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]> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>> >>> >> >
