Re: [kwant] test

2013-09-10 Thread christoph . groth
test-reply through NNTP with CC

Re: [Kwant] Tutorial files - 500 – Internal Server Error

2013-09-29 Thread Christoph Groth
Hi Benjamin, > I am trying to follow the kwant tutorial but there is a problem when > downloading tutorial files. Thanks for letting us now. It should work now. (The problem was due to a misconfiguration of the web server that treated .py files as CGI scripts.) > I am working on my own impleme

Re: [Kwant] Tutorial files - 500 – Internal Server Error

2013-09-30 Thread Christoph Groth
Benjamín Santos writes: > Is the Knitting algorithm  (K. Kazymyrenko, X. Waintal, Phys. Rev. B > 77, 115119 (2008)) implemented in kwant? It's not, as the available MUMPS-based sparse solver is more efficient. However, for very large systems (i.e. long wires) where the MUMPS-solver runs out of m

Re: [Kwant] kwant version on PyPi incorrect

2013-10-03 Thread christoph . groth
I've debugged this somewhat weird issue together with Joseph. It's not related in any way to pip. Joseph was extracting the Kwant tarball und building it inside some _other_ git repository. Now, in order to determine its version, Kwant's setup.py checks whether it lives inside a git repository a

[Kwant] Recursive Green's function method and Kwant

2013-10-16 Thread christoph . groth
Hi Benjamin (and anyone else who is interested), I have made available an unfinished RGF module for Kwant in the repository http://git.kwant-project.org/experimental/kwant-rgf/. This code was written by our former student Daniel Jaschke and myself. It is not at all ready to be included into Kwan

Re: [Kwant] dual transverse wave functions and mode velocities

2013-10-18 Thread christoph . groth
Anton Akhmerov writes: > > While what you want is not implemented directly in Kwant, but you > > can get * Wave functions, momenta and velocities of the propagating > > modes, from the function kwant.physics.modes Alexander Croy writes: > Excuse my possibly stupid question, but how would I go ab

Re: [Kwant] Possible system?

2013-11-25 Thread christoph . groth
Hi Sebastien, Sebastien Guissart writes: > It is possible to study impurity or something like in a 2d infinity > system by defining a finite system with impurity and add "lead" with 2 > translational symmetry? What observable would you like to calculate? The builder does in fact allow to defin

Re: [Kwant] Possible system?

2013-11-26 Thread Christoph Groth
Hi Sebastien, Do I understand you correctly that you'd like to calculate the LDOS of a system that contains an impurity, and that is periodic in two dimensions? So your system would look something like this . ..*.. . infinitely tiled both in up/down and left/right directions to arrive a

Re: [Kwant] Possible system?

2013-11-26 Thread Christoph Groth
Hi, Sebastien Guissart writes: > But I hope the impurity changes the system in reasonable size and at a > reasonable distance of the impurity the system stay unperturbed. so i > hope the LDOS near the impurity in this system . . . > > ...

Re: [Kwant] 1D Leads

2013-12-17 Thread christoph . groth
Hi Thomas, Thomas Schmidt writes: > I'm trying out Kwant, and I've encountered a problem when investigating > 1D leads. The problem that you encounter can be boiled down to the following program import kwant, numpy kwant.physics.modes(numpy.array([[2]]), numpy.array([[-1]])) You are asking fo

Re: [Kwant] Normal metal - P Wave interface

2014-01-20 Thread christoph . groth
Hi Baris, Baris Pekerten writes: > (...) > > Because of the term linear in p, you can't take it directly to > zero. For example: Define the p-wave parameter to be zero in the > hopping between sites x=0 and x=1 (with lattice spacing=1). Then > define the hopping between sites x=1 and x=2 to to b

Re: [Kwant] How the spin is positioned in the Smatrix?

2014-03-06 Thread christoph . groth
Hi Qingtian, I suggest to put spin-up and spin-down on separate lattices, like in http://kwant-project.org/doc/1.0/tutorial/tutorial5#lattice-description-using-different-lattices This will split each lead into a spin-up and a spin-down lead and you can easily calculate transmission between them.

Re: [Kwant] Propagating mode

2014-03-13 Thread christoph . groth
Hi, An addition to Joseph’s reply: If all you want to do is to save the wave function, you will probably not want to build a dictionary, but simply loop over the wave function array and the list of sites while writing both to a file. For example like this (with spin): sites = fsys.leads[lea

Re: [Kwant] launch the kwnat.test()

2014-04-07 Thread christoph . groth
Hi Loïc, I am new to the project, and I try to launch the first test. Unfortunately when I do : python -c 'import kwant; kwant.test()', that doesn't work : ImportError: cannot import name lapack but I have already installed liblapack-dev, I'am on Debian. Did you leave the root directory o

Re: [Kwant] Kwant error

2014-05-06 Thread christoph . groth
Hi Bas, Thank you for reporting these two problems. I've fixed the Cython issue in http://git.kwant-project.org/kwant/commit/?id=707bfa2073. The other issue has been noted in http://git.kwant-project.org/kwant/commit/?id=e110d01f99. Best, Christoph

Re: [Kwant] Quantum transport in system with periodic boundary condition.

2014-05-26 Thread christoph . groth
Dear all, Sébastien and Julien tried to attach leads with periodic boundary conditions to a scattering region with periodic boundary conditions. This is something that Kwant does not support well yet, as finalized builders may only have a single symmetry vector. On an earlier occasion we sh

Re: [Kwant] gauge invariance

2014-06-17 Thread christoph . groth
Dear Zhang Bing, The gauge that is used for each lead _must_ be such that the hoppings are translation invariant for that lead. If you have leads with different directions, this means that you need to use different adopted gauges. It is possible to interpolate between the different gauges u

Re: [Kwant] actual grid position

2014-06-30 Thread christoph . groth
Dear Jerzy, "Jerzy Wrobel" writes: how to get local_dos at (i,j) space position from 1d Numpy array, on a simple rectangular grid? The order of sites in a finalized system is random, as there is no useful order in the general case. It’s straightforward to look-up the site object given a s

Re: [Kwant] actual grid position

2014-06-30 Thread christoph . groth
"Jerzy Wrobel" writes: Interestingly enough, when kwant.plotter.map(sys, ldos_array) is called again, AFTER dictionary creation, the resulting picture is changed to a random patchwork of colourful rectangles. The creation of ldos_dict should not have any side-effects. Can you show us a sc

[Kwant] Paper, screencast, bugfix release 1.0.1

2014-07-04 Thread christoph . groth
, Christoph Groth -- To upgrade kwant in macports, do sudo port upgrade py27-kwant (or py26-kwant, depending on whether you are using python 2.6 or 2.7). Follow the instructions for additional commands you have to execute. To upgrade Mac homebrew

Re: [Kwant] Please help: Kwant installation on Mac OSX 10.9

2014-08-12 Thread christoph . groth
Dear Chagaan Baatar, Chagaan Baatar writes: I’m doing the MacPorts installation and got stuck at the following error message: (...) Currently it's vacation high season and no one of us has access to a Mac and the time to look into this issue. So, unfortunately, I cannot promise you quick h

Re: [Kwant] question on parallelization

2014-08-23 Thread christoph . groth
Hi Luis, Luis Foa Torres writes: In the kwant paper it is mentioned that "a few additional lines of code allow us to parallelize the script for a multi-core workstation or cluster". I was wondering if you could share any tip in this direction. As Kwant is simply a Python library, you can u

Re: [Kwant] Symmetry and leads

2014-10-30 Thread christoph . groth
Joseph Weston wrote: - A more general solution is to do what Anton proposed. I include a sample script below. sym.add_site_family(lat.sublattices[0], other_vectors=[(-1, 2)]) sym.add_site_family(lat.sublattices[1], other_vectors=[(-1, 2)]) Thanks for this. I had tried do do the following:

[Kwant] Scope of this mailing list

2014-11-25 Thread christoph . groth
Dear Anant, This mailing list is a forum for exchange about the Kwant code. Everybody is welcome to discuss how to do something with Kwant, i.e. how to best implement some physical system in Kwant, or how Kwant itself could be improved. We're glad to see that recently a few questions were an

Re: [Kwant] Contour plot of the conductance

2014-12-04 Thread christoph . groth
Dear Lee Kwok-Long, To be able to work with Kwant there's no way around learning the basics of Python. There are plenty of good tutorials available on the internet. We recommend the official Python tutorial (https://docs.python.org/2/tutorial/index.html) and “Software carpentry” (http://so

Re: [Kwant] Contour plot of the conductance

2014-12-05 Thread Christoph Groth
Dear Kwok-Long Lee, You wrote: I have another question about " smatrix = kwant.smatrix(sys, energy, args=[-welldepth])", and I found in tutorial 2.3.2 the expression "kwant.smatrix allows us to specify a list, *args*, that will be passed additional arguments to the functions that provide the

Re: [Kwant] About dispersion relation

2014-12-05 Thread Christoph Groth
Hi Anant, You wrote: Is there any way in KWANT that I can plot a 3-d graph of dispersion relation? In the tutorial it is given that the infinite system is quasi 1-d system. Indeed, in Kwant 1.x low-level systems (e.g. finalized builders) can only be either finite or quasi-1-d. This is bec

[Kwant] Graphene dispersion example script

2014-12-05 Thread Christoph Groth
Dear all, Due to a bug in my e-mail program, the attached script had some errors (from was capitalized). I send the script again, this time without signing the email message. This should avoid the problem. Best Christoph import cmath from collections import defaultdict import kwant import

Re: [Kwant] About bans structure for 3d

2014-12-09 Thread Christoph Groth
Hi Anant, You are setting the values of your sites and hoppings to “None”. That is, you define the structure of your Hamiltonian matrix but not its values. Note that I also use “None” in my graphene band structure example, but only in the ancillary system that is not used for calculations.

Re: [Kwant] Unable to update to Tinyarray 1.0.5

2015-01-30 Thread Christoph Groth
Bas Nijholt wrote: Michael might already change it, but with the current Homebrew formulas tinyarray 1.0.2 is installed.  For Kwant it doesn’t matter whether you use tinyarray 1.0.2 or 1.0.5. Christoph smime.p7s Description: S/MIME cryptographic signature

Re: [Kwant] Building Kwant from tarball on Mac OSX

2015-02-09 Thread Christoph Groth
Michael Wimmer wrote: very hard to say what the problem is. I couldn't find a Mac with OSX 10.6, so I cannot reproduce the error. Dear Pol, If everything fails, you can also install Kwant inside a Virtualbox virtual machine running some variant of GNU/Linux (Ubuntu is probably the easiest).

Re: [Kwant] Building Kwant from tarball on Mac OSX

2015-02-09 Thread Christoph Groth
Hi Pol, I am developing Kwant on a computer that runs Debian “testing” and we run it in our lab on our cluster that runs Debian “stable”. Anton (and I believe Michael) are using Ubuntu. Debian-based Linuxes are the platform where Kwant is at home. You said that you don’t like Ubuntu’s Unity

[Kwant] Confusing error messages

2015-03-03 Thread Christoph Groth
Bas Nijholt wrote: I’ve found a bug in add_site_family(), the input for other_vectors should be a list, but I used a tulpe, the error message I got is not correct. Hi Bas, Thanks for having reported this. I’ve fixed this issue in the development version of Kwant that will become version 1.

Re: [Kwant] Query about longitudinal and hall conductance in 4 terminal

2015-03-18 Thread Christoph Groth
Sudin Ganguly wrote: nonlocal_resistance = np.linalg.solve(cm, [1, 0, -1])[1] Why did you put the currents I_0=1, I_1=0 and I_2=-1? The code line you cite is taken from the valve.py example script From the Kwant paper. Did you have a look at the full example that can be downloaded at http:

Re: [Kwant] Lead around a corner

2015-03-19 Thread Christoph Groth
Pijnenburg Jana wrote: I have a rectangular shaped system that should be completely coupled to leads at one side . This means I have leads attached along the horizontal direction as well as the vertical direction. Now, the corners (the transition between the vertical and horizontal leads) ac

Re: [Kwant] Adding leads to a 4-layer system

2015-03-23 Thread Christoph Groth
Dear Kowk-Long Lee, There’s no limitation for the number of lattices (“site families”) of the sites of Builder objects (i. e. systems or leads). What you want to achieve should be perfectly possible. Let us know if there are any problems. Instead of using four stacked 2-d square lattices y

Re: [Kwant] bug in plotting a 3D system (matplotlib 1.4.3)

2015-03-25 Thread Christoph Groth
Cześć Rafał, The bug you describe has been fixed for Kwant 1.0.2. Unfortunately, the version available for Ubuntu right now is still 1.0.1. I plan to make a newer version available soon. If you need an immediate fix, you can install Kwant >= 1.0.2 directly from source, it’s easy. Krzysiek

Re: [Kwant] reproducing graphene magnetoresistance curve (Novoselov paper)

2015-04-01 Thread Christoph Groth
Hi Anant, You are welcome to ask for advice on this list about specific problems that you encounter while using Kwant. Please describe the problem that you experience and what you have already done about it. “My program does not work” is not a specific problem. Christoph smime.p7s Descri

Re: [Kwant] attaching 1D lead to 2D lattice

2015-04-15 Thread Christoph Groth
Hi Sergey, Currently kwant.plotter.map() only works when site positions are 2-d. We could add a pos_transform argument (like in kwant.plot()). I've made a note about this. For now, the cleanest solution will be to build your system as you did originally, i.e. with a 2-d scattering region a

Re: [Kwant] attaching 1D lead to 2D lattice

2015-04-15 Thread Christoph Groth
Hi Sergey, You could have used the search box of the kwant documentation to find out what is Site. Site refers to kwant.builder.Site. Please see the reference documentation of this class. To get the real-space position of a site, use its attribute “pos”, i.e. sys.sites[12].pos is the posi

Re: [Kwant] precision of calculations

2015-04-26 Thread Christoph Groth
Sergey Slizovskiy wrote: Another question is about parallel computations: are there any examples of it's use with kwant? Hello Sergey, did you find the following post from some time ago? http://article.gmane.org/gmane.comp.science.kwant.user/157 Christoph smime.p7s Description: S/MIME cryp

Re: [Kwant] Appcrash for very large systems

2015-04-28 Thread Christoph Groth
Hello Sam, Thanks for your compliment about Kwant. The conductance calculation in your script needs about 1.4 GiB of RAM on my machine (Debian GNU/Linux, amd64 architecture). So while 500x1000 is large system, it should run with 2 GiB of RAM. See Fig. 7 of the Kwant paper for memory usage of

Re: [Kwant] what is the wave function inside the system?

2015-04-28 Thread Christoph Groth
Dear Mariya, Kwant’s wave_function routine will give you the wave functions inside the scattering region due to all the modes of a lead that are incoming and propagating. Does this answer your question? Christoph smime.p7s Description: S/MIME cryptographic signature

Re: [Kwant] suggestion

2015-04-30 Thread Christoph Groth
Sergey wrote: It would be convenient to improve the method kwant.lattice.Monatomic.n_closest to include an argument "range" or even two arguments: range_min = 0 and range_max so that it returns the sites within a range from the given point. This is useful to e.g. specify the hoppings b

[Kwant] Incommensurate lattices in Kwant

2015-04-30 Thread Christoph Groth
Sergey, I’d like to add something to my post of a few minutes ago. The way I understood your request is that you suggested Monatomic.n_closest to return all the points (of all lattices?) that are in some given range around a point. But you probably simply meant to keep it working as it does

Re: [Kwant] bug in kwant installation requirement in PyPi

2015-05-04 Thread Christoph Groth
Hi Rafał, Thanks for letting us know about the problems with “pip”. The state of python packaging has been messy, only recently there has been some progress [1]. The way Kwant is packaged reflects the documentation on Python packaging for Python 2.7. We’ll see how we can improve things. C

Re: [Kwant] bug in kwant installation requirement in PyPi

2015-05-04 Thread Christoph Groth
Joseph Weston wrote: Unfortunately it's not a 1-line fix just to add the dependencies, as numpy is imported within the setup.py script itself (so that we can get the numpy C headers; used for compiling the kwant modules written in Cython). I can't see a way around this using the current tools

Re: [Kwant] Package for ubuntu vivid

2015-05-06 Thread Christoph Groth
Hi David, I’m aware that Kwant is not yet available in Ubuntu 15.04. It’s on my list of things to do, but frankly I have been too busy the last weeks to take care of it. I hope to have time next week to deal with it. For now you can try to install Kwant from source. This is very easy on

[Kwant] Kwant user survey

2015-06-02 Thread Christoph Groth
Dear all, We have prepared a short (5 min) anonymous survey for users of Kwant. Please consider helping us by filling it out and do not hesitate to spread the word to others who might not be on this list. The survey is linked from the top of http://kwant-project.org/. It can be also access

Re: [Kwant] Install want on CentOS 6.4

2015-06-08 Thread Christoph Groth
Hi Michael, Can you please post a complete log of all that you did (including output and error messages)? Christoph smime.p7s Description: S/MIME cryptographic signature

Re: [Kwant] Install want on CentOS 6.4

2015-06-09 Thread Christoph Groth
Dear Michael, You wrote: This is all the log reported from the terminal: [beconcini@goldrake01 kwant-1.0.2]$ python setup.py build (...) /usr/bin/ld: cannot find -llapack So the problem is that the setup script cannot link with LAPACK. You need some kind of LAPACK to build Kwant. Sometimes

[Kwant] 2 PhD positions in computational quantum theory (Grenoble)

2015-06-09 Thread Christoph Groth
at the Institute for Nanoscience and Cryogenics (INAC) of CEA Grenoble (France) over the course of three years under the supervision of Christoph Groth and Xavier Waintal in close collaboration with Michael Wimmer and Anton Akhmerov of Delft University of Technology (Netherlands). The city of

Re: [Kwant] suggestion

2015-07-10 Thread Christoph Groth
Sergey wrote: I use the following construction to connect the incommensurate lattices: lat_e (graphene) and lat_e1 (square) for x in list(lat_e1.shape(rectangle1, (0, 0))()): for neighbour in lat_e.sublattices[0].n_closest(x.pos): sys[(x, lat_e.sublattices[0](*neighbou

Re: [Kwant] suggestion

2015-07-10 Thread Christoph Groth
Sergey wrote: Yes, such function would be definitely useful. Sometimes, it is useful to play with some reasonable, but a bit ad-hoc hoppings. I propose that that the function "connect" must take a function name "crit" as an input parameter. Where "crit" is a function taking two sites as para

Re: [Kwant] [PATCH] initialize numpy arrays to zero

2015-07-28 Thread Christoph Groth
Applied. Thanks for finding this! smime.p7s Description: S/MIME cryptographic signature

[Kwant] Everybody is invited to participate in discussions on this list

2015-07-31 Thread Christoph Groth
Dear all, This mailing list is often used to ask questions about Kwant. Naturally, such questions will be often answered by developers of Kwant, but I would like to emphasize that this list is meant as a forum of exchange of ideas for all users of Kwant. There are many experienced Kwant user

Re: [Kwant] Python 3 support

2015-08-07 Thread Christoph Groth
Hi Joe, I think it’s OK if we require Python 3.4 for the Python 3 version of Kwant. This decision would only hurt people who are keen to use Python 3 with Kwant now, but who for some reason are bound to older versions of it. And these (very few or none, I suppose) people can just continue t

[Kwant] Discussing kwant development

2015-08-19 Thread Christoph Groth
Dear all, We would like to make it easier for the community to see what is going on in terms of Kwant development. We hope that this will provide useful feedback and lower the barrier for participation. As a first step, we have created a new mailing list called “kwant-devel”. The new list

Re: [Kwant] Band structure for bulk material

2015-09-09 Thread Christoph Groth
Jonas Nascimento wrote: When comes kwant 2.0? It will come when it’s ready. Kwant is an open-source project, everyone is welcome to help. If you are interested, please let us know on this mailing list. Cheers Christoph smime.p7s Description: S/MIME cryptographic signature

Re: [Kwant] AUR build scripts for kwant and tinyarray

2015-09-10 Thread Christoph Groth
Hi Jörg, Thanks a lot for updating Arch Linux packaging of Kwant! Are you planning to maintain them for some time in future? Your scripts look fine to me. I just noticed that we were still using *.sig for the signatures of the tinyarray tarballs. I now renamed those to *.asc (which seems

Re: [Kwant] AUR build scripts for kwant and tinyarray

2015-09-10 Thread Christoph Groth
Jörg wrote: I assume the documentation build process needs sphinx, is that correct? If so it might be easiest to factor out a documentation into a separate python2-kwant-doc package. Indeed, and that's why we separate the two for Debian as well. There's python-kwant, and python-kwant-doc.

Re: [Kwant] AUR build scripts for kwant and tinyarray

2015-09-11 Thread Christoph Groth
Jörg Behrmann wrote: How can I actually test whether Kwant uses mumps? Try to “import kwant.solvers.mumps”. If this fails, the Kwant MUMPS solver does not work. The only warning I get is about my scipy missing umfpack. Is that the appropriate runtime warning? No, this is an independent

Re: [Kwant] AUR build scripts for kwant and tinyarray

2015-09-16 Thread Christoph Groth
Hi Jörg, Thank you for updating the Arch packaging. I’ve updated the installation instructions following your suggestion. Christoph smime.p7s Description: S/MIME cryptographic signature

Re: [Kwant] AUR build scripts for kwant and tinyarray

2015-09-16 Thread Christoph Groth
Jörg Behrmann wrote: much appreciated. Could you maybe add the link [1] on "Arch install scripts" (the first three words of the paragraph)? Right, the link got lost during the change. Fixed. smime.p7s Description: S/MIME cryptographic signature

Re: [Kwant] About hoppingkind and Translational symmetry in hexagonal lattice

2015-09-17 Thread Christoph Groth
Hi Anant, lat.neighbors() returns nothing else than a list of HoppingKind instances. You can simply print it and have a look. In your case, the three HoppingKind objects that you create manually are identical to the ones returned by lat.neighbors(). Check it! The problem with your script

Re: [Kwant] Package for ubuntu vivid

2015-09-17 Thread Christoph Groth
David Abergel wrote: Is there any chance you could package it for {,k,x}ubuntu 15.04? I tried installing kwant in that linux today, using the 14.10 package, and I am getting a bunch of errors from Tkinter and matplotlib when I use kwant's inbuilt plotter. Up-to-date Kwant packages are now a

Re: [Kwant] del sys[a(0,0)]

2015-10-09 Thread Christoph Groth
Dedi Setiabudidaya wrote: I would like to modify the scattering region by deleting some atoms.For example, I would like to delete 10 atoms and I did it by inserting ten lines of del sys [(,)] in my codes.I was wandering if there is a concise way to do that. Kwant builders behave like python

Re: [Kwant] Energy eigenvalue of graphene edge states

2015-10-12 Thread Christoph Groth
T.C. Wu wrote: Concerning the graphene dot example shown in http://kwant-project.org/doc/1.0/tutorial/tutorial6, may I know the way to find the corresponding energy eigenvalue for the state shown (the edge state)? Check out the documentation for the function that is used: scipy.linalg.eigh

[Kwant] Kwant 1.1 has been released

2015-10-22 Thread Christoph Groth
Hello, We are happy to announce the release of Kwant 1.1. The user-visible changes are: • Harmonize Bands with modes • New option add_cells of attach_lead • New method conductance_matrix • Deduction of transmission probabilities • Clearer error messages • New option pos_transform of map See

[Kwant] Kwant 1.1 has been released

2015-10-22 Thread Christoph Groth
Hello, We are happy to announce the release of Kwant 1.1. The user-visible changes are: • Harmonize Bands with modes • New option add_cells of attach_lead • New method conductance_matrix • Deduction of transmission probabilities • Clearer error messages • New option pos_transform of map See

[Kwant] APS March meeting 2016 tutorial: Introduction to computational quantum nanoelectronics

2015-10-22 Thread Christoph Groth
ors…). We particularly encourage participation of experimentalists wanting to develop their own modeling of their experiments. Basic knowledge of quantum mechanics, statistical physics and condensed matter would help to fully benefit from the tutorial. Organizer Christoph Groth, CEA Greno

Re: [Kwant] Kwant 1.1 has been released

2015-10-22 Thread Christoph Groth
Jörg Behrmann wrote: I've just updated the kwant package build to 1.1.0 on the AUR. Thanks! I saw 1.1.1 is already tagged in the git, will there be a notice when it hits http://downloads.kwant-project.org/kwant/ ? Right… it is now. By the way, the only difference between 1.1.0 and 1.1.1 i

Re: [Kwant] problem loading MUMPS: build.conf?

2015-10-27 Thread Christoph Groth
Becuwe Stefan wrote: I have installed (in non standard directories) * MUMPS 5.0.1 * * SCOTCH 6.0.4 * METIS 5.1.0 (...) However, it seems something is going wrong since MUMPS cannot be loaded. I tried both kwant 1.0.5 and 1.1.1. (...) from kwant.linalg import mumps Traceback (mo

Re: [Kwant] problem loading MUMPS: build.conf?

2015-10-28 Thread Christoph Groth
Becuwe Stefan wrote: So far so good, but … import kwant Current memory used: 416 bytes Maximum memory used: 416 bytes ***Memory allocation failed for OMETIS: cptr. Requested size: 3435973836824 bytes Segmentation fault (core dump made) Any ideas? Weird! 34359738368

Re: [Kwant] Non-interrupted leads

2015-11-26 Thread Christoph Groth
Oscar Erlandsson wrote: Let's say I want to model a 2D system with 'wide leads' like illustrated in the attached figure, i.e. with leads wider than the scattering region, It is possible to realize such a system in Kwant. However, one has to respect Kwant’s convention that leads are connecte

Re: [Kwant] Hopping parameters for multilayered system

2015-11-26 Thread Christoph Groth
Sergey Nikolaev wrote: Could you please explain me how I can put hopping parameters for a multilayered system with  kwant.builder.HoppingKind(). The difficulty is that the intralayer hopping parameters are different for each layer and depend on the layer's position z. T he hopping integrals b

Re: [Kwant] Quantum Hall effect in graphene

2015-12-02 Thread Christoph Groth
T.C. Wu wrote: (...) because I cannot recover the conductance steps in QHE. Please check the QHE example in the Kwant paper. That example calculates conductance steps. Christoph smime.p7s Description: S/MIME cryptographic signature

Re: [Kwant] Quantum Hall effect in graphene

2015-12-02 Thread Christoph Groth
Christoph Groth wrote: T.C. Wu wrote: (...) because I cannot recover the conductance steps in QHE. Please check the QHE example in the Kwant paper. That example calculates conductance steps. I attach a honeycomb-lattice version of qhe.py that does show conductance steps. import math

[Kwant] Kwant 1.2 has been released

2015-12-16 Thread Christoph Groth
Hello, We are happy to announce the release of Kwant 1.2 [1]. Kwant 1.2 is identical to Kwant 1.1 except that it has been updated to run on Python 3.4 and above. Bugfix releases for the 1.1 and 1.2 series will mirror each other, i.e. 1.1.3 and 1.2.3 will fix the same bugs. Starting with Kw

Re: [Kwant] Kwant 1.2 has been released

2015-12-19 Thread Christoph Groth
Hi Jörg, Thanks! I’ve updated http://kwant-project.org/install#arch-linux. Christoph smime.p7s Description: S/MIME cryptographic signature

Re: [Kwant] kwant and Anaconda distribution

2015-12-22 Thread Christoph Groth
Hi Jessica, What error do you get exactly? Can you post the full message? Is the Python interpreter that you are using provided by Ubuntu or by Conda? If it's provided by Conda (let's say it can be launched as "conda-python"), you can try to use pip with that interpreter to build kwant from

Re: [Kwant] kwant and Anaconda distribution

2015-12-24 Thread Christoph Groth
Anton Akhmerov wrote: You probably can find a workaround it by setting the PYTHONPATH environment variable, but this may cause further troubles due to conflicts between different versions of numpy and python. I do not think that there would be any conflicts. I believe that the only question

Re: [Kwant] Installing Kwant on Windows

2016-01-03 Thread Christoph Groth
Jerzy Wrobel wrote: The command, which is suggested on Kwant webpage pip3 install --no-deps *.whl generates (python 3.4 and win7) the following error message: Requirement '*.whl' looks like a filename, but the file does not exist *.whl is not a valid filename. Are there any other p

Re: [Kwant] How resource dependent is Kwant?

2016-01-03 Thread Christoph Groth
siddheshwar chopra wrote: Can anybody tell me HOW resource intensive is KWant? I mean, as compared to DFT calculations. For DFT, computer has to be quite powerful. Any suggestion or explanation is welcomed. Especially in terms of number of atoms. Please have a look at section 7 (“benchmark”

Re: [Kwant] Installing Kwant on Windows

2016-01-04 Thread Christoph Groth
Hi, I just had the idea that the lack of wildcard support in the default Windows shell could be worked-around using Python's own means. Could someone who has access to a Windows machine please try whether the Windows installation instructions [1] work when the command pip3 install --no-dep

Re: [Kwant] Installing Kwant on Windows

2016-01-04 Thread Christoph Groth
Hi Siddheshwar, Thanks for trying. Did you download the *.whl files from Christoph Gohlke's site as described in [1]? You need to execute the command that I gave in the same directory into which these files have been put. Christoph [1] http://kwant-project.org/install#microsoft-windows

Re: [Kwant] Installing Kwant on Windows

2016-01-04 Thread Christoph Groth
Jerzy Wrobel wrote: BTW, 2to3 converter does not exist in my windows installations, nevertheless python scrips are so far interpreted correctly On Windows it seems that you have to use something like: python C:\Python34\Tools\scripts\2to3.py -w script.py but apparently six-1.10.0-py2.py3-no

[Kwant] How strict should we take backwards compatibility?

2016-01-04 Thread Christoph Groth
Dear all, With Kwant, we strive to keep backwards compatibility across major versions: a script that only uses the documented API and works with Kwant 1.x should continue to work unchanged with Kwant 1.y, for any y >= x. Still, we have a bunch of ideas that require breaking strict compatibi

Re: [Kwant] How strict should we take backwards compatibility?

2016-01-06 Thread Christoph Groth
Anton Akhmerov wrote: Thanks a lot, that is exactly what we need to know! Your scripts would indeed be influenced by the change. Well, we will most likely provide syst.graph.num_nodes, and it might be actually possible to have syst.graph.out_neighbors with reasonable (log) efficency as well

Re: [Kwant] How strict should we take backwards compatibility?

2016-01-07 Thread Christoph Groth
Koen Reijnders wrote: By the way, just for curiosity, it is easy to say what the current efficiency of syst.graph.out_neighbors is? Or is it more or less instantaneous? Currently it’s very fast, just a few lookups in integer tables that are done in Cython. The time it takes does not depend

Re: [Kwant] (help request) Windows 7 Install:

2016-01-15 Thread Christoph Groth
Hi Brendan, The error message that you get [1] signals that the module kwant.linalg.lapack cannot be imported. This is the extension module that is created from the source file kwant/linalg/lapack.pyx. On Windows it should have the file name kwant/linalg/lapack.dll, I believe. Can you tel

Re: [Kwant] GPU speedup via PyCUDA

2016-01-25 Thread Christoph Groth
Anton Akhmerov wrote: Finally speeding up the solution of the sparse problem also seems possible on GPU's, but it's a matter of ongoing research, quick googling yielded this for example: https://www.oerc.ox.ac.uk/sites/default/files/uploads/sparse_direct_gpu.pdf Another approach (that is not

[Kwant] Should we disable implicit overwriting in Builder?

2016-02-03 Thread Christoph Groth
Dear Kwant users, Right now it is possible to overwrite bits of a builder, i.e.: syst[lat(0, 0)] = 1 # Create a new site. syst[lat(0, 1)] = 1 # Create another site. syst[lat(0, 0)] = 2 # Overwrite the first site. Kwant builders behave like this because they are mimicking Python’s diction

Re: [Kwant] Should we disable implicit overwriting in Builder?

2016-02-04 Thread Christoph Groth
Anton Akhmerov wrote: Firstly, overwriting hoppings is handy, and we even use it in Kwant tutorial: http://kwant-project.org/doc/1/tutorial/tutorial2#nontrivial-shapes Sure it is handy. That’s why I don’t want to disallow it, only to make it explicit in order to avoid things getting overwri

Re: [Kwant] Kwant for bulk system

2016-02-07 Thread Christoph Groth
Weiyuan Tong wrote: I want to calculate the conductance and the band structure of a bulk graphene system. Finalized systems in current Kwant can only handle a single direction of translational symmetry. We are working on removing this restriction, but this unfortunately requires modifying s

Re: [Kwant] Kwant for bulk system

2016-02-07 Thread Christoph Groth
For people who do not use git, the code can be found directly at https://gitlab.kwant-project.org/cwg/wraparound/raw/master/wraparound.py (To get there from the main page https://gitlab.kwant-project.org/cwg/wraparound, use the "files" link on the left side.) smime.p7s Description: S/MIME cry

Re: [Kwant] Should we disable implicit overwriting in Builder?

2016-02-08 Thread Christoph Groth
Chagaan Baatar wrote: I also like to chime in and vote with Anton on this. What I try to do with Kwant is to build nanographene or polycyclic aromatic hydrocarbon (PAH) molecular structures by combining smaller structures/molecules, sometimes in a hierarchical way. With overwrite, when I fuse

Re: [Kwant] Kwant for bulk system

2016-02-10 Thread Christoph Groth
Weiyuan Tong wrote: Thanks for your code. Can I run it on kwant 1.0 ? When I run your code on my computer I get some error message: The code will work with Kwant 1.0 as well. The test fails because the convention for the sign of momentum of kwant.physics.Bands changed in Kwant 1.1 [1]. "w

Re: [Kwant] Kwant for bulk system

2016-02-12 Thread Christoph Groth
weiyuanphysics wrote: I had tried to install kwant 1.1 after its release, but it showed some error message like "lack of lapack". Do I need to install lapack before I install all the kwant codes? It seems i do not need to do this for kwant 1.0. Are you perhaps referring to the Microsoft Wind

Re: [Kwant] Conda packages for Kwant

2016-02-19 Thread Christoph Groth
Hi Bas, Thanks for packaging Kwant for conda! Do these packages include MUMPS? Do you think you could continue to maintain these packages for a while? If yes, and if no grave problems show up after a few days or so, you would be very welcome to update http://kwant-project.org/install. (Y

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