Messages

151

General Questions and Answers / Re: Ph.-DOS /transmission eigen values

« on: July 7, 2015, 09:12 »

For the Stillinger-Weber and Tersoff-potentials the default values usually work well. You don't need to specify the maximum interaction range in the DynamicalMatrix parameters.

In your case, I'd rather suspect that there is something odd with the structure. Negative frequencies mean that there are soft modes present in the system, either by atoms sitting in a local saddle point.
You could try to calculate the phonon bandstructure (without checking Accoustic sum rule and Symmetrize) and then the location of the negative frequencies might give you some hints. If the negative frequencies occur at gamma, then you might need to increase the maximum interaction range, if the negative frequencies occur elsewhere, then it is likely that your structure is not in a local minimum.

152

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

« on: July 6, 2015, 18:27 »

Just as an information, if you want to use constraints together with the Image-dependent pair potential or the Halgren-Lipscomb method in ATK2014, you can tag the group of constrained atoms using the tag name 'constrained'. Then the NEB builder will automatically recognize these tagged atoms and keep them fixed.
In ATK2015, the NEB builder will have a proper constraints widget similar to OptimizeGeometry or MolecularDynamics.

153

General Questions and Answers / Re: Ph.-DOS /transmission eigen values

« on: July 6, 2015, 15:04 »

The maximum interaction range is an optional parameter that can be set in the DynamicalMatrix analysis object. When calculating the dynamical matrix, this parameter specifies the distance around a displaced central atom (i) in which the derivative of the forces on atoms (j)  are taken into account to calculate d^2 U / dr_i dr_j .
If this parameter is not specified, the default values are used (which are the covalent distances multiplied by a fuzz factor of 4.0).  In most cases this works well, but when e.g. a classical potential is used, which has a large cutoff radius (e.g. CoulombDSF (http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.coulombdsf.html) with a default of 9 Angstrom), then the maximum interaction range parameter has to be increased to be larger than this cutoff radius, i.e. larger than 9 Angstrom, to avoid discontinuities.
You can find out if large cutoff values are used by your potential, if you send the script to the Editor with the "Script details" parameter set to "Show defaults". Then all the details of the classical potential are reflected in the script.
Which exact potential are you using?

Apart from that, negative frequencies might also occur if you are sitting exactly at a local maximum (e.g. due to symmetries in your structure). In this case, small random displacements to the atoms followed by another accurate geometry optimization should lead you to a minimum.

154

General Questions and Answers / Re: Ph.-DOS /transmission eigen values

« on: July 6, 2015, 12:39 »

Most likely, the atomic positions in your structure are not accurately optimized before calculating the PhononDOS.
If that still does not help, and if you are using classical potentials with a long range (e.g. Coulomb interactions) then you need to increase the maximum interaction range parameter to be larger than the largest cutoff distance of the potential.

155

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

« on: July 1, 2015, 16:34 »

Can you tell me if any optimization steps had been performed, before the error message popped up? Could you maybe send me the full log file?
Also, if you remove the line

device_configuration.update()

in line 1293 of your script, then the error message should pop up immediately. Do you see this?

Regarding the parallelization:
As stated in the Note at the beginning of the NEB-tutorial, the image-parallelization works only in ATK2015, not in ATK2014.

156

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

« on: July 1, 2015, 11:37 »

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.

157

General Questions and Answers / Re: Presure calculations

« on: April 14, 2015, 09:36 »

For a static system (i.e. obtained from a geometry optimization), the pressure can be calculated from the stress tensor via P = -1/3 (s_xx + s_yy + s_zz) (see attached script).
At finite temperature (i.e. in a molecular dynamics run) there would be an additional contribution of the kinetic energy: P = 2/3 E_kin/V - 1/3 (s_xx + s_yy + s_zz).

If you want to compare the enthalpy of two systems, you have to simulate them at the desired target pressure. In a molecular dynamics simulation, this can easily be achieved by employing one the NPT-methods. If you intend to obtain the structures via a geometry optimization, you have to optimize the cell until the desired target stress is reached. In ATK2015, this can easily be achieved via the target_stress parameter.

158

General Questions and Answers / Re: Bond angle distribution plot

« on: April 1, 2015, 09:04 »

There will be an bond angle analysis in the MD-Analyzer plugin in ATK-2015, which makes it possible to obtain such a plot with few clicks.
In ATK-2014, it is unfortunately only possible by writing a python script .

159

General Questions and Answers / Re: Can ATK simulate the relation between temperature and transport property(I-V)?

« on: March 26, 2015, 10:25 »

Ideally, the snapshots obtained from an equilibrium MD simulation will be sampled from canonical distribution automatically (ergodicity theorem).  Therefore, no additional weighting is necessary. The configurations with high energy and low exp(-E/kT) weight will be correspondingly rare in the MD simulation anyway. Of course, for shorter MD simulations this holds only approximately.

160

General Questions and Answers / Re: Optimization geometry at different electron temperature

« on: March 6, 2015, 19:31 »

Hi Jenny,

Unless you are explicitly interested in thermal or temperature dependent properties (e.g. thermal expansion), performing a geometry optimization at 0K and then calculating the desired properties based on the final structure is in fact the most common approach, in particular when you are interested in electronic-structure-related properties.
I see that your MD temperature is 50 K, and for this low temperature I would expect the difference to the 0K-structure to be very small.
The disadvantage of finite-temperature-structures is that there is no unique structure but rather an ensemble of configurations that you would have to average over.
If you really want to use finite temperature structures, then in your case, you would have to use the the NPTMelchionna-thermostat isntead of the NPTBerendsen-thermostat. The reason is that you have an anisotropic structure that is only periodic in z-direction, and NPTBerendsen treats everything as isotropic (cf. MD-tutorial), which probably causes your error message.
So you'd have to use something like:

method = NPTMelchionna(
    time_step=1*femtoSecond,
    reservoir_temperature=50*Kelvin,
    external_stress=1*bar,
    thermostat_timescale=100*femtoSecond,
    barostat_timescale=100*femtoSecond,
    bulk_modulus=1e+06*bar,
    initial_velocity=initial_velocity,
    mask=[[False, False, False], [False, False, False], [False, False, True]]
)

161

General Questions and Answers / Re: al2o3 cif file

« on: January 30, 2015, 09:48 »

Sorry, the file was indeed missing. It is attached to the tutorial now.

162

General Questions and Answers / Re: vacancy formation energy

« on: November 19, 2014, 16:19 »

It's essentially all in the tutorial (cf. "Summarizing the calculations").
The total energy corresponds to LaMnO3, but the contributions (in energy, forces and stress) arising from the difference, e.g. between O being simulated inside the basis set of LaMnO3-x and as a single atom, are removed. Vice versa for LaMnO3-x .
Now, you have to optimize LaMnO3 with BSSE correction and get the total energy E(LaMnO3). Then you optimize and calculate  E (LaMnO3-x) and E(O) with the same settings but without BSSE.
Then you do the same thing for O2 (with BSSE) and O (without). and get the BSSE-corrected O2 binding energy from E(O2-binding) = E(O2)-2E(O).

Finally, you combine everything as shown in Ref. 4 in the tutorial to get the vacancy formation energy:
E(vac)= E(LaMnO3-x) - E(LaMnO3) + E(O) + 1/2 E(O2 - binding) 

163

General Questions and Answers / Re: vacancy formation energy

« on: November 19, 2014, 13:19 »

You can for example calculate the vacancy formation energy as described in Ref. 4 in the BSSE-tutorial (J. Theor. Comput. Chem. 11, 1261 (2012)) using a single oxygen atom as intermediate step.
Following the tutorial, when calculating the LaMnO3 system, the LaMnO3-x part of the system would then correspond to "layer1" in the tutorial, and the oxygen atom would correspond to "layer2".
Similarly, the two oxygen atoms in the O2-molecule atom would be "layer1" and "layer2", respectively.