When I run a tranSIESTA calculation, the SCF converges, and the TBtrans output shows the following error:
************************
* WELCOME TO TBtrans *
************************
reinit: Reading from scat.fdf
reinit: -------------------------------------------------------------------
reinit: System Name: scat
reinit: -----------------------------------------------------------------------
reinit: System Label: scat
reinit: -------------------------------------------------------------------
Kpoints in: 1 . Kpoints trimmed: 1
tbt: Number of transport k-points = 1
tbt: Method = Monkhorst-Pack grid.
tbt: k-grid: Supercell and displacements
tbt: 1 0 0 0.000
tbt: 0 1 0 0.000
tbt: 0 0 1 0.000
tbt: **************************************************************
tbt: Electronic temperature (reference) = 299.9869 K
tbt: No applied bias
tbt: Calculate transmission only using diag(Gf) = F
tbt: Saving bulk transmission for electrodes = F
tbt: Saving DOS from bulk electrodes = F
tbt: Saving DOS from Green function = T
tbt: Saving DOS from all spectral functions = T
tbt: Saving bond currents (orb-orb) = F
tbt: Saving DM from Green function = F
tbt: Saving DM from spectral functions = F
tbt: Saving COOP from Green function = F
tbt: Saving COOP from spectral functions = F
tbt: Saving COHP from Green function = F
tbt: Saving COHP from spectral functions = F
tbt: Calc. # transmission eigenvalues = 0
tbt: Calc. T between all electrodes = F
tbt: Calc. total T out of electrodes = F
tbt: Non-polarized Hamiltonian
tbt: BTD creation algorithm = speed
tbt: BTD spectral function algorithm = propagation
tbt: Divide and conquer diagonalization = F
tbt: Assume LAPACK <i|S|j> = delta_ij = F
tbt: Saving downfolded self-energies = F
tbt: No delta Hamiltonian
tbt: No delta self-energy
tbt: Data files stored in current folder
tbt: No compression of TBT.nc files
tbt: Default NetCDF precision = single
tbt: Use parallel MPI-IO for NetCDF file = F
tbt: >> Electrodes <<
tbt: >> Left
tbt: Electrode cell pivoting: E1, E2, E3 = A1, A2, A3
tbt: In-core self-energy calculation
tbt: Electrode TSHS file = ./elec.TSHS
tbt: # atoms used in electrode = 44
tbt: Electrode Bloch unity [E1 x E2 x E3] = 1 x 1 x 1
tbt: Position in geometry = 1 -- 44
tbt: Semi-infinite direction for electrode = negative wrt. E3
tbt: Chemical shift = 0.000000 eV
tbt: Electronic temperature = 299.986869 K
tbt: Gamma-only electrode = T
tbt: Bulk H, S in electrode region = T
tbt: Electrode self-energy imaginary Eta = 0.1000E-03 eV
tbt: Electrode self-energy accuracy = 0.1000E-13 eV
tbt: Electrode inter-layer distance (semi-inf) = 1.3874 Ang
tbt: >> Right
tbt: Electrode cell pivoting: E1, E2, E3 = A1, A2, A3
tbt: In-core self-energy calculation
tbt: Electrode TSHS file = ./elec.TSHS
tbt: # atoms used in electrode = 44
tbt: Electrode Bloch unity [E1 x E2 x E3] = 1 x 1 x 1
tbt: Position in geometry = 265 -- 308
tbt: Semi-infinite direction for electrode = positive wrt. E3
tbt: Chemical shift = 0.000000 eV
tbt: Electronic temperature = 299.986869 K
tbt: Gamma-only electrode = T
tbt: Bulk H, S in electrode region = T
tbt: Electrode self-energy imaginary Eta = 0.1000E-03 eV
tbt: Electrode self-energy accuracy = 0.1000E-13 eV
tbt: Electrode inter-layer distance (semi-inf) = 1.3874 Ang
ts: >> TBtrans contour <<
ts: Device Green function imaginary Eta = 0.000 eV
ts: Contour name = TBT.Contour.line
ts: line contour E_min = -2.0000 eV
ts: line contour E_max = 2.0000 eV
ts: line contour points = 400
ts: line contour method = Mid-rule
tbt: **************************************************************
tbt: <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
%block TBT.Contours
line
%endblock TBT.Contours
%block TBT.Contour.line
part line
from -2. eV to 2. eV
delta 0.01 eV
method mid-rule
%endblock TBT.Contour.line
tbt: <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
************************ Begin: TBT CHECKS AND WARNINGS ************************
** Speed up the execution by utilizing parallel I/O
> TBT.CDF.MPI true
************************ End: TBT CHECKS AND WARNINGS **************************
Device information (full):
<sparsity:scat.TSHS
nrows_g=3780 nrows=3780 sparsity=.1129 nnzs=1613836, refcount: 3>
Electrode information:
<sparsity:./elec.TSHS
nrows_g=540 nrows=540 sparsity=.7906 nnzs=230548, refcount: 3>
<sparsity:(TM [--,--, 0] of: ./elec.TSHS)
nrows_g=540 nrows=540 sparsity=.3644 nnzs=106260, refcount: 3>
<sparsity:(TM [--,--,-1] of: ./elec.TSHS)
nrows_g=540 nrows=540 sparsity=.2131 nnzs=62144, refcount: 3>
Left principal cell is perfect!
<sparsity:./elec.TSHS
nrows_g=540 nrows=540 sparsity=.7906 nnzs=230548, refcount: 3>
<sparsity:(TM [--,--, 0] of: ./elec.TSHS)
nrows_g=540 nrows=540 sparsity=.3644 nnzs=106260, refcount: 3>
<sparsity:(TM [--,--, 1] of: ./elec.TSHS)
nrows_g=540 nrows=540 sparsity=.2131 nnzs=62144, refcount: 3>
Right principal cell is perfect!
tbt: Analyzing electrode sparsity pattern and electrode pivot-tables
*** WARNING! Removed 124288 elements which connect electrodes across the device region!
tbt: BTD pivoting scheme for electrode (Left): atom+Left
Region (2700): [O]-calculation
[ 541 -- 3240 ]
Region (540): Connect-Graph ()
[ 1 -- 540 ]
The electrode down-folding region is 0 in the device region. Please expand your device region.
The electrode down-folding region is 0 in the device region. Please expand your device region.
Stopping Program from Node: 0
Stopping Program from Node: 0
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
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.
--------------------------------------------------------------------------
This is the input calculation:
SolutionMethod Transiesta
SystemName scat
SystemLabel scat
==================================================
==================================================
# SPECIES AND BASIS
# Number of species
PAO.BasisSize DZP
PAO.EnergyShift 0.005 Ry
XC.functional GGA
XC.authors PBE
# ---------------------------------------------------------------------------
# Lattice
# ---------------------------------------------------------------------------
LatticeConstant 1.00 Ang
%block LatticeVectors
38.6768100000 0.0000000000 0.0000000000
0.0000000000 18.6851730000 0.0000000000
0.0000000000 0.0000000000 30.1042280000
%endblock LatticeVectors
# ---------------------------------------------------------------------------
# Species and Atoms
# ---------------------------------------------------------------------------
NumberOfSpecies 2
NumberOfAtoms 308
%block ChemicalSpeciesLabel
1 6 C
2 1 H
%endblock ChemicalSpeciesLabel
# ---------------------------------------------------------------------------
# Atomic Coordinates
# ---------------------------------------------------------------------------
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
2.382124030 9.947903380 1.477394770 1
4.860867040 9.947902900 1.485178540 1
7.333441770 9.947895520 1.480987940 1
9.809049030 9.947897240 1.482661500 1
12.280587220 9.947898690 1.483191640 1
14.754631820 9.947904150 1.481319140 1
17.227337500 9.947904520 1.483830520 1
19.697489200 9.947908640 1.481879250 1
22.174671570 9.947905950 1.480422050 1
24.621016910 9.947904870 1.510384170 1
1.166765930 9.947910660 3.653015820 1
3.618228130 9.947908220 3.623496400 1
6.099269120 9.947906590 3.625171600 1
8.570402150 9.947903840 3.627024140 1
11.044726030 9.947905640 3.623946660 1
13.518976140 9.947911980 3.626830320 1
15.988974480 9.947911870 3.625958590 1
18.464420820 9.947912110 3.624170140 1
20.934451480 9.947911350 3.628550790 1
23.408430950 9.947912850 3.621127820 1
1.166795710 9.947899270 0.739807800 1
3.618257410 9.947900570 0.769353230 1
6.099266620 9.947895170 0.767652400 1
8.570396160 9.947895340 0.765752800 1
11.044719240 9.947894900 0.768777320 1
13.518967180 9.947899740 0.765973090 1
15.988982230 9.947901030 0.766886840 1
18.464416860 9.947904980 0.768749590 1
20.934469120 9.947903800 0.764402670 1
23.408449860 9.947903490 0.771834920 1
2.382114000 9.947907190 2.915416910 1
4.860857660 9.947904120 2.907667790 1
7.333442290 9.947900740 2.911778090 1
9.809077290 9.947901710 2.910068240 1
12.280579530 9.947907490 2.909559000 1
14.754651260 9.947907930 2.911525370 1
17.227316290 9.947909520 2.909089240 1
19.697500000 9.947912290 2.911037910 1
22.174666730 9.947909110 2.912556810 1
24.621010220 9.947912200 2.882607540 1
0.201256320 9.947903870 1.256218750 2
0.201235990 9.947915730 3.136550830 2
25.582822460 9.947911930 3.402598090 2
25.582829770 9.947901560 0.990383820 2
2.382124030 9.947903380 27.281018770 1
4.860867040 9.947902900 27.288802540 1
7.333441770 9.947895520 27.284611940 1
9.809049030 9.947897240 27.286285500 1
12.280587220 9.947898690 27.286815640 1
14.754631820 9.947904150 27.284943140 1
17.227337500 9.947904520 27.287454520 1
19.697489200 9.947908640 27.285503250 1
22.174671570 9.947905950 27.284046050 1
24.621016910 9.947904870 27.314008170 1
1.166765930 9.947910660 29.456639820 1
3.618228130 9.947908220 29.427120400 1
6.099269120 9.947906590 29.428795600 1
8.570402150 9.947903840 29.430648140 1
11.044726030 9.947905640 29.427570660 1
13.518976140 9.947911980 29.430454320 1
15.988974480 9.947911870 29.429582590 1
18.464420820 9.947912110 29.427794140 1
20.934451480 9.947911350 29.432174790 1
23.408430950 9.947912850 29.424751820 1
1.166795710 9.947899270 26.543431800 1
3.618257410 9.947900570 26.572977230 1
6.099266620 9.947895170 26.571276400 1
8.570396160 9.947895340 26.569376800 1
11.044719240 9.947894900 26.572401320 1
13.518967180 9.947899740 26.569597090 1
15.988982230 9.947901030 26.570510840 1
18.464416860 9.947904980 26.572373590 1
20.934469120 9.947903800 26.568026670 1
23.408449860 9.947903490 26.575458920 1
2.382114000 9.947907190 28.719040910 1
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7.333442290 9.947900740 28.715402090 1
9.809077290 9.947901710 28.713692240 1
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17.227316290 9.947909520 28.712713240 1
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22.174666730 9.947909110 28.716180810 1
24.621010220 9.947912200 28.686231540 1
0.201256320 9.947903870 27.059842750 2
0.201235990 9.947915730 28.940174830 2
25.582822460 9.947911930 29.206222090 2
25.582829770 9.947901560 26.794007820 2
2.382124030 9.947903380 22.980414770 1
4.860867040 9.947902900 22.988198540 1
7.333441770 9.947895520 22.984007940 1
9.809049030 9.947897240 22.985681500 1
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14.754631820 9.947904150 22.984339140 1
17.227337500 9.947904520 22.986850520 1
19.697489200 9.947908640 22.984899250 1
22.174671570 9.947905950 22.983442050 1
24.621016910 9.947904870 23.013404170 1
1.166765930 9.947910660 25.156035820 1
3.618228130 9.947908220 25.126516400 1
6.099269120 9.947906590 25.128191600 1
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11.044726030 9.947905640 25.126966660 1
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15.988974480 9.947911870 25.128978590 1
18.464420820 9.947912110 25.127190140 1
20.934451480 9.947911350 25.131570790 1
23.408430950 9.947912850 25.124147820 1
1.166795710 9.947899270 22.242827800 1
3.618257410 9.947900570 22.272373230 1
6.099266620 9.947895170 22.270672400 1
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11.044719240 9.947894900 22.271797320 1
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2.382114000 9.947907190 24.418436910 1
4.860857660 9.947904120 24.410687790 1
7.333442290 9.947900740 24.414798090 1
9.809077290 9.947901710 24.413088240 1
12.280579530 9.947907490 24.412579000 1
14.754651260 9.947907930 24.414545370 1
17.227316290 9.947909520 24.412109240 1
19.697500000 9.947912290 24.414057910 1
22.174666730 9.947909110 24.415576810 1
24.621010220 9.947912200 24.385627540 1
0.201256320 9.947903870 22.759238750 2
0.201235990 9.947915730 24.639570830 2
25.582822460 9.947911930 24.905618090 2
25.582829770 9.947901560 22.493403820 2
2.382124030 9.947903380 18.679810770 1
4.860867040 9.947902900 18.687594540 1
7.333441770 9.947895520 18.683403940 1
9.809049030 9.947897240 18.685077500 1
12.280587220 9.947898690 18.685607640 1
14.754631820 9.947904150 18.683735140 1
17.227337500 9.947904520 18.686246520 1
19.697489200 9.947908640 18.684295250 1
22.174671570 9.947905950 18.682838050 1
24.621016910 9.947904870 18.712800170 1
1.166765930 9.947910660 20.855431820 1
3.618228130 9.947908220 20.825912400 1
6.099269120 9.947906590 20.827587600 1
8.570402150 9.947903840 20.829440140 1
11.044726030 9.947905640 20.826362660 1
13.518976140 9.947911980 20.829246320 1
15.988974480 9.947911870 20.828374590 1
18.464420820 9.947912110 20.826586140 1
20.934451480 9.947911350 20.830966790 1
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1.166795710 9.947899270 17.942223800 1
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6.099266620 9.947895170 17.970068400 1
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11.044719240 9.947894900 17.971193320 1
13.518967180 9.947899740 17.968389090 1
15.988982230 9.947901030 17.969302840 1
18.464416860 9.947904980 17.971165590 1
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0.201235990 9.947915730 20.338966830 2
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2.382124030 9.947903380 14.379206770 1
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7.333441770 9.947895520 14.382799940 1
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14.754631820 9.947904150 14.383131140 1
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19.697489200 9.947908640 14.383691250 1
22.174671570 9.947905950 14.382234050 1
24.621016910 9.947904870 14.412196170 1
1.166765930 9.947910660 16.554827820 1
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18.464420820 9.947912110 16.525982140 1
20.934451480 9.947911350 16.530362790 1
23.408430950 9.947912850 16.522939820 1
1.166795710 9.947899270 13.641619800 1
3.618257410 9.947900570 13.671165230 1
6.099266620 9.947895170 13.669464400 1
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18.464416860 9.947904980 13.670561590 1
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23.408449860 9.947903490 13.673646920 1
2.382114000 9.947907190 15.817228910 1
4.860857660 9.947904120 15.809479790 1
7.333442290 9.947900740 15.813590090 1
9.809077290 9.947901710 15.811880240 1
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0.201256320 9.947903870 14.158030750 2
0.201235990 9.947915730 16.038362830 2
25.582822460 9.947911930 16.304410090 2
25.582829770 9.947901560 13.892195820 2
2.382124030 9.947903380 10.078602770 1
4.860867040 9.947902900 10.086386540 1
7.333441770 9.947895520 10.082195940 1
9.809049030 9.947897240 10.083869500 1
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14.754631820 9.947904150 10.082527140 1
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19.697489200 9.947908640 10.083087250 1
22.174671570 9.947905950 10.081630050 1
24.621016910 9.947904870 10.111592170 1
1.166765930 9.947910660 12.254223820 1
3.618228130 9.947908220 12.224704400 1
6.099269120 9.947906590 12.226379600 1
8.570402150 9.947903840 12.228232140 1
11.044726030 9.947905640 12.225154660 1
13.518976140 9.947911980 12.228038320 1
15.988974480 9.947911870 12.227166590 1
18.464420820 9.947912110 12.225378140 1
20.934451480 9.947911350 12.229758790 1
23.408430950 9.947912850 12.222335820 1
1.166795710 9.947899270 9.341015800 1
3.618257410 9.947900570 9.370561230 1
6.099266620 9.947895170 9.368860400 1
8.570396160 9.947895340 9.366960800 1
11.044719240 9.947894900 9.369985320 1
13.518967180 9.947899740 9.367181090 1
15.988982230 9.947901030 9.368094840 1
18.464416860 9.947904980 9.369957590 1
20.934469120 9.947903800 9.365610670 1
23.408449860 9.947903490 9.373042920 1
2.382114000 9.947907190 11.516624910 1
4.860857660 9.947904120 11.508875790 1
7.333442290 9.947900740 11.512986090 1
9.809077290 9.947901710 11.511276240 1
12.280579530 9.947907490 11.510767000 1
14.754651260 9.947907930 11.512733370 1
17.227316290 9.947909520 11.510297240 1
19.697500000 9.947912290 11.512245910 1
22.174666730 9.947909110 11.513764810 1
24.621010220 9.947912200 11.483815540 1
0.201256320 9.947903870 9.857426750 2
0.201235990 9.947915730 11.737758830 2
25.582822460 9.947911930 12.003806090 2
25.582829770 9.947901560 9.591591820 2
2.382124030 9.947903380 5.777998770 1
4.860867040 9.947902900 5.785782540 1
7.333441770 9.947895520 5.781591940 1
9.809049030 9.947897240 5.783265500 1
12.280587220 9.947898690 5.783795640 1
14.754631820 9.947904150 5.781923140 1
17.227337500 9.947904520 5.784434520 1
19.697489200 9.947908640 5.782483250 1
22.174671570 9.947905950 5.781026050 1
24.621016910 9.947904870 5.810988170 1
1.166765930 9.947910660 7.953619820 1
3.618228130 9.947908220 7.924100400 1
6.099269120 9.947906590 7.925775600 1
8.570402150 9.947903840 7.927628140 1
11.044726030 9.947905640 7.924550660 1
13.518976140 9.947911980 7.927434320 1
15.988974480 9.947911870 7.926562590 1
18.464420820 9.947912110 7.924774140 1
20.934451480 9.947911350 7.929154790 1
23.408430950 9.947912850 7.921731820 1
1.166795710 9.947899270 5.040411800 1
3.618257410 9.947900570 5.069957230 1
6.099266620 9.947895170 5.068256400 1
8.570396160 9.947895340 5.066356800 1
11.044719240 9.947894900 5.069381320 1
13.518967180 9.947899740 5.066577090 1
15.988982230 9.947901030 5.067490840 1
18.464416860 9.947904980 5.069353590 1
20.934469120 9.947903800 5.065006670 1
23.408449860 9.947903490 5.072438920 1
2.382114000 9.947907190 7.216020910 1
4.860857660 9.947904120 7.208271790 1
7.333442290 9.947900740 7.212382090 1
9.809077290 9.947901710 7.210672240 1
12.280579530 9.947907490 7.210163000 1
14.754651260 9.947907930 7.212129370 1
17.227316290 9.947909520 7.209693240 1
19.697500000 9.947912290 7.211641910 1
22.174666730 9.947909110 7.213160810 1
24.621010220 9.947912200 7.183211540 1
0.201256320 9.947903870 5.556822750 2
0.201235990 9.947915730 7.437154830 2
25.582822460 9.947911930 7.703202090 2
25.582829770 9.947901560 5.290987820 2
%endblock AtomicCoordinatesAndAtomicSpecies
# K-points
%block kgrid_Monkhorst_Pack
1 0 0 0.0
0 1 0 0.0
0 0 100 0.0
%endblock kgrid_Monkhorst_Pack
==================================================
==================================================
# SCF variables
DM.MixSCF1 T
MaxSCFIterations 30000 # Maximum number of SCF iter
DM.MixingWeight 0.05 # New DM amount for next SCF cycle
DM.Tolerance 1.d-4 # Tolerance in maximum difference
DM.UseSaveDM true # to use continuation files
DM.NumberPulay 5
==================================================
==================================================
# MD variables
MD.FinalTimeStep 1
MD.TypeOfRun CG
MD.NumCGsteps 000
MD.UseSaveXV .true.
==================================================
==================================================
# Output variables
WriteMullikenPop 1
WriteBands .false.
SaveRho .true.
SaveDeltaRho .true.
SaveHS .true.
SaveElectrostaticPotential .true.
SaveTotalPotential .true.
WriteCoorXmol .true.
WriteMDXmol .true.
WriteMDhistory .false.
WriteEigenvalues .true.
XML.Write .true.
SaveBaderCharge .true.
==================================================
==================================================
#Other options
TS.HS.Save .true.
TS.DE.Save .true.
ParallelOverK .true.
User.Basis .true.
Diag.ParallelOverK .true.
==================================================
==================================================
#####################TRANSIESTA###################
# Bias voltage
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.Elecs.Bulk true
TS.Elecs.DM.Update none
TS.Elecs.GF.ReUse false
%block TS.Elecs
Left
Right
%endblock TS.Elecs
%block TS.Elec.Left
TSHS ./elec.TSHS
chem-pot Left
semi-inf-dir -a3
elec-pos begin 1
%endblock TS.Elec.Left
%block TS.Elec.Right
TSHS ./elec.TSHS
chem-pot Right
semi-inf-dir +a3
elec-pos end -1
%endblock TS.Elec.Right
TS.Contours.Eq.Pole 2.5 eV
%block TS.Contour.c-Left
part circle
from -40.00000 eV + V/2 to -10. kT + V/2
points 30
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 -40.00000 eV - V/2 to -10. kT - V/2
points 30
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
TS.Contours.nEq.Eta 0.0001 eV
%block TS.Contours.nEq
neq
%endblock TS.Contours.nEq
%block TS.Contour.nEq.neq
part line
from -|V|/2 - 5 kT to |V|/2 + 5 kT
delta 0.01 eV
method mid-rule
%endblock TS.Contour.nEq.neq
#%block LocalDensityOfStates
#-2.21 0.00 eV
#%endblock LocalDensityOfStates
TBT.DOS.A.All T
TBT.DOS.Gf T
TS.SolutionMethod btd
TS.BTD.Pivot atom+Left
TS.Elecs.Neglect.Principal true
==================================================
==================================================
How can I solve this error?
