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Messages - Julian Schneider

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121
General Questions and Answers / Re: Molecular Dynamics Error
« on: January 19, 2016, 15:14 »
Yes, you are right, you are using DFT so the forces are probably not totally wrong.
I made some tests, and it looks as if the problem is that you initially have quite large forces on the atoms of the molecule, as the molecule is a little compressed (it expands quite a bit if you optimize the molecule alone).
That means that in the beginning of your MD the large forces accelerate the atoms in the molecule away from the center of the molecule.
Then you use zero initial velocities (initial_velocities=None). As the average temperature is below the target temperature of 300K the thermostat additionally accelerates the atoms in order to reach the target temperature. This will cause that the atoms of the molecule will be driven apart even further, and for a moment it looks as if the bonds are broken.
However, remember that the bonds in the viewer are just a graphical representation based on the atom distance, and it doesn't necessarily mean that the bonds really are broken. If you'd continue the MD for longer times they'd very likely find their equilibrium bond lengths in the end.
To prevent this effect, I suggest you use the Langevin thermostat instead of the NVT Berendsen thermostat. The Langevin  thermostat couples each atom more tightly to the heat bath and the friction force prevents that atoms become accelerated to much (see the MD tutorial http://www.docs.quantumwise.com/tutorials/md_basics.html).

122
General Questions and Answers / Re: Molecular Dynamics Error
« on: January 14, 2016, 10:45 »
It is generally not recommended to perform MD simulations at constant pressure (i.e. NPT simulations) on DeviceConfigurations, especially not NPTBerendsen, (see last paragraph in the MD tutorial www.docs.quantumwise.com/tutorials/md_basics.html). You should use constant volume simulations (i.e. NVE or NVT) instead.
If you want to optimize the cell of the device with respect to the stress you should adopt the scheme outlined in the device relaxation tutorial (www.docs.quantumwise.com/tutorials/device_relaxation.html).
However, it should technically be possible to run NPT on a device configuration, and the error you see seems to be a bug, which we'll fix.

123
General Questions and Answers / Re: Virtual Nanolab not reading energies and velocity from LAMMPS
« on: January 4, 2016, 14:20 »
From the missing energy data in the MovieTool, I suppose the corresponding LabFloor item is a Trajectory instead of an MDTrajectory object, correct?

From the input file you posted everything looks ok, and the LAMMPS trajectory should be loaded as an MDTrajectory.
It is difficult to find the error without more information or the remaining files.
Is the original "pt-pd.data" file present in the current directory?
Are the atoms in the MovieTool displayed as the correct elements?
Did you rename any of the output files?



124
General Questions and Answers / Re: Chemical potential and molecular dynamics
« on: December 15, 2015, 16:58 »
Yes, that is possible using a hook function during Molecular Dynamics.
To do so, you first have to define a suitable hook function in your script, e.g.

Code
def chemical_potential_hook(step, time, configuration):
    """ 
    Hook function to calculate and print the chemical potential at 
    every MD step.
    """
    chemical_potential = ChemicalPotential(configuration)
    nlprint(chemical_potential)

Then, you define your MD simulation as usual, but with the additional argument
Code
post_step_hook=chemical_potential_hook

e.g.

Code
md_trajectory = MolecularDynamics(
    bulk_configuration,
    trajectory_filename='trajectory.nc',
    steps=100000,
    log_interval=2,
    post_step_hook=chemical_potential_hook,
    method=method
)
The hook function will now be called after each MD step and the specified operation, in this case the calculation and printing of the chemical potential, will be performed.
Of course, the calculator that you use for running molecular dynamics must support the calculation of the chemical potential (i.e. it must be an electronic-structure-based calculator such as the LCAOCalculator, as this is the electronic chemical potential).

125
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.

126
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.

127
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).

128
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.

129
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!

130
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. 

131
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.

132
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?

133
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

134
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.

135
General Questions and Answers / Re: How to generate amorphous structures of activated carbon in VNL/ATK
« on: October 19, 2015, 11:42 »
Quote from: reallusion on October 18, 2015, 15:25

(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.

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