Siesta Version  : 4.1.5
Architecture    : intel-mpi-mkl
Compiler version: ifort (IFORT) 2021.6.0 20220226
Compiler flags  : mpiifort -O2 -fPIC -fp-model source
PP flags        : -DMPI -DFC_HAVE_ABORT
Libraries       :  -L/opt/intel/oneapi/mkl/2022.1.0/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blaccs_intelmpi_lp64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread -lm -ldl
PARALLEL version

* Running on 8 nodes in parallel
>> Start of run:   7-OCT-2026  22:49:46

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

reinit: Reading from standard input
reinit: Dumped input in INPUT_TMP.82536
************************** Dump of input data file ****************************
SystemName       GNR_6unit       # Descriptive name of the system
SystemLabel      scat            # Short name for naming files
%include STRUCT.fdf
%include BASIS.fdf
%include TS.fdf
SolutionMethod      transiesta
XC.functional       GGA
XC.authors          PBE
MeshCutoff          100.0 Ry
SaveHS              T
MaxSCFIterations      500           # Default: 50
DM.MixingWeight       0.10          # Default: 0.25
DM.NumberPulay        3             # Default: 0
DM.PulayOnFile        F             # SystemLabel.P1, SystemLabel.P2
DM.Tolerance          1.d-4         # Default: 1.d-4
DM.UseSaveDM          T             # because of the bug
Diag.ParallelOverK    T
TS.SCF.DM.Tolerance 1.d-4
TS.SCF.dQ.Tolerance 1.d-0
************************** End of input data file *****************************

reinit: -----------------------------------------------------------------------
reinit: System Name: GNR_6unit
reinit: -----------------------------------------------------------------------
reinit: System Label: scat
reinit: -----------------------------------------------------------------------

initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Species number:   1 Atomic number:    6 Label: C
 
Ground state valence configuration:   2s02  2p02
Reading pseudopotential information in formatted form from C.psf

Valence configuration for pseudopotential generation:
2s( 2.00) rc: 1.54
2p( 2.00) rc: 1.54
3d( 0.00) rc: 1.54
4f( 0.00) rc: 1.54
For C, standard SIESTA heuristics set lmxkb to 2
 (one more than the basis l, including polarization orbitals).
Use PS.lmax or PS.KBprojectors blocks to override.

<basis_specs>
===============================================================================
C                    Z=   6    Mass=  12.010        Charge= 0.17977+309
Lmxo=1 Lmxkb= 2    BasisType=split      Semic=F
L=0  Nsemic=0  Cnfigmx=2
          i=1  nzeta=1  polorb=0  (2s)
            splnorm:   0.15000    
               vcte:    0.0000    
               rinn:    0.0000    
               qcoe:    0.0000    
               qyuk:    0.0000    
               qwid:   0.10000E-01
                rcs:    0.0000    
            lambdas:    1.0000    
L=1  Nsemic=0  Cnfigmx=2
          i=1  nzeta=1  polorb=0  (2p)
            splnorm:   0.15000    
               vcte:    0.0000    
               rinn:    0.0000    
               qcoe:    0.0000    
               qyuk:    0.0000    
               qwid:   0.10000E-01
                rcs:    0.0000    
            lambdas:    1.0000    
-------------------------------------------------------------------------------
L=0  Nkbl=1  erefs: 0.17977+309
L=1  Nkbl=1  erefs: 0.17977+309
L=2  Nkbl=1  erefs: 0.17977+309
===============================================================================
</basis_specs>

atom: Called for C                     (Z =   6)

read_vps: Pseudopotential generation method:
read_vps: ATM3      Troullier-Martins                       
Valence charge for ps generation:    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=  1.5227
V l=1 = -2*Zval/r beyond r=  1.5227
V l=2 = -2*Zval/r beyond r=  1.5227
All V_l potentials equal beyond r=  1.5227
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r=  1.5227

VLOCAL1: 99.0% of the norm of Vloc inside     18.722 Ry
VLOCAL1: 99.9% of the norm of Vloc inside     42.668 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge    1.83678
atom: Maximum radius for r*vlocal+2*Zval:    1.58088
GHOST: No ghost state for L =  0
GHOST: No ghost state for L =  1
GHOST: No ghost state for L =  2

KBgen: Kleinman-Bylander projectors: 
   l= 0   rc=  1.704034   el= -1.009801   Ekb=  5.335044   kbcos=  0.316824
   l= 1   rc=  1.704034   el= -0.388707   Ekb= -3.785862   kbcos= -0.366464
   l= 2   rc=  1.791422   el=  0.001971   Ekb= -0.970471   kbcos= -0.009212

KBgen: Total number of Kleinman-Bylander projectors:    9
atom: -------------------------------------------------------------------------

atom: SANKEY-TYPE ORBITALS:

SPLIT: Orbitals with angular momentum L= 0

SPLIT: Basis orbitals for state 2s

SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift=  0.020000 Ry

   izeta = 1
                 lambda =    1.000000
                     rc =    4.088342
                 energy =   -0.989105
                kinetic =    0.904439
    potential(screened) =   -1.893544
       potential(ionic) =   -5.484581

SPLIT: Orbitals with angular momentum L= 1

SPLIT: Basis orbitals for state 2p

SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift=  0.020000 Ry

   izeta = 1
                 lambda =    1.000000
                     rc =    4.870301
                 energy =   -0.368906
                kinetic =    2.520369
    potential(screened) =   -2.889275
       potential(ionic) =   -6.370528
atom: Total number of Sankey-type orbitals:  4

atm_pop: Valence configuration (for local Pseudopot. screening):
 2s( 2.00)                                                            
 2p( 2.00)                                                            
Vna: chval, zval:    4.00000   4.00000

Vna:  Cut-off radius for the neutral-atom potential:   4.870301
comcore: Pseudo-core radius Rcore=  1.791422

atom: _________________________________________________________________________

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

PAO.BasisType split     

%block ChemicalSpeciesLabel
    1    6 C                       # Species index, atomic number, species label
%endblock ChemicalSpeciesLabel

%block PAO.Basis                 # Define Basis set
C                     2                    # Species label, number of l-shells
 n=2   0   1                         # n, l, Nzeta 
   4.088   
   1.000   
 n=2   1   1                         # n, l, Nzeta 
   4.870   
   1.000   
%endblock PAO.Basis

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

coor:   Atomic-coordinates input format  =     Cartesian coordinates
coor:                                          (in Angstroms)

siesta: Atomic coordinates (Bohr) and species
siesta:     18.89727   0.00000   0.00000  1        1
siesta:     18.89727   0.00000   2.67396  1        2
siesta:     18.89727   2.31572   4.01095  1        3
siesta:     18.89727   2.31572   6.68491  1        4
siesta:     18.89727   0.00000   8.02189  1        5
siesta:     18.89727   0.00000  10.69585  1        6
siesta:     18.89727   2.31572  12.03284  1        7
siesta:     18.89727   2.31572  14.70680  1        8
siesta:     18.89727   0.00000  16.04378  1        9
siesta:     18.89727   0.00000  18.71774  1       10
siesta:     18.89727   2.31572  20.05473  1       11
siesta:     18.89727   2.31572  22.72869  1       12
siesta:     18.89727   0.00000  24.06567  1       13
siesta:     18.89727   0.00000  26.73964  1       14
siesta:     18.89727   2.31572  28.07662  1       15
siesta:     18.89727   2.31572  30.75058  1       16
siesta:     18.89727   0.00000  32.08756  1       17
siesta:     18.89727   0.00000  34.76153  1       18
siesta:     18.89727   2.31572  36.09851  1       19
siesta:     18.89727   2.31572  38.77247  1       20
siesta:     18.89727   0.00000  40.10945  1       21
siesta:     18.89727   0.00000  42.78342  1       22
siesta:     18.89727   2.31572  44.12040  1       23
siesta:     18.89727   2.31572  46.79436  1       24

siesta: System type = slab      

initatomlists: Number of atoms, orbitals, and projectors:     24    96   216

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                                 =   F
redata: Number of Atomic Species                    =        1
redata: Charge density info will appear in .RHO file
redata: Write Mulliken Pop.                         = NO
redata: Matel table size (NRTAB)                    =     1024
redata: Mesh Cutoff                                 =   100.0000 Ry
redata: Net charge of the system                    =     0.0000 |e|
redata: Min. number of SCF Iter                     =        0
redata: Max. number of SCF Iter                     =      500
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 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                        = 3
mix.SCF:    Linear mixing weight                 =     0.100000
mix.SCF:    Mixing weight                        =     0.100000
mix.SCF:    SVD condition                        = 0.1000E-07
redata: ***********************************************************************

%block SCF.Mixers
  Pulay
%endblock SCF.Mixers

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

  # Mixing options
  weight 0.1000
  weight.linear 0.1000
  history 3
%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:    96.000000
Total ionic charge:    96.000000

* ProcessorY, Blocksize:    2  12


* Orbital distribution balance (max,min):    12    12

 Kpoints in:            1 . Kpoints trimmed:            1

siesta: k-grid: Number of k-points =     1
siesta: k-grid: Cutoff (effective) =     1.225 Ang
siesta: k-grid: Supercell and displacements
siesta: k-grid:    1   0   0      0.000
siesta: k-grid:    0   1   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                  =   T
diag: Parallel block-size                           = 12
diag: Parallel distribution                         =     2 x     4
diag: Used triangular part                          = Lower
diag: Absolute tolerance                            =  0.100E-15
diag: Orthogonalization factor                      =  0.100E-05
diag: Memory factor                                 =  1.0000
 
 WARNING !!!
 TS kgrid determined first with 3D cell !!!
 Specifying only cutoff in Electrode AND Scattering calculations might lead to p
 roblems !!
 Kpoints in:            1 . Kpoints trimmed:            1

transiesta: k-grid: Number of Green function k-points =     1
transiesta: k-grid: Supercell and displacements
transiesta: k-grid:    1   0   0      0.000
transiesta: k-grid:    0   1   0      0.000
transiesta: k-grid:    0   0   1      0.000
Incompatible k-grids...
Electrode file k-grid:
   1    0    0   0.0000
   0  240    0   0.0000
   0    0   35   0.0000
System k-grid:
   1    0    0   0.0000
   0    1    0   0.0000
   0    0    1   0.0000
Electrode file k-grid should probably be:
   1    0    0   0.0000
   0    1    0   0.0000
   0    0   35   0.0000
Erroneous electrode setup, check out-put
Erroneous electrode setup, check out-put
Erroneous electrode setup, check out-put
Erroneous electrode setup, check out-put
Erroneous electrode setup, check out-put
Erroneous electrode setup, check out-put
Stopping Program from Node:    0
Erroneous electrode setup, check out-put
Stopping Program from Node:    4
Stopping Program from Node:    5
Stopping Program from Node:    6
Stopping Program from Node:    7
Stopping Program from Node:    1
Stopping Program from Node:    3
Erroneous electrode setup, check out-put
Stopping Program from Node:    2

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 4 PID 620564 RUNNING AT n015
=   KILLED BY SIGNAL: 9 (Killed)
===================================================================================
