Messages

16

General Questions and Answers / where is the unit cell in the view interface?

« on: January 18, 2016, 11:09 »

Recently itested the tutorial http://www.quantumwise.com/documents/tutorials/latest/GrapheneBloch/index.html/chap.spin.html.When i analyse the nc in the viewer to visualize the Spin up (right) and down (left) states at the Z point  in Fig6. I couldn't find theUnit cell ,i.e, I couldn't find the cell tick.All the subsequent analyse such as Electron density ,i couldn.t see the unit cell in the viewer .Hope anyone could help me!
attachments are the analyse nc file.

17

General Questions and Answers / Re: How to save selfconsistent_configurations for every voltage

« on: January 17, 2016, 13:14 »

Thanks for your kind reply , i whill check  it  tonight .I have already  solved  it in another way ,the code is :

Code

# -------------------------------------------------------------
# IV Curve
# -------------------------------------------------------------
calculator=device_configuration.calculator()

biases = [0.000000, 0.100000, 0.200000, 0.300000, 0.400000, 0.500000,
          0.600000, 0.700000, 0.800000, 0.900000, 1.000000]*Volt
for bias in biases:
    calculator=calculator(
            electrode_voltages=(bias/2, -bias/2))

    device_configuration.setCalculator(
          calculator(),
          initial_state=device_configuration)
    device_configuration.update()
    nlsave("ivcurve_selfconsistent_configurations_bias_%g.nc" % bias.inUnitsOf(Volt), device_configuration)
    
#----------------------------------------
# Transmission spectrum
#----------------------------------------
for bias in biases:
    configurations = nlread('ivcurve_selfconsistent_configurations_bias_%g.nc' % bias.inUnitsOf(Volt), DeviceConfiguration)
    for device_configuration in configurations:
           transmission_spectrum = TransmissionSpectrum(
               configuration=device_configuration,
               energies=numpy.linspace(-2,2,201)*eV,
               kpoints=MonkhorstPackGrid(4, 4),
               energy_zero_parameter=AverageFermiLevel,
               infinitesimal=1e-06*eV,
               self_energy_calculator=RecursionSelfEnergy(),
               )
           nlsave("TS_analysis.nc", transmission_spectrum)
           nlprint(transmission_spectrum)

This way to save the checkpoint is very helpful and it's easy to restart from the I-V converged state .Hope it could help the new learnrers.

18

General Questions and Answers / Re: problem about restarting from a check point

« on: January 17, 2016, 13:08 »

The jobs stopped instanly and  a another occurred :

Code

Traceback (most recent call last):
  File "Device.py", line 494, in <module>
    device_configuration = nlread("checkpoint-2.nc", DeviceConfiguration)[0]
IndexError: list index out of range

, i clear the

• and another error occurred:
  Code

  Traceback (most recent call last):[/li][/list]
    File "Device.py", line 495, in <module>
      device_configuration.setCalculator(DeviceLCAOCalculator(), initial_state= device_configuration)
  AttributeError: 'list' object has no attribute 'setCalculator'

  i will test the restarting function after running a long time .Did anyone can explain why i can't restart?

19

General Questions and Answers / How to save selfconsistent_configurations for every voltage

« on: January 10, 2016, 11:21 »

Dear sir:
       Recently i tested to  restart I-V calculations from a checkpoint . i learned from http://quantumwise.com/forum/index.php?topic=3306.msg15142#msg15142 andhttp://quantumwise.com/forum/index.php?topic=1358.msg9062#msg9062 about how to restart a suspended job.i modify the code as

Code

# -------------------------------------------------------------
# IV Curve
# -------------------------------------------------------------
calculator=device_configuration.calculator()

biases = [0.000000, 0.100000, 0.200000, 0.300000, 0.400000, 0.500000,
          0.600000, 0.700000, 0.800000, 0.900000, 1.000000]*Volt
for bias in biases:
    calculator=calculator(
            electrode_voltages=(bias/2, -bias/2))

    device_configuration.setCalculator(
          calculator(),
          initial_state=device_configuration)
    device_configuration.update()
    nlsave("ivcurve_selfconsistent_configurations.nc", device_configuration)
    
#----------------------------------------
# Transmission spectrum
#----------------------------------------
configurations = nlread('ivcurve_selfconsistent_configurations.nc', DeviceConfiguration)
     for device_configuration in configurations:
         transmission_spectrum = TransmissionSpectrum(
             configuration=device_configuration,
             energies=numpy.linspace(-2,2,201)*eV,
             kpoints=MonkhorstPackGrid(4, 4),
             energy_zero_parameter=AverageFermiLevel,
             infinitesimal=1e-06*eV,
             self_energy_calculator=RecursionSelfEnergy(),
             )
         nlsave("TS_analysis.nc", transmission_spectrum)
         nlprint(transmission_spectrum)

.

So here is my idea:
For the initial calculation script(not restaring script) i want to use "nlsave" statement to make a new file for each converged bias and calculate the transmission spectrum for each bias using each converged bias(i want to exactly know output bias file and restart from it ),
my problem is :
How to modify the above code in the I-V and transmission module  to realise the these two underlined functions.

20

General Questions and Answers / Re: problem about restarting from a check point

« on: January 9, 2016, 06:53 »

The modified code i restart the job is

Code

device_configuration = nlread("checkpoint-2.nc",)[0]
device_configuration.setCalculator(DeviceLCAOCalculator(), initial_state= device_configuration)
nlprint(device_configuration)
device_configuration.update(force_restart=True)
nlsave('Device Gold.nc', device_configuration)

21

General Questions and Answers / problem about restarting from a check point

« on: January 9, 2016, 06:48 »

Hello,recently i run a test script[Device.py] to set the

Code

DeviceLCAOCalculator( checkpoint_handler= CheckpointHandler('checkpoint-2.nc', 1*Minute),

and kille the job for restarting the jobs.i also get the [checkpoint-2.nc],but when i run the new py script[Device-restart.py], i get the  error message instantly

Code

Traceback (most recent call last):
  File "Device.py", line 495, in <module>
    device_configuration.setCalculator(DeviceLCAOCalculator(), initial_state= device_configuration)
  File "./zipdir/NL/CommonConcepts/Configurations/AtomicConfiguration.py", line 1222, in setCalculator
  File "./zipdir/NL/CommonConcepts/Calculator.py", line 58, in _supportConfiguration
  File "./zipdir/NL/CommonConcepts/Calculator.py", line 48, in _supportConfigurationType
  File "./zipdir/NL/Analysis/AnalysisUtilities.py", line 78, in checkConfiguration
NL.ComputerScienceUtilities.Exceptions.NLTypeError: The parameter, configuration, must be an instance of one of the following SurfaceConfiguration, DeviceConfiguration, NudgedElasticBand.

I have already read the Restarting stopped calculations toturial ,forum ,and the manual and i can't fix the problem in my code. Hope anyone could help! me!

22

General Questions and Answers / how to print out the default parameter in the .out file

« on: December 18, 2015, 04:57 »

Hello,i am eager to know the default Double Contour Integral Parameters ,ie .fermi_ function_poles 、circle_points， and fermi_line_points.but i am not farmiliar with the python language.Can anyone tell me what code should i use in .py to print out it.

23

General Questions and Answers / Re: transmission-spectrum output differences running on cluster using VNL-ATK2015

« on: December 16, 2015, 03:20 »

Thank you very much for your reply to this thread.I changed the basis sets  as you said  and fixed the problem.

24

General Questions and Answers / transmission-spectrum output differences running on cluster using VNL-ATK2015

« on: December 15, 2015, 06:00 »

Hello,i tested the example on the quantumwise website-Transmission spectrum of a graphene nanoribbon with a distortion  on our cluster by parallel computing(i watched the viedo and follow the steps and set the same parameter as it sets).I found the apparent differences of  transmission-spectrum output  .Hope anyone can explain it , thanks a lot .

25

General Questions and Answers / How to get the transmission spectrum data by K-point average

« on: December 10, 2015, 14:29 »

I used VNL-ATK 2015 to calculate the transmission spectrum ,but i don't understand the export  data of the  transmisison spectrum .What  does the data in  Line2D(_line0,1,2,3,4,5,6) mean?It is extraordinary  to see that data corresponding to  line6 only has two lines(see the attachment [transmission in ATK]).In addition ,what code should i write in the input  py  script to  get the transmision data averaged by K-point (see the attachments [input.py,transmission in siesta]).

26

General Questions and Answers / Question about difference between ATK and Siesta transmission spectrum data

« on: December 9, 2015, 15:25 »

Dear QuantumWise Staff :
              I used  ATK  and Siesta to  run transmission spectrum of the same gold-dtb-gold device under zero bias voltage .When i compare the two  transmisison coefficient data and graph ,i am confused with several differences between  the two graphs and datas:
             1. T(e,v) <1  in SIESTA .T(e,v) can be 2 or more in ATK. I learned the transmission spectrum in ATK is the sum of probabilities for all the states that exist at the given energy, but i don't know what the T(e,v) means in SIESTA exactly and
             2. the two graph has two instinct  differences under E<-1.5 and E=1.8
             3  i don't understand the ATK output  transmission spectrum data .In detail ,why it has line 0 -6  ,ie,seven group data ,and how should i pick the correct line to analyse my system. In addition , i used the Line2D(_line0) data in the graph plotted above .
              4.how do i use the transmission spectrum to analyse my system.

              Hope for your answers sincerely! Thank you very much !