QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: lida on June 4, 2012, 13:27

Title: run error, please help
Post by: lida on June 4, 2012, 13:27

Dear everyone，
I am a newcomer in ATK using, when I calculated the transmission spectrum of Au-Si two-probe system, I encountered the problem like this:
error message:
Traceback (most recent call last):
  File ".\zipdir\NL\Calculators\DeviceCalculatorInterface.py", line 257, in _update
  File ".\zipdir\NL\Calculators\LCAOCalculator\LCAOCalculator.py", line 1092, in scfLoop
  File ".\zipdir\NL\Calculators\LCAOCalculator\LCAOCalculator.py", line 799, in scfLoopHamiltonian
  File ".\zipdir\NL\Calculators\GenericParameters\CheckpointHandler.py", line 131, in _storeIfNecessary
  File ".\zipdir\NL\IO\IOUtilityFunctions.py", line 1142, in setupForOverwrite
  File ".\zipdir\NL\IO\MetaCDFFile.py", line 241, in __init__
  File ".\zipdir\NL\IO\MetaCDFFile.py", line 891, in _read
  File ".\zipdir\NL\IO\MetaCDFFile.py", line 977, in _readVariables
NLIOError: Error: unexpected header encountered when reading variables
I am not sure what is wrong, is there any problem in device structure or calculation script?
Another question, in my calculation script, where can the checkpointfile statements locate?
In addtion, I run atk_windows_32bit in my 64bit OS with 4Gb memory, whether the program only use 2Gb memory like in 32bit OS?
The following is my script. Thank you very much for your help.

Title: Re: run error, please help
Post by: Anders Blom on June 4, 2012, 13:48

You already have a checkpoint statement in the script, and it seems this is where it crashes. Does the file you specify as checkpoint already access? Does the directory D:/checkpoint exist?

Yes, the 32-bit version of ATK can only use 2 GB of RAM, you should download and install the 64-bit version.

Title: Re: run error, please help
Post by: lida on June 5, 2012, 10:58

okay, I got it. Indeed, the checkpoint file have already exist in my directory which I ignored when doing the calculation. Thanks a lot for your helpful reply.

Title: Re: run error, please help
Post by: satendra kumar gautam on December 11, 2015, 08:52

Traceback (most recent call last):
  File "/tmp/3534094636938398.py", line 41, in <module>
    nlsave('analysis.nc', bulk_configuration)
  File "./zipdir/NL/IO/NLSaveUtilities.py", line 213, in nlsave
  File "./zipdir/NL/IO/MetaCDFFile.py", line 439, in close
  File "./zipdir/NL/IO/MetaCDFFile.py", line 483, in flush
  File "./zipdir/NL/IO/MetaCDFFile.py", line 982, in _readVariables
NL.ComputerScienceUtilities.Exceptions.NLIOError: Error: unexpected header encountered when reading variables

I have calculated energy for Ge but this error comes when I calculated Energy  for Aluminium, Please help me in sorting this problem and same type of error came in calculating the complex band structure

Title: Re: run error, please help
Post by: Jess Wellendorff on December 11, 2015, 11:55

Could you upload the script so that we may take a look at it?

Title: Re: run error, please help
Post by: Anders Blom on December 11, 2015, 14:29

Try a different filename,, simply. Probably (although I can basically only guess) you are mixing different versions of ATK, so the file "analysis.nc" already exists and has data in it that was generated with a newer version (or older, but that's less likely).