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Messages - kaypu

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16
General Questions and Answers / Re: Calculate the electron density for a specific band-by atk 14.3
« on: November 9, 2015, 09:26 »
thank you prof. Umberto Martinez, the tutorial only contains how to calculate blochstate at one k-point. however, i want to get the electron density for a specific band, it means the summation of blochstate from G-Z.  how to modify the script?

17
General Questions and Answers / Calculate the electron density for a specific band-by atk 14.3
« on: November 9, 2015, 08:29 »
Dear Quantumwise staff:

according to the page from http://quantumwise.com/forum/index.php?topic=2203.msg10537#msg10537
i try to do it using atk 14.3, but something wrong with it. the script as follows:
**********************************************
from NanoLanguage import *
import NLEngine

def makeGridValues(datagrid, cell, origin, unit):

    n0, n1, n2 = datagrid.shape
    gA, gB, gC = cell
    u0 = NLEngine.Cartesian3D(gA[0],gA[1],gA[2])
    u1 = NLEngine.Cartesian3D(gB[0],gB[1],gB[2])
    u2 = NLEngine.Cartesian3D(gC[0],gC[1],gC[2])
    cell_origin = NLEngine.Cartesian3D(origin[0],origin[1],origin[2])

    grid_descriptor = NLEngine.GridDescriptor(n0,n1,n2,
                                              NLEngine.UnitCell(u0,u1,u2,cell_origin))
    grid3d = NLEngine.RealGrid3D(grid_descriptor,
                                 NLEngine.doubleSequenceToRealVector(datagrid.flatten()),True)

    return GridValues(grid3d,unit)

bulk_configuration = nlread("C:\Users\kaypu\Desktop/zigzag12-band.nc", BulkConfiguration)[0]
conf = nlread("C:\Users\kaypu\Desktop/zigzag12-band.nc", BulkConfiguration, read_state=False)[0]

dm = bulk_configuration.calculator()._densityMatrixCalculator()
number_of_electrons = int(dm.fermiDistribution().numberOfElectrons())

LUMO = number_of_electrons/2
LLUMO = LUMO+1

# Which state to compute?
spin = Spin.Up
state = LUMO
filename = "bloch_z12_LUMO_up.nc"

# Number of points to sample from G to Z
Nk = 100

density = None
for kz in numpy.linspace(0.2,0.5,Nk):
    b = BlochState(bulk_configuration, quantum_number=state, k_point=[0,0,kz], spin=spin)
    psi = b.toArray()
    if density == None:
        density = (psi*psi.conj()).real
    else:
        density += (psi*psi.conj()).real

cell = conf.bravaisLattice().primitiveVectors().inUnitsOf(Bohr)
origin = conf.bravaisLattice().origin().inUnitsOf(Bohr)
grid = makeGridValues(density,cell,origin,unit = eV/eV)

nlsave(filename, grid)
nlsave(filename, conf)
******************************************************
the wrong message shows as follows:

Traceback (most recent call last):
  File "c:\users\kaypu\appdata\local\temp\1676064135181985.py", line 52, in <module>
    grid = makeGridValues(density,cell,origin,unit = eV/eV)
  File "c:\users\kaypu\appdata\local\temp\1676064135181985.py", line 12, in makeGridValues
    u0 = NLEngine.Cartesian3D(gA[0],gA[1],gA[2])
AttributeError: 'module' object has no attribute 'Cartesian3D'

what's wrong with it, i use 2014.3

18
General Questions and Answers / Question on antiresonance in transmission
« on: May 8, 2015, 05:33 »
Dear QuantumWise staff

Following your advice(http://quantumwise.com/forum/index.php?topic=3385.0), I increase the scattering region and recalculate the s-PDOS. The negative s-PDOS is gone. thank you

in the attachment, there is a dip in the Fermi energy, is that QI or numerical artifact?
near -1.8eV, is there Fano resonance? how to explain it?

thank you

19
General Questions and Answers / Question on negative s-PDOS
« on: May 4, 2015, 08:57 »
Dear QuantumWise staff:

In the attachment, the device is composed of carbon nanotube(m=n=4) and anthracene (certral molecule). all the device has been optmized using LBFGS(z vetor is not fixed).The corresponding script is also in the attachment. The self-energy is chosen recursionself energy to avoid negative transmission appearing. Integral lower bound is set to 4.0 hartree to  eliminate charge missing problem.

but there are still some problem...

in the s-PDOS.jpg, near -1 eV, the PDOS of s state is negative, is that right? could  you help me to figure out this problem?

                                             Thanks

20
General Questions and Answers / Re: Question on PDOS
« on: April 29, 2015, 13:04 »
thank you pro zh
i want to project the density to px, py, pz, how to write angular_momenta? 1 means p,but how to project to px or py?

21
General Questions and Answers / Question on PDOS
« on: April 29, 2015, 08:52 »
Dear QuantumWise staff
Whether it is possible for ATK(2014.2) to calculate PDOS and project the density to s, px, py, pz of certain atom? if it is, how to compile  the script,
 thank you

22
General Questions and Answers / How the left/right electrodes are modeled?
« on: March 7, 2015, 13:15 »
Dear QuantumWise staff:
    How the left/right electrodes are modeled? it is done through a self-energy(Recursion self-energy)? And i want to know which model is used for it (wide band approximation, absorbing potential, etc.) in ATK

Thanks

23
General Questions and Answers / Re: Questions on Energy dependent LDOS
« on: November 10, 2014, 01:00 »
thank you, but still didn't work.  i replace "convertTo" by "inUnitsOf" in line 9, right?
******************
Traceback (most recent call last):
  File "LDOS-plot2014.py", line 10, in <module>
    dz = dZ.norm()
AttributeError: 'numpy.ndarray' object has no attribute 'norm'
*****************

24
General Questions and Answers / Questions on Energy dependent LDOS
« on: November 9, 2014, 14:16 »
hi:
 i use this py(in the attachment) to plot the Energy dependent LDOS at bias of 0.4V. the LDOS in the different energy(-1eV~1eV) are saved to LDOS1-LDOS4. but it doesn't work.
*******************
File "LDOS-plot.py", line 25, in <module>
    X, Y = numpy.meshgrid(z, energies)
  File "./build/lib/python2.7/site-packages/numpy/lib/function_base.py", line 3379, in meshgrid
  File "./zipdir/NL/CommonConcepts/PhysicalQuantity.py", line 456, in __mul__
  File "./zipdir/NL/CommonConcepts/PhysicalQuantity.py", line 249, in unit
AttributeError: 'PhysicalQuantity' object has no attribute '_PhysicalQuantity__unit'
*******************
atk version 2014.1

what's wrong? need to modify the py?

thanks

25
General Questions and Answers / Re: Question about Electrostatic Potential and Electrostatic Difference Potential
« on: December 20, 2013, 01:46 »
thank you  professor zh   

understood

26
General Questions and Answers / Question about Electrostatic Potential and Electrostatic Difference Potential
« on: December 19, 2013, 08:49 »
Dear QuantumWise staff
             
      What does the Electrostatic Potential consist of when the bias is applied? Does it equal to the Hartree energy?  or equal to the sum of Hartree energy and the electro-static external potential (bias potential)?

27
General Questions and Answers / Re: Question about zero charge at 0 bias
« on: December 18, 2013, 01:26 »
Thank you professor Anders and Shinji

28
General Questions and Answers / Re: Question about zero charge at 0 bias
« on: December 17, 2013, 09:05 »
i will upload the new file

29
General Questions and Answers / Re: Question about zero charge at 0 bias
« on: December 17, 2013, 01:20 »
atk 12.8.2

30
General Questions and Answers / 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?

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