3 questions about: import initial _state; export data from .nc; debug in python.

[fangyongxinxi]

Dear Sir,
Question1:
Import the initial calculation is helpful to calculate efficiently, I am familiar with ATK2008.10, but stange to ATK 2010.8,
I wrote a script, part of it is shown blow, I wonder is it right ?  and what's the use of the " device_configuration.update() " ?
I also have a question on the manual page 109, as the attach shows. First,  v = 0 V, the imported initial_state is just a device_configuration.(just contains the xyz_file, not scf process ). When the 0V calculation is done, but no "nlsave" to store the scf calculation ( I don't know it's right to say like this ), so when v = 0.1, the imported initial_state is the same xyz_file, no scf process. Am I right ? If I am wrong, how to understand the initial_state ?
Question2:
Could you give us some script on how to export the data , especially how to deal with these data. ( for example, how to draw a "v-scan I-V" picture by script. ), just like the previous topics on ATK 2008.10.
Qestion3:
a question about python. How to debug a python script efficiently ? I know how to use " try--except ", but that's not help me too much on how to debug a script. I like the debug in matlab, that's convenient.

Thank you.


#----------------------------------------
# Device Calculator
#----------------------------------------
v=0
calculator = DeviceLCAOCalculator(
        electrode_calculators=
        [left_electrode_calculator, right_electrode_calculator],
        electrode_voltages=( v*Volt, 0.0*Volt)
       )
device_configuration.setCalculator(calculator) ## time cost , this is the v=0 scf done.
device_configuration.update()
nlsave("analysis-%.1f.nc"  % v, device_configuration)  

opt_configuration = OptimizeGeometry(
        device_configuration,
        maximum_forces=0.05*eV/Ang,
        constraints=[ 0, 1, 2, 3, 4, 5,  8, 9, 10, 11, 12,13],
        trajectory_filename="analysis-%.1f.nc" % v )
nlsave("analysis-%.1f.nc"  % v, opt_configuration)

forces = Forces(device_configuration)
nlsave("analysis-%.1f.nc"  % v, forces)
print  " ### 0 is done ####"


v= 0.2
calculator = DeviceLCAOCalculator(
        electrode_calculators=
        [left_electrode_calculator, right_electrode_calculator],
        electrode_voltages=( v*Volt, 0.0*Volt)
       )
device_configuration.setCalculator(calculator,
                                   initial_state = device_configuration )   # I set the initial_stat here is right ? and after this scipt ,the v=0.2 scf is stored in device_configration, right?
device_configuration.update()
nlsave("analysis-%.1f.nc"  % v,device_configuration)

opt_configuration = OptimizeGeometry(
        device_configuration,
        maximum_forces=0.05*eV/Ang,
        constraints=[ 0, 1, 2, 3, 4, 5,  8, 9, 10, 11, 12,13],
        trajectory_filename= "analysis-%.1f.nc"  % v )
nlsave("analysis-%.1f.nc"  % v, opt_configuration)

forces = Forces(device_configuration)
nlsave("analysis-%.1f.nc"  % v,forces)
print "########0.2 is done########"

v=0.4....../v=0.6......

[fangyongxinxi]

In my script, I understand it like this:
 first I use
"device_configuration.setCalculator(calculator)"
to get the v=0 scf, and this is stored in device_configuration, which will be used by 0.2V (right ?)
then, I use the stored device_configuration to do the optimization and calculate the force.

v = 0.2 V, we set
" device_configuration.setCalculator(calculator, initial_state = device_configuration )"
to get the v=0 scf with the v=0.2 "calculator", at this same time v=0.2 scf is stored in device_configuration, which will be used by 0.4 V .

so that's the loop. right ?

[Anders Blom]

Debugging in Python can be done e.g. in Eclipse.

It seems you have indeed understood the voltage loop correctly. Post further questions if there's anything else you wonder about.