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Kind regards Nick Papior On 11 May 2016 08:24, "Seyed Mohammad Tabatabaei" <[email protected]> wrote: > > Thank you very much for your help. > > Do I have change this and recompile transiesta? Yes. > > 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? No, that is correct, would you expect otherwise? > > 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 >>>> >>>> >>> >
