Re: [Kwant] wave function at each site

2016-04-18 Thread Abbout Adel
the intensity at each site > plotted by > > kwant.plot(sys, site_color=wf, site_symbol=family_shape, >site_size=0.5, hop_lw=0, cmap='gist_heat_r') > > can be obtained from wf without attaching the leads right? Thanks again > for your time. > > Best, > Johnny

Re: [Kwant] wave function at each site

2016-04-18 Thread Abbout Adel
; > I obtained the wavefunction of the system by using > ham = sys.hamiltonian_submatrix() > evecs = la.eigh(ham)[1] > > Is the wavefunction corresponding to site i given by evecs[i] ? Thanks! > > Best, > Johnny > > On 18 April 2016 at 03:44, Abbout Adel <abb

Re: [Kwant] closed graphene system - PBCs in one direction - dispersion

2016-07-20 Thread Abbout Adel
persion relation E(k_y) of such a closed system > with periodic boundary conditions in y-direction (I did it by hand) and > hard-wall in x-direction. I guess I need to do the Fourier transform in > y-direction by hand. Or, are there some built-in functions to do this? > > Thank you for eventual answer or pointing me to duplicate question. > > Tibor > -- Abbout Adel

Re: [Kwant] (no subject)

2017-02-08 Thread Abbout Adel
if sys[site]==edge_potential: > return 'green' > else: return 'black' > > def site_size(site): > if sys[site]==edge_potential: > return 0.35 > else:return 0.2 > kwant.plot(sys,site_color=family_color,site_size=site_size) > # Finalize the system. > sys = sys.finalized() > > > # Compute number of neighbors > i=sys.sites.index(graphene(5,6)) > all_the_neighbors=sys.graph.out_neighbors(i) > > > > # Call the main function if the script gets executed (as opposed to imported). > # See <http://docs.python.org/library/__main__.html> > <http://docs.python.org/library/__main__.html>. > if __name__ == '__main__': > main() > > > -- Abbout Adel

Re: [Kwant] Using Kwant for finding tunneling probability from metal to vacuum

2017-02-14 Thread Abbout Adel
ne wave is normal to the barrier). Could you give me some advice on how > to achieve this? > > Best regards, > Kristjan > > On Mon, Dec 19, 2016 at 8:15 PM, Abbout Adel <abbout.a...@gmail.com> > wrote: > >> >> >> Dear Kristjan, >> >> >

Re: [Kwant] Using Kwant for finding tunneling probability from metal to vacuum

2017-02-14 Thread Abbout Adel
solve it easily. your conductance is the sum of all the conductances (Actually the sum is an integral (you need to divide over the number of modes to go from the sum to the Riemann integral)) I hope that this helps Adel On Tue, Feb 14, 2017 at 2:36 PM, Abbout Adel <abbout.a...@gmail.com>

Re: [Kwant] Plotting Hamiltonian for overlapping lattices

2016-11-08 Thread Abbout Adel
t looks completely random. > > > > I hope my explanation was understandable. > > > > Best, > > Camilla > > > -- Abbout Adel # Tutorial 2.6.2. "Lattice description": using different lattices # ==

Re: [Kwant] a step tripping up Kwant

2016-10-17 Thread Abbout Adel
gies - V0)/hbar**2) > T = 4*k1*k2/(k1+k2)**2 > T[energies <= V0] = 0 > > plt.figure() > plt.plot(energies, data, energies, T) > plt.legend(('numerical','exact'), loc=4) > plt.xlabel("energy [V0]") > plt.ylabel("Transmission") > plt.show() > return data, T > > > # In[6]: > > stepNumerical, stepExact = plot_conductance(sys,linspace(1e-9,2*V0,201)) > > > # In[7]: > > print(stepNumerical) > > -- Abbout Adel

Re: [Kwant] Curved Quantum Wire

2016-12-08 Thread Abbout Adel
> appreciated. Thank you. > > > > > -- > Oliver B. Generalao > > M.S. Physics student > Structure and Dynamics Group > National Institue of Physics > University of the Philippines > Diliman, Quezon City > Trunkline: +63-2-981-8500 > Mobile: +63-927-4033966 > -- Abbout Adel

Re: [Kwant] A question regarding the conductance formula in Kwant paper

2016-12-07 Thread Abbout Adel
; > > # Check that the system looks as intended. > > # kwant.plot(sys) > > > > # Finalize the system. > > sys = sys.finalized() > > > > en = 3 > > sm = kwant.smatrix(sys, en) > > > > print('transmission by kwant: ',sm.transmission(0,0)) > > > > smatrix = sm.data > > sdags = (smatrix.conj().T) > > # As from Eq. (10) in kwant paper > > print((sdags[0,0]*smatrix[0,0] + sdags[0,1]*smatrix[0,1] + > sdags[1,1]*smatrix[1,1]+ sdags[1,0]*smatrix[1,0])) > > # As from Eq. (47) in buttiker > > print(sdags[0,0]*smatrix[0,0]+sdags[1,1]*smatrix[1,1] - 2) > > > > # 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() > -- Abbout Adel

Re: [Kwant] How can I use kwant.plotter.map when using an orbital description

2016-12-15 Thread Abbout Adel
bar=False, oversampling=1) > > syst = make_system() > kwant.plot(syst) > syst = syst.finalized() > plot_conductance(syst, energies=[-0.25 + 0.005 * i for i in range(100)]) > plot_wave_function(syst) > > > Currently, I get the error "The number of sites doesn't match the number > of provided values." > > ​Thanks, > Eric​ > > -- Abbout Adel

Re: [Kwant] putting disorder (kwant.digest.uniform) in graphene with shape function

2017-01-13 Thread Abbout Adel
> Thank you for the quick reply. I think my institute mail is not working > properly, so I used this mail-id. > > By using the line: lambda site: sys_2['sys'][site] > > I got another error massage, which says that, "TypeError: 'int' object is > not callable". > > With

Re: [Kwant] On-site potential only at the edge of the sample in Kwant

2017-01-03 Thread Abbout Adel
any example code from which I can learn to use this function? > > > Best, > Dongwook. -- Abbout Adel

Re: [Kwant] STM tip as lead

2017-01-08 Thread Abbout Adel
above a 2D > system? > I'm guessing that I have to use a 3D system where the system is in the XY > plane and the lead has a translational symmetry in the Z direction. > > Thanks, > Eric > -- Abbout Adel

Re: [Kwant] virtual lead

2017-07-31 Thread Abbout Adel
(3)] for i in > range(3)]) > voltage = linalg.solve(cond, [1, -1, 0]) > > How do I calculate the conductance then? > > Regards > Patrik > > On 27 July 2017 at 17:13, Abbout Adel <abbout.a...@gmail.com> wrote: > >> Dear Patrik, >> >> I have some

Re: [Kwant] Current in a closed system

2017-07-18 Thread Abbout Adel
can arise in other > contexts. > > In the future we want to make it easier to work with these different > quantities without having to put the burden of bookkeeping on the user, but > it's difficult to do this while trying to keep things simple. If anybody > has any suggestions we are very open to them! > > Happy Kwanting, > > Joe > > > [1]: https://kwant-project.org/doc/1/tutorial/operators#using- > bind-for-speed > > -- Abbout Adel

Re: [Kwant] Importing coordinates of the scattering region

2017-07-09 Thread Abbout Adel
es[0]] = syst[sites[1]] = 2 >> syst[sites[1], sites[0]] = 1 >> >> kwant.plot(syst) >> ----- >> >> Of course it's now your responsibility to specify the Hamiltonian, >> leads, attaching leads, etc. >> >> Best, >> Anton >> >> On Thu, Jul 6, 2017 at 4:12 PM, Patrik Arvoy <arv...@gmail.com> wrote: >> > >> > Dear users and developers, >> > >> > I was wondering if I can import the coordinates of a scattering region >> > without any particular symmetry and compute the conductance via kwant. >> > If yes, how does one do that? >> > Let's say the scattering region does not have any symmetry after >> optimizing >> > the structure via MD or ... and I have a list of coordinates of all the >> > sites. >> > I appreciate any help. >> > >> > Regards >> > Patrik >> > > -- Abbout Adel

Re: [Kwant] virtual lead

2017-07-27 Thread Abbout Adel
= t0*sigma_0 > syst.attach_lead(up_lead) > > system=kwant.plot(syst, site_lw=0.1, site_color=family_color, > hop_lw=hopping_lw) > > > trans=True > if trans: > syst = syst.finalized() > energies = [] > datau = [] > datad = [] > > for ie in range(-320,520): > energy = ie * 0.001 > smatrix = kwant.smatrix(syst, energy=energy) > energies.append(energy) > Gu=smatrix.transmission((1, 0), 0) > Gd=smatrix.transmission((1, 1), 0) > datau.append(Gu) > datad.append(Gd) > > fig = pyplot.figure() > pyplot.plot(energies, datau, 'r--') > pyplot.plot(energies, datad, 'b:') > pyplot.legend(['Gu', 'Gd'], loc='upper left') > pyplot.xlim([-0.4,0.65]) > pyplot.ylim([-0.03,1.0]) > pyplot.show() > > > -- Abbout Adel

Re: [Kwant] Plotting 2D maps for 3D systems

2017-04-26 Thread Abbout Adel
took from the post referenced at the start, and it > gives a syntax error. I'm not really sure how to fix it as it looks fine to > me. What's wrong there? > > And more importantly, once this is fixed, how can one then make a > kwant.plotter.map type of plot at this x-z plane? > -- Abbout Adel

[Kwant] small correction in the documentation

2017-07-30 Thread Abbout Adel
Dear all, In the section "Computing local quantities: densities and currents", the function field_direction(pos,r0,delta) is defined with the condition: if r==0: m_i=[0,0,1] This should be m_i =[0,0,-1] This explains why we get some strange pattern in the present figures on the online

Re: [Kwant] eigenvalues test in wraparound module

2017-05-15 Thread Abbout Adel
Thank you Joseph for the highlight. It make sens since the tests on a square lattice seemed working fine. I checked the 'plot_2d_bands' function but could not identify the transformation you were mentioning. Could you help me in this please? Just to check my understanding for this module,

Re: [Kwant] use of a function to define the on-site energy in the leads

2017-05-24 Thread Abbout Adel
t; >> There is a warning in the Kwant tutorial about this exact topic [1]. >> Any value function used by leads *must* have the declared symmetry >> of the lead -- Kwant evaluates the lead Hamiltonian over an arbitrary >> unit cell, so you will not get what you expect if your value functions >> do not satisfy this symmetry. >> >> Do you think that we could make this warning more prominent in the >> tutorial? >> >> >> Happy Kwanting, >> >> Joe >> >> >> [1]: https://kwant-project.org/doc/1/tutorial/tutorial2#spatially >> -dependent-values-through-functions >> > > -- Abbout Adel

Re: [Kwant] How to plot the local dos for both the scattering region and leads

2017-09-19 Thread Abbout Adel
te(site, pot=0): >> > return 4 * t + potential(site, pot) >> > >> > sys[(lat(x, y) for x in range(L) for y in range(W))] = onsite >> > sys[lat.neighbors()] = -t >> > >> > Define and attach the leads. >> > lead = kwant.Builder(kwant.TranslationalSymmetry((-a, 0))) >> > lead[(lat(0, j) for j in range(W))] = 4 * t >> > lead[lat.neighbors()] = -t >> > sys.attach_lead(lead) >> > sys.attach_lead(lead.reversed()) >> > >> > return sys >> > >> > def main(): >> > >> > sys = make_system() >> > >> > # Check that the system looks as intended. >> > kwant.plot(sys) >> > >> > # Finalize the system. >> > sys = sys.finalized() >> > >> > # Calculate ldos at a given energy >> > well_depth = 0.55 >> > ldos = kwant.ldos(sys, energy=0.25, args=[-well_depth]) >> > kwant.plotter.map(sys, ldos, num_lead_cells=10) >> > >> > if __name__ == '__main__': >> > main() >> > >> > > -- Abbout Adel

Re: [Kwant] lead_info

2017-09-20 Thread Abbout Adel
nts) is for the use of the > intended recipient only and may contain confidential information and/or > copyright material. If you are not the intended recipient, please notify > the sender immediately and delete this email and all copies from your > system. Any unauthorized use, disclosure, reproduction, copying, > distribution, or other form of unauthorized dissemination of the contents > is expressly prohibited. > -- Abbout Adel

Re: [Kwant] A weird result of 1D quantum wire

2017-09-05 Thread Abbout Adel
t_lead.finalized()) > > #finalize the system for conductivity computation > sys=sys.finalized() > return energies,kwant.smatrix(sys,0.0001).transmission(1,0) > > das=np.linspace(0,10,51) > > ts=[] > defect=[1000] > #energies,data,t=conduct(mu=0.0,da=0.0) > #pyplot.plot(energies,data) > for tda in das: > energies,t=conduct(mu=0,da=tda) > ts.append(t) > > #plot the conductance > > > > > > #pyplot.ylim([0,1]) > pyplot.show() > pyplot.figure() > pyplot.plot(das,ts) > pyplot.xlabel('A') > pyplot.ylabel('conductance[e^2/h]') > > > Best regards, > Feng Liu > > -- Abbout Adel

Re: [Kwant] How to build a phosphorene lattice

2017-12-16 Thread Abbout Adel
ke to help me to find the bug? Thank you! > > Regards, > > Qiao Chen > > > University of Antwerp > Condensed Matter Theory > Department of Physics > -- Abbout Adel

Re: [Kwant] Hamiltonian not hermician for an infinite wire with random complex hopping

2018-05-22 Thread Abbout Adel
ut not for the hoppings ? (it > also doesn't work for random real nearest neighbors hopping terms) > > I will try to fix it by hand, by specifying the hopping terms between the > cells, and see if it works. > > Best regards, > Alexandre > > --

Re: [Kwant] Coupling Matrix between Lead and Conductor

2018-06-10 Thread Abbout Adel
and had overlooked the >> phase part. A noob mistake. >> >> Appreciate your help! >> >> Shivang >> >> On Thu, Jun 7, 2018 at 11:53 AM Abbout Adel >> wrote: >> >>> Dear Shivang, >>> >>> To get the matrix Gamma you can do: >&

Re: [Kwant] Coupling Matrix between Lead and Conductor

2018-06-07 Thread Abbout Adel
is confusing! I hope this helps. Adel [1] https://mailman-mail5.webfaction.com/pipermail/kwant-discuss/2015-May/000355.html Abbout Adel On Wed, Jun 6, 2018 at 11:53 PM, Shivang Agarwal < shivang.agar...@iitgn.ac.in> wrote: > Hello authors, > > I am trying to perform an eigenc

Re: [Kwant] Energy dispersion of MoS2

2018-01-03 Thread Abbout Adel
uilder.HoppingKind(*hopping2_MX)] = t2_MX > > sys[kwant.builder.HoppingKind(*hopping3_MX)] = t3_MX > > def family_colors(site): > > return 0 if (site.family == M) else 1 > > def hopping_lw(site1, site2): > > return 0.05 if site1.family == site2.family else 0.1 > > def hopping_color(site1,site2): > > return 'g' if site1.family==site2.family else 'b' > > kwant.plot(sys,site_color=family_colors,site_lw=0.05, > hop_lw=hopping_lw,hop_color=hopping_color,colorbar=False) > > return sys > > > > > > def main(): > > lead = make_lead().finalized() > > kwant.plotter.bands(lead, show=False) > > pyplot.xlabel("momentum [(lattice constant)^-1]") > > pyplot.ylabel("energy [eV]") > > 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() > > > -- Abbout Adel

Re: [Kwant] getting less number of peaks in transmission for 1D chain

2018-01-23 Thread Abbout Adel
that. (This is true for tc <<1). I hope this helps Abbout Adel On Tue, Jan 23, 2018 at 7:53 AM, SUDIN GANGULY <sudingang...@gmail.com> wrote: > Dear Sir, > > Recently I was doing a problem on a 1D chain. The problem I faced is as > follows. > > For a 1D chain

Re: [Kwant] Saving a figure of the system

2018-02-07 Thread Abbout Adel
-- > > > > If anyone knows whether the problem is with the system or with the > plotting it would be greatly appreciated. > > Regards > > > > -- > Dr. Eleni Chatzikyriakou > Computational Physics lab > Aristotle University of Thessaloniki > elch...@auth.gr - tel:+30 2310 998109 > > -- Abbout Adel

Re: [Kwant] Conductance for a rectangular geometry

2018-02-22 Thread Abbout Adel
) > #transmission from left 2 leads to right lead > > pyplot.figure() > pyplot.plot(energies, data) > pyplot.xlabel("energy [t]") > pyplot.ylabel("conductance [e^2/h]") > pyplot.show() > energies=[-3+i*0.02 for i in range(100)] > plot_conductance(sys,energies) > -- Abbout Adel

Re: [Kwant] Conductance for a rectangular geometry

2018-02-24 Thread Abbout Adel
y. I have another query here. Can I add > these two system together incorporating missing hopping elements? > -- Abbout Adel

Re: [Kwant] (no subject)

2018-08-10 Thread Abbout Adel
his lead always) for calculating the > scattering matrix. > Please, suggest me what is the code of voltage. (How to apply the voltage) > Best, > Rohit > -- Abbout Adel

Re: [Kwant] Profiles of incoming transverse waveguide modes

2018-03-14 Thread Abbout Adel
rix.transmission(1,2) ) > #transmission from left 2 leads to right lead > > pyplot.figure() > pyplot.plot(energies, data) > pyplot.xlabel("energy [t]") > pyplot.ylabel("conductance [e^2/h]") > pyplot.show() > energies=[-3+i*0.02 for i in range(100)] > plot_conductance(sys,energies) > > > -- Abbout Adel

Re: [Kwant] Coordinates of spatial greens function

2018-03-21 Thread Abbout Adel
gt; > if (x-25*a)**2+(y-9*a)**2<8: > > return -m*sz+0*sx > > elif y>-0.1*a: > > return m*sz+0*sx > > else: > > return np.zeros([2,2]) > > > > > > sys[lat.shape(disk,(0,0))]=onsite > > sys[lat.neighbors()]=-s0*2/3 > > sys[A.neighbors()]=hopp > > sys[B.neighbors()]=hopp2 > > > > lead0=kwant.Builder(kwant.TranslationalSymmetry((-a,0))) > > lead0[lat.shape(edge,(0,0))]=onsite > > lead0[lat.neighbors()]=-s0*2/3 > > lead0[A.neighbors()]=hopp > > lead0[B.neighbors()]=hopp2 > > sys.attach_lead(lead0) > > sys.attach_lead(lead0.reversed()) > > > > kwant.plot(sys, fig_size=(30, 12)) > > > > sys=sys.finalized() > > > > gf=kwant.greens_function(sys,0).submatrix(1,0) > > ## > -- Abbout Adel

Re: [Kwant] Units of density

2018-10-22 Thread Abbout Adel
ut > overall I'm not so sure of the units. > > > Thank you again for your help. > > > Kind regards, > > > Marc > -- Abbout Adel

Re: [Kwant] plotting band structure of bulk 2D material along high symmetry lines in the Brillouin zone

2018-10-24 Thread Abbout Adel
> Can anyone give some useful solutions to my concern? Your help is much > appreciated. > > Thank you and best regards, > Kuangyia Lee > > > -- Abbout Adel

Re: [Kwant] attach-lead

2019-01-23 Thread Abbout Adel
; Can you give me some hints? > > Maybe my description is not clear, I attach the code in the e-mail to > reproduce this question. > > Best wishes. > Jinlong Zhang > jlzhang1...@163.com > > > > -- Abbout Adel

Re: [Kwant] Ynt: Re: Datta’s ballistic transport formalism vs KWANT

2019-01-23 Thread Abbout Adel
tta’s transmission expression? >> > >> >> Nice question! >> >> Looking at your results it seems that the energies at which new modes >> open is shifted with respect to Datta's result. >> >> I believe that this is simply due to the fact that your discretization >> is not fine enough. Datta's result is valid in the continuum limit, >> whereas the Kwant simulation (in the case presented) uses a >> finite-difference discretization to render the problem discrete. If you >> decrease the 'a' parameter, you should see the discrepancy between the >> two result decrease. >> >> >> Happy Kwanting, >> >> Joe >> > > > -- > Abbout Adel > -- Abbout Adel

Re: [Kwant] Ynt: Re: Datta’s ballistic transport formalism vs KWANT

2019-01-22 Thread Abbout Adel
tion (in the case presented) uses a > finite-difference discretization to render the problem discrete. If you > decrease the 'a' parameter, you should see the discrepancy between the > two result decrease. > > > Happy Kwanting, > > Joe > -- Abbout Adel

Re: [Kwant] The right way to build up a system?

2018-11-19 Thread Abbout Adel
la.eigh(ham)[1] > psi=evecs[:, n] > > J_0 = kwant.operator.Current(syst) > current=J_0(psi) > print(len(current)) > kwant.plotter.current(syst, current, colorbar=False) > > wf = abs(psi)**2 > def site_size(i): > return wf[i] / wf.max() > > kwant.plot(syst, site_size=site_size, site_color=(0, 0, 1, 0.3), >hop_lw=0.1) > > def main(): > syst=make_system() > plot_data(syst,900) > syst2=make_system2() > plot_data(syst2,900) > > if __name__ == '__main__': > main() > > -- Abbout Adel

Re: [Kwant] Fixing min and max values of colormap using kwant.plot

2018-11-19 Thread Abbout Adel
s and best regards, > Shivang Agarwal > > -- > *Shivang Agarwal* > Senior Undergraduate > Coordinator - Academic Discussion Hours > Discipline of Electrical Engineering > IIT Gandhinagar > > Contact: +91-9869321451 > -- Abbout Adel

Re: [Kwant] Question about leads

2019-03-05 Thread Abbout Adel
dagger} > since I am starting with Kwant, > I prefer to understand the low-level programming, first. > > Thank you very much again > > L. > > > Il giorno mar 5 mar 2019 alle ore 10:20 Abbout Adel > ha scritto: > > > > Dear Luca, > > > > Lookin

Re: [Kwant] Dephasing effect

2019-03-20 Thread Abbout Adel
SFpUZDZe_NmpizjAUd5aDVWfJ1pWtaEWkmo95Kor8QVS> > no > longer hermite ? > > -- > Jinlong Zhang > jlzh...@163.com > > > > -- Abbout Adel

Re: [Kwant] help on constructing a one-dimensional tight-binding chain using kwant

2019-03-18 Thread Abbout Adel
this seemly simple problem. > > Thank you very much for your help in advance. > > Hanning Chen, Ph.D. > Assistant Professor > Department of Chemistry > George Washington University > Washington, DC 20052 > http://www.chenlagbwu.net > > > > > -- Abbout Adel

Re: [Kwant] Problem with semimetals

2019-03-22 Thread Abbout Adel
a_0 > > > right_lead[lat(i, 1, k), lat(i, 0, k)] = -t*sigma_0 > > > # I close hopping in x-direction, connecting W-1 and 0 > for k in range(W): > right_lead[lat(0, 0, k), lat(W-1, 0, k)] = -t*sigma_0 > > # I close hopping in z-direction, connecting W-1 > for i in range(W): > right_lead[lat(i, 0, 0), lat(i, 0, W-1)] = -t*sigma_0 > > > syst.attach_lead(right_lead) > left_lead = right_lead.reversed() > syst.attach_lead(left_lead) > -- Abbout Adel

Re: [Kwant] Advanced green's function

2019-04-14 Thread Abbout Adel
; your archive. But when I have tried to execute it didn't work. > > -- Abbout Adel

Re: [Kwant] Advanced green's function

2019-04-15 Thread Abbout Adel
> line 98, in main > Ga = conj((Gr).T) #a for advanced > NameError: name 'conj' is not defined > > Best, > Sayan > > > -- > *From:* Abbout Adel > *Sent:* Monday, April 15, 2019 1:27:01 AM > *To:* SAYAN MONDAL; kwant-discuss > *Subject:*

Re: [Kwant] About Calculating density of states in transport system

2019-05-17 Thread Abbout Adel
gt; Hence, there’s something wrong with the calculation. I don’t know how to > solve the warning. > > > > Please help me solve my bewilderment , Thanks! > > > > Best regard, > > > > Yan > > -- Abbout Adel

Re: [Kwant] Infinite Slab and wraparound

2019-06-08 Thread Abbout Adel
hen you find a solution. We are particularly > interested if you find some problem with Kwant (or its documentation). > > Owocnego Kwantowania! > > Krzysiek > -- Abbout Adel

Re: [Kwant] Density Operator & Current Operator for 3D systems

2019-06-11 Thread Abbout Adel
an *ValueError: Only 2D systems can be plotted this >> > way.* Please suggest me if there is a way to plot probability density >> > for 3D system having only an orbital degree of freedom per site. >> >> Kwant's plotting submodule is based on matplotlib, whose 3D features are >> very rudimentary and slow. And anyway, what kind of plot do you have in >> mind? There are many different ways to plot 3D densities, appropriate >> for different situations/data. >> >> For serious 3D plotting, I suggest using a separate library. For >> example, you could give MayaVi a try. >> > > > -- > > > With Best Regards > NAVEEN YADAV > Ph.D Research Scholar > Deptt. Of Physics & Astrophysics > University Of Delhi. > -- Abbout Adel

Re: [Kwant] bounds on KPM

2019-06-17 Thread Abbout Adel
is > possible to get the correct DOS with limited energy window. > > Best, > Antonio > > Em dom, 16 de jun de 2019 às 05:11, Abbout Adel > escreveu: > >> Dear Antonio, >> >> Without an example, your problem may be not very clear. Could you provid

Re: [Kwant] Current and hopping index relationship

2019-06-23 Thread Abbout Adel
so, I'm not sure that if I want to calculate the current at a certain > energy (like "-1" above), > do I have to calculate the current at all the wavefunction (like for all p > of wf(0)[p]) > or I have to calculate the current only at the wavefunction with "negivate > velocity"? > > Thanks in advance for your help. > Hang Zang > -- Abbout Adel

Re: [Kwant] Density Operator & Current Operator for 3D systems

2019-06-10 Thread Abbout Adel
> > > > > > Naveen > Department of Physics & Astrophysics > University of Delhi > New Delhi-110007 > -- Abbout Adel

Re: [Kwant] build polyatomic model with different orbital number on each site

2019-05-19 Thread Abbout Adel
0.0)] = -4.0 > syst[basis[0](0.0 , 0.0 , 0.0) , basis[2](8.0 , 0.0 , 0.0)] = -4.0 > syst[basis[0](0.0 , 0.0 , 0.0) , basis[3](8.0 , 0.0 , 0.0)] = -4.0 > syst[basis[0](0.0 , 0.0 , 0.0) , basis[4](8.0 , 0.0 , 0.0)] = -4.0 > > kwant.plot(syst) > > syst = builder.finalized() > > sparse_mat = syst.hamiltonian_submatrix(sparse=False) > print(np.matrix(sparse_mat)) > evs = scipy.sparse.linalg.eigs(sparse_mat,3)[0] > print(evs.real) > > === > > > -- Abbout Adel

Re: [Kwant] Regarding the NNN term in bilayer graphene across the layer

2019-04-30 Thread Abbout Adel
ind I had given is right or wrong. Is there > any way to visualize those hoppings in the 3d plot (as we can see in the 2d > plot). > > > Ah, that's a good point. Perhaps you could make the 2 lattices in 2D but > put an offset in the x-y positions of the sites in one of the layers of the > bilayer. This way you can still visualize the hoppings using kwant.plot and > the sites occupy distinct positions in space. Because we are limited by > matplotlib's poor 3D rendering we cannot display the hoppings in 3D plots. > > > Happy Kwanting, > > > Joe > -- Abbout Adel

Re: [Kwant] Mobius Structure using Kwant

2019-07-09 Thread Abbout Adel
2, 1, projection='3d') > ax.plot_trisurf(x, y, z, triangles=tri.triangles) > ax.set_zlim(-1, 1) > > plt.show() > > > -- Abbout Adel

Re: [Kwant] 答复: Problem in Kwant1.4

2019-04-23 Thread Abbout Adel
ere is a hopping > integral missing in the left lead. > > > > Otherwise, I writing the same lead which I don’t replace *lead1* with* > sys* in the symmetric direction, there is no error here. > > > > Please help me solve this problem,Thanks! > > > > In the attachment, I will attach my program. > > > > Sincerely yours, > > F.X. Yan > > > > 发送自 Windows 10 版邮件 <https://go.microsoft.com/fwlink/?LinkId=550986>应用 > > > > > -- Abbout Adel

Re: [Kwant] leads not properly attached in a one-dimensional system

2019-04-23 Thread Abbout Adel
print(np.matrix(sparse_mat)) > evs = scipy.sparse.linalg.eigs(sparse_mat,10)[0] > print(evs.real) > > #conductance calculation through transmission matrix > energies = [] > transmission = [] > > for ie in range(100): > energy = ie * 0.01 > smatrix = kwant.smatrix(device, energy) > energies.append(energy) > transmission.append(smatrix.transmission(1,0)) > > plt.figure() > plt.plot(energies,transmission) > plt.xlabel("energy") > plt.ylabel("conductance") > plt.show() > > > -- Abbout Adel

Re: [Kwant] How to feed a portion of a finite system to kwant.plotter.interpolate_density

2019-08-17 Thread Abbout Adel
uot;ch_densities", which is basically a vector of > length=len(sys_f.sites). > > > > For complexity reason, I'd like to feed a slice of sys_f to the > interpolate_density() as: > > > > >> kwant.plotter.interpolate_density(syst=sys_p, density=ch_densities_p) > > > > where sys_p is a slice of sys_f and ch_densities_p is the corresponding > density vector. > > Could you please let me know how to do it? > > > > Best regards, > > Hadi > -- Abbout Adel

Re: [Kwant] Kwant scattering wave function vs Green's function comparison

2019-09-15 Thread Abbout Adel
t with this email. > > Does anyone know the reason behind the discrepancy between the two > methods?I would greatly appreciate any comments/suggestions on how we can > resolve this error? > > Thanks! > > > > -- Abbout Adel

Re: [Kwant] Kwant scattering wave function vs Green's function comparison

2019-09-18 Thread Abbout Adel
“or” use “and”). > > > I would really appreciate if we could resolve this discrepancy. I look > forward to any suggestions. > > Thanks for your time! > > On Sun, Sep 15, 2019 at 7:27 AM Abbout Adel wrote: > >> Dear Amrit, >> >> You wrote: >> &qu

Re: [Kwant] Plotting energy as a function of magnetic field in 3D.

2019-09-08 Thread Abbout Adel
ict(B=B), sparse=True)ev, evec = > sla.eigsh(ham_mat.tocsc(), k=20, sigma=0)energies.append(ev) > #print(energies)plt.figure()plt.plot(Bfields, energies) > plt.xlabel("magnetic field [${10^-3 h/e}$]")plt.ylabel("energy [t]") > plt.ylim(0, 0.11)plt.showdef main():syst = make_system() > analyze_system()main()* > > > > > -- > > > With Best Regards > NAVEEN YADAV > Ph.D Research Scholar > Deptt. Of Physics & Astrophysics > University Of Delhi. > -- Abbout Adel

Re: [Kwant] Plotting energy as a function of magnetic field in 3D.

2019-09-08 Thread Abbout Adel
t (energies)plt.figure()plt.plot(Bfields, energies) > plt.xlabel("magnetic field [${10^-3 h/e}$]")plt.ylabel("energy [t]") > plt.ylim(0, 0.11)plt.show()def main():syst = make_system() > analyze_system(syst, [B * 0.2 for B in range(101)])main()* &g

Re: [Kwant] How to solve the Hamiltonian matrix with off-diagonal terms?

2019-09-10 Thread Abbout Adel
in_block” in “lead=kwant.Builder()” > > > > The program can not work, and prompt error: > > > > IndexError: index 2 is out of bounds for axis 0 with size 2 > > > > Please help me. > > > > Thank you, > > > > Kind regards, > > X.F.Yan > > > > > > > -- Abbout Adel

Re: [Kwant] Difference between hop[0].tag and hop[1].tag

2019-09-10 Thread Abbout Adel
mple >> def circle(pos): rsq = pos[0] ** 2 + pos[1] ** 2 >> depends on pos >> >> Because when creating a shape in realspace you typically only care about >> the position, whereas your onsite matrix elements could potentially depend >> on other things (e.g. the lattice that the site is from) >> >> >> Happy Kwanting, >> >> >> Joe >> > -- Abbout Adel

Re: [Kwant] Hopping for random sites

2019-10-02 Thread Abbout Adel
PM Ali Asgharpour wrote: > Hello, > > Would you please let me know how I can add nn and nnn hoppings for > random sites (not all) in graphene? > > Best regards, > > Ali > -- Abbout Adel

Re: [Kwant] Current and hopping index relationship

2019-06-30 Thread Abbout Adel
ang > > On Sun, Jun 23, 2019 at 8:22 AM Abbout Adel wrote: > >> Dear Zang, >> >> If you do not specify the region where you want to calculate the current, >> kwant will do that for all the hoppings in your system. In your case, I >> guess that your system ha

Re: [Kwant] The unit of current of kwant.operator.Current

2019-06-30 Thread Abbout Adel
lear with the unit of the output current. > > Besides, is the current calculated by the second method should be equal to > the first method? > > Thanks in advance for your help. > Hang Zang > -- Abbout Adel

Re: [Kwant] (no subject)

2019-11-04 Thread Abbout Adel
rn arccos(-1+abs(E/2)) Energies=linspace(-2,2,200) pyplot.plot(Energies,T(Energies)) pyplot.show() ### On Sun, Oct 27, 2019 at 2:42 PM Abbout Adel wrote: > Dear Hosein, > >

Re: [Kwant] Surface in 3D space using kwant.

2019-11-23 Thread Abbout Adel
ystem? > > > In the manuals there are just examples for "cubic" 3d system but what I > hope is to analyze 2D structures embedded in the R3. > > > Best regards, > > Eudes. > -- Abbout Adel

Re: [Kwant] Access to eigenvalue, eigenvector and number of points in each unit cell

2019-11-23 Thread Abbout Adel
; and "unit cell", so I presume that you are trying to create a > system with translational symmetry, and that each Kwant *site* corresponds > to a single atom. > > > > It is not 100% clear to me what you want when you say "the eigenvectors > and eigenvalue" of your Hamiltonian; if your system has translational > symmetry then presumably you want the eigen-decomposition *at a given > quasi-momentum*, but you do not explicitly state this, so I am not sure. > > > > Posting a complete code example is useful because it is more precise than > describing your problem with words. > > > > Happy Kwanting, > > > > Joe > -- Abbout Adel

Re: [Kwant] matrix

2019-12-07 Thread Abbout Adel
appreciate. > > Best, > Nafise > -- Abbout Adel

Re: [Kwant] scattering matrix

2019-12-14 Thread Abbout Adel
plt.grid(True) > plt.title("Conductance eqhop temp=0.1") > plt.legend() > plt.ylabel("G_[G_0]") > plt.xlabel(r'$\phi [2\pi / L]$') > plt.show() > > > > def main(): > syst = make_system() > syst = syst.finalized() > plot_conductance(syst) > > > if __name__ == "__main__": > main() > -- Abbout Adel

Re: [Kwant] Transmission spectrum for a reverse bias

2019-12-14 Thread Abbout Adel
g the direction of measurement lead1 to lead0? > Thanks, > > Paul > -- Abbout Adel

Re: [Kwant] armchair nanoribbon with defect

2019-10-27 Thread Abbout Adel
and > lead but the results are not same. > > Would you please help me what is a problem. Would you please let me know > if symmetry vector (sym = kwant.TranslationalSymmetry(latt.vec((-1,2 > > used is ok? > > Best wishes, > > Sajad > -- Abbout Adel

Re: [Kwant] (no subject)

2019-10-27 Thread Abbout Adel
anks in advance. The definition of incident angle is shown in the > attached Fig.1, the band structure for my bulk system is shown in attached > Fig.2 and the Tranmission vs ky is shown in Fig.3 (I do not know how the > set the values for ky). > Regards, > Hosein Khani > > > -- Abbout Adel

Re: [Kwant] How to add Hopping to a curved surface?

2019-11-30 Thread Abbout Adel
see: > > (Site((None, 1), array([-3.472, -9.108, > 1.205])), Site(kwant.lattice.Monatomic([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], > [0.0, 0.0, 1.0]], [0.0, 0.0, 0.0], '', 3), array([-3, -9, 1]))) > > and array([-3, -9, 1]) should be array([-3.472, -9.108, 1.205]). Why > lattices accept only integer values? > > > > > > > > > > > > > > > > -- Abbout Adel

Re: [Kwant] Access to eigenvalue, eigenvector and number of points in each unit cell

2019-12-02 Thread Abbout Adel
alized() > Sites= list(fsys.sites) #list of all the sites in the scattering region > number_of_sites=len(Sites) > > kwant code gives us the number of sites of the scattering region in terms > of the line with pink color. I need in the scattering region just have one > hole li

Re: [Kwant] Access to eigenvalue, eigenvector and number of points in each unit cell

2019-12-01 Thread Abbout Adel
response. I am trying to use your Instructions for > finding all site in the scattering region and also finding eigenvalu but I > can not. That is very kind of you if you send me a short example of these > problem. Would you please? > > Best regard > > Sajad > *From: *

Re: [Kwant] question

2019-10-31 Thread Abbout Adel
gt;>>>>> lead[[kwant.builder.HoppingKind((0,0),a,b)]] =t >>>>>> >>>>>> lead[[kwant.builder.HoppingKind((0,1),a,b)]] =t >>>>>> >>>>>> lead[[kwant.builder.HoppingKind((-1,1),a,b)]] =t >>>>&

Re: [Kwant] question

2019-10-10 Thread Abbout Adel
ad.reversed(),add_cells=3) >>> >>> ax=kwant.plot(syst); >>> >>> Best wishes, >>> Nafise >>> >>> On Sat, Oct 5, 2019 at 12:57 PM Joseph Weston >>> wrote: >>> >>>> Hi Nafise >>>> >>>> >>>> I need to make a periodic lattice with hole. In fact I should make holes >>>> on the scattering region and also on the leads. Although I can make this >>>> kind of lattice by kwant, I have problem about the distances between >>>> holes. I want to make a periodic holes on the nanoribbon but the distance >>>> between holes in the scattering region is different from the distance >>>> between holes in the other regions. Would you please let me know How Can I >>>> make a same distance between holes? Should I work on the translational >>>> symmetry in the leads? >>>> >>>> >>>> Because the leads need to be translationally invariant if you want a >>>> very large distance between defects then your unit cell in the leads needs >>>> to be correspondingly large. >>>> >>>> If you post a code example of what your problem is specifically we may >>>> be able to help more. >>>> >>>> >>>> Happy Kwanting, >>>> >>>> Joe >>>> >>>> >>>> P.S. sorry for the double reply; I forgot to send to the mailing list >>>> also >>>> >>>> -- Abbout Adel

Re: [Kwant] Realistic values of hopping parameters

2020-02-05 Thread Abbout Adel
tight-binding approximation of p electrons, there are two types of > hopping integrals: Vppσ, and Vppπ, so I’m wondering if it’s possible to > simulate the effect of both hoppings? > > Thanks a lot for reading my questions! > Cheers, > Yu Li > -- Abbout Adel

Re: [Kwant] Problems to add disorder to the Kitaev chain

2020-02-03 Thread Abbout Adel
= kitaev(L,t,mub,Delta,W,salt) > systb = systb.finalized() > hamatb = systb.hamiltonian_submatrix(sparse = False) > evalsb, evecsb = la.eigh(hamatb) > > creates the Kitaev code with just one specific configuration for > the random onsite offset, right ? > > Thank you very much again and best > > L. > -- Abbout Adel

Re: [Kwant] Problems to add disorder to the Kitaev chain

2020-02-04 Thread Abbout Adel
,Delta,W,salt) > systb = systb.finalized() > hamatb = systb.hamiltonian_submatrix(sparse = False) > evalsb, evecsb = la.eigh(hamatb) > > > > > is it sufficient to add a For cycle on the value of salt ? > Say, from 1 to Nmax, where Nmax is the number of configurat

Re: [Kwant] site value is changing after finalizing the system

2020-04-17 Thread Abbout Adel
[site],colorbar=True, cmap=None) > > if __name__ == '__main__': > main() > # > > I can resolve this issue by collecting the site positions from the array > named my_list in the given code and then assign the site values > accordingly. Howe

Re: [Kwant] site value is changing after finalizing the system

2020-04-16 Thread Abbout Adel
e=list(line) > line=sort(line) > > > i=1 > for site in sys.expand(lat.shape(cross(W,L), (0, 0))): >for j in range(0,no_of_line+1,2): >line_no=j > if (site.pos[1]==line[line_no] or site.pos[1]==line[line_no+1]): >sys[site]=i >i=i+1 > > > With Regards, > Sudin > -- Abbout Adel

Re: [Kwant] discontinuity between lead and scattering region

2020-05-18 Thread Abbout Adel
d.reversed()) > sys = kwant.wraparound.wraparound(sys, keep=None) > kwant.plot(sys) > sysf=sys.finalized() > ham_mat = sysf.hamiltonian_submatrix() > ev = sla.eigsh(ham_mat, k=31, which='SM') > evecs = ev[1] > prob_dens = np.abs(evecs[:, 30])**2 > #print(prob_dens) > #Sites=list(s

Re: [Kwant] discontinuity between lead and scattering region

2020-05-07 Thread Abbout Adel
; -- > Best Regards, > Naveen Yadav > Research Scholar > Department of Physics & Astrophysics > University Of Delhi > New Delhi-110007 > -- Abbout Adel

Re: [Kwant] discontinuity between lead and scattering region

2020-05-07 Thread Abbout Adel
Yadav > Research Scholar > Department of Physics & Astrophysics > University of Delhi > New Delhi-110007 > > On Thu, May 7, 2020, 19:06 Abbout Adel wrote: > >> Dear Naveen, >> >> What you get is what is expected. You do not have translational symmetry. >&

Re: [Kwant] discontinuity between lead and scattering region

2020-05-08 Thread Abbout Adel
hysics & Astrophysics > University of Delhi > New Delhi-110007 > > On Thu, May 7, 2020, 20:37 Abbout Adel wrote: > >> Hi again, >> >> I f you want translational symmetry, you need to use wraparound module >> and you will need to find your result only on one uni

Re: [Kwant] Number of equidistant neighbors on honeycomb lattice

2020-05-03 Thread Abbout Adel
Nuclear Research, > Materials Research Laboratory, > ul. Andrzeja Sołtana 7, > 05-400 Otwock-Świerk, Polandhttp://nanophysics.pl > mobile: +48 507 330 216 > > > -- Abbout Adel