Messages

121

General Questions and Answers / Re: Au tip electrodes

« on: November 26, 2015, 09:24 »

We also have a Tip Builder plugin. You have to download the SCAITools Addon (formerly ATK-CLASSICAL plugin) via the Addon-Manager and the Tip Builder will be available in the VNL-Builder under Builders. With this plugin you can build various kinds of STM-tips.

122

General Questions and Answers / Re: about Non-Equilibrium Momentum ExchangeType

« on: November 20, 2015, 09:05 »

No, for this technique it is generally not possible to explicitly set the temperatures in the heat source and sink regions. You can only indirectly modify the temperature difference by changing the exchange interval.

If you really want to explicitly set a temperature difference, you can invoke a NVTNoseHooverChain thermostat with two thermostatted regions, e.g. something like

NVTNoseHooverChain(initial_velocity=ConfigurationVelocities(),
                 time_step=1.0*fs,
                 reservoir_temperatures=[('heat_source' , 400.0*Kelvin), ('heat_sink', 200.0*Kelvin)]
                 )
               
where the two regions are marked by tags.
However, the total momentum will probably not be conserved in such a simulation, and your system will start drifting. To avoid this, you might need to constrain at least one atom in one of the thermostatted regions.

123

General Questions and Answers / Re: Some files do not appear in the lab floor

« on: November 10, 2015, 18:29 »

Do you have some hidden file starting with ".#" (some emacs temporary file), or something similar in your project folder?
You can find this by typing ls -a in your terminal (if you're using linux).

124

General Questions and Answers / Re: Problem about ploting temperature profile

« on: November 10, 2015, 12:58 »

The fix will be included in the ATK-2015.1 version, which will be released soon.
Unfortunately, the bug is in the backengine itself, so there is no easy workaround in ATK.
If it's an urgent matter for you, I can provide a temporary script to calculate the temperature profile for the large cell.

125

General Questions and Answers / Re: Problem about ploting temperature profile

« on: November 9, 2015, 12:44 »

Yes, I see it, as well. This is a bug. We'll fix it asap.
Thanks for pointing it out!

126

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

« on: November 5, 2015, 21:38 »

If you have imaginary frequencies at the gamma point (if you switch off ASR correction), then this is often caused by the max_interaction_range. In your case, I would not suspect the max_interaction_range in the first place, although I wouldn't completely rule out this possibility. 

127

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

« on: November 5, 2015, 13:43 »

The accoustic sum rule correction corrects the non-zero accoustic frequencies at the gamma point. However, your gamma point frequencies are all zero. The negative bulge appears at finite wavevectors.
Assuming that it is not a numerical effect, and you have optimized your forces sufficiently, there is still the chance that the structure is not in a minimum but at a saddle point, e.g. stabilized by the symmetry.
In this case further optimization does not help, but you might try and rattle the atoms a bit to break the symmetry and then optimize again. If the resulting structure is different from the original structure, then this might be the origin for the negative frequencies.
Moreover, although it is generally possible to calculate phonon frequencies for strained systems, a compressed cell sometimes enhances such effects (see e.g. the tutorial http://www.quantumwise.com/documents/tutorials/latest/Phonon/index.html), especially for lower dimensional systems, such as graphene, which tends to buckle if you compress the cell. In this case, optimizing the cell can help to remove negative frequencies (I don't know if you already tried optimizing your cell).
Finally, be aware that you optimize the small cell, whereas the actual phonon calculations are carried out in the repeated supercell. If you have instabilities that occur at a larger scale, they may be stabilized by the periodicity of the small cell. A good example for such behaviour is again the graphene sheet that tends to buckle (e.g. because you compress the cell). You won't see the buckling in the small cell, because the wavelength of the buckling is larger than the cell length, but in the repeated supercell, the buckling may well be possible.
It don't know if any of these causes apply to your system, but it is something to think about when you encounter negative phonon frequencies.

128

General Questions and Answers / Re: Rigid v/s. Fixed

« on: October 30, 2015, 10:00 »

The reason for this is that in order to enable rotational motions of the rigid bodies, we would have to switch from normal Newton-dynamics to Newton-Euler-dynamics, which would require to implement completely different equations of motion. Although this is planned for some time in the future, right now only translational motions are allowed, which can be implemented into our regular dynamics and optimization framework.
Are you considering a system which explicitly requires rotational motions of rigid bodies, as well?

129

General Questions and Answers / Re: comb potential

« on: October 23, 2015, 09:05 »

Actually, I just saw that all COMB potential classes are now in the reference manual.

Just have a look here:
http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.tremolox.html#ref.nanolanguage.potentialclasses

130

General Questions and Answers / Re: comb potential

« on: October 23, 2015, 09:02 »

Yes, this is true, we have COMB potentials classes implemented in the ATK-Classical/TremoloX-calculator in ATK-2015.
We also have some predefined COMB-potentials such as:
COMB_OSi_2010 : Shan, T., Devine B., Hawkins, J., Asthagiri, A., Phillpot, S., Sinnot, S., "Second-generation charge-optimized many-body potential for Si/SiO2 and amorphous silica",  Pysical Review  B 82, 235302 (2010),
COMB_OSi_2007 : Yu, J., Sinnott, S., Phillpot, S., "Charge optimized many-body potential for the Si/SiO2 system",    Pysical Review  B 75, 085311 (2007)
You can directly use them from the ScriptGenerator.

I think the reference manual has not been updated to 2015 yet, that's why the classes are not in it. But, this will be changed very soon, and then you can also define your own COMB potential.

And yes, you can also use semi-empirical calculators for MD simulations. Just change the calculator in the ScriptGenerator and run the MD simulation as usual.

131

General Questions and Answers / Re: How to generate amorphous structures of activated carbon in VNL/ATK

« on: October 19, 2015, 11:42 »

(1) Would you please give me a simple example on how to introduce constraints on the structures.

Currently, you can only use fixed-atoms constraints, i.e. fix an atom to its initial position, or rigid-body constraints, i.e. treat a groups of atoms as rigid body by allowing only translational motion of its center-of-mass. This can be done in the constraints editor in the MolecularDynamics widget. You may also have a look at the basic MD tutorial.

Unfortunately, it is currently not possible to use or implement other types of constraints, such as fixed angles, etc. Support for more general constraints will probably be available from ATK-2016.

132

General Questions and Answers / Re: How to generate amorphous structures of activated carbon in VNL/ATK

« on: October 9, 2015, 10:29 »

First of all, such porous carbon structures require considerably large system sizes, which is why you very likely need to use classical potentials to model the system.
You could follow the procedure outlined in the paper
http://homepages.rpiscrews.us/~shiy2/publications/jcp.porous.pdf

Although we do not have the exact potential of this paper implemented, you could use one of our Tersoff or Brenner potentials for Carbon.
Then, you essentially need to create a random arrangement of carbon atoms at the desired density.
You can do this e.g. by taking a diamond cell, repeating it to obtain the desired number of atoms, then increasing the lattice constants to obtain the desired atomic density (while keeping the fractional coordinates constant). As a new plugin in ATK-2015, you can also use the new Amorphous prebuilder plugin after downloading the SCAITools AddOn.

This initial structure has to be annealed at very high temperatures (in the paper they use 21 000 K) in a NVT thermostat e.g. Langevin or NVT Nose Hoover Chain to randomize the atomic arrangement. Such high temperatures require a very small time step e.g. 0.1 fs or smaller.
Then you can basically follow the instructions in the paper, by cooling the system to lower temperatures. In ATK-2015 this can easily be achieved in the NVT Nose Hoover Chain thermostat by choosing an initial temperature (e.g. 21 000 K and a final temperature, e.g. 1000 K). In ATK-2014 you need to run a series of constant temperature simulations, e.g. with the Langevin thermostat, as described in the amorphous systems tutorial.
Choose a sufficiently large number of steps, ideally resulting in several nanoseconds simulation time, to achieve a relatively slow quenching. Remember also to set the log interval parameter to something like 1000 or even larger, otherwise your trajectory file will become huge and the simulation very slow.
The atoms will move around wildly due to the high temperatures, so in order to be able to inspect your structures properly you need to send the final structure of the MD simulation from the Movie Tool to the Builder and wrap all atoms back into the cell via 'Bulk Tools > Wrap' .

133

General Questions and Answers / Re: Phase Transition in Materials

« on: September 29, 2015, 10:25 »

Some additional remarks:

If you want to see the phase transition in an MD simulation you need to use a constant pressure simulation, in this case NPT Melchionna. Using NVT you will never see the phase transformation because the cell size won't change. Currently, NPT does not support increasing the temperature during the simulation, so you have to run a new simulation a each temperature point.
A good general example how phase transformations can be simulated using MD can be found in this paper:
http://dx.doi.org/10.1063/1.2038747.

Before you run the simulation you should check if your calculator/parameter set can reasonably well reproduce all phases that you expect to see, i.e. that they are reasonably stable under a geometry and cell optimization. If not, you cannot expect to encounter this structure in a dynamical simulation.

To check the total energy, the simplest way is to view your MDTrajectory in the Movie Tool, where all energy contributions, as well as the temperature are automatically plotted.

134

General Questions and Answers / Re: Tremolox Package

« on: September 28, 2015, 09:32 »

1. To use the external ReaxFF-file, you have to copy the downloaded ReaxFF-file into the Quantumwise installation under lib/python2.7/site-packages/tremolox/potentials/ReaxFF (under Linux, under Windows the path may be slightly different). Then you have to specify the following lines in the script to define the calculator:

potentialSet = TremoloXPotentialSet(name='ReaxFF_AuSCH')
potentialSet.addParticleType(ParticleType(symbol='H', mass=1.00794 * atomic_mass_unit, charge=None, sigma=None, sigma14=None, epsilon=None, epsilon14=None, atomicNumber=1))
potentialSet.addParticleType(ParticleType(symbol='Au', mass=196.967 * atomic_mass_unit, charge=None, sigma=None, sigma14=None, epsilon=None, epsilon14=None, atomicNumber=79))
potentialSet.addParticleType(ParticleType(symbol='C', mass=12.011 * atomic_mass_unit, charge=None, sigma=None, sigma14=None, epsilon=None, epsilon14=None, atomicNumber=6))
potentialSet.addParticleType(ParticleType(symbol='S', mass=32.06 * atomic_mass_unit, charge=None, sigma=None, sigma14=None, epsilon=None, epsilon14=None, atomicNumber=16))

# Add the ReaxFF potential to the potential set
potential = ReaxFFPotential(file='ffield_AuSCH',
                                          qeq=True,
                                          qeqEps=1.000000e-06,
                                          qeqMaxIter=200,
                                          lgvdw=False,
                                          bond_rcut=5.0*Angstrom,
                                          hbond_rcut=7.5*Angstrom,
                                          thb_bond_rcut=0.001000,
                                          thb_bond_rcutsq=0.000010,
                                          multiwell=False,
                                          strict_bondpairs=True)
potentialSet.addPotential(potential)

calculator = TremoloXCalculator(parameters=potentialSet)

The ReaFFpotential options may have to be adapted as needed.
Furthermore, when I tried to run the calculation, the potential file did not work out of the box, because apparently a line is missing. So you have to open the potential file in an Editor and add the following line as the second line:

4 C 6 H 1 S 16 Au 79

so that the beginning of the file reads like

Reactive MD-force field: AuSCH as published in T. T. Jarvi et al., J. Phys. Chem. A, doi: 10.1021/jp201496x
4 C 6 H 1 S 16 Au 79
 39       ! Number of general parameters                                       
   50.0000 !p(boc1)                                                             
    9.5469 !p(boc2)                                                             
   26.5405 !p(coa2)

This is to let the calculator know how many and which atoms it should expect.
However, you are strongly encouraged to test the potential, whether it gives the correct results before using it, because I haven't made any tests!

2. No, it is currently not possible to use more than one ReaxFF-potentials in the same calculator.

135

General Questions and Answers / Re: Mimicking decomposition of Silicon on 6H-SiC(000-1)

« on: September 15, 2015, 10:33 »

Yes, in this case it (0001) and (000-1) distinguish between a C-terminated surface and a Si-terminated surface. So, in simple words, whether you use the top or the bottom surface of the slab.