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Topics - yongjunwinwin

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General Questions and Answers / The calculation of Indium Arsenide

« on: August 6, 2012, 04:13 »

I used ATK to calculate the band structure of Indium Arsenide (the script and result is attached) under two different k point sampling, however, I found the band gap I got is ~0.7 which is larger than reported 0.35 eV. In addition, the split off band did not show in my calculated band structure.

I also found the the zero energy level shift with different k point sampling (3*3*3 and 6*6*6), what would be the reason for the phenomenon I mention?

General Questions and Answers / Plot separate transmission eigenstate in the same picture

« on: April 12, 2012, 12:32 »

In the version of ATK 11.8.2, the transmission eigenstate is calucated with separate contribution from left and right. Therefore, how to show the eigenstate of the whole device in the same device configuration?

General Questions and Answers / About the energy window of transmission spectrum calculation

« on: February 10, 2012, 13:24 »

The current is obtained by integrating the transmission spectrum at a given bias voltage(e.g. -1 V) and the range of integration is the chemical potential of the right and left electrode. So is it reasonable to define the energy window for transmission spectrum by the bias( e.g. [-0.5, 0.5] and zero energy is aligned to average Fermi level) thus reduce calculation time.

I notice one tutorial "Graphene Junction Device" (page 11)mention that both valence and conduction band edges of the central region should within the energy range of the transmission spectrum to obtain accurate conductance, so I am a little confused that whether the strategy I mention before is improper or not?

General Questions and Answers / A puzzle of stop of ATK

« on: October 6, 2011, 08:29 »

When a calculation goes for a few hours, the windows report "vnl.exe stop working" and the related files are as follows:

C:\Users\liyongjun\AppData\Local\Temp\WER375B.tmp.WERInternalMetadata.xml
C:\Users\liyongjun\AppData\Local\Temp\WER5289.tmp.appcompat.txt
C:\Users\liyongjun\AppData\Local\Temp\WER54FA.tmp.mdmp

what's wrong with it? and is something related to my models? (the script is attached)

General Questions and Answers / A warning about convergence when calculating transport properties

« on: July 30, 2011, 12:33 »

I calculate the transport properties of the bulk MoS2 with a N atom substitute S in the central region, there is no warning when the bias is 0 or 0.2 V, but when the electrode bias is 0.4V, I got the following warning(just part of the log)

Quote

| 83 S [ 5.000 , 7.298 , 21.330 ] 6.08322 0.08322 |
+------------------------------------------------------------------------------+
| 99 E = -177.533 dE = 2.215149e-01 dH = 3.054094e-01 |
+------------------------------------------------------------------------------+
########################################################
# #
# Warning: The calculation did not converge to the requested tolerance! #
# #
########################################################

the script is also attached
What is the problem and how to solve the problem of the convergence of my system?
As there is comment saying the upload is full, I have to paste my script below

Code

# -------------------------------------------------------------
# TwoProbe configuration
# -------------------------------------------------------------

# -------------------------------------------------------------
# Left electrode
# -------------------------------------------------------------

# Set up lattice
vector_a = [13.172, 0.0, 0.0]*Angstrom
vector_b = [0.0, 10.94656, 0.0]*Angstrom
vector_c = [0.0, 0.0, 9.48]*Angstrom
left_electrode_lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
left_electrode_elements = [Molybdenum, Sulfur, Sulfur, Sulfur, Sulfur, Molybdenum, Molybdenum,
                           Sulfur, Sulfur, Sulfur, Sulfur, Molybdenum, Sulfur, Molybdenum,
                           Sulfur, Sulfur, Molybdenum, Sulfur, Molybdenum, Molybdenum, Sulfur,
                           Sulfur, Sulfur, Sulfur, Sulfur, Molybdenum, Molybdenum, Sulfur,
                           Sulfur, Sulfur, Sulfur, Molybdenum, Sulfur, Sulfur, Sulfur,
                           Molybdenum]

# Define coordinates
left_electrode_coordinates = [[  6.586     ,   0.912215  ,   0.79      ],
                              [  8.172     ,   4.561065  ,   0.79      ],
                              [  8.172     ,  10.034345  ,   0.79      ],
                              [  5.        ,  10.034345  ,   0.79      ],
                              [  5.        ,   4.561065  ,   0.79      ],
                              [  6.586     ,   6.385495  ,   0.79      ],
                              [  6.586     ,   9.122135  ,   2.37      ],
                              [  8.172     ,   1.824425  ,   2.37      ],
                              [  8.172     ,   7.297705  ,   2.37      ],
                              [  5.        ,   7.297705  ,   2.37      ],
                              [  5.        ,   1.824425  ,   2.37      ],
                              [  6.586     ,   3.648855  ,   2.37      ],
                              [  8.172     ,   4.561065  ,   3.95      ],
                              [  6.586     ,   6.385495  ,   3.95      ],
                              [  5.        ,   4.561065  ,   3.95      ],
                              [  5.        ,  10.034345  ,   3.95      ],
                              [  6.586     ,   0.912215  ,   3.95      ],
                              [  8.172     ,  10.034345  ,   3.95      ],
                              [  6.586     ,   9.122135  ,   5.53      ],
                              [  6.586     ,   3.648855  ,   5.53      ],
                              [  5.        ,   7.297705  ,   5.53      ],
                              [  8.172     ,   1.824425  ,   5.53      ],
                              [  8.172     ,   7.297705  ,   5.53      ],
                              [  5.        ,   1.824425  ,   5.53      ],
                              [  8.17273822,   4.5597421 ,   7.10893146],
                              [  6.58779066,   6.38548616,   7.10976081],
                              [  6.586     ,   0.912215  ,   7.11      ],
                              [  5.        ,  10.034345  ,   7.11      ],
                              [  8.172     ,  10.034345  ,   7.11      ],
                              [  5.01682695,   4.55707024,   7.14298238],
                              [  8.1721717 ,   1.82501485,   8.68790182],
                              [  6.586     ,   9.122135  ,   8.69      ],
                              [  8.17229847,   7.29879878,   8.69131041],
                              [  5.01731892,   1.85637138,   8.70283463],
                              [  5.01756127,   7.27016182,   8.71088609],
                              [  6.62346376,   3.68354863,   8.74905406]]*Angstrom

# Set up configuration
left_electrode = BulkConfiguration(
    bravais_lattice=left_electrode_lattice,
    elements=left_electrode_elements,
    cartesian_coordinates=left_electrode_coordinates
    )

# -------------------------------------------------------------
# Right electrode
# -------------------------------------------------------------

# Set up lattice
vector_a = [13.172, 0.0, 0.0]*Angstrom
vector_b = [0.0, 10.94656, 0.0]*Angstrom
vector_c = [0.0, 0.0, 9.48]*Angstrom
right_electrode_lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
right_electrode_elements = [Sulfur, Sulfur, Molybdenum, Sulfur, Molybdenum, Sulfur, Molybdenum,
                            Sulfur, Sulfur, Molybdenum, Sulfur, Sulfur, Sulfur, Sulfur,
                            Sulfur, Sulfur, Molybdenum, Molybdenum, Molybdenum, Sulfur, Sulfur,
                            Molybdenum, Sulfur, Sulfur, Molybdenum, Molybdenum, Sulfur, Sulfur,
                            Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Molybdenum, Molybdenum,
                            Sulfur]

# Define coordinates
right_electrode_coordinates = [[  5.01688382,   4.5571484 ,   0.75677638],
                               [  5.        ,  10.034345  ,   0.79      ],
                               [  6.586     ,   0.912215  ,   0.79      ],
                               [  8.172     ,  10.034345  ,   0.79      ],
                               [  6.58766598,   6.38544301,   0.790323  ],
                               [  8.17260236,   4.55959415,   0.79112081],
                               [  6.586     ,   9.122135  ,   2.37      ],
                               [  5.        ,   1.824425  ,   2.37      ],
                               [  8.172     ,   7.297705  ,   2.37      ],
                               [  6.586     ,   3.648855  ,   2.37      ],
                               [  8.172     ,   1.824425  ,   2.37      ],
                               [  5.        ,   7.297705  ,   2.37      ],
                               [  8.172     ,   4.561065  ,   3.95      ],
                               [  8.172     ,  10.034345  ,   3.95      ],
                               [  5.        ,  10.034345  ,   3.95      ],
                               [  5.        ,   4.561065  ,   3.95      ],
                               [  6.586     ,   0.912215  ,   3.95      ],
                               [  6.586     ,   6.385495  ,   3.95      ],
                               [  6.586     ,   9.122135  ,   5.53      ],
                               [  8.172     ,   7.297705  ,   5.53      ],
                               [  5.        ,   1.824425  ,   5.53      ],
                               [  6.586     ,   3.648855  ,   5.53      ],
                               [  5.        ,   7.297705  ,   5.53      ],
                               [  8.172     ,   1.824425  ,   5.53      ],
                               [  6.586     ,   0.912215  ,   7.11      ],
                               [  6.586     ,   6.385495  ,   7.11      ],
                               [  5.        ,  10.034345  ,   7.11      ],
                               [  5.        ,   4.561065  ,   7.11      ],
                               [  8.172     ,  10.034345  ,   7.11      ],
                               [  8.172     ,   4.561065  ,   7.11      ],
                               [  8.172     ,   7.297705  ,   8.69      ],
                               [  8.172     ,   1.824425  ,   8.69      ],
                               [  5.        ,   1.824425  ,   8.69      ],
                               [  6.586     ,   9.122135  ,   8.69      ],
                               [  6.586     ,   3.648855  ,   8.69      ],
                               [  5.        ,   7.297705  ,   8.69      ]]*Angstrom

# Set up configuration
right_electrode = BulkConfiguration(
    bravais_lattice=right_electrode_lattice,
    elements=right_electrode_elements,
    cartesian_coordinates=right_electrode_coordinates
    )

# -------------------------------------------------------------
# Central region
# -------------------------------------------------------------

# Set up lattice
vector_a = [13.172, 0.0, 0.0]*Angstrom
vector_b = [0.0, 10.94656, 0.0]*Angstrom
vector_c = [0.0, 0.0, 22.12]*Angstrom
central_region_lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
central_region_elements = [Molybdenum, Sulfur, Sulfur, Sulfur, Sulfur, Molybdenum, Molybdenum,
                           Sulfur, Sulfur, Sulfur, Sulfur, Molybdenum, Sulfur, Molybdenum,
                           Sulfur, Sulfur, Molybdenum, Sulfur, Molybdenum, Molybdenum, Sulfur,
                           Sulfur, Sulfur, Sulfur, Sulfur, Molybdenum, Molybdenum, Sulfur,
                           Sulfur, Sulfur, Sulfur, Molybdenum, Sulfur, Sulfur, Sulfur,
                           Molybdenum, Molybdenum, Nitrogen, Sulfur, Sulfur, Sulfur,
                           Molybdenum, Molybdenum, Sulfur, Sulfur, Sulfur, Molybdenum, Sulfur,
                           Sulfur, Sulfur, Molybdenum, Sulfur, Molybdenum, Sulfur, Molybdenum,
                           Sulfur, Sulfur, Molybdenum, Sulfur, Sulfur, Sulfur, Sulfur,
                           Sulfur, Sulfur, Molybdenum, Molybdenum, Molybdenum, Sulfur, Sulfur,
                           Molybdenum, Sulfur, Sulfur, Molybdenum, Molybdenum, Sulfur, Sulfur,
                           Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Molybdenum, Molybdenum,
                           Sulfur]

# Define coordinates
central_region_coordinates = [[  6.586     ,   0.912215  ,   0.79      ],
                              [  8.172     ,   4.561065  ,   0.79      ],
                              [  8.172     ,  10.034345  ,   0.79      ],
                              [  5.        ,  10.034345  ,   0.79      ],
                              [  5.        ,   4.561065  ,   0.79      ],
                              [  6.586     ,   6.385495  ,   0.79      ],
                              [  6.586     ,   9.122135  ,   2.37      ],
                              [  8.172     ,   1.824425  ,   2.37      ],
                              [  8.172     ,   7.297705  ,   2.37      ],
                              [  5.        ,   7.297705  ,   2.37      ],
                              [  5.        ,   1.824425  ,   2.37      ],
                              [  6.586     ,   3.648855  ,   2.37      ],
                              [  8.172     ,   4.561065  ,   3.95      ],
                              [  6.586     ,   6.385495  ,   3.95      ],
                              [  5.        ,   4.561065  ,   3.95      ],
                              [  5.        ,  10.034345  ,   3.95      ],
                              [  6.586     ,   0.912215  ,   3.95      ],
                              [  8.172     ,  10.034345  ,   3.95      ],
                              [  6.586     ,   9.122135  ,   5.53      ],
                              [  6.586     ,   3.648855  ,   5.53      ],
                              [  5.        ,   7.297705  ,   5.53      ],
                              [  8.172     ,   1.824425  ,   5.53      ],
                              [  8.172     ,   7.297705  ,   5.53      ],
                              [  5.        ,   1.824425  ,   5.53      ],
                              [  8.17273822,   4.5597421 ,   7.10893146],
                              [  6.58779066,   6.38548616,   7.10976081],
                              [  6.586     ,   0.912215  ,   7.11      ],
                              [  5.        ,  10.034345  ,   7.11      ],
                              [  8.172     ,  10.034345  ,   7.11      ],
                              [  5.01682695,   4.55707024,   7.14298238],
                              [  8.1721717 ,   1.82501485,   8.68790182],
                              [  6.586     ,   9.122135  ,   8.69      ],
                              [  8.17229847,   7.29879878,   8.69131041],
                              [  5.01731892,   1.85637138,   8.70283463],
                              [  5.01756127,   7.27016182,   8.71088609],
                              [  6.62346376,   3.68354863,   8.74905406],
                              [  6.5876179 ,   0.91130968,  10.26983443],
                              [  5.59827839,   4.56059523,  10.26994231],
                              [  8.172     ,  10.034345  ,  10.27      ],
                              [  5.        ,  10.034345  ,  10.27      ],
                              [  8.33498485,   4.56088264,  10.27000223],
                              [  6.62327856,   6.31588444,  10.27037848],
                              [  6.62338152,   3.68355084,  11.79065483],
                              [  5.0172326 ,   7.27047134,  11.82955335],
                              [  5.01735904,   1.85679472,  11.83687065],
                              [  8.17237071,   7.29879284,  11.84963777],
                              [  6.586     ,   9.122135  ,  11.85      ],
                              [  8.17218961,   1.82494187,  11.85192361],
                              [  5.01688382,   4.5571484 ,  13.39677638],
                              [  5.        ,  10.034345  ,  13.43      ],
                              [  6.586     ,   0.912215  ,  13.43      ],
                              [  8.172     ,  10.034345  ,  13.43      ],
                              [  6.58766598,   6.38544301,  13.430323  ],
                              [  8.17260236,   4.55959415,  13.43112081],
                              [  6.586     ,   9.122135  ,  15.01      ],
                              [  5.        ,   1.824425  ,  15.01      ],
                              [  8.172     ,   7.297705  ,  15.01      ],
                              [  6.586     ,   3.648855  ,  15.01      ],
                              [  8.172     ,   1.824425  ,  15.01      ],
                              [  5.        ,   7.297705  ,  15.01      ],
                              [  8.172     ,   4.561065  ,  16.59      ],
                              [  8.172     ,  10.034345  ,  16.59      ],
                              [  5.        ,  10.034345  ,  16.59      ],
                              [  5.        ,   4.561065  ,  16.59      ],
                              [  6.586     ,   0.912215  ,  16.59      ],
                              [  6.586     ,   6.385495  ,  16.59      ],
                              [  6.586     ,   9.122135  ,  18.17      ],
                              [  8.172     ,   7.297705  ,  18.17      ],
                              [  5.        ,   1.824425  ,  18.17      ],
                              [  6.586     ,   3.648855  ,  18.17      ],
                              [  5.        ,   7.297705  ,  18.17      ],
                              [  8.172     ,   1.824425  ,  18.17      ],
                              [  6.586     ,   0.912215  ,  19.75      ],
                              [  6.586     ,   6.385495  ,  19.75      ],
                              [  5.        ,  10.034345  ,  19.75      ],
                              [  5.        ,   4.561065  ,  19.75      ],
                              [  8.172     ,  10.034345  ,  19.75      ],
                              [  8.172     ,   4.561065  ,  19.75      ],
                              [  8.172     ,   7.297705  ,  21.33      ],
                              [  8.172     ,   1.824425  ,  21.33      ],
                              [  5.        ,   1.824425  ,  21.33      ],
                              [  6.586     ,   9.122135  ,  21.33      ],
                              [  6.586     ,   3.648855  ,  21.33      ],
                              [  5.        ,   7.297705  ,  21.33      ]]*Angstrom

# Set up configuration
central_region = BulkConfiguration(
    bravais_lattice=central_region_lattice,
    elements=central_region_elements,
    cartesian_coordinates=central_region_coordinates
    )

device_configuration = DeviceConfiguration(
    central_region,
    [left_electrode, right_electrode]
    )

In the setting,the k-point sampling is kA=1,KB=3,Kc=100,and the nA, nB in transmission spectrum calculation is 1 and 100 respectively.

General Questions and Answers / Different results by LDA and GGA

« on: July 23, 2011, 13:15 »

I calculated the band structure of monolayer MoTe2 respectively with LDA and GGA, but got the complete different result! The band structure by LDA suggest metal property while GGA suggest semiconductor property with a direct band gap of 1.118 eV. What cause the difference and which result is right? (The results and the script of the unite cell of monolayer MoTe2 is attached)

General Questions and Answers / Model about mismatch of lattice constant

« on: July 13, 2011, 14:26 »

I want to construct a model that is graphene is absorbed on the metal surface but the problem I come across is that the graphene lattice is inconsistent with the metal lattice like Au, then the question is how to model such system?

Another question is when I utilize the 'cleave' option in 'transform' panel of the builder tool to obtain Ag(111) surface of the metal, but i was confused which surface is the (111) surface (xy, yz or xz?)

General Questions and Answers / A question about optimization

« on: July 11, 2011, 10:45 »

I have a few questions in doing structure optimization:
1.When should we constrain the cell and when we should untick the constrain, for example when I build a super cell, in which one carbon is substituted by other atoms or a molecule is absorbed on the surface of the graphene, whether should I constrain the cell or not in optimization.
2.If the case is not bulk material, but nanoribbon, what about the same problem mentioned above?

General Questions and Answers / A question about Brillrouin zone route

« on: July 10, 2011, 12:46 »

When I calculate the band structure using the unit cell of bulk graphene, which contain two carbon atoms, the brillrouin zone route can be set to G,M,K,G, just as the tutorials suggest. But as I enlarge the cell using repetition ( because I want to substitute boron atom for one carbon atoms ), but when I want to calculate the band structure of it, the default Brillouin zone route is G, Z ,but as far as I know such BZ is used in graphene nanoribbon andI cannot change to G,M,K,G, the cell used in calculation and the band structure is attached. Could anyone explain what was the prolbem? Thanks in advance!

General Questions and Answers / how to export the data of bloch state

« on: June 4, 2011, 18:19 »

If I want to plot the isosurface of bloch state with other software like origin. Is there anyway to export the data for plotting because through the 'export' in result viewer panel, I cannot get the detailed data for plotting.

General Questions and Answers / questions about transmission eigenvalue and eigenstate

« on: May 24, 2011, 06:37 »

I don't quite understand the concept of transmission eigenvalue and transmission eigenstate. Could anyone explain to me these two concepts and how to make use of them to do analysis about transport properties?

General Questions and Answers / about calculate bandstructure of the graphene nanoribbon

« on: May 14, 2011, 12:57 »

In using the ATK, I found that the bandstructure of GNR depends on the lengh of the ribbon, when using the example in the tutorials, I got the same bandstructure in the example, but when I increase the length with the same settings, I got a totally different result. Is that right? or I have to change the settings like the k points sampling?

General Questions and Answers / Is AFM magnetization of zGNR necessary to be included for calculation

« on: May 9, 2011, 05:13 »

I have beening conducting calculation on zigzag graphene nanoribbon, as I have seen many papers concering the ordering of magnetizaion on the edges of zigzag GNR? I am wondering it is necessary to add AFM magnetization on the edge of the zigzag GNR in order to make the result more reliable? Then what about armchair GNR or Bilayer GNR?