Topics

16

General Questions and Answers / Hückel convergence in 0 steps

« on: August 31, 2011, 16:11 »

When calculating a perfect infinite CNT, using the Hückel method (defaults + cerda_graphite_basis) I get (here a (6,0) CNT as example):

Code

+------------------------------------------------------------------------------+
| Density Matrix Report                        V_H         DM        DD        |
+------------------------------------------------------------------------------+
|   0   C   [  8.400 ,  6.050 ,  2.842 ]    0.00000 Ha   4.00001   0.00001     |
|   1   C   [  8.085 ,  7.225 ,  3.552 ]    0.00000 Ha   4.00000  -0.00000     |
|   2   C   [  8.400 ,  6.050 ,  1.421 ]    0.00000 Ha   4.00001   0.00001     |
|   3   C   [  7.225 ,  8.085 ,  2.842 ]    0.00000 Ha   4.00000  -0.00000     |
|   4   C   [  6.050 ,  8.400 ,  3.552 ]    0.00000 Ha   4.00001   0.00001     |
|   5   C   [  8.085 ,  7.225 ,  0.710 ]    0.00000 Ha   4.00000  -0.00000     |
|   6   C   [  7.225 ,  8.085 ,  1.421 ]    0.00000 Ha   4.00000  -0.00000     |
|   7   C   [  4.875 ,  8.085 ,  2.842 ]    0.00000 Ha   4.00000  -0.00000     |
|   8   C   [  4.015 ,  7.225 ,  3.552 ]    0.00000 Ha   4.00000  -0.00000     |
|   9   C   [  6.050 ,  8.400 ,  0.710 ]    0.00000 Ha   4.00001   0.00001     |
|  10   C   [  4.875 ,  8.085 ,  1.421 ]    0.00000 Ha   4.00000  -0.00000     |
|  11   C   [  3.700 ,  6.050 ,  2.842 ]    0.00000 Ha   4.00001   0.00001     |
|  12   C   [  4.015 ,  4.875 ,  3.552 ]    0.00000 Ha   4.00000  -0.00000     |
|  13   C   [  4.015 ,  7.225 ,  0.710 ]    0.00000 Ha   4.00000  -0.00000     |
|  14   C   [  3.700 ,  6.050 ,  1.421 ]    0.00000 Ha   4.00001   0.00001     |
|  15   C   [  4.875 ,  4.015 ,  2.842 ]    0.00000 Ha   4.00000  -0.00000     |
|  16   C   [  6.050 ,  3.700 ,  3.552 ]    0.00000 Ha   4.00001   0.00001     |
|  17   C   [  4.015 ,  4.875 ,  0.710 ]    0.00000 Ha   4.00000  -0.00000     |
|  18   C   [  4.875 ,  4.015 ,  1.421 ]    0.00000 Ha   4.00000  -0.00000     |
|  19   C   [  7.225 ,  4.015 ,  2.842 ]    0.00000 Ha   4.00000  -0.00000     |
|  20   C   [  8.085 ,  4.875 ,  3.552 ]    0.00000 Ha   4.00000  -0.00000     |
|  21   C   [  6.050 ,  3.700 ,  0.710 ]    0.00000 Ha   4.00001   0.00001     |
|  22   C   [  7.225 ,  4.015 ,  1.421 ]    0.00000 Ha   4.00000  -0.00000     |
|  23   C   [  8.085 ,  4.875 ,  0.710 ]    0.00000 Ha   4.00000  -0.00000     |
+------------------------------------------------------------------------------+
|   0 E = -51.7466 dE =  8.096459e-01 dM =  5.335291e-06 dH =  0.000000e+00    |
+------------------------------------------------------------------------------+
| Calculation Converged in 0 steps                                             |
|                                                                              |
| Fermi Level  = -5.328540 eV                                                  |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
|                                                                              |
| Huckel Calculation  [Finished Wed Aug 31 15:58:53 2011]                      |
|                                                                              |
+------------------------------------------------------------------------------+

Could you give me a hint, why it stops at this point?
If we look at

Code

|   0 E = -51.7466 dE =  8.096459e-01 dM =  5.335291e-06 dH =  0.000000e+00    |

the energy difference (and also dH) are well above default tolerance. When I change the CNT structure a bit (shifting some atoms around), then there is really some convergence loop visible and dE, dM and dH go down.

17

General Questions and Answers / Obtaining the radial parts of DFT-orbitals

« on: August 18, 2011, 17:11 »

VNL-Viewer allows to inspect the radial parts of the DFT-orbitals.
Is there a hack to obtain those from within atkpython to plot them in some different way?
Thanks.

18

General Questions and Answers / Shape of Slater type orbitals

« on: August 18, 2011, 17:09 »

In the ATK Reference (http://quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/chap.atkse.html#sect1.atkse.intro) the shape of the orbitals used within the Hückel-Method is given as



Therein n, l and m are the principal, angular and magnetic qunatum numbers, respectivley:

1s :  n=1, l=0, m=0
2s :  n=2, l=0, m=0
2p :  n=2, l=1, m=-1,0,1
3s :  n=3, l=0, m=0
3p :  n=3, l=1, m=-1,0,1
3d :  n=3, l=2, m=-2,-1,0,1,2
...


The radial part R_nl(r) is given as a superposition of two (double zeta) Slater type orbitals (STOs):



The constants C1, C2, eta1, eta2 are the orbital weights and slater coefficients fitted by different authors and tabulated within the ATK-manual.

My question is now: why does the radial part depend on the angular momentum? In literature I often see STOs (here only single zeta for simplicity) of the form:

R_n(r) = N*r^(n-1)*exp(-eta*r)

with

N={ ( [2eta]^[2n+1] ) / (2n)! }^(1/2) .

The difference is the missing r^-l and a square root on some prefactors (N={...}^(1/2)).

By using the Cerda carbon graphite parameters of the 2p orbitals as an example (as given in a paper of Cerda and also in the ATK reference), I calculated the integral over Conjugate[phi]*phi  (phi being the whole orbital, including the spherical harmonics) and found out, that only by dropping the angular dependency and including the mentioned square roots, the orbitals are normalized.

Any comments would be highly recommended, as I want to plot the orbitals I'm using and I want to be sure that everything is OK.
Thanks.

19

General Questions and Answers / Some comments on the new version of VNL

« on: July 13, 2011, 16:55 »

Hallo,

I am testing the new version 11.2 of VNL (on WinXP) and have to say:
1.) It is nice to have some bonds between the atoms now.
2.) Maybe because of those bonds, the 3D output (e.g. rotating a molecule around) is very slow on my notebook, while it was quite fast at the previous versions.
3.) There could be an option to turn down the graphics quality for the purpose of previewing and playing with big structures (I know I should use a reasonable GPU anyway...)
4.) I could not find any way to totally hide the electrodes in a two-probe setup:
     a) If I uncheck Bond->Visible, only the central region bonds disappear
     b) If I uncheck Electrode1->Bulk config.->Visible, only the electrode atoms disappear but the bonds stay
     --> To summarize: I can not find a way to change the visual properties of the electrode bonds (Plots->Properties->Bonds should change the visual properties of all bonds)
5.) I have a custom builder. When I set the central region of my two-probe-setup invisible and change some parameter of the setup, it happens sometimes that the hidden atoms get visible automatically. I do not know why someone wants to hide the central region, but anyway, I would classify this behaviour as a bug.
6.) I personally would like the following feature: A small menu or whatever, where you can change the view in a controlled way (not only be dragging the mouse). Like turning the camera around a given axis by a user specified number of degrees (while keep looking at the molecule), or shifting the view along a given axis by a given distance. In principle it would be nice to be able to do everything that you can do with the mouse, also from within some menu.

Kind regards,
ziand

20

General Questions and Answers / Problem: Wrong Tcl version while plotting with atkpython (version 11.2.3)

« on: July 5, 2011, 17:49 »

When I try to plot something manually, by using atkpython 11.2.3  [Build 3085], I get the following (input and output):

Code

Atomistix ToolKit 11.2.3 [Build 3085]

In [1]: import pylab

In [2]: pylab.plot((1,2,3))
---------------------------------------------------------------------------
TclError                                  Traceback (most recent call last)

C:\Dokumente und Einstellungen\ziand\<ipython console> in <module>()

D:\Software\QuantumWise\atk-11.2.3\atkpython\lib\site-packages\matplotlib-0.99.3-py2.6-win32.egg\matplotlib\pyplot.pyc in plot(*args, **kwargs)

D:\Software\QuantumWise\atk-11.2.3\atkpython\lib\site-packages\matplotlib-0.99.3-py2.6-win32.egg\matplotlib\pyplot.pyc in gca(**kwargs)

D:\Software\QuantumWise\atk-11.2.3\atkpython\lib\site-packages\matplotlib-0.99.3-py2.6-win32.egg\matplotlib\pyplot.pyc in gcf()

D:\Software\QuantumWise\atk-11.2.3\atkpython\lib\site-packages\matplotlib-0.99.3-py2.6-win32.egg\matplotlib\pyplot.pyc in figure(num, figsize, dpi, facecolor, edgecolor, frameon, FigureClass, **kwargs)

D:\Software\QuantumWise\atk-11.2.3\atkpython\lib\site-packages\matplotlib-0.99.3-py2.6-win32.egg\matplotlib\backends\backend_tkagg.pyc in new_figure_manager(num, *args, **kwargs)

D:\Software\QuantumWise\atk-11.2.3\atkpython\lib\lib-tk\Tkinter.pyc in __init__(self, screenName, baseName, className, useTk, sync, use)

TclError: Can't find a usable init.tcl in the following directories:
    D:/Software/Python26/lib/tcl8.5 D:/Software/QuantumWise/atk-11.2.3/atkpython/lib/tcl8.5 D:/Software/QuantumWise/atk-11.2.3/lib/tcl8.5 D:/Software/QuantumWise/atk-11.2.3/atkpython/library D:/Software/QuantumWise/atk-11.2.3/library D:/Software/QuantumWise/atk-11.2.3/tcl8.5.2/library D:/Software/QuantumWise/tcl8.5.2/library

D:/Software/QuantumWise/atk-11.2.3/atkpython/lib/tcl8.5/init.tcl: version conflict for package "Tcl": have 8.5.2, need exactly 8.5.8
version conflict for package "Tcl": have 8.5.2, need exactly 8.5.8
    while executing
"package require -exact Tcl 8.5.8"
    (file "D:/Software/QuantumWise/atk-11.2.3/atkpython/lib/tcl8.5/init.tcl" line 20)
    invoked from within
"source D:/Software/QuantumWise/atk-11.2.3/atkpython/lib/tcl8.5/init.tcl"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list source $tclfile]"


This probably means that Tcl wasn't installed properly.


In [3]:

atkpython-10.8.2 works fine. Any suggestions?

21

General Questions and Answers / Back Engine exception 92 and some ather questions

« on: March 8, 2011, 11:28 »

Hallo,
I am testing the new version (still ATK 11.2.b2 in the moment, we will buy new hardware for replacing our extremly old and unreliable license server soon and ask for a 11.2.0 license after that).

1.) Are there major differences between 11.2.b2 and 11.2.0 / 11.2.r1?

2.) At the beginning of the transmission spectrum calculation, I got the following error:

** Back Engine Exception 92 : Too large a difference in calculated transmissions has been detected among processes
** Location : calculatetransmissioncoefficient.cpp:166

What could be the reason?
I have to mention that the device density matrix calculation did not converge and there were large difference density values on some atoms.

3.) As I'm often dealing with long metallic systems I am curious about the new Kerker preconditioner. The documentation there is a bit confusing to me. In the explanation of energy_q0 what do you mean with "i.e 0.5*q0*q0" ? Or "energyQ0(): Return 0.5*q0*q0".   Is enegry_q0 equal to q0 or is energy_q0 equal to 0.5*q0*q0 ?

4.) Some things about the ReferenceManual: In the DeviceCalculator sections there is no hint about the new FFT2D solver. On some pages (e.g. 97, 98, 101, ...) in the new Manual there is lots of red text that looks as it should be formatted in a different way.

22

General Questions and Answers / Problem: Fatal error in MPI_Allreduce

« on: February 11, 2011, 16:49 »

Hello,

very recently I am getting the error below. Im using ATK 10.8.2 doing a parallel calulation on 25 nodes, 1 MPI per node, 4 OpenMP threads per MPI-process. My feeling is that it is not a problem of ATK. There might be someting wrong with the network. However I post here because I would like the hear your opinion about it. (There are 2 similar topics, but they deal with some "Message truncated" error.) Thank you very much.


+------------------------------------------------------------------------------+
|                                                                              |
| Atomistix ToolKit 10.8.0                                                     |
|                                                                              |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
|                                                                              |
| Device Calculation  [Started Fri Feb 11 15:18:12 2011]                       |
|                                                                              |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
|                                                                              |
| Left Electrode Calculation  [Started Fri Feb 11 15:18:39 2011]               |
|                                                                              |
+------------------------------------------------------------------------------+

                            |--------------------------------------------------|
Calculating Eigenvalues    : ==================================================
Calculating Density Matrix : ==================================================
Fatal error in MPI_Allreduce: Other MPI error, error stack:
MPI_Allreduce(773)................: MPI_Allreduce(sbuf=0x9ff43c0, rbuf=0x2aaab80aa650, count=2205, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD) failed
MPIR_Allreduce(445)...............:
MPIC_Sendrecv(164)................:
MPIC_Wait(513)....................:
MPIDI_CH3I_Progress(150)..........:
MPID_nem_mpich2_blocking_recv(948):
MPID_nem_tcp_connpoll(1709).......: Communication error
rank 9 in job 1  chic2i38_33252   caused collective abort of all ranks
  exit status of rank 9: killed by signal 9

### JOB - END ########################################

MPD: killing mpd daemons
Fri Feb 11 15:34:18 CET 2011

### PBS - END ########################################

23

General Questions and Answers / Meaning of electrode_constraint_length

« on: February 3, 2011, 18:52 »

Hello,

could you please clarify the meaning of the electrode_constraint_length for example in: initial_density_type = NeutralAtom(electrode_constraint_length = 10.0 * Ang). The manual says: "The part of the initial density matrix that is overwritten by the electrode density matrix." The central region has to include copies of the electrodes anyway. Wouldn't it be natural to just overwrite the density of those atoms? What is the effect of different electrode_constraint_length values? (I think the effect is small, because it only infuences the initial guess, but what would be if I'd perform a non-selfconsistent calculation?)

Thank you.

24

General Questions and Answers / Timing reports after job execution

« on: February 2, 2011, 13:35 »

Hello.

When an ATK-Job is finished, there is always a timing-report. I noticed, that the sum of timings is often far below 100%.
For example:
Timing:                          Total     Per Step        %
--------------------------------------------------------------------------------
Density Matrix (EQ)     :    7445.76 s     148.92 s      17.40% |========|
Transmission Spectrum   :    4647.48 s     929.50 s      10.86% |====|
Real Space Density      :    1049.96 s       4.20 s       2.45% ||
Self-Energies           :     128.05 s       2.56 s       0.30% |
Diagonalization         :      91.14 s      18.23 s       0.21% |
Hartree Potential       :      24.08 s       0.10 s       0.06% |
Setting Density Matrix  :       2.86 s       0.57 s       0.01% |
Mixing                  :       0.09 s       0.00 s       0.00% |
Laplace Kernel          :       0.02 s       0.00 s       0.00% |
Density Matrix (NEQ)    :       0.00 s       0.00 s       0.00% |
--------------------------------------------------------------------------------
Total                   :   42802.05 s (11h53m22.05s)

After a closer look, I think that some (?) of the timing results printed at the end of a job are those from the LAST SCF-calculation while others maybe for the whole job. To clearify: There is a simple loop inside my script that does 5 repeated TransmissionSpectrum-calculations and the last calculation took 50 steps.
Density Matrix (EQ): 148.92 * 50 = 7445.76  (time spent for last calculation???)
But
Transmission Spectrum: 929.50 * 5 = 4647.48  (time spent for ALL 5 calculations???)

Could you please commtent an those numbers?

It would be nice to have a command that can be called within an ATK-script to print such a timing-report (and maybe reset the times to zero afterwards), to have multiple reports within one log-file.

Thanks.

25

General Questions and Answers / Damaged nc-file

« on: September 9, 2010, 11:21 »

Hallo,

I did several subsequent calculations and wrote results to one big nc-file. My object_id's look like this:

Code

object_id= 'angle' + str(int(angle)).rjust(2, '0')

Angle is 0.0, 1.0, ... so I get object id's like 'angle-000', 'angle-001', ...

My nc-file is very big ~4.3GB. When I wanted to read a configuration I got the following error

  File "./zipdir/NL/IO/NLSaveUtilities.py", line 252, in nlread
  File "./zipdir/NL/IO/NetCDFFile.py", line 156, in __init__
  File "./zipdir/NL/IO/NetCDFFile.py", line 369, in _read
  File "./zipdir/NL/IO/NetCDFFile.py", line 440, in _read_var_array

If a have a wrong object_id, the output of nlread is an empty array []. But not such an error.
Did you see someting like this before? Could it be related to the file-size being too large?
Normally VNL is able to quickly print the object_id's of an nc-file. But it does not work here. Is there a way to find out the object-id's manually with atkpython?
Is this file unrepairably damaged or could there be a way to still get some data out of it?

26

General Questions and Answers / Question about padding_length

« on: September 8, 2010, 20:09 »

Hallo,

recently I have made some basic testing on a Carbon dimer. I plotted the molecular spectrum (only 5 lowest states) as a function of C-C distance (see attachement: horizontal black lines are the states of a single carbon atom, dashed black line is the fermi level (which changes with C-C-distance), dotted vertical line could be the equilibrium distance). We see that the spectrum changes over the whole range and approaches the single atom spectrum (but twofold degenerate) for big distances.

In a second test, I plotted the spectrum at C-C-dist = 1.27 Ang as a function of padding_length. This gives me straight lines: no dependency. Why is this so? The default padding_length in ATK 10.8 seems to be zero. Is this right?

ATK performs a bulk calculation for molecules too. So there is a big but finite unitcell. For the carbon dimer it is:

Code

C = MoleculeConfiguration(elements=[Carbon,],cartesian_coordinates=[[0,0,0],[0,0,1]]*Ang)
Cb = C._bulkConfiguration()
coord = Cb.cartesianCoordinates()
# now coord == PhysicalQuantity([[0.77, 0.77, 0.77],[0.77, 0.77, 1.77]], Ang)

The size of that cell is not too big (1.54 Ang in x and y), compared to the C-C-dist range that I have plotted. Different padding_length should have an influence.

27

General Questions and Answers / Cu-CNT-TwoProbe refuses to converge (version 10.8)

« on: August 16, 2010, 11:05 »

Hello,

I have a very small device which I am using for testing purposes (see attached picture (2x2 unitcells in A-B-plane for visualization only, one copper and one carbon atom is marked, together with its artificial copies)). I scripted the structure manually. The electordes are made of copper (111)-planes perpendicular to the z-direction with 4 atoms per plane. I have one copy of each electrode in the center and two extra layers at the central carbon, which is a (1,1)CNT (which is no real CNT at all). This will be bigger later.

I left most of the parameters default expect the following:

Code

numAcc = NumericalAccuracyParameters(electron_temperature = 3000.0 * Kelvin, k_point_sampling = (5, 5, 100))
itCon = IterationControlParameters(damping_factor = 0.01, number_of_history_steps = 20)
left_electrode_calculator = LCAOCalculator(numerical_accuracy_parameters = numAcc, iteration_control_parameters = itCon,)
right_electrode_calculator = LCAOCalculator(numerical_accuracy_parameters = numAcc, iteration_control_parameters = itCon,)
calculator = DeviceLCAOCalculator(numerical_accuracy_parameters = numAcc,
                                  iteration_control_parameters = itCon,
                                  electrode_calculators = [left_electrode_calculator, right_electrode_calculator])

device.setCalculator(calculator)
nlprint(device)
device.update()
nlsave('Test02.nc', device, labels=['SCF_T3000_k_5_5_100'])

But it refuses to converge within 100 steps. Below is the output I got with " cat outputfile | grep 'dE' ":

Code

|   0 E = -9.28358 dE =  1.000000e+00 dH =  1.957292e+00                       |  <- Left Electrode
|   1 E =  -24.951 dE =  1.566745e+01 dH =  1.907528e+00                       |
|   2 E =  -25.092 dE =  1.409716e-01 dH =  6.698269e-02                       |
|   3 E = -24.1539 dE =  9.380961e-01 dH =  1.352402e-01                       |
|   4 E = -26.3725 dE =  2.218593e+00 dH =  2.031978e-01                       |
|   5 E = -26.0375 dE =  3.350403e-01 dH =  3.761344e-02                       |
|   6 E =  -26.053 dE =  1.554116e-02 dH =  1.293788e-03                       |
|   7 E = -26.0527 dE =  3.278675e-04 dH =  2.380394e-03                       |
|   8 E = -26.0526 dE =  9.655686e-05 dH =  2.350997e-03                       |
|   9 E = -26.0525 dE =  4.599861e-05 dH =  2.342983e-03                       |
|  10 E = -26.0525 dE =  2.811217e-05 dH =  2.339151e-03                       |
|  11 E = -26.0525 dE =  1.601581e-05 dH =  2.336802e-03                       |
|  12 E = -26.0525 dE =  1.225662e-05 dH =  2.335474e-03                       |
|  13 E = -26.0525 dE =  7.343548e-06 dH =  2.334443e-03                       |
|  14 E = -26.0525 dE =  7.625876e-06 dH =  2.333822e-03                       |
|  15 E = -26.0525 dE =  6.076573e-06 dH =  2.333187e-03                       |
|  16 E = -26.0524 dE =  5.043814e-06 dH =  2.332684e-03                       |
|  17 E = -26.0524 dE =  3.063014e-06 dH =  2.332262e-03                       |
|  18 E = -26.0524 dE =  2.385551e-06 dH =  2.332006e-03                       |
|  19 E = -26.0524 dE =  2.247365e-07 dH =  2.331799e-03                       |
|  20 E = -25.9834 dE =  6.905499e-02 dH =  2.331780e-03                       |
|  21 E = -26.0532 dE =  6.977171e-02 dH =  5.553639e-03                       |
|  22 E = -26.0383 dE =  1.490374e-02 dH =  2.506854e-03                       |
|  23 E = -26.0384 dE =  1.791781e-04 dH =  5.323370e-04                       |
|  24 E = -26.0346 dE =  3.818816e-03 dH =  5.479463e-04                       |
|  25 E = -26.0331 dE =  1.542964e-03 dH =  1.825500e-04                       |
|  26 E = -26.0328 dE =  2.212606e-04 dH =  2.140062e-05                       |
|  27 E = -26.0328 dE =  3.735856e-06 dH =  2.014998e-06                       |
|   0 E = -52.1175 dE =  1.000000e+00 dH =  8.002716e+01                       |  <- Equiv. Bulk
|   1 E = -55.3747 dE =  3.257236e+00 dH =  3.539836e+01                       |
|   2 E = -62.5345 dE =  7.159738e+00 dH =  2.484458e+01                       |
|   3 E = -65.5368 dE =  3.002383e+00 dH =  1.020375e+01                       |
|   4 E = -75.9371 dE =  1.040029e+01 dH =  6.905815e+00                       |
|   5 E = -77.6137 dE =  1.676524e+00 dH =  9.486269e+00                       |
|   6 E = -97.0482 dE =  1.943454e+01 dH =  1.526916e+01                       |
|   7 E =  -103.99 dE =  6.941399e+00 dH =  1.421917e+01                       |
|   8 E = -107.827 dE =  3.837587e+00 dH =  1.230399e+01                       |
|   9 E = -108.742 dE =  9.152131e-01 dH =  1.833487e+01                       |
|  10 E = -108.767 dE =  2.463842e-02 dH =  1.092078e+01                       |
|  11 E = -112.023 dE =  3.256113e+00 dH =  1.132742e+01                       |
|  12 E = -110.458 dE =  1.564945e+00 dH =  1.592230e+01                       |
|  13 E = -109.914 dE =  5.440599e-01 dH =  5.424236e+00                       |
|  14 E = -110.002 dE =  8.817741e-02 dH =  3.900751e+00                       |
|  15 E =  -109.62 dE =  3.827935e-01 dH =  4.127336e+00                       |
|  16 E = -109.139 dE =  4.809340e-01 dH =  2.165962e+00                       |
|  17 E = -109.734 dE =  5.956971e-01 dH =  2.356494e+00                       |
|  18 E = -109.805 dE =  7.118364e-02 dH =  3.485979e+00                       |
|  19 E = -109.908 dE =  1.021554e-01 dH =  5.150541e+00                       |
|  20 E = -110.168 dE =  2.603592e-01 dH =  4.826544e-01                       |
|  21 E = -110.408 dE =  2.397511e-01 dH =  1.881110e+00                       |
|  22 E = -110.048 dE =  3.597512e-01 dH =  2.535395e+00                       |
|  23 E = -109.552 dE =  4.960595e-01 dH =  7.478923e-01                       |
|  24 E = -109.772 dE =  2.198320e-01 dH =  2.761119e-01                       |
|  25 E = -109.983 dE =  2.116189e-01 dH =  2.909817e-01                       |
|  26 E = -110.022 dE =  3.888809e-02 dH =  2.134411e-01                       |
|  27 E = -110.059 dE =  3.632988e-02 dH =  2.336451e-01                       |
|  28 E = -110.117 dE =  5.861831e-02 dH =  2.787550e-01                       |
|  29 E = -110.108 dE =  9.665085e-03 dH =  1.978950e-01                       |
|  30 E = -110.131 dE =  2.338280e-02 dH =  7.858236e-02                       |
|  31 E = -110.121 dE =  9.874759e-03 dH =  2.802419e-02                       |
|  32 E = -110.119 dE =  1.730446e-03 dH =  2.785925e-02                       |
|  33 E = -110.119 dE =  9.733476e-05 dH =  7.508533e-03                       |
|  34 E =  -110.13 dE =  1.097536e-02 dH =  2.656777e-02                       |
|  35 E = -110.129 dE =  1.208967e-03 dH =  6.615630e-03                       |
|  36 E = -110.133 dE =  3.893389e-03 dH =  9.248499e-03                       |
|  37 E = -110.133 dE =  1.889237e-04 dH =  3.382227e-03                       |
|   0 E = -102.621 dE =  1.000000e+00 dH =  7.157121e-01                       |  <- TwoProbe
|   1 E = -102.584 dE =  3.646259e-02 dH =  3.409074e-01                       |
|   2 E = -102.274 dE =  3.098169e-01 dH =  3.312632e-01                       |
|   3 E =  -102.25 dE =  2.418133e-02 dH =  2.492674e-02                       |
|   4 E = -102.264 dE =  1.352417e-02 dH =  1.225670e-02                       |
|   5 E = -102.332 dE =  6.785265e-02 dH =  1.140780e-02                       |
|   6 E = -102.345 dE =  1.320389e-02 dH =  6.749163e-02                       |
|   7 E = -102.338 dE =  6.884866e-03 dH =  5.286386e-02                       |
|   8 E = -102.335 dE =  2.798107e-03 dH =  1.675101e-02                       |
|   9 E = -102.375 dE =  4.025102e-02 dH =  1.578997e-02                       |
|  10 E = -102.413 dE =  3.751979e-02 dH =  2.275917e-02                       |
|  11 E = -102.429 dE =  1.652063e-02 dH =  5.412494e-02                       |
|  12 E = -102.489 dE =  6.002332e-02 dH =  6.115327e-02                       |
|  13 E = -102.507 dE =  1.729930e-02 dH =  1.882245e-02                       |
|  14 E = -102.608 dE =  1.017362e-01 dH =  1.453195e-02                       |
|  15 E = -102.487 dE =  1.217324e-01 dH =  4.059554e-02                       |
|  16 E = -102.575 dE =  8.794406e-02 dH =  3.813336e-02                       |
|  17 E = -102.285 dE =  2.892916e-01 dH =  4.278893e-02                       |
|  18 E = -102.166 dE =  1.192052e-01 dH =  4.539961e-02                       |
|  19 E = -102.196 dE =  2.971796e-02 dH =  4.290032e-02                       |
|  20 E = -101.991 dE =  2.053542e-01 dH =  3.926788e-02                       |
|  21 E = -102.628 dE =  6.375890e-01 dH =  3.400972e-02                       |
|  22 E = -103.718 dE =  1.089482e+00 dH =  4.566194e-02                       |
|  23 E = -103.083 dE =  6.348282e-01 dH =  1.873589e-01                       |
|  24 E = -102.153 dE =  9.296264e-01 dH =  7.185801e-02                       |
|  25 E = -102.056 dE =  9.735942e-02 dH =  6.939121e-02                       |
|  26 E = -100.228 dE =  1.827633e+00 dH =  6.461525e-02                       |
|  27 E = -99.9976 dE =  2.305169e-01 dH =  3.685884e-01                       |
|  28 E = -100.314 dE =  3.161853e-01 dH =  3.695522e-01                       |
|  29 E =  -101.36 dE =  1.046606e+00 dH =  2.896509e-01                       |
|  30 E = -101.363 dE =  2.479714e-03 dH =  1.283334e-01                       |
|  31 E = -101.324 dE =  3.864634e-02 dH =  1.472880e-01                       |
|  32 E = -101.458 dE =  1.334152e-01 dH =  1.493884e-01                       |
|  33 E = -102.228 dE =  7.706878e-01 dH =  1.339231e-01                       |
|  34 E = -102.342 dE =  1.133917e-01 dH =  1.048693e-01                       |
|  35 E = -102.721 dE =  3.792269e-01 dH =  1.042257e-01                       |
|  36 E = -103.016 dE =  2.954290e-01 dH =  1.152679e-01                       |
|  37 E = -103.013 dE =  3.582533e-03 dH =  1.341734e-01                       |
|  38 E = -103.031 dE =  1.777184e-02 dH =  1.304675e-01                       |
|  39 E = -103.013 dE =  1.746905e-02 dH =  1.330147e-01                       |
|  40 E = -102.942 dE =  7.090189e-02 dH =  1.315609e-01                       |
|  41 E = -102.941 dE =  1.088833e-03 dH =  1.242441e-01                       |
|  42 E =   -102.9 dE =  4.090990e-02 dH =  1.240422e-01                       |
|  43 E = -102.896 dE =  4.641878e-03 dH =  1.179475e-01                       |
|  44 E = -102.983 dE =  8.695819e-02 dH =  1.193143e-01                       |
|  45 E = -102.818 dE =  1.648690e-01 dH =  1.258797e-01                       |
|  46 E = -102.707 dE =  1.106669e-01 dH =  1.138266e-01                       |
|  47 E = -102.636 dE =  7.069018e-02 dH =  1.105154e-01                       |
|  48 E = -102.569 dE =  6.743514e-02 dH =  1.084540e-01                       |
|  49 E = -102.065 dE =  5.042223e-01 dH =  1.077418e-01                       |
|  50 E = -102.279 dE =  2.145969e-01 dH =  1.076242e-01                       |
|  51 E =  -102.34 dE =  6.102456e-02 dH =  1.032777e-01                       |
|  52 E = -101.539 dE =  8.014810e-01 dH =  1.032364e-01                       |
|  53 E =  -101.62 dE =  8.083190e-02 dH =  1.447540e-01                       |
|  54 E = -101.042 dE =  5.775699e-01 dH =  1.281750e-01                       |
|  55 E = -100.581 dE =  4.612885e-01 dH =  2.054891e-01                       |
|  56 E = -101.522 dE =  9.411875e-01 dH =  2.758580e-01                       |
|  57 E =  -102.04 dE =  5.181671e-01 dH =  1.312995e-01                       |
|  58 E = -101.189 dE =  8.508337e-01 dH =  1.145268e-01                       |
|  59 E = -100.577 dE =  6.119079e-01 dH =  1.904290e-01                       |
|  60 E = -101.524 dE =  9.467545e-01 dH =  2.782521e-01                       |
|  61 E = -101.686 dE =  1.623138e-01 dH =  1.343176e-01                       |
|  62 E = -102.107 dE =  4.207239e-01 dH =  1.297906e-01                       |
|  63 E = -101.178 dE =  9.294024e-01 dH =  1.146502e-01                       |
|  64 E = -101.892 dE =  7.140627e-01 dH =  1.940070e-01                       |
|  65 E = -102.334 dE =  4.424037e-01 dH =  1.172509e-01                       |
|  66 E = -102.306 dE =  2.852777e-02 dH =  1.142363e-01                       |
|  67 E =  -102.21 dE =  9.591331e-02 dH =  1.130270e-01                       |
|  68 E = -102.284 dE =  7.386085e-02 dH =  1.134358e-01                       |
|  69 E = -101.687 dE =  5.967967e-01 dH =  1.138563e-01                       |
|  70 E = -100.917 dE =  7.699771e-01 dH =  1.402786e-01                       |
|  71 E = -100.626 dE =  2.911824e-01 dH =  2.284667e-01                       |
|  72 E = -100.802 dE =  1.761745e-01 dH =  2.682293e-01                       |
|  73 E = -100.672 dE =  1.302223e-01 dH =  2.311967e-01                       |
|  74 E =  -100.75 dE =  7.836917e-02 dH =  2.601875e-01                       |
|  75 E =  -100.78 dE =  3.001792e-02 dH =  2.411524e-01                       |
|  76 E = -100.817 dE =  3.747257e-02 dH =  2.382292e-01                       |
|  77 E = -100.878 dE =  6.017445e-02 dH =  2.316780e-01                       |
|  78 E = -100.832 dE =  4.595723e-02 dH =  2.216465e-01                       |
|  79 E = -100.945 dE =  1.134485e-01 dH =  2.312301e-01                       |
|  80 E = -101.031 dE =  8.574788e-02 dH =  2.110932e-01                       |
|  81 E = -100.945 dE =  8.641087e-02 dH =  2.001982e-01                       |
|  82 E = -100.875 dE =  6.974777e-02 dH =  2.150934e-01                       |
|  83 E = -100.986 dE =  1.109005e-01 dH =  2.248064e-01                       |
|  84 E = -101.515 dE =  5.293752e-01 dH =  2.057519e-01                       |
|  85 E = -101.642 dE =  1.274513e-01 dH =  1.434845e-01                       |
|  86 E = -101.554 dE =  8.890799e-02 dH =  1.384801e-01                       |
|  87 E = -101.888 dE =  3.340234e-01 dH =  1.467488e-01                       |
|  88 E =  -102.02 dE =  1.323257e-01 dH =  1.231425e-01                       |
|  89 E =  -102.39 dE =  3.698263e-01 dH =  1.205212e-01                       |
|  90 E = -101.968 dE =  4.215551e-01 dH =  1.171929e-01                       |
|  91 E = -101.973 dE =  5.219843e-03 dH =  1.238743e-01                       |
|  92 E = -101.957 dE =  1.681175e-02 dH =  1.216673e-01                       |
|  93 E = -101.981 dE =  2.420225e-02 dH =  1.222801e-01                       |
|  94 E = -102.066 dE =  8.529214e-02 dH =  1.212431e-01                       |
|  95 E = -101.894 dE =  1.721380e-01 dH =  1.177741e-01                       |
|  96 E = -101.491 dE =  4.031971e-01 dH =  1.261367e-01                       |
|  97 E = -101.604 dE =  1.130753e-01 dH =  1.566322e-01                       |
|  98 E = -102.052 dE =  4.485234e-01 dH =  1.396589e-01                       |
|  99 E = -101.873 dE =  1.790571e-01 dH =  1.193218e-01                       |  <- Did not converge!

I also tried

Code

numAcc = NumericalAccuracyParameters(electron_temperature = 1000.0 * Kelvin, k_point_sampling = (10, 10, 100))

with default iteration control and left it running over the weekend and it did not converge within >450 steps. The total energy more or less fluctuates up and down.

1.) Is the reason for the non-convergence related to the unrealistic structure?
2.) What are reasonable parameters for such a copper-carbon system (maybe with a more reasonable CNT)? What should I change according to the defaults (especially for saving computation time without too much accuracy loss)? --> With a bigger (diameter) CNT and a good spacing, I need LOTS of copper atoms  so I can not afford to do extensive parameter space searches to find the best speed/accuracy combination.
3.) How much can I reduce the numbers of k-points kx and ky when I go to bigger unitcells (more copper atoms in the A-B-plane)?

Thank you very much for some hints!

28

Installation and License Questions / Error when installing ATK 10.8.0

« on: July 28, 2010, 19:01 »

Hallo,

when I tried to install ATK 10.8 (atk-10.8.0.5054-windows.exe) on Windows XP, a strange error appeared. The Installation process was nearly finished when the attached message appeared (see vcredist_error.png).

Before the installation I downloaded atk-10.8.0.5054-windows.exe to my local home directory, at drive C: and I want to intsall it to D:\Software\Quantumwise\atk-10.8.0 which is also on a local drive.

Another strange thing: After I cancelled the installation, there was a cryptic folder D:\04fcc5f34a9040a95a3fe3a679 with files inside that sound like they have something to do with this vcredist stuff (like some eula-texts, some dlls, vc_red.cap, vcredist.bmp, and others).

Anyway, I will mostly use the linux version (which I try to install next), so I just write this topic to help you fixing what looks like a bug.