Zeynab,
and one more thing, in order to check that the TranSIESTA calculation
restarts properly, you should look at whether the energies, convergence
of the density matrix and Fermi energy for the first SCF steps are very
close to those of the last SCF steps of your previous run. The SCF
counter simply starts from 1 again as Nick points out.
regards,
SIMUNE support team
El 03/07/16 a las 16:50, Carlos Sanz escribió:
Hi Zeynab,
the *.TSHS files are built in a previous stage, during the Electrodes
calculations (which is actually a pure SIESTA calculation with a high
number of k-points in the transport direction), and then used when the
Scattering Region calculation starts to describe the electrodes, but
it is true that they do not change anymore at this last stage.
regards,
Carlos
El 03/07/16 a las 11:21, zeynab mohamad hoseyni escribió:
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]
<mailto:[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
> T.: +34 943 57 40 42 | [email protected] | www.simune.eu
<http://www.simune.eu/>
>
>
--
SIMUNE Atomistic Simulations
Support
Simune Atomistics
Tolosa Hiribidea 76 | 20018 Donostia - San Sebastián | Spain
T.: +34 943 57 40 42 | [email protected] | www.simune.eu
<http://www.simune.eu> SIMUNE Atomistic Simulations
<http://www.simune.eu/>
--
SIMUNE Atomistic Simulations
Support
Simune Atomistics
Tolosa Hiribidea 76 | 20018 Donostia - San Sebastián | Spain
T.: +34 943 57 40 42 | [email protected] <mailto:[email protected]> |
www.simune.eu <http://www.simune.eu> SIMUNE Atomistic Simulations
<http://www.simune.eu/>
