if not Grain_Boundary:
unit_slab = crack.build_unit_slab()
pot_dir = os.environ['POTDIR']
pot_file = os.path.join(pot_dir, crack_info['param_file'])
mm_pot = Potential('IP EAM_ErcolAd do_rescale_r=T r_scale=1.00894848312', param_filename=pot_file, cutoff_skin=2.0)
# gb_frac.py will generate the frac_cell.xyz file which contains
# a crack_cell:
if Grain_Boundary:
unit_slab = Atoms('frac_cell.xyz')
unit_slab.set_calculator(mm_pot)
#calculate the elasticity tensor:
crack.calculate_c(mm_pot)
surface = crack.build_surface(mm_pot)
E_surf = surface.get_potential_energy()
bulk = bcc(2.82893)
bulk.set_atoms(26)
bulk.info['adsorbate_info']=None
bulk.set_calculator(mm_pot)
E_bulk = bulk.get_potential_energy()/len(bulk)
area = (surface.get_cell()[0,0]*surface.get_cell()[2,2])
print E_surf, E_bulk
gamma = (E_surf - E_bulk*len(surface))/(2.0*area)
print('Surface energy of %s surface %.4f J/m^2\n' %
(crack.cleavage_plane, gamma/(units.J/units.m**2)))
crack_slab = crack.build_crack_cell(unit_slab, mm_pot)
crack.write_crack_cell(crack_slab, mm_pot)
(0.25, 0.75, 0.75),
(0.75, 0.25, 0.75),
(0.75, 0.75, 0.25)])
atoms.set_cell([a,a,a], scale_atoms=True)
return atoms
xc = 'GLLB'
a = 5.404 # Si
if 1:
# 2 atom unit cell
bulk = diamond2('Si', a)
calc = GPAW(nbands=2*3,
width=0.01,
kpts=(32, 32, 32), h = 0.3, xc=xc)
bulk.set_calculator(calc)
E2_tot = bulk.get_potential_energy()
calc.write('Si2_GLLB.gpw')
response = calc.hamiltonian.xc.xcs['RESPONSE']
response.calculate_delta_xc()
Eks2, Dxc2 = response.calculate_delta_xc_perturbation()
"""
# 4 atom unit cell
bulk = diamond4('Si', a)
calc = GPAW(nbands=4*3,
width=0.01,
kpts=(24, 24, 20), h = 0.2, xc=xc)
bulk.set_calculator(calc)
E4_tot = bulk.get_potential_energy()
calc.write('Si4_GLLB.gpw')
response = calc.hamiltonian.xc.xcs['RESPONSE']
from gpaw.xc.rpa_correlation_energy import RPACorrelation
from gpaw.test import equal
kpts = monkhorst_pack((4,4,4))
kpts += np.array([1/8., 1/8., 1/8.])
bulk = bulk('Na', 'bcc', a=4.23)
ecut = 350
calc = GPAW(mode=PW(ecut),dtype=complex, basis='dzp', kpts=kpts,
parallel={'domain': 1}, txt='gs_occ_pw.txt', nbands=4,
occupations=FermiDirac(0.01),
setups={'Na': '1'},
)
bulk.set_calculator(calc)
bulk.get_potential_energy()
calc.write('gs_occ_pw.gpw')
calc = GPAW('gs_occ_pw.gpw',txt='gs_pw.txt', parallel={'band': 1})
calc.diagonalize_full_hamiltonian(nbands=520)
calc.write('gs_pw.gpw', 'all')
ecut = 120
calc = GPAW('gs_pw.gpw', communicator=serial_comm, txt=None)
rpa = RPACorrelation(calc, txt='rpa_%s.txt' %(ecut))
E = rpa.get_rpa_correlation_energy(ecut=ecut,
skip_gamma=False,
directions=[[0,1.0]],
kcommsize=size,
dfcommsize=size)
bulk = bulk('Na', 'bcc', a=4.23)
ecut = 350
calc = GPAW(
mode=PW(ecut),
dtype=complex,
basis='dzp',
kpts={
'size': (4, 4, 4),
'gamma': True
},
parallel={'domain': 1},
txt='gs_occ_pw.txt',
nbands=4,
occupations=FermiDirac(0.01),
setups={'Na': '1'},
)
bulk.set_calculator(calc)
bulk.get_potential_energy()
calc.write('gs_occ_pw.gpw')
calc = GPAW('gs_occ_pw.gpw', txt='gs_pw.txt', parallel={'band': 1})
calc.diagonalize_full_hamiltonian(nbands=520)
calc.write('gs_pw.gpw', 'all')
ecut = 120
calc = GPAW('gs_pw.gpw', communicator=serial_comm, txt=None)
rpa = RPACorrelation(calc, txt='rpa_%s.txt' % ecut)
E = rpa.calculate(ecut=[ecut])
equal(E, -1.106, 0.005)
unit_slab = crack.build_unit_slab()
pot_dir = os.environ['POTDIR']
pot_file = os.path.join(pot_dir, crack_info['param_file'])
mm_pot = Potential('IP EAM_ErcolAd do_rescale_r=T r_scale=1.00894848312',
param_filename=pot_file,
cutoff_skin=2.0)
# gb_frac.py will generate the frac_cell.xyz file which contains
# a crack_cell:
if Grain_Boundary:
unit_slab = Atoms('frac_cell.xyz')
unit_slab.set_calculator(mm_pot)
#calculate the elasticity tensor:
crack.calculate_c(mm_pot)
surface = crack.build_surface(mm_pot)
E_surf = surface.get_potential_energy()
bulk = bcc(2.82893)
bulk.set_atoms(26)
bulk.info['adsorbate_info'] = None
bulk.set_calculator(mm_pot)
E_bulk = bulk.get_potential_energy() / len(bulk)
area = (surface.get_cell()[0, 0] * surface.get_cell()[2, 2])
print E_surf, E_bulk
gamma = (E_surf - E_bulk * len(surface)) / (2.0 * area)
print('Surface energy of %s surface %.4f J/m^2\n' %
(crack.cleavage_plane, gamma / (units.J / units.m**2)))
crack_slab = crack.build_crack_cell(unit_slab, mm_pot)
crack.write_crack_cell(crack_slab, mm_pot)
