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Messages - carbn9

Pages: [1] 2
1
General Questions and Answers / Re: Building graphene shell in VNL
« on: June 12, 2012, 09:19 »
Thanks Nordland. The structure you built seems really good.

One thing: In the builder, which menu should I use? Or is there a tutorial on this?

Thanks again...

2
General Questions and Answers / Re: Building graphene shell in VNL
« on: June 11, 2012, 16:16 »
Thanks Anders Blom.

"deform it into an ellipsoidal shape by compressing the cell in one direction while keeping the fractional coordinates fixed" Sorry but how to do this?  ::)

Best regards and fingers crossed...

3
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

4
Scripts, Tutorials and Applications / Re: Script for creating nanotubes
« on: April 16, 2009, 15:47 »
Thanks Anders, but how can we insert screening layers in perfect nanotube two probe geometry of the code of this thread?

Cheers,
Serhan

5
General Questions and Answers / Re: Lattice vectors and lattice constant of electrode and scattering region
« on: March 12, 2009, 07:39 »
Thank you sir.

6
Scripts, Tutorials and Applications / Re: Script for creating nanotubes
« on: March 11, 2009, 23:30 »
Thank tou for your answers Sir.

7
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
    )

8
Scripts, Tutorials and Applications / Re: Script for creating nanotubes
« on: March 11, 2009, 12:30 »
Dear all, When I tried to generate a (3,3) CNT as TwoProbe, the script gave the following error. How can I correct it? Regards, Maresh

Code
Traceback (most recent call last):
  File "c:/docume~1/master1/locals~1/temp/tmplp9jqf.nl", line 254, in ?
    nanotube = createPerfectNanotubeAsTwoProbe (n,m,1,(element1,element2),aCC)
  File "c:/docume~1/master1/locals~1/temp/tmplp9jqf.nl", line 232, in createPerfectNanotubeAsTwoProbe
    electrode = createNanotubeAsPAC (n,m,elec_reps,elements,bondlength)
  File "c:/docume~1/master1/locals~1/temp/tmplp9jqf.nl", line 187, in createNanotubeAsPAC
    elements = myTube.siteCount()*[elements[0],]+myTube.siteCount()*[elements[1],]
AttributeError: PhysicalQuantity instance has no attribute '__getitem__'
Terminated Abnormally

9
Scripts, Tutorials and Applications / Re: Exporting electron density etc to XYZ file for plotting in other software
« on: February 23, 2009, 08:05 »
Thanks.

10
Scripts, Tutorials and Applications / Re: Exporting electron density etc to XYZ file for plotting in other software
« on: February 22, 2009, 20:06 »
Hi again. Thanks for yur post.
When I extract the real space electron density, I get 126 z-coordinate points. How can I increase this number in simulation, i.e. how can we increase the number of mesh in the z-axis?
Maresh

11
General Questions and Answers / Re: Check parallel performance
« on: February 21, 2009, 08:13 »
Hi friends, I tried the (5,5) CNT simulation sent by Anders Blom. I see that the simulation file, there are 64 C atoms in the scattering region with 16 C atoms in the electrode. Unit cell of a (5,5) CNT has 20 atoms as VNL shows. How did you construct this simulation file? With 4 unit cells? Moreover, how can we construct a two-probe system from another CNT i.e. how can we specify the electrode atoms and electrode unit cell? Thanks...

12
Scripts, Tutorials and Applications / Re: Exporting electron density etc to XYZ file for plotting in other software
« on: February 19, 2009, 16:14 »
Hello Nordland, vey thanks but  I tried the new script but it still gives the x coordinate first :( Can you post it again please ? :)

13
Scripts, Tutorials and Applications / Re: Exporting electron density etc to XYZ file for plotting in other software
« on: February 19, 2009, 08:01 »
Dear sirs, I tried to modify the script export3d in order to make it write the z-coordinate first like

z(Bohr)     x(Bohr)     y(Bohr)    Value
--------------------------------------
0               0              0           some value
0               0.00121     0           some value
0               0.00124     0           some value


......

I could not make it work. Could you help me how to modify the script to do this?

Maresh

14
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

15
General Questions and Answers / Re: How to optimize two-probe
« on: February 9, 2009, 19:45 »
Thank you.

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