Dear Nick,
Thanks a lot for your prompt reply and your guidance..
All the Best,
Zeynab
On Monday, July 4, 2016 6:58 AM, Nick Papior <[email protected]> wrote:
Sometimes restarting from a not-so-well converged density matrix ends
up going out of the convergence basin. This seems to be what happens
here.
Secondly, it seems you should change some of your calculation
parameters. It converges with very low rate.
Regarding transiesta convergence, please see previous mails on the
mailing list.
2016-07-04 7:02 GMT+02:00 zeynab mohamad hoseyni <[email protected]
<mailto:[email protected]>>:
Hi Carlos,
Thanks a lot for the answer. As you said I had a look at the last
lines of the OUTPUT.fdf for the first run and the first lines of
that of
continuation run. I think the energies aren't that much close.
Would be thankful to let me know your idea about it:
Here I copy the last lines of the first run:
transiesta: TSiscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax
Ef(eV)
transiesta: 59 -27749.7793 -27802.2693 -27802.2693 0.6819 -3.5816
TranSiesta: Qsol,Qtot: 715.511 713.000 1.000
transiesta: 60 -27829.2053 -27817.4318 -27817.4318 0.7644 -3.5816
TranSiesta: Qsol,Qtot: 715.936 713.000 1.000
transiesta: 61 -27805.3324 -27808.0481 -27808.0481 0.9509 -3.5816
TranSiesta: Qsol,Qtot: 715.196 713.000 1.000
transiesta: 62 -27809.7837 -27812.0000 -27812.0000 0.7693 -3.5816
TranSiesta: Qsol,Qtot: 715.049 713.000 1.000
transiesta: 63 -27820.2730 -27817.4024 -27817.4024 0.7280 -3.5816
TranSiesta: Qsol,Qtot: 714.691 713.000 1.000
And here is the one of continuation run:
transiesta: TSiscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax
Ef(eV)
transiesta: 1 -26177.9898 -26389.7478 -26389.7478 9.5642 -3.5816
timer: Routine,Calls,Time,% = IterSCF 1 0.000 0.00
elaps: Routine,Calls,Wall,% = IterSCF 1 0.000 0.00
timer: Routine,Calls,Time,% = TS 1 6109.618 15.80
elaps: Routine,Calls,Wall,% = TS 1 127.847 15.83
timer: Routine,Calls,Time,% = IterSCF 1 38369.594 99.21
elaps: Routine,Calls,Wall,% = IterSCF 1 801.301 99.21
TranSiesta: Qsol,Qtot: 868.854 713.000 1.000
transiesta: 2 4588.1213 -1130.8881 -1130.8881 22.0851 -3.5816
TranSiesta: Qsol,Qtot: 767.213 713.000 1.000
transiesta: 3 -33998.9321 -24075.0873 -24075.0873 11.8589 -3.5816
TranSiesta: Qsol,Qtot: 720.054 713.000 1.000
transiesta: 4 -28365.1093 -27515.3187 -27515.3187 4.6533 -3.5816
TranSiesta: Qsol,Qtot: 727.959 713.000 1.000
transiesta: 5 -27507.8708 -27520.8220 -27520.8220 4.0404 -3.5816
TranSiesta: Qsol,Qtot: 737.516 713.000 1.000
transiesta: 6 -26131.8016 -25891.0284 -25891.0284 16.7552 -3.5816
TranSiesta: Qsol,Qtot: 713.770 713.000 1.000
transiesta: 7 -26949.2847 -27274.1379 -27274.1379 6.1382 -3.5816
TranSiesta: Qsol,Qtot: 717.130 713.000 1.000
transiesta: 8 -27697.9093 -27604.8120 -27604.8120 1.7657 -3.5816
TranSiesta: Qsol,Qtot: 712.777 713.000 1.000
transiesta: 9 -27595.7559 -27600.6101 -27600.6101 1.9578 -3.5816
TranSiesta: Qsol,Qtot: 744.675 713.000 1.000
transiesta: 10 -24264.7612 -23823.9262 -23823.9262 24.9160 -3.5816
TranSiesta: Qsol,Qtot: 727.493 713.000 1.000
transiesta: 11 -27053.7951 -27406.1813 -27406.1813 6.4667 -3.5816
TranSiesta: Qsol,Qtot: 720.304 713.000 1.000
transiesta: 12 -27569.4696 -27643.9851 -27643.9851 1.7944 -3.5816
TranSiesta: Qsol,Qtot: 714.457 713.000 1.000
I also see the following options in the OUTPUT.fdf of Continuation
run, which I guess they confirm it is really a
continuation job:
New_DM. Step: 1
Initializing Density Matrix...
ts_iodm: Reading Density Matrix from files
TRANSIESTA: Continuation run
All the Best,
Zeynab
On Sunday, July 3, 2016 4:55 PM, Carlos Sanz <[email protected]
<mailto:[email protected]>> wrote:
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]> <mailto:[email protected]> wrote:
Hi zeynab,
See comments in line.
--
Kind regards Nick Papior
On 3 Jul 2016 10:13, "zeynab mohamad hoseyni"
<[email protected] <mailto:[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]
<mailto:[email protected]> | www.simune.eu <http://www.simune.eu/>
>
>
--
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/>
--
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/>
--
Kind regards Nick
