Dear Nick, Thank you for your response. The only way to ensure this is by adding vacuum to lattice vectors (transverse directions)? Am I right? For example:
1) This is for the original electrode cell (bulk like): LatticeConstant 1.0 Ang % block LatticeVectors 11.540 0.000 0.000 5.770 9.994 0.000 0.0 0.0 7.06705 % endblock LatticeVectors 2) This is for electrode cell "chain like" (bulk like + 20 Angstroms) LatticeConstant 1.0 Ang % block LatticeVectors 31.540 0.000 0.000 25.770 29.994 0.000 0.0 0.0 7.06705 % endblock LatticeVectors Is this right? Nick once again thank you. 2015-08-20 9:20 GMT-03:00 Nick Papior <[email protected]>: > > > 2015-08-20 14:14 GMT+02:00 leoqmc . <[email protected]>: > >> Dear Nick, >> >> I read the paper you recommended. The author recommends adding more >> electrode atoms in the transversal direction in order to reduce the >> effect of interference due to device images. My question: >> >> 1) What is the problem in adding vacuum in the transverse directions? I >> think it would reduce the effect of interference due to device images. >> > Yes, sure you would remove the interference, but it would not be a bulk > (periodic) electrode, rather it would be an electrode "chain". > >> >> >> Since already very Thank you. >> >> Leone Carmo Garcia >> >> >> >> 2015-08-19 14:51 GMT-03:00 leoqmc . <[email protected]>: >> >>> Dear Nick, >>> >>> Thank you. I'll read the paper. >>> >>> Leone Carmo Garcia >>> >>> 2015-08-19 14:36 GMT-03:00 Nick Papior <[email protected]>: >>> >>>> >>>> >>>> 2015-08-19 17:14 GMT+00:00 leoqmc . <[email protected]>: >>>> >>>>> Dear Nick, >>>>> >>>>> I prepared my inputs following your tips and test inputs. I'm waiting >>>>> for the calculations to complete. But one question remains. >>>>> >>>>> 1) I want to get the transport properties in a single molecule and not >>>>> added vacuum in either direction (as the tests that you recommended). The >>>>> results will not be influenced by the "images" of my device? >>>>> >>>> Sure they will. :) >>>> >>>>> >>>>> >>>>> 2) I have seen examples that use large vacuum in the x and y >>>>> directions. When this is recommended? >>>>> >>>> This is a drawback of the supercell approach, however, please look >>>> through litterature for this. >>>> This article touches upon that: 10.1103/PhysRevB.72.033401, as well as >>>> how to circumvent 1). >>>> >>>>> >>>>> >>>>> From already thank you very much. >>>>> >>>>> Leone Carmo Garcia >>>>> >>>>> 2015-08-19 8:47 GMT-03:00 leoqmc . <[email protected]>: >>>>> >>>>>> Dear Nick, >>>>>> >>>>>> I am very grateful for your help. I will follow the tips. >>>>>> >>>>>> Leone Carmo Garcia >>>>>> >>>>>> 2015-08-18 16:42 GMT-03:00 Nick Papior <[email protected]>: >>>>>> >>>>>>> >>>>>>> >>>>>>> 2015-08-18 19:27 GMT+00:00 leoqmc . <[email protected]>: >>>>>>> >>>>>>>> Dear Nick and transiesta users, >>>>>>>> >>>>>>>> I am interested in transport calculations in single-molecule >>>>>>>> two-probe systems[Au(111)-Molecule-Au(111)]. I searched in the list >>>>>>>> for the >>>>>>>> following questions, but I think that these questions were not >>>>>>>> explicitly >>>>>>>> solved for a beginner. Please help me. >>>>>>>> >>>>>>>> 1) Charge: The Molecule is charged(charge +2). Not make sense uses >>>>>>>> the option (NetCharge 2.0) in the transiesta calculation, since that >>>>>>>> the >>>>>>>> charge will be screened. I'm right? >>>>>>>> >>>>>>> No that will most likely not work, currently this is not an easy >>>>>>> task. >>>>>>> >>>>>>>> >>>>>>>> 2) Setup for the electrodes: >>>>>>>> a) The third lattice's vector (z-direction) should have length >>>>>>>> minimal possible, namely it should be enough for the atoms+basis >>>>>>>> functions. >>>>>>>> I'm right? >>>>>>>> >>>>>>> In your case, make the z-direction periodic. >>>>>>> >>>>>>>> b) The lattice's vectors in x,y direction should include large >>>>>>>> vacuum (~20 Angstroms). I'm right? >>>>>>>> >>>>>>> No, not necessarily, here you can also impose periodicity. Please >>>>>>> look at the examples in the test directory, an example of gold, >>>>>>> gold-chain, >>>>>>> gold is shown. That could be the basis for your further geometry >>>>>>> creation. >>>>>>> See example ts_au_100, both the repetition and non-repeated structure. >>>>>>> >>>>>>>> c) Usually you use how many units ("N") of the electrodes (N * >>>>>>>> ABC)? >>>>>>>> >>>>>>> In your 111 direction I would think a single ABC stacking should be >>>>>>> enough. This depends on your basis range, you need to check this >>>>>>> your-self. >>>>>>> >>>>>>>> >>>>>>>> 3) Setup for complete device (Electrodes + Molecule): >>>>>>>> >>>>>>>> a) My electrodes are equal. In this case it is mandatory to >>>>>>>> include vacuum in the z direction, such that the device is not >>>>>>>> affected by >>>>>>>> their image in the calculation of siesta prior to the calculation of >>>>>>>> transiesta? >>>>>>>> >>>>>>> Please re-read 2a. If electrodes are the same, having a periodic >>>>>>> setup is far better than the alternative. Again refer to the example as >>>>>>> suggested in 2b. >>>>>>> >>>>>>>> >>>>>>>> Thanks in advance. >>>>>>>> >>>>>>>> Leone Carmo Garcia >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Kind regards Nick >>>>>>> >>>>>> >>>>>> >>>>> >>>> >>>> >>>> -- >>>> Kind regards Nick >>>> >>> >>> >> > > > -- > Kind regards Nick >
