16
General Questions and Answers / Re: how can I get the results from the .nc file?
« on: August 2, 2009, 10:32 »
thank you ! 
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17
General Questions and Answers / Re: how can I get the results from the .nc file?
« on: August 2, 2009, 08:05 »
hi, doctor Blom,
is the follow script correct?
is the follow script correct?
Quote
for voltage in numpy.arange(0.0, 5.01, 0.1):please check it. thank you !
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 = (voltage, 0)*Volt,
algorithm_parameters = two_probe_algorithm_parameters
)
runtime_parameters = runtimeParameters(
verbosity_level = 10,
checkpoint_filename = 'C:/Users/617/Desktop/lih2li1_%g.nc' %voltage
)
if processIsMaster(): nlPrint(voltage)
# Using initial density from self consistent calculation
scf = executeSelfConsistentCalculation(
twoprobe_configuration,
two_probe_method,
initial_calculation = scf,
runtime_parameters = runtime_parameters
)
######################################################################
# Calculate physical properties
######################################################################
current = calculateCurrent(
self_consistent_calculation = scf,
brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters((1, 1)),
green_function_infinitesimal = 1.0e-5*electronVolt,
number_of_points = 100
)
if processIsMaster(): print "Voltage: %g V, Current: %g A" % (voltage.inUnitsOf(Volt), current.inUnitsOf(Ampere))
if processIsMaster(): file.addToSample(current, 'twoprobe_configuration', 'Current at %g V bias' % voltage)
18
General Questions and Answers / Re: how can I get the results from the .nc file?
« on: July 30, 2009, 10:41 »
thank you doctor Blom very much!
I will chang it as soon as possible and post it. thank you again!
I will chang it as soon as possible and post it. thank you again!
19
General Questions and Answers / Re: how can I get the results from the .nc file?
« on: July 30, 2009, 09:57 »
there is only 1 .nc file
and the code is as follow:
for voltage in numpy.arange(0.0, 5.01, 0.1):
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 = (voltage, 0)*Volt,
algorithm_parameters = two_probe_algorithm_parameters
)
if processIsMaster(): nlPrint(voltage)
runtime_parameters = runtimeParameters(
verbosity_level = 10,
checkpoint_filename = 'C:/Users/617/Desktop/lih2li1.nc'
)
# Using initial density from self consistent calculation
scf = executeSelfConsistentCalculation(
twoprobe_configuration,
two_probe_method,
initial_calculation = scf,
runtime_parameters = runtime_parameters
)
######################################################################
# Calculate physical properties
######################################################################
current = calculateCurrent(
self_consistent_calculation = scf,
brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters((1, 1)),
green_function_infinitesimal = 1.0e-5*electronVolt,
number_of_points = 100
)
if processIsMaster(): nlPrint(current)
if processIsMaster(): file.addToSample(current, 'twoprobe_configuration', 'Current')
and the code is as follow:
for voltage in numpy.arange(0.0, 5.01, 0.1):
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 = (voltage, 0)*Volt,
algorithm_parameters = two_probe_algorithm_parameters
)
if processIsMaster(): nlPrint(voltage)
runtime_parameters = runtimeParameters(
verbosity_level = 10,
checkpoint_filename = 'C:/Users/617/Desktop/lih2li1.nc'
)
# Using initial density from self consistent calculation
scf = executeSelfConsistentCalculation(
twoprobe_configuration,
two_probe_method,
initial_calculation = scf,
runtime_parameters = runtime_parameters
)
######################################################################
# Calculate physical properties
######################################################################
current = calculateCurrent(
self_consistent_calculation = scf,
brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters((1, 1)),
green_function_infinitesimal = 1.0e-5*electronVolt,
number_of_points = 100
)
if processIsMaster(): nlPrint(current)
if processIsMaster(): file.addToSample(current, 'twoprobe_configuration', 'Current')
20
General Questions and Answers / Re: how can I get the results from the .nc file?
« on: July 27, 2009, 14:26 »
oh! my god! all the values of the current cost two weeks.Does it mean that I should spend two weeks in calculating the values again? 
21
General Questions and Answers / how can I get the results from the .nc file?
« on: July 27, 2009, 04:31 »
Hi,
I have calculated my job which calculated the I-V curve by making a loop, but I closed the .log file. Now, I want to see the results again, but when I put the .vnl file into the results browser, I cant no t see the all the results any more, it just show the last value of the current. How can I get all the values of the current under different bias?
I have calculated my job which calculated the I-V curve by making a loop, but I closed the .log file. Now, I want to see the results again, but when I put the .vnl file into the results browser, I cant no t see the all the results any more, it just show the last value of the current. How can I get all the values of the current under different bias?
22
General Questions and Answers / is the reults of current correct?
« on: May 11, 2009, 11:35 »
hi, everybody.
I calculate the I-V characteristic using the method as follow:
1. calculate the current under zero bias and get the zerobias.nc
2. calculate the current under a high bias such as 4 Voltage and get the 4voltage.nc using the date of zerobias.nc.
3. then the bias descrease in the step of 0.5 Voltage. serials valence of current under different bias can be got using the date of 4voltage.nc as the initial data. I find that the convergence can be quickly attained.
so, I don't sure the results of current is precise? can anybody give a some suggestion?
I calculate the I-V characteristic using the method as follow:
1. calculate the current under zero bias and get the zerobias.nc
2. calculate the current under a high bias such as 4 Voltage and get the 4voltage.nc using the date of zerobias.nc.
3. then the bias descrease in the step of 0.5 Voltage. serials valence of current under different bias can be got using the date of 4voltage.nc as the initial data. I find that the convergence can be quickly attained.
so, I don't sure the results of current is precise? can anybody give a some suggestion?
23
General Questions and Answers / Re: How can I rerun the job?
« on: May 10, 2009, 09:35 »
doctor blom,
does the former bpcur1-0.5.nc file be used as the initial datas for Equivalent Bulk Calculationcalculation?
Equivalent Bulk Calculationcalculation seem be restart without using the former bpcur1-0.5.nc file. the content of the results is as follows:
# ----------------------------------------------------------------
# Electrodes Calculation
# ----------------------------------------------------------------
# sc 0 : Fermi Energy = 0.00000 Ry
# sc 1 : Fermi Energy = -0.37496 Ry dRho = 1.8700E+00
# sc 2 : Fermi Energy = -0.35694 Ry dRho = 1.2413E-02
# sc 3 : Fermi Energy = -0.27741 Ry dRho = 6.2172E-02
# sc 4 : Fermi Energy = -0.27699 Ry dRho = 1.2709E-02
# sc 5 : Fermi Energy = -0.25859 Ry dRho = 1.4290E-02
# sc 6 : Fermi Energy = -0.27538 Ry dRho = 9.5796E-03
# sc 7 : Fermi Energy = -0.27439 Ry Etot = -416.24910 Ry dRho = 6.9657E-04
# sc 8 : Fermi Energy = -0.27486 Ry Etot = -416.24909 Ry dRho = 3.6515E-04 dEtot = 9.7646E-07 Ry
# sc 0 : Fermi Energy = 0.00000 Ry
# sc 1 : Fermi Energy = -0.37496 Ry dRho = 1.8700E+00
# sc 2 : Fermi Energy = -0.35694 Ry dRho = 1.2413E-02
# sc 3 : Fermi Energy = -0.27741 Ry dRho = 6.2172E-02
# sc 4 : Fermi Energy = -0.27699 Ry dRho = 1.2709E-02
# sc 5 : Fermi Energy = -0.25859 Ry dRho = 1.4290E-02
# sc 6 : Fermi Energy = -0.27538 Ry dRho = 9.5796E-03
# sc 7 : Fermi Energy = -0.27439 Ry Etot = -416.24910 Ry dRho = 6.9657E-04
# sc 8 : Fermi Energy = -0.27486 Ry Etot = -416.24909 Ry dRho = 3.6515E-04 dEtot = 9.7646E-07 Ry
# ----------------------------------------------------------------
# Equivalent Bulk Calculation (Initial Density for TwoProbe)
# ----------------------------------------------------------------
# sc 0 : Fermi Energy = 0.00000 Ry
# sc 1 : Fermi Energy = -0.44262 Ry dRho = 3.6372E+02
# sc 2 : Fermi Energy = -0.37231 Ry dRho = 1.6327E+01
# sc 3 : Fermi Energy = -0.33476 Ry dRho = 1.7550E+01
dose the job run correctly? if it does, what is the main difference between the original calculation and the later calculation.
does the former bpcur1-0.5.nc file be used as the initial datas for Equivalent Bulk Calculationcalculation?
Equivalent Bulk Calculationcalculation seem be restart without using the former bpcur1-0.5.nc file. the content of the results is as follows:
# ----------------------------------------------------------------
# Electrodes Calculation
# ----------------------------------------------------------------
# sc 0 : Fermi Energy = 0.00000 Ry
# sc 1 : Fermi Energy = -0.37496 Ry dRho = 1.8700E+00
# sc 2 : Fermi Energy = -0.35694 Ry dRho = 1.2413E-02
# sc 3 : Fermi Energy = -0.27741 Ry dRho = 6.2172E-02
# sc 4 : Fermi Energy = -0.27699 Ry dRho = 1.2709E-02
# sc 5 : Fermi Energy = -0.25859 Ry dRho = 1.4290E-02
# sc 6 : Fermi Energy = -0.27538 Ry dRho = 9.5796E-03
# sc 7 : Fermi Energy = -0.27439 Ry Etot = -416.24910 Ry dRho = 6.9657E-04
# sc 8 : Fermi Energy = -0.27486 Ry Etot = -416.24909 Ry dRho = 3.6515E-04 dEtot = 9.7646E-07 Ry
# sc 0 : Fermi Energy = 0.00000 Ry
# sc 1 : Fermi Energy = -0.37496 Ry dRho = 1.8700E+00
# sc 2 : Fermi Energy = -0.35694 Ry dRho = 1.2413E-02
# sc 3 : Fermi Energy = -0.27741 Ry dRho = 6.2172E-02
# sc 4 : Fermi Energy = -0.27699 Ry dRho = 1.2709E-02
# sc 5 : Fermi Energy = -0.25859 Ry dRho = 1.4290E-02
# sc 6 : Fermi Energy = -0.27538 Ry dRho = 9.5796E-03
# sc 7 : Fermi Energy = -0.27439 Ry Etot = -416.24910 Ry dRho = 6.9657E-04
# sc 8 : Fermi Energy = -0.27486 Ry Etot = -416.24909 Ry dRho = 3.6515E-04 dEtot = 9.7646E-07 Ry
# ----------------------------------------------------------------
# Equivalent Bulk Calculation (Initial Density for TwoProbe)
# ----------------------------------------------------------------
# sc 0 : Fermi Energy = 0.00000 Ry
# sc 1 : Fermi Energy = -0.44262 Ry dRho = 3.6372E+02
# sc 2 : Fermi Energy = -0.37231 Ry dRho = 1.6327E+01
# sc 3 : Fermi Energy = -0.33476 Ry dRho = 1.7550E+01
dose the job run correctly? if it does, what is the main difference between the original calculation and the later calculation.
24
General Questions and Answers / Re: How can I rerun the job?
« on: May 10, 2009, 06:33 »
doctor blom, I have edited the script following what you told me. the code
# Restore self consistent calculation from check point file
oldscf = restoreSelfConsistentCalculation(
filename = '/home/ms/bpcur1-0.5.nc'
)
scf = executeSelfConsistentCalculation(self_consistent_calculation=oldscf)
runtime_parameters = runtimeParameters(
verbosity_level = 1,
checkpoint_filename = '/home/ms/xv/bpcur1.nc'
)
voltages = numpy.arange(0.,5.01,0.5)*Volt
ivcurve.runIVcurve (
twoprobe_configuration,
two_probe_method,
runtime_parameters,
voltages,
vnl_filename='/home/ms/xv/bp_iv.vnl', sample_name='bp_iv',
current_k_point_sampling = (10,10),
current_number_of_points = 100
)
when the job run, the electrode is calculted. the content of the calculted result is as follows:
# ----------------------------------------------------------------
# Electrodes Calculation
# ----------------------------------------------------------------
# sc 0 : Fermi Energy = 0.00000 Ry
# sc 1 : Fermi Energy = -0.37496 Ry dRho = 1.8700E+00
# sc 2 : Fermi Energy = -0.35694 Ry dRho = 1.2413E-02
# sc 3 : Fermi Energy = -0.27741 Ry dRho = 6.2172E-02
# sc 4 : Fermi Energy = -0.27699 Ry dRho = 1.2709E-02
# sc 5 : Fermi Energy = -0.25859 Ry dRho = 1.4290E-02
# sc 6 : Fermi Energy = -0.27538 Ry dRho = 9.5796E-03
# sc 7 : Fermi Energy = -0.27439 Ry Etot = -416.24910 Ry dRho = 6.9657E-04
# sc 8 : Fermi Energy = -0.27486 Ry Etot = -416.24909 Ry dRho = 3.6515E-04 dEtot = 9.7646E-07 Ry
# sc 0 : Fermi Energy = 0.00000 Ry
# sc 1 : Fermi Energy = -0.37496 Ry dRho = 1.8700E+00
# sc 2 : Fermi Energy = -0.35694 Ry dRho = 1.2413E-02
dose the job run rightly? does the former bpcur1-0.5.nc file be used as the initial datas for calculation?
# Restore self consistent calculation from check point file
oldscf = restoreSelfConsistentCalculation(
filename = '/home/ms/bpcur1-0.5.nc'
)
scf = executeSelfConsistentCalculation(self_consistent_calculation=oldscf)
runtime_parameters = runtimeParameters(
verbosity_level = 1,
checkpoint_filename = '/home/ms/xv/bpcur1.nc'
)
voltages = numpy.arange(0.,5.01,0.5)*Volt
ivcurve.runIVcurve (
twoprobe_configuration,
two_probe_method,
runtime_parameters,
voltages,
vnl_filename='/home/ms/xv/bp_iv.vnl', sample_name='bp_iv',
current_k_point_sampling = (10,10),
current_number_of_points = 100
)
when the job run, the electrode is calculted. the content of the calculted result is as follows:
# ----------------------------------------------------------------
# Electrodes Calculation
# ----------------------------------------------------------------
# sc 0 : Fermi Energy = 0.00000 Ry
# sc 1 : Fermi Energy = -0.37496 Ry dRho = 1.8700E+00
# sc 2 : Fermi Energy = -0.35694 Ry dRho = 1.2413E-02
# sc 3 : Fermi Energy = -0.27741 Ry dRho = 6.2172E-02
# sc 4 : Fermi Energy = -0.27699 Ry dRho = 1.2709E-02
# sc 5 : Fermi Energy = -0.25859 Ry dRho = 1.4290E-02
# sc 6 : Fermi Energy = -0.27538 Ry dRho = 9.5796E-03
# sc 7 : Fermi Energy = -0.27439 Ry Etot = -416.24910 Ry dRho = 6.9657E-04
# sc 8 : Fermi Energy = -0.27486 Ry Etot = -416.24909 Ry dRho = 3.6515E-04 dEtot = 9.7646E-07 Ry
# sc 0 : Fermi Energy = 0.00000 Ry
# sc 1 : Fermi Energy = -0.37496 Ry dRho = 1.8700E+00
# sc 2 : Fermi Energy = -0.35694 Ry dRho = 1.2413E-02
dose the job run rightly? does the former bpcur1-0.5.nc file be used as the initial datas for calculation?
25
General Questions and Answers / Re: How can I rerun the job?
« on: May 10, 2009, 03:52 »
thank you, doctor blom!
26
General Questions and Answers / How can I rerun the job?
« on: May 9, 2009, 06:52 »
hello, verybody.
I want to ask that when the running job is broken, I want to continue this job after its break. How can I retart the job?
I want to ask that when the running job is broken, I want to continue this job after its break. How can I retart the job?
27
Scripts, Tutorials and Applications / Re: Voltage sweep (I-V curve)
« on: May 5, 2009, 05:05 »
thank you ! I will try it again. if there is any problem, would you like helping again? 
you are so kind person. thank you again. best regards. have a good trip! by the way, do you like the chinese culture? I hope you can have a trip in china. 
welcome to china! I am in china.
you are so kind person. thank you again. best regards. have a good trip! by the way, do you like the chinese culture? I hope you can have a trip in china. welcome to china! I am in china.
28
Scripts, Tutorials and Applications / Re: Voltage sweep (I-V curve)
« on: May 5, 2009, 04:36 »
I am so sorry not to post the content of error. I can run properly in serial on Windows or Linux via the VNL Job Manager, but it fails in parallel on Linux. I do download the the new ivcurve.py file and replace the existing file.
the code:
# Opening vnlfile
if processIsMaster(): file = VNLFile('/home/ms/b-pcur/lih.vnl')
ivcurve.runIVcurve (
twoprobe_configuration,
two_probe_method,
runtime_parameters,
voltages,
vnl_filename='/home/ms/b-pcur/lih.vnl', sample_name='lih',
current_k_point_sampling = (1,1),
current_number_of_points = 100
)
iv = ivcurve.extractIVcurveFromVNLFile('/home/ms/b-pcur/lih.vnl','lih')
but the error is as follows;
Traceback (most recent call last):
File "<string>", line 226, in ?
File "/home/ms/vnl-2008.10.0/atk/lib/python2.4/site-packages/ivcurve.py", line 80, in runIVcurve
if processIsMaster: f.addToSample(current,sample_name,'Current at %s V bias' % voltage.inUnitsOf(Volt))
OSError: [Errno 2] No such file or directory: '/home/ms/b-pcur/lih.vnl'
the path of the "lih.vnl" file have a problem? please help me? the job run on Linux system with the command "$ mpiexec -n 4 /home/ms/vnl-2008.10.0/atk/bin/atk /home/ms/b-pcur/lih.py"
the code:
# Opening vnlfile
if processIsMaster(): file = VNLFile('/home/ms/b-pcur/lih.vnl')
ivcurve.runIVcurve (
twoprobe_configuration,
two_probe_method,
runtime_parameters,
voltages,
vnl_filename='/home/ms/b-pcur/lih.vnl', sample_name='lih',
current_k_point_sampling = (1,1),
current_number_of_points = 100
)
iv = ivcurve.extractIVcurveFromVNLFile('/home/ms/b-pcur/lih.vnl','lih')
but the error is as follows;
Traceback (most recent call last):
File "<string>", line 226, in ?
File "/home/ms/vnl-2008.10.0/atk/lib/python2.4/site-packages/ivcurve.py", line 80, in runIVcurve
if processIsMaster: f.addToSample(current,sample_name,'Current at %s V bias' % voltage.inUnitsOf(Volt))
OSError: [Errno 2] No such file or directory: '/home/ms/b-pcur/lih.vnl'
the path of the "lih.vnl" file have a problem? please help me? the job run on Linux system with the command "$ mpiexec -n 4 /home/ms/vnl-2008.10.0/atk/bin/atk /home/ms/b-pcur/lih.py"
29
Scripts, Tutorials and Applications / Re: Voltage sweep (I-V curve)
« on: May 5, 2009, 03:09 »
dear doctor blom, I have download the script and replace the existing file. however, when my script run, it does not work and the same error comes out.
I want to ask whether the ivcurve.py file works well. do you test it ? Now, I really don't know what can I do? please help me agian. thank you very much.
I want to ask whether the ivcurve.py file works well. do you test it ? Now, I really don't know what can I do? please help me agian. thank you very much.
30
Scripts, Tutorials and Applications / Re: Voltage sweep (I-V curve)
« on: May 4, 2009, 15:53 »
thank you! I will try it again.