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Topics - John

Pages: [1]
1
General Questions and Answers / How to design the gate electrode
« on: January 11, 2012, 14:42 »
Dear Sir,
   Can you give any suggestions about the gate electrode, e.g., in the graphene device tutorial, how to decide the thickness of metallic and dielectric region and the distance between the graphene and dielectric region?

2
Installation and License Questions / ATK can not work
« on: October 27, 2011, 16:39 »
Dear Sir,
   It works well before the restart of our server. However, unfortuantly, recently, our linux server had been restarted, and atk (11.2.3) can not work after the restart. I had tried to reinstall it, while it still does not work. After the installation, when I executive the commond "atkpython", it displays the error information

"License Error: (Internal: 292 Feature: ATKPython)

(Err: 9) Feature not found

For further assistance consult the manual or contact QuantumWise.
"

Note: The service license file had been put into the installation path /home/user1/bin/atk/license, and I had tried to start the license server using the commend "lmx-serv-quantum -b -l /home/user1/bin/atk/license/qw_license.lic -lf /home/user1/bin/atk/license/lmxserver.log".

Can you give any suggestion?

Thank you very much.

3
General Questions and Answers / two-probe model in new version
« on: July 10, 2011, 09:28 »
Dear Sir,
   In the new version 11.2.3, when building one two-probe model like the Au-S-alkene-S-Au (the example in Custom->Molecular Junction, as shown inthe attachment), it seems that the central molecule is always tilted (the X and Y positions of the two end S atoms are not same).
Whether is there one  convemient way to tune the molecule position, so that when one new molecule (like S-molecule-S) is dropped to "Drop configure here" the two end S atoms are automatically moved to one hollow site near the center of the electrode sections,respectively, and have same X and Y positions.

Thank you.


4
General Questions and Answers / how to hide the unit cell
« on: March 18, 2011, 03:57 »
Dear Sir,
    For the newest version 11.2.1, I want to know how to hide the unit cell like that the Axes can be hiden.  Thank you.

5
General Questions and Answers / losing the configure when displaying the LDOS
« on: March 13, 2011, 16:28 »
Dear Sir,
    For the ATK11.2 version, it seems unable to display the device or two-probe configure when viewing the LDOS. It could be better to control the display of configure,not only the space distribution of real-space density of states.
    Thanks.

6
General Questions and Answers / One error occured when calculating the DOS
« on: March 12, 2011, 02:02 »
Dear Sir,
    One error occured when I calculate the Device DOS of my two-probe system, which have 270 atoms (Carbon or Hydrogen) using the 2X2 CPUs. The error is following, can you give any suggestion? It is run by the newest version 11.2.  Thanks.

+------------------------------------------------------------------------------+
|                                                                              |
| Transmission Spectrum Analysis                                               |
|                                                                              |
+------------------------------------------------------------------------------+

                            |--------------------------------------------------|
Calculating Transmission   : ==================================================

+----------------------------------------------------------+
| Transmission Spectrum Report                             |
| -------------------------------------------------------- |
| Left electrode Fermi level  = -3.993602e+00 eV           |
| Right electrode Fermi level = -3.993602e+00 eV           |
| Energy zero                 = -3.993602e+00 eV           |
+----------------------------------------------------------+
   energy       T(up)
     eV
 -2.000000e+00   8.812919e-01
 -1.990000e+00   8.925038e-01
 -1.980000e+00   9.001541e-01

...........................................

  1.980000e+00   9.576673e-01
  1.990000e+00   9.638053e-01
  2.000000e+00   9.703618e-01
+----------------------------------------------------------+
+------------------------------------------------------------------------------+
|                                                                              |
| Device Density of States                                                     |
|                                                                              |
+------------------------------------------------------------------------------+

                            |--------------------------------------------------|
Calculating DOS            : =================================================Fatal error in MPI_Allreduce: Message truncated, error stack:
MPI_Allreduce(773).......: MPI_Allreduce(sbuf=0x95abc30, rbuf=0x1c820e0, count=4, MPI_INT, MPI_SUM, MPI_COMM_WORLD) failed
MPIR_Reduce(764).........:
MPIR_Reduce_binomial(172):
do_cts(490)..............: Message truncated; 1405104 bytes received but buffer size is 16
rank 0 in job 17  node18_42298   caused collective abort of all ranks
  exit status of rank 0: killed by signal 9

7
General Questions and Answers / some questions about the newest version
« on: March 10, 2011, 16:31 »
Dear friends,
     When I did one test about the transport properties of Li-H2-Li system by the both methods ATK-DFT and Device Extended Huckel using the newest version ATK11.2 released on 3 March, some errors occurred:
     1.   It seems that the method Device Extend Huckel can not do the optimization of one two-probe system.
     2.   Some analysises can not be obtained by the Device Extend Huckel method, such as the ElectronDensity, Forces, LocalDeviceDensityOfStates, Effective potential, and stress (also for ATK-DFT)
     3.   For one spin non-polarized transport calculation, some parameters are only alternative, up or down, such as for the calculation effective potential, Eigenstate, TransmissionEigenstate, TransmissionPathways,
     4.   About the TransmissionPathways researches,  for one spin non-polarized transport calculation, Four situations should be inverstigated, such as Left+Up, Left+Down, Right+Up, and Right+Down.
     5.   For the ATK-DFT calculation, I have a trouble to decide the Poisson Slover parameters, for 1D Graphene nanoribbon transport calculation, which one is better for such system, Multi-grid, FFT2D, or FFT?
     Thanks.

8
General Questions and Answers / how to regulate the energy range of energyband diagram
« on: March 6, 2011, 06:42 »
Dear friends,
  It seems difficult to regulate the energy range of the energyband diagram.  Can you give one easy way to extract the energyband data to plot it easily by other drawing tools, such as Origin.  For the version 2008.10 or 11.2. Thanks.

9
General Questions and Answers / the unit of isovalue
« on: January 8, 2011, 03:08 »
Dear Sir,
    Here I have the question about the unit of isovalue of eigenstates and LDOS:
        For eigenstates, the unit of isovalue is Angstrom^(-3/2) ?
        For LDOS, the unit of isovalue is Ang^(-3) * eV^(-1) ?
     Right?
     Thanks!

10
General Questions and Answers / Real Space Effective Potential Voltage Drop
« on: November 2, 2010, 15:06 »
Dear everyone,
    When I plot the voltage drop, all the atoms can not be displayed, only the scale value can be shown, as shown in the following figure.  Anyone can give the possible reasons, and how to deal with the problem?  Thanks! (I use the version of ATK2008.10, and the two-probe model (Aubulk-Molecule-Aubulk) and input file are both produced by VNL).


11
Scripts, Tutorials and Applications / some questions about the Etot
« on: July 31, 2010, 02:16 »
Dear everyone,
     I have a question about the printed Total energy for one two-probe system calculation. How to understand the Total energy, and which part it indicates, left+scattering region+right, or scattering region, etc. it seems that the printed Total energy is often smaller than that of Equivalent Bulk or scattering region.

Thanks!

12
Installation and License Questions / error happend when install
« on: July 28, 2010, 04:57 »
Dear everyone,
   When I install the new version 10.8 on our server, the error happens:
" /opt/intel/mkl/9.1.021/lib/em64t/libmkl_mc.so: undefined symbol: mkl_dft_commit_descriptor_core", while we can run it well for the version 2008.10.

how to deal with it?

thank you!

13
General Questions and Answers / some questions about the new version
« on: July 21, 2010, 16:04 »
Dear everyone,
    For the new version, I have some questions that,
(1)Monkhorst-Pack Grid for the calculations on DOS and Transmission spectrum: there are only two indexes (KA and KB) in the vnl panel, while the input file always includes three indexes, like that kpoints=MonkhorstPackGrid(n, m, 1),  whether the third “1” needs to be modified.
(2)It seems that the function “Restore SCF calculation and Only use initial density” is difficult to achieve, like that in 2008.10, how to calculate the SCF and Transmission spectrum under high bias using the low bias initial density, or restore calculation?
(3)If choosing the method SGGA+U or LSDA+U, how to decide the U values. Why I only find two kinds of normconserving pseudopotentials LDA.PZ and GGA.PBE, although I have tested one job using SGGA.PW91 exchange correlation, and there are not errors happened.  

Thank you!

14
General Questions and Answers / question in the new version
« on: July 8, 2010, 03:56 »
Dear everyone,
    1)In the new version, it seems that the electrodes formations are always changed with the changes of electrode copy length, and the left and right periodic lead parts are not same like 2008.10, how do understand it.
    2) If I want to run the job in parallel on Windows XP(one machine with 4 CPUs), whether I need to install the mpich2, and how to assgin the CPUs(just now I use the trial license, does it support the parallel)
   Thank you!

15
General Questions and Answers / some questions about MO
« on: May 17, 2010, 07:08 »
Dear everyone,

      when calculating the spin transport properties of one magnetic  molecule, the MPSH energy spectrum is list
# -----------------------------------------------------------------------------
# Energy Spectrum
# -----------------------------------------------------------------------------
# Spin-Up Energy (eV)  Spin-Down Energy (eV)
               -18.49                 -18.51
               -17.76                 -17.76
               -17.31                 -17.31
-----------------------------------------
                -1.94                  -0.79
                -1.83                  -0.50
                -1.36                  -0.40
                -1.32                   0.02
                -0.01                  1.24
                 0.02                  1.49
                 1.75                   1.92
------------------------------------------
I have some questions that:

(1) Is the Fermi level same for spin up state and spin down state(E_fermi=0?)
(2) Now, how can we decide the quantum numebers to calculate the MPSH HOMO and LUMO, here, for spin up state, the energy -0.01 and 0.02 correspond to HOMO and LUMO, respectively, and for spin down state -0.40 and 0.02 correspond to HOMO and LUMO? Is it alway right?
(3)Due to the smearing effect, whether the Fermi level could be brodened, and results -0.01 and 0.02 could be treated as 0. if so, sometimes it could be difficult to accurately judge the quantum number of HOMO and LUMO, even due to annexation of energy level.   Now, whether it is effective to judge it according to the different spin stats electron occupation.
(4) Usually, whether are there any obvious differences between the spatial distribution of HOMO or LUMO of one isolated molecule   and that of its MPSH MOs when coulped into two electrodes?

thank you!

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