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
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
