Messages

31

General Questions and Answers / Charge density around the Fermi energy?

« on: December 26, 2011, 22:46 »

Hi,

How can we get the charge density, for each spin direction, at energies close to the Fermi energy (or for a specific energy interval) for a two probe system?

32

General Questions and Answers / Re: Mulliken population

« on: October 21, 2011, 10:52 »

Thanks...

33

General Questions and Answers / Re: Mulliken population

« on: October 19, 2011, 16:07 »

Hi,

The code above doesn't work in ATK 11.2.3. How can we write a this code in ATK 11.2.3?
or is there a way to get total up and down mulliken population?

Thanks

34

General Questions and Answers / Re: Exporting images in eps, in ATK 11.2.3

« on: August 10, 2011, 12:01 »

Hi,

Thanks for your replies. The main problem is to get higher resolution in eps. I have tried the GIMP and some other softwares to convert the png to eps, but resolution is not so good. It would be better if we are able to export the images in eps directly in ATK. Do you think GIMP is the best in converting? or is there any better software?

Thanks,

35

General Questions and Answers / Exporting images in eps, in ATK 11.2.3

« on: August 8, 2011, 12:26 »

Hi,

In ATK 11.2.3, it is not possible to export images (transmission spectrum, device configuration etc.) in eps format to be used in latex. Is there a way to export in this format?

Thanks,

36

General Questions and Answers / NLScopeExecutionError: global name 'len' is not defined

« on: April 20, 2011, 07:25 »

Hi,

I am using ATK 11.2.2. I have written a script (regarding construction of a bulk configuration) which works, without any problem, upon sending it directly to the job manager. However when I drop it on "Builder" or "Viewer" it gives an error:
 
global name 'len' is not defined

In detailed error:

Traceback (most recent call last):
  File "./zipdir/NL/GUI/DragAndDrop/DropReceiver.py", line 41, in handleDrop
  File "./zipdir/NL/NanoLanguage/ScopeExecuter.py", line 59, in execute
NLScopeExecutionError: global name 'len' is not defined

Thanks for you reply.

37

General Questions and Answers / NanoLanguageScript execution failure

« on: November 9, 2010, 13:14 »

Hi,

I am trying to consider the transport properties of some systems consisting of Na atoms. The job starts and makes calculations regading device, left and right electrode. But when the calculation, concerning Equivalent Bulk, starts the job almost freezes and after a while gives the following error:

Equivalent Bulk  [Started Tue Nov  9 11:24:41 2010]                          |
|                                                                              |
+------------------------------------------------------------------------------+
/home/scaliskan/QuantumWise/atk-10.8.0/atkpython/bin/atkpython: line 3:  5046 Killed                  PSEUDOPOTENTIALS_PATH=$EXEC_DIR/../share/pseudopotentials GPAW_SETUP_PATH=$EXEC_DIR/../share/gpaw-setups/ PYTHONHOME=$EXEC_DIR/.. PYTHONPATH= LD_LIBRARY_PATH=$EXEC_DIR/../lib $EXEC_DIR/atkpython_exec $*
NanoLanguageScript execution failure
+------------------------------------------------------------------------------+
| NanoLanguageScript execution finished                                        |
+---------------------------------------------------------------

By the way I continue to run 10.8.0, since in 10.8.2  VNL closes down (in linux64) directly without giving any error(topic=816)

Thanks,

38

Installation and License Questions / Re: Import error:.../_path.so: undefined symbol: _ZNSs4_Rep20_S_empty_rep_storageE

« on: October 8, 2010, 15:54 »

Yes I have this library....

39

Installation and License Questions / Re: Import error:.../_path.so: undefined symbol: _ZNSs4_Rep20_S_empty_rep_storageE

« on: October 8, 2010, 15:24 »

Actually, of course, I can also use other plotting software but I have intended to employ the pylab in my script.
Upon using grep the log file (file2.log) is attached.

I hope the problem will be resolved soon.

Thanks,

40

Installation and License Questions / Re: Import error:.../_path.so: undefined symbol: _ZNSs4_Rep20_S_empty_rep_storageE

« on: October 8, 2010, 14:53 »

Thanks for your quick reply,

I use RHEL 5 and I have just installed ATK 10.8.2 with floating license server. Actually in ATK 10.8.0 there was no such a problem and everything was OK.

By the way, I have done what you have indicated in your Reply#3.  But the log file that I get has a size of 33 MB! So I think it is impossible to send it.

I think the main problem originates from the pylab which is taken place at the end of my script, for which we use import pylab.

Thanks,

41

Installation and License Questions / Import error:.../_path.so: undefined symbol: _ZNSs4_Rep20_S_empty_rep_storageE

« on: October 8, 2010, 09:44 »

Hi,
I have installed ATK 10.8.2. At the end of the calculation the following error appears:

Traceback (most recent call last):
  File "/tmp/0835619392553552.py", line 33, in <module>
    import pylab
  File "./build/atkpython/lib/python2.6/site-packages/pylab.py", line 1, in <module>
  File "./build/atkpython/lib/python2.6/site-packages/matplotlib/pylab.py", line 216, in <module>
  File "./build/atkpython/lib/python2.6/site-packages/matplotlib/mpl.py", line 1, in <module>
  File "./build/atkpython/lib/python2.6/site-packages/matplotlib/artist.py", line 6, in <module>
  File "./build/atkpython/lib/python2.6/site-packages/matplotlib/transforms.py", line 34, in <module>
ImportError: /home/scaliskan/QuantumWise/atk-10.8.2/atkpython/lib/python2.6/site-packages/matplotlib/_path.so: undefined symbol: _ZNSs4_Rep20_S_empty_rep_storageE
NanoLanguageScript execution failure

How can I resolve that problem?

Thanks,

42

Installation and License Questions / ATK 10.8, 'GLIBC_2.4' not found (required by ./lmx-serv-quantum)

« on: July 9, 2010, 14:28 »

Hi,

In ATK 10.8, while running the lmx-serv-quantum, I get the error:

./lmx-serv-quantum: /lib64/tls/libc.so.6: version `GLIBC_2.4' not found (required by ./lmx-serv-quantum)

I use:

red hat 4:  2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST 2006 x86_64 x86_64 x86_64 GNU/Linux

Thanks for your reply,

43

Scripts, Tutorials and Applications / Re: Relaxation under bias

« on: April 27, 2010, 22:33 »

Hi Anders,

Thanks for your comment on the problem. The issue has been resolved after making a few modifications in the script...

44

Scripts, Tutorials and Applications / Re: Relaxation under bias

« on: April 24, 2010, 22:19 »

 Dear Dr. Blom,

The script that you have written is really good. But I have written a script where a few atoms in the scattering region have spins. Thus the script gives an error related to spin dimensions:

Traceback (most recent call last):
  File "My_File_relaxOpt.py", line 107, in ?
    fixed_atoms = fixed_atoms,
  File "/data1/clusterfs/users/scaliskan/vnl-2008.10.0/atk/lib/python2.4/site-packages/CalculateOptimizedTwoProbeGeometry.py", line 248, in calculateOptimizedTwoProbeGeometry
    initial_calculation = initial_calculation
NLValueError: The two system has different spin dimensions

How can we include spin in your script to avoid this problem?

Thanks

45

General Questions and Answers / Re: KeyError

« on: February 18, 2010, 12:03 »

Dr. Blom,

Sorry for late reply, I was dealing with some reports....Actually I have just realized that upon defining the exact path of the vnl file, the code that you have written works!

Thanks,