Messages

796

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

« on: December 21, 2008, 23:23 »

It is my experience that one of the lattice types that is notorious hard to perform good calculations of the lattices constants on
is the semi-conducting wurtzite crystals. Again I have tryed only with the default parameters to see how good the agreement is between experimental values
and calculation.

# ----------------------------------------
# Lattices parameters (Hexagonal)
# ----------------------------------------
# A = 3.20426776283 Ang
# C = 5.21758120909 Ang
# ----------------------------------------
# Fractional coordinates
# -----------------------------------------
# Index  Element  x (frac)   y (frac)   z (frac)
#    0      Ga       0.333378051061      0.666729233831       0.0040187886993
#    1      Ga       0.666698321157      0.333359730274       0.504110187473
#    2       N        0.333371154227      0.66669569163         0.380881963248
#    3       N        0.66671438049        0.333401955497       0.880886063456

The experimential values are A = 3.18 Ang, C = 5.1660 Ang and U = 0.385.
The errors for A is 0.7%, and the errors for C is 1%,  and for U is also 1%

Again this is done using the default parameters, it can properly be done even better if the parameters are tuned to
give better results for GaN.

797

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

« on: December 21, 2008, 23:14 »

I have applied this functionality on Si(fcc) to see how good agreement, you can get by using only the default parameters
of ATK, between the calculated lattice constant and the experimental value.

# ----------------------------------------
# Lattices parameters (FaceCenteredCubic)
# ----------------------------------------
# A = 5.41146687312 Ang

The experimental value is 5.4306 Ang, and therefore the errors is only 0.3%! and that is using only default parameters!
I have attached the script for reproducing these results ( as well the results )

798

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

« on: December 21, 2008, 23:09 »

Hey everyone.

I have created a script for calculating the approximative stress on the unitcell for bulk crystal. I have combined this
with the relaxation module that comes with ATK, and tries to use the same interface as the one official included.

Given a bulk configuration and method to be used, it will first optimized the internal structure of the unitcell according to
the forces on the atoms, and then it will calculate the approximative stress on the unitcell, and scale the unitcell according to
the stress. It will then calculate the optimized internal geometry again, and calculate the stress again and repeat this cycle until
all the forces and stress are below a certain threshold.

Normally the fastest way to calculate the optimized geometry for bulk configuration in ATK is using the equation of state,
however for more complex systems like wurtzite ZnO, it requires alot of calculations! In these cases I think this script is
superior, however for simple systems like Si(FCC) the equation of states is properly better.

However when the goal is to determine the effect of pressure and strain on the unitcell on the band gap etc, it is important that the unitcell
is in equilibrium, and therefore I find this script quite usefull.

The usage is pretty straight forward - download this script and use it in the following way:

from stress_optimizers import *
....
optimized_conf = calculateOptimizedBulkConfiguration(configuration,
                                                                                         method,
                                                                                         runtime_parameters,
                                                                                         geometric_optimization_parameters,
                                                                                         stress_tolerance = 5.0e-3*Units.eV/Units.Ang**3,
                                                                                         maximum_iterations = 100)

• The configuration is the bulk configuration to be optimized.
• The method is the KohnShamMethod to be used for this optimization.
• The runtime parameters for control the verbosity and checkpoint file.
• The geometric_optimization_parameters is the ATK geometric optimization parameters for the forces.
• The stress tolerance thresshold for the optimization - default 5.0e-3 ev/Ang**3
• Maximum iterations is the maximum number of iterations of the unitcell optimization.

Feel free to use.

Updated 1:
Updated the script to correctly support cells where the conventional cell and the primitive cell is not identical.

Updated 2:
Updated with version that are MPI safe and allows the user to constrain atoms.

799

General Questions and Answers / Re: How to make a model from other soft

« on: December 21, 2008, 19:54 »

And by the way do you have access to the newest version of VNL?

800

General Questions and Answers / Re: How to make a model from other soft

« on: December 21, 2008, 19:30 »

I am not sure there exist any other program for building nanowires,
but it is possible to build structures in external programs and input them into VNL.

However I have made a python builder for atomic wires, that can create defects and strains,
if it has any value for you, I can try to find it.

801

Scripts, Tutorials and Applications / Re: How to apply a force on the bulk system

« on: December 19, 2008, 01:46 »

It depends on what you want to study - if you want to see how the band gap for instance behave under pressure,
you could just make two calculations with very close lattice constants and then compare the difference in energy bandgap
to determinethe stress.

However if you want strain or stress analysis it requires some thing and somre sparetime.

802

General Questions and Answers / Re: the NLTypeError and how to find the bandgap??

« on: December 18, 2008, 14:40 »

Hej Rosen.

You can either perform a bulk calculation of the twoprobe system as described here (Equivalent Bulk Calculation of TwoProbe) and the use my script for finding the bandgap.

However if it is a molecular junction you are modelling, then I suggest making a seperate calculation of the molecule alone, and use the molecular spectrum to determine the band gap.

803

General Questions and Answers / Re: the NLTypeError and how to find the bandgap??

« on: December 18, 2008, 14:33 »

Hey Rosen.

I have posted a script for calculating the band gap in bulk systems.
You can find it here - ( Band gap for bulk systems )

For molecule it is straight forward, you simply perform a calculation on the desired molecule, and
calculate the molecular spectrum. The substract the first positive energy from the last negative and you get the homo-lumo:

molecular_energy_spectrum = calculateMolecularEnergySpectrum(self_consistent_calculation = scf)
nlPrint(molecular_energy_spectrum)

For the H2 molecule this gives the following output:

# -----------------------------------------------------------------------------
# Energy Spectrum
# -----------------------------------------------------------------------------
# Energy (eV)
       -10.17
         2.84
         8.41
        12.92
        12.92
        16.42
        31.75
        32.56
        32.56
        70.26

So in this case the band gap is 2.84 - (-10.17) = 13.01 eV.

804

Scripts, Tutorials and Applications / Script for calculate the bandgap.

« on: December 18, 2008, 14:24 »

If you want to calculate the bandgap of a semi-conductor or an insulator I have created a small script
that does it for you and I have attached it to this post.

Simple perform a calculation, and store the results in a NetCDF file,
and edit the script bandgap.py to point at this netcdf file, and the run it as normal:
atk bandgap.py

It will produced the following output ( based on ZnSe calculation ):

Band Gap =  1.18165139396 eV

For test purposes I have also attached the script for performing calculation on znse

Edit:
Updated the scripted in a slight faster version, but it also calculates the indirect band gap now.

805

Scripts, Tutorials and Applications / Re: Script for calculating the atomization energies of molecule.

« on: December 18, 2008, 11:22 »

I also did it for a calculation for Acetylene (C2H2) and compare the values to Blaha et al.

LDA.PZ     =  20.2639146361 eV
GGA.PBE    =  18.5128556649 eV
GGA.revPBE =  18.2398891734 eV

The all-electron calculation gives 17.9944 and reports a 17.5608 for the experimental value.

806

General Questions and Answers / Re: the NLTypeError and how to find the bandgap??

« on: December 18, 2008, 09:33 »

The reason for the error is that the system has converged to some unphysical state.
This is either a geometry issue or insufficient parameters. Perhaps if you posted your
script, I could help in trying to fix this issue.

Regarding the band gap - is it a molecule or is it bulk you are trying to determine the band gap in?

807

Scripts, Tutorials and Applications / How to install ASE in ATK 2008.10

« on: December 18, 2008, 00:28 »

For those experts, that want to use ASE inside ATK 2008.10, I have written a small guide for installation of ASE into ATK 2008.10.
It is very straight forward, it requires 3 shell commands and you need to insert a small piece of code into the setup.py of ASE.

Use at own risk - but it should be risk-free.

0) Download and unpack ASE from (Atomic Simulatoin Environment)
1) Execute in a shell "mkdir -p PATH_TO_YOUR_ATK/lib/python2.4/config"
2) Execute in a shell "touch PATH_TO_YOUR_ATK/lib/python2.4/config/Makefile"
3) Enter the unpacked ASE directory and edit the file setup.py - Go to line 11 where it writes "import sys".
    Insert the following line "sys.argv = sys.argv[1:]" on line 12. Save and exit.
4) Now install just like your would normally "ATH_TO_YOUR_ATK/bin/atk setup.py install"

And now you can start up ATK and write from ase import * and you are ready to use ASE from within ATK.

Note:
   Other similar python packages can be installed in the exact same way!

808

Scripts, Tutorials and Applications / Re: Script for calculating the atomization energies of molecule.

« on: December 17, 2008, 23:59 »

For the methane case using default parameters I found the following:

LDA.PZ = 20.622076671 eV
GGA.PBE = 18.9564183782 eV
GGA.revPBE = 18.7426438569 eV

The experimental value is 18.16 eV and Bhala et al gets it to be 18.21 eV.
Again the error is only around 3-4%, however it is clear that you must use the revPBE functional in order to get good atomization energies as the error for LDA is in the order of 20%!

Please feel free to post your own atomization energy calculations!

809

Scripts, Tutorials and Applications / Re: Script for calculating the atomization energies of molecule.

« on: December 17, 2008, 23:57 »

I did a calculation of the atomization energy of a Hydrogen molecule (H2).
I got the following values for the atomization energy of the molecule using default parameters.

LDA.PZ = 4.79218961857 eV
GGA.PBE = 4.47776121909 eV
GGA.revPBE = 4.50626999466 eV

According to Blaha et al, the all-electron calculation gives 4.54 eV.
Futhermore I found this experimental value to be 4.7 eV, so I think it is quite close.

I have attached the script to perform the calculation.

810

Scripts, Tutorials and Applications / Script for calculating the atomization energies of molecule.

« on: December 17, 2008, 23:54 »

Hey everyone.

I just wanted to share with you a script that I made for calculating the atomization energy of molecules using NanoLanguage.
You can use the script either by copying the code directly into your own program or
 you can also just download the script and store it along your other scripts and use it by writing:

from AtomizationEnergy import *
E = calculateAtomizationEnergy(molecule, method, verbosity)

Please feel free to use and share!