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
previousTranSiesta file (it is called "elec.TSHS").
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
runstops at number 63 and I expect the continuation run start from 64 and not
63..
Can you guess what is wrong?
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-04UseSaveData
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 TDM.UseSaveDM
true
Diag.ParallelOverK F
PAO.EnergyShift 50 meV PAO.SplitNorm
0.1500000000 PAO.BasisType split
PAO.BasisSize DZP WriteMullikenPop
0WriteBands FSaveRho
.true.SaveDeltaRho .true.SaveHS
.true.SaveElectrostaticPotential .true. SaveTotalPotential
yesWriteCoorXmol .true.WriteMDXmol
.true.WriteMDhistory .false.WriteEigenvalues
yesWriteDM T
%include POSITIONS.fdf
# Transiesta informationSolutionMethod Transiesta # GENGF
OPTIONSTS.ComplexContour.Emin -24 eV TS.ComplexContour.NPoles
16TS.ComplexContour.NCircle 16TS.ComplexContour.NLine 10 # BIAS
OPTIONSTS.biasContour.NumPoints 10
# TS OPTIONSTS.Voltage 0.00 eV
# TBT OPTIONSTS.TBT.Emin -3 eVTS.TBT.Emax +3 eVTS.TBT.NPoints 500TS.TBT.NEigen
3TS.TBT.Eta 0.000001 Ry
# Write electrode hamiltonianTS.SaveHS .true.TS.SaveLead .true.
TS.MixH TTS.UpdateDMCROnly TSCFMustConverge T
# LEFT ELECTRODETS.HSFileLeft ./elec.TSHS TS.NumUsedAtomsLeft
12TS.BufferAtomsLeft 0
# RIGHT ELECTRODETS.HSFileRight ./elec.TSHS TS.NumUsedAtomsRight
12TS.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
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