Author Topic: self-consistent (Read 6459 times)

qnsyhanjiu · « **on:** April 7, 2011, 08:08 »

# Total Charge (Spin Down) = 767.00537
#-------------------------------------------------------------------------------
# sc 20 : Fermi Energy = -0.20291 Ry dRho = 1.3457E-02
#-------------------------------------------------------------------------------
# Mulliken Population for sc 20
#-------------------------------------------------------------------------------
# Spin Up
I computer the self-consistent,when the result is Mulliken Population for sc 20,the result is stop,but top,the computer is still running why? Thank you!

qnsyhanjiu · « **Reply #1 on:** April 7, 2011, 08:16 »

This is my scripter:

from ATK.TwoProbe import *
from ATK.MPI import processIsMaster

# Generate time stamp
if processIsMaster():
import platform, time
print '#',time.ctime()
print '#',platform.node(),platform.platform()+'\n'

# Scattering elements and coordinates
scattering_elements = [Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Carbon, Carbon, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon,
Hydrogen, Hydrogen, Hydrogen, Hydrogen,
Hydrogen, Hydrogen, Hydrogen, Hydrogen,
Iron, Carbon, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon,
Carbon, Hydrogen, Hydrogen, Hydrogen,
Hydrogen, Hydrogen, Hydrogen, Hydrogen,
Hydrogen, Iron, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon,
Carbon, Carbon, Hydrogen, Hydrogen,
Hydrogen, Hydrogen, Hydrogen, Hydrogen,
Hydrogen, Hydrogen, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold]
scattering_coordinates = [[ 0. , 0. , 4.07800007],
[ 0. , 2.8835814 , 4.07800007],
[ 0. , 5.7671628 , 4.07800007],
[ 0. , 8.65074444, 4.07800007],
[ 2.8835814 , 0. , 4.07800007],
[ 2.8835814 , 2.8835814 , 4.07800007],
[ 2.8835814 , 5.7671628 , 4.07800007],
[ 2.8835814 , 8.65074444, 4.07800007],
[ 5.7671628 , 0. , 4.07800007],
[ 5.7671628 , 2.8835814 , 4.07800007],
[ 5.7671628 , 5.7671628 , 4.07800007],
[ 5.7671628 , 8.65074444, 4.07800007],
[ 8.65074444, 0. , 4.07800007],
[ 8.65074444, 2.8835814 , 4.07800007],
[ 8.65074444, 5.7671628 , 4.07800007],
[ 8.65074444, 8.65074444, 4.07800007],
[ 1.4417907 , 1.4417907 , 6.1170001 ],
[ 1.4417907 , 4.32537222, 6.1170001 ],
[ 1.4417907 , 7.20895386, 6.1170001 ],
[ 1.4417907 , 10.09253502, 6.1170001 ],
[ 4.32537222, 1.4417907 , 6.1170001 ],
[ 4.32537222, 4.32537222, 6.1170001 ],
[ 4.32537222, 7.20895386, 6.1170001 ],
[ 4.32537222, 10.09253502, 6.1170001 ],
[ 7.20895386, 1.4417907 , 6.1170001 ],
[ 7.20895386, 4.32537222, 6.1170001 ],
[ 7.20895386, 7.20895386, 6.1170001 ],
[ 7.20895386, 10.09253502, 6.1170001 ],
[ 10.09253502, 1.4417907 , 6.1170001 ],
[ 10.09253502, 4.32537222, 6.1170001 ],
[ 10.09253502, 7.20895386, 6.1170001 ],
[ 10.09253502, 10.09253502, 6.1170001 ],
[ 3.02664982, 5.03114932, 11.19394743],
[ 3.64980839, 3.62328051, 11.19235987],
[ 5.08596092, 3.06840383, 11.19343848],
[ 6.49382888, 3.69155847, 11.19655144],
[ 7.04870211, 5.1277089 , 11.1998752 ],
[ 6.42554365, 6.53557764, 11.20146275],
[ 4.98939115, 7.09045445, 11.20038415],
[ 3.58152317, 6.46729969, 11.19727121],
[ 1.89673768, 5.00402291, 11.19228215],
[ 2.87002312, 2.80513106, 11.18980259],
[ 5.11309019, 1.93849217, 11.19148725],
[ 7.31198059, 2.91177164, 11.19634923],
[ 8.17861425, 5.15483531, 11.20154048],
[ 7.20532905, 7.35372721, 11.20402003],
[ 4.96226188, 8.22036587, 11.2023354 ],
[ 2.76337134, 7.24708663, 11.1974734 ],
[ 5.03538535, 5.07661079, 12.79707573],
[ 3.02206932, 5.02551366, 14.39372049],
[ 3.64522778, 3.61764489, 14.39213286],
[ 5.08138034, 3.06276821, 14.39321146],
[ 6.48924826, 3.68592285, 14.39632449],
[ 7.04412161, 5.12207324, 14.39964829],
[ 6.42096316, 6.52994202, 14.40123592],
[ 4.98481057, 7.08481871, 14.40015731],
[ 3.57694267, 6.46166407, 14.39704428],
[ 1.89215718, 4.99838725, 14.39205513],
[ 2.86544262, 2.79949556, 14.38957558],
[ 5.10850961, 1.93285667, 14.39126024],
[ 7.30740009, 2.9061359 , 14.39612231],
[ 8.17403375, 5.14919965, 14.40131364],
[ 7.20074831, 7.34809147, 14.40379319],
[ 4.9576813 , 8.21473037, 14.40210853],
[ 2.75879084, 7.24145089, 14.39724646],
[ 5.03080556, 5.07097611, 15.99629293],
[ 3.01748859, 5.019878 , 17.5934938 ],
[ 3.64064716, 3.61200927, 17.59190593],
[ 5.07679976, 3.05713259, 17.59298454],
[ 6.48466765, 3.68028723, 17.59609733],
[ 7.03954099, 5.11643758, 17.59942136],
[ 6.41638254, 6.52430628, 17.60100875],
[ 4.98022999, 7.07918297, 17.59993015],
[ 3.57236205, 6.45602845, 17.59681735],
[ 1.88757645, 4.9927516 , 17.59182821],
[ 2.86086188, 2.79385983, 17.58934865],
[ 5.10392903, 1.92722093, 17.59103332],
[ 7.3028196 , 2.90050017, 17.59589515],
[ 8.16945325, 5.14356399, 17.60108648],
[ 7.19616781, 7.34245573, 17.60356603],
[ 4.95310072, 8.20909463, 17.60188136],
[ 2.75421034, 7.23581539, 17.59701953],
[ 0. , 0. , 22.67700092],
[ 0. , 2.8835814 , 22.67700092],
[ 0. , 5.7671628 , 22.67700092],
[ 0. , 8.65074444, 22.67700092],
[ 2.8835814 , 0. , 22.67700092],
[ 2.8835814 , 2.8835814 , 22.67700092],
[ 2.8835814 , 5.7671628 , 22.67700092],
[ 2.8835814 , 8.65074444, 22.67700092],
[ 5.7671628 , 0. , 22.67700092],
[ 5.7671628 , 2.8835814 , 22.67700092],
[ 5.7671628 , 5.7671628 , 22.67700092],
[ 5.7671628 , 8.65074444, 22.67700092],
[ 8.65074444, 0. , 22.67700092],
[ 8.65074444, 2.8835814 , 22.67700092],
[ 8.65074444, 5.7671628 , 22.67700092],
[ 8.65074444, 8.65074444, 22.67700092],
[ 1.4417907 , 1.4417907 , 24.71600096],
[ 1.4417907 , 4.32537222, 24.71600096],
[ 1.4417907 , 7.20895386, 24.71600096],
[ 1.4417907 , 10.09253502, 24.71600096],
[ 4.32537222, 1.4417907 , 24.71600096],
[ 4.32537222, 4.32537222, 24.71600096],
[ 4.32537222, 7.20895386, 24.71600096],
[ 4.32537222, 10.09253502, 24.71600096],
[ 7.20895386, 1.4417907 , 24.71600096],
[ 7.20895386, 4.32537222, 24.71600096],
[ 7.20895386, 7.20895386, 24.71600096],
[ 7.20895386, 10.09253502, 24.71600096],
[ 10.09253502, 1.4417907 , 24.71600096],
[ 10.09253502, 4.32537222, 24.71600096],
[ 10.09253502, 7.20895386, 24.71600096],
[ 10.09253502, 10.09253502, 24.71600096]]*Angstrom

electrode_elements = [Gold, Gold]
electrode_coordinates = [[ 0. , 0. , 0. ],
[ 1.44179073, 1.44179073, 2.039 ]]*Angstrom

electrode_cell = [[ 2.88358145, 0. , 0. ],
[ 0. , 2.88358145, 0. ],
[ 0. , 0. , 4.078 ]]*Angstrom

# Set up electrodes
electrode_configuration = PeriodicAtomConfiguration(
electrode_cell,
electrode_elements,
electrode_coordinates
)

# Set up two-probe configuration
twoprobe_configuration = TwoProbeConfiguration(
(electrode_configuration,electrode_configuration),
scattering_elements,
scattering_coordinates,
electrode_repetitions=[[4,4],[4,4]],
equivalent_atoms=([0,0],[1,98])
)
if processIsMaster(): nlPrint(twoprobe_configuration)

######################################################################
# Central region parameters
######################################################################
exchange_correlation_type = GGA.revPBE

iteration_mixing_parameters = iterationMixingParameters(
algorithm = IterationMixing.Pulay,
diagonal_mixing_parameter = 0.1,
quantity = IterationMixing.Hamiltonian,
history_steps = 6
)

electron_density_parameters = electronDensityParameters(
mesh_cutoff = 150.0*Rydberg,
initial_scaled_spin = [ 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.,
0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.,
0., 0., 0., 0., 0., 0., 1., 1., 1., 1., 1., 1., 1.,
1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.,
1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.,
1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.,
1., 1., 1., 1., 0., 0., 0., 0., 0., 0., 0., 0., 0.,
0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.,
0., 0., 0., 0., 0., 0., 0., 0., 0., 0. ]
)

basis_set_parameters_Common = basisSetParameters(
type = DoubleZetaPolarized,
radial_sampling_dr = 0.001*Bohr,
energy_shift = 0.01*Rydberg,
delta_rinn = 0.8,
v0 = 40.0*Rydberg,
charge = 0.0,
split_norm = 0.15
)

basis_set_parameters_Gold = basisSetParameters(
type = SingleZetaPolarized,
energy_shift = 0.01*Rydberg,
delta_rinn = 0.8,
v0 = 40.0*Rydberg,
charge = 0.0,
split_norm = 0.15,
element = Gold
)

basis_set_parameters = [
basis_set_parameters_Common,
basis_set_parameters_Gold
]

iteration_control_parameters = iterationControlParameters(
tolerance = 1e-005,
criterion = IterationControl.TotalEnergy,
max_steps = 100
)

electrode_voltages = (0.0,0.0)*Volt

two_probe_algorithm_parameters = twoProbeAlgorithmParameters(
electrode_constraint = ElectrodeConstraints.Off,
initial_density_type = InitialDensityType.EquivalentBulk
)

energy_contour_integral_parameters = energyContourIntegralParameters(
circle_points = 30,
integral_lower_bound = 3*Rydberg,
fermi_line_points = 10,
fermi_function_poles = 4,
real_axis_infinitesimal = 0.01*electronVolt,
real_axis_point_density = 0.02*electronVolt
)

two_center_integral_parameters = twoCenterIntegralParameters(
cutoff = 2500.0*Rydberg,
points = 1024
)

######################################################################
# Left electrode parameters
######################################################################
left_electrode_electron_density_parameters = electronDensityParameters(
mesh_cutoff = 200.0*Rydberg,
initial_scaled_spin = [ 0., 0. ]
)

left_electrode_iteration_control_parameters = iterationControlParameters(
tolerance = 1e-005,
criterion = IterationControl.TotalEnergy,
max_steps = 100
)

left_electrode_brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters(
monkhorst_pack_parameters = (30, 30, 100)
)

left_electrode_iteration_mixing_parameters = iterationMixingParameters(
algorithm = IterationMixing.Pulay,
diagonal_mixing_parameter = 0.1,
quantity = IterationMixing.Hamiltonian,
history_steps = 6
)

left_electrode_eigenstate_occupation_parameters = eigenstateOccupationParameters(
temperature = 1000.0*Kelvin
)

######################################################################
# Collect left electrode parameters
######################################################################
left_electrode_parameters = ElectrodeParameters(
brillouin_zone_integration_parameters = left_electrode_brillouin_zone_integration_parameters,
electron_density_parameters = left_electrode_electron_density_parameters,
eigenstate_occupation_parameters = left_electrode_eigenstate_occupation_parameters,
iteration_mixing_parameters = left_electrode_iteration_mixing_parameters,
iteration_control_parameters = left_electrode_iteration_control_parameters
)

######################################################################
# Right electrode parameters
######################################################################
right_electrode_electron_density_parameters = electronDensityParameters(
mesh_cutoff = 150.0*Rydberg,
initial_scaled_spin = [ 0., 0. ]
)

right_electrode_iteration_control_parameters = iterationControlParameters(
tolerance = 1e-005,
criterion = IterationControl.TotalEnergy,
max_steps = 100
)

right_electrode_brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters(
monkhorst_pack_parameters = (30, 30, 100)
)

right_electrode_iteration_mixing_parameters = iterationMixingParameters(
algorithm = IterationMixing.Pulay,
diagonal_mixing_parameter = 0.1,
quantity = IterationMixing.Hamiltonian,
history_steps = 6
)

right_electrode_eigenstate_occupation_parameters = eigenstateOccupationParameters(
temperature = 1000.0*Kelvin
)

######################################################################
# Collect right electrode parameters
######################################################################
right_electrode_parameters = ElectrodeParameters(
brillouin_zone_integration_parameters = right_electrode_brillouin_zone_integration_parameters,
electron_density_parameters = right_electrode_electron_density_parameters,
eigenstate_occupation_parameters = right_electrode_eigenstate_occupation_parameters,
iteration_mixing_parameters = right_electrode_iteration_mixing_parameters,
iteration_control_parameters = right_electrode_iteration_control_parameters
)

######################################################################
# Initialize self-consistent field calculation
######################################################################
two_probe_method = TwoProbeMethod(
electrode_parameters = (left_electrode_parameters,right_electrode_parameters),
exchange_correlation_type = exchange_correlation_type,
iteration_mixing_parameters = iteration_mixing_parameters,
electron_density_parameters = electron_density_parameters,
basis_set_parameters = basis_set_parameters,
iteration_control_parameters = iteration_control_parameters,
energy_contour_integral_parameters = energy_contour_integral_parameters,
two_center_integral_parameters = two_center_integral_parameters,
electrode_voltages = electrode_voltages,
algorithm_parameters = two_probe_algorithm_parameters
)
if processIsMaster(): nlPrint(two_probe_method)

runtime_parameters = runtimeParameters(
verbosity_level = 10,
checkpoint_filename = 'AuFe2COT3Au-scf.nc'
)

# Perform self-consistent field calculation
scf = executeSelfConsistentCalculation(
twoprobe_configuration,
two_probe_method,
runtime_parameters = runtime_parameters
)

Anders Blom · « **Reply #2 on:** April 7, 2011, 09:07 »

Sounds like a spurious error. I suggest you just rerun it, possible restarting from the checkpoint NC file.

qnsyhanjiu · « **Reply #3 on:** April 7, 2011, 10:50 »

the script is not any questions? This computer I have been computer five days,it may be the setting up is not right?

Anders Blom · « **Reply #4 on:** April 7, 2011, 10:54 »

An error in the script would not really cause such a problem.

However, in general, the electrode is too short. You should have at least 4 layers of gold.

qnsyhanjiu · « **Reply #5 on:** April 7, 2011, 17:15 »

electrode_repetitions=[[4,4],[4,4]],
this set is not the electrode's parameger? Or having the other setting up ? Thank you!

Anders Blom · « **Reply #6 on:** April 7, 2011, 21:37 »

4,4 is the repetition in the XY plane. The problem is in the Z direction, you only have 2 layers, you need 4 or maybe 6.

qnsyhanjiu · « **Reply #7 on:** April 8, 2011, 12:15 »

when I setup 6 6 for the x,y; the Z if at least to set 6 or 8,how can I chose x ,y,z for computering two-probe system.

Anders Blom · « **Reply #8 on:** April 8, 2011, 12:41 »

The same way you set up the original system, only with 4 or 6 electrode layers instead. 8 is probably overkill.

qnsyhanjiu · « **Reply #9 on:** April 9, 2011, 03:04 »

when self-consistent finished,I computer the transmission spectrum,the transmission cofficient is 0 .This is my script:
from ATK.TwoProbe import *
from ATK.MPI import processIsMaster

# Generate time stamp
if processIsMaster():
import platform, time
print '#',time.ctime()
print '#',platform.node(),platform.platform()+'\n'

# Opening vnlfile
if processIsMaster(): file = VNLFile('AuFeCOT2Au_trans.vnl')

# Scattering elements and coordinates
scattering_elements = [Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Carbon, Carbon, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon,
Hydrogen, Hydrogen, Hydrogen, Hydrogen,
Hydrogen, Hydrogen, Hydrogen, Hydrogen,
Iron, Carbon, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon,
Carbon, Hydrogen, Hydrogen, Hydrogen,
Hydrogen, Hydrogen, Hydrogen, Hydrogen,
Hydrogen, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold]
scattering_coordinates = [[ 0. , 0. , 4.07800007],
[ 0. , 2.8835814 , 4.07800007],
[ 0. , 5.7671628 , 4.07800007],
[ 0. , 8.65074444, 4.07800007],
[ 2.8835814 , 0. , 4.07800007],
[ 2.8835814 , 2.8835814 , 4.07800007],
[ 2.8835814 , 5.7671628 , 4.07800007],
[ 2.8835814 , 8.65074444, 4.07800007],
[ 5.7671628 , 0. , 4.07800007],
[ 5.7671628 , 2.8835814 , 4.07800007],
[ 5.7671628 , 5.7671628 , 4.07800007],
[ 5.7671628 , 8.65074444, 4.07800007],
[ 8.65074444, 0. , 4.07800007],
[ 8.65074444, 2.8835814 , 4.07800007],
[ 8.65074444, 5.7671628 , 4.07800007],
[ 8.65074444, 8.65074444, 4.07800007],
[ 1.4417907 , 1.4417907 , 6.1170001 ],
[ 1.4417907 , 4.32537222, 6.1170001 ],
[ 1.4417907 , 7.20895386, 6.1170001 ],
[ 1.4417907 , 10.09253502, 6.1170001 ],
[ 4.32537222, 1.4417907 , 6.1170001 ],
[ 4.32537222, 4.32537222, 6.1170001 ],
[ 4.32537222, 7.20895386, 6.1170001 ],
[ 4.32537222, 10.09253502, 6.1170001 ],
[ 7.20895386, 1.4417907 , 6.1170001 ],
[ 7.20895386, 4.32537222, 6.1170001 ],
[ 7.20895386, 7.20895386, 6.1170001 ],
[ 7.20895386, 10.09253502, 6.1170001 ],
[ 10.09253502, 1.4417907 , 6.1170001 ],
[ 10.09253502, 4.32537222, 6.1170001 ],
[ 10.09253502, 7.20895386, 6.1170001 ],
[ 10.09253502, 10.09253502, 6.1170001 ],
[ 3.00554715, 5.06825432, 11.02264016],
[ 3.60000394, 3.64764951, 11.01966818],
[ 5.02483884, 3.06347858, 11.00989404],
[ 6.44540297, 3.65794097, 10.99904331],
[ 7.02954911, 5.08280861, 10.99347218],
[ 6.43509244, 6.50341343, 10.99644416],
[ 5.01025753, 7.08758436, 11.0062183 ],
[ 3.58969341, 6.49312197, 11.01706904],
[ 1.8750888 , 5.06416577, 11.03102176],
[ 2.80354606, 2.84538208, 11.02637995],
[ 5.02893651, 1.9329897 , 11.01111413],
[ 7.24765669, 2.86145579, 10.99416681],
[ 8.16001021, 5.08689752, 10.9854655 ],
[ 7.23155295, 7.30568133, 10.99010731],
[ 5.00616257, 8.21807347, 11.00537313],
[ 2.78744231, 7.28960739, 11.02232045],
[ 5.02913646, 5.07703446, 12.60752008],
[ 3.02872382, 5.0712603 , 14.22156797],
[ 3.6231805 , 3.6506555 , 14.21859584],
[ 5.04801539, 3.06648456, 14.20882187],
[ 6.46857952, 3.66094695, 14.19797096],
[ 7.05272566, 5.0858146 , 14.19239984],
[ 6.45826899, 6.50641941, 14.19537196],
[ 5.03343408, 7.09059034, 14.20514593],
[ 3.61286997, 6.49612795, 14.21599684],
[ 1.89826261, 5.0671714 , 14.22957454],
[ 2.82671987, 2.84838759, 14.22493277],
[ 5.05211035, 1.93599545, 14.20966706],
[ 7.2708305 , 2.86446153, 14.19271956],
[ 8.18318401, 5.08990314, 14.18401823],
[ 7.25472699, 7.30868684, 14.18866024],
[ 5.0293364 , 8.22107922, 14.20392595],
[ 2.81061636, 7.29261314, 14.22087321],
[ 0. , 0. , 19.71699968],
[ 0. , 2.8835814 , 19.71699968],
[ 0. , 5.7671628 , 19.71699968],
[ 0. , 8.65074444, 19.71699968],
[ 2.8835814 , 0. , 19.71699968],
[ 2.8835814 , 2.8835814 , 19.71699968],
[ 2.8835814 , 5.7671628 , 19.71699968],
[ 2.8835814 , 8.65074444, 19.71699968],
[ 5.7671628 , 0. , 19.71699968],
[ 5.7671628 , 2.8835814 , 19.71699968],
[ 5.7671628 , 5.7671628 , 19.71699968],
[ 5.7671628 , 8.65074444, 19.71699968],
[ 8.65074444, 0. , 19.71699968],
[ 8.65074444, 2.8835814 , 19.71699968],
[ 8.65074444, 5.7671628 , 19.71699968],
[ 8.65074444, 8.65074444, 19.71699968],
[ 1.4417907 , 1.4417907 , 21.75599972],
[ 1.4417907 , 4.32537222, 21.75599972],
[ 1.4417907 , 7.20895386, 21.75599972],
[ 1.4417907 , 10.09253502, 21.75599972],
[ 4.32537222, 1.4417907 , 21.75599972],
[ 4.32537222, 4.32537222, 21.75599972],
[ 4.32537222, 7.20895386, 21.75599972],
[ 4.32537222, 10.09253502, 21.75599972],
[ 7.20895386, 1.4417907 , 21.75599972],
[ 7.20895386, 4.32537222, 21.75599972],
[ 7.20895386, 7.20895386, 21.75599972],
[ 7.20895386, 10.09253502, 21.75599972],
[ 10.09253502, 1.4417907 , 21.75599972],
[ 10.09253502, 4.32537222, 21.75599972],
[ 10.09253502, 7.20895386, 21.75599972],
[ 10.09253502, 10.09253502, 21.75599972]]*Angstrom

electrode_elements = [Gold, Gold]
electrode_coordinates = [[ 0. , 0. , 0. ],
[ 1.44179073, 1.44179073, 2.039 ]]*Angstrom

electrode_cell = [[ 2.88358145, 0. , 0. ],
[ 0. , 2.88358145, 0. ],
[ 0. , 0. , 4.078 ]]*Angstrom

# Set up electrodes
electrode_configuration = PeriodicAtomConfiguration(
electrode_cell,
electrode_elements,
electrode_coordinates
)

# Set up two-probe configuration
twoprobe_configuration = TwoProbeConfiguration(
(electrode_configuration,electrode_configuration),
scattering_elements,
scattering_coordinates,
electrode_repetitions=[[4,4],[4,4]],
equivalent_atoms=([0,0],[1,81])
)
if processIsMaster(): nlPrint(twoprobe_configuration)
if processIsMaster(): file.addToSample(twoprobe_configuration, 'AuFeCOT2Au')

######################################################################
# Central region parameters
######################################################################
exchange_correlation_type = GGA.revPBE

iteration_mixing_parameters = iterationMixingParameters(
algorithm = IterationMixing.Pulay,
diagonal_mixing_parameter = 0.1,
quantity = IterationMixing.Hamiltonian,
history_steps = 6
)

electron_density_parameters = electronDensityParameters(
mesh_cutoff = 150.0*Rydberg,
initial_scaled_spin = [ 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.,
0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.,
0., 0., 0., 0., 0., 0., 1., 1., 1., 1., 1., 1., 1.,
1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.,
1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.,
0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.,
0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.,
0., 0., 0., 0., 0., 0. ]
)

basis_set_parameters_Common = basisSetParameters(
type = DoubleZetaPolarized,
radial_sampling_dr = 0.001*Bohr,
energy_shift = 0.01*Rydberg,
delta_rinn = 0.8,
v0 = 40.0*Rydberg,
charge = 0.0,
split_norm = 0.15
)

basis_set_parameters_Gold = basisSetParameters(
type = SingleZetaPolarized,
energy_shift = 0.01*Rydberg,
delta_rinn = 0.8,
v0 = 40.0*Rydberg,
charge = 0.0,
split_norm = 0.15,
element = Gold
)

basis_set_parameters = [
basis_set_parameters_Common,
basis_set_parameters_Gold
]

iteration_control_parameters = iterationControlParameters(
tolerance = 1e-005,
criterion = IterationControl.TotalEnergy,
max_steps = 100
)

electrode_voltages = (0.0,0.0)*Volt

two_probe_algorithm_parameters = twoProbeAlgorithmParameters(
electrode_constraint = ElectrodeConstraints.Off,
initial_density_type = InitialDensityType.EquivalentBulk
)

energy_contour_integral_parameters = energyContourIntegralParameters(
circle_points = 30,
integral_lower_bound = 3*Rydberg,
fermi_line_points = 10,
fermi_function_poles = 4,
real_axis_infinitesimal = 0.01*electronVolt,
real_axis_point_density = 0.02*electronVolt
)

two_center_integral_parameters = twoCenterIntegralParameters(
cutoff = 2500.0*Rydberg,
points = 1024
)

######################################################################
# Left electrode parameters
######################################################################
left_electrode_electron_density_parameters = electronDensityParameters(
mesh_cutoff = 150.0*Rydberg,
initial_scaled_spin = [ 0., 0. ]
)

left_electrode_iteration_control_parameters = iterationControlParameters(
tolerance = 1e-005,
criterion = IterationControl.TotalEnergy,
max_steps = 100
)

left_electrode_brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters(
monkhorst_pack_parameters = (30, 30, 100)
)

left_electrode_iteration_mixing_parameters = iterationMixingParameters(
algorithm = IterationMixing.Pulay,
diagonal_mixing_parameter = 0.1,
quantity = IterationMixing.Hamiltonian,
history_steps = 6
)

left_electrode_eigenstate_occupation_parameters = eigenstateOccupationParameters(
temperature = 300.0*Kelvin
)

######################################################################
# Collect left electrode parameters
######################################################################
left_electrode_parameters = ElectrodeParameters(
brillouin_zone_integration_parameters = left_electrode_brillouin_zone_integration_parameters,
electron_density_parameters = left_electrode_electron_density_parameters,
eigenstate_occupation_parameters = left_electrode_eigenstate_occupation_parameters,
iteration_mixing_parameters = left_electrode_iteration_mixing_parameters,
iteration_control_parameters = left_electrode_iteration_control_parameters
)

######################################################################
# Right electrode parameters
######################################################################
right_electrode_electron_density_parameters = electronDensityParameters(
mesh_cutoff = 150.0*Rydberg,
initial_scaled_spin = [ 0., 0. ]
)

right_electrode_iteration_control_parameters = iterationControlParameters(
tolerance = 1e-005,
criterion = IterationControl.TotalEnergy,
max_steps = 100
)

right_electrode_brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters(
monkhorst_pack_parameters = (30, 30, 100)
)

right_electrode_iteration_mixing_parameters = iterationMixingParameters(
algorithm = IterationMixing.Pulay,
diagonal_mixing_parameter = 0.1,
quantity = IterationMixing.Hamiltonian,
history_steps = 6
)

right_electrode_eigenstate_occupation_parameters = eigenstateOccupationParameters(
temperature = 300.0*Kelvin
)

######################################################################
# Collect right electrode parameters
######################################################################
right_electrode_parameters = ElectrodeParameters(
brillouin_zone_integration_parameters = right_electrode_brillouin_zone_integration_parameters,
electron_density_parameters = right_electrode_electron_density_parameters,
eigenstate_occupation_parameters = right_electrode_eigenstate_occupation_parameters,
iteration_mixing_parameters = right_electrode_iteration_mixing_parameters,
iteration_control_parameters = right_electrode_iteration_control_parameters
)

######################################################################
# Initialize self-consistent field calculation
######################################################################
two_probe_method = TwoProbeMethod(
electrode_parameters = (left_electrode_parameters,right_electrode_parameters),
exchange_correlation_type = exchange_correlation_type,
iteration_mixing_parameters = iteration_mixing_parameters,
electron_density_parameters = electron_density_parameters,
basis_set_parameters = basis_set_parameters,
iteration_control_parameters = iteration_control_parameters,
energy_contour_integral_parameters = energy_contour_integral_parameters,
two_center_integral_parameters = two_center_integral_parameters,
electrode_voltages = electrode_voltages,
algorithm_parameters = two_probe_algorithm_parameters
)
if processIsMaster(): nlPrint(two_probe_method)

# Restore self consistent calculation from check point file
scf = restoreSelfConsistentCalculation(
filename = 'AuFeCOT2Au-scf.nc'
)
######################################################################
# Calculate physical properties
######################################################################
import numpy
transmission_spectrum = calculateTransmissionSpectrum(
self_consistent_calculation = scf,
energies = numpy.arange(-2.0, 2.0, 0.01)*electronVolt,
brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters((30, 30)),
green_function_infinitesimal = 1.0e-5*electronVolt
)
if processIsMaster(): nlPrint(transmission_spectrum)
if processIsMaster(): file.addToSample(transmission_spectrum, 'AuFeCOT2Au', 'Transmission Spectrum')

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Re: self-consistent

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Re: self-consistent

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Re: self-consistent

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Re: self-consistent