Siesta Version: siesta-4.0--500
Architecture  : i686-pc-linux-gnu--unknown
Compiler flags: f95 -g -O2
PP flags      : -DFC_HAVE_FLUSH -DFC_HAVE_ABORT 
SERIAL version

* Running in serial mode
>> Start of run:   4-JUL-2016  19:42:20

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

reinit: Reading from standard input
************************** Dump of input data file ****************************
SystemName          Water molecule
SystemLabel         h2o
NumberOfAtoms       3
NumberOfSpecies     2
%block ChemicalSpeciesLabel
 1  8  O      # Species index, atomic number, species label
 2  1  H
%endblock ChemicalSpeciesLabel
AtomicCoordinatesFormat  Ang
%block AtomicCoordinatesAndAtomicSpecies
 0.000  0.000  0.000  1
 0.757  0.586  0.000  2
-0.757  0.586  0.000  2
%endblock AtomicCoordinatesAndAtomicSpecies
xc.functional                   GGA
xc.authors                      PBE
************************** End of input data file *****************************

reinit: -----------------------------------------------------------------------
reinit: System Name: Water molecule
reinit: -----------------------------------------------------------------------
reinit: System Label: h2o                                                         
reinit: -----------------------------------------------------------------------

initatom: Reading input for the pseudopotentials and atomic orbitals ----------
 Species number:            1  Label: O Atomic number:           8
 Species number:            2  Label: H Atomic number:           1
Ground state valence configuration:   2s02  2p04
Reading pseudopotential information in formatted form from O.psf

Pseudopotential generated from a relativistic atomic calculation
There are spin-orbit pseudopotentials available
Spin-orbit interaction is not included in this calculation

Valence configuration for pseudopotential generation:
2s( 2.00) rc: 1.14
2p( 4.00) rc: 1.14
3d( 0.00) rc: 1.14
4f( 0.00) rc: 1.14
Ground state valence configuration:   1s01
Reading pseudopotential information in formatted form from H.psf

Pseudopotential generated from a relativistic atomic calculation
There are spin-orbit pseudopotentials available
Spin-orbit interaction is not included in this calculation

Valence configuration for pseudopotential generation:
1s( 1.00) rc: 1.09
2p( 0.00) rc: 1.09
3d( 0.00) rc: 1.09
4f( 0.00) rc: 1.09
For O, 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 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.

<basis_specs>
===============================================================================
O                    Z=   8    Mass=  16.000        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 O                     (Z =   8)

read_vps: Pseudopotential generation method:
read_vps: ATM3      Troullier-Martins                       
Total valence charge:    6.00000

xc_check: Exchange-correlation functional:
xc_check: GGA Perdew, Burke & Ernzerhof 1996
V l=0 = -2*Zval/r beyond r=  1.1420
V l=1 = -2*Zval/r beyond r=  1.1420
V l=2 = -2*Zval/r beyond r=  1.1420
V l=3 = -2*Zval/r beyond r=  1.1420
All V_l potentials equal beyond r=  1.1278
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r=  1.1420

VLOCAL1: 99.0% of the norm of Vloc inside     34.126 Ry
VLOCAL1: 99.9% of the norm of Vloc inside     77.774 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge    1.37759
atom: Maximum radius for r*vlocal+2*Zval:    1.18566
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=  1.278025   el= -1.759792   Ekb=  9.084139   kbcos=  0.329569
   l= 1   rc=  1.262145   el= -0.663799   Ekb= -7.981946   kbcos= -0.392569
   l= 2   rc=  1.791199   el=  0.002031   Ekb= -1.973642   kbcos= -0.003480
   l= 3   rc=  2.107308   el=  0.003153   Ekb= -0.869991   kbcos= -0.000331

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 =    3.305093
                 energy =   -1.742190
                kinetic =    1.636125
    potential(screened) =   -3.378315
       potential(ionic) =  -11.352901

   izeta = 2
                 rmatch =    2.479194
              splitnorm =    0.150000
                 energy =   -1.461984
                kinetic =    2.528197
    potential(screened) =   -3.990181
       potential(ionic) =  -12.565919

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 =    3.937239
                 energy =   -0.645821
                kinetic =    4.987367
    potential(screened) =   -5.633188
       potential(ionic) =  -13.409643

   izeta = 2
                 rmatch =    2.541963
              splitnorm =    0.150000
                 energy =   -0.356533
                kinetic =    7.472349
    potential(screened) =   -7.828882
       potential(ionic) =  -16.506091

POLgen: Perturbative polarization orbital with L=  2

POLgen: Polarization orbital for state 2p

   izeta = 1
                     rc =    3.937239
                 energy =    2.424640
                kinetic =    4.743467
    potential(screened) =   -2.318828
       potential(ionic) =   -8.626408
atom: Total number of Sankey-type orbitals: 13

atm_pop: Valence configuration (for local Pseudopot. screening):
 2s( 2.00)                                                            
 2p( 4.00)                                                            
Vna: chval, zval:    6.00000   6.00000

Vna:  Cut-off radius for the neutral-atom potential:   3.937239

atom: _________________________________________________________________________

<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: ATM3      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=  1.0754
V l=1 = -2*Zval/r beyond r=  1.0620
V l=2 = -2*Zval/r beyond r=  1.0620
All V_l potentials equal beyond r=  1.0754
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r=  1.0754

VLOCAL1: 99.0% of the norm of Vloc inside     37.534 Ry
VLOCAL1: 99.9% of the norm of Vloc inside     85.540 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge    1.26560
atom: Maximum radius for r*vlocal+2*Zval:    1.06202
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=  1.234287   el= -0.477184   Ekb= -2.219172   kbcos= -0.300759
   l= 1   rc=  1.585560   el=  0.001076   Ekb= -0.508658   kbcos= -0.016807
   l= 2   rc=  1.889267   el=  0.002010   Ekb= -0.204834   kbcos= -0.001615

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 =   -0.457736
                kinetic =    0.990127
    potential(screened) =   -1.447864
       potential(ionic) =   -1.976652

   izeta = 2
                 rmatch =    3.759707
              splitnorm =    0.150000
                 energy =   -0.338970
                kinetic =    1.603674
    potential(screened) =   -1.942644
       potential(ionic) =   -2.493467

POLgen: Perturbative polarization orbital with L=  1

POLgen: Polarization orbital for state 1s

   izeta = 1
                     rc =    4.708991
                 energy =    0.764558
                kinetic =    1.470191
    potential(screened) =   -0.705634
       potential(ionic) =   -1.198294
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: _________________________________________________________________________

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

PAO.BasisType split     

%block ChemicalSpeciesLabel
    1    8 O                       # Species index, atomic number, species label
    2    1 H                       # Species index, atomic number, species label
%endblock ChemicalSpeciesLabel

%block PAO.Basis                 # Define Basis set
O                     2                    # Species label, number of l-shells
 n=2   0   2                         # n, l, Nzeta 
   3.305      2.479   
   1.000      1.000   
 n=2   1   2 P   1                   # n, l, Nzeta, Polarization, NzetaPol
   3.937      2.542   
   1.000      1.000   
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   
%endblock PAO.Basis

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

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

siesta: Atomic coordinates (Bohr) and species
siesta:      0.00000   0.00000   0.00000  1        1
siesta:      1.43052   1.10738   0.00000  2        2
siesta:     -1.43052   1.10738   0.00000  2        3

siesta: Automatic unit cell vectors (Ang):
siesta:    7.147558    0.000000    0.000000
siesta:    0.000000    5.677525    0.000000
siesta:    0.000000    0.000000    5.482158

siesta: System type = molecule  

initatomlists: Number of atoms, orbitals, and projectors:      3    23    34

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: 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          =       50
redata: Mix DM or H after convergence    =     F
redata: Recompute H after scf cycle      =     F
redata: Mixing is linear
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             =     0.2500
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    =     F
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
 Kpoints in:            1 . Kpoints trimmed:            1

siesta: k-grid: Number of k-points =     1
siesta: k-grid: Cutoff (effective) =     2.741 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

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

outcell: Unit cell vectors (Ang):
        7.147558    0.000000    0.000000
        0.000000    5.677525    0.000000
        0.000000    0.000000    5.482158

outcell: Cell vector modules (Ang)   :    7.147558    5.677525    5.482158
outcell: Cell angles (23,13,12) (deg):     90.0000     90.0000     90.0000
outcell: Cell volume (Ang**3)        :    222.4684
New_DM. Step:     1
Initializing Density Matrix...
New grid distribution:   1
           1       1:   24    1:   18    1:   18

InitMesh: MESH =    48 x    36 x    36 =       62208
InitMesh: (bp) =    24 x    18 x    18 =        7776
InitMesh: Mesh cutoff (required, used) =   100.000   111.119 Ry
ExtMesh (bp) on 0 =    60 x    50 x    54 =      162000
PhiOnMesh: Number of (b)points on node 0 =                 7776
PhiOnMesh: nlist on node 0 =                38628

stepf: Fermi-Dirac step function

siesta: Program's energy decomposition (eV):
siesta: Ebs     =      -121.959346
siesta: Eions   =       821.677655
siesta: Ena     =       178.018554
siesta: Ekin    =       342.888076
siesta: Enl     =       -49.035369
siesta: DEna    =        -0.000002
siesta: DUscf   =         0.000000
siesta: DUext   =         0.000000
siesta: Exc     =      -112.922910
siesta: eta*DQ  =         0.000000
siesta: Emadel  =         0.000000
siesta: Emeta   =         0.000000
siesta: Emolmec =         0.000000
siesta: Ekinion =         0.000000
siesta: Eharris =      -467.597485
siesta: Etot    =      -462.729306
siesta: FreeEng =      -462.729306

   scf: iscf   Eharris(eV)      E_KS(eV)   FreeEng(eV)    dDmax  Ef(eV)
   scf:    1     -467.5975     -462.7293     -462.7293  1.37586 -4.1445
timer: Routine,Calls,Time,% =    IterSCF     1       0.112   6.97
   scf:    2     -468.2009     -466.2516     -466.2516  0.20424  0.1350
   scf:    3     -467.0759     -466.5203     -466.5203  0.05945 -1.4116
   scf:    4     -466.9789     -466.6407     -466.6407  0.02173 -1.8521
   scf:    5     -466.9693     -466.7234     -466.7234  0.01082 -1.9799
   scf:    6     -466.9682     -466.7847     -466.7847  0.00631 -2.0149
   scf:    7     -466.9681     -466.8306     -466.8306  0.00412 -2.0227
   scf:    8     -466.9680     -466.8649     -466.8649  0.00287 -2.0232
   scf:    9     -466.9680     -466.8907     -466.8907  0.00219 -2.0221
   scf:   10     -466.9680     -466.9100     -466.9100  0.00165 -2.0209
   scf:   11     -466.9680     -466.9245     -466.9245  0.00124 -2.0200
   scf:   12     -466.9680     -466.9354     -466.9354  0.00093 -2.0194
   scf:   13     -466.9680     -466.9436     -466.9436  0.00070 -2.0190
   scf:   14     -466.9680     -466.9497     -466.9497  0.00053 -2.0187
   scf:   15     -466.9680     -466.9543     -466.9543  0.00040 -2.0185
   scf:   16     -466.9680     -466.9577     -466.9577  0.00030 -2.0184
   scf:   17     -466.9680     -466.9603     -466.9603  0.00023 -2.0183
   scf:   18     -466.9680     -466.9622     -466.9622  0.00017 -2.0183
   scf:   19     -466.9680     -466.9637     -466.9637  0.00013 -2.0182
   scf:   20     -466.9680     -466.9648     -466.9648  0.00010 -2.0182
   scf:   21     -466.9680     -466.9656     -466.9656  0.00008 -2.0182

SCF Convergence by dMax criterion
max |DM_out - DM_in|:     0.00007633
SCF cycle converged after   21 iterations

Using DM_out to compute the final energy and forces

siesta: E_KS(eV) =             -466.9680

siesta: E_KS - E_eggbox =      -466.9680

siesta: Atomic forces (eV/Ang):
----------------------------------------
   Tot   -0.000000    0.032669   -0.000000
----------------------------------------
   Max    0.811101
   Res    0.456593    sqrt( Sum f_i^2 / 3N )
----------------------------------------
   Max    0.811101    constrained

Stress-tensor-Voigt (kbar):       -7.01       -3.70       -0.53        0.00        0.00       -0.00
(Free)E + p*V (eV/cell)     -466.4480
Target enthalpy (eV/cell)     -466.9680

siesta: Program's energy decomposition (eV):
siesta: Ebs     =      -103.484586
siesta: Eions   =       821.677655
siesta: Ena     =       178.018554
siesta: Ekin    =       353.326815
siesta: Enl     =       -58.450283
siesta: DEna    =        -2.825552
siesta: DUscf   =         0.746459
siesta: DUext   =         0.000000
siesta: Exc     =      -116.106360
siesta: eta*DQ  =         0.000000
siesta: Emadel  =         0.000000
siesta: Emeta   =         0.000000
siesta: Emolmec =         0.000000
siesta: Ekinion =         0.000000
siesta: Eharris =      -466.968021
siesta: Etot    =      -466.968021
siesta: FreeEng =      -466.968021

siesta: Final energy (eV):
siesta:  Band Struct. =    -103.484586
siesta:       Kinetic =     353.326815
siesta:       Hartree =     382.817677
siesta:    Ext. field =       0.000000
siesta:   Exch.-corr. =    -116.106360
siesta:  Ion-electron =   -1071.795186
siesta:       Ion-ion =     -15.210967
siesta:       Ekinion =       0.000000
siesta:         Total =    -466.968021

siesta: Atomic forces (eV/Ang):
siesta:      1    0.000000   -0.811101    0.000000
siesta:      2    0.656672    0.421885   -0.000000
siesta:      3   -0.656672    0.421885   -0.000000
siesta: ----------------------------------------
siesta:    Tot   -0.000000    0.032669   -0.000000

siesta: Stress tensor (static) (eV/Ang**3):
siesta:    -0.004373    0.000000    0.000000
siesta:     0.000000   -0.002306   -0.000000
siesta:    -0.000000    0.000000   -0.000333

siesta: Cell volume =        222.468374 Ang**3

siesta: Pressure (static):
siesta:                Solid            Molecule  Units
siesta:           0.00002546          0.00000137  Ry/Bohr**3
siesta:           0.00233751          0.00012613  eV/Ang**3
siesta:           3.74514157          0.20207973  kBar
(Free)E+ p_basis*V_orbitals  =        -466.414943
(Free)Eharris+ p_basis*V_orbitals  =        -466.414943

siesta: Electric dipole (a.u.)  =    0.000000    0.534678    0.000000
siesta: Electric dipole (Debye) =    0.000000    1.359017    0.000000

timer: Elapsed wall time (sec) =       4.225
timer: CPU execution times (sec):

Routine            Calls   Time/call    Tot.time        %
siesta                 1       3.884       3.884   100.00
Setup                  1       0.236       0.236     6.08
bands                  1       0.000       0.000     0.00
KSV_init               1       0.000       0.000     0.00
IterGeom               1       3.648       3.648    93.92
state_init             1       0.220       0.220     5.66
hsparse                1       0.000       0.000     0.00
overlap                1       0.220       0.220     5.66
Setup_H0               1       1.040       1.040    26.78
naefs                  2       0.000       0.000     0.00
MolMec                 2       0.000       0.000     0.00
kinefsm                2       0.104       0.208     5.36
nlefsm                 2       0.380       0.760    19.57
DHSCF_Init             1       0.072       0.072     1.85
DHSCF1                 1       0.012       0.012     0.31
INITMESH               1       0.000       0.000     0.00
DHSCF2                 1       0.060       0.060     1.54
REMESH                 1       0.000       0.000     0.00
REORD                 52       0.000       0.004     0.10
PHION                  1       0.048       0.048     1.24
COMM_BSC              47       0.000       0.004     0.10
POISON                23       0.004       0.092     2.37
fft                   46       0.001       0.056     1.44
IterSCF               21       0.106       2.216    57.05
setup_H               21       0.105       2.200    56.64
DHSCF                 22       0.108       2.368    60.97
DHSCF3                22       0.104       2.296    59.11
rhoofd                22       0.007       0.164     4.22
cellXC                22       0.088       1.944    50.05
vmat                  22       0.003       0.064     1.65
compute_dm            21       0.001       0.012     0.31
diagon                21       0.001       0.012     0.31
r-eigvec              21       0.001       0.012     0.31
r-buildHS             21       0.000       0.000     0.00
rdiag                 21       0.001       0.012     0.31
rdiag1                21       0.000       0.004     0.10
rdiag2                21       0.000       0.000     0.00
rdiag3                21       0.000       0.008     0.21
rdiag4                21       0.000       0.000     0.00
r-buildD              21       0.000       0.000     0.00
MIXER                 20       0.000       0.000     0.00
WriteDM               21       0.000       0.000     0.00
PostSCF                1       0.172       0.172     4.43
DHSCF4                 1       0.072       0.072     1.85
dfscf                  1       0.056       0.056     1.44
overfsm                1       0.000       0.000     0.00
state_analysis         1       0.000       0.000     0.00
siesta_move            1       0.000       0.000     0.00
optical                1       0.000       0.000     0.00
  
>> End of run:   4-JUL-2016  19:42:24
