Dear Bibhas,
As Leo mentioned, you should just shift the original coordination to what
you got from your output file,i.e (AtomicCoordinatesFormat Ang
%block AtomicCoordinatesOrigin
1.6556 0.0009 0.0000
%endblock AtomicCoordinatesOrigin)...put it in your .fdf file.
Or you can shift the x coordinates to the positive coordinates in order to
solve this problem.
Regards,
Esmaeil.
On Mon, Nov 6, 2017 at 7:34 AM, Bibhas Manna <[email protected]> wrote:
> Dear Leonardo,
>
> Thanking you for your quick response.
>
> I was trying to solve the problem following your suggestions. But, I
> failed every time. I have also checked the atomic coordinate positions
> using VNL GUI. In all the cases, it seems to me that the atomic positions
> are within the unit cells, but I got the same error message. My transiesta
> input file looks like:
>
> # ------------------------------------------------------------
> ---------------
> # Name and Label
> # ------------------------------------------------------------
> ---------------
> SolutionMethod transiesta
> SystemName Left Electrode for Graphene
> SystemLabel Scat_G_Opt
>
> # ------------------------------------------------------------
> ---------------
> # Lattice
> # ------------------------------------------------------------
> ---------------
>
> LatticeConstant 1.00 Ang
>
> %block LatticeVectors
> 9.896615 -17.142261 0.000000
> 4.947479 8.570652 0.000000
> 0.000000 0.000000 18.000000
> %endblock LatticeVectors
>
> %block kgrid_Monkhorst_Pack
> 1 0 0 0.0
> 0 10 0 0.0
> 0 0 1 0.0
> %endblock kgrid_Monkhorst_Pack
>
> # ------------------------------------------------------------
> ---------------
> # Species and Atoms
> # ------------------------------------------------------------
> ---------------
>
> NumberOfSpecies 1
> NumberOfAtoms 64
>
> %block ChemicalSpeciesLabel
> 1 6 C
> %endblock ChemicalSpeciesLabel
>
> # ------------------------------------------------------------
> ---------------
> # Atomic Coordinates
> # ------------------------------------------------------------
> ---------------
>
> AtomicCoordinatesFormat Ang
>
> %block AtomicCoordinatesAndAtomicSpecies
> -0.00000041 0.00000463 0.00000000 1 #1 C
> 1.23686930 2.14266679 0.00000000 1 #3 C
> 2.47373901 4.28532895 0.00000000 1 #5 C
> 3.71060872 6.42799121 0.00000000 1 #7 C
> 1.23707646 -2.14277714 0.00000000 1 #9 C
> 2.47394618 -0.00011498 0.00000000 1 #11 C
> 3.71081589 2.14254718 0.00000000 1 #13 C
> 4.94768560 4.28520934 0.00000000 1 #15 C
> 1.23693835 0.71418545 0.00000000 1 #33 C
> 2.47380807 2.85684771 0.00000000 1 #35 C
> 3.71067778 4.99950987 0.00000000 1 #37 C
> 4.94754749 7.14217203 0.00000000 1 #39 C
> 2.47401523 -1.42859632 0.00000000 1 #41 C
> 3.71088494 0.71406584 0.00000000 1 #43 C
> 4.94775465 2.85672810 0.00000000 1 #45 C
> 6.18462437 4.99939026 0.00000000 1 #47 C
> 4.94830195 -8.57103523 0.00000000 1 #2 C
> 6.18517162 -6.42837184 0.00000000 1 #4 C
> 7.42204133 -4.28570960 0.00000000 1 #6 C
> 8.65891106 -2.14304739 0.00000000 1 #8 C
> 6.18540520 -10.71390543 0.00000000 1 #10 C
> 7.42227487 -8.57124206 -0.00000000 1 #12 C
> 8.65914459 -6.42857985 -0.00000000 1 #14 C
> 9.89601431 -4.28591757 0.00000000 1 #16 C
> 2.47417423 -4.28563042 0.00000000 1 #17 C
> 3.71104390 -2.14296705 0.00000000 1 #19 C
> 4.94791361 -0.00030488 0.00000000 1 #21 C
> 6.18478334 2.14235736 0.00000000 1 #23 C
> 3.71122197 -6.42828885 0.00000000 1 #25 C
> 4.94809164 -4.28562542 0.00000000 1 #27 C
> 6.18496135 -2.14296324 0.00000000 1 #29 C
> 7.42183108 -0.00030103 0.00000000 1 #31 C
> 6.18522814 -7.85699769 -0.00000000 1 #34 C
> 7.42209786 -5.71433541 0.00000000 1 #36 C
> 8.65896758 -3.57167320 0.00000000 1 #38 C
> 9.89583724 -1.42900983 -0.00000000 1 #40 C
> 7.42232463 -9.99975752 -0.00000000 1 #42 C
> 8.65919435 -7.85709531 -0.00000000 1 #44 C
> 9.89606407 -5.71443308 0.00000000 1 #46 C
> 11.13293377 -3.57176963 0.00000000 1 #48 C
> 3.71112009 -3.57138709 0.00000000 1 #49 C
> 4.94798981 -1.42872488 -0.00000000 1 #51 C
> 6.18485953 0.71393730 0.00000000 1 #53 C
> 7.42172919 2.85660073 0.00000000 1 #55 C
> 4.94814250 -5.71415374 -0.00000000 1 #57 C
> 6.18501223 -3.57149149 0.00000000 1 #59 C
> 7.42188195 -1.42882931 0.00000000 1 #61 C
> 8.65875161 0.71383406 -0.00000000 1 #63 C
> 7.42246443 -12.85669135 0.00000000 1 #18 C
> 8.65933414 -10.71402919 0.00000000 1 #20 C
> 9.89620385 -8.57136702 0.00000000 1 #22 C
> 11.13307356 -6.42870486 0.00000000 1 #24 C
> 8.65954130 -14.99947321 0.00000000 1 #26 C
> 9.89641102 -12.85681095 0.00000000 1 #28 C
> 11.13328073 -10.71414879 0.00000000 1 #30 C
> 12.37015044 -8.57148663 0.00000000 1 #32 C
> 8.65940319 -12.14251053 0.00000000 1 #50 C
> 9.89627291 -9.99984837 0.00000000 1 #52 C
> 11.13314262 -7.85718621 0.00000000 1 #54 C
> 12.37001233 -5.71452395 0.00000000 1 #56 C
> 9.89648007 -14.28529230 0.00000000 1 #58 C
> 11.13334978 -12.14263014 0.00000000 1 #60 C
> 12.37021949 -9.99996797 0.00000000 1 #62 C
> 13.60708921 -7.85730581 0.00000000 1 #64 C
> %endblock AtomicCoordinatesAndAtomicSpecies
>
> # END OF VNL EXPORT
> # ------------------------------------------------------------
> ---------------
> # ------------------------------------------------------------
> ---------------
>
> PAO.BasisType split
> PAO.BasisSize DZP
> PAO.SplitNorm 0.15
> PAO.EnergyShift 275 meV
>
> MeshCutoff 200. Ry
> XC.functional GGA
> XC.authors PBE
> SolutionMethod transiesta
>
> ElectronicTemperature 300 K
> OccupationFunction FD
>
> MinSCFIterations 3
> MaxSCFIterations 200
> DM.MixingWeight 0.1
> DM.Tolerance 0.0001
> DM.NumberPulay 6
> DM.UseSaveDM .true.
> DM.MixSCF1 .true.
>
> MD.NumCGSteps 0
>
> Diag.ParallelOverK T
>
> WriteMullikenPop 1
> WriteForces T
> SaveHS T
>
> TS.Voltage 0.0 eV
> %block TS.ChemPots
> Left
> Right
> %endblock TS.ChemPots
>
> %block TS.ChemPot.Left
> mu V/2
> contour.eq
> begin
> C-Left
> T-Left
> end
> %endblock TS.ChemPot.Left
> %block TS.ChemPot.Right
> mu -V/2
> contour.eq
> begin
> C-Right
> T-Right
> end
> %endblock TS.ChemPot.Right
>
> TS.Contours.Eq.Pole 2.5 eV
> %block TS.Contour.C-Left
> part circle
> from -40. eV + V/2 to -10 kT + V/2
> points 25
> method g-legendre
> %endblock TS.Contour.C-Left
> %block TS.Contour.T-Left
> part tail
> from prev to inf
> points 10
> method g-fermi
> %endblock TS.Contour.T-Left
> %block TS.Contour.C-Right
> part circle
> from -40. eV -V/2 to -10 kT -V/2
> points 25
> method g-legendre
> %endblock TS.Contour.C-Right
> %block TS.Contour.T-Right
> part tail
> from prev to inf
> points 10
> method g-fermi
> %endblock TS.Contour.T-Right
>
> %block TS.Contours.nEq
> neq-1
> %endblock TS.Contours.nEq
> %block TS.Contour.nEq.neq-1
> part line
> from -|V|/2 - 5 kT to |V|/2 + 5 kT
> delta 0.01 eV
> method mid-rule
> %endblock TS.Contour.nEq.neq-1
>
> # We have 2 electrodes
> %block TS.Elecs
> Left
> Right
> %endblock TS.Elecs
>
> %block TS.Elec.Left
> TSHS ./ElecLeft_Opt.TSHS
> chemical-potential Left
> semi-inf-direction -a1
> electrode-position 1
> %endblock TS.Elec.Left
> %block TS.Elec.Right
> TSHS ./ElecLeft_Opt.TSHS
> chemical-potential Right
> semi-inf-direction +a1
> electrode-position end -1
> %endblock TS.Elec.Right
>
>
>
> # TBtrans allows k-points along self-energy directions
> # when using mis-aligned electrodes.
> # Hence you MUST specify the k-grid
> %block TBT.k
> diag 1 10 1
> %endblock
> TBT.DOS.A T
>
> %block TBT.Contours
> line
> %endblock TBT.Contours
> %block TBT.Contour.line
> part line
> from -1. eV to 1. eV
> delta 0.01 eV
> method mid-rule
> %endblock TBT.Contour.line
>
>
> Could you please spend some time from your busy schedule to check my above
> input file. Because, I am not really able to clean the error.
>
> I am eagerly waiting for your valuable reply. Sorry for my bad English.
>
>
> Thanking you.
> With regards,
> Bibhas
>
>
>
>
>
>
> On Sat, Oct 21, 2017 at 3:01 AM, Leonardo Fonseca <[email protected]>
> wrote:
>
>> Dear Bibhas,
>>
>> The error message is self-explanatory. The contour integration would
>> benefit by adding 5 more energy points without increasing the computational
>> load. However this is not an error, just a suggestion. The error is in your
>> atomic coordinates. I am unable to open your included files, but most
>> likely you have atomic coordinates that are outside the unit cell. For
>> example, you could have negative z coordinates or x or y values that go
>> beyond the unit cell vectors. For band structure calculation you don't have
>> to worry about this since the system is periodic, but for transport you do.
>> The message even tells you how to fix the problem. Just add the suggested
>> block to shift all atomic coordinates automatically, so you don't have to
>> fix it atom by atom.
>>
>> Good luck!
>>
>> Leo
>>
>> 2017-10-20 5:10 GMT-02:00 Bibhas Manna <[email protected]>:
>>
>>> Dear Transiesta Users,
>>>
>>> I am very new to run the transiesta code. I have successfully computed
>>> .TSHS file for the left electrode at the first step. Assuming that my right
>>> and left electrodes are equivalent, I then move on to run the scattering
>>> region file using .TSHS for left electrode as an input. However, I faced
>>> some fatal errors related to transiesta run. Errors are as follows:
>>>
>>> ************************ Begin: TS CHECKS AND WARNINGS
>>> ************************
>>> Without loosing performance you can increase the equilibrium integration
>>> precision.
>>> You can add 5 more energy points in the equilibrium contours, for FREE!
>>> This is 5 more energy points per chemical potential.
>>> 5(1=-1) 7(1=-1)
>>> atom(cell-dir=neighbour-cell)
>>> *** Device atomic coordinates are not inside unit-cell.
>>> *** This is a requirement for bias calculations
>>> as the Poisson equation cannot be correctly handled
>>> due to inconsistencies with the grid and atomic coordinates
>>> *** Will continue, but will die when running V /= 0 ***
>>> Electrode: Left lies outside the unit-cell.
>>> Please shift the entire structure using the following recipe:
>>> If you already have AtomicCoordinatesFormat, add these
>>> AtomicCoordinatesFormat Ang
>>> %block AtomicCoordinatesOrigin
>>> 1.6556 0.0009 0.0000
>>> %endblock AtomicCoordinatesOrigin
>>> ************************ End: TS CHECKS AND WARNINGS
>>> **************************
>>>
>>> ****************************************
>>> TRANSIESTA REPORTED IMPORTANT WARNINGS
>>> ****************************************
>>>
>>> ******************************
>>> TRANSIESTA REPORTED ERRORS
>>> ******************************
>>> One or more errors have occured doing transiesta initialization, check
>>> the output
>>> Stopping Program from Node: 0
>>> ------------------------------------------------------------
>>> --------------
>>> MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 3
>>> CREATE FROM 0
>>> with errorcode 1.
>>>
>>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>>> You may or may not see output from other processes, depending on
>>> exactly when Open MPI kills them.
>>>
>>>
>>> I have tried to find the origin of such errors but failed every time.
>>>
>>> Please suggest me with some solution for this problem. Any help in this
>>> regard is highly appreciable.
>>> I am also attaching my input and output file of scattering region for
>>> your kind consideration.
>>>
>>> Thanking you.
>>> With regards,
>>> Bibhas
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
>
