Messages

16

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.

17

General Questions and Answers / Re: One error occured when calculating the DOS

« on: March 13, 2011, 03:27 »

Dear Sir,
    My MPI is mpich2.1.0.8.
    I have tested the simple Li-H2-Li system, Almost no errors occured in parallel calculation for all kinds of analysises, including LDOS and DOS calculation.
    Maybe, like ajaramil said,"This is most likely an MPI coding problem in  ATK 11.2.0 when calculating the LDOS, DOS, and Transmissionpathways of one big system (such as my 200 atoms) in parallel (2X2 nodes). It worked fine when running the same calculation (LDOS, DOS, and Transmissionpathways ) on a single processor.

18

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

19

General Questions and Answers / Re: some questions about the newest version

« on: March 11, 2011, 15:35 »

Thank you, Anders Blom.
    Whether are there any bugs for the newest version ATK11.2 for Windows 32-bit. The spin parameters of the Transmission Pathways calculation have only two choices, "Up or Down", like Figure1, but more parameter "Total" can be found in the the VNL tutorial(Page 24). Maybe,other properties calculations , should also have the "Total" parameter, like Eigenstate and TransmissionEigenstate calculations.
     Thank you.  

20

General Questions and Answers / Re: some questions about the newest version

« on: March 11, 2011, 01:41 »

Thank you, Anders Blom.
     For these properties ,such as the effective potential, Eigenstate, TransmissionEigenstate, and TransmissionPathways of one spin non-polarized transport calculation, I think it could be better if the sum results (up + down)can be also obtained. Like that there are three options when calculating the ElectronDensity, Sum, Up, or Down.  For one Spin polarized, the Up and Down results can be analyzed, respectively. While for one spin non-polarized calculation, Whether is it better to only analyze the sum results (Up+down)?
    Another question, It seems unable to automatically display the bond length when the mouse points at it.
    

21

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.

22

Installation and License Questions / Re: parall in Windows XP system

« on: March 9, 2011, 15:43 »

Dear Sir,
    I want to know now whether can the newest version ATK11.2 do the calculation in parall on Windows XP system? If yes, how to carry out? (My PC is one Four-core Windows XP SP3 system)
    Thanks!

23

General Questions and Answers / Re: how to regulate the energy range of energyband diagram

« on: March 7, 2011, 03:34 »

Thank you. 

24

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.

25

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!

26

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).

27

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!

28

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!

29

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!

30

General Questions and Answers / Re: question in the new version

« on: July 9, 2010, 15:06 »

Ok, thank you Anders Blom! The Linux cluster should be the first and best choice for HPC.