Thank you very much for your help. Do I have change this and recompile transiesta?
Also I have used 0 for MD.NumCGsteps and the positions were not updated by any means in the program. Is that a numerical issue in siesta? Bests, On Wed, May 11, 2016 at 10:11 AM, Nick Papior <[email protected]> wrote: > You may change this line > real(dp), parameter :: EPS = 1.0d-4 > In m_ts_electrode.F90 to a lower value, say, 1e-3 or so. > As you can see from your output there are some differences in the > coordinates, although small. > > -- > > Kind regards Nick Papior > On 11 May 2016 07:13, "Seyed Mohammad Tabatabaei" <[email protected]> > wrote: > >> This is also the POSITIONS.fdf input file for my left electrode. >> >> On Wed, May 11, 2016 at 9:25 AM, Seyed Mohammad Tabatabaei < >> [email protected]> wrote: >> >>> Thank you for your time. >>> >>> The older version is "siesta-3.2-pl-5". >>> >>> I have checked my coordinates several times and I think they are >>> currently "equivalent with respect to a common translational vector." so I >>> would be really grateful if you explain to me the cause of this error. >>> >>> The inputs to both versions are identical so I only attach the output >>> files. I have also attached the output file for left electrode calculation. >>> Bests, >>> Mohammad, >>> >>> On Tue, May 10, 2016 at 11:26 PM, Nick Papior <[email protected]> >>> wrote: >>> >>>> Dear Mohammad, >>>> >>>> 2016-05-10 17:46 GMT+02:00 Seyed Mohammad Tabatabaei <[email protected]> >>>> : >>>> >>>>> Dear all, >>>>> >>>>> I have the two latest versions of transiesta installed on my computer. >>>>> The older version does not print any errors for my electrode positions >>>>> but the newer version (siesta-4.0b-485) prints this error for a 100 >>>>> percent identical calculation: "The electrodes are not situated in the >>>>> same coordinates. Please correct." and stops. >>>>> >>>> Which version is the old version? >>>> >>>>> >>>>> I have read a similar thread about this issue and the suggestions >>>>> therein but I think the newer version of transiesta falls short of >>>>> understanding the fact that the positions of the electrodes may not be >>>>> identical (same/equal) but they can be equivalent. Particularly, this >>>>> sentence can be found in the manual of both versions: >>>>> ".... Here, equivalent means that they can be made equal by a simple >>>>> translation in space." >>>> >>>> Yes, this sentence is true. The electrode coordinates need not be >>>> EXACTLY the same. They only need to be equivalent with respect to a common >>>> translational vector. >>>> >>>>> >>>> >>>> >>>>> I would be really thankful to anyone who helps me understand the issue. >>>>> >>>> We need more information, input/output of both the old and new version. >>>> >>>> >>>>> Bests, >>>>> Mohammad, >>>>> >>>> >>>> >>>> >>>> -- >>>> Kind regards Nick >>>> >>> >>> >>
