how to optimize two probe system with functional groups

[sweta]

Hi,

I want to work on functionalized 2 probe molecular system. But when I optimize  functionalized dithiol sandwitched between two gold electrodes (having total 67 atoms using two electrode layers) in device configuration  (the procedure you given in the optimizing two probe mini tutorial). This program show run time error.
Why it shows this problem either it is parameters problem or 32-bit system problem???
I have taken mesh cutoff=150Rydberg,k-points=3,3,50, iteration steps=200, stress=.001, also tick no self iteration.

Please help me how to optimize functionalized two probe system??? and what parameters I should use so it will converge and optimize easily

[kstokbro]

please attach your script else it is difficult to help you.
Which calculator are you using?

[sweta]

I am using ATK-DFT(Device) calculator.
Please find the attached script

[zh]

Please check your script file carefully. The parameters in "OptimizeGeometry()" called in your script file is wrong:

Code

device_configuration = OptimizeGeometry(
        device_configuration,
        max_forces=0.05*eV/Ang,
        max_stress=0.001*eV/Ang**3,
        max_steps=200,
        max_step_length=0.5*Ang,
        trajectory_filename=None,
        )

The "max_forces" and "max_stress" should be changed into "maximum_forces" and "maximum_stress". see the manual here: http://quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.optimizegeometry.html

Code

#----------------------------------------
# Iteration Control Settings
#----------------------------------------
device_iteration_control_parameters = NonSelfconsistent

The "NonSelfconsistent" is not defined in your script file. If you don't know how to define, you may simply remove the above line in your script file.

[sweta]

Its not working.

Can anyone send me the full script of optimizing the two probe system by taking dithiol molecule sandwitched between two gold electrodes.

Please help!

[zh]

The suggestions made in reply are based on the error messages in the test running of your script file.

Since you said that they didn't help you, please show your error messages.

[sweta]

Hi,

It is showing run time error.
The script i am using may or may not be the right script for optimization of two probe system. Since I dont know the right procedure for the same.
Can you please send me the right procedure or the whole script for two probe system optimization by taking dithiol sandwitched  between two gold electrodes??

[Anders Blom]

Can you do the opposite, please send us the script you are running which doesn't work, then we can figure out why.

[sweta]

Hello Dr. Blom,

Please find the attached script and tell me why it is not running...

[Anders Blom]

I can't say exactly why it doesn't run, without running it - which I don't want to because the system is not correctly set up. What I mean is, that maybe there is an issue with memory, but before getting into that, the geometry needs to be corrected.

If you inspect the structure you will find that you have a Cu atom embedded inside the gold matrix in the right electrode, and a similar effect is seen on the left electrode. These atoms have been placed too close to the surface.

I have attached an improved structure, which hopefully will run better (I didn't have time to run it myself)!