Dear Nick, Thank you very much.
Leone Carmo Garcia 2015-08-20 10:26 GMT-03:00 Nick Papior <[email protected]>: > If you want a chain electrode, then yes, it seems correct, but check for > your self (always check!). > > 2015-08-20 15:08 GMT+02:00 leoqmc . <[email protected]>: > >> 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 >>> >> >> > > > -- > Kind regards Nick >
