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Topics - carbn9

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General Questions and Answers / Building graphene shell in VNL

« on: June 10, 2012, 08:05 »

Hi,

I need to build the graphene shell shown in the second or the final step of the following image:

which is from the publication of http://www.sciencedirect.com/science/article/pii/S0021999111007042

I know and I can build a graphene sheet with NanoSheet command and I studied the corresponding tutorial. However could you please help me for connecting upper and lower graphene sheets to form a shell like structure?

Best regards,
Maresh

General Questions and Answers / Lattice vectors and lattice constant of electrode and scattering region

« on: March 11, 2009, 23:28 »

Dear friends, I have generated a CNT of (4,4) using the code posted in this forum. The electrode and scattering region information that ATK generated are shown below. My question is: according to this information, what are the lattice constant and lattice vectors of electrodes and scattering region? Thanx.

Code

# Scattering elements and coordinates
scattering_elements = [Carbon, Carbon, Carbon, Carbon, 
                       Carbon, Carbon, Carbon, Carbon, 
                       Carbon, Carbon, Carbon, Carbon, 
                       Carbon, Carbon, Carbon, Carbon, 
                       Carbon, Carbon, Carbon, Carbon, 
                       Carbon, Carbon, Carbon, Carbon, 
                       Carbon, Carbon, Carbon, Carbon, 
                       Carbon, Carbon, Carbon, Carbon, 
                       Carbon, Carbon, Carbon, Carbon, 
                       Carbon, Carbon, Carbon, Carbon, 
                       Carbon, Carbon, Carbon, Carbon, 
                       Carbon, Carbon, Carbon, Carbon, 
                       Carbon, Carbon, Carbon, Carbon, 
                       Carbon, Carbon, Carbon, Carbon, 
                       Carbon, Carbon, Carbon, Carbon, 
                       Carbon, Carbon, Carbon, Carbon]
scattering_coordinates = [[  7.00668,   4.29086,   2.46298],
                          [  6.21123,   6.21123,   3.69446],
                          [  4.29086,   7.00668,   2.46298],
                          [  2.37048,   6.21123,   3.69446],
                          [  1.57504,   4.29086,   2.46298],
                          [  2.37048,   2.37048,   3.69446],
                          [  4.29086,   1.57504,   2.46298],
                          [  6.21123,   2.37048,   3.69446],
                          [  6.64283,   5.64877,   2.46298],
                          [  4.99376,   6.91414,   3.69446],
                          [  2.93295,   6.64283,   2.46298],
                          [  1.66758,   4.99376,   3.69446],
                          [  1.93889,   2.93295,   2.46298],
                          [  3.58795,   1.66758,   3.69446],
                          [  5.64877,   1.93889,   2.46298],
                          [  6.91414,   3.58795,   3.69446],
                          [  7.00668,   4.29086,   4.92595],
                          [  6.21123,   6.21123,   6.15744],
                          [  4.29086,   7.00668,   4.92595],
                          [  2.37048,   6.21123,   6.15744],
                          [  1.57504,   4.29086,   4.92595],
                          [  2.37048,   2.37048,   6.15744],
                          [  4.29086,   1.57504,   4.92595],
                          [  6.21123,   2.37048,   6.15744],
                          [  6.64283,   5.64877,   4.92595],
                          [  4.99376,   6.91414,   6.15744],
                          [  2.93295,   6.64283,   4.92595],
                          [  1.66758,   4.99376,   6.15744],
                          [  1.93889,   2.93295,   4.92595],
                          [  3.58795,   1.66758,   6.15744],
                          [  5.64877,   1.93889,   4.92595],
                          [  6.91414,   3.58795,   6.15744],
                          [  7.00293,   4.27934,   7.39446],
                          [  6.21109,   6.20773,   8.61571],
                          [  4.28956,   6.99758,   7.38242],
                          [  2.37035,   6.21122,   8.62154],
                          [  1.5713 ,   4.28428,   7.40271],
                          [  2.36689,   2.37054,   8.6444 ],
                          [  4.28467,   1.56604,   7.41475],
                          [  6.20764,   2.36705,   8.63857],
                          [  6.6403 ,   5.63756,   7.38693],
                          [  4.99426,   6.91173,   8.61337],
                          [  2.93132,   6.63497,   7.38665],
                          [  1.66635,   4.99442,   8.62985],
                          [  1.93393,   2.92606,   7.41024],
                          [  3.58373,   1.66654,   8.64673],
                          [  5.64291,   1.92865,   7.41053],
                          [  6.91164,   3.58386,   8.63025],
                          [  7.00668,   4.29086,   9.8531 ],
                          [  6.21123,   6.21123,  11.0846 ],
                          [  4.29086,   7.00668,   9.8531 ],
                          [  2.37048,   6.21123,  11.0846 ],
                          [  1.57504,   4.29086,   9.8531 ],
                          [  2.37048,   2.37048,  11.0846 ],
                          [  4.29086,   1.57504,   9.8531 ],
                          [  6.21123,   2.37048,  11.0846 ],
                          [  6.64283,   5.64877,   9.8531 ],
                          [  4.99376,   6.91414,  11.0846 ],
                          [  2.93295,   6.64283,   9.8531 ],
                          [  1.66758,   4.99376,  11.0846 ],
                          [  1.93889,   2.93295,   9.8531 ],
                          [  3.58795,   1.66758,  11.0846 ],
                          [  5.64877,   1.93889,   9.8531 ],
                          [  6.91414,   3.58795,  11.0846 ]]*Angstrom
        

electrode_elements = [Carbon, Carbon, Carbon, Carbon, 
                      Carbon, Carbon, Carbon, Carbon, 
                      Carbon, Carbon, Carbon, Carbon, 
                      Carbon, Carbon, Carbon, Carbon]
electrode_coordinates = [[ 7.00668,  4.29086,  0.     ],
                         [ 6.21123,  6.21123,  1.23149],
                         [ 4.29086,  7.00668,  0.     ],
                         [ 2.37048,  6.21123,  1.23149],
                         [ 1.57504,  4.29086,  0.     ],
                         [ 2.37048,  2.37048,  1.23149],
                         [ 4.29086,  1.57504,  0.     ],
                         [ 6.21123,  2.37048,  1.23149],
                         [ 6.64283,  5.64877,  0.     ],
                         [ 4.99376,  6.91414,  1.23149],
                         [ 2.93295,  6.64283,  0.     ],
                         [ 1.66758,  4.99376,  1.23149],
                         [ 1.93889,  2.93295,  0.     ],
                         [ 3.58795,  1.66758,  1.23149],
                         [ 5.64877,  1.93889,  0.     ],
                         [ 6.91414,  3.58795,  1.23149]]*Angstrom

electrode_cell = [[ 12.8726 ,   0.     ,   0.     ],
                  [  0.     ,  12.8726 ,   0.     ],
                  [  0.     ,   0.     ,   2.46298]]*Angstrom

# Set up electrodes
electrode_configuration = PeriodicAtomConfiguration(
    electrode_cell,
    electrode_elements,
    electrode_coordinates
    )

General Questions and Answers / Parallel code

« on: February 14, 2009, 19:32 »

Hi firends,

I tried to see the paralellization of ATK how much it speeds up calculations? I runned the Li-H2-Li two-probe example on single core and then at six cores. But while 1 core completed in 2:38 mins, 6 cores completed in 5:51 mins. I am very surprised since parallelization made things slower. I looked at the system performance during runs, when running in parallel, most of the time is spent during MPI communication more than real calculation I think. I concluded that for small systems, MPI parallelization may have negative effect, is this true, or am I making sth wrong? Is there a trick that must be used during parallel calculation? I gave the command:

mpiexec -n 6 /ATK dir /file name after connection all cores using mpd. I used the Li.py given in the manual without modifying the code. Is there anything to add in order to order ATK to parallelize??

Maresh

General Questions and Answers / How to optimize two-probe

« on: February 8, 2009, 13:40 »

Hi,

I've read the optimization for two-probe geometries from the manual. There optimization is defined as the rearrangement of the specified scattering region atoms while keeping electrodes fixed if I understood right.

My problem is that I want to fix the scattering region atoms' positions with respect to each other and fixing the electrode crystal type but, to optimize the distance of scattering region to electrodes (the optimum distance between electrodes). How can I impose these constraints to optimization?

General Questions and Answers / Current calculation comparison with Smeagol

« on: December 6, 2008, 18:04 »

Dear ATK users,

First of all, I'm very happy since new versions of ATK will be released by Quantumwise. Thanks.

I addition, I'd like to ask a question that I asked at Smeagol discuss group but could not get a satisfactory answer there:

"
I've just installed Smeagol and tried the Au nanowire example provided by the package. The current calculation is as follows (.CUR file)

0.00000000D+00 0.00000000D+00
0.24148777D-01 0.25318921D-04
0.48728283D-01 0.50981350D-04
0.73308789D-01 0.76277083D-04

Thus, as I understand, for a bias of 1V, the current is 7.6277083E-05. Is it right?

On the other hand, I have made an input file describing the Au nanowire of the example of Smeagol. The input file of ATK for Au nanowire I have created is attached. I have applied a 1V bias to nanowire just as in Smeagol. The output of ATK is also given as attachement. But I get a current value of 3.4018175915e-005 A. That is lower than the half of the value calculated using Smeagol. Where can this difference come from?

Thank you for your interest.

Maresh Kubar".

The answer on Smeagol forum was:

"the wire has about 1 quantum of conductance (transmission =1), so that
the current at 1 volt is about

I=1/12900 A = 77 microAmpere

This is approximately what smeagol gives as result. This system is
unphysical anyway, since you can not apply one Volt on such a 1D chain,
it is just an example to test the code. It is therefore probably not the
best system to compare results at finite bias for different codes"

Could you please give an idea on this question?

Regards,
Maresh