Messages

31

General Questions and Answers / Re: how to display the MPSH picture?

« on: August 19, 2009, 09:15 »

it has some imformation about MPSH, however, it was dropped the nanorope, it didn't see except configuratoin! why? I am very worry about it!

32

General Questions and Answers / how to explain this? is it wrong?

« on: August 19, 2009, 08:24 »

Recently, I calculated a two-probe system and find its DOS and Transmission Spectrum are like as the figure,  which display a disagreement with each other, how to explain this?  is it wrong? it is noted that all calculation are calculated well to be 1e-5!

33

General Questions and Answers / how to display the MPSH picture?

« on: August 19, 2009, 08:13 »

Today, I face to a strange problem: in our calculation file(vnl) including MPSH, whose size is up to 20M, however, when I place it to vnl, and it only can see the two-probe system, it didn't have something about MPSH! WHy?

34

General Questions and Answers / strange transmission spectrum and energy levels! why?

« on: August 6, 2009, 14:24 »

Recently, I face to a strange problem and after I relaxed the two-probe system, and calculated its transmission and energy level, it shows like:
 -2.00        0.0000
        -1.99        0.0000
        -1.98        0.0000
        -1.97        0.0000
        -1.96        0.0000
        -1.95        0.0000
        -1.94        0.0000
        -1.93        0.0000
        -1.92        0.0000
        -1.91        0.0000
        -1.90        0.0000
        -1.89        0.0000
        -1.88        0.0000
        -1.87        0.0000
        -1.86        0.0000
        -1.85        0.0000
        -1.84        0.0000
        -1.83        0.0000
        -1.82        0.0000
        -1.81        0.0000
        -1.80        0.0000
        -1.79        0.0000
        -1.78        0.0000
        -1.77        0.0000
        -1.76        0.0000
......
          1.91        0.0000
         1.92        0.0000
         1.93        0.0000
         1.94        0.0000
         1.95        0.0000
         1.96        0.0000
         1.97        0.0000
         1.98        0.0000
         1.99        0.0000
         2.00        0.0000
and the energy level:
   # -----------------------------------------------------------------------------
# Energy Spectrum
# -----------------------------------------------------------------------------
# Energy (eV)
     -4396.36
     -4390.27
     -4384.25
     -4376.04
     -4371.64
     -4366.54
     -4365.30
     -4363.47
     -4362.17
     -4361.41
     -4359.66
     -4359.01
     -4358.58
     -4358.01
     -4354.00
     -4349.05
     -4345.41
     -4341.87
     -4340.59
     -4333.43
     -4331.80
     -4324.20
     -4317.41
     -4316.14
     -4303.11
......
   
why? how to solve it?
I checked carefully the configuration and it is correct! 
Thanks!

35

Installation and License Questions / Re: a error when running ATK-SE

« on: July 25, 2009, 05:05 »

Thank you for your help!
Let me try again!

36

Installation and License Questions / Re: ATK-semi library

« on: July 24, 2009, 02:50 »

http://rpm.pbone.net/index.php3/stat/3/srodzaj/1/search/libc.so.6(GLIBC_2.4)
Here a lot of RPM are shown,
which one for our linux system ?

37

Installation and License Questions / a error when running ATK-SE

« on: July 22, 2009, 02:59 »

I install the ATK-SE, as mentioned above, I face  the problem when runing:
/home/atk2009/atk-2009.06/nlpython/bin/nlpython_exec: /lib64/tls/libc.so.6: version `GLIBC_2.4' not found (required by /home/atk2009/atk-2009.06/nlpython/bin/../lib/libpython2.6.so.1.0)
How to slove it?
My linux:
Linux node11 2.6.9-78.ELsmp #1 SMP Wed Jul 9 15:46:26 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
Thank you very much!!!

38

Installation and License Questions / Re: ATK-semi library

« on: July 22, 2009, 02:51 »

I install the ATK-SE, as mentioned above, I face  the problem when runing:
/home/atk2009/atk-2009.06/nlpython/bin/nlpython_exec: /lib64/tls/libc.so.6: version `GLIBC_2.4' not found (required by /home/atk2009/atk-2009.06/nlpython/bin/../lib/libpython2.6.so.1.0)
How to slove it?
My linux:
Linux node11 2.6.9-78.ELsmp #1 SMP Wed Jul 9 15:46:26 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
Thank you very much!!!

39

General Questions and Answers / Re: two-probe device temperture

« on: July 16, 2009, 15:38 »

Thank you very much!!! I see a bit, hehe

40

General Questions and Answers / two-probe device temperture

« on: July 16, 2009, 14:36 »

We know it often is treated at zero temperture for ab inito calculation, however, in ATK manual, it says
the electron temperature has nothing to do with the lattice temperture
or phonons, but is strictly related to the electron distribution function.
At last, what is the temperture for two-probe in ATK? is it zero, 300k or other?
Thank you for your attention!!!

41

General Questions and Answers / Pulay mixing inversion failed.Using only last step.

« on: May 2, 2009, 09:10 »

these days, I face to a problem as the following:
when I calculate scf or current, it always display on ATK command:

#Pulay mixing inversion failed.Using only last step.
#Pulay mixing inversion failed.Using only last step.
#Pulay mixing inversion failed.Using only last step.
...       

And the output file .log as:
# ----------------------------------------------------------------
# TwoProbe Calculation
# ----------------------------------------------------------------
# sc  0 : q =  499.75484 e
# sc  1 : q =  494.11790 e  dRho = 5.0430E-001
# sc  2 : q =  505.26125 e  dRho = 4.1534E-001
# sc  3 : q =  505.26125 e  dRho = 0.0000E+000
# sc  4 : q =  493.40165 e  Etot =   -1.#IND0 Ry  dRho = 3.0489E-001
# sc  5 : q =  493.40165 e  Etot =   -1.#IND0 Ry  dRho = 4.2188E-015  dEtot = -1.#INDE+000 Ry
# sc  6 : q =  505.06675 e  Etot =   -1.#IND0 Ry  dRho = 3.1876E-001  dEtot = -1.#INDE+000 Ry
# sc  7 : q =  505.06675 e  Etot =   -1.#IND0 Ry  dRho = 2.1649E-015  dEtot = -1.#INDE+000 Ry
# sc  8 : q =  493.87468 e  Etot =   -1.#IND0 Ry  dRho = 2.6356E-001  dEtot = -1.#INDE+000 Ry
# sc  9 : q =  493.87468 e  Etot =   -1.#IND0 Ry  dRho = 1.2768E-014  dEtot = -1.#INDE+000 Ry
#
the configuration is relaxed on two-probe, and I try to decrease electrode lays and middle
regions lays but remains failed, why? how to solve it? Thank you very much!!!

42

General Questions and Answers / a mpi calculation error, why?

« on: April 19, 2009, 08:43 »

recently, I use mpi-atk(v2008.10.0)  to calculation for nano systems, however, I face to a problem, when two-probe calculation reached 2 steps, however, it displays in outfile .log:
# ----------------------------------------------------------------
# TwoProbe Calculation
# ----------------------------------------------------------------
# sc  0 : q =  791.88962 e
# sc  1 : q =  834.52211 e  dRho =  5.2383E-01
mpiexec_node08: mpd_uncaught_except_tb handling:
  exceptions.IOError: [Errno 5] Input/output error
    /opt/mpich2/bin/mpiexec  1051  handle_cli_stderr_input
        sys.stderr.write(msg)
    /opt/mpich2/bin/mpdlib.py  762  handle_active_streams
        handler(stream,*args)
    /opt/mpich2/bin/mpiexec  515  mpiexec
        rv = streamHandler.handle_active_streams(timeout=1.0)
    /opt/mpich2/bin/mpiexec  1423  ?
        mpiexec()

how to solve this involved problem?Thank you very much!!!

43

General Questions and Answers / how to deal with the install problem? Thank you very much!

« on: April 16, 2009, 16:19 »

 when I run "atk" in linux and it displays:

Traceback (most recent call last):
  File "<string>", line 1, in ?
  File "./ATK/__init__.py", line 16, in ?
  File "./NL/InputOutput/NLObjectFormatter.py", line 24, in ?
  File "./NL/InputOutput/FormatterFunctions.py", line 16, in ?
  File "./NL/DensityFunctionalTheory/Methods/CalculationType.py", line 6, in ?
  File "./PyATK.py", line 5, in ?
ImportError: libiomp5.so: cannot open shared object file: No such file or directory

then I run"chcon -t texrel_shlib_t lib/python2.4/_PyATK.so " in directory /atk-2008.10.0/lib
and displays an error:
chcon: can't apply partial context to unlabeled file lib/python2.4/_PyATK.so

How to deal with? Thank you very much!!!

44

General Questions and Answers / how does the deformation effect every term in Hamiltonian?

« on: April 9, 2009, 15:32 »

Recently, I face to a problem about Hamiltonian: As far as I know, the systemic
Hamiltonian can be written as following:
H=T+V(NA)+V(NL)+V(eff)
above four terms are kinetic energy, neutral atom potential, non-local potential and effictive potential, respectively.
and V(eff)=V(ext)+V(xc)+V(H)
three terms are external potential, exchange-corrlation term and Hartree term, respectively.
If I deformed our structure such as CNT(9,0), and produced a nano-device, how does the deformation effect every term in Hamiltonian? Are there some differences for device under or/not external bias voltage?
Thank you very much!
I am worried about it for long time!

45

General Questions and Answers / can not run by atk or vnl

« on: March 25, 2009, 16:46 »

when I run atk, it displays:
Warning: Could not to rename file c:vnl\gnr_zigzag_band2_HKNDKE.nc to c:vnl\gnr_zigzag_band2.nc !
and then it stops!
Why? How to deal with it ?
Thanks everyone!