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Messages - marmotte

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16
General Questions and Answers / Re: Grimme's DFT-D2 semi-empirical model for van der Waals interactions
« on: August 28, 2013, 12:02 »
I did it using Vnl and also with new project. But still have problem with it

+------------------------------------------------------------------------------+
| NanoLanguageScript execution started                                         |
+------------------------------------------------------------------------------+
# ------------------------------------------------------------ #
# This time-limited preview version will expire on 2013-10-01. #
# ------------------------------------------------------------ #
+------------------------------------------------------------------------------+
|                                                                              |
| Atomistix ToolKit 13.8.b1 [Build a1c2415]                                    |
|                                                                              |
+------------------------------------------------------------------------------+
Traceback (most recent call last):
  File "/tmp/4479250470234043.py", line 4, in <module>
    from DFTD2 import extendedCalculatorWithDFTD2
ImportError: No module named DFTD2
+------------------------------------------------------------------------------+
| NanoLanguageScript execution finished                                        |
+----------------------------------------------------------------------------

could you please help me ?

Many thanks

17
General Questions and Answers / Re: Grimme's DFT-D2 semi-empirical model for van der Waals interactions
« on: August 28, 2013, 09:48 »
Hi Anders,
I followed your instruction and I'm getting this error

                            |--------------------------------------------------|
Calculating Kinetic Matrix : ==================================================
Traceback (most recent call last):
  File "graphene.py", line 68, in <module>
    optimizer_method=QuasiNewton(),
  File "./zipdir/NL/Dynamics/Optimization/OptimizeGeometry.py", line 211, in OptimizeGeometry
  File "./zipdir/NL/Dynamics/Optimization/OptimizeGeometry.py", line 263, in runRelaxation
  File "./zipdir/NL/Dynamics/ASEAtomsInterface.py", line 173, in get_forces
  File "./zipdir/NL/Dynamics/ASEAtomsInterface.py", line 97, in _update
  File "./zipdir/NL/Analysis/TotalEnergy.py", line 26, in __init__
  File "/home/goumris/D2-DFT/graphene/DFTD2.py", line 173, in _calculateTotalEnergy
    translation = NLEngine.Cartesian3DDouble()
AttributeError: 'module' object has no attribute 'Cartesian3DDouble'

Timing:                          Total     Per Step        %

--------------------------------------------------------------------------------

Exchange-Correlation    :       6.53 s       0.65 s      25.53% |=============|
Valence Density         :       3.73 s       0.37 s      14.59% |=======|
Real Space Integral     :       3.65 s       0.37 s      14.29% |=======|
Diagonalization         :       3.06 s       0.34 s      11.97% |======|
Constant Terms          :       0.74 s       0.74 s       2.89% |=|
Difference Density      :       0.68 s       0.07 s       2.67% ||
Basis Set Generation    :       0.48 s       0.48 s       1.88% ||
Real Space Basis        :       0.27 s       0.27 s       1.06% ||
Core Density            :       0.11 s       0.01 s       0.44% |
Neutral Atom Potential  :       0.07 s       0.07 s       0.26% |
Hartree Potential       :       0.04 s       0.00 s       0.17% |
Mixing                  :       0.04 s       0.00 s       0.17% |
Setting Density Matrix  :       0.00 s       0.00 s       0.01% |
Hubbard Term            :       0.00 s       0.00 s       0.00% |
--------------------------------------------------------------------------------

and when I want to run the script graphne.py from the VNL interface, I have also this error

+------------------------------------------------------------------------------+
| NanoLanguageScript execution started                                         |
+------------------------------------------------------------------------------+
# ------------------------------------------------------------ #
# This time-limited preview version will expire on 2013-10-01. #
# ------------------------------------------------------------ #
+------------------------------------------------------------------------------+
|                                                                              |
| Atomistix ToolKit 13.8.b1 [Build a1c2415]                                    |
|                                                                              |
+------------------------------------------------------------------------------+
Traceback (most recent call last):
  File "/tmp/1866424033809726.py", line 4, in <module>
    from DFTD2 import extendedCalculatorWithDFTD2
ImportError: No module named DFTD2
+------------------------------------------------------------------------------+
| NanoLanguageScript execution finished                                        |
+------------------------------------------------------------------------------+

Thx

18
General Questions and Answers / Re: Grimme's DFT-D2 semi-empirical model for van der Waals interactions
« on: August 27, 2013, 14:22 »
Hi Anders, Thank you  ! I think I will wait for your tutorial and may be an upgraded version because I still have problem when running these script such as "import extendedCalculatorWithDFTD2" ...please advise if we need to add/on some extra module for that.

19
General Questions and Answers / Phonon in the new version
« on: August 27, 2013, 14:19 »
Dear ATK team,

since I have installed the new version. I'm trying to test it and compare it with other tools. The new module about the phonon seems to be very slowing down. For a simple Silicon, see the output. It seems that the new ATK is considering a supercell (repetitive unit) automatically. could you please check again from your side.

+------------------------------------------------------------------------------+
| NanoLanguageScript execution started                                         |
+------------------------------------------------------------------------------+
# ------------------------------------------------------------ #
# This time-limited preview version will expire on 2013-10-01. #
# ------------------------------------------------------------ #
+------------------------------------------------------------------------------+
|                                                                              |
| Atomistix ToolKit 13.8.b1 [Build a1c2415]                                    |
|                                                                              |
+------------------------------------------------------------------------------+
+----------------------------------------------------------+
| Bulk Bravais lattice                                     |
+----------------------------------------------------------+
Type:
FaceCenteredCubic

Lattice constants:
a =     5.430600 Ang
b =     5.430600 Ang
c =     5.430600 Ang

Lattice angles:
alpha =    90.000000 deg
beta  =    90.000000 deg
gamma =    90.000000 deg

Primitive vectors:
u_1 =      0.000000      2.715300      2.715300 Ang
u_2 =      2.715300      0.000000      2.715300 Ang
u_3 =      2.715300      2.715300      0.000000 Ang

+----------------------------------------------------------+
| Bulk: Cartesian (Angstrom) / fractional                  |
+----------------------------------------------------------+
2
Bulk
Si    0.000000e+00  0.000000e+00  0.000000e+00    0.00000  0.00000  0.00000
Si    1.357650e+00  1.357650e+00  1.357650e+00    0.25000  0.25000  0.25000
+------------------------------------------------------------------------------+
|                                                                              |
| DFT Calculation  [Started Tue Aug 27 14:51:54 2013]                          |
|                                                                              |
+------------------------------------------------------------------------------+

                            |--------------------------------------------------|
Calculating Nonlocal Part  : ==================================================

                            |--------------------------------------------------|
Calculating Kinetic Matrix : ==================================================

+------------------------------------------------------------------------------+
| Checkpoint Handler                                                           |
| Filename : /tmp/checkpoint56593951.nc                                        |
| Interval : 0.5 h                                                             |
+------------------------------------------------------------------------------+

                            |--------------------------------------------------|
Calculating Eigenvalues    : ==================================================
Calculating Density Matrix : ==================================================

+------------------------------------------------------------------------------+
| Density Matrix Report                       DM        DD                     |
+------------------------------------------------------------------------------+
|   0  Si   [  0.000 ,  0.000 ,  0.000 ]    4.00006   0.00006                  |
|   1  Si   [  1.358 ,  1.358 ,  1.358 ]    3.99994  -0.00006                  |
+------------------------------------------------------------------------------+
|   0 E =  -2.1635 dE =  1.000000e+00 dH =  4.795576e-02                       |
+------------------------------------------------------------------------------+

                            |--------------------------------------------------|
Calculating Eigenvalues    : ==================================================
Calculating Density Matrix : ==================================================

+------------------------------------------------------------------------------+
| Density Matrix Report                       DM        DD                     |
+------------------------------------------------------------------------------+
|   0  Si   [  0.000 ,  0.000 ,  0.000 ]    4.00004   0.00004                  |
|   1  Si   [  1.358 ,  1.358 ,  1.358 ]    3.99996  -0.00004                  |
+------------------------------------------------------------------------------+
|   1 E = -1.88072 dE =  2.827811e-01 dH =  4.287798e-02                       |
+------------------------------------------------------------------------------+

                            |--------------------------------------------------|
Calculating Eigenvalues    : ==================================================
Calculating Density Matrix : ==================================================

+------------------------------------------------------------------------------+
| Density Matrix Report                       DM        DD                     |
+------------------------------------------------------------------------------+
|   0  Si   [  0.000 ,  0.000 ,  0.000 ]    3.99993  -0.00007                  |
|   1  Si   [  1.358 ,  1.358 ,  1.358 ]    4.00007   0.00007                  |
+------------------------------------------------------------------------------+
|   2 E = -1.89473 dE =  1.401719e-02 dH =  8.079464e-04                       |
+------------------------------------------------------------------------------+

                            |--------------------------------------------------|
Calculating Eigenvalues    : ==================================================
Calculating Density Matrix : ==================================================

+------------------------------------------------------------------------------+
| Density Matrix Report                       DM        DD                     |
+------------------------------------------------------------------------------+
|   0  Si   [  0.000 ,  0.000 ,  0.000 ]    4.00017   0.00017                  |
|   1  Si   [  1.358 ,  1.358 ,  1.358 ]    3.99983  -0.00017                  |
+------------------------------------------------------------------------------+
|   3 E = -1.88415 dE =  1.058724e-02 dH =  1.527243e-03                       |
+------------------------------------------------------------------------------+

                            |--------------------------------------------------|
Calculating Eigenvalues    : ==================================================
Calculating Density Matrix : ==================================================

+------------------------------------------------------------------------------+
| Density Matrix Report                       DM        DD                     |
+------------------------------------------------------------------------------+
|   0  Si   [  0.000 ,  0.000 ,  0.000 ]    4.00009   0.00009                  |
|   1  Si   [  1.358 ,  1.358 ,  1.358 ]    3.99991  -0.00009                  |
+------------------------------------------------------------------------------+
|   4 E = -1.88431 dE =  1.666973e-04 dH =  7.235547e-05                       |
+------------------------------------------------------------------------------+

                            |--------------------------------------------------|
Calculating Eigenvalues    : ==================================================
Calculating Density Matrix : ==================================================

+------------------------------------------------------------------------------+
| Density Matrix Report                       DM        DD                     |
+------------------------------------------------------------------------------+
|   0  Si   [  0.000 ,  0.000 ,  0.000 ]    3.99999  -0.00001                  |
|   1  Si   [  1.358 ,  1.358 ,  1.358 ]    4.00001   0.00001                  |
+------------------------------------------------------------------------------+
|   5 E = -1.88433 dE =  1.858881e-05 dH =  3.727075e-05                       |
+------------------------------------------------------------------------------+
| Calculation Converged in 5 steps                                             |
|                                                                              |
| Fermi Level  = -2.228177 eV                                                  |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
|                                                                              |
| DFT Calculation  [Finished Tue Aug 27 14:52:02 2013]                         |
|                                                                              |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Phonon: Automatically detected repetitions = [7 7 7]                         |
+------------------------------------------------------------------------------+

                            |--------------------------------------------------|
Calculating Nonlocal Part  : ==================================================

                            |--------------------------------------------------|
Calculating Kinetic Matrix : ==================================================
+------------------------------------------------------------------------------+
|                                                                              |
| DFT Calculation  [Started Tue Aug 27 14:52:54 2013]                          |
|                                                                              |
+------------------------------------------------------------------------------+

                            |--------------------------------------------------|
Calculating Nonlocal Part  : ==================================================

                            |--------------------------------------------------|
Calculating Kinetic Matrix : ==================================================

+------------------------------------------------------------------------------+
| Checkpoint Handler                                                           |
| Filename : /tmp/checkpoint56593951.nc                                        |
| Interval : 0.5 h                                                             |
+------------------------------------------------------------------------------+

                            |--------------------------------------------------|
Calculating Eigenvalues    : ==================================================
Calculating Density Matrix : ==================================================

20
General Questions and Answers / Grimme's DFT-D2 semi-empirical model for van der Waals interactions
« on: August 27, 2013, 10:28 »
Dear ATK team,

Many thanks for the new version 13.8.b1. It is really and excellent version. :D

I need to know how to setup calculations with D2-DFT ? Could you please help on how to set-up these calculations ?

Thank you

21
General Questions and Answers / about the passivation-shortcuts
« on: July 30, 2013, 12:27 »
Dear QWise developper,

I'm interested in the method of passivation iii-v nanowire, as described before the forum, for example for an InAs nanowire.

    * Build the InAs wire you want passivated. (OK)
    * Select all In atoms add the tag "In" for these atoms (shortcut needed)
    * Select all As atoms add the tag "As" for these atoms (shortcut needed)
    * Select all atoms and change the element to Si (OK)
    * Select all atoms with tag "In" and press change element to In (how to do it ?, could you please more details, or give printscreen shot of that)
    * Select all atoms with tag "As" and press change element to As (how to do it ?, could you please more details, or give printscreen shot of that)

Thank you

22
General Questions and Answers / Re: How to ripple a graphene ?
« on: May 14, 2013, 14:14 »
sounds good, thank you so much

23
General Questions and Answers / Re: How to ripple a graphene ?
« on: May 13, 2013, 13:27 »
Dear Anders,

Thank you for clarifications. I understand that by buckling the graphene ( depending on  periods and amplitude), we may have a ripple structure.

I was working on the script under "Funwith graphene" and I can understand how we can buckle a graphene by considering the cooridinate x of an atom and also two periods (in length and width in z and y directions) as well as the amplitude. I need just to have the correct expression of the : Function for converting a nanosheet coordinate into a wobbled graphene nano-sheet. From the script, we may have the phases phi (y and z directions), but for a publication, it is important for the reader to have this function.  I need you help help.

Best regards,

24
General Questions and Answers / How to ripple a graphene ?
« on: May 8, 2013, 11:00 »
Dear ATK times,

Could you please give some examples on how to obtain a rippled structure of graphene ? I have already installed the plugging and I know how to do buckling and twisting.

Thank you

25
General Questions and Answers / meaning of poalrization values
« on: April 15, 2013, 13:16 »
Hello,

could you please tell me the meaning of the output of the polarization : Pe, Pi, Pt ?

 Polarization                                                                 |
+------------------------------------------------------------------------------+
|       [  4.18743352e-02 ]                                                    |
|  Pe=  [ -2.61147429e-02 ]                                                    |
|       [ -2.25682826e-06 ]                                                    |
+------------------------------------------------------------------------------+
|       [ -3.55271368e-15 ]                                                    |
|  Pi=  [ -3.55271368e-15 ]                                                    |
|       [  0.00000000e+00 ]                                                    |
+------------------------------------------------------------------------------+
|       [  4.18743352e-02 ]                                                    |
|  Pt=  [ -2.61147429e-02 ]                                                    |
|       [ -2.25682826e-06 ]                                                    |
+------------------------------------------------------------------------------+
|       [ -1.84660694e-02 ]                                                    |
|  Pt=  [  1.84648436e-02 ] C/Meter**2                                         |
|       [  8.55220819e-03 ]                                                    |
+------------------------------------------------------------------------------+


Thanks

26
General Questions and Answers / band structure decomposition
« on: April 9, 2013, 13:54 »
Dear ATK team,

I run band-structre calculation for a simple bulk material and I'd like to know if there is a script or tool under ATK 2012.8 able to give me which band is the valence band or conduction band. Is it possible to do a decomposition of the bandstructure such as with DOS ?

Best regards,

27
General Questions and Answers / Re: dipole matrix element in Coulomb-meter (Cm)
« on: April 9, 2013, 13:21 »
Dear Anders and ATK team,

I need your help again. From these dipole matrix calculation I need to know this transition between what and what?  If the code does not give the symmetry but tells what the dipole is, for example : <Band1|Z|Band2> and <Band1|X|Band2>  ?  is it possible to know from which band ? I need to know for each relevand band.

28
General Questions and Answers / Re: dipole matrix element in Coulomb-meter (Cm)
« on: April 9, 2013, 09:31 »
One more question about the unit of dipole moment matrix. With ATK, we have e*Bohr – is this electric charge in CGS times Hydrogen Bohr Radius in Angstroms?

Thank you !

29
General Questions and Answers / Re: dipole matrix element in Coulomb-meter (Cm)
« on: April 3, 2013, 09:47 »
This works fine ! Thank you Anders

30
General Questions and Answers / dipole matrix element in Coulomb-meter (Cm)
« on: April 2, 2013, 14:07 »
Dear Developers of ATK,

is it possible to extract or save the dipole matrix element(in Coulomb-meter(Cm)) ?

best regards


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