Topics

61

General Questions and Answers / saving calcs with device?

« on: January 24, 2012, 22:23 »

It seems that when you set the device calculator object, then save the object, it does not save the calculator .. is this correct? 

example: 

Code

	device_configuration = nlread(outFileName,DeviceConfiguration)[0]
	device_configuration.setCalculator(calculator)
	device_configuration.update()
	nlsave(outFileName, device_configuration, object_id="cfg")

when i open the "cfg" object later and try to run a calc it says i did not set a calculator ... why?

62

General Questions and Answers / MKL ?

« on: January 23, 2012, 20:42 »

on this page: http://quantumwise.com/documents/tutorials/latest/ParallelGuide/index.html/chap.quick.html

it talks about parallel implementation, then at the bottom it mentions:

"MKL will detect the presence of a multi-core processor and enable OpenMP automatically. It is recommended to let the software figure out itself how many threads to use optimally."

So I have a machine which has an equivalent of 24 cores ... so then should I run my jobs with the mpiexec -n parameter or not? should I .. "let the software figure out itself" ?

 

63

General Questions and Answers / Error message - mem error running in parallel

« on: January 20, 2012, 21:05 »

I am running atk in parallel on a machine with an equivalent of 24 cores ...

i got the following after an hour:


  File "./zipdir/NL/Calculators/DeviceCalculatorInterface.py", line 287, in _update
  File "./zipdir/NL/Calculators/DeviceCalculatorInterface.py", line 287, in _update
  File "./zipdir/NL/Calculators/LCAOCalculator/DeviceLCAOCalculator.py", line 1632, in scfLoopDevice
  File "./zipdir/NL/Calculators/LCAOCalculator/DeviceLCAOCalculator.py", line 588, in scfLoopDeviceHamiltonian
  File "./zipdir/NL/Calculators/CommonBuilder/DeviceBuilder.py", line 461, in createElectrostaticCalculator
  File "./zipdir/NL/Calculators/LCAOCalculator/DeviceLCAOCalculator.py", line 1632, in scfLoopDevice
  File "./zipdir/NL/Calculators/LCAOCalculator/DeviceLCAOCalculator.py", line 588, in scfLoopDeviceHamiltonian
  File "./zipdir/NL/Calculators/CommonBuilder/DeviceBuilder.py", line 461, in createElectrostaticCalculator
  File "./zipdir/NL/CommonConcepts/PoissonSolvers/MultigridSolver.py", line 55, in calculateFunctionOnGrid
MemoryError
  File "./zipdir/NL/CommonConcepts/PoissonSolvers/MultigridSolver.py", line 55, in calculateFunctionOnGrid
MemoryError



Now there are still many processes running, so ... i am not sure, will the results be valid, or if i got this i should kill the processes and start over?

64

General Questions and Answers / imports

« on: January 20, 2012, 05:43 »

I wanted to organize my code where i put parameters into a parms.py file, then use the following in the main program file:

Code

from parms import *

but i am having a problem where some of my parms use NanoLanguage units, etc .. and they are not available there ... i tried importing numpy and NanoLanguage but it is not working ... how can I accomplish this?

65

General Questions and Answers / GNR topology

« on: January 17, 2012, 07:34 »

I have reviewed over 50 papers on graphene and GNR based FETs, and I believe in all these papers, AGNR ribbons are presented with alternating widths within the ribbon, ... atk creates a sort of staggered topology ... the attachment shows what i mean by "alternating" ... if you count the rings (as a simple way to see this), the wdith from left to right is 6, 5, 6, 5, 6, 5 to create the AGNR .... ATK seems to produce 6, 6, 6, 6, 6, 6, 6, where the armchair part is made by "staggerring" the rings, as opposed to alternating the widths ... does that make sense?  my question is how to make the topology so commonly used in research papers ... do I have to do it manually?  IF I make a GNR of width W, I want it to be the same as is done in published research papers

66

General Questions and Answers / null calculator

« on: January 16, 2012, 22:22 »

I am getting an error after reading in a file ...

File "C:\Users\patakye\Documents\EP_EDU\GradSchool\UMN\KiaResearch\QuantumSimulations\ATK\ATKSIMS\gnr_12_0_AGNR_z10.py", line 672, in doCalcs2
    calculator(electrode_voltages=(-0.1*Volt,0.1*Volt)),
TypeError: 'NoneType' object is not callable

My setup is like this ... I create the device in one function and save it as:

Code

	#----------------------------------------
	# Device Calculator
	#----------------------------------------
	calculator = DeviceHuckelCalculator(
		basis_set=basis_set,
		electrode_voltages=(-0.1*Volt,0.1*Volt),
		electrode_calculators=
			[left_electrode_calculator, right_electrode_calculator],
		)

	device_configuration.setCalculator(calculator)
	nlprint(device_configuration)
	device_configuration.update()
	nlsave(outFileName, device_configuration)

then in another function:

Code

	#read in the old configuration
	device_configuration = nlread(outFileName,DeviceConfiguration)[0]
	calculator = device_configuration.calculator()

This is where I get an error that the calculator object is null ... am i doing this incorrectly?

67

General Questions and Answers / Angstrom vs Ang

« on: January 16, 2012, 21:22 »

Maybe I am just not familiar with the unit "Ang", but when I try to modify values that are in Angstroms the program keeps giving me errors that I am not using Ang units ... How do we know when to use "Ang" and when to use "Angstrom"?   I tested 1*Ang == 1*Angstrom and it returned true, so ... are they the same or not?

68

General Questions and Answers / gate electrodes

« on: January 15, 2012, 04:39 »

I have been reading over these tutorials and I cannot seem to piece together how to add a gate to a simple GNR FET type device ... am I correct that this cannot be done in the GUI and has to be done programatically?