Show Posts

This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.


Messages - Inaoton

Pages: 1 [2] 3 4 ... 8
16
General Questions and Answers / Error message
« on: May 8, 2018, 15:10 »
Hello
After one running the script for 39 minutes, I got this error. What is this error for?


Traceback (most recent call last):
  File "4x4x4 supercell-270Ha-band-toten.py", line 925, in <module>
    bulk_configuration.update()
  File "zipdir/NL/CommonConcepts/Configurations/AtomicConfiguration.py", line 1675, in update
  File "zipdir/NL/Calculators/Interfaces/BulkCalculatorInterface.py", line 273, in _update
  File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/LCAOCalculator.py", line 1340, in scfLoop
  File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/SCFLoop.py", line 263, in scfLoopHamiltonian
  File "zipdir/NL/ComputerScienceUtilities/Flowchart.py", line 660, in execute
  File "zipdir/NL/ComputerScienceUtilities/Flowchart.py", line 652, in executeBlock
  File "zipdir/NL/Calculators/Blocks/Checkpoint.py", line 43, in execute
  File "zipdir/NL/Calculators/GenericParameters/CheckpointHandler.py", line 238, in _storeIfNecessary
  File "zipdir/NL/ComputerScienceUtilities/ParallelTools/ParallelTools.py", line 1104, in wrapper
  File "zipdir/NL/IO/HDF5.py", line 387, in _repack
OSError: [Errno 2] No such file or directory

Timing:                          Total     Per Step        %

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

Diagonalization         :    1324.93 s     662.47 s      55.87% |=============|
Real Space Integral     :     504.21 s     168.07 s      21.26% |====|
Difference Density      :     185.20 s      37.04 s       7.81% |=|
Exchange-Correlation    :     100.71 s      33.57 s       4.25% ||
Neutral Atom Potential  :      90.58 s      90.58 s       3.82% ||
Real Space Basis        :      83.13 s      83.13 s       3.51% ||
Valence Density         :      42.05 s      14.02 s       1.77% |
Constant Terms          :      21.33 s      21.33 s       0.90% |
Hartree Potential       :       6.83 s       2.28 s       0.29% |
Core Density            :       2.99 s       2.99 s       0.13% |
Loading Modules + MPI   :       1.46 s       1.46 s       0.06% |
Mixing                  :       0.21 s       0.11 s       0.01% |
Basis Set Generation    :       0.06 s       0.06 s       0.00% |
Setting Density Matrix  :       0.02 s       0.02 s       0.00% |
Hubbard Term            :       0.00 s       0.00 s       0.00% |
Fixed Spins Term        :       0.00 s       0.00 s       0.00% |
--------------------------------------------------------------------------------
Total                   :    2371.58 s (39m31.58s)

** Back Engine Exception : PETSc error 270090288 of type 1 in Real_PetscCommDestroy:231: 
** Location of Exception : petsc_impl.h:90

17
General Questions and Answers / Re: Substitutional doping
« on: April 23, 2018, 12:39 »
  The reason why I asked the question is that the system under consideration consists of 96 atoms and so it takes a lot of computational time during optimization of the system which has substituted atoms if I start from the beginning (pristine) each time. I was just guessing  if it could work that way..

18
General Questions and Answers / Re: Substitutional doping
« on: April 23, 2018, 08:43 »
Hello  :)
 I have replace X atoms in the optimized pristine structure with 0.25% of  Y atoms, and then optimized it.
 Can I use the resultant optimized structure ( with 0.25% of Y)  as initial structure for 0.50% substitution by adding more  Y atoms?

19
General Questions and Answers / Re: Substitutional doping
« on: April 21, 2018, 13:00 »
Thanks Petr again . I understood

20
General Questions and Answers / Re: Substitutional doping
« on: April 21, 2018, 12:18 »
So it means that if the global charge of the system is positive because I have substituted a +2 oxidation state atom with +3 oxidation atom, the calculation is still valid??

21
General Questions and Answers / Re: Substitutional doping
« on: April 20, 2018, 19:25 »
hello again Petr
           If I substitute an atom in the structure with another atom of different Oxidation/valence state, what things I have to consider?
           1. Does the whole system needs to be neutrally charged for DFT calculations?
           2. Or Can I run the system by changing calculator settings?

22
General Questions and Answers / Re: Substitutional doping
« on: April 16, 2018, 17:04 »
Thanks Petr

23
General Questions and Answers / Substitutional doping
« on: April 16, 2018, 16:11 »
Dear ATK team
                                  I want to dope a particular atom in a crystal by some fraction. And I cannot do so in the unit cell because there is only one atom (the one I want to replace)  in the unit cell. In order to do so, I have to create a super  cell. My question is:
                                 1. Should I optimize the pristine crystal, create super cell  , dope  and then optimize it?
                                                                   "OR"
                                 2. Create a super cell and dope it, then optimize it?

24
General Questions and Answers / Trajectory for Optimize Geometry
« on: April 12, 2018, 08:05 »
Dear ATK team
                  I forgot to save the trajectory. Can a trajectory be generated using the initial and the optimized structure?

25
General Questions and Answers / Effective band structure
« on: April 9, 2018, 12:45 »
Dear ATK team
                  I have built a super cell using a relaxed unit cell. The resulting super cell reconstructs upon ion relaxation. After that I have varied the lattice constant to obtain the equilibrium lattice. Now  I want to calculate the effective band structure.
Should I  drag the the relaxed unit cell onto the effective band structure block for the calculation?

26
General Questions and Answers / Re: Solar Cell device simulation
« on: April 8, 2018, 07:51 »
Thanks Petr

27
General Questions and Answers / Re: how to acesss "how to simulate interfaces in electronics at the atomic scale"
« on: April 8, 2018, 07:46 »
    Check out this link https://docs.quantumwise.com/webinars/webinars.html

28
General Questions and Answers / Re: Solar Cell device simulation
« on: April 7, 2018, 09:37 »
 
 Each  layer has a thickness ranging from 50 to 500 nm. And primarily I want to measure the  I-V characteristics under illumination.

29
General Questions and Answers / Re: Supercell optical calculations
« on: April 7, 2018, 08:14 »
Quote from: Petr Khomyakov on April  5, 2018, 09:20
You just have to increase the number of bands, do the optical spectrum calculation, and then verify if there is any significant difference with your calculations with less bands. And you do it until the optical spectrum is converged within the tolerance you set yourself.
Yes I am getting a value of static dielectric constant which approaches the experimental value by increasing the number of bands. The number of bands has been increased to 500 for both above and below EF. Can I estimate  the required number of bands from the band structure itself?

30
General Questions and Answers / Solar Cell device simulation
« on: April 6, 2018, 17:03 »
Dear ATK team
                  I want to compute device characteristics  of the whole hybrid organic-inorganic perovskite solar cell ( consisting of 4 or more layers) in ATK. Is it possible to do so?
                 
                 

Pages: 1 [2] 3 4 ... 8