Messages

16

General Questions and Answers / Re: NEB calculation help: CO migration on Cu(111)

« on: July 5, 2015, 08:28 »

In general, the reported error message means that you are using constraints on a part of the system but the positions of the constrained atoms are not exactly the same in all NEB-images. This can happen when you use the NEB creator with the IDPP or Halgren-Lipscomb method to create your initial NEB images.
However, in your system (as given in the file neb_input.py) everything looks ok, i.e. all constrained atoms have constant positions across all images. Accordingly, I could not reproduce your error message, running your file neb_input.py in ATK2014.2. Are you sure that this is the file that generated the error?

Another point, in ATK2014 there is no possibility to parallelize over the NEB images, so during the geometry optimization the images would be calculated sequentially, using 14 MPI processes for each DFT calculation. Parallelization over the NEB images will be available in ATK2015.

"This can happen when you use the NEB creator with the IDPP or Halgren-Lipscomb method to create your initial NEB images. "

this is the reason.
When I create initial NEB images with linear method,
the calculation goes one well. No errors.


Thanks for your help.

17

General Questions and Answers / Re: NEB calculation help: CO migration on Cu(111)

« on: July 1, 2015, 13:26 »

In general, the reported error message means that you are using constraints on a part of the system but the positions of the constrained atoms are not exactly the same in all NEB-images. This can happen when you use the NEB creator with the IDPP or Halgren-Lipscomb method to create your initial NEB images.
However, in your system (as given in the file neb_input.py) everything looks ok, i.e. all constrained atoms have constant positions across all images. Accordingly, I could not reproduce your error message, running your file neb_input.py in ATK2014.2. Are you sure that this is the file that generated the error?

Another point, in ATK2014 there is no possibility to parallelize over the NEB images, so during the geometry optimization the images would be calculated sequentially, using 14 MPI processes for each DFT calculation. Parallelization over the NEB images will be available in ATK2015.

Thanks for your reply.
1.
I run the script like "mpiexe -n 14 atk14 input.py > out.log"
The script can run for about one hour, and the stopped. I am sure that is the error message.

why I use 14 processes, that is the tutorial said so. I do not know atk14 can not Parallelization over the NEB images.
2.
You finish the calculation with my input file ?
I suggest you set the "Max_force = 0.2" in the input file ( in order to finished the calculation quickly), and run the script.


Thanks, and look forward to you reply.

18

General Questions and Answers / NEB calculation help: CO migration on Cu(111)

« on: June 30, 2015, 12:58 »

Dear Sir,

I have a prolbem when I do neb calculation with atk_14_version.

the system is CO migration on Cu(111), and four files are listed in the attachment.

ini.txt, is the initial structure,
final.txt, is the final structure,
neb_input.txt, is the calculation file generated by ATK neb toolbox,
error.txt, is the error file.

there are seven images in the neb calculation, so I use "mpiexe -n 14 input.py > out.log" to do the calculation.
the calculation is stopped after a few minites.
I check the error message, but I can not solve the problem by myself.

could you have a check for the input file ?
and I want to know what's wrong with my input file.

Thanks!

19

General Questions and Answers / Re: Optimization and Total energy calculation with " did not converge"

« on: June 26, 2015, 14:03 »

Thanks for your reply.
Next, I do as you said.

The optimized structure may or may not be ok if it is based on minimizing forces from a non-converged Kohn-Sham Hamiltonian. The only way you can know for sure if the structure is ok is to get the forces from a well converged calculation.

I suggest increasing the maximum number of allowed SCF steps and and/or changing the damping factor in the SCF loop.

The ATK manual tells you how to do this (and many other useful things):
http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.iterationcontrolparameters.html

20

General Questions and Answers / Optimization and Total energy calculation with " did not converge"

« on: June 25, 2015, 16:44 »

Dear, I have a problem when I calculate optmization and total energy calculation.

The input file is show in the attachment. In the scritp,  both optimize and total energy are calculated.
then I run the script like "atk14version input.py > out.log"

when the calculation finished,
I use:
"grep Force out.log" to check how is the optmization going,
and then I use
"grep did out.log", (here "did" means if the calculation did not converge, the word "did" will show in out.log), to check the converge.

As the attachment shows,
after six steps, the Force on each atom is less than 0.05 eV/A, and the optimization is stopped. And the the total E is calculated.

However, for each optimize step, and for Total E calculation, the SCF is not converged in 100 cycle.
so when I did "grep did out.log",  there is seven lines:
" Warning, the calculation did not converge to the requested tolerance !"

So,  my question is :
the optimizatied structure is ok ?
the number of the total energy is ok ?

If they are not ok, is there some calculation parameters should be reset to avoid the converge problem ?

Thanks

21

General Questions and Answers / Re: Question: vacancy formation energy with charged state

« on: June 24, 2015, 02:39 »

Happy to know that!

22

General Questions and Answers / Re: Question: vacancy formation energy with charged state

« on: June 23, 2015, 05:19 »

Thanks for your reply!

It is very good to see the vacancy formation energy calculation in ATK tutorial, it helps me alot.
http://quantumwise.com/publications/tutorials/item/864-calculation-of-formation-energies

However, I still do not know how to calculate the formation energy of charged vacancy.
hope to see related tutorial.

First of all, you have to understand the physics concept (or definition) of Fermi energy (or Fermi level, particularly for the Fermi energy of a semiconductor) and chemical potential of a gas molecule.

The average potential in your mentioned papers may be the average electrostatic potential.  This can be obtained by do a specific average of  the calculated ElectrostaticDifferencePotential.

The chemical potential of a gas molecule is usually  calculated based on the ideal-gas approximation.  You can refer to the following webpage, which gives nice explanation on the background of the calculation of chemical  potential of a gas molecule
https://wiki.fysik.dtu.dk/ase/ase/thermochemistry/thermochemistry.html

The Fermi energy in the formation energy of  a charged defect is indeed the chemical potential of electron reservoir. Its value in the range of valence band minimum (VBM) and  conduction band maximum (CBM) is more interesting to be studied.  The VBM could be chosen as a reference for the zero energy. This is why people plot the formation energy versus Fermi energy in the range of 0 and band gap.

23

General Questions and Answers / Question: vacancy formation energy with charged state

« on: June 20, 2015, 09:07 »

Dear Sir,

I have a problem on how to calculate the formation energy of charged vacancy.

For this problem, I checked some papers, and found How other people did before.
Follow the description in this paper: Phys. Rev. B 68, 205213
First-principles study on structures and energetics of intrinsic vacancies in SrTiO3
The formation energy could be write as that in pic_1,
It conneted with:
Total energy of defective supercell with charge q, Etotal(defect:q)
Total energy of perfect supercell, Etotal(perfect:0)
atom chemical potential, eg. Oxygen vacancy, u(oxygen)
Femi energy, Ef
Energy of Valence-band maximum of defective supercell, E(VBM)
Average Potentials at a number of atomic sites in supercell, V(av)(defect/perfect)
Total energy of perfect supercell with charge q, Etotal(perfect:q)

I don know how to get these things in ATK:
u(oxygen),  Ef, and Average Potentials at a number of atomic sites in supercell, V(av)(defect/perfect)

In my case, I want to get the oxygen (Voxygen(+1)) formation energy in MgO,
Firstly, I make supercell, and calculate the total energy of supercell. E(total, perfect,q=0),
Next, I move away one oxygen atom, and set: Charge = +1, calculate total energy of the defective supercell, get E(total, defect,q=1),
Question is :
How to get the, oxygen chemical potential, Femi energy, and Average Potentials at a number of atomic sites in supercell, V(av)(defect/perfect) ?

So, could you give me an example on how to calculate the vacancy formation energy (with charge) in ionic crystal ?


There are two more papers talked about the formation energy of vacancy  (I did not get how they did in detail)
1. Ab initio calculation of the formation energy of charged vacancies in germanium
http://www.sciencedirect.com/science/article/pii/S0921452607006953?np=y

2. First-principles calculations for defects and impurities: Applications to III-nitrides
http://scitation.aip.org/content/aip/journal/jap/95/8/10.1063/1.1682673

Thanks.

24

Future Releases / Suggestion about Page Shrink in VNL

« on: May 19, 2015, 15:54 »

Dear,
I have one suggestion about vnl.

using VNL in my PC, when I finish my script in "Editor", I click the arrow, send the script to "Builder"
at this moment, the "Builder" page will show, and the "Editor" page will Shrink to the bottom of the table.
In my view, I'd like the "Editor" page to stay just behind the "Builder" page, not shrink to the bottom of the table.

Fang Yong

25

General Questions and Answers / export DOS from large nc file; set pressure in bulk calculation in DFT engine

« on: May 3, 2015, 03:12 »

Dear, I have two question when I use atk2014.

the first one is:
my system is 500 atoms, after calculation, i want to get the total dos and  dos of single atom, the problem is I just can get the total dos, can not get the dos for single atom. (as the attachshow). there is no calculation model in the right corner, so I can not choose single atom; even I set the "atom index", I can still not get the dos for the choosed index atom.

I guess the reason is that my system is too big (because for small system, there is no problem). So, is there a script to export the dos for single atom ? like:
dos = export_dos('*.nc', atom_index(1,2,3,)) ?

the second question is:
In some other softwares, like vasp, I can optimize the bulk system with pressure (eg, 2oGPa) with DFT calculation engine. Now, it is possible to do the similar thing in atk2014? I checked the "optimizeGeometry", find no pressure.


Thanks for you time.

26

General Questions and Answers / Re: charged point defects (F center)

« on: April 24, 2015, 11:43 »

1- from the link I posted before: "The charge of the system, a charge of -1 corresponds to one extra electron."

2- the two papers state the same.
You can also check this one which deals with these defects @ MgO(100) surfaces: http://dx.doi.org/10.1021/jp7108016

Remove a neutral O atom and you will have two electron in your cell (O is O2- in MgO) which supposedly they will be trapped in the vacancy : F(0)
The whole cell is still neutral so far.
Remove one electron with the charge parameters and you will get a F+ (given that you converge to that state)
Note that depending on your basis set you may need to add a ghost atom in the center of the vacancy.

Dear Umberto Martinez
thanks for your help.

according to your reply, my understanding is:
remove one O atom, and set charge = 0, get F(0)
remove one O atom, and set charge =+1, (take away one electron form system) , get F(+)
remove one O atom, and set charge = +2, get F(2+)
Is that right ?

By the way, I find you published lot of good papers about point defects in oxides, and I am reading these papers now, and they help me alot for my own works.

Sincerely FangYong
2015-4-24

27

General Questions and Answers / Re: charged point defects (F center)

« on: April 24, 2015, 04:49 »

You can add/remove an extra charge to your bulk configuration with the charge parameter in the LCAOCalculator
http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.lcaocalculator.html

Dear, I have more questions about build the color center in bulk materials.

qeustion-1,

we can use the following script to set the charge of a system.
LCAOCalculator(
basis_set,
exchange_correlation,
charge,
numerical_accuracy_parameters,
iteration_control_parameters,
poisson_solver,
checkpoint_handler,
dynamical_matrix_parameters,
correction_extension,
algorithm_parameters,
hamiltonian_derivatives_parameters
)

the question is: the charge is positive charge or negative charge ?
eg.
charge = 1
means we put one extral electron to system, or we move one electron away from the system ?



question-2. 
how to build color center model in bulk material. (this question is more relatively to my own work)

In other people's work about MgO (see the attachment picture), the author said like follows:

"Oxygen vacancies exists in three possible variants, depending on the charge of the defect. the removal of neutral
oxygen leads to a F0 color center, with two electrons trapped in the cavity; the removal of O(-) or O(2-) ions leads
to F(+) or F(2+) centers, with only one or no electrons trapped in the cavity, respectively"

another paper said:
"color centers can also form in oxides such as MgO. When a single electron is trapped at an anion vacancy in MgO, the defect is positively charged and refferred to as F(+) center. An F center in MgO is a vacancy with two elctrons"


My understanding like this:
eg, for a 100-atom MgO supercell model,
if i want to get a F(0) center, I just need to remove one oxygen atom, nothing else to do. The " two electrons
trapped in the cavity" are from one Mg atom in the 99-atom model.
(or, I should set "charge=2" for F(0) center ?)
if i want to get a F(+) center, I need to remove one oxygen atom, and set "charge = 1", which means I put one extral
electron to the 99-atom system.
if i want to get a F(2+) center, I need to remove one oxygen atom, and set "charge = 2", which means I put two
extral electrons to the 99-atom system.
is that right?

what's more, how can I get the total number of electrons in the log file ?


looking forward to reply.

28

General Questions and Answers / Re: When publish paper, how to cite ATK software ?

« on: April 22, 2015, 15:40 »

http://quantumwise.com/publications/referencing

thanks for your reply, it helps me alot~

29

General Questions and Answers / Re: charged point defects (F center)

« on: April 22, 2015, 15:40 »

You can add/remove an extra charge to your bulk configuration with the charge parameter in the LCAOCalculator
http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.lcaocalculator.html

thanks for your reply, it helps me alot~

30

General Questions and Answers / When publish paper, how to cite ATK software ?

« on: April 22, 2015, 09:43 »

Dear,

when publish papers with ATK software, of course we have the copyright,

usually, we write the following things in paper:

 " ***** using the DFT calculation engine in ATK [ref]"

how to wirte the " ref"
is there any papers, or something, we should cite ?
I checked some papers in the publication list, did not find a good answer.


thanks