pbe-spn-rrkjus_psl.1.0.0.UPF'}
input_data = {'smearing': 'gaussian'}
calc = Espresso(
pseudopotentials=pseudopotentials,
label='scf/fe', # 'scf/fe' is the directory, 'fe' is the prefix
ecutwfc=40,
occupations='smearing',
degauss=0.03,
input_data=input_data,
kpts=(6, 6, 6))
atoms.calc = calc
e = atoms.get_potential_energy()
print('Energy: {0:1.3f}'.format(e))
'''
Energy: -3368.488
'''
'ecutwfc': 70.0,
'ecutrho': 840.0,
'occupations': 'smearing',
'degauss': 0.01,
'nspin': 2,
'lda_plus_u': True,
'input_ntyp': input_ntyp,
}
queue = {'nodes': 1, 'ntasks-per-node': 4, 'account': 'dcb',
'partition': 'all', 'time': '0:10:00'}
pseudopotentials = {
'Mn1': 'Mn.pbesol-spn-rrkjus_psl.0.3.1.UPF',
'Mn2': 'Mn.pbesol-spn-rrkjus_psl.0.3.1.UPF',
'Mn3': 'Mn.pbesol-spn-rrkjus_psl.0.3.1.UPF',
'Mn4': 'Mn.pbesol-spn-rrkjus_psl.0.3.1.UPF',
'O' : 'O.pbesol-n-rrkjus_psl.1.0.0.UPF',
'O1' : 'O.pbesol-n-rrkjus_psl.1.0.0.UPF',
'Sr' : 'Sr.pbesol-spn-rrkjus_psl.1.0.0.UPF',
}
# print(queue)
calc = Espresso(pseudopotentials = pseudopotentials,
package = 'pw',
parallel = '-nk 2 -nt 4 -nd 144', # parallel parameters
queue = queue,
label = 'scf/mno',
input_data = input_data, kpts=(6, 6, 6))
atoms.set_calculator(calc)
e = atoms.get_potential_energy()
print('Energy: ', e)
atoms.arrays['species'][0] = 'Fe'
atoms.arrays['species'][1] = 'Fe1'
print(atoms.arrays['species'])
input_ntyp = {
'starting_magnetization': {
'Fe': 1.0,
'Fe1': -1.0,
}
}
pseudopotentials = {
'Fe': 'Fe.pbe-spn-rrkjus_psl.1.0.0.UPF',
'Fe1': 'Fe.pbe-spn-rrkjus_psl.1.0.0.UPF',
}
calc = Espresso(
pseudopotentials=pseudopotentials,
label='scf/fe-afm',
ecutwfc=40,
occupations='smearing',
degauss=0.02,
nspin=2,
input_data={'input_ntyp': input_ntyp},
kpts=(4, 4, 4),
debug=True,
)
atoms.calc = calc
e = atoms.get_potential_energy()
print('Energy {0:1.3f}'.format(e))
'''
Energy -6737.189
'''
queue = {'nodes': 2, 'ntasks-per-node': 20, 'partition': 'debug', 'time': '00:10:00'}
paras = {
'pseudopotentials': rrkjus_psl,
'calculation':'relax',
'ecutwfc': 40.0,
'ecutrho': 320.0,
'occupations': 'smearing',
'degauss': 0.02,
'kpts': (8, 8, 8),
'queue': queue,
'debug': True,
'parallel': '-nk 4',
}
atoms = bulk('Li')
calc = Espresso(label = 'vc-relax/li', **paras)
atoms.calc = calc
e = atoms.get_potential_energy()
print('energy: ', e)
#
paras.update({'calculation': 'scf', 'conv_thr': 1e-10})
atoms = calc.results['atoms']
calc = Espresso(label = 'scf/li', **paras)
atoms.calc = calc
e = atoms.get_potential_energy()
print('energy: ', e)
# Phonon calculations at gamma
input = {
'tr2_ph':1.0e-14,
'epsil':True,
}
def dfpt(self):
'''
'''
atoms = self.atoms
self.log('-'*60)
self.log('Submit job {0}'.format(job))
self.log.print_atoms(atoms)
calc = Espresso(
label = os.path.join(self.label, job),
**self.calculator,
)
calc.parameters['input_data']['prefix'] = job
atoms.calc = calc
energy = atoms.get_potential_energy()
# dos
calc.post(queue = queue,
package = 'ph',
tr2_ph = 1e-14,
ldisp = True,
nq1 = 4,
nq2 = 4,
nq3 = 3,
)
calc.post(queue = queue,
fildyn = 'matdyn',
package = 'q2r',
zasr = 'simple',
flfrc = '%s.fc'%job,
)
calc.post(queue = queue,
package = 'matdyn',
asr = 'simple',
dos = True,
flfrc = '%s.fc'%job,
fldos = '%s.phdos'%job,
nk1 = 40,
nk2 = 40,
nk3 = 30,
)
calc.plot_phdos(fldos = '%s'%job,
output = 'images/%s-phdos.png'%job)
pass
'degauss': 0.03,
'nspin': 2,
'input_ntyp': input_ntyp,
#
'mixing_beta': 0.3,
'conv_thr': 1.0e-8,
}
# queue = {'nodes': 1, 'ntasks-per-node': 4, 'account': 'dcb', 'partition': 'all', 'time': '0:59:00'}
queue = None
pseudopotentials = {
'H': 'H.pbe-rrkjus_psl.1.0.0.UPF',
}
calc = Espresso(
pseudopotentials=pseudopotentials,
# queue = queue,
label='relax/initial',
input_data=input_data,
kpts=(1, 1, 1),
debug=True,
)
atoms.calc = calc
e = atoms.get_potential_energy()
print('Initial energy: ', e)
#=============================================================
# start NEB
initial = calc.results['atoms']
final = initial.copy()
final.positions[1] = [3.0 - final[1].x, 0, 0]
images = [initial, final]
# view images before neb calculation
from ase.build import bulk
from ase.visualize import view
from xespresso import Espresso
from xespresso.dos import DOS
from xespresso.tools import get_nbnd
import matplotlib.pyplot as plt
atoms = bulk('Fe')
pseudopotentials = {'Fe': 'Fe.pbe-spn-rrkjus_psl.1.0.0.UPF'}
calc = Espresso(pseudopotentials = pseudopotentials,
label = 'scf/fe', # 'scf/fe' is the directory, 'fe' is the prefix
ecutwfc = 40,
occupations = 'smearing',
degauss = 0.03,
kpts=(6, 6, 6))
atoms.calc = calc
e = atoms.get_potential_energy()
fermi = calc.get_fermi_level()
#===============================================================
# # nscf calculation
# calc.nscf(kpts=(8, 8, 8))
# calc.nscf_calculate()
# # post calculation
# calc.post(package='dos', Emin = fermi - 20, Emax = fermi + 10, DeltaE = 0.1)
# calc.post(package='projwfc', Emin = fermi - 20, Emax = fermi + 10, DeltaE = 0.1)
# # # DOS analysis
# dos = DOS(calc)
# dos.read_dos()
# dos.plot_dos()
# plt.show()
#
import matplotlib.pyplot as plt
atoms = molecule('CO')
atoms.center(5)
atoms.pbc = [True, True, True]
pseudopotentials = {
'O': 'O.pbe-n-rrkjus_psl.1.0.0.UPF',
'C': 'C.pbe-n-rrkjus_psl.1.0.0.UPF'
}
queue = None
calc = Espresso(
label='scf/co',
pseudopotentials=pseudopotentials,
ecutwfc=30,
occupations='smearing',
degauss=0.03,
kpts=(1, 1, 1),
debug=True,
)
atoms.calc = calc
e = atoms.get_potential_energy()
print('Energy = {0:1.3f} eV'.format(e))
#===============================================================
# start nscf calculation
fe = calc.get_fermi_level()
print('fermi level: ', fe)
calc.nscf(occupations='tetrahedra', kpts=(3, 3, 3))
calc.nscf_calculate()
# dos, projwfc
calc.post(package='dos', Emin=fe - 30, Emax=fe + 30, DeltaE=0.01)
from ase.build import molecule
from xespresso import Espresso
h2 = molecule('H2')
h2.cell = [8, 8, 8]
h2.pbc = [True, True, True]
pseudopotentials = {'H': 'H.pbe-rrkjus_psl.1.0.0.UPF',}
calc = Espresso(pseudopotentials = pseudopotentials,
label = 'scf/h2', # 'scf/fe' is the directory, 'fe' is the prefix
ecutwfc = 40,
occupations = 'smearing',
degauss = 0.03,
kpts=(1, 1, 1))
h2.calc = calc
e = h2.get_potential_energy()
print('Energy: {0:1.3f}'.format(e))
'''
Energy: -3368.488
'''
from ase.build import molecule
from xespresso import Espresso
from xespresso.dos import DOS
import matplotlib.pyplot as plt
atoms = molecule('CO')
atoms.center(5)
atoms.pbc = [True, True, True]
pseudopotentials = {
'O': 'O.pbe-n-rrkjus_psl.1.0.0.UPF',
'C': 'C.pbe-n-rrkjus_psl.1.0.0.UPF'
}
calc = Espresso(
label='scf/co',
pseudopotentials=pseudopotentials,
ecutwfc=30,
kpts=(1, 1, 1),
)
atoms.calc = calc
e = atoms.get_potential_energy()
calc.read_results()
print('Energy = {0:1.3f} eV'.format(e))
#===============================================================
# start nscf calculation, and dos, projwfc
calc.read_results()
fermi = calc.get_fermi_level()
calc.nscf(kpts=(1, 1, 1))
calc.nscf_calculate()
calc.post(package='dos', Emin=fermi - 20, Emax=fermi + 10, DeltaE=0.1)
# DOS analysis
dos = DOS(calc)