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Messages - Zexter

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1
General Questions and Answers / accuracy 32 bit/64 bit atk
« on: March 15, 2011, 14:55 »
I want to know whether running atk linux 32 bit software on a 32 bit OS would produce a different result(the places after the decimal point)when compared to running the same input in atk linux 64 bit on a 64 bit OS ......If so how to get same accuracy in 32 bit os 32 bit atk.




2
General Questions and Answers / Re: Effect of long range forces in cnt interaction
« on: March 4, 2011, 18:22 »
I will do it. thanks all

3
General Questions and Answers / Re: Effect of long range forces in cnt interaction
« on: March 3, 2011, 10:07 »
I tried with a tolerance level of 1e-6, but it doesn't show any improvement in values for the total energy of the individual nanotubes. The value of total energy of an isolated nanotube is around -15711.2 for a tolerance level of 4e-5, and the same value -15711.2 for a level of 1e-6.The same value occurs even changing the tolerance limit. So is this because I am computing the energy of isolated nanotube the tolerance limit is not having any effect

4
General Questions and Answers / Re: Effect of long range forces in cnt interaction
« on: March 3, 2011, 05:01 »
Sir I got it.I will reduce the tolerance from my current value of 4e-5 to 1e-6 and reply back.

5
General Questions and Answers / Re: Effect of long range forces in cnt interaction
« on: March 2, 2011, 11:12 »
Dear all,
    I got the following values for the total energy (without subtracting the energy from the individual nanotubes).I think the minimum value is close around 3 Angstrom matching the MD result of 3.345 Angstrom.

But one thing that intrigues me is that the total energy values of the nanotube doesn't vary much especially left to the decimal point. Is this change acceptable or is it wrong. I have attached a screen shot of my system. The total energy of the system is plotted for various separation distances between the two nanotubes.

6
General Questions and Answers / Re: Effect of long range forces in cnt interaction
« on: February 28, 2011, 10:46 »
The paper you are refering gives good idea, but still I have a doubt. The paper you mentioned deals only with planar structure, but the nanotube case, the structure is actually a hemisphere with a curvature coming into picture. But still is it possible to expect a DFT to give some correct result?

I tried to do but the atom count 0f 200 make the calculation time consuming.

7
General Questions and Answers / Effect of long range forces in cnt interaction
« on: February 23, 2011, 08:13 »
Dear all
       In a carbon nanotube with capped end facing each other the interaction is complex with a multitude of forces acting.So when calculated with DFT calculations the interaction energy shows only the energy contribution from only the non-dispersion corrected part.the contribution from the dispersion forces is missed out. Is there any possible way of including this long range dispersion forces so that I can effectively compute the interaction between the capped cnt ends.

The DFT calculations underestimate the equilibrium positions in such a configuration since the dispersion equations are not included.Is this opinion is correct?

8
General Questions and Answers / query regarding Ion and Ioff for graphene transistors
« on: February 15, 2011, 12:34 »
i plotted the curve of Id vs Vg for a graphene transistor where Id was obtained in nA units.what is this value in log terms and in normal Id i.e is it nA/nm or um...

1.i wanted to know the length dimensions(if it is nA/um/mm) over which the current(nA) is obtained...

2.i then wanted to calculate Ion and Ioff values.for this i want to know how will Vth be defined i.e in some cases its defined as the point where Id=1mA/mm...so if i get the current in nA,how will Vth be determined?

9
General Questions and Answers / van der waals force calculation in atk 11.2
« on: January 24, 2011, 11:28 »
hi all
    So with the Atk 11.2s atk classical engine we can compute with classical potentials(brenner potential).Is it possible to introduce user defined pairwise potentials say Van der waals term or so which would be of great use with a classical md tool.


10
General Questions and Answers / exporting atomic coordinates to lammps
« on: January 18, 2011, 05:58 »
Dear all
        Is there any possible ways to export atomic coordinates created in ATK exported to lammps?If so what's the procedure to do so?

11
General Questions and Answers / Re: calculation of end-end interaction energy nanotubes
« on: January 18, 2011, 05:57 »
I am computing the total energy for each distance of separation being created separately.If the problem is with the script file then it should affect the separation distance of 2.5 to 3 Angstroms also.But the positive energy comes only for separation greater than 3Angstroms.Is there any other problem that can be attributed to this conflict.The files for separation distances 2.5,3,and 3.35 Angstroms are here.

12
General Questions and Answers / Re: calculation of end-end interaction energy nanotubes
« on: January 11, 2011, 10:52 »
the files are here. I have each file made separately with varying the distance between them.

13
General Questions and Answers / Re: calculation of end-end interaction energy nanotubes
« on: January 11, 2011, 07:46 »
the minima in this configuration is hard to find.thecurve is ever decreasing and not changing the slope.

14
General Questions and Answers / Re: calculation of end-end interaction energy nanotubes
« on: December 29, 2010, 13:56 »
Hi
  I calculated the total energy of the structure with vaccum level at the edge of the central region as 0 and my gate biased at 6v,
left and right electrode at 0v
gate dielectric epsr=1
electrodes with 40 atoms 2.41 Angstroms
I have here attached my ever decreasing total energy curve. So what's strange with my system.Please help me in untangling this mystery.
my variation of distance is from 3to 4 Angstroms for which I get positive values of total energy :o :o :o
for 2.5 to 2.9 i get negative values, which is around -8500eV

So my questions are
1. What's the reason for positive values of total energy in the region 3 to 4.Is it right to get a positve energy value when the system is biased with the above configuration.
2. why my energy in 2.5 to 2.9 alone is negative.(I haven't tried below 2.5Angstroms)
3. whether applying  a bias would drive the energy to positive value of potential energy (which is unacceptable)

15
General Questions and Answers / electrode coordinates mismatch
« on: December 28, 2010, 06:37 »
Hi
 I have coordinates of the central region.Based on the central region I define the electrodes.The left electrode has no problem with it as the coordinates of my first 30 atoms make up the coordinates of my electrodes.But my right electrode shows some conflict.Here is my central region coordinates

cartesian_coordinates = numpy.array([[ 11.78410677,   8.39205339,   0.        ],
                                     [ 11.49084835,   9.77172579,   0.        ],
                                     [ 11.13628222,  10.38585234,   1.23050086],
                                     [ 10.08808008,  11.32965779,   1.23050086],
                                     [  9.44025553,  11.61808786,   0.        ],
                                     [  8.03748726,  11.76552475,   0.        ],
                                     [  7.34385124,  11.61808786,   1.23050086],
                                     [  6.12232665,  10.91284031,   1.23050086],
                                     [  5.64782455,  10.38585234,   0.        ],
                                     [  5.0741245 ,   9.09730094,   0.        ],
                                     [  5.        ,   8.39205339,   1.23050086],
                                     [  5.29325842,   7.01238098,   1.23050086],
                                     [  5.64782455,   6.39825443,   0.        ],
                                     [  6.69602669,   5.45444898,   0.        ],
                                     [  7.34385124,   5.16601891,   1.23050086],
                                     [  8.74661951,   5.01858202,   1.23050086],
                                     [  9.44025553,   5.16601891,   0.        ],
                                     [ 10.66178013,   5.87126646,   0.        ],
                                     [ 11.13628222,   6.39825443,   1.23050086],
                                     [ 11.70998227,   7.68680583,   1.23050086],
                                     [ 11.78410677,   8.39205339,   2.46100171],
                                     [ 11.49084835,   9.77172579,   2.46100171],
                                     [ 11.13628222,  10.38585234,   3.69150257],
                                     [  9.44025553,  11.61808786,   2.46100171],
                                     [   8.03748726,  11.76552475,   2.46100171],
                                     [  7.34385124,  11.61808786,   3.69150257],
                                     [  5.64782455,  10.38585234,   2.46100171],
                                     [  5.0741245 ,   9.09730094,   2.46100171],
                                     [  5.        ,   8.39205339,   3.69150257],
                                     [  5.64782455,   6.39825443,   2.46100171],
                                     [  6.69602669,   5.45444898,   2.46100171],
                                     [  8.74661951,   5.01858202,   3.69150257],
                                     [  9.44025553,   5.16601891,   2.46100171],
                                     [ 10.66178013,   5.87126646,   2.46100171],
                                     [ 11.70998227,   7.68680583,   3.69150257],
                                     [ 10.40042677,   8.88880475,   6.96812],
                                     [ 11.30777677,   8.45569475,   5.191936],
                                     [  9.51582677,   7.98203475,   7.54074],
                                     [ 11.29134677,   7.13432475,   5.48832],
                                     [ 11.39062677,   6.83183475,   4.07066257],
                                     [ 11.42394677,   9.53401475,   4.95221],
                                     [  7.72150677,   9.66815475,   7.51415],
                                     [  8.64598677,  10.61579475,   6.91579],
                                     [  8.14669677,   8.38042475,   7.81981],
                                     [  9.95586677,  10.23483475,   6.64888],
                                     [ 10.58825677,  10.63352475,   5.40304],
                                     [  7.90947677,  11.41236475,   5.949],
                                     [  8.51457677,  11.79387475,   4.75709257],
                                     [  9.88366677,  11.39586475,   4.47817257],
                                     [  6.03219677,   7.44738475,   6.97001],
                                     [  5.58782677,   8.79318475,   6.65067],
                                     [  7.28322677,   7.24547475,   7.54167],
                                     [  6.41376677,   9.87907475,   6.9168],
                                     [  6.52994677,  10.95687475,   5.94947],
                                     [  4.84106677,   8.73603475,   5.40539],
                                     [  4.95214677,   9.76732475,   4.47995257],
                                     [  5.81524677,  10.90237475,   4.75816257],
                                     [  7.66702677,   5.29566475,   6.08772],
                                     [  6.35955677,   5.50656475,   5.4904],
                                     [  8.11872677,   6.14570475,   7.09069],
                                     [  5.56009677,   6.55864475,   5.92184],
                                     [  4.82410677,   7.35499475,   4.95483],
                                     [  6.45916677,   5.20353475,   4.07273257],
                                     [  5.75485677,   5.96538475,   3.14755257],
                                     [  4.91914677,   7.06490475,   3.59846257],
                                     [ 10.36669677,   6.18659475,   6.08648],
                                     [  9.89460677,   5.29812475,   5.03836],
                                     [  9.49850677,   6.60097475,   7.09004],
                                     [  8.57462677,   4.86238475,   5.03899],
                                     [  7.82823677,   4.80552475,   3.79374257],
                                     [ 10.52758677,   5.69679475,   3.79263257],
                                     [  6.44770677,  11.30104475,   3.51245257],
                                     [  9.98296677,  11.09329475,   3.06063257]])

cartesian_coordinates1 = numpy.array([[ 11.78410677,   8.39205339,   7.27452],
                                     [ 11.49084835,   9.77172579,   7.27452],
                                     [ 11.13628222,  10.38585234,   6.04402],
                                     [ 10.08808008,  11.32965779,   6.04402],
                                     [  9.44025553,  11.61808786,   7.27452],
                                     [  8.03748726,  11.76552475,   7.27452],
                                     [  7.34385124,  11.61808786,   6.04402],
                                     [  6.12232665,  10.91284031,   6.04402],
                                     [  5.64782455,  10.38585234,   7.27452],
                                     [  5.0741245 ,   9.09730094,   7.27452],
                                     [  5.        ,   8.39205339,   6.04402],
                                     [  5.29325842,   7.01238098,   6.04402],
                                     [  5.64782455,   6.39825443,   7.27452],
                                     [  6.69602669,   5.45444898,   7.27452],
                                     [  7.34385124,   5.16601891,   6.04402],
                                     [  8.74661951,   5.01858202,   6.04402],
                                     [  9.44025553,   5.16601891,   7.27452],
                                     [ 10.66178013,   5.87126646,   7.27452],
                                     [ 11.13628222,   6.39825443,   6.04402],
                                     [ 11.70998227,   7.68680583,   6.04402],
                                     [ 11.78410677,   8.39205339,   4.81351829],
                                     [ 11.49084835,   9.77172579,   4.81351829],
                                     [ 11.13628222,  10.38585234,   3.58301743],
                                     [  9.44025553,  11.61808786,   4.81351829],
                                     [  8.03748726,  11.76552475,   4.81351829],
                                     [  7.34385124,  11.61808786,   3.58301743],
                                     [  5.64782455,  10.38585234,   4.81351829],
                                     [  5.0741245 ,   9.09730094,   4.81351829],
                                     [  5.        ,   8.39205339,   3.58301743],
                                     [  5.64782455,   6.39825443,   4.81351829],
                                     [  6.69602669,   5.45444898,   4.81351829],
                                     [  8.74661951,   5.01858202,   3.58301743],
                                     [  9.44025553,   5.16601891,   4.81351829],
                                     [ 10.66178013,   5.87126646,   4.81351829],
                                     [ 11.70998227,   7.68680583,   3.58301743],
                                     [ 10.40042677,   8.88880475,   0.3064    ],
                                     [ 11.30777677,   8.45569475,   2.082584  ],
                                     [  9.51582677,   7.98203475,   -0.26622],
                                     [ 11.29134677,   7.13432475,   1.7862    ],
                                     [ 11.39062677,   6.83183475,   3.20385743],
                                     [ 11.42394677,   9.53401475,   2.32231   ],
                                     [  7.72150677,   9.66815475,   -0.2396368237342],
                                     [  8.64598677,  10.61579475,   0.35873   ],
                                     [  8.14669677,   8.38042475,   -0.54529],
                                     [  9.95586677,  10.23483475,   0.62564   ],
                                     [ 10.58825677,  10.63352475,   1.87148   ],
                                     [  7.90947677,  11.41236475,   1.32552   ],
                                     [  8.51457677,  11.79387475,   2.51742743],
                                     [  9.88366677,  11.39586475,   2.79634743],
                                     [  6.03219677,   7.44738475,   0.30451   ],
                                     [  5.58782677,   8.79318475,   0.62385   ],
                                     [  7.28322677,   7.24547475,   -0.26715],
                                     [  6.41376677,   9.87907475,   0.35772   ],
                                     [  6.52994677,  10.95687475,   1.32505   ],
                                     [  4.84106677,   8.73603475,   1.86913   ],
                                     [  4.95214677,   9.76732475,   2.79456743],
                                     [  5.81524677,  10.90237475,   2.51635743],
                                     [  7.66702677,   5.29566475,   1.1868    ],
                                     [  6.35955677,   5.50656475,   1.78412   ],
                                     [  8.11872677,   6.14570475,   0.18383   ],
                                     [  5.56009677,   6.55864475,   1.35268   ],
                                     [  4.82410677,   7.35499475,   2.31969   ],
                                     [  6.45916677,   5.20353475,   3.20178743],
                                     [  5.75485677,   5.96538475,   4.12696743],
                                     [  4.91914677,   7.06490475,   3.67605743],
                                     [ 10.36669677,   6.18659475,   1.18804   ],
                                     [  9.89460677,   5.29812475,   2.23616   ],
                                     [  9.49850677,   6.60097475,   0.18448   ],
                                     [  8.57462677,   4.86238475,   2.23553   ],
                                     [  7.82823677,   4.80552475,   3.48077743],
                                     [ 10.52758677,   5.69679475,   3.48188743],
                                     [  6.44770677,  11.30104475,   3.76206743],
                                     [  9.98296677,  11.09329475,   4.21388743]])


cartesian_coordinates=cartesian_coordinates+numpy.array([0,0,0])
cartesian_coordinates1=cartesian_coordinates1+numpy.array([0,0,10.5651])
cartesiand=cartesian_coordinates1
cartesian_coordinates=cartesian_coordinates.tolist()
cartesian_coordinates1=cartesian_coordinates1.tolist()
elements = [Carbon,]*len(cartesian_coordinates+cartesian_coordinates1)

ccordinates=(cartesian_coordinates + cartesian_coordinates1)*Ang


my left electrode coordinates
left_electrode_coordinates = [[ 11.78410677,   8.39205339,   0.        ],
                                     [ 11.49084835,   9.77172579,   0.        ],
                                     [ 11.13628222,  10.38585234,   1.23050086],
                                     [ 10.08808008,  11.32965779,   1.23050086],
                                     [  9.44025553,  11.61808786,   0.        ],
                                     [  8.03748726,  11.76552475,   0.        ],
                                     [  7.34385124,  11.61808786,   1.23050086],
                                     [  6.12232665,  10.91284031,   1.23050086],
                                     [  5.64782455,  10.38585234,   0.        ],
                                     [  5.0741245 ,   9.09730094,   0.        ],
                                     [  5.        ,   8.39205339,   1.23050086],
                                     [  5.29325842,   7.01238098,   1.23050086],
                                     [  5.64782455,   6.39825443,   0.        ],
                                     [  6.69602669,   5.45444898,   0.        ],
                                     [  7.34385124,   5.16601891,   1.23050086],
                                     [  8.74661951,   5.01858202,   1.23050086],
                                     [  9.44025553,   5.16601891,   0.        ],
                                     [ 10.66178013,   5.87126646,   0.        ],
                                     [ 11.13628222,   6.39825443,   1.23050086],
                                     [ 11.70998227,   7.68680583,   1.23050086],
                                     [ 11.78410677,   8.39205339,   2.46100171],
                                     [ 11.49084835,   9.77172579,   2.46100171],
                                     [ 11.13628222,  10.38585234,   3.69150257],
                                     [  9.44025553,  11.61808786,   2.46100171],
                                     [   8.03748726,  11.76552475,   2.46100171],
                                     [  7.34385124,  11.61808786,   3.69150257],
                                     [  5.64782455,  10.38585234,   2.46100171],
                                     [  5.0741245 ,   9.09730094,   2.46100171],
                                     [  5.        ,   8.39205339,   3.69150257],
                                     [  5.64782455,   6.39825443,   2.46100171]]*Angstrom

my right electrode
right_electrode_coordinates = numpy.array([[  8.14669677,   8.38042475,   -0.54529],
                                     [  9.95586677,  10.23483475,   0.62564   ],
                                     [ 10.58825677,  10.63352475,   1.87148   ],
                                     [  7.90947677,  11.41236475,   1.32552   ],
                                     [  8.51457677,  11.79387475,   2.51742743],
                                     [  9.88366677,  11.39586475,   2.79634743],
                                     [  6.03219677,   7.44738475,   0.30451   ],
                                     [  5.58782677,   8.79318475,   0.62385   ],
                                     [  7.28322677,   7.24547475,   -0.26715],
                                     [  6.41376677,   9.87907475,   0.35772   ],
                                     [  6.52994677,  10.95687475,   1.32505   ],
                                     [  4.84106677,   8.73603475,   1.86913   ],
                                     [  4.95214677,   9.76732475,   2.79456743],
                                     [  5.81524677,  10.90237475,   2.51635743],
                                     [  7.66702677,   5.29566475,   1.1868    ],
                                     [  6.35955677,   5.50656475,   1.78412   ],
                                     [  8.11872677,   6.14570475,   0.18383   ],
                                     [  5.56009677,   6.55864475,   1.35268   ],
                                     [  4.82410677,   7.35499475,   2.31969   ],
                                     [  6.45916677,   5.20353475,   3.20178743],
                                     [  5.75485677,   5.96538475,   4.12696743],
                                     [  4.91914677,   7.06490475,   3.67605743],
                                     [ 10.36669677,   6.18659475,   1.18804   ],
                                     [  9.89460677,   5.29812475,   2.23616   ],
                                     [  9.49850677,   6.60097475,   0.18448   ],
                                     [  8.57462677,   4.86238475,   2.23553   ],
                                     [  7.82823677,   4.80552475,   3.48077743],
                                     [ 10.52758677,   5.69679475,   3.48188743],
                                     [  6.44770677,  11.30104475,   3.76206743],
                                     [  9.98296677,  11.09329475,   4.21388743]])
                                    
right_electrode_coordinates=right_electrode_coordinates+numpy.array([0,0,10.5651])
right_electrode_coordinates=right_electrode_coordinates.tolist()
right_electrode_coordinates=right_electrode_coordinates*Angstrom

when I use the above coordinates the error comes out as
"The last 30 atoms of the central region must match the last 30 atoms of the right electrode region. Atom 116 of the central region was C at (8.14669677 Ang, 8.38042475 Ang, 10.01981 Ang), it should have been C at (8.14669677 Ang, 8.38042475 Ang, 25.39840829 Ang)"

But still my last 30 central region  coordinates are same as my right electrode coordinates.

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