Siesta

The electrode connectivity problem of siesta running SiP bias

Asked by Jinye Lv

I wanted to use transiesta to calculate the transfer characteristics of SiP under different bias, but an error occurred during the running of the.sh file. The error was:Electrode connectivity is not perfect, refer to the manual for achieving a perfect electrode.I looked at the.out file for the central area and found the following statement：

Left principal cell is extending out with 12716 elements:
    Atom 3 connects with atom 16
    Orbital 27 connects with orbital 144
    Hamiltonian value: |H(27,792)|@R=-2 = 0.105 eV
    Overlap : S(27,792)|@R=-2 = 0.121E-02
Electrode connectivity is not perfect, refer to the manual for achieving a perfect electrode.

And I want to know how to solve this problem,Is it a problem of SiP modeling structure or a problem of parameter setting in subsequent. Elec and. Scat?

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Jinye Lv (rrredstone) said : 		#1

This is my.out file:

Siesta Version : v4.1-b4
Architecture : Intel_composer_xe_2013_update2+OpenMPI(2.1.0)@SUSE-10.2_X86-64
Compiler version: ifort (IFORT) 13.1.0 20130121
Compiler flags : mpif90 -O3 -i-static
PP flags : -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DMPI -DGRID_DP -DPHI_GRID_SP -DCDF -DNCDF -DNCDF_4
Libraries : libncdf.a libfdict.a -L/home/lv/intel/composer_xe_2013.2.146/mkl/lib/intel64 -lmkl_scalapack_lp64 -L/home/lv/intel/composer_xe_2013.2.146/mkl/lib/intel64 -lmkl_blacs_openmpi_lp64 -L/home/lv/intel/composer_xe_2013.2.146/mkl/lib/intel64 -lmkl_sequential -lmkl_core -L/home/lv/intel/composer_xe_2013.2.146/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz
PARALLEL version
NetCDF support
NetCDF-4 support

* Running on 2 nodes in parallel
>> Start of run: 25-APR-2019 18:23:39

                           ***********************
                           * WELCOME TO SIESTA *
                           ***********************

reinit: Reading from standard input
reinit: Dumped input in INPUT_TMP.16322
************************** Dump of input data file ****************************
SolutionMethod Transiesta
SystemName SiP_scat
SystemLabel SiP_scat
==================================================
==================================================
# SPECIES AND BASIS
# Number of species
NumberOfSpecies 2
%block ChemicalSpeciesLabel
  1 14 Si
  2 15 P
%endblock ChemicalSpeciesLabel
PAO.BasisSize SZP
PAO.EnergyShift 275 meV
XC.functional GGA
XC.authors PBE
MeshCutoff 300.00000000 Ry # default value
==================================================
==================================================
# K-points
%block kgrid_Monkhorst_Pack
 1 0 0 0.0
 0 10 0 0.0
 0 0 1 0.0
%endblock kgrid_Monkhorst_Pack
==================================================
==================================================
# Structure
NumberOfAtoms 120
LatticeConstant 1.0 Ang
%block LatticeVectors
     17.605000 0.000000 0.00000
     0.0000000 20.47900 0.00000
     0.0000000 0.000000 25.0000
%endblock LatticeVectors
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.826793964 6.405363 10.859704 1
0.826906964 6.479372 13.261764 1
0.826952964 8.67376 10.383837 2
0.826962964 18.090289 13.908239 2
0.827016964 11.619284 13.971085 2
0.827084964 13.888055 13.496212 1
0.827119964 13.814794 11.094005 1
0.827127964 4.626704 14.65555 2
0.827188964 19.236014 11.874205 1
0.827252964 1.057441 12.480765 1
0.827269964 15.666657 9.699298 2
0.827297964 2.202867 10.446642 2
2.587290964 5.432484 9.699313 2
2.587341964 7.857543 13.907422 2
2.587351964 11.295483 12.483414 1
2.587363964 8.998883 11.871285 1
2.587463964 16.712573 13.261543 1
2.587474964 18.909185 10.386933 2
2.587511964 12.437001 10.447608 2
2.587561964 3.653609 13.495236 1
2.587597964 1.384375 13.968026 2
2.587602964 14.860746 14.656604 2
2.587643964 3.580434 11.093508 1
2.587739964 16.640054 10.859589 1
4.347793964 6.405363 10.859704 1
4.347906964 6.479372 13.261764 1
4.347952964 8.67376 10.383837 2
4.347962964 18.090289 13.908239 2
4.348016964 11.619284 13.971085 2
4.348084964 13.888055 13.496212 1
4.348119964 13.814794 11.094005 1
4.348127964 4.626704 14.65555 2
4.348188964 19.236014 11.874205 1
4.348252964 1.057441 12.480765 1
4.348269964 15.666657 9.699298 2
4.348297964 2.202867 10.446642 2
6.108290964 5.432484 9.699313 2
6.108341964 7.857543 13.907422 2
6.108351964 11.295483 12.483414 1
6.108363964 8.998883 11.871285 1
6.108463964 16.712573 13.261543 1
6.108474964 18.909185 10.386933 2
6.108511964 12.437001 10.447608 2
6.108561964 3.653609 13.495236 1
6.108597964 1.384375 13.968026 2
6.108602964 14.860746 14.656604 2
6.108643964 3.580434 11.093508 1
6.108739964 16.640054 10.859589 1
7.868793964 6.405363 10.859704 1
7.868906964 6.479372 13.261764 1
7.868952964 8.67376 10.383837 2
7.868962964 18.090289 13.908239 2
7.869016964 11.619284 13.971085 2
7.869084964 13.888055 13.496212 1
7.869119964 13.814794 11.094005 1
7.869127964 4.626704 14.65555 2
7.869188964 19.236014 11.874205 1
7.869252964 1.057441 12.480765 1
7.869269964 15.666657 9.699298 2
7.869297964 2.202867 10.446642 2
9.629290964 5.432484 9.699313 2
9.629341964 7.857543 13.907422 2
9.629351964 11.295483 12.483414 1
9.629363964 8.998883 11.871285 1
9.629463964 16.712573 13.261543 1
9.629474964 18.909185 10.386933 2
9.629511964 12.437001 10.447608 2
9.629561964 3.653609 13.495236 1
9.629597964 1.384375 13.968026 2
9.629602964 14.860746 14.656604 2
9.629643964 3.580434 11.093508 1
9.629739964 16.640054 10.859589 1
11.38979396 6.405363 10.859704 1
11.38990696 6.479372 13.261764 1
11.38995296 8.67376 10.383837 2
11.38996296 18.090289 13.908239 2
11.39001696 11.619284 13.971085 2
11.39008496 13.888055 13.496212 1
11.39011996 13.814794 11.094005 1
11.39012796 4.626704 14.65555 2
11.39018896 19.236014 11.874205 1
11.39025296 1.057441 12.480765 1
11.39026996 15.666657 9.699298 2
11.39029796 2.202867 10.446642 2
13.15029096 5.432484 9.699313 2
13.15034196 7.857543 13.907422 2
13.15035196 11.295483 12.483414 1
13.15036396 8.998883 11.871285 1
13.15046396 16.712573 13.261543 1
13.15047496 18.909185 10.386933 2
13.15051196 12.437001 10.447608 2
13.15056196 3.653609 13.495236 1
13.15059796 1.384375 13.968026 2
13.15060296 14.860746 14.656604 2
13.15064396 3.580434 11.093508 1
13.15073996 16.640054 10.859589 1
14.91079396 6.405363 10.859704 1
14.91090696 6.479372 13.261764 1
14.91095296 8.67376 10.383837 2
14.91096296 18.090289 13.908239 2
14.91101696 11.619284 13.971085 2
14.91108496 13.888055 13.496212 1
14.91111996 13.814794 11.094005 1
14.91112796 4.626704 14.65555 2
14.91118896 19.236014 11.874205 1
14.91125296 1.057441 12.480765 1
14.91126996 15.666657 9.699298 2
14.91129796 2.202867 10.446642 2
16.67129096 5.432484 9.699313 2
16.67134196 7.857543 13.907422 2
16.67135196 11.295483 12.483414 1
16.67136396 8.998883 11.871285 1
16.67146396 16.712573 13.261543 1
16.67147496 18.909185 10.386933 2
16.67151196 12.437001 10.447608 2
16.67156196 3.653609 13.495236 1
16.67159796 1.384375 13.968026 2
16.67160296 14.860746 14.656604 2
16.67164396 3.580434 11.093508 1
16.67173996 16.640054 10.859589 1
%endblock AtomicCoordinatesAndAtomicSpecies
==================================================
==================================================
# SCF variables
SCF.Mix.Method Pulay
DM.NumberPulay 5
DM.MixSCF1 T
SCF.Mix Hamiltonian
MaxSCFIterations 100 # Maximum number of SCF iter
DM.MixingWeight 0.05 # New DM amount for next SCF cycle
DM.UseSaveDM true # to use continuation files
MixHamiltonian yes
==================================================
==================================================
# MD variables
# MD.FinalTimeStep 1
# MD.TypeOfRun CG
# MD.NumCGsteps 000
# MD.UseSaveXV .true.
==================================================
==================================================
# Output variables
LongOutput .true.
WriteCoorXmol .true.
SaveTotalPotential T
SaveElectrostaticPotential T
SaveRho T
SaveDeltaRho T
WriteDenchar .true. # Write information for DENCHAR
Denchar.TypeOfRun 2D
Denchar.PlotCharge T
==================================================
==================================================
# Bias voltage
TS.Voltage 0.5 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 ./SiP_elec.TSHS
  chem-pot Left
  semi-inf-dir -a1
  elec-pos begin 1
  used-atoms 24
%endblock TS.Elec.Left
%block TS.Elec.Right
  TSHS ./SiP_elec.TSHS
  chem-pot Right
  semi-inf-dir +a1
  elec-pos end -1
  used-atoms 24
%endblock TS.Elec.Right
TS.Contours.Eq.Pole 2.5 eV
%block TS.Contour.c-Left
  part circle
   from -40.0000 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 #from -|V|/2 to |V|/2
    delta 0.01 eV
     method mid-rule
%endblock TS.Contour.nEq.neq
%block Geometry.Charge
 plane 0.0 charge
   gauss 1. 2. Ang
    0. 6. 20. Ang
    0. 0. 1.
%endblock Geometry.Charge
%block TBT.Contours
line
%endblock TBT.Contours
%block TBT.Contour.line
from -5. eV to 5. eV
delta 0.04 eV
method mid-rule
%endblock TBT.Contour.line
TBT.DOS.Elecs .true.
TBT.DOS.Gf .true.
TBT.DOS.A .true.
TBT.DOS.A.All .true.
TBT.T.All .true.
TBT.T.Out .true.
#TBT.Atoms.Device [17 -- 64]
#TBT.Current.Orb .true.
************************** End of input data file *****************************

reinit: -----------------------------------------------------------------------
reinit: System Name: SiP_scat
reinit: -----------------------------------------------------------------------
reinit: System Label: SiP_scat
reinit: -----------------------------------------------------------------------

initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Species number: 1 Atomic number: 14 Label: Si
Species number: 2 Atomic number: 15 Label: P

Ground state valence configuration: 3s02 3p02
Reading pseudopotential information in formatted form from Si.psf

Valence configuration for pseudopotential generation:
3s( 2.00) rc: 1.75
3p( 2.00) rc: 1.94
3d( 0.00) rc: 2.09
4f( 0.00) rc: 2.09
Ground state valence configuration: 3s02 3p03
Reading pseudopotential information in formatted form from P.psf

Valence configuration for pseudopotential generation:
3s( 2.00) rc: 1.70
3p( 3.00) rc: 1.88
3d( 0.00) rc: 2.00
4f( 0.00) rc: 2.00
For Si, standard SIESTA heuristics set lmxkb to 3
 (one more than the basis l, including polarization orbitals).
Use PS.lmax or PS.KBprojectors blocks to override.
For P, standard SIESTA heuristics set lmxkb to 3
 (one more than the basis l, including polarization orbitals).
Use PS.lmax or PS.KBprojectors blocks to override.

<basis_specs>
===============================================================================
Si Z= 14 Mass= 28.090 Charge= 0.17977+309
Lmxo=1 Lmxkb= 3 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=3
          n=1 nzeta=1 polorb=0
            splnorm: 0.15000
               vcte: 0.0000
               rinn: 0.0000
               qcoe: 0.0000
               qyuk: 0.0000
               qwid: 0.10000E-01
                rcs: 0.0000
            lambdas: 1.00000
L=1 Nsemic=0 Cnfigmx=3
          n=1 nzeta=1 polorb=1
            splnorm: 0.15000
               vcte: 0.0000
               rinn: 0.0000
               qcoe: 0.0000
               qyuk: 0.0000
               qwid: 0.10000E-01
                rcs: 0.0000
            lambdas: 1.00000
-------------------------------------------------------------------------------
L=0 Nkbl=1 erefs: 0.17977+309
L=1 Nkbl=1 erefs: 0.17977+309
L=2 Nkbl=1 erefs: 0.17977+309
L=3 Nkbl=1 erefs: 0.17977+309
===============================================================================
</basis_specs>

atom: Called for Si (Z = 14)

read_vps: Pseudopotential generation method:
read_vps: ATM3 Troullier-Martins
Total valence charge: 4.00000

read_vps: Pseudopotential includes a core correction:
read_vps: Pseudo-core for xc-correction

xc_check: Exchange-correlation functional:
xc_check: GGA Perdew, Burke & Ernzerhof 1996
V l=0 = -2*Zval/r beyond r= 2.0104
V l=1 = -2*Zval/r beyond r= 2.0873
V l=2 = -2*Zval/r beyond r= 2.1670
V l=3 = -2*Zval/r beyond r= 2.1670
All V_l potentials equal beyond r= 2.0613
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r= 2.1670

VLOCAL1: 99.0% of the norm of Vloc inside 10.216 Ry
VLOCAL1: 99.9% of the norm of Vloc inside 23.282 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 2.45560
atom: Maximum radius for r*vlocal+2*Zval: 2.14012
GHOST: No ghost state for L = 0
GHOST: No ghost state for L = 1
GHOST: No ghost state for L = 2
GHOST: No ghost state for L = 3

KBgen: Kleinman-Bylander projectors:
   l= 0 rc= 2.306811 el= -0.791441 Ekb= 5.289775 kbcos= 0.291595
   l= 1 rc= 2.394965 el= -0.300632 Ekb= 1.944256 kbcos= 0.287657
   l= 2 rc= 2.549439 el= 0.001958 Ekb= -1.788485 kbcos= -0.056492
   l= 3 rc= 2.782581 el= 0.003046 Ekb= -0.472620 kbcos= -0.006203

KBgen: Total number of Kleinman-Bylander projectors: 16
atom: -------------------------------------------------------------------------

atom: SANKEY-TYPE ORBITALS:

SPLIT: Orbitals with angular momentum L= 0

SPLIT: Basis orbitals for state 3s

SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.020212 Ry

   izeta = 1
                 lambda = 1.000000
                     rc = 5.007352
                 energy = -0.772735
                kinetic = 0.581259
    potential(screened) = -1.353994
       potential(ionic) = -3.769451

SPLIT: Orbitals with angular momentum L= 1

SPLIT: Basis orbitals for state 3p

SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.020212 Ry

   izeta = 1
                 lambda = 1.000000
                     rc = 6.270866
                 energy = -0.282590
                kinetic = 0.876421
    potential(screened) = -1.159012
       potential(ionic) = -3.390735

POLgen: Perturbative polarization orbital with L= 2

POLgen: Polarization orbital for state 3p

   izeta = 1
                     rc = 6.270866
                 energy = 0.439433
                kinetic = 1.304939
    potential(screened) = -0.865506
       potential(ionic) = -2.929821
atom: Total number of Sankey-type orbitals: 9

atm_pop: Valence configuration (for local Pseudopot. screening):
 3s( 2.00)
 3p( 2.00)
Vna: chval, zval: 4.00000 4.00000

Vna: Cut-off radius for the neutral-atom potential: 6.270866
comcore: Pseudo-core radius Rcore= 2.999314

atom: _________________________________________________________________________

<basis_specs>
===============================================================================
P Z= 15 Mass= 30.970 Charge= 0.17977+309
Lmxo=1 Lmxkb= 3 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=3
          n=1 nzeta=1 polorb=0
            splnorm: 0.15000
               vcte: 0.0000
               rinn: 0.0000
               qcoe: 0.0000
               qyuk: 0.0000
               qwid: 0.10000E-01
                rcs: 0.0000
            lambdas: 1.00000
L=1 Nsemic=0 Cnfigmx=3
          n=1 nzeta=1 polorb=1
            splnorm: 0.15000
               vcte: 0.0000
               rinn: 0.0000
               qcoe: 0.0000
               qyuk: 0.0000
               qwid: 0.10000E-01
                rcs: 0.0000
            lambdas: 1.00000
-------------------------------------------------------------------------------
L=0 Nkbl=1 erefs: 0.17977+309
L=1 Nkbl=1 erefs: 0.17977+309
L=2 Nkbl=1 erefs: 0.17977+309
L=3 Nkbl=1 erefs: 0.17977+309
===============================================================================
</basis_specs>

atom: Called for P (Z = 15)

read_vps: Pseudopotential generation method:
read_vps: ATM3 Troullier-Martins
Total valence charge: 5.00000

read_vps: Pseudopotential includes a core correction:
read_vps: Pseudo-core for xc-correction

xc_check: Exchange-correlation functional:
xc_check: GGA Perdew, Burke & Ernzerhof 1996
V l=0 = -2*Zval/r beyond r= 1.8764
V l=1 = -2*Zval/r beyond r= 1.9481
V l=2 = -2*Zval/r beyond r= 1.9974
V l=3 = -2*Zval/r beyond r= 1.9974
All V_l potentials equal beyond r= 1.9726
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r= 1.9974

VLOCAL1: 99.0% of the norm of Vloc inside 11.155 Ry
VLOCAL1: 99.9% of the norm of Vloc inside 25.423 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 2.37948
atom: Maximum radius for r*vlocal+2*Zval: 2.07377
GHOST: No ghost state for L = 0
GHOST: No ghost state for L = 1
GHOST: No ghost state for L = 2
GHOST: No ghost state for L = 3

KBgen: Kleinman-Bylander projectors:
   l= 0 rc= 2.180107 el= -1.021271 Ekb= 6.416696 kbcos= 0.303324
   l= 1 rc= 2.263420 el= -0.405531 Ekb= 2.368759 kbcos= 0.295942
   l= 2 rc= 2.349916 el= 0.002048 Ekb= -2.202332 kbcos= -0.057366
   l= 3 rc= 2.532950 el= 0.003178 Ekb= -0.567893 kbcos= -0.005281

KBgen: Total number of Kleinman-Bylander projectors: 16
atom: -------------------------------------------------------------------------

atom: SANKEY-TYPE ORBITALS:

SPLIT: Orbitals with angular momentum L= 0

SPLIT: Basis orbitals for state 3s

SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.020212 Ry

   izeta = 1
                 lambda = 1.000000
                     rc = 4.558135
                 energy = -1.003686
                kinetic = 0.730692
    potential(screened) = -1.734377
       potential(ionic) = -5.317595

SPLIT: Orbitals with angular momentum L= 1

SPLIT: Basis orbitals for state 3p

SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.020212 Ry

   izeta = 1
                 lambda = 1.000000
                     rc = 5.567355
                 energy = -0.387087
                kinetic = 1.179303
    potential(screened) = -1.566390
       potential(ionic) = -4.902418

POLgen: Perturbative polarization orbital with L= 2

POLgen: Polarization orbital for state 3p

   izeta = 1
                     rc = 5.567355
                 energy = 0.582313
                kinetic = 1.738827
    potential(screened) = -1.156514
       potential(ionic) = -4.227359
atom: Total number of Sankey-type orbitals: 9

atm_pop: Valence configuration (for local Pseudopot. screening):
 3s( 2.00)
 3p( 3.00)
Vna: chval, zval: 5.00000 5.00000

Vna: Cut-off radius for the neutral-atom potential: 5.567355
comcore: Pseudo-core radius Rcore= 2.730239

atom: _________________________________________________________________________

prinput: Basis input ----------------------------------------------------------

PAO.BasisType split

%block ChemicalSpeciesLabel
    1 14 Si # Species index, atomic number, species label
    2 15 P # Species index, atomic number, species label
%endblock ChemicalSpeciesLabel

%block PAO.Basis # Define Basis set
Si 2 # Species label, number of l-shells
 n=3 0 1 # n, l, Nzeta
   5.007
   1.000
 n=3 1 1 P 1 # n, l, Nzeta, Polarization, NzetaPol
   6.271
   1.000
P 2 # Species label, number of l-shells
 n=3 0 1 # n, l, Nzeta
   4.558
   1.000
 n=3 1 1 P 1 # n, l, Nzeta, Polarization, NzetaPol
   5.567
   1.000
%endblock PAO.Basis

prinput: ----------------------------------------------------------------------

Dumping basis to NetCDF file Si.ion.nc
Dumping basis to NetCDF file P.ion.nc
coor: Atomic-coordinates input format = Cartesian coordinates
coor: (in Angstroms)

siesta: Atomic coordinates (Bohr) and species
siesta: 1.56241 12.10439 20.52187 1 1
siesta: 1.56263 12.24424 25.06111 1 2
siesta: 1.56272 16.39104 19.62262 2 3
siesta: 1.56273 34.18571 26.28277 2 4
siesta: 1.56284 21.95727 26.40153 2 5
siesta: 1.56296 26.24463 25.50415 1 6
siesta: 1.56303 26.10619 20.96464 1 7
siesta: 1.56305 8.74321 27.69499 2 8
siesta: 1.56316 36.35081 22.43900 1 9
siesta: 1.56328 1.99827 23.58524 1 10
siesta: 1.56331 29.60570 18.32902 2 11
siesta: 1.56337 4.16282 19.74130 2 12
siesta: 4.88927 10.26591 18.32905 2 13
siesta: 4.88937 14.84861 26.28123 2 14
siesta: 4.88939 21.34538 23.59024 1 15
siesta: 4.88941 17.00543 22.43349 1 16
siesta: 4.88960 31.58220 25.06069 1 17
siesta: 4.88962 35.73320 19.62847 2 18
siesta: 4.88969 23.50254 19.74313 2 19
siesta: 4.88979 6.90432 25.50231 1 20
siesta: 4.88985 2.61609 26.39575 2 21
siesta: 4.88986 28.08275 27.69698 2 22
siesta: 4.88994 6.76604 20.96370 1 23
siesta: 4.89012 31.44516 20.52166 1 24
siesta: 8.21614 12.10439 20.52187 1 25
siesta: 8.21636 12.24424 25.06111 1 26
siesta: 8.21644 16.39104 19.62262 2 27
siesta: 8.21646 34.18571 26.28277 2 28
siesta: 8.21656 21.95727 26.40153 2 29
siesta: 8.21669 26.24463 25.50415 1 30
siesta: 8.21676 26.10619 20.96464 1 31
siesta: 8.21677 8.74321 27.69499 2 32
siesta: 8.21689 36.35081 22.43900 1 33
siesta: 8.21701 1.99827 23.58524 1 34
siesta: 8.21704 29.60570 18.32902 2 35
siesta: 8.21710 4.16282 19.74130 2 36
siesta: 11.54300 10.26591 18.32905 2 37
siesta: 11.54310 14.84861 26.28123 2 38
siesta: 11.54312 21.34538 23.59024 1 39
siesta: 11.54314 17.00543 22.43349 1 40
siesta: 11.54333 31.58220 25.06069 1 41
siesta: 11.54335 35.73320 19.62847 2 42
siesta: 11.54342 23.50254 19.74313 2 43
siesta: 11.54351 6.90432 25.50231 1 44
siesta: 11.54358 2.61609 26.39575 2 45
siesta: 11.54359 28.08275 27.69698 2 46
siesta: 11.54367 6.76604 20.96370 1 47
siesta: 11.54385 31.44516 20.52166 1 48
siesta: 14.86987 12.10439 20.52187 1 49
siesta: 14.87008 12.24424 25.06111 1 50
siesta: 14.87017 16.39104 19.62262 2 51
siesta: 14.87019 34.18571 26.28277 2 52
siesta: 14.87029 21.95727 26.40153 2 53
siesta: 14.87042 26.24463 25.50415 1 54
siesta: 14.87049 26.10619 20.96464 1 55
siesta: 14.87050 8.74321 27.69499 2 56
siesta: 14.87062 36.35081 22.43900 1 57
siesta: 14.87074 1.99827 23.58524 1 58
siesta: 14.87077 29.60570 18.32902 2 59
siesta: 14.87082 4.16282 19.74130 2 60
siesta: 18.19673 10.26591 18.32905 2 61
siesta: 18.19683 14.84861 26.28123 2 62
siesta: 18.19685 21.34538 23.59024 1 63
siesta: 18.19687 17.00543 22.43349 1 64
siesta: 18.19706 31.58220 25.06069 1 65
siesta: 18.19708 35.73320 19.62847 2 66
siesta: 18.19715 23.50254 19.74313 2 67
siesta: 18.19724 6.90432 25.50231 1 68
siesta: 18.19731 2.61609 26.39575 2 69
siesta: 18.19732 28.08275 27.69698 2 70
siesta: 18.19740 6.76604 20.96370 1 71
siesta: 18.19758 31.44516 20.52166 1 72
siesta: 21.52360 12.10439 20.52187 1 73
siesta: 21.52381 12.24424 25.06111 1 74
siesta: 21.52390 16.39104 19.62262 2 75
siesta: 21.52392 34.18571 26.28277 2 76
siesta: 21.52402 21.95727 26.40153 2 77
siesta: 21.52415 26.24463 25.50415 1 78
siesta: 21.52422 26.10619 20.96464 1 79
siesta: 21.52423 8.74321 27.69499 2 80
siesta: 21.52435 36.35081 22.43900 1 81
siesta: 21.52447 1.99827 23.58524 1 82
siesta: 21.52450 29.60570 18.32902 2 83
siesta: 21.52455 4.16282 19.74130 2 84
siesta: 24.85046 10.26591 18.32905 2 85
siesta: 24.85055 14.84861 26.28123 2 86
siesta: 24.85057 21.34538 23.59024 1 87
siesta: 24.85060 17.00543 22.43349 1 88
siesta: 24.85079 31.58220 25.06069 1 89
siesta: 24.85081 35.73320 19.62847 2 90
siesta: 24.85088 23.50254 19.74313 2 91
siesta: 24.85097 6.90432 25.50231 1 92
siesta: 24.85104 2.61609 26.39575 2 93
siesta: 24.85105 28.08275 27.69698 2 94
siesta: 24.85113 6.76604 20.96370 1 95
siesta: 24.85131 31.44516 20.52166 1 96
siesta: 28.17733 12.10439 20.52187 1 97
siesta: 28.17754 12.24424 25.06111 1 98
siesta: 28.17763 16.39104 19.62262 2 99
siesta: 28.17765 34.18571 26.28277 2 100
siesta: 28.17775 21.95727 26.40153 2 101
siesta: 28.17788 26.24463 25.50415 1 102
siesta: 28.17794 26.10619 20.96464 1 103
siesta: 28.17796 8.74321 27.69499 2 104
siesta: 28.17807 36.35081 22.43900 1 105
siesta: 28.17820 1.99827 23.58524 1 106
siesta: 28.17823 29.60570 18.32902 2 107
siesta: 28.17828 4.16282 19.74130 2 108
siesta: 31.50419 10.26591 18.32905 2 109
siesta: 31.50428 14.84861 26.28123 2 110
siesta: 31.50430 21.34538 23.59024 1 111
siesta: 31.50432 17.00543 22.43349 1 112
siesta: 31.50451 31.58220 25.06069 1 113
siesta: 31.50453 35.73320 19.62847 2 114
siesta: 31.50460 23.50254 19.74313 2 115
siesta: 31.50470 6.90432 25.50231 1 116
siesta: 31.50477 2.61609 26.39575 2 117
siesta: 31.50478 28.08275 27.69698 2 118
siesta: 31.50485 6.76604 20.96370 1 119
siesta: 31.50504 31.44516 20.52166 1 120

siesta: System type = slab

initatomlists: Number of atoms, orbitals, and projectors: 120 1080 1920

coxmol: Writing XMOL coordinates into file SiP_scat.xyz

siesta: ******************** Simulation parameters ****************************
siesta:
siesta: The following are some of the parameters of the simulation.
siesta: A complete list of the parameters used, including default values,
siesta: can be found in file out.fdf
siesta:
redata: Spin configuration = none
redata: Number of spin components = 1
redata: Time-Reversal Symmetry = T
redata: Spin-spiral = F
redata: Long output = T
redata: Number of Atomic Species = 2
redata: Charge density info will appear in .RHO file
redata: Write Mulliken Pop. = Atomic and Orbital charges
redata: Matel table size (NRTAB) = 1024
redata: Mesh Cutoff = 300.0000 Ry
redata: Net charge of the system = 0.0000 |e|
redata: Min. number of SCF Iter = 0
redata: Max. number of SCF Iter = 100
redata: SCF convergence failure will abort job
redata: SCF mix quantity = Hamiltonian
redata: Mix DM or H after convergence = F
redata: Recompute H after scf cycle = F
redata: Mix DM in first SCF step = T
redata: Write Pulay info on disk = F
redata: New DM Mixing Weight = 0.0500
redata: New DM Occupancy tolerance = 0.000000000001
redata: No kicks to SCF
redata: DM Mixing Weight for Kicks = 0.5000
redata: Require Harris convergence for SCF = F
redata: Harris energy tolerance for SCF = 0.000100 eV
redata: Require DM convergence for SCF = T
redata: DM tolerance for SCF = 0.000100
redata: Require EDM convergence for SCF = F
redata: EDM tolerance for SCF = 0.001000 eV
redata: Require H convergence for SCF = T
redata: Hamiltonian tolerance for SCF = 0.001000 eV
redata: Require (free) Energy convergence for SCF = F
redata: (free) Energy tolerance for SCF = 0.000100 eV
redata: Using Saved Data (generic) = F
redata: Use continuation files for DM = T
redata: Neglect nonoverlap interactions = F
redata: Method of Calculation = Transiesta
redata: Fix the spin of the system = F
redata: Dynamics option = Single-point calculation
mix.SCF: Pulay mixing = Pulay
mix.SCF: Variant = stable
mix.SCF: History steps = 5
mix.SCF: Linear mixing weight = 0.050000
mix.SCF: Mixing weight = 0.050000
mix.SCF: SVD condition = 0.1000E-07
redata: Save all siesta data in one NC = F
redata: ***********************************************************************

%block SCF.Mixers
  Pulay
%endblock SCF.Mixers

%block SCF.Mixer.Pulay
  # Mixing method
  method pulay
  variant stable

  # Mixing options
  weight 0.0500
  weight.linear 0.0500
  history 5
%endblock SCF.Mixer.Pulay

DM_history_depth set to one: no extrapolation allowed by default for geometry relaxation
Size of DM history Fstack: 1
Total number of electrons: 540.000000
Total ionic charge: 540.000000

* ProcessorY, Blocksize: 1 24

* Orbital distribution balance (max,min): 552 528

k-point displ. along 2 input, could be: 0.00 0.50
 Kpoints in: 6 . Kpoints trimmed: 6

siesta: k-point coordinates (Bohr**-1) and weights:
siesta: 1 0.000000 0.000000 0.000000 0.100000
siesta: 2 0.000000 0.016236 0.000000 0.200000
siesta: 3 0.000000 0.032471 0.000000 0.200000
siesta: 4 0.000000 0.048707 0.000000 0.200000
siesta: 5 0.000000 0.064943 0.000000 0.200000
siesta: 6 0.000000 0.081179 0.000000 0.100000

siesta: k-grid: Number of k-pSiesta Version : v4.1-b4
Architecture : Intel_composer_xe_2013_update2+OpenMPI(2.1.0)@SUSE-10.2_X86-64
Compiler version: ifort (IFORT) 13.1.0 20130121
Compiler flags : mpif90 -O3 -i-static
PP flags : -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DMPI -DGRID_DP -DPHI_GRID_SP -DCDF -DNCDF -DNCDF_4
Libraries : libncdf.a libfdict.a -L/home/lv/intel/composer_xe_2013.2.146/mkl/lib/intel64 -lmkl_scalapack_lp64 -L/home/lv/intel/composer_xe_2013.2.146/mkl/lib/intel64 -lmkl_blacs_openmpi_lp64 -L/home/lv/intel/composer_xe_2013.2.146/mkl/lib/intel64 -lmkl_sequential -lmkl_core -L/home/lv/intel/composer_xe_2013.2.146/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz
PARALLEL version
NetCDF support
NetCDF-4 support

* Running on 2 nodes in parallel
>> Start of run: 25-APR-2019 18:23:39

                           ***********************
                           * WELCOME TO SIESTA *
                           ***********************

reinit: Reading from standard input
reinit: Dumped input in INPUT_TMP.16322
************************** Dump of input data file ****************************
SolutionMethod Transiesta
SystemName SiP_scat
SystemLabel SiP_scat
==================================================
==================================================
# SPECIES AND BASIS
# Number of species
NumberOfSpecies 2
%block ChemicalSpeciesLabel
  1 14 Si
  2 15 P
%endblock ChemicalSpeciesLabel
PAO.BasisSize SZP
PAO.EnergyShift 275 meV
XC.functional GGA
XC.authors PBE
MeshCutoff 300.00000000 Ry # default value
==================================================
==================================================
# K-points
%block kgrid_Monkhorst_Pack
 1 0 0 0.0
 0 10 0 0.0
 0 0 1 0.0
%endblock kgrid_Monkhorst_Pack
==================================================
==================================================
# Structure
NumberOfAtoms 120
LatticeConstant 1.0 Ang
%block LatticeVectors
     17.605000 0.000000 0.00000
     0.0000000 20.47900 0.00000
     0.0000000 0.000000 25.0000
%endblock LatticeVectors
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.826793964 6.405363 10.859704 1
0.826906964 6.479372 13.261764 1
0.826952964 8.67376 10.383837 2
0.826962964 18.090289 13.908239 2
0.827016964 11.619284 13.971085 2
0.827084964 13.888055 13.496212 1
0.827119964 13.814794 11.094005 1
0.827127964 4.626704 14.65555 2
0.827188964 19.236014 11.874205 1
0.827252964 1.057441 12.480765 1
0.827269964 15.666657 9.699298 2
0.827297964 2.202867 10.446642 2
2.587290964 5.432484 9.699313 2
2.587341964 7.857543 13.907422 2
2.587351964 11.295483 12.483414 1
2.587363964 8.998883 11.871285 1
2.587463964 16.712573 13.261543 1
2.587474964 18.909185 10.386933 2
2.587511964 12.437001 10.447608 2
2.587561964 3.653609 13.495236 1
2.587597964 1.384375 13.968026 2
2.587602964 14.860746 14.656604 2
2.587643964 3.580434 11.093508 1
2.587739964 16.640054 10.859589 1
4.347793964 6.405363 10.859704 1
4.347906964 6.479372 13.261764 1
4.347952964 8.67376 10.383837 2
4.347962964 18.090289 13.908239 2
4.348016964 11.619284 13.971085 2
4.348084964 13.888055 13.496212 1
4.348119964 13.814794 11.094005 1
4.348127964 4.626704 14.65555 2
4.348188964 19.236014 11.874205 1
4.348252964 1.057441 12.480765 1
4.348269964 15.666657 9.699298 2
4.348297964 2.202867 10.446642 2
6.108290964 5.432484 9.699313 2
6.108341964 7.857543 13.907422 2
6.108351964 11.295483 12.483414 1
6.108363964 8.998883 11.871285 1
6.108463964 16.712573 13.261543 1
6.108474964 18.909185 10.386933 2
6.108511964 12.437001 10.447608 2
6.108561964 3.653609 13.495236 1
6.108597964 1.384375 13.968026 2
6.108602964 14.860746 14.656604 2
6.108643964 3.580434 11.093508 1
6.108739964 16.640054 10.859589 1
7.868793964 6.405363 10.859704 1
7.868906964 6.479372 13.261764 1
7.868952964 8.67376 10.383837 2
7.868962964 18.090289 13.908239 2
7.869016964 11.619284 13.971085 2
7.869084964 13.888055 13.496212 1
7.869119964 13.814794 11.094005 1
7.869127964 4.626704 14.65555 2
7.869188964 19.236014 11.874205 1
7.869252964 1.057441 12.480765 1
7.869269964 15.666657 9.699298 2
7.869297964 2.202867 10.446642 2
9.629290964 5.432484 9.699313 2
9.629341964 7.857543 13.907422 2
9.629351964 11.295483 12.483414 1
9.629363964 8.998883 11.871285 1
9.629463964 16.712573 13.261543 1
9.629474964 18.909185 10.386933 2
9.629511964 12.437001 10.447608 2
9.629561964 3.653609 13.495236 1
9.629597964 1.384375 13.968026 2
9.629602964 14.860746 14.656604 2
9.629643964 3.580434 11.093508 1
9.629739964 16.640054 10.859589 1
11.38979396 6.405363 10.859704 1
11.38990696 6.479372 13.261764 1
11.38995296 8.67376 10.383837 2
11.38996296 18.090289 13.908239 2
11.39001696 11.619284 13.971085 2
11.39008496 13.888055 13.496212 1
11.39011996 13.814794 11.094005 1
11.39012796 4.626704 14.65555 2
11.39018896 19.236014 11.874205 1
11.39025296 1.057441 12.480765 1
11.39026996 15.666657 9.699298 2
11.39029796 2.202867 10.446642 2
13.15029096 5.432484 9.699313 2
13.15034196 7.857543 13.907422 2
13.15035196 11.295483 12.483414 1
13.15036396 8.998883 11.871285 1
13.15046396 16.712573 13.261543 1
13.15047496 18.909185 10.386933 2
13.15051196 12.437001 10.447608 2
13.15056196 3.653609 13.495236 1
13.15059796 1.384375 13.968026 2
13.15060296 14.860746 14.656604 2
13.15064396 3.580434 11.093508 1
13.15073996 16.640054 10.859589 1
14.91079396 6.405363 10.859704 1
14.91090696 6.479372 13.261764 1
14.91095296 8.67376 10.383837 2
14.91096296 18.090289 13.908239 2
14.91101696 11.619284 13.971085 2
14.91108496 13.888055 13.496212 1
14.91111996 13.814794 11.094005 1
14.91112796 4.626704 14.65555 2
14.91118896 19.236014 11.874205 1
14.91125296 1.057441 12.480765 1
14.91126996 15.666657 9.699298 2
14.91129796 2.202867 10.446642 2
16.67129096 5.432484 9.699313 2
16.67134196 7.857543 13.907422 2
16.67135196 11.295483 12.483414 1
16.67136396 8.998883 11.871285 1
16.67146396 16.712573 13.261543 1
16.67147496 18.909185 10.386933 2
16.67151196 12.437001 10.447608 2
16.67156196 3.653609 13.495236 1
16.67159796 1.384375 13.968026 2
16.67160296 14.860746 14.656604 2
16.67164396 3.580434 11.093508 1
16.67173996 16.640054 10.859589 1
%endblock AtomicCoordinatesAndAtomicSpecies
==================================================
==================================================
# SCF variables
SCF.Mix.Method Pulay
DM.NumberPulay 5
DM.MixSCF1 T
SCF.Mix Hamiltonian
MaxSCFIterations 100 # Maximum number of SCF iter
DM.MixingWeight 0.05 # New DM amount for next SCF cycle
DM.UseSaveDM true # to use continuation files
MixHamiltonian yes
==================================================
==================================================
# MD variables
# MD.FinalTimeStep 1
# MD.TypeOfRun CG
# MD.NumCGsteps 000
# MD.UseSaveXV .true.
==================================================
==================================================
# Output variables
LongOutput .true.
WriteCoorXmol .true.
SaveTotalPotential T
SaveElectrostaticPotential T
SaveRho T
SaveDeltaRho T
WriteDenchar .true. # Write information for DENCHAR
Denchar.TypeOfRun 2D
Denchar.PlotCharge T
==================================================
==================================================
# Bias voltage
TS.Voltage 0.5 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 ./SiP_elec.TSHS
  chem-pot Left
  semi-inf-dir -a1
  elec-pos begin 1
  used-atoms 24
%endblock TS.Elec.Left
%block TS.Elec.Right
  TSHS ./SiP_elec.TSHS
  chem-pot Right
  semi-inf-dir +a1
  elec-pos end -1
  used-atoms 24
%endblock TS.Elec.Right
TS.Contours.Eq.Pole 2.5 eV
%block TS.Contour.c-Left
  part circle
   from -40.0000 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 #from -|V|/2 to |V|/2
    delta 0.01 eV
     method mid-rule
%endblock TS.Contour.nEq.neq
%block Geometry.Charge
 plane 0.0 charge
   gauss 1. 2. Ang
    0. 6. 20. Ang
    0. 0. 1.
%endblock Geometry.Charge
%block TBT.Contours
line
%endblock TBT.Contours
%block TBT.Contour.line
from -5. eV to 5. eV
delta 0.04 eV
method mid-rule
%endblock TBT.Contour.line
TBT.DOS.Elecs .true.
TBT.DOS.Gf .true.
TBT.DOS.A .true.
TBT.DOS.A.All .true.
TBT.T.All .true.
TBT.T.Out .true.
#TBT.Atoms.Device [17 -- 64]
#TBT.Current.Orb .true.
************************** End of input data file *****************************

reinit: -----------------------------------------------------------------------
reinit: System Name: SiP_scat
reinit: -----------------------------------------------------------------------
reinit: System Label: SiP_scat
reinit: -----------------------------------------------------------------------

initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Species number: 1 Atomic number: 14 Label: Si
Species number: 2 Atomic number: 15 Label: P

Ground state valence configuration: 3s02 3p02
Reading pseudopotential information in formatted form from Si.psf

Valence configuration for pseudopotential generation:
3s( 2.00) rc: 1.75
3p( 2.00) rc: 1.94
3d( 0.00) rc: 2.09
4f( 0.00) rc: 2.09
Ground state valence configuration: 3s02 3p03
Reading pseudopotential information in formatted form from P.psf

Valence configuration for pseudopotential generation:
3s( 2.00) rc: 1.70
3p( 3.00) rc: 1.88
3d( 0.00) rc: 2.00
4f( 0.00) rc: 2.00
For Si, standard SIESTA heuristics set lmxkb to 3
 (one more than the basis l, including polarization orbitals).
Use PS.lmax or PS.KBprojectors blocks to override.
For P, standard SIESTA heuristics set lmxkb to 3
 (one more than the basis l, including polarization orbitals).
Use PS.lmax or PS.KBprojectors blocks to override.

<basis_specs>
===============================================================================
Si Z= 14 Mass= 28.090 Charge= 0.17977+309
Lmxo=1 Lmxkb= 3 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=3
          n=1 nzeta=1 polorb=0
            splnorm: 0.15000
               vcte: 0.0000
               rinn: 0.0000
               qcoe: 0.0000
               qyuk: 0.0000
               qwid: 0.10000E-01
                rcs: 0.0000
            lambdas: 1.00000
L=1 Nsemic=0 Cnfigmx=3
          n=1 nzeta=1 polorb=1
            splnorm: 0.15000
               vcte: 0.0000
               rinn: 0.0000
               qcoe: 0.0000
               qyuk: 0.0000
               qwid: 0.10000E-01
                rcs: 0.0000
            lambdas: 1.00000
-------------------------------------------------------------------------------
L=0 Nkbl=1 erefs: 0.17977+309
L=1 Nkbl=1 erefs: 0.17977+309
L=2 Nkbl=1 erefs: 0.17977+309
L=3 Nkbl=1 erefs: 0.17977+309
===============================================================================
</basis_specs>

atom: Called for Si (Z = 14)

read_vps: Pseudopotential generation method:
read_vps: ATM3 Troullier-Martins
Total valence charge: 4.00000

read_vps: Pseudopotential includes a core correction:
read_vps: Pseudo-core for xc-correction

xc_check: Exchange-correlation functional:
xc_check: GGA Perdew, Burke & Ernzerhof 1996
V l=0 = -2*Zval/r beyond r= 2.0104
V l=1 = -2*Zval/r beyond r= 2.0873
V l=2 = -2*Zval/r beyond r= 2.1670
V l=3 = -2*Zval/r beyond r= 2.1670
All V_l potentials equal beyond r= 2.0613
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r= 2.1670

VLOCAL1: 99.0% of the norm of Vloc inside 10.216 Ry
VLOCAL1: 99.9% of the norm of Vloc inside 23.282 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 2.45560
atom: Maximum radius for r*vlocal+2*Zval: 2.14012
GHOST: No ghost state for L = 0
GHOST: No ghost state for L = 1
GHOST: No ghost state for L = 2
GHOST: No ghost state for L = 3

KBgen: Kleinman-Bylander projectors:
   l= 0 rc= 2.306811 el= -0.791441 Ekb= 5.289775 kbcos= 0.291595
   l= 1 rc= 2.394965 el= -0.300632 Ekb= 1.944256 kbcos= 0.287657
   l= 2 rc= 2.549439 el= 0.001958 Ekb= -1.788485 kbcos= -0.056492
   l= 3 rc= 2.782581 el= 0.003046 Ekb= -0.472620 kbcos= -0.006203

KBgen: Total number of Kleinman-Bylander projectors: 16
atom: -------------------------------------------------------------------------

atom: SANKEY-TYPE ORBITALS:

SPLIT: Orbitals with angular momentum L= 0

SPLIT: Basis orbitals for state 3s

SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.020212 Ry

   izeta = 1
                 lambda = 1.000000
                     rc = 5.007352
                 energy = -0.772735
                kinetic = 0.581259
    potential(screened) = -1.353994
       potential(ionic) = -3.769451

SPLIT: Orbitals with angular momentum L= 1

SPLIT: Basis orbitals for state 3p

SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.020212 Ry

   izeta = 1
                 lambda = 1.000000
                     rc = 6.270866
                 energy = -0.282590
                kinetic = 0.876421
    potential(screened) = -1.159012
       potential(ionic) = -3.390735

POLgen: Perturbative polarization orbital with L= 2

POLgen: Polarization orbital for state 3p

   izeta = 1
                     rc = 6.270866
                 energy = 0.439433
                kinetic = 1.304939
    potential(screened) = -0.865506
       potential(ionic) = -2.929821
atom: Total number of Sankey-type orbitals: 9

atm_pop: Valence configuration (for local Pseudopot. screening):
 3s( 2.00)
 3p( 2.00)
Vna: chval, zval: 4.00000 4.00000

Vna: Cut-off radius for the neutral-atom potential: 6.270866
comcore: Pseudo-core radius Rcore= 2.999314

atom: _________________________________________________________________________

<basis_specs>
===============================================================================
P Z= 15 Mass= 30.970 Charge= 0.17977+309
Lmxo=1 Lmxkb= 3 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=3
          n=1 nzeta=1 polorb=0
            splnorm: 0.15000
               vcte: 0.0000
               rinn: 0.0000
               qcoe: 0.0000
               qyuk: 0.0000
               qwid: 0.10000E-01
                rcs: 0.0000
            lambdas: 1.00000
L=1 Nsemic=0 Cnfigmx=3
          n=1 nzeta=1 polorb=1
            splnorm: 0.15000
               vcte: 0.0000
               rinn: 0.0000
               qcoe: 0.0000
               qyuk: 0.0000
               qwid: 0.10000E-01
                rcs: 0.0000
            lambdas: 1.00000
-------------------------------------------------------------------------------
L=0 Nkbl=1 erefs: 0.17977+309
L=1 Nkbl=1 erefs: 0.17977+309
L=2 Nkbl=1 erefs: 0.17977+309
L=3 Nkbl=1 erefs: 0.17977+309
===============================================================================
</basis_specs>

atom: Called for P (Z = 15)

read_vps: Pseudopotential generation method:
read_vps: ATM3 Troullier-Martins
Total valence charge: 5.00000

read_vps: Pseudopotential includes a core correction:
read_vps: Pseudo-core for xc-correction

xc_check: Exchange-correlation functional:
xc_check: GGA Perdew, Burke & Ernzerhof 1996
V l=0 = -2*Zval/r beyond r= 1.8764
V l=1 = -2*Zval/r beyond r= 1.9481
V l=2 = -2*Zval/r beyond r= 1.9974
V l=3 = -2*Zval/r beyond r= 1.9974
All V_l potentials equal beyond r= 1.9726
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r= 1.9974

VLOCAL1: 99.0% of the norm of Vloc inside 11.155 Ry
VLOCAL1: 99.9% of the norm of Vloc inside 25.423 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 2.37948
atom: Maximum radius for r*vlocal+2*Zval: 2.07377
GHOST: No ghost state for L = 0
GHOST: No ghost state for L = 1
GHOST: No ghost state for L = 2
GHOST: No ghost state for L = 3

KBgen: Kleinman-Bylander projectors:
   l= 0 rc= 2.180107 el= -1.021271 Ekb= 6.416696 kbcos= 0.303324
   l= 1 rc= 2.263420 el= -0.405531 Ekb= 2.368759 kbcos= 0.295942
   l= 2 rc= 2.349916 el= 0.002048 Ekb= -2.202332 kbcos= -0.057366
   l= 3 rc= 2.532950 el= 0.003178 Ekb= -0.567893 kbcos= -0.005281

KBgen: Total number of Kleinman-Bylander projectors: 16
atom: -------------------------------------------------------------------------

atom: SANKEY-TYPE ORBITALS:

SPLIT: Orbitals with angular momentum L= 0

SPLIT: Basis orbitals for state 3s

SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.020212 Ry

   izeta = 1
                 lambda = 1.000000
                     rc = 4.558135
                 energy = -1.003686
                kinetic = 0.730692
    potential(screened) = -1.734377
       potential(ionic) = -5.317595

SPLIT: Orbitals with angular momentum L= 1

SPLIT: Basis orbitals for state 3p

SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.020212 Ry

   izeta = 1
                 lambda = 1.000000
                     rc = 5.567355
                 energy = -0.387087
                kinetic = 1.179303
    potential(screened) = -1.566390
       potential(ionic) = -4.902418

POLgen: Perturbative polarization orbital with L= 2

POLgen: Polarization orbital for state 3p

   izeta = 1
                     rc = 5.567355
                 energy = 0.582313
                kinetic = 1.738827
    potential(screened) = -1.156514
       potential(ionic) = -4.227359
atom: Total number of Sankey-type orbitals: 9

atm_pop: Valence configuration (for local Pseudopot. screening):
 3s( 2.00)
 3p( 3.00)
Vna: chval, zval: 5.00000 5.00000

Vna: Cut-off radius for the neutral-atom potential: 5.567355
comcore: Pseudo-core radius Rcore= 2.730239

atom: _________________________________________________________________________

prinput: Basis input ----------------------------------------------------------

PAO.BasisType split

%block ChemicalSpeciesLabel
    1 14 Si # Species index, atomic number, species label
    2 15 P # Species index, atomic number, species label
%endblock ChemicalSpeciesLabel

%block PAO.Basis # Define Basis set
Si 2 # Species label, number of l-shells
 n=3 0 1 # n, l, Nzeta
   5.007
   1.000
 n=3 1 1 P 1 # n, l, Nzeta, Polarization, NzetaPol
   6.271
   1.000
P 2 # Species label, number of l-shells
 n=3 0 1 # n, l, Nzeta
   4.558
   1.000
 n=3 1 1 P 1 # n, l, Nzeta, Polarization, NzetaPol
   5.567
   1.000
%endblock PAO.Basis

prinput: ----------------------------------------------------------------------

Dumping basis to NetCDF file Si.ion.nc
Dumping basis to NetCDF file P.ion.nc
coor: Atomic-coordinates input format = Cartesian coordinates
coor: (in Angstroms)

siesta: Atomic coordinates (Bohr) and species
siesta: 1.56241 12.10439 20.52187 1 1
siesta: 1.56263 12.24424 25.06111 1 2
siesta: 1.56272 16.39104 19.62262 2 3
siesta: 1.56273 34.18571 26.28277 2 4
siesta: 1.56284 21.95727 26.40153 2 5
siesta: 1.56296 26.24463 25.50415 1 6
siesta: 1.56303 26.10619 20.96464 1 7
siesta: 1.56305 8.74321 27.69499 2 8
siesta: 1.56316 36.35081 22.43900 1 9
siesta: 1.56328 1.99827 23.58524 1 10
siesta: 1.56331 29.60570 18.32902 2 11
siesta: 1.56337 4.16282 19.74130 2 12
siesta: 4.88927 10.26591 18.32905 2 13
siesta: 4.88937 14.84861 26.28123 2 14
siesta: 4.88939 21.34538 23.59024 1 15
siesta: 4.88941 17.00543 22.43349 1 16
siesta: 4.88960 31.58220 25.06069 1 17
siesta: 4.88962 35.73320 19.62847 2 18
siesta: 4.88969 23.50254 19.74313 2 19
siesta: 4.88979 6.90432 25.50231 1 20
siesta: 4.88985 2.61609 26.39575 2 21
siesta: 4.88986 28.08275 27.69698 2 22
siesta: 4.88994 6.76604 20.96370 1 23
siesta: 4.89012 31.44516 20.52166 1 24
siesta: 8.21614 12.10439 20.52187 1 25
siesta: 8.21636 12.24424 25.06111 1 26
siesta: 8.21644 16.39104 19.62262 2 27
siesta: 8.21646 34.18571 26.28277 2 28
siesta: 8.21656 21.95727 26.40153 2 29
siesta: 8.21669 26.24463 25.50415 1 30
siesta: 8.21676 26.10619 20.96464 1 31
siesta: 8.21677 8.74321 27.69499 2 32
siesta: 8.21689 36.35081 22.43900 1 33
siesta: 8.21701 1.99827 23.58524 1 34
siesta: 8.21704 29.60570 18.32902 2 35
siesta: 8.21710 4.16282 19.74130 2 36
siesta: 11.54300 10.26591 18.32905 2 37
siesta: 11.54310 14.84861 26.28123 2 38
siesta: 11.54312 21.34538 23.59024 1 39
siesta: 11.54314 17.00543 22.43349 1 40
siesta: 11.54333 31.58220 25.06069 1 41
siesta: 11.54335 35.73320 19.62847 2 42
siesta: 11.54342 23.50254 19.74313 2 43
siesta: 11.54351 6.90432 25.50231 1 44
siesta: 11.54358 2.61609 26.39575 2 45
siesta: 11.54359 28.08275 27.69698 2 46
siesta: 11.54367 6.76604 20.96370 1 47
siesta: 11.54385 31.44516 20.52166 1 48
siesta: 14.86987 12.10439 20.52187 1 49
siesta: 14.87008 12.24424 25.06111 1 50
siesta: 14.87017 16.39104 19.62262 2 51
siesta: 14.87019 34.18571 26.28277 2 52
siesta: 14.87029 21.95727 26.40153 2 53
siesta: 14.87042 26.24463 25.50415 1 54
siesta: 14.87049 26.10619 20.96464 1 55
siesta: 14.87050 8.74321 27.69499 2 56
siesta: 14.87062 36.35081 22.43900 1 57
siesta: 14.87074 1.99827 23.58524 1 58
siesta: 14.87077 29.60570 18.32902 2 59
siesta: 14.87082 4.16282 19.74130 2 60
siesta: 18.19673 10.26591 18.32905 2 61
siesta: 18.19683 14.84861 26.28123 2 62
siesta: 18.19685 21.34538 23.59024 1 63
siesta: 18.19687 17.00543 22.43349 1 64
siesta: 18.19706 31.58220 25.06069 1 65
siesta: 18.19708 35.73320 19.62847 2 66
siesta: 18.19715 23.50254 19.74313 2 67
siesta: 18.19724 6.90432 25.50231 1 68
siesta: 18.19731 2.61609 26.39575 2 69
siesta: 18.19732 28.08275 27.69698 2 70
siesta: 18.19740 6.76604 20.96370 1 71
siesta: 18.19758 31.44516 20.52166 1 72
siesta: 21.52360 12.10439 20.52187 1 73
siesta: 21.52381 12.24424 25.06111 1 74
siesta: 21.52390 16.39104 19.62262 2 75
siesta: 21.52392 34.18571 26.28277 2 76
siesta: 21.52402 21.95727 26.40153 2 77
siesta: 21.52415 26.24463 25.50415 1 78
siesta: 21.52422 26.10619 20.96464 1 79
siesta: 21.52423 8.74321 27.69499 2 80
siesta: 21.52435 36.35081 22.43900 1 81
siesta: 21.52447 1.99827 23.58524 1 82
siesta: 21.52450 29.60570 18.32902 2 83
siesta: 21.52455 4.16282 19.74130 2 84
siesta: 24.85046 10.26591 18.32905 2 85
siesta: 24.85055 14.84861 26.28123 2 86
siesta: 24.85057 21.34538 23.59024 1 87
siesta: 24.85060 17.00543 22.43349 1 88
siesta: 24.85079 31.58220 25.06069 1 89
siesta: 24.85081 35.73320 19.62847 2 90
siesta: 24.85088 23.50254 19.74313 2 91
siesta: 24.85097 6.90432 25.50231 1 92
siesta: 24.85104 2.61609 26.39575 2 93
siesta: 24.85105 28.08275 27.69698 2 94
siesta: 24.85113 6.76604 20.96370 1 95
siesta: 24.85131 31.44516 20.52166 1 96
siesta: 28.17733 12.10439 20.52187 1 97
siesta: 28.17754 12.24424 25.06111 1 98
siesta: 28.17763 16.39104 19.62262 2 99
siesta: 28.17765 34.18571 26.28277 2 100
siesta: 28.17775 21.95727 26.40153 2 101
siesta: 28.17788 26.24463 25.50415 1 102
siesta: 28.17794 26.10619 20.96464 1 103
siesta: 28.17796 8.74321 27.69499 2 104
siesta: 28.17807 36.35081 22.43900 1 105
siesta: 28.17820 1.99827 23.58524 1 106
siesta: 28.17823 29.60570 18.32902 2 107
siesta: 28.17828 4.16282 19.74130 2 108
siesta: 31.50419 10.26591 18.32905 2 109
siesta: 31.50428 14.84861 26.28123 2 110
siesta: 31.50430 21.34538 23.59024 1 111
siesta: 31.50432 17.00543 22.43349 1 112
siesta: 31.50451 31.58220 25.06069 1 113
siesta: 31.50453 35.73320 19.62847 2 114
siesta: 31.50460 23.50254 19.74313 2 115
siesta: 31.50470 6.90432 25.50231 1 116
siesta: 31.50477 2.61609 26.39575 2 117
siesta: 31.50478 28.08275 27.69698 2 118
siesta: 31.50485 6.76604 20.96370 1 119
siesta: 31.50504 31.44516 20.52166 1 120

siesta: System type = slab

initatomlists: Number of atoms, orbitals, and projectors: 120 1080 1920

coxmol: Writing XMOL coordinates into file SiP_scat.xyz

siesta: ******************** Simulation parameters ****************************
siesta:
siesta: The following are some of the parameters of the simulation.
siesta: A complete list of the parameters used, including default values,
siesta: can be found in file out.fdf
siesta:
redata: Spin configuration = none
redata: Number of spin components = 1
redata: Time-Reversal Symmetry = T
redata: Spin-spiral = F
redata: Long output = T
redata: Number of Atomic Species = 2
redata: Charge density info will appear in .RHO file
redata: Write Mulliken Pop. = Atomic and Orbital charges
redata: Matel table size (NRTAB) = 1024
redata: Mesh Cutoff = 300.0000 Ry
redata: Net charge of the system = 0.0000 |e|
redata: Min. number of SCF Iter = 0
redata: Max. number of SCF Iter = 100
redata: SCF convergence failure will abort job
redata: SCF mix quantity = Hamiltonian
redata: Mix DM or H after convergence = F
redata: Recompute H after scf cycle = F
redata: Mix DM in first SCF step = T
redata: Write Pulay info on disk = F
redata: New DM Mixing Weight = 0.0500
redata: New DM Occupancy tolerance = 0.000000000001
redata: No kicks to SCF
redata: DM Mixing Weight for Kicks = 0.5000
redata: Require Harris convergence for SCF = F
redata: Harris energy tolerance for SCF = 0.000100 eV
redata: Require DM convergence for SCF = T
redata: DM tolerance for SCF = 0.000100
redata: Require EDM convergence for SCF = F
redata: EDM tolerance for SCF = 0.001000 eV
redata: Require H convergence for SCF = T
redata: Hamiltonian tolerance for SCF = 0.001000 eV
redata: Require (free) Energy convergence for SCF = F
redata: (free) Energy tolerance for SCF = 0.000100 eV
redata: Using Saved Data (generic) = F
redata: Use continuation files for DM = T
redata: Neglect nonoverlap interactions = F
redata: Method of Calculation = Transiesta
redata: Fix the spin of the system = F
redata: Dynamics option = Single-point calculation
mix.SCF: Pulay mixing = Pulay
mix.SCF: Variant = stable
mix.SCF: History steps = 5
mix.SCF: Linear mixing weight = 0.050000
mix.SCF: Mixing weight = 0.050000
mix.SCF: SVD condition oints = 6
siesta: k-grid: Cutoff (effective) = 8.803 Ang
siesta: k-grid: Supercell and displacements
siesta: k-grid: 1 0 0 0.000
siesta: k-grid: 0 10 0 0.000
siesta: k-grid: 0 0 1 0.000

diag: Algorithm = D&C
diag: Parallel over k = F
diag: Use parallel 2D distribution = F
diag: Parallel block-size = 24
diag: Parallel distribution = 1 x 2
diag: Used triangular part = Lower
diag: Absolute tolerance = 0.100E-15
diag: Orthogonalization factor = 0.100E-05
diag: Memory factor = 1.0000

superc: Internal auxiliary supercell: 3 x 3 x 1 = 9
superc: Number of atoms, orbitals, and projectors: 1080 9720 17280

k-point displ. along 2 input, could be: 0.00 0.50
 Kpoints in: 6 . Kpoints trimmed: 6

transiesta: ts_k-point coordinates (Bohr**-1) and weights:
transiesta: 1 0.000000 0.000000 0.000000 0.100000
transiesta: 2 0.000000 0.016236 0.000000 0.200000
transiesta: 3 0.000000 0.032471 0.000000 0.200000
transiesta: 4 0.000000 0.048707 0.000000 0.200000
transiesta: 5 0.000000 0.064943 0.000000 0.200000
transiesta: 6 0.000000 0.081179 0.000000 0.100000

transiesta: k-grid: Number of Green function k-points = 6
transiesta: k-grid: Supercell and displacements
transiesta: k-grid: 1 0 0 0.000
transiesta: k-grid: 0 10 0 0.000
transiesta: k-grid: 0 0 1 0.000

ts: **************************************************************
ts: Voltage = 0.5000 Volts
ts: Save H and S matrices = T
ts: Electronic temperature = 299.986869 K
ts: Transport along unit-cell vector = A1
ts: Transport along Cartesian vector = X
ts: Fixing Hartree potential at electrode-plane = Right
ts: Fix Hartree potential fraction = 1.0000
ts: Hartree potential offset = 0.000000 eV
ts: Solution method = BTD
ts: BTD pivoting method = atom+Left
ts: BTD creation algorithm = speed
ts: BTD spectral function algorithm = propagation
ts: SCF.TS DM tolerance = 0.100E-03
ts: SCF.TS Hamiltonian tolerance = 0.001000 eV
ts: Initialize DM by = diagon
ts: Initial DM for electrodes = this
ts: Hartree potential as linear ramp
ts: Hartree potential ramp across central region
ts: Thermal non-equilibrium in distributions = F
ts: Non-equilibrium contour weight method = orb-orb
ts: Non-equilibrium contour weight k-method = Correlated k-points
ts: Will not correct charge fluctuations
ts: TS.SCF mixing options same as SCF
ts: >> Electrodes <<
ts: >> Left
ts: Electrode cell pivoting: E1, E2, E3 = A1, A2, A3
ts: GF file = SiP_scat.TSGFLeft
ts: Reuse existing GF-file = T
ts: Electrode TSHS file = ./SiP_elec.TSHS
ts: # atoms used in electrode = 24
ts: Electrode Bloch unity [E1 x E2 x E3] = 1 x 1 x 1
ts: Position in geometry = 1 -- 24
ts: Semi-infinite direction for electrode = negative wrt. E1
ts: Chemical shift = 0.250000 eV
ts: Electronic temperature = 299.986869 K
ts: Gamma-only electrode = F
ts: Bulk H, S in electrode region = T
ts: Cross-terms are updated
ts: Hamiltonian E-C Ef fractional shift = 0.0000
ts: Electrode self-energy imaginary Eta = 0.1000E-03 eV
ts: Electrode self-energy accuracy = 0.1000E-13 eV
ts: Electrode inter-layer distance (semi-inf) = 1.7601 Ang
ts: >> Right
ts: Electrode cell pivoting: E1, E2, E3 = A1, A2, A3
ts: GF file = SiP_scat.TSGFRight
ts: Reuse existing GF-file = T
ts: Electrode TSHS file = ./SiP_elec.TSHS
ts: # atoms used in electrode = 24
ts: Electrode Bloch unity [E1 x E2 x E3] = 1 x 1 x 1
ts: Position in geometry = 97 -- 120
ts: Semi-infinite direction for electrode = positive wrt. E1
ts: Chemical shift = -0.250000 eV
ts: Electronic temperature = 299.986869 K
ts: Gamma-only electrode = F
ts: Bulk H, S in electrode region = T
ts: Cross-terms are updated
ts: Hamiltonian E-C Ef fractional shift = 0.0000
ts: Electrode self-energy imaginary Eta = 0.1000E-03 eV
ts: Electrode self-energy accuracy = 0.1000E-13 eV
ts: Electrode inter-layer distance (semi-inf) = 1.7601 Ang
ts: ----------------- Contour -----------------
ts: >> Residual contour <<
ts: Pole chemical potential = 0.2500 eV
ts: Chemical potential temperature = 299.9869 K
ts: Number of poles = 16
ts: Top energy point = 2.5988 eV
ts: Pole chemical potential = -0.2500 eV
ts: Chemical potential temperature = 299.9869 K
ts: Number of poles = 16
ts: Top energy point = 2.5988 eV
ts: >> Equilibrium contour <<
ts: Contour name = TS.Contour.c-Left
ts: circle contour E_min = -39.7500 eV
ts: circle contour E_max = -0.0085 eV
ts: circle contour points = 30
ts: circle contour method = Gauss-Legendre
ts: Contour name = TS.Contour.t-Left
ts: tail contour E_min = -0.0085 eV
ts: tail contour E_max = Infinity
ts: tail contour points = 10
ts: tail contour method = Gauss-Fermi (0kT)
ts: Contour name = TS.Contour.c-Right
ts: circle contour E_min = -40.2500 eV
ts: circle contour E_max = -0.5085 eV
ts: circle contour points = 30
ts: circle contour method = Gauss-Legendre
ts: Contour name = TS.Contour.t-Right
ts: tail contour E_min = -0.5085 eV
ts: tail contour E_max = Infinity
ts: tail contour points = 10
ts: tail contour method = Gauss-Fermi (0kT)
ts: >> non-Equilibrium contour <<
ts: Device Green function imaginary Eta = 0.1000E-03 eV
ts: Fermi-function cut-off = 5.000 kT
ts: Contour name = TS.Contour.nEq.neq
ts: line contour E_min = -0.3793 eV
ts: line contour E_max = 0.3793 eV
ts: line contour points = 76
ts: line contour method = Mid-rule
ts: **************************************************************

************************ Begin: TS CHECKS AND WARNINGS ************************
************************ End: TS CHECKS AND WARNINGS **************************

>>> TranSiesta block information for FDF-file START <<<

%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
%block TS.Contour.c-Left
  part circle
     from -40.0000 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
%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

>>> TranSiesta block information for FDF-file END <<<

transiesta: Regions of atoms:
   ## (24): Elec.Left
     [ 1 -- 24 ]
   ## (24): Elec.Right
     [ 97 -- 120 ]
   -- (72): Device
     [ 25 -- 96 ]

  <sparsity:./SiP_elec.TSHS
    nrows_g=216 nrows=216 sparsity=2.5316 nnzs=118112, refcount: 3>
  <sparsity:(TM [ 0,--,--] of: ./SiP_elec.TSHS)
    nrows_g=216 nrows=216 sparsity=.6999 nnzs=32656, refcount: 3>
  <sparsity:(TM [-1,--,--] of: ./SiP_elec.TSHS)
    nrows_g=216 nrows=216 sparsity=.6433 nnzs=30012, refcount: 3>
 Left principal cell is extending out with 12716 elements:
    Atom 3 connects with atom 16
    Orbital 27 connects with orbital 144
    Hamiltonian value: |H(27,792)|@R=-2 = 0.105 eV
    Overlap : S(27,792)|@R=-2 = 0.121E-02
Electrode connectivity is not perfect, refer to the manual for achieving a perfect electrode.
Stopping Program from Node: 0
Electrode connectivity is not perfect, refer to the manual for achieving a perfect electrode.
Stopping Program from Node: 1
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 1 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.
--------------------------------------------------------------------------

Revision history for this message
Nick Papior (nickpapior) said : 		#2

Please see Sec. 10.4.2 in the siesta manual.

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