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 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 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 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
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,
fileout='stm1_1eV.cube')
# ========================
# Creates: 2d.png, 2d_I.png, line.png, dIdV.png
from ase.dft.stm import STM
from ase.io.cube import read_cube_data