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
