Siesta Version  : v4.0.2
Architecture    : x86_64-unknown-linux-gnu--unknown
Compiler version: GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.10) 5.4.0 20160609
Compiler flags  : /usr/bin/mpif90 -g -O2
PP flags        : -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DMPI -DGRID_DP -DPHI_GRID_SP 
PARALLEL version

* Running on    4 nodes in parallel
>> Start of run:   7-SEP-2019  17:41:28

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

reinit: Reading from standard input
************************** Dump of input data file ****************************
SystemName        system
SystemLabel       system
NumberOfAtoms     5
NumberOfSpecies   2
WriteForces       T
WriteCoorStep     T
WriteCoorXmol     T
WriteMDXmol       T
WriteMDHistory    T
# SCF options
MeshCutoff             300 Ry
MaxSCFIterations       40           # Maximum number of SCF iter
DM.MixingWeight       0.05          # New DM amount for next SCF cycle
DM.Tolerance          1.000000e-04  # Tolerance in maximum difference between input and output DM
DM.UseSaveDM          true          # to use continuation files
DM.NumberPulay         5
MD.UseSaveXV           T
# MD options
XC.functional          GGA
XC.authors             PBE
DM.UseSaveDM           F
WriteDM                F
WriteDM.NetCDF         F
WriteDMHS.NetCDF       F
%block Chemical_Species_label
1	1	H
2	6	C
%endblock Chemical_Species_label
%block kgrid_Monkhorst_Pack
	2	0	0	0.0
	0	2	0	0.0
	0	0	2	0.0
%endblock kgrid_Monkhorst_Pack
LatticeConstant    1.00 Ang
%block LatticeVectors
	10.269574816504	0.000000000000	0.000000000000
	-0.255659971217	9.882867516503	0.000000000000
	0.112990394520	-0.148018909925	9.809640850409
%endblock LatticeVectors
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
	5.36586	4.05415	3.59848	1
	3.92611	4.82628	4.42448	1
	5.5636	5.65033	4.43064	1
	5.28729	4.14347	5.36703	1
	5.01936	4.68879	4.44103	2
%endblock AtomicCoordinatesAndAtomicSpecies
************************** End of input data file *****************************

reinit: -----------------------------------------------------------------------
reinit: System Name: system
reinit: -----------------------------------------------------------------------
reinit: System Label: system                                                      
reinit: -----------------------------------------------------------------------

initatom: Reading input for the pseudopotentials and atomic orbitals ----------
 Species number:            1  Label: H Atomic number:           1
 Species number:            2  Label: C Atomic number:           6
Ground state valence configuration:   1s01
Reading pseudopotential information in formatted form from H.psf

Valence configuration for pseudopotential generation:
1s( 1.00) rc: 1.33
2p( 0.00) rc: 1.33
3d( 0.00) rc: 0.37
4f( 0.00) rc: 1.33
Ground state valence configuration:   2s02  2p02
Reading pseudopotential information in formatted form from C.psf

Valence configuration for pseudopotential generation:
2s( 2.00) rc: 1.56
2p( 2.00) rc: 1.56
3d( 0.00) rc: 1.56
4f( 0.00) rc: 1.56
For H, 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.
For C, 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>
===============================================================================
H                    Z=   1    Mass=  1.0100        Charge= 0.17977+309
Lmxo=0 Lmxkb= 2    BasisType=split      Semic=F
L=0  Nsemic=0  Cnfigmx=1
          n=1  nzeta=2  polorb=1
            splnorm:   0.15000    
               vcte:    0.0000    
               rinn:    0.0000    
               qcoe:    0.0000    
               qyuk:    0.0000    
               qwid:   0.10000E-01
                rcs:    0.0000      0.0000    
            lambdas:    1.0000      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 H                     (Z =   1)

read_vps: Pseudopotential generation method:
read_vps: ATM 3.2.2 Troullier-Martins                       
Total valence charge:    1.00000

xc_check: Exchange-correlation functional:
xc_check: GGA Perdew, Burke & Ernzerhof 1996
V l=0 = -2*Zval/r beyond r=  1.2656
V l=1 = -2*Zval/r beyond r=  1.2498
V l=2 = -2*Zval/r beyond r=  0.3563
All V_l potentials equal beyond r=  1.2656
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r=  1.2656

VLOCAL1: 99.0% of the norm of Vloc inside     27.100 Ry
VLOCAL1: 99.9% of the norm of Vloc inside     61.762 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge    1.48935
atom: Maximum radius for r*vlocal+2*Zval:    1.24984
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=  1.398961   el= -0.477209   Ekb= -2.001853   kbcos= -0.352188
   l= 1   rc=  1.470814   el=  0.001006   Ekb= -0.423408   kbcos= -0.024395
   l= 2   rc=  1.489346   el=  0.001895   Ekb= -0.481957   kbcos= -0.001574

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

atom: SANKEY-TYPE ORBITALS:
atom: Selected multiple-zeta basis: split     

SPLIT: Orbitals with angular momentum L= 0

SPLIT: Basis orbitals for state 1s

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

   izeta = 1
                 lambda =    1.000000
                     rc =    4.708991
                 energy =   -0.457764
                kinetic =    0.979534
    potential(screened) =   -1.437298
       potential(ionic) =   -1.965615

   izeta = 2
                 rmatch =    3.759707
              splitnorm =    0.150000
                 energy =   -0.339003
                kinetic =    1.582546
    potential(screened) =   -1.921548
       potential(ionic) =   -2.471878

POLgen: Perturbative polarization orbital with L=  1

POLgen: Polarization orbital for state 1s

   izeta = 1
                     rc =    4.708991
                 energy =    0.764951
                kinetic =    1.476882
    potential(screened) =   -0.711931
       potential(ionic) =   -1.204335
atom: Total number of Sankey-type orbitals:  5

atm_pop: Valence configuration (for local Pseudopot. screening):
 1s( 1.00)                                                            
Vna: chval, zval:    1.00000   1.00000

Vna:  Cut-off radius for the neutral-atom potential:   4.708991

atom: _________________________________________________________________________

<basis_specs>
===============================================================================
C                    Z=   6    Mass=  12.010        Charge= 0.17977+309
Lmxo=1 Lmxkb= 3    BasisType=split      Semic=F
L=0  Nsemic=0  Cnfigmx=2
          n=1  nzeta=2  polorb=0
            splnorm:   0.15000    
               vcte:    0.0000    
               rinn:    0.0000    
               qcoe:    0.0000    
               qyuk:    0.0000    
               qwid:   0.10000E-01
                rcs:    0.0000      0.0000    
            lambdas:    1.0000      1.0000    
L=1  Nsemic=0  Cnfigmx=2
          n=1  nzeta=2  polorb=1
            splnorm:   0.15000    
               vcte:    0.0000    
               rinn:    0.0000    
               qcoe:    0.0000    
               qyuk:    0.0000    
               qwid:   0.10000E-01
                rcs:    0.0000      0.0000    
            lambdas:    1.0000      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
L=3  Nkbl=1  erefs: 0.17977+309
===============================================================================
</basis_specs>

atom: Called for C                     (Z =   6)

read_vps: Pseudopotential generation method:
read_vps: ATM 3.2.2 Troullier-Martins                       
Total valence charge:    4.00000

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
V l=3 = -2*Zval/r beyond r=  1.5227
All V_l potentials equal beyond r=  1.4851
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     19.682 Ry
VLOCAL1: 99.9% of the norm of Vloc inside     44.856 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge    1.79142
atom: Maximum radius for r*vlocal+2*Zval:    1.54183
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=  1.661951   el= -1.010689   Ekb=  5.289847   kbcos=  0.316429
   l= 1   rc=  1.661951   el= -0.388490   Ekb= -4.102504   kbcos= -0.351025
   l= 2   rc=  1.747182   el=  0.001971   Ekb= -1.006005   kbcos= -0.008530
   l= 3   rc=  1.791422   el=  0.003065   Ekb= -0.421399   kbcos= -0.001072

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

atom: SANKEY-TYPE ORBITALS:
atom: Selected multiple-zeta basis: split     

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 =   -0.990050
                kinetic =    0.909804
    potential(screened) =   -1.899854
       potential(ionic) =   -5.513925

   izeta = 2
                 rmatch =    3.347176
              splitnorm =    0.150000
                 energy =   -0.836186
                kinetic =    1.375045
    potential(screened) =   -2.211230
       potential(ionic) =   -6.057915

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 =   -0.368677
                kinetic =    2.532104
    potential(screened) =   -2.900781
       potential(ionic) =   -6.401132

   izeta = 2
                 rmatch =    3.475094
              splitnorm =    0.150000
                 energy =   -0.205777
                kinetic =    3.787472
    potential(screened) =   -3.993249
       potential(ionic) =   -7.860448

POLgen: Perturbative polarization orbital with L=  2

POLgen: Polarization orbital for state 2p

   izeta = 1
                     rc =    4.870301
                 energy =    1.296521
                kinetic =    2.641128
    potential(screened) =   -1.344607
       potential(ionic) =   -4.300412
atom: Total number of Sankey-type orbitals: 13

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

atom: _________________________________________________________________________

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

PAO.BasisType split     

%block ChemicalSpeciesLabel
    1    1 H                       # Species index, atomic number, species label
    2    6 C                       # Species index, atomic number, species label
%endblock ChemicalSpeciesLabel

%block PAO.Basis                 # Define Basis set
H                     1                    # Species label, number of l-shells
 n=1   0   2 P   1                   # n, l, Nzeta, Polarization, NzetaPol
   4.709      3.760   
   1.000      1.000   
C                     2                    # Species label, number of l-shells
 n=2   0   2                         # n, l, Nzeta 
   4.088      3.347   
   1.000      1.000   
 n=2   1   2 P   1                   # n, l, Nzeta, Polarization, NzetaPol
   4.870      3.475   
   1.000      1.000   
%endblock PAO.Basis

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

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

ioxv: Reading coordinates and velocities from file
! Info in XV file prevails over previous structure input

siesta: Atomic coordinates (Bohr) and species
siesta:     10.14001   7.66124   6.80014  1        1
siesta:      7.41928   9.12035   8.36106  1        2
siesta:     10.51368  10.67758   8.37270  1        3
siesta:      9.99153   7.83003  10.14222  1        4
siesta:      9.48522   8.86053   8.39233  2        5

siesta: System type = molecule  

initatomlists: Number of atoms, orbitals, and projectors:      5    33    52

coxmol: Writing XMOL coordinates into file system.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: Non-Collinear-spin run           =     F
redata: SpinPolarized (Up/Down) run      =     F
redata: Number of spin components        =     1
redata: Long output                      =     F
redata: Number of Atomic Species         =        2
redata: Charge density info will appear in .RHO file
redata: Write Mulliken Pop.              =     NO
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          =       40
redata: Mix DM or H after convergence    =     F
redata: Recompute H after scf cycle      =     F
redata: Performing Pulay mixing using    =     5 iterations
redata: Mix DM in first SCF step ?       =     F
redata: Write Pulay info on disk?        =     F
redata: Discard 1st Pulay DM after  kick =     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: DM Tolerance for SCF             =     0.000100
redata: Require (free) Energy convergence in SCF =     F
redata: DM (free)Energy tolerance for SCF =     0.000010 eV
redata: Require Harris convergence for SCF =     F
redata: DM Harris energy tolerance for SCF =     0.000010 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: Divide and Conquer               =     T
redata: Electronic Temperature           =     0.0019  Ry
redata: Fix the spin of the system       =     F
redata: Dynamics option                  =     Single-point calculation
redata: ***********************************************************************
Total number of electrons:     8.000000
Total ionic charge:     8.000000

* ProcessorY, Blocksize:    2   9


* Orbital distribution balance (max,min):     9     6

k-point displ. along   1 input, could be:     0.00    0.50
k-point displ. along   2 input, could be:     0.00    0.50
k-point displ. along   3 input, could be:     0.00    0.50
 Kpoints in:            8 . Kpoints trimmed:            8

siesta: k-grid: Number of k-points =     8
siesta: k-grid: Cutoff (effective) =     9.811 Ang
siesta: k-grid: Supercell and displacements
siesta: k-grid:    2   0   0      0.000
siesta: k-grid:    0   2   0      0.000
siesta: k-grid:    0   0   2      0.000
Naive supercell factors:     2    2    2

superc: Internal auxiliary supercell:     2 x     2 x     2  =       8
superc: Number of atoms, orbitals, and projectors:     40    264    416

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

outcoor: Atomic coordinates (Ang):                          
    5.36586000    4.05415000    3.59848000   1       1  H
    3.92611000    4.82628000    4.42448000   1       2  H
    5.56360000    5.65033000    4.43064000   1       3  H
    5.28729000    4.14347000    5.36703000   1       4  H
    5.01936000    4.68879000    4.44103000   2       5  C

superc: Internal auxiliary supercell:     2 x     2 x     2  =       8
superc: Number of atoms, orbitals, and projectors:     40    264    416

outcell: Unit cell vectors (Ang):
       10.269575    0.000000    0.000000
       -0.255660    9.882868    0.000000
        0.112990   -0.148019    9.809641

outcell: Cell vector modules (Ang)   :   10.269575    9.886174    9.811408
outcell: Cell angles (23,13,12) (deg):     90.8812     89.3402     91.4819
outcell: Cell volume (Ang**3)        :    995.6084
New_DM. Step:     1
Initializing Density Matrix...
New grid distribution:   1
           1       1:   54    1:   27    1:   27
           2       1:   54    1:   27   28:   54
           3       1:   54   28:   54    1:   27
           4       1:   54   28:   54   28:   54

InitMesh: MESH =   108 x   108 x   108 =     1259712
InitMesh: (bp) =    54 x    54 x    54 =      157464
InitMesh: Mesh cutoff (required, used) =   300.000   305.906 Ry
ExtMesh (bp) on 0 =   110 x    87 x    87 =      832590
New grid distribution:   2
           1       1:   54    1:   26    1:   25
           2       1:   54    1:   26   26:   54
           3       1:   54   27:   54    1:   25
           4       1:   54   27:   54   26:   54
New grid distribution:   3
           1       1:   54    1:   26    1:   25
           2       1:   54    1:   26   26:   54
           3       1:   54   27:   54    1:   25
           4       1:   54   27:   54   26:   54
Setting up quadratic distribution...
ExtMesh (bp) on 0 =   110 x    86 x    85 =      804100
PhiOnMesh: Number of (b)points on node 0 =                35100
PhiOnMesh: nlist on node 0 =                83033

stepf: Fermi-Dirac step function

siesta: Program's energy decomposition (eV):
siesta: Ebs     =      -111.060811
siesta: Eions   =       338.948826
siesta: Ena     =        77.930585
siesta: Ekin    =       146.974218
siesta: Enl     =       -14.753712
siesta: DEna    =        -0.000000
siesta: DUscf   =         0.000000
siesta: DUext   =         0.000000
siesta: Exc     =       -80.216229
siesta: eta*DQ  =         0.000000
siesta: Emadel  =         0.000000
siesta: Emeta   =         0.000000
siesta: Emolmec =         0.000000
siesta: Ekinion =         0.000000
siesta: Eharris =      -220.171745
siesta: Etot    =      -209.013965
siesta: FreeEng =      -209.013965

   scf: iscf   Eharris(eV)      E_KS(eV)   FreeEng(eV)    dDmax  Ef(eV)
   scf:    1     -220.1717     -209.0140     -209.0140  1.98614  0.4290
timer: Routine,Calls,Time,% =    IterSCF     1       0.620  18.39
   scf:    2     -220.3271     -218.2922     -218.2922  0.33579 -4.6077
   scf:    3     -219.6173     -217.1323     -217.1323  0.31890 -5.6210
   scf:    4     -219.2354     -218.6344     -218.6344  0.08127 -6.1900
   scf:    5     -219.1746     -218.8551     -218.8551  0.01456 -6.8789
   scf:    6     -219.1643     -218.9768     -218.9768  0.00847 -6.7477
   scf:    7     -219.1640     -219.1127     -219.1127  0.00187 -6.7556
   scf:    8     -219.1640     -219.1270     -219.1270  0.00148 -6.7555
   scf:    9     -219.1640     -219.1572     -219.1572  0.00026 -6.7517
   scf:   10     -219.1640     -219.1597     -219.1597  0.00030 -6.7520
   scf:   11     -219.1640     -219.1604     -219.1604  0.00032 -6.7521
   scf:   12     -219.1640     -219.1639     -219.1639  0.00002 -6.7526

SCF Convergence by dMax criterion
max |DM_out - DM_in|:     0.00001998
SCF cycle converged after   12 iterations

Using DM_out to compute the final energy and forces

siesta: E_KS(eV) =             -219.1640

siesta: E_KS - E_eggbox =      -219.1640

siesta: Atomic forces (eV/Ang):
     1   -0.219766    0.230163    0.000242
     2    0.013220    0.102811   -0.156756
     3   -0.166877    0.011241   -0.056008
     4   -0.040521    0.111642    0.032408
     5    0.412697   -0.457364    0.181026
----------------------------------------
   Tot   -0.001247   -0.001507    0.000911
----------------------------------------
   Max    0.457364
   Res    0.199186    sqrt( Sum f_i^2 / 3N )
----------------------------------------
   Max    0.457364    constrained

Stress-tensor-Voigt (kbar):        0.31        0.29       -0.05       -0.01        0.15       -0.24
(Free)E + p*V (eV/cell)     -219.2787
Target enthalpy (eV/cell)     -219.1640

coxmol: Writing XMOL coordinates into file system.xyz                                                      

siesta: Program's energy decomposition (eV):
siesta: Ebs     =       -87.939375
siesta: Eions   =       338.948826
siesta: Ena     =        77.930585
siesta: Ekin    =       168.648331
siesta: Enl     =       -32.727854
siesta: DEna    =        -9.204808
siesta: DUscf   =         1.226371
siesta: DUext   =         0.000000
siesta: Exc     =       -86.087826
siesta: eta*DQ  =         0.000000
siesta: Emadel  =         0.000000
siesta: Emeta   =         0.000000
siesta: Emolmec =         0.000000
siesta: Ekinion =         0.000000
siesta: Eharris =      -219.164027
siesta: Etot    =      -219.164027
siesta: FreeEng =      -219.164027

siesta: Final energy (eV):
siesta:  Band Struct. =     -87.939375
siesta:       Kinetic =     168.648331
siesta:       Hartree =     284.640131
siesta:    Ext. field =       0.000000
siesta:   Exch.-corr. =     -86.087826
siesta:  Ion-electron =    -714.389220
siesta:       Ion-ion =     128.024557
siesta:       Ekinion =       0.000000
siesta:         Total =    -219.164027

siesta: Atomic forces (eV/Ang):
siesta:      1   -0.219766    0.230163    0.000242
siesta:      2    0.013220    0.102811   -0.156756
siesta:      3   -0.166877    0.011241   -0.056008
siesta:      4   -0.040521    0.111642    0.032408
siesta:      5    0.412697   -0.457364    0.181026
siesta: ----------------------------------------
siesta:    Tot   -0.001247   -0.001507    0.000911

siesta: Stress tensor (static) (eV/Ang**3):
siesta:     0.000195   -0.000004   -0.000150
siesta:    -0.000004    0.000183    0.000093
siesta:    -0.000150    0.000093   -0.000032

siesta: Cell volume =        995.608381 Ang**3

siesta: Pressure (static):
siesta:                Solid            Molecule  Units
siesta:          -0.00000125         -0.00000001  Ry/Bohr**3
siesta:          -0.00011520         -0.00000092  eV/Ang**3
siesta:          -0.18457250         -0.00147983  kBar
(Free)E+ p_basis*V_orbitals  =        -218.058510
(Free)Eharris+ p_basis*V_orbitals  =        -218.058510

siesta: Electric dipole (a.u.)  =    0.003125   -0.004703    0.004943
siesta: Electric dipole (Debye) =    0.007944   -0.011954    0.012563
>> End of run:   7-SEP-2019  17:41:42
Job completed
