Messages

31

Future Releases / Re: Display number of atoms

« on: July 27, 2015, 14:34 »

Nice plugin. Very useful information just a click away. If there's a way of using this in the 2D plot window it'd be very cool.

What I meant by "you get the list of atoms at the top" is the "Atom Indices" list you get in the 2D plot window (just above the tick boxes to select the types of orbitals). I've tried using len() on that list to get the number of atoms I have selected but it's a lot of hassle when you are doing several sets to be honest.

Thanks for this plugin!

32

General Questions and Answers / Re: Convergence of dE and dH

« on: July 27, 2015, 13:41 »

Well I thought convergence of both quantities (dE & dH) would still be required. So if dE is converged and you have to wait for dH to be that's perfectly fine. I just wondered if it's necessary the other way around (i.e., does it make sense to wait for dE once dH is converged or is it a waste of time?).

I am not an expert on these things of course it just occurred to me that if we require two quantities to be converged to the same level they should be comparable. And if dE is extensive (scales with the total number of atoms) and dH isn't it seems strange to me.

You may encounter a situation in which you have many atoms and even though the individual H matrix elements are converged you still struggle to get E to converge to the desired threshold. If we're using, for example, a 1.e-6 tolerance, and we have 1000 atoms we could have at some point dH < 1.e-6 and dE ~ 1.e-5. There being 1.e3 atoms I would think that dE is actually converged to the same level of accuracy (if not more) as dH since that 1.e-5 refers to 1000 atoms whereas dH refers to individual matrix elements.

Just a thought anyway, I'm no expert. I'll have to think a bit more about E being the weighted sum of occupied states and what that means for convergence of the quantity. Very interesting reading your replies though so thank you for taking the time.

33

Future Releases / Display number of atoms

« on: July 26, 2015, 15:34 »

It'd be nice if you could tick a box somewhere to display the number of atoms whenever you visualize structures. It could also show the number of selected atoms (if any).

Maybe I'm missing something but in the builder the only way I know of knowing the number of selected atoms is by clicking Graphics > Properties... and looking at the "Editing X atoms" at the bottom of the Scene Properties window.

It'd be useful not only in the builder but also in windows like the 2D plot... tool. If you are for example visualising the local density of states of a subset of atoms using this tool it'd be nice to see how many atoms you have selected as with big structures and atoms being behind other atoms it can get tricky. I know you get the list of atoms at the top anyway and you can count them (or len() the list if you have many atoms) but being able to see the number right there would be a nice feature.

34

General Questions and Answers / Convergence of dE and dH

« on: July 26, 2015, 15:19 »

I have a question regarding the convergence of these two reported values (dE & dH). When running DFT calculations with 1000+ atoms I notice that often the convergence of dH gets below tolerance (by default 1.e-5 iirc) much before dE. The difference also tends to be a couple of orders of magnitude.

I wonder if this is because dE refers to the total system energy (extensive property) whereas dH is per matrix element which if I understand correctly shouldn't scale with the number of atoms in the system.

If so, wouldn't it make sense to set all tolerances to be per atom?

I understand that calculations usually converge dE in a few more steps anyway but when dealing with large systems each extra iteration might mean a sizeable amount of time.

Thanks for your time

35

General Questions and Answers / Re: Translate 2D silicon atoms to fit trigonal or hexagonal shape

« on: July 26, 2015, 14:49 »

You can always copy the graphene hexagonal lattice available in VNL's structure database. By importing graphene into the builder you get something like:

Code

# Set up lattice
lattice = Hexagonal(2.4612*Angstrom, 6.709*Angstrom)

# Define elements
elements = [Carbon, Carbon]

# Define coordinates
fractional_coordinates = [[ 0.            ,  0.            ,  0.            ],
                          [ 0.333333333333,  0.666666666667,  0.            ]]

# Set up configuration
bulk_configuration = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    fractional_coordinates=fractional_coordinates
    )

If I understand your question correctly you could get what you're looking for by changing that 2.4612 to match the bond length of Si, change the C parameter (6.709) to however much vaccum you think is appropriate for your calculation, and change elements to Silicon instead of Carbon . Hope this helps.

36

General Questions and Answers / Re: Transmission of periodic systems

« on: June 22, 2015, 21:32 »

Thank you Dr. Blom, much appreciated.

37

General Questions and Answers / Re: Transmission of periodic systems

« on: June 22, 2015, 12:47 »

Could anyone clarify this for me? My question is:

Can a bulk crystalline system have non-integer transmission?

In case the previous post was too long. Thanks in advance.

38

Future Releases / Rotation along one axis

« on: June 16, 2015, 23:00 »

It would be nice if you could rotate structures along a specific axis when you're visualising them. Another software I use has this and I find it useful: if you hold 'x' while right clicking the structure it's only allowed to rotate along the X axis, and so on for 'y' and 'z'.

Maybe more people would find this useful as rotating structures can sometimes get out of hand (at least for me)  and then I have to reset the view and start trying again to find the angle I want. I've found that "decomposing" the rotations by axis makes it much easier. 

39

General Questions and Answers / Transmission of periodic systems

« on: June 16, 2015, 20:12 »

Hi,

I've been reading around and it is quite clear to me that for perfectly periodic systems the transmission at a certain energy & transverse k-point must be an integer. But should the total transmission at a certain energy be an integer always?

In order to investigate this issue I have been trying to calculate the TransmissionSpectrum of bulk copper. I can see with the transmission analyzer that the number of channels at a particular (E,k) is always an integer ("numerical" integers anyway, e.g. 0.999999...) but then the "total" transmission can be non-integer. Is the total transmission a brillouin zone integration of the  values along the transverse directions and can be non-integer?

It isn't clear to me whether this is a physical result or it just means my calculation isn't  converged (my electrode is too small or not enough k-points, etc). I tried calculating this TransmissionSpectrum in both Device & Bulk Configurations. In both cases I'm getting non-integers. The bulk configuration I used was just one conventional cell and the device configuration included 2x conventional cells along the Z direction as electrodes and 3x as the central region. In all cases the size of both transverse directions was just 1 conventional cell.

Thanks in advance

40

General Questions and Answers / Self energy calculator for transmission pathways

« on: June 11, 2015, 17:06 »

Hi,

I've been reading around about self energy calculators and found that in this thread:

http://quantumwise.com/forum/index.php?topic=3178

Dr. Anders Blom mentions that the Direct calculator is mostly included for historical reasons and that Recursion should be the standard reliable calculator. So my question is:

Is there a reason why the default calculator for TransmissionPathways is DirectSelfEnergy()?

For TransmissionSpectrum the default is RecursionSelfEnergy() in agreement with Dr. Blom's post.

Thanks for your help

41

General Questions and Answers / Re: Checkpoint file in restarted calculations

« on: June 8, 2015, 13:52 »

Very nice. Thanks!

42

General Questions and Answers / Checkpoint file in restarted calculations

« on: June 5, 2015, 15:31 »

Hi all,

When running a restarted calculation with a script like:

configuration = nlread('original_checkpoint_file.nc')[0]
configuration.setCalculator(configuration.calculator(), initial_state=configuration)
configuration.update(force_restart=True)
nlsave('output.nc', configuration)

How can one specify the checkpoint file to write to? Since there's no explicit specification of the calculator I don't know how to do it. Is there a way using the setCalculator method?

Thanks!