Hi Nick!
Thanks a lot for your attention.. So much happy.. ;-)
All the Best,Zeynab
On Sunday, July 3, 2016 10:14 AM, Nick Papior <[email protected]> wrote:
Hi zeynab,
See comments in line. --Kind regards Nick Papior
On 3 Jul 2016 10:13, "zeynab mohamad hoseyni" <[email protected]> wrote:
>
> Hi Carlos,
>
> Thanks a lot for the reply. Nobody answered my question and I really didn't
> know what should I do.
> I progressed well and don't want to switch to another software due to this
> simple problem..
>
> I've enabled all the options you mentioned in my input.fdf (I copy it in the
> following) file.
> I had a look into my directory where I ran previous TranSiesta job. When I
> list *.TSDE I find "scat.TSDE" file,
> but when I list *.TSHS I can't find such file except for the one I already
> put there as the input for previous
> TranSiesta file (it is called "elec.TSHS").
In fact, TSHS file isn't used for a continuation run.
>
> Another point is that when I run the continuation job, inside the produced
> OUTPUT.fdf file it is written "Continuation run".
> But as soon as the section "transiesta: TSiscf" is printed out, it starts
> from number 1 while the previous run
> stops at number 63 and I expect the continuation run start from 64 and not
> 63..
A continuation run does not know what the previous runs Scf count is, so it
starts over.
If it says it has read in the TSDE file, then it is a continuation run.
>
> Can you guess what is wrong?
So I would guess nothing is wrong and it actually behaves as expected. :)
>
> All the Best and thanks again for your time,
> Zeynab
>
> P.S.
> INPUT.fdf file :
> **********************************
> SystemName scat
>
> SystemLabel scat
>
> %block kgrid_Monkhorst_Pack
> 1 0 0 0.0
> 0 1 0 0.0
> 0 0 5 0.0
> %endblock kgrid_Monkhorst_Pack
>
>
> xc.functional GGA
> xc.authors PBE
>
> MeshCutoff 1000.00000000 Ry
> SolutionMethod Transiesta
> OccupationFunction MP
> ElectronicTemperature 300 K
>
> SpinPolarized F
> FixSpin F
>
> MaxSCFIterations 1000
>
> DM.NumberPulay 6
> DM.NumberBroyden 0
> DM.MixingWeight 0.05
> DM.OccupancyTolerance 0.1000000000E-11
> DM.NumberKick 0
> DM.KickMixingWeight 0.5000000000
> DM.Tolerance 1.000000000E-04
> UseSaveData T
>
> MD.NumCGsteps 0
> MD.TypeOfRun CG
> MD.VariableCell F
> MD.MaxCGDispl 0.2000000000 Bohr
> MD.MaxForceTol 0.05 eV/Ang
> #MD.MaxStressTol 0.0001 eV/Ang**3
> MD.UseSaveXV .true.
> MD.UseSaveCG T
> DM.UseSaveDM true
>
> Diag.ParallelOverK F
> PAO.EnergyShift 50 meV
> PAO.SplitNorm 0.1500000000
> PAO.BasisType split
> PAO.BasisSize DZP
>
> WriteMullikenPop 0
> WriteBands F
> SaveRho .true.
> SaveDeltaRho .true.
> SaveHS .true.
> SaveElectrostaticPotential .true.
> SaveTotalPotential yes
> WriteCoorXmol .true.
> WriteMDXmol .true.
> WriteMDhistory .false.
> WriteEigenvalues yes
> WriteDM T
>
>
>
> %include POSITIONS.fdf
>
>
> # Transiesta information
> SolutionMethod Transiesta
> # GENGF OPTIONS
> TS.ComplexContour.Emin -24 eV
> TS.ComplexContour.NPoles 16
> TS.ComplexContour.NCircle 16
> TS.ComplexContour.NLine 10
> # BIAS OPTIONS
> TS.biasContour.NumPoints 10
>
>
> # TS OPTIONS
> TS.Voltage 0.00 eV
>
> # TBT OPTIONS
> TS.TBT.Emin -3 eV
> TS.TBT.Emax +3 eV
> TS.TBT.NPoints 500
> TS.TBT.NEigen 3
> TS.TBT.Eta 0.000001 Ry
>
> # Write electrode hamiltonian
> TS.SaveHS .true.
> TS.SaveLead .true.
>
> TS.MixH T
> TS.UpdateDMCROnly T
> SCFMustConverge T
>
> # LEFT ELECTRODE
> TS.HSFileLeft ./elec.TSHS
> TS.NumUsedAtomsLeft 12
> TS.BufferAtomsLeft 0
>
> # RIGHT ELECTRODE
> TS.HSFileRight ./elec.TSHS
> TS.NumUsedAtomsRight 12
> TS.BufferAtomsRight 0
>
> DM.UseSaveDM T
>
>
>
>
> ==================================================
> ==================================================
>
>
> On Saturday, July 2, 2016 11:24 AM, Carlos Sanz <[email protected]> wrote:
>
>
>
> Dear Zeynab,
>
> as in any SIESTA run, you will have to set up the typical restarting
> parameters in the fdf file such as
>
> DM.UseSaveDM .true. (during a TranSIESTA run, the .DM values are used for
> the density matrix in the buffer (if used)
> and electrode regions)
>
> DM.UseSaveXV .true.
>
> etc... In addition, and what really makes a specific TranSIESTA restarting,
> you must check that you have the *.TSHS and *.TSDE files from the previous
> run in the directory where you are going to restart TranSIESTA. By the way,
> TS.SaveHS is true by default, so you should find the *.TSHS from the previous
> run unless you set up TS.SaveHS false previously.
>
> - The *.TSHS file contains the information (e.g.: Hamiltonian matrix once
> self consistency is achieved and overlap matrix) necessary for the scattering
> region calculation. If both electrodes are identical structures, the same
> .*.TSHS can be used to describe both. In general, however, the electrodes can
> be different and therefore you will have two different *.TSHS files; one for
> the left electrode and and another for the right electrode.
>
> - The *.TSDE file contains the density matrix for the TranSIESTA
> calculations. It is equivalent to the *.DM file for SIESTA (i.e., density
> matrix with periodic boundary conditions in all directions and no voltage),
> but the density and energy matrix stored in *.TSDE has open boundary
> conditions and bias potential.
>
> best regards,
>
> SIMUNE support team
>
> El 02/07/16 a las 07:08, zeynab mohamad hoseyni escribió:
>>
>> Dear all,
>>
>> I would really appreciate if someone kindly answer to my question:
>> How I can restart a TranSiesta job from the previous run? Is there any
>> option
>> that I have to enable in the .fdf file so that continuing a job from
>> previous job
>> which has been stopped due to lack of wall-time?
>>
>> Would be so much thankful to help me on that.
>>
>> All the Best,
>> Zeynab
>>
>
> --
> Support
> Simune Atomistics
> Tolosa Hiribidea 76 | 20018 Donostia - San Sebastián | Spain
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>
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