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Offline kaypu

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Question about zero charge at 0 bias
« on: December 16, 2013, 07:35 »
Dear QuantumWise staff:

    i want to test the polarization transport of the two-probe system of Ni-benzene-Ni.  but all the charges in the center scattering area are zero, as shown in the following:

+------------------------------------------------------------------------------+
| Density Matrix Report                         DM     DM[D]      DD        |
+------------------------------------------------------------------------------+
|   0  Ni   [   0.623 ,   0.622 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   1  Ni   [   3.115 ,   0.622 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   2  Ni   [   5.608 ,   0.622 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   3  Ni   [   0.623 ,   3.115 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   4  Ni   [   3.115 ,   3.115 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   5  Ni   [   5.608 ,   3.115 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   6  Ni   [   0.623 ,   5.607 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   7  Ni   [   3.115 ,   5.607 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   8  Ni   [   5.608 ,   5.607 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   9  Ni   [   1.869 ,   1.869 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  10  Ni   [   4.361 ,   1.869 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  11  Ni   [   6.854 ,   1.869 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  12  Ni   [   1.869 ,   4.361 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  13  Ni   [   4.361 ,   4.361 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  14  Ni   [   6.854 ,   4.361 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  15  Ni   [   1.869 ,   6.854 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  16  Ni   [   4.361 ,   6.854 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  17  Ni   [   6.854 ,   6.854 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  18  Ni   [   0.623 ,   0.622 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  19  Ni   [   3.115 ,   0.622 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  20  Ni   [   5.608 ,   0.622 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  21  Ni   [   0.623 ,   3.115 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  22  Ni   [   3.115 ,   3.115 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  23  Ni   [   5.608 ,   3.115 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  24  Ni   [   0.623 ,   5.607 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  25  Ni   [   3.115 ,   5.607 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  26  Ni   [   5.608 ,   5.607 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  27  Ni   [   1.869 ,   1.869 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  28  Ni   [   4.361 ,   1.869 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  29  Ni   [   6.854 ,   1.869 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  30  Ni   [   1.869 ,   4.361 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  31  Ni   [   4.361 ,   4.361 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  32  Ni   [   6.854 ,   4.361 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  33  Ni   [   1.869 ,   6.854 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  34  Ni   [   4.361 ,   6.854 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  35  Ni   [   6.854 ,   6.854 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  36  Ni   [   0.623 ,   0.622 ,   7.977 ]   -0.00000  -0.00000 -10.00000     |
|  37  Ni   [   3.125 ,   0.623 ,   7.977 ]   -0.00000  -0.00000 -10.00000     |
|  38  Ni   [   5.598 ,   0.623 ,   7.977 ]   -0.00000  -0.00000 -10.00000     |
|  39  Ni   [   0.623 ,   3.123 ,   7.971 ]   -0.00000  -0.00000 -10.00000     |
|  40  Ni   [   3.084 ,   3.081 ,   8.044 ]   -0.00000  -0.00000 -10.00000     |
|  41  Ni   [   5.640 ,   3.081 ,   8.044 ]   -0.00000  -0.00000 -10.00000     |
|  42  Ni   [   0.623 ,   5.599 ,   7.971 ]   -0.00000  -0.00000 -10.00000     |
|  43  Ni   [   3.083 ,   5.642 ,   8.043 ]   -0.00000  -0.00000 -10.00000     |
|  44  Ni   [   5.641 ,   5.643 ,   8.043 ]   -0.00000  -0.00000 -10.00000     |
|  45   S   [   4.364 ,   4.366 ,   9.313 ]   -0.00000  -0.00000  -6.00000     |
|  46   C   [   4.364 ,   4.368 ,  11.106 ]   -0.00000  -0.00000  -4.00000     |
|  47   H   [   4.367 ,   6.532 ,  11.228 ]   -0.00000  -0.00000  -1.00000     |
|  48   H   [   4.367 ,   2.204 ,  11.228 ]   -0.00000  -0.00000  -1.00000     |
|  49   C   [   4.367 ,   3.145 ,  11.808 ]   -0.00000  -0.00000  -4.00000     |
|  50   C   [   4.366 ,   5.592 ,  11.807 ]   -0.00000  -0.00000  -4.00000     |
|  51   C   [   4.369 ,   5.591 ,  13.208 ]   -0.00000  -0.00000  -4.00000     |
|  52   C   [   4.369 ,   3.145 ,  13.208 ]   -0.00000  -0.00000  -4.00000     |
|  53   H   [   4.374 ,   2.203 ,  13.783 ]   -0.00000  -0.00000  -1.00000     |
|  54   H   [   4.374 ,   6.534 ,  13.783 ]   -0.00000  -0.00000  -1.00000     |
|  55   C   [   4.369 ,   4.368 ,  13.913 ]   -0.00000  -0.00000  -4.00000     |
|  56   S   [   4.368 ,   4.368 ,  15.711 ]   -0.00000  -0.00000  -6.00000     |
|  57  Ni   [   0.624 ,   0.624 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  58  Ni   [   3.116 ,   0.624 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  59  Ni   [   5.609 ,   0.624 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  60  Ni   [   0.624 ,   3.116 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  61  Ni   [   3.116 ,   3.116 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  62  Ni   [   5.609 ,   3.116 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  63  Ni   [   0.624 ,   5.609 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  64  Ni   [   3.116 ,   5.609 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  65  Ni   [   5.609 ,   5.609 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  66  Ni   [   1.870 ,   1.870 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  67  Ni   [   4.362 ,   1.870 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  68  Ni   [   6.855 ,   1.870 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  69  Ni   [   1.870 ,   4.362 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  70  Ni   [   4.362 ,   4.362 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  71  Ni   [   6.855 ,   4.362 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  72  Ni   [   1.870 ,   6.855 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  73  Ni   [   4.362 ,   6.855 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  74  Ni   [   6.855 ,   6.855 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  75  Ni   [   0.624 ,   0.624 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  76  Ni   [   3.116 ,   0.624 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  77  Ni   [   5.609 ,   0.624 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  78  Ni   [   0.624 ,   3.116 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  79  Ni   [   3.116 ,   3.116 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  80  Ni   [   5.609 ,   3.116 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  81  Ni   [   0.624 ,   5.609 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  82  Ni   [   3.116 ,   5.609 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  83  Ni   [   5.609 ,   5.609 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  84  Ni   [   1.870 ,   1.870 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  85  Ni   [   4.362 ,   1.870 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  86  Ni   [   6.855 ,   1.870 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  87  Ni   [   1.870 ,   4.362 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  88  Ni   [   4.362 ,   4.362 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  89  Ni   [   6.855 ,   4.362 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  90  Ni   [   1.870 ,   6.855 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  91  Ni   [   4.362 ,   6.855 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  92  Ni   [   6.855 ,   6.855 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
+------------------------------------------------------------------------------+
|  15 E =  0.000508546 dE =  7.311566e-08 dH =  7.445477e-05  

          
The script is in the attachment

whar's wrong with it? should i increase the integral lower bound?
« Last Edit: December 17, 2013, 09:06 by kaypu »
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Offline Anders Blom

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Re: Question about zero charge at 0 bias
« Reply #1 on: December 16, 2013, 09:13 »
Which ATK version=?
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Offline kaypu

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Re: Question about zero charge at 0 bias
« Reply #2 on: December 17, 2013, 01:20 »
atk 12.8.2
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Offline Shinji Usui

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Re: Question about zero charge at 0 bias
« Reply #3 on: December 17, 2013, 02:25 »
I could not get the py file you put.  The size is Zero kilobyte.
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Offline kaypu

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Re: Question about zero charge at 0 bias
« Reply #4 on: December 17, 2013, 09:05 »
i will upload the new file
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Offline Anders Blom

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Re: Question about zero charge at 0 bias
« Reply #5 on: December 17, 2013, 11:45 »
The script is a bit odd, the calculator is defined twice. Also, I recommend not using Krylov, just stick to the Recursion method. The problem happens earlier, so it will be necessary to see the whole log to troubleshoot.
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Offline Shinji Usui

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Re: Question about zero charge at 0 bias
« Reply #6 on: December 17, 2013, 14:40 »
Dear kaypu

I could get a converged result at least for the first scf step.
1.  I used a Recursion method as Anders mentioned
2.  Add extra surface layers in the central region

See input and output files I attached (compressed).

 
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Offline kaypu

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Re: Question about zero charge at 0 bias
« Reply #7 on: December 18, 2013, 01:26 »
Thank you professor Anders and Shinji
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