Messages

46

General Questions and Answers / Re: Thermal conductivity: dependence on temperature

« on: April 6, 2017, 21:42 »

Anharmonic effects are not included in phonon transmission calculated via non-equilibrium Green's functions. Everything is purely harmonic. Therefore NEGF is primarily suited for interfacial thermal conductance (where scattering at the interface is the main contribution to thermal resistance) and not so much for bulk conductivity (where inelastic phonon-phonon-scattering is the main contribution to resistance).

Non-equilibrium MD, on the other hand fully includes anharmonic effects and can therefore be used to calculate both interface conductance and bulk conductivity.
So what you observe makes perfect sense.

Have a look at our recent webinar on thermal transport simulations http://docs.quantumwise.com/webinars/webinars.html

47

General Questions and Answers / Re: Wrong result as per theoretical formula

« on: April 6, 2017, 09:27 »

VNL calculates the Young's modulus as Y_i = 1/S_ii  (i=x,y,z) where S is the inverse of the elastic constants matrix.
We do not calculate the bulk modulus and the shear modulus directly, but from the elastic constants, as well. Since there are several conventions how to do this exactly (Hill, Voigt, Reuss) which all use slightly different formulas, it is more straightforward to calculate the Young's modulus from the elastic compliance matrix, since that does not rely on any of these conventions.

48

General Questions and Answers / Re: Calculation of thermal conductivity of a graphene layer

« on: March 28, 2017, 23:15 »

Sorry for the late answer, I took me some to look into your system.

1. What do you think the suitable momentum exchange interval? I used 150 intervals for the simulation. When we used 150 intervals, the temperature was increased.

150 should be fine in general, although it depends a bit on your system. Generally, the exchange interval allows you to modify the magnitude of the thermal current. For a system with a small cross section, the same thermal current can lead to a larger thermal flux and thus a larger temperature gradient. The temperature gradient should ideally not be too large, on the other hand large enough so that it can be measured with sufficient accuracy. 

2. How can we decide the convergence or steady state of the temperature profile? Are there any criteria for that? For my case, the temperature gradient is changed in a short time, and it is hard to figure out the convergence of the temperature profile.

You should plot your temperature profile at different time intervals during the simulation. If you don't see a difference between the temperature profiles of subsequent time intervals then you can assume that your temperature profile has reached a steady-state.

3. In the tutorial of the calculating interfacial thermal conductance using molecular dynamics, you compared the two temperature profiles. Are there a proper time range for the integration of the temperature profile? The temperature gradient is changed when we modify the time range.

At first, I would recommend you to use a smaller log interval than 10 000, e.g. something like 500 or 1000. This will make the temperature profile a lot smoother, as you will have more snapshots to average over. Remember, for your system you have to calculate the profile along the B-direction, not the default C-direction.
Yes, the temperature profile will depend on the chosen time interval. On the one hand, as for a small time interval your average might not be very good and the profile can become fuzzy. On the other hand, as long as you haven't reached a steady state, changing the length of the time interval will also include snapshots from different phases of the simulation, which will result in a different profile, that's just the nature of the non-equilibrium simulation. So, as a rule of thumb, you could use intervals of 50-100 ps to check for convergence, and once you know that you have reached a steady-sate, you should average the profile over several 100 ps, to get a smooth profile.
If your profile is too fuzzy you can also try and increase the bin width a bit.

4. Can you tell me the reason why the increase of the system temperature during the simulation of the non-equilibrium momentum exchange? In the case, the system is isolated, and no energy can be provided.

I can reproduce your problem, and it actually seems that the total energy increases during time. Although I'm not 100% sure, I would guess a major part of the problem is that the time step is too large and the conservation of total energy is not given any more. In this case a smaller time step, maybe 0.5 fs, might at least fix the problem to some extent. Furhtermore, the system is very soft and buckles quite a lot during the simulation which might make it additionally difficult.

5. What is the meaning of "truncated content"? I saw the warning in my log file of the simulation.

That is just a message that the output line in the log file is longer than the width of the terminal. You can ignore that.

49

General Questions and Answers / Re: Calculation of thermal conductivity of a graphene layer

« on: March 20, 2017, 11:46 »

The kinetic energy should not increase significantly  during the simulation. By increasing the time step, do you mean the total number of MD steps or the actual time step  (e.g. 1 fs)?
The latter should not be increased. Increasing it to e.g. 5 fs can in fact lead to energy conservation being violated.
If you just increased the number if MD steps and the energy increases, then the system may not be sufficiently equilibrated before the NEMD simulation. Or your temperature gradient has become so large that part of the system experiences such a high temperature that it runs out of equilibrium.

50

General Questions and Answers / Re: what't the difference bwteen NVT-Nose-Hoover-chain and NVT-Nose-Hoover in 2015?

« on: March 13, 2017, 12:25 »

The NVTNoseHooveChain in ATK-2015 is essentially the same as the new NVTNoseHoover thermostat in ATK-2016.
The old NVTNoseHoover in ATK-2015 thermostat does not exists any more in ATK-2016, as it was using an older algorithm which is not state-of-the-art.
In ATK-2015 you should use the NVTNoseHooverChain thermostat.

51

General Questions and Answers / Re: Calculation of thermal conductivity of a graphene layer

« on: March 9, 2017, 20:11 »

1)    I know that the nanosheet is 2D and periodic in the y and z directions. Is it required to set the periodic boundary condition for the top and bottom side additionally? If the boundary condition is periodic, there are no scattering effects related on the phonon or electrons because the top and bottom side are not terminated anymore, Right? I expect for the case; there are no dependencies on the width of the structure for the thermal conductivity. I want to know about this.

With ATK-Classical you cannot switch off the periodic boundary conditions, so you should make sure that you have a sufficiently large vacuum buffer on top of th graphene layer if you want to simulate an isolated layer.

2)    For the non-equilibrium momentum exchange, should we set the fixed boundary at the left and right side of the structure besides the heat sink and source?

You have two options how to set up the boundaries in transport direction:
a) Add some vacuum buffer in transport direction and fix the outermost terminating atoms. This way you'd only have periodicity in the in-plane direction perpendicular to the transport direction.
b) You treat the system periodic in the transport direction, as well. Then the thermal current runs in both directions. Here you in principle don't need to fix anything.

3)     For the Nose-Hoover thermostat, the temperature gradient can be generated using reservoir temperature. Is there are no problem to obtain the thermal conductivity of the graphene layer although some synchronization issues are between the heat source and sink.

In principle you could just set two thermostats on heat sink and source to obtain the gradient. However, in this case you'd have no straightforward way to measure the magnitude of the thermal flux. So, I'd recommend using the NonEquilibriumMomentumExchange method.

4)    I read a several papers about NEMD for the calculation of the thermal conductivity by LAMMPS. In that case, the method is similar methods kinds of setting the different reservoir temperature on both sides for the Nose-Hoover thermostat.

According to recent papers, the alternative way to using NonEquilibriumMomentumExchange  not really setting reservoir temperatures, but to set achieve a specified thermal by heating and cooling the heat and sink with a constant heating power, which at steady state has the same magnitude as the thermal curent in the system. This method will be available in the upcoming ATK-2017 release.

5)    Please comment about the procedure of simulation, some notes and missing point and so on.

To obtain reliable bulk conductivity values, you may have to run a series of simulations at increasing system sizes and then extrapolate to infinite lengths, as described e.g. in http://aip.scitation.org/doi/abs/10.1063/1.4767516.
As, Petr said, for more explanations and details, you may want to look at our tutorials and the webinar.

52

General Questions and Answers / 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.

53

General 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 http://docs.quantumwise.com/manuals/Types/HTSTEvent/HTSTEvent.html#htstevent-c). 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.

54

General Questions and Answers / Re: Error in emulating wrap and hook function

« on: February 14, 2017, 12:08 »

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.

55

General Questions and Answers / Re: Error in emulating wrap and hook function

« on: February 13, 2017, 14:59 »

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.

56

General Questions and Answers / Re: Is that ok to do MD relax then put the relaxed coordinate for DFT calculations?

« on: February 12, 2017, 19:49 »

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.

57

General Questions and Answers / Re: how to convert a unit cell in LAMMPS ?

« on: January 28, 2017, 17:13 »

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.

58

General Questions and Answers / 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.

59

General Questions and Answers / Re: how to convert a unit cell in LAMMPS ?

« on: January 24, 2017, 11:51 »

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 http://docs.quantumwise.com/tutorials/lammps_trajectories/lammps_trajectories.html

60

General 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

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.