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  23:07:01

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

reinit: Reading from standard input
reinit: Dumped input in INPUT_TMP.30611
************************** Dump of input data file ****************************
SystemName       GRP_electrode   # Descriptive name of the system
SystemLabel      elec            # Short name for naming files
%include STRUCT.fdf
%include BASIS.fdf
%include KPT.fdf
%block kgrid_Monkhorst_Pack
 1    0    0    0.0
 0   30    0    0.0
 0    0   35    0.0
%endblock kgrid_Monkhorst_Pack
SolutionMethod      diagon
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.HS.Save .true.
TS.DE.Save .true.
************************** End of input data file *****************************

reinit: -----------------------------------------------------------------------
reinit: System Name: GRP_electrode
reinit: -----------------------------------------------------------------------
reinit: System Label: elec
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   4.63144   0.00000  1        2
siesta:     18.89727   0.00000   2.67396  1        3
siesta:     18.89727   4.63144   2.67396  1        4
siesta:     18.89727   2.31572   4.01095  1        5
siesta:     18.89727   6.94716   4.01095  1        6
siesta:     18.89727   2.31572   6.68491  1        7
siesta:     18.89727   6.94716   6.68491  1        8

siesta: System type = slab      

initatomlists: Number of atoms, orbitals, and projectors:      8    32    72

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                       = Diagonalization
redata: Electronic Temperature                      =   299.9869 K
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:    32.000000
Total ionic charge:    32.000000

* ProcessorY, Blocksize:    2   4


* Orbital distribution balance (max,min):     4     4

k-point displ. along   2 input, could be:     0.00    0.50
 Kpoints in:          540 . Kpoints trimmed:          526

siesta: k-grid: Number of k-points =   526
siesta: k-grid: Cutoff (effective) =    10.000 Ang
siesta: k-grid: Supercell and displacements
siesta: k-grid:    1   0   0      0.000
siesta: k-grid:    0  30   0      0.000
siesta: k-grid:    0   0  35      0.000
 
diag: Algorithm                                     = D&C
diag: Parallel over k                               =   T
diag: Use parallel 2D distribution                  =   T
diag: Parallel block-size                           = 4
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

superc: Internal auxiliary supercell:     1 x     3 x     5  =      15
superc: Number of atoms, orbitals, and projectors:    120    480   1080
 
 
ts: **************************************************************
ts: Save H and S matrices                           =    T
ts: Save DM and EDM matrices                        =    T
ts: Only save the overlap matrix S                  =    F
ts: **************************************************************
 
************************ Begin: TS CHECKS AND WARNINGS ************************
************************ End: TS CHECKS AND WARNINGS **************************


                     ====================================
                        Single-point calculation
                     ====================================

superc: Internal auxiliary supercell:     1 x     3 x     5  =      15
superc: Number of atoms, orbitals, and projectors:    120    480   1080

outcell: Unit cell vectors (Ang):
       20.000000    0.000000    0.000000
        0.000000    4.901704    0.000000
        0.000000    0.000000    4.245000

outcell: Cell vector modules (Ang)   :   20.000000    4.901704    4.245000
outcell: Cell angles (23,13,12) (deg):     90.0000     90.0000     90.0000
outcell: Cell volume (Ang**3)        :    416.1547
<dSpData1D:S at geom step 0
  <sparsity:sparsity for geom step 0
    nrows_g=32 nrows=4 sparsity=.5781 nnzs=592, refcount: 7>
  <dData1D:(new from dSpData1D) n=592, refcount: 1>
refcount: 1>
new_DM -- step:     1
Initializing Density Matrix...
 
Attempting to read DM from file... Failed...
DM filled with atomic data:
<dSpData2D:DM initialized from atoms
  <sparsity:sparsity for geom step 0
    nrows_g=32 nrows=4 sparsity=.5781 nnzs=592, refcount: 8>
  <dData2D:DM n=592 m=1, refcount: 1>
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps:      13      52
New grid distribution:   1
           1       1:   64    1:    8    1:    4
           2       1:   64    1:    8    5:    8
           3       1:   64    1:    8    9:   12
           4       1:   64    1:    8   13:   15
           5       1:   64    9:   15    1:    4
           6       1:   64    9:   15    5:    8
           7       1:   64    9:   15    9:   12
           8       1:   64    9:   15   13:   15

InitMesh: MESH =   128 x    30 x    30 =      115200
InitMesh: (bp) =    64 x    15 x    15 =       14400
InitMesh: Mesh cutoff (required, used) =   100.000   103.526 Ry
ExtMesh (bp) on 0 =   100 x    40 x    44 =      176000
New grid distribution:   2
           1      37:   64    1:   15    1:   15
           2      34:   35    1:   15    1:   15
           3      31:   31    1:   15    1:   15
           4      32:   32    1:   15    1:   15
           5       1:   28    1:   15    1:   15
           6      29:   30    1:   15    1:   15
           7      36:   36    1:   15    1:   15
           8      33:   33    1:   15    1:   15
New grid distribution:   3
           1      39:   64    1:   15    1:   15
           2      35:   36    1:   15    1:   15
           3      37:   38    1:   15    1:   15
           4      27:   28    1:   15    1:   15
           5       1:   26    1:   15    1:   15
           6      33:   34    1:   15    1:   15
           7      29:   30    1:   15    1:   15
           8      31:   32    1:   15    1:   15
Setting up quadratic distribution...
ExtMesh (bp) on 0 =    64 x    47 x    55 =      165440
PhiOnMesh: Number of (b)points on node 0 =                 6300
PhiOnMesh: nlist on node 0 =                15254

stepf: Fermi-Dirac step function

siesta: Program's energy decomposition (eV):
siesta: Ebs     =      -502.386871
siesta: Eions   =      2044.779007
siesta: Ena     =       424.462072
siesta: Ekin    =       820.239748
siesta: Enl     =       -79.558352
siesta: Eso     =         0.000000
siesta: Edftu   =         0.000000
siesta: DEna    =        28.013515
siesta: DUscf   =         0.981978
siesta: DUext   =         0.000000
siesta: Exc     =      -436.920900
siesta: eta*DQ  =         0.000000
siesta: Emadel  =         0.000000
siesta: Emeta   =         0.000000
siesta: Emolmec =         0.000000
siesta: Ekinion =         0.000000
siesta: Eharris =     -1276.811107
siesta: Etot    =     -1287.560946
siesta: FreeEng =     -1287.561083

        iscf     Eharris(eV)        E_KS(eV)     FreeEng(eV)     dDmax    Ef(eV) dHmax(eV)
   scf:    1    -1276.811107    -1287.560946    -1287.561083  1.441036 -4.571772  1.853669
timer: Routine,Calls,Time,% = IterSCF        1       0.184  40.31
   scf:    2    -1287.562294    -1287.561620    -1287.561757  0.000818 -4.723268  1.666599
   scf:    3    -1287.567254    -1287.564459    -1287.564597  0.007235 -6.078102  0.006061
   scf:    4    -1287.564475    -1287.564471    -1287.564608  0.000318 -6.078351  0.001205
   scf:    5    -1287.564471    -1287.564471    -1287.564609  0.000018 -6.078586  0.000679

SCF Convergence by DM+H criterion
max |DM_out - DM_in|         :     0.0000178394
max |H_out - H_in|      (eV) :     0.0006789898
SCF cycle converged after 5 iterations

Using DM_out to compute the final energy and forces
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps:      13      52

siesta: E_KS(eV) =            -1287.5645

siesta: E_KS - E_eggbox =     -1287.5645

siesta: Atomic forces (eV/Ang):
----------------------------------------
   Tot   -0.000000   -0.000000   -0.000000
----------------------------------------
   Max    0.011118
   Res    0.004947    sqrt( Sum f_i^2 / 3N )
----------------------------------------
   Max    0.011118    constrained

Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar):        0.19      -70.84      -69.61        0.00       -0.00       -0.00
(Free)E + p*V (eV/cell)    -1275.4211
Target enthalpy (eV/cell)    -1287.5646

siesta: Program's energy decomposition (eV):
siesta: Ebs     =      -502.075339
siesta: Eions   =      2044.779007
siesta: Ena     =       424.462072
siesta: Ekin    =       821.171123
siesta: Enl     =       -80.269852
siesta: Eso     =         0.000000
siesta: Edftu   =         0.000000
siesta: DEna    =        27.834486
siesta: DUscf   =         0.978740
siesta: DUext   =         0.000000
siesta: Exc     =      -436.962031
siesta: eta*DQ  =         0.000000
siesta: Emadel  =         0.000000
siesta: Emeta   =         0.000000
siesta: Emolmec =         0.000000
siesta: Ekinion =         0.000000
siesta: Eharris =     -1287.564471
siesta: Etot    =     -1287.564471
siesta: FreeEng =     -1287.564609

siesta: Final energy (eV):
siesta:  Band Struct. =    -502.075339
siesta:       Kinetic =     821.171123
siesta:       Hartree =    6156.561288
siesta:       Edftu   =       0.000000
siesta:       Eso     =       0.000000
siesta:    Ext. field =       0.000000
siesta:   Exch.-corr. =    -436.962031
siesta:  Ion-electron =  -13146.292286
siesta:       Ion-ion =    5317.957435
siesta:       Ekinion =       0.000000
siesta:         Total =   -1287.564471
siesta:         Fermi =      -6.078586

siesta: Stress tensor (static) (eV/Ang**3):
siesta:     0.000118   -0.000000    0.000000
siesta:    -0.000000   -0.044214    0.000000
siesta:    -0.000000    0.000000   -0.043445

siesta: Cell volume =        416.154670 Ang**3

siesta: Pressure (static):
siesta:                Solid            Molecule  Units
siesta:           0.00031781          0.00031796  Ry/Bohr**3
siesta:           0.02918018          0.02919446  eV/Ang**3
siesta:          46.75230649         46.77518318  kBar
(Free)E+ p_basis*V_orbitals  =       -1286.424942
(Free)Eharris+ p_basis*V_orbitals  =       -1286.424942

siesta: Electric dipole (a.u.)  =   -0.000000    0.000000    0.000000
siesta: Electric dipole (Debye) =   -0.000000    0.000000    0.000000

cite: Please see "elec.bib" for an exhaustive BiBTeX file.
cite: Please clearly indicate Siesta version in published work: 4.1.5
cite: This calculation has made use of the following articles
cite: which are encouraged to be cited in a published work.
        Primary SIESTA paper
          DOI: www.doi.org/10.1088/0953-8984/14/11/302
 
>> End of run:   7-OCT-2026  23:07:02
Job completed
