[Smeagol-discuss] Smeagol examples
Ivan Rungger
runggeri at tcd.ie
Tue Apr 21 10:42:31 IST 2009
Hello Kou Iiangzhi,
since the solution is found self-consistently, it is OK if two
calculations take a different path to get to the solution. The important
thing is that the final solution is correct, which is the case in your
calculation.
The current version of smeagol has some problems when restarting the
calculation, we have now an updated version, where this problem is
fixed. We will make it available as development version in the next
future, for now you can use the code you have, just always check that
the charge is conserved.
Cheers,
Ivan
寇良志 wrote:
> Dear Ivan
>
> Thanks for your suggestions.
> The first problem you mentioned in the following is successfully
> solved after recompiling atom.f with -00.
> The second problems is also solved after setting the DM.NumberPulay to
> 1. At this time, the calculated result is absolutely same to yours.
> However, When DM.NumberPulay equal to 5, the problem still exsit(*.CHR
> file converges to a solution with only 53 electrons instead of 93).
> The software version we used is siesta1.3flp, and smeagol.1.0b.
> What is the reason? And what should i do?
> Thanks
>
> Cheers
>
> Kou liangzhi
>
>
> 2009-04-17
> ------------------------------------------------------------------------
> 寇良志
> ------------------------------------------------------------------------
> *发件人：* Ivan Rungger
> *发送时间：* 2009-04-17 16:54:10
> *收件人：* 寇良志
> *抄送：* smeagol-discuss
> *主题：* Re: [Smeagol-discuss] Smeagol examples
> Hello 寇良志,
> there are two problems:
> 1)the difference in the energy: if you are using the pgf compiler, it is
> probably due to the fact that with that compiler if you use -O3 or some
> similar optimization, part of the energy is wrong. I think it is enough
> just to recompile atom.f with -O0, and then the energy should be OK.
> 2)The second problem is more serious, i.e. your TRC is definitely wrong.
> The reason is that you converge to a wrong solution. I compared my
> buffer.out and *CHR file, and they are identical to yours for the first
> few iterations, but then they start to differ (you converge to a
> solution with only 53 electrons instead of 93). What code exactly are
> you using, is it smeagol-1.0b with the two patches applied (and which
> siesta version is it based on)? If yes, try to rerun the calculation
> with DM.NumberPulay 1 (and remove any saved DM files). And also:
> try to compile the whole code with -O0 (i.e. no optimization), and see
> what you get.
> I think once you converge to the right solution, you should also get the
> same TRC and CUR.
> Cheers,
> Ivan
> 寇良志 wrote:
> > Dear Ivan and every smeagol user
> >
> > I have run the smeagol examples. However, there are some differences
> > comparing with your attached output files.
> >
> > For the first two examples (Au_wire_1kp and Au_wire_4kp), the results
> > (including the *.TRC, *.CUR etl) are almost same to yours. But we note
> > that, there are some discrepancys for the following energy parameters
> > in the "out" file:
> > Our results are:
> > siesta: Ena = 15.344394
> > siesta: Eharris = -1647.976798
> > siesta: Etot = -1648.041394
> > siesta: FreeEng = -1648.041394
> > Your results are:
> > siesta: Ena = 731.942850
> > siesta: Eharris = -930.824171
> > siesta: Etot = -922.648096
> > siesta: FreeEng = -922.648096
> >
> > However, the serious problems occure in the third example. The datas
> > in the *.TRC and *.CUR files we obtained are at least 3 or 4 orders of
> > magnitude lower than your datas. In addition, the energy differents
> > described above still exist.
> >
> > I attached the five output files of the third example we obtained.
> >
> > Could you please provide some suggestions, and tell us what is the
> > problem?
> >
> > Thanks a lot !
> >
> > PS: All of the parameters and pseudopotentials we used are exactly
> > those you provided. The soft version to run the examples is
> > siesta13flp+smeagol1.1.0.b
> >
> > 2009-04-17
> > ------------------------------------------------------------------------
> > Kou Liangzhi
> > Institute of NanoScience, NanJing University of Aeronautics and
> > Astronautics, NanJing, China.
> > ------------------------------------------------------------------------
> > *发件人：* Ivan Rungger
> > *发送时间：* 2009-04-14 23:31:28
> > *收件人：* smeagol-discuss
> > *抄送：*
> > *主题：* [Smeagol-discuss] Smeagol examples
> > Hello,
> > since different smeagol users have asked me to provide some simple
> > example systems with which to check whether the output of the code they
> > compiled is correct, here I post a tar archive with 3 different test
> > systems:
> > 1)Au_wire_1kp: A gold wire with 8 gold atoms
> > 2)Au_wire_1kp: A gold wire with 8 gold atoms, 4 k-points are used in the
> > plane perpendicular to the transport. There is no need to use k-points
> > for a wire, here I just added them for testing the k-points routines.
> > The results must be identical to the ones without k-points.
> > 3)Au_Au3_Au: a gold cacitor with 3 gold atoms joining the two gold
> > surfaces. The conductance of this wire at the Fermi energy is about one.
> > Whereas the bias was applied in an artificial way in the first two
> > examples (which are modified versions of those provided with the smeagol
> > source code), this example represents a real physical system.
> > All the directories contain the necessary leads and scattering-region
> > input files, and also the used Au pseudopotential. These systems are
> > intended for small tests, the aim is not to simulate real physical
> > systems (especially the gold wires are completely unphysical at finite
> > bias). All the calculations were run with the parallel version of the
> > code (I suggest using that one). In the output directory there is the
> > main output of the code. It contains the following files:
> > 1)out: standard output
> > 2)buffer.out
> > 3).CHR file
> > 4).TRC: transmission coefficient. There is also a rescaled *.TRC file
> > called *.TRC.rescaled, where the transmission has been divided by the
> > number of k-points, the Fermi energy has been set to 0 and the units of
> > the energy axis are in eV.
> > 5).CUR file for the current.
> > These output files can be used as reference to check the calculated results.
> > Cheers,
> > Ivan
> > --
> > =================================================
> > Ivan Rungger,
> > School of Physics and CRANN,
> > Trinity College Dublin,
> > Dublin 2, IRELAND
> > Phone: +353-1-8968454
> > Email: runggeri at tcd.ie
> > =================================================
> > _______________________________________________
> > Smeagol-discuss mailing list
> > Smeagol-discuss at lists.tchpc.tcd.ie
> > http://lists.tchpc.tcd.ie/listinfo/smeagol-discuss
> --
> =================================================
> Ivan Rungger,
> School of Physics and CRANN,
> Trinity College Dublin,
> Dublin 2, IRELAND
> Phone: +353-1-8968454
> Email: runggeri at tcd.ie
> =================================================
--
=================================================
Ivan Rungger,
School of Physics and CRANN,
Trinity College Dublin,
Dublin 2, IRELAND
Phone: +353-1-8968454
Email: runggeri at tcd.ie
=================================================
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