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