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« on: May 4, 2009, 12:29 »
dear doctor Blom,
I edit the script to calculate the I-V curve using this method. the code:
from ATK.TwoProbe import *
from ATK.MPI import processIsMaster
import ivcurve
import numpy
# Generate time stamp
if processIsMaster():
import platform, time
print '#',time.ctime()
print '#',platform.node(),platform.platform()+'\n'
# Opening vnlfile
if processIsMaster(): file = VNLFile('C:/Users/617/Desktop/lih.vnl')
# Scattering elements and coordinates
scattering_elements = [lithium, Lithium, Lithium, Hydrogen,
Hydrogen, Lithium, Lithium, Lithium]
scattering_coordinates = [[ 4.35 , 4.35 , 11.6 ],
[ 4.35 , 4.35 , 14.5000001 ],
[ 4.35 , 4.35 , 17.40000019],
[ 4.35 , 4.35 , 19.76600037],
[ 4.35 , 4.35 , 20.57000027],
[ 4.35 , 4.35 , 22.93600044],
[ 4.35 , 4.35 , 25.83600006],
[ 4.35 , 4.35 , 28.73599968]]*Angstrom
electrode_elements = [lithium, Lithium, Lithium, Lithium]
electrode_coordinates = [[ 4.3499999 , 4.3499999 , 0. ],
[ 4.3499999 , 4.3499999 , 2.9000001 ],
[ 4.3499999 , 4.3499999 , 5.80000019],
[ 4.3499999 , 4.3499999 , 8.69999981]]*Angstrom
electrode_cell = [[ 8.7, 0. , 0. ],
[ 0. , 8.7, 0. ],
[ 0. , 0. , 11.6]]*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=[[1,1],[1,1]],
equivalent_atoms=([0,0],[3,7])
)
if processIsMaster(): nlPrint(twoprobe_configuration)
if processIsMaster(): file.addToSample(twoprobe_configuration, 'twoprobe_configuration')
######################################################################
# Central region parameters
######################################################################
exchange_correlation_type = LDA.PZ
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
)
basis_set_parameters = 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
)
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
)
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 = (1, 1, 500)
)
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
)
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 = (1, 1, 500)
)
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)
runtime_parameters = runtimeParameters(
verbosity_level = 1,
checkpoint_filename = 'C:/Users/617/Desktop/lih.nc'
)
voltages = numpy.arange(0.,1.01,0.1)*Volt
ivcurve.runIVcurve (
twoprobe_configuration,
two_probe_method,
runtime_parameters,
voltages,
vnl_filename='lih.vnl', sample_name='lih',
current_k_point_sampling = (1,1),
current_number_of_points = 100
)
iv = ivcurve.extractIVcurveFromVNLFile('lih.vnl','lih')
ivcurve.plotIVCurve(iv,'iv.png')
import matplotlib
matplotlib.use('Agg')
import pylab as P
from numpy import array
X = array(iv)[:,0]
Y = array(iv)[:,1]
P.plot(X,Y)
P.xlabel('Bias (Volt)')
P.ylabel('Current (Ampere)')
P.title('I-V curve for lih')
P.savefig('lih.png')
when I drag this script into in Job manage icon, after the job finish, a i-v photo can be got. but when I run the job with the ATK using the command "$ mpiexec -n 4 /home/ms/vnl-2008.10.0/atk/bin/atk /home/ms/b-pcur/lih.py"
an error comes out as follows:
Traceback (most recent call last):
File "<string>", line 218, in ?
File "/home/ms/vnl-2008.10.0/atk/lib/python2.4/site-packages/ivcurve.py", line 79, in runIVcurve
f.addToSample(current,sample_name,'Current at %s V bias' % voltage.inUnitsOf(Volt))
OSError: [Errno 2] No such file or directory: 'lih.vnl'
I run the VNL on linux system,
what is the problem? please help me to solve it. thank you !
how can I solve it ? is there any method?
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