No,system type is a chain means it is isolated in the other directions(here ,x and y axis) ,but not isolated in the z axis .
2014-08-27 12:41 GMT+08:00 邵德喜 <[email protected]>: > No,system is a chain means it is isolated in the other directions(here > ,x and y axis) ,but not isolated in the z axis .the system is bulk.you can > set some vaccum layers to achieve your goal. > But I advise you to not > > > 2014-08-27 11:46 GMT+08:00 joyce79928cc . <[email protected]>: > > my siesta said that my system is a chain, >> this is wrong, right? >> so I can't isolate my system in x & y direction? >> I should make my system continuously in x & y direction? >> thank you >> >> -- >> Best Regards >> >> 邱芳瑜 Chiu Fang Yu >> 國立成功大學 材料科學與工程學系碩一 >> MOBILE：0930287221(中華) >> GMAIL：[email protected] <[email protected]> >> >> >> >> >> 2014-08-27 8:45 GMT+08:00 邵德喜 <[email protected]>: >> >> You can look for in the OUTPUT file the system type to get whether it is >>> isolated . >>> Best wishes. >>> >>> >>> 2014-08-26 23:56 GMT+08:00 joyce79928cc . <[email protected]>: >>> >>> so if I choose isolate one, >>>> when I calculate my electrode using TranSiesta, >>>> it is also isolate in x and y direction? >>>> should I fixed some atoms? will the side atoms in x and y direction act >>>> as surface? >>>> thanks >>>> >>>> >>>> -- >>>> Best Regards >>>> >>>> 邱芳瑜 Chiu Fang Yu >>>> 國立成功大學 材料科學與工程學系碩一 >>>> MOBILE：0930287221(中華) >>>> GMAIL：[email protected] <[email protected]> >>>> >>>> >>>> >>>> >>>> 2014-08-26 23:35 GMT+08:00 邵德喜 <[email protected]>: >>>> >>>> In fact , isolate in x-y direction or continuous with PBC are both >>>>> ok,it just depends on your decision. But if you want to get a bulk >>>>> one,just >>>>> choose continuous with PBC ,then set your k grids large enough. >>>>> Best wishes. >>>>> >>>>> >>>>> 2014-08-26 22:44 GMT+08:00 joyce79928cc . <[email protected]>: >>>>> >>>>> thank you for typing me this. >>>>>> but I don't know what's x1+10 to x9+10 and z1 mean... >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Best Regards >>>>>> >>>>>> 邱芳瑜 Chiu Fang Yu >>>>>> 國立成功大學 材料科學與工程學系碩一 >>>>>> MOBILE：0930287221(中華) >>>>>> GMAIL：[email protected] <[email protected]> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> 2014-08-26 21:58 GMT+08:00 toufik esssakhri <[email protected]>: >>>>>> >>>>>> here you have a base formed by seven atoms, right?? >>>>>>> in this case you should do something like this : >>>>>>> %block LatticeVectors # in angestrom >>>>>>> 25.00 0.00 0.00 >>>>>>> 0.00 25.00 0.00 >>>>>>> 0.00 0.00 your z position taking into account periodic >>>>>>> conditions >>>>>>> %endblock LatticeVectors >>>>>>> >>>>>>> AtomicCoordinatesFormat Ang >>>>>>> %block AtomicCoordinatesAndAtomicSpecies >>>>>>> #First layer >>>>>>> atom1 x1+10 y1+10 0.00 >>>>>>> atom2 x2+10 y2+10 0.00 >>>>>>> atom3 x3+10 y3+10 0.00 >>>>>>> atom4 x4+10 y4+10 0.00 >>>>>>> atom5 x5+10 y5+10 0.00 >>>>>>> atom6 x6+10 y6+10 0.00 >>>>>>> atom7 x7+10 y7+10 0.00 >>>>>>> #Second layer >>>>>>> atom8 x8+10 y8+10 z1 >>>>>>> atom2 x9+10 y9+10 z1 >>>>>>> ...... >>>>>>> ....... >>>>>>> %endblock AtomicCoordinatesAndAtomicSpecies >>>>>>> >>>>>>> ------------------------------ >>>>>>> Date: Tue, 26 Aug 2014 21:35:55 +0800 >>>>>>> From: [email protected] >>>>>>> >>>>>>> To: [email protected] >>>>>>> Subject: Re: [SIESTA-L] electrode model calculation >>>>>>> >>>>>>> Dear: >>>>>>> >>>>>>> so if I build by electrode like the pic. attached, is that OK? >>>>>>> the z direction is in (111) direction >>>>>>> >>>>>>> -- >>>>>>> Best Regards >>>>>>> >>>>>>> 邱芳瑜 Chiu Fang Yu >>>>>>> 國立成功大學 材料科學與工程學系碩一 >>>>>>> MOBILE：0930287221(中華) >>>>>>> GMAIL：[email protected] <[email protected]> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> 2014-08-26 21:26 GMT+08:00 toufik esssakhri <[email protected]>: >>>>>>> >>>>>>> dear, >>>>>>> >>>>>>> PBC = Periodic Bondairy Condition >>>>>>> >>>>>>> in my knowledge, the electrode should be periodic only in the >>>>>>> z-direction (z here is the direction of transport) >>>>>>> >>>>>>> ------------------------------ >>>>>>> Date: Tue, 26 Aug 2014 21:18:58 +0800 >>>>>>> From: [email protected] >>>>>>> To: [email protected] >>>>>>> Subject: Re: [SIESTA-L] electrode model calculation >>>>>>> >>>>>>> >>>>>>> What is so called "PBC" here? >>>>>>> >>>>>>> >>>>>>> 2014-08-26 11:55 GMT+08:00 joyce79928cc . <[email protected]>: >>>>>>> >>>>>>> Dear: >>>>>>> >>>>>>> I want to do a transiesta calculation. >>>>>>> I know I should use transiesta to calculate electrode >>>>>>> with SolutionMethod=Diagon first. >>>>>>> since my electrode model is a (111) direction Al, I have 3 layer(ABC >>>>>>> sequence) and 9 atoms for a plane. >>>>>>> should I set my electrode isolate in x-y direction or continuous >>>>>>> with PBC?( is transiesta have PBC in x-y direction?) >>>>>>> but if I choose isolate electrode , the side of the electrode will >>>>>>> become surface right? >>>>>>> >>>>>>> the files attached are isolate electrode and continuous electrode. >>>>>>> thank you! >>>>>>> >>>>>>> -- >>>>>>> Best Regards >>>>>>> >>>>>>> 邱芳瑜 Chiu Fang Yu >>>>>>> 國立成功大學 材料科學與工程學系碩一 >>>>>>> MOBILE：0930287221(中華) >>>>>>> GMAIL：[email protected] <[email protected]> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >
