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Messages - Julian Schneider

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General Questions / Re: postprocessing analysis
« on: March 5, 2017, 20:09 »
You get an error when running the simulation, that's why the files do not show up.
The script you are using works only with VNL-versions 2015 and older.
For the 2016-version you have make a two tiny changes in the python file.
I have attached the fixed script.

Questions and Answers / Re: AKMC or KMC simulations
« on: February 28, 2017, 09:28 »
The way we calculate barriers in AMKC does not take into account temperature, as in NEB everything is calculated at 0K. Temperature only comes into play when the rate constants are calculated, which we do using the harmonic transition state theory (HTST) formalism in our HTSTEvent analysis object.

If you have a single transition for which you have calculated an NEB, and you want to study the effect of temperature on the forward and reverse rate constants of this transition, you can directly use this HTSTEvent analysis object ( see Once you have calculated and stored this analysis object, we have a LabFloor plugin called HTST Rates which calculates a variety of properties for this transition.

The script is correct, it is a small bug in the MD-functionality. We'll try and fix it as soon as possible.

For now, the workaround is to include all atoms the W-surface (i.e. also the constrained bottom atoms) into the group "substrate", as shown  in the attached script.

The script looks ok at first glance, we'll need to look into this a bit more. We'll let you know as soon as we have found the problem.

Don't think you will get the same level of accuracy with MD optimization as with DFT. Unless it's a Really GOOD classical potential which fits very well with DFT. So it's material and as a consequence parameter dependen
Actually, running an MD simulation does not mean you are using classical potentials. You can run both MD and optimization with classical potentials OR DFT (or basically any method that gives you reasonable forces).

So, if the question was if you could use MD with DFT instead of Geometry Optimization using DFT, to speed up your optimization, I would say in most cases  running an actual geometry optimization is more efficient. You could run a few steps MD simulation to reduce initial large forces, which in some tricky cases may help to converge a subsequent geometry optimization. However, in MD you have no control over the max. forces, and therefore no control over how much your final configuration deviates from the true optimized configuration, so, unless you just want to have a very coarse guess of your structure, I would suggest running an optimization before you calculate any properties via DFT.

If your question was related to using classical potentials with to relax your configuration, then it can actually make sense to run a pre-relaxation with classical potentials, but, to be in the safe side, I would at least run a DFT force calculation before calculating any properties with DFT, to check if the residual DFT-forces are sufficiently small.

i did not get LAMMPS option in the export option. but i installed LAMMPS plug in
You might have to scroll down a bit when choosing the file format to export. The LAMMPS option is normally a bit further down in the list of export options.

General Questions / Re: Combining RearFF potential with other?
« on: January 25, 2017, 10:20 »
It is currently not possible to combine ReaxFF-potentials with other potentials in ATK-Classical. We are planning to make that work in the future, though.

If you have your configuration open in the Builder, in the menu, click "File" -> "Export Configuration". Then the export dialog pops up. Here, you need to select the LAMMPS format in the lower right-hand-corner. Then you select a suitable file name and click save. The your LAMMPS data file will be saved. Note that the produced data file is only compatible with the LAMMPS atom_style atomic. If you want to use a different atom style you may have to modify the data file, e.g. by adding charges.

If you want to import your LAMMPS simulation trajectory into VNL again, you should have a look at the tutorial

Questions and Answers / Re: Exceptions.NLNotImplementedError
« on: January 17, 2017, 21:08 »
If you use the tags-parameter in the potential, the potential acts only on the tagged atoms, not on the gold atoms, which do not belong to this tagged group. Without having seen your script, I suppose in your case not all atoms belong to the tagged group 'layer1' and that means that there is no potential defined for the rest of the system. This is what the error message means.
To fix it define another Tersoff potential for the remaining part of the system (assuming this part has the tag 'layer2'):
Code: [Select]
eam_layer1 = Tersoff_Au_2012(tags='layer1')
eam_layer2= Tersoff_Au_2012(tags='layer2')
calculator = TremoloXCalculator(parameters=[eam_layer1, eam_layer2])

If this does not solve your error, please post the script that you want to run.

Support for EAM-potentials and tags is something that we plan to add hopefully soon.

Questions and Answers / Re: Youngs modulus for buckyball
« on: January 3, 2017, 10:04 »
Anders, as far as I see it, you cannot really do an optimization under external stress/pressure here, because this quantity is not well-defined for a molecule in a vacuum-padded cell, since the stress is normalized to the volume of the cell, which is arbitrary in a vacuum padded cell (unless you consider a crystal of may interacting buckyballs).

The only reasonable picture, I could think of, is that when you consider the buckyball as a kind of spherical macroscopic solid, which can be strained by clamping the two ends. Then you are right, one could approximate the stress as the sum of all local stresses, normalized by the volume of the  sphere (that is actually equivalent to what I did in the script).
But that assumption may already be a far-fetched approximation for such a microscopic molecule.

Questions and Answers / Re: Youngs modulus for buckyball
« on: January 2, 2017, 17:50 »
It is still a tricky case because enclosing it in a bulk configuration does not make it a bulk system, for which you can calculate a well-defined stress tensor.

One possibility is that you optimize the buckyball, calculate the stress, then strain the cell in one direction, calculate the stress again and then get the Young's modulus as
(stress_strained - stress_unstrained)/strain

Note that the stress is normalized to the volume of the cell, which is arbitrary, so  you have to correct the stress for the actual volume of the buckyball.
How you define that volume depends very much on what you want to do with the Young's modulus.
One could think of using the volume of a sphere with the same diameter as the buckyball, but you really need to think carefully yourself, whether this fits your application.
I have attached an example script which assumes the volume of a solid sphere.

Please remember again, that there is no real straightforward definition for the Young's modulus in your system, and we can only give you one possible auxiliary way to estimate a quantity, which could be used as a Young's modulus, but you should carefully review whether this makes sense in your application!

The case of device configurations is a bit more tricky. For normal MD and Optimization calculations, the periodic boundary conditions are only active in x- and y-direction, whereas there is no PBC in z-direction.
For NEGF-phonon-transmisson calculations, however, the z-direction is semi-periodic (similar to a DFT-device), meaning that the periodicity on both sides is given by the periodic electrodes. In practice, this is achieved by adding the atoms of the electrodes on both sides to the central regions and using this extended system to calculate the dynamical matrix of the central region. The  dynamical matrices of the electrodes are calculated as regular 3D-periodic bulk configurations.

In the ATK-Classical calculator, the boundary conditions are periodic for BulkConfiguration and a vacuum-padded cell for MoleculeConfigurations.
If you want to switch off periodic boundary conditions for a bulk-configuration in certain directions, you can increase the length of the cell vector in this direction to add a vacuum padding, which is larger than the interaction range of the potential, so that one side of the configuration does not interact with the opposite side.

If you want to impose more specialized boundary conditions, which e.g. modify the forces on the atoms (e.g. walls), you can do this using a hook function.

General Questions / Re: Polycrystal Builder
« on: December 13, 2016, 10:44 »
No, this can be any arbitrary number. This number is used to initialize the random number generator. The name "seed" might be a bit misleading here, but it does not refer to the seeds of the grains.

Questions and Answers / Re: partial charges calculation
« on: December 8, 2016, 13:07 »
The partial charges analysis in ATK just gives you the partial charges that you have defined in the classical potential for the system. If no partial charges are defined then the output will be zero (see

The only exception is if you use a ReaxFF potential. In that case the charges are calculated self-consistently, based on the charge-equilibration method (see and the output of partial charges will give you the calculated charges.

Generally, if you implement a potential from a paper, it should have partial charges defined with the definition of the potential, and you should use these.
If you want to develop your own potential, it is important that the non-Coulomb potential terms and parameters need to be chosen and adjusted to work with the chosen set of partial charges.
You normally cannot just use any arbitrary combination of partial charges and non-Coulomb potentials.
An initial guess for partial charges could be obtained e.g. from the Bader ( or Mulliken  ( charges.

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