Messages

61

Scripts, Tutorials and Applications / Re: Improved relaxation of bulk systems using approximative stress.

« on: January 26, 2010, 13:55 »

 
This method is powerful and beautiful, but I have a problem about the relaxation of bulk system : I have a supercell bulk system, and I want to optimize only the C lattice constant and also the atom coordinates(may be we also need constrain on atom in some case) in series as this: optimize C then used the optimized C optimize the atom coordinates, and repeated the above two steps , ...... , until the C lattice constant and the atom coordinates are all well optimized ,but the a lattice constant and b lattice constant are all fixed in the whole process.

Could someone help me? Thanks a lot!

62

General Questions and Answers / Re: Why scf calculation for a two probe system only converge for the SZ basis set?

« on: January 21, 2010, 03:20 »

In the error txt, it is clear see where is the problem with the last sentence "ATKError: Exceeded maximum number of self-consistent iterations."
so please increase the Max Steps in the Iteration Control option with default number "100".

By the way ,from the scf.out file I also doubt whether the two-probe system you built was correct or not, for example, do you have enough screen layers in surface or do you have enough vacuum in the transverse plane at central region to screen the interaction of the repeated Li2Pc molecules? I suggest you check your geometry careful. And if you don't want others to see your structure,you can send your geometry to Anders Blom , if not,you can demonstrate it here,which will be convenient to see the real problem.

63

General Questions and Answers / Re: Why scf calculation for a two probe system only converge for the SZ basis set?

« on: January 20, 2010, 03:14 »

 
I think you'd better send your error message or the log file to here,which may  be easy see where is the problem.

By the way ,I think your system or the parameters that you choose in your scf may be so big which make the scf out of memory in your computer.

64

General Questions and Answers / one question about the MOLECULAR BUILDER in ATK-SE 2009.12

« on: January 15, 2010, 10:30 »

 
Hi,

In ATK-SE 2009.12 I didn't find the MOLECULAR BUILDER ,and I am puzzled about how can we conveniently build the Molecule through the function of join 、fuse and others as the early version of ATK?

65

General Questions and Answers / Re: one question about the CUSTOM BUILDER SCRIPT in ATK-SE 2009.12

« on: January 15, 2010, 09:36 »

 
Thanks a lot for your's timely reply, the new version of ATK-SE 2009.12 is so powerful, and I greatly appreciate it!
I aslo think it will be more popular!

66

General Questions and Answers / one question about the CUSTOM BUILDER SCRIPT in ATK-SE 2009.12

« on: January 15, 2010, 07:42 »

  Hi,everyone:
   First, I congratulate the released of the  new version of ATK-SE 2009.12.The new version has so many powerful tools , and I think it will be more popular.
  When I use the CUSTOM BUILDER in Custom,I have encounter one problem:
  the append file is a script that CEO Kurt Stokbro wrote in HeFei of China, it  worked well of the time in HeFei, however, when I dragged it into the CUSTOM BUILDER in Custom of ATK-SE 2009.12,it does't work, and it give the follow error message:
Traceback (most recent call last):
  File ".\zipdir\NL\GUI\Core\Runner.py", line 232, in run
  File "<string>", line 20, in configuration
AttributeError: 'BulkConfiguration' object has no attribute 'get_bravais_lattice'

Info: Script generator function does not generate a valid configuration.

how can I solve it ?

By the way,maybe we want to write some other scripts like above which has the parameters that influence the lattice constants or the coordinates of the atoms, i.e. maybe the lattice constants or the coordinates of the atoms in our own scripts are dynamic ,how can I do so that we can conveniently control the parameters in our own scripts?

67

General Questions and Answers / Re: How can we get the detailed MullikenPopulations after scf ?

« on: November 19, 2009, 09:33 »

    Thanks your detailed reply, you are so kind and clever.

In the reply you have been mentioned "running ATK interactively ", I am very interested in this and I want to know how can I running ATK interactively ?

you also mentioned "it's more tricky about array"   I want to know what are they?

Thanks a lot

68

General Questions and Answers / How can we get the detailed MullikenPopulations after scf ?

« on: November 17, 2009, 15:23 »

Hi ,every one
 

I have finished the scf, and have the convergence .nc files,but I have not save the log files (I know we can get the detailed MullikenPopulations using verbosity level 10),so how can do to get  the detailed MullikenPopulations as (0 H q = 1.00000 [ s: 1.014, s: -0.014, y: 0.000, z: 0.000, x: 0.000 ),not the H 1.14273929774 by using calculateMullikenPopulation?

 May be we only need the scattering region elements's detailed MullikenPopulations ,so I  want to know why when I ues twoprobe_configuration.scattering_elements() is not right to print but the twoprobe_configuration.elements can implement to print, in this  I am confused  that twoprobe_configuration.elements represent the  scattering_elements or all the twoprobe configuration's elements?

By the way , I want to know how can we expertly use the RETURNED OBJECT METHODS in ATK ? Could someone show me the trick?

69

Future Releases / Re: My suggestion to the next VNL version about optimization

« on: November 15, 2009, 10:16 »

First,Thanks zh's detailed reply about optimization.


2,for some reasons(for example: the suppress of the lattice coordinates in plane by substrates),so we need to fix the XY lattice coordinates and the xy coordinates of the atoms
so we need conveniently optimize the lattice constants and the coordinates of atoms in the bulk system with one direction(for example , the transport direction,i.e. Z direction) , in that process we also need  we can impose the constraint on the other directions of the lattice constants and the coordinates of atoms in the bulk system .

Not sure what the difference between "one time" and "same time" is

But, to optimize the lattice constants (efficiently) you need to compute the strain, and ATK doesn't support this today. It will, however, be added very soon.

Constraints are a completely separate issue, in a sense, and although natively ATK only support fixing atoms completely, one can, with some effort, get it to constrain the movement of the atom in certain directions (when using the steepest descent method, at least).

70

Future Releases / Re: My suggestion to the next VNL version about optimization

« on: November 12, 2009, 04:52 »

Thanks you noted

as 2) mentioned above, we need conveniently optimize the lattice constants and the coordinates of atoms in the bulk system with one direction(for example , the transport direction,i.e. Z direction) at one time,but the other directions of the lattice constants and the coordinates of atoms in the bulk system  we can impose the constraint at the same time .Could we do this in ATK now or the next version?
Because we need to this before we calculate the properties of the two-probe system.

Thanks a lot

71

Future Releases / My suggestion to the next VNL version about optimization

« on: November 11, 2009, 16:11 »

 
Hi, everyone

I think may be you need strengthen the function of the optimization in the next VNl version:
1,we can conveniently optimize the lattice constants and the coordinates of atoms in the bulk system at one time , of course we also can optimize one of them at one time;
2,we can conveniently optimize the lattice constants and the coordinates of atoms in the bulk system with one direction(for example , the transport direction,i.e. Z direction) ,but the other directions of the lattice constants and the coordinates of atoms in the bulk system  we can impose the constraint.

Wish you best and succeed!

72

General Questions and Answers / Re: How can I bulid such two-probe system as the append files?

« on: November 11, 2009, 12:14 »

  Thanks a lot.
I have learned many useful trick of ATK from you ,you are so kind and earnest to help me. Thanks agin.

Whish you good luck.

73

General Questions and Answers / Re: How can I bulid such two-probe system as the append files?

« on: November 11, 2009, 04:17 »

    you make a trick in the problem I have been mentioned,  
The  passivation problem I can solve in another way : I can passivate the molecular in the Molecular Builder ,then I append the hydrogen atoms in the Atomic Manipulator by hand through compare the relative coordinates of the middle end canbon atoms and the passivated hydrogen atoms in the Molecular Builder .

My aim is want to know how can we solve the bad alignment problem of the  Molecular Builder, because we may be do another operation(for example :  modify the configuration or the shape  of the central region in the Molecular Builder) not only the passivation ?

In short, may be we can solve this problem in two ways:

1,Could we constrain  it messes up the alignment in the  Molecular Builder when we do some operation in it ?

2,May be you can write a nice new tutorial  and a script which is about the alignment that we can alignment  the molecular through  the axis of arbitrary two atoms of the molecular and the arbitrary atom of the molecular  as the origin of the axis? It seems another question and a powerful function?

All is my  crude thought, I think you are very clever and best

74

General Questions and Answers / Re: How can I bulid such two-probe system as the append files?

« on: November 10, 2009, 09:30 »

It seem the structure is only rotated in an inconvenient way about its own axis, i.e. we don't need to realign the axis itself?

In that case, you can quite easily rotate it about the z axis in the Atomic Manipulator. The question is, of course, by what exact angle... Can you attach the electrodes too, so we can compare?

May be ,but I am not sure.may be you can drag the 55nanotube_Equivalent_bulk_molecular into the Atomic Manipulator which have a cleaving (5,5)nanotube ,then you can compare .
Th append files is only a sketch map, which is wrong of the width of the central region .


The electrodes you can get from cleaving a (5,5) nanotube in theAtomic Manipulator ,which you can adjust the width of the central region  appropriate.

And our aim is to join the molecular with two electrodes appropriateway.

75

General Questions and Answers / Re: How can I bulid such two-probe system as the append files?

« on: November 10, 2009, 09:04 »

  Thanks a lot, you are so kind and zealous .

The two electrodes and the screen layers you can get through cleaving a (5,5) nanotube  in the Atomic Manipulator.
The apppend files is the (5,5) nanotube molecular saturating with hydrogen atoms ,which is a part of central region I want to join with the electrodes.But it  rotated in a bad way, after MB.So 0....
By the way,The 55nanotube_Equivalent_bulk_molecular is get from the way I have been mentioned above.

I make a grateful acknowledgement for you to give me the trick, thanks a lot.

wish you best!