Kwant-discuss June 2015

kwant-discuss@python.org

11 participants
17 discussions

kwant.linalg.lapack.LinAlgError
by Michael Beconcini 18 Jun '15

18 Jun '15

Dear all, I have made a code to compute the transmission matrices for many close values of energies for a graphene sheet. At a certain value of energy the program stops returning the following error: Traceback (most recent call last): File "4leads_grap_mag.py", line 308, in <module> main() File "4leads_grap_mag.py", line 289, in main print_smatrix(sys, energies, maglist, t_0=t_0) File "4leads_grap_mag.py", line 181, in print_smatrix smatrix = kwant.smatrix(sys, en, args=[t, Phi]) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/kwant/solvers/common.py", line 338, in smatrix check_hermiticity, False) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/kwant/solvers/common.py", line 173, in _make_linear_sys prop, stab = lead.modes(energy, args) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/kwant/system.py", line 213, in modes return physics.modes(ham, self.inter_cell_hopping(args)) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/kwant/physics/leads.py", line 590, in modes evan_vecs = ord_schur(evanselect)[:, :nevan] File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/kwant/physics/leads.py", line 391, in <lambda> calc_ev=False)[2] File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/kwant/linalg/decomp_schur.py", line 495, in order_gen_schur return tgsen(select, s, t, q, z, calc_ev) File "kwant/linalg/lapack.pyx", line 1861, in kwant.linalg.lapack.dtgsen (kwant/linalg/lapack.c:30475) kwant.linalg.lapack.LinAlgError: Reordering failed; problem is very ill-conditioned I’ve tried to run the same code on a different computer, where kwant is installed without umfpack and without mumps, and the programs stops returning exactly the same error, but at a different value of energy. This value of energy at which this second computer stops had not given any problems in the first computer, that instead is able to use umfpack and mumps. Can you suggest a solution? Thank you, Michael

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Attaching leads to a 3D system
by WU Tsz Chun 15 Jun '15

15 Jun '15

Dear Sir/Madam, I am now working with kwant to build my system. I have a question concerning how to attach leads to a 3D system, say a cuboid (the same as that shown in documentation). We cannot accomplish it by using the method for a 2D system: sym_right_lead = kwant.TranslationalSymmetry((a, 0)) right_lead = kwant.Builder(sym_right_lead) for j in xrange(W): right_lead[lat(0, j)] = 4 * t if j > 0: right_lead[lat(0, j), lat(0, j - 1)] = -t right_lead[lat(1, j), lat(0, j)] = -t sys.attach_lead(right_lead) I will be very grateful if you can help me with this. I look forward for your reply. Thank you. Yours faithfully, T.C. Wu

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kwant.plotter.map for lead
by Sergey 15 Jun '15

15 Jun '15

Dear Kwant developers, I have found that plot works for unfinalized lead Builder, while kwant.plotter.map does not. (the aim of the code below is to print a wave-function of the mode in the lead) Could you propose a fix, please. Thank you, Sergey import numpy as np import kwant from numpy import pi, sqrt, tanh, log, sin, cos, exp import scipy.sparse.linalg as sla import scipy.sparse as sparse # For plotting from matplotlib import pyplot def make_lead(W=10): sin_30=0.5 cos_30=sqrt(3)/2.0 lat_r = kwant.lattice.general([(1, 0), (sin_30, cos_30)], [(0, 0), (0, 1.0 / sqrt(3))]) ar,br=lat_r.sublattices ##same, but shifted by bond length in y direction lat_l = kwant.lattice.general([(1, 0), (sin_30, cos_30)], [(0, -1/sqrt(3)), (0, 1.0 / sqrt(3) - 1/sqrt(3))]) al,bl=lat_l.sublattices ##graphene - left and right lattices sym = kwant.TranslationalSymmetry(lat_l.vec((1, 0))) def leadl_shape(pos): x, y = pos return (0 > y >= - W * sqrt(3)/2.0 ) lead = kwant.Builder(sym) lead[lat_l.shape(leadl_shape, (0, 0))] = 0.0 lead[lat_l.neighbors()] = 1 def leadr_shape(pos): x, y = pos return (0 <= y <= W * sqrt(3)/2.0) lead[lat_r.shape(leadr_shape, (0, 0))] = 0.0 lead[lat_r.neighbors()] = 1 lead[al(0,0),ar(0,0)]=1 def family_color(site): return 'black' if site.family == a else 'white' kwant.plot(lead,num_lead_cells=3,hop_lw=0.1,site_size=0.1,show=False) return lead def plot_bandstructure(flead, momenta): bands = kwant.physics.Bands(flead) energies = [bands(k) for k in momenta] pyplot.figure() pyplot.plot(momenta, energies) pyplot.xlabel("momentum [(lattice constant)^-1]") pyplot.ylabel("energy [t]") # pyplot.show() def main(): barelead=make_lead(3) lead = make_lead(3).finalized() plot_bandstructure(lead, momenta=np.linspace(-np.pi, np.pi, 101)) propagating, stabilized = lead.modes(energy=0.2) print propagating.wave_functions print propagating.momenta print propagating.velocities mode1=abs(propagating.wave_functions)[:,1] print mode1 kwant.plot(barelead,num_lead_cells=3,hop_lw=0.1,site_size=0.1,show=False) ####This gives Error. kwant.plotter.map(barelead, mode1) pyplot.show() # Call the main function if the script gets executed (as opposed to imported). # See <http://docs.python.org/library/__main__.html>. if __name__ == '__main__': main()

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2 PhD positions in computational quantum theory (Grenoble)
by Christoph Groth 09 Jun '15

09 Jun '15

Dear all, Please take note of this announcement and forward it to anyone who might be interested. Thank you. This summer/fall we are going to hire two PhD students to work with us on new computational approaches to quantum transport. Candidates should have a strong background in theoretical physics (ideally condensed matter / quantum transport) as well as experience in software design and development. Each PhD project will consist of three overlapping phases: (1) Prototyping of a new computational approach for quantum transport problems. (2) Implementation of the new approach within the framework of the Kwant code [1]. (3) Application of the newly gained capabilities to unsolved physical problems, in close collaboration with experts in the particular fields. The two subjects are introduced in some detail at the bottom of this message. The research will take place 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 Grenoble offers a superb combination of a rich international scientific environment with a unique natural and cultural setting. Grenoble is home to a vibrant nanoscience research community [2], several international research institutions (ESRF synchrotron, ILL neutron source, and others) and 60,000 university students. The city is literally surrounded by the French alps that offer numerous possibilities for outdoor activities. Interested candidates are invited to send an application to Christoph Groth [3] with the subject “PhD application Kwant 2015”. Applications should include: • a CV, • Email addresses of persons that can be asked for a recommendation, • an example of theoretical physical work done by the applicant (e.g. a project, or a master thesis), Applicants are invited to also provide the source code of a program that highlights their software engineering experience. Sincerely Christoph Groth and Xavier Waintal [1] http://kwant-project.org/ [2] http://www.fondation-nanosciences.fr/RTRA/en/14/vocation.html [3] mailto:christoph.groth@cea.fr Subject 1: Scalable electrostatics computations Both single-particle simulations of quantum nanoelectronics and pure electrostatics simulations are a standard problem. However, in order to accurately simulate complex quantum systems, one needs to combine both approaches. This transforms the linear electrostatic problem into a non-linear integro-differential system of equations with rapidly growing complexity. Current approaches at exactly solving the combined problem are limited to small systems of around 10 nanometers in linear size. Advancing the state of the art is becoming increasingly important to improve our understanding of modern experiments (e.g. spin qubits, mesoscale transport). Subject 2: Multidimensional scattering Traditionally, quantum transport codes have focused on the 1-d scattering problem: a finite scattering region with attached semi-infinite quasi-1-d electrodes. While this suffices to calculate the basic experimental observables (for example conductance), solving the more general n-dimensional case would allow to • characterize disordered materials with a non-spherical band structure, • calculate transport properties of crystallographic defects, • treat hybrid systems with different dimensionalities (e.g. a 1-d nanowire coupled to a 3-d superconductor). The first two capabilities would greatly aid in the analysis of realistic systems and materials that in practice contain disorder, dislocations and impurities. The last capability would be highly valuable for example for studies of Majorana fermions.

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Install want on CentOS 6.4
by Michael Beconcini 09 Jun '15

09 Jun '15

Dear all, I’m a PhD student and I need to install kwant on the server of my university dedicated to big numerical calculations. On this server it is installed a CentOS distribution, release 6.4, and I don’t know exactly how to do it. I have tried to install the source from the file kwant-1.0.2.tar.gz, but without success. Is there a simple way to do it? Thank you for your attention. Best regards, Michael Beconcini

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Problem with drawing picture
by Iwona Janus-Zygmunt 06 Jun '15

06 Jun '15

Good morning, I am PhD student and I have small problem with drawing picture. I would like to get picture where attachment between site number 3 to 6 would be thin line, and in other places wider line. Because I would like small coupling and bigger coupling. I was trying with 'def hopping_lw', but it didn't get good picture. Please bear with me. I am a beginner in programming Best regards, Iwona Janus-Zygmunt This is code: from matplotlib import pyplot import kwant # First, define the tight-binding system sys = kwant.Builder() # Here, we are only working with square lattices a = 1 lat = kwant.lattice.square(a) t = 1.0 # - bigger coupling tt=0.1 # - smaller coupling W = 3 L = 10 # Define the scattering region for i in xrange(L): for j in xrange(W): # On-site Hamiltonian sys[lat(i, j)] = 4 * t if i in xrange(3,6): # Hopping in y-direction if j > 0: sys[lat(i, j), lat(i, j - 1)] = -tt # Hopping in x-direction if L-1 > i > 1: sys[lat(i, j), lat(i - 1, j)] = -tt else: # Hopping in y-direction if j > 0: sys[lat(i, j), lat(i, j - 1)] = -t # Hopping in x-direction if L-1 > i > 1: sys[lat(i, j), lat(i - 1, j)] = -t # Then, define and attach the leads: # First the lead to the left # (Note: TranslationalSymmetry takes a real-space vector) sym_left_lead = kwant.TranslationalSymmetry((-a, 0)) left_lead = kwant.Builder(sym_left_lead) for j in xrange(W): left_lead[lat(0, j)] = 4 * t if j > 0: left_lead[lat(0, j), lat(0, j - 1)] = -t left_lead[lat(1, j), lat(0, j)] = -t sys.attach_lead(left_lead) # Then the lead to the right sym_right_lead = kwant.TranslationalSymmetry((a, 0)) right_lead = kwant.Builder(sym_right_lead) for j in xrange(W): right_lead[lat(0, j)] = 4 * t if j > 0: right_lead[lat(0, j), lat(0, j - 1)] = -t right_lead[lat(1, j), lat(0, j)] = -t sys.attach_lead(right_lead) def hopping_lw(site1, site2): return 0.04 if site1.family == site2.family else 0.1 # Plot it, to make sure it's OK kwant.plot(sys,hop_lw=hopping_lw,file='picture.png') # Finalize the system sys = sys.finalized()

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Kwant user survey
by Christoph Groth 02 Jun '15

02 Jun '15

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 accessed directly at http://kwant-project.org/2015-survey. Thanks, your feedback is highly appreciated. Christoph on behalf of the authors of Kwant

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Kwant-discuss June 2015