def run_dftb(system, c, records):
calc = Dftb(
label='graphene',
atoms=graphene,
kpts=(1, 1, 1),
run_manyDftb_steps=False,
# Specific DFTB+ keywords
Hamiltonian_SCC='Yes',
Hamiltonian_SCCTolerance=1E-5,
Hamiltonian_Charge=-1.0,
Hamiltonian_Filling_='Fermi',
Hamiltonian_Filling_Temperature='1E-6',
Hamiltonian_SpinPolarisation_='Colinear',
Hamiltonian_SpinPolarisation_UnpairedElectrons=1.0,
Hamiltonian_SpinConstants_='',
Hamiltonian_SpinConstants_C='{ -0.023}',
Hamiltonian_ElectricField_='',
Hamiltonian_ElectricField_PointCharges_='',
Hamiltonian_ElectricField_PointCharges_CoordsAndCharges_='DirectRead',
Hamiltonian_ElectricField_PointCharges_CoordsAndCharges_Records=records,
Hamiltonian_ElectricField_PointCharges_CoordsAndCharges_File=
'charges.dat')
graphene.set_calculator(calc)
calc.calculate(system)
return ()
def main():
'''Main driver routine.'''
system = read(GEO_PATH, format='gen')
calc = Dftb(label='H2O_cluster',
atoms=system,
Hamiltonian_SCC='Yes',
Hamiltonian_SCCTolerance='1.00E-010',
Driver_='ConjugateGradient',
Driver_MaxForceComponent='1.00E-008',
Driver_MaxSteps=1000,
Hamiltonian_MaxAngularMomentum_='',
Hamiltonian_MaxAngularMomentum_O='"p"',
Hamiltonian_MaxAngularMomentum_H='"s"')
system.set_calculator(calc)
calc.calculate(system)
final = read('geo_end.gen')
forces = system.get_forces()
energy = system.get_potential_energy()
def dftb_calc(path, calc_folder, sys):
os.chdir(path)
i = 0
if os.path.exists(calc_folder):
calc_folder += '_{0}'.format(i)
while os.path.exists(calc_folder):
i += 1
last_underscore = calc_folder.rfind('_')
calc_folder = calc_folder[:last_underscore+1] + str(i)
os.makedirs(calc_folder)
os.chdir(calc_folder)
# Assuming C and H are always present
args = {}
if 'N' in sys.get_chemical_symbols():
args['Hamiltonian_MaxAngularMomentum_N'] = '"p"'
if 'O' in sys.get_chemical_symbols():
args['Hamiltonian_MaxAngularMomentum_O'] = '"p"'
calc = Dftb(label=calc_folder,
atoms=sys,
run_manyDftb_steps=True,
# WriteResultsTag='Yes',
Driver_='ConjugateGradient',
Driver_MaxForceComponent='1E-4',
Driver_MaxSteps=1000,
Hamiltonian_MaxAngularMomentum_='',
Hamiltonian_MaxAngularMomentum_C='"p"',
Hamiltonian_MaxAngularMomentum_H='"s"',
**args)
sys.set_calculator(calc)
sys.write('geo_start.xyz')
calc.calculate(sys)
os.chdir(os.pardir)
return calc
from ase.calculators.dftb import Dftb
from ase.io import write, read
from ase.build import molecule
atoms = molecule('H2O')
calc = Dftb(atoms=atoms,
label='h2o',
Driver_='ConjugateGradient',
Driver_MaxForceComponent=1e-4,
Driver_MaxSteps=1000,
Hamiltonian_MaxAngularMomentum_='',
Hamiltonian_MaxAngularMomentum_O='p',
Hamiltonian_MaxAngularMomentum_H='s')
atoms.set_calculator(calc)
calc.calculate(atoms)
final = read('geo_end.gen')
write('final.xyz', final)
from ase.calculators.dftb import Dftb
from ase.io import write, read
from ase.build import molecule
system = molecule('H2O')
calc = Dftb(label='h2o', atoms=system,
run_manyDftb_steps=True,
Driver_='ConjugateGradient',
Driver_MaxForceComponent='1E-4',
Driver_MaxSteps=1000,
Hamiltonian_MaxAngularMomentum_='',
Hamiltonian_MaxAngularMomentum_O='"p"',
Hamiltonian_MaxAngularMomentum_H='"s"')
system.set_calculator(calc)
calc.calculate(system)
final = read('geo_end.gen')
write('test.final.xyz', final)
from ase.calculators.dftb import Dftb
from ase.io import write, read
from ase.build import molecule
system = molecule('H2O')
calc = Dftb(label='h2o',
atoms=system,
run_manyDftb_steps=True,
Driver_='ConjugateGradient',
Driver_MaxForceComponent='1E-4',
Driver_MaxSteps=1000,
Hamiltonian_MaxAngularMomentum_='',
Hamiltonian_MaxAngularMomentum_O='"p"',
Hamiltonian_MaxAngularMomentum_H='"s"')
system.set_calculator(calc)
calc.calculate(system)
final = read('geo_end.gen')
write('test.final.xyz', final)
def test_dftb_bandstructure():
import os
import subprocess
from unittest import SkipTest
from ase.test import require
from ase.test.testsuite import datafiles_directory
from ase.calculators.dftb import Dftb
from ase.build import bulk
require('dftb')
os.environ['DFTB_PREFIX'] = datafiles_directory
# We need to get the DFTB+ version to know
# whether to skip this test or not.
# For this, we need to run DFTB+ and grep
# the version from the output header.
cmd = os.environ['ASE_DFTB_COMMAND'].split()[0]
proc = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
lines = ''
for line in proc.stdout:
l = line.decode()
if 'DFTB+' in l and ('version' in l.lower() or 'release' in l.lower()):
version = l[l.index('DFTB+'):]
break
lines += l + '\n'
else:
raise RuntimeError('Could not parse DFTB+ version ' + lines)
if '17.1' not in version:
msg = 'Band structure properties not present in results.tag for ' + version
raise SkipTest(msg)
# The actual testing starts here
calc = Dftb(label='dftb',
kpts=(3, 3, 3),
Hamiltonian_SCC='Yes',
Hamiltonian_SCCTolerance=1e-5,
Hamiltonian_MaxAngularMomentum_Si='d')
atoms = bulk('Si')
atoms.set_calculator(calc)
atoms.get_potential_energy()
efermi = calc.get_fermi_level()
assert abs(efermi - -2.90086680996455) < 1.
# DOS does not currently work because of
# missing "get_k_point_weights" function
#from ase.dft.dos import DOS
#dos = DOS(calc, width=0.2)
#d = dos.get_dos()
#e = dos.get_energies()
#print(d, e)
calc = Dftb(atoms=atoms,
label='dftb',
kpts={
'path': 'WGXWLG',
'npoints': 50
},
Hamiltonian_SCC='Yes',
Hamiltonian_MaxSCCIterations=1,
Hamiltonian_ReadInitialCharges='Yes',
Hamiltonian_MaxAngularMomentum_Si='d')
atoms.set_calculator(calc)
calc.calculate(atoms)
calc.results['fermi_levels'] = [efermi]
calc.band_structure()
