Siesta Version : v4.1-b4-351
Architecture : x86_64-linux-n-62-26-19
Compiler version: GNU Fortran (GCC) 9.3.0
Compiler flags : mpifort -m64 -fPIC -O3 -march=native -ftree-vectorize -fexpensive-optimizatioons -funroll-loops -fprefetch-loop-arrays -fno-second-underscore -flto
PP flags : -I/dtu/sw/dcc/SL73/2020-aug/generic/build-tools/1.0/include -I/dtu/sw/dcc/SL773/2020-aug/generic/gcc/9.3.0/include -I/dtu/sw/dcc/SL73/2020-aug/generic/gcc/9.3.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/zlib/1.2.11/include -I/dtu/sw/dcc/SL73/2020-aug/generic/numactl/2.0.12/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/libxml2/2.9.10/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/hwloc/2.2.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/knem/1.1.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/ucx/1.8.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/openmpi/4.0.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/szip/2.1.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/hdf5/1.12.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/pnetcdf/1.12.1/include -I/dtu/sw/dcc/SL73/2020-aug/generic/gen-zlib/1.2.11/include -I/dtu/sw/dcc/SL73/2020-aug/generic/openssl/1.1.1/include -I/dtu/sw/dcc/SL73/2020-aug/generic/libssh2/1.8.2/include -I/dtu/sw/dcc/SL73/2020-aug/generic/curl/7.65.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/netcdf/4.7.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/fftw/3.3.8/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/parmetis/4.0.3/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/scalapack/2.1.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/lapack/3.9.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/blis/0.7.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/scotch/6.0.9/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/mumps/5.3.3/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/elpa/2020.05.001/include -DSIESTA__ELPA -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DCDF4 -DSIESTA__FLOOK -DNCDF -DNCDF_4 -DNCDF_PARALLEL -DTS_NOCHECKS -DSIESTA__METIS -DSIESTA__MUMPS -DSIESTA__MRRR -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/elpa/2020.05.001/include/elpa
Libraries : libncdf.a libfdict.a -lnetcdff -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lz -lzmuumps -lmumps_common -lesmumps -lscotch -lscotcherr -lpord -lparmetis -lmetis -lelpa -lscalapack -llapack -lblis -L/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/lib -Wl,-rpath=/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/lib -lflookall -ldl -flto -fuse-linker-plugin -lmetis
PARALLEL version
NetCDF support
NetCDF-4 support
NetCDF-4 MPI-IO support
METIS ordering support
Lua support
* Running on 8 nodes in parallel
>> Start of run: 22-JAN-2021 23:12:41
***********************
* WELCOME TO SIESTA *
***********************
reinit: Reading from standard input
reinit: Dumped input in INPUT_TMP.93070
************************** Dump of input data file ****************************
SystemName Water molecule -- md verlet
SystemLabel h2o
NumberOfAtoms 3
NumberOfSpecies 2
MeshCutoff 100 Ry
%block ChemicalSpeciesLabel
1 8 O # Species index, atomic number, species label
2 1 H
%endblock ChemicalSpeciesLabel
LatticeConstant 8.0 Ang
%block LatticeVectors
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 0.8
%endblock LatticeVectors
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
Solution.Method diagon
MeshCutoff 100 Ry
WriteCoorStep .true.
WriteForces .true.
WriteMDHistory .true.
MD.UseSaveXV T
MD.TypeOfRun Verlet
MD.InitialTemperature 600 K
MD.Initial.Time.Step 1
MD.Final.Time.Step 20
MD.Length.Time.Step 0.2 fs
************************** End of input data file *****************************
reinit: -----------------------------------------------------------------------
reinit: System Name: Water molecule -- md verlet
reinit: -----------------------------------------------------------------------
reinit: System Label: h2o
reinit: -----------------------------------------------------------------------
initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Species number: 1 Atomic number: 8 Label: O
Species number: 2 Atomic number: 1 Label: H
Ground state valence configuration: 2s02 2p04
Reading pseudopotential information in formatted form from O.psf
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
Valence configuration for pseudopotential generation:
1s( 1.00) rc: 1.25
2p( 0.00) rc: 1.25
3d( 0.00) rc: 1.25
4f( 0.00) rc: 1.25
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.
===============================================================================
O Z= 8 Mass= 16.000 Charge= 0.17977+309
Lmxo=1 Lmxkb= 3 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=2
i=1 nzeta=2 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 0.0000
lambdas: 1.0000 1.0000
L=1 Nsemic=0 Cnfigmx=2
i=1 nzeta=2 polorb=1 (2p)
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
===============================================================================
atom: Called for O (Z = 8)
read_vps: Pseudopotential generation method:
read_vps: ATM3 Troullier-Martins
Valence charge for ps generation: 6.00000
xc_check: Exchange-correlation functional:
xc_check: Ceperley-Alder
V l=0 = -2*Zval/r beyond r= 1.1278
V l=1 = -2*Zval/r beyond r= 1.1278
V l=2 = -2*Zval/r beyond r= 1.1278
V l=3 = -2*Zval/r beyond r= 1.1138
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= 1.1278
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= 1.294105 el= -1.742414 Ekb= 9.135903 kbcos= 0.326910
l= 1 rc= 1.294105 el= -0.676589 Ekb= -8.124878 kbcos= -0.395047
l= 2 rc= 1.448233 el= 0.002386 Ekb= -2.039267 kbcos= -0.003484
l= 3 rc= 1.561052 el= 0.003508 Ekb= -0.799141 kbcos= -0.000344
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 = -1.723766
kinetic = 1.614911
potential(screened) = -3.338677
potential(ionic) = -11.304675
izeta = 2
rmatch = 2.510382
splitnorm = 0.150000
energy = -1.471299
kinetic = 2.446434
potential(screened) = -3.917732
potential(ionic) = -12.476133
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 = -0.658841
kinetic = 5.005986
potential(screened) = -5.664827
potential(ionic) = -13.452360
izeta = 2
rmatch = 2.541963
splitnorm = 0.150000
energy = -0.367441
kinetic = 7.530509
potential(screened) = -7.897949
potential(ionic) = -16.611953
POLgen: Perturbative polarization orbital with L= 2
POLgen: Polarization orbital for state 2p
izeta = 1
rc = 3.937239
energy = 2.398520
kinetic = 4.716729
potential(screened) = -2.318209
potential(ionic) = -8.603170
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: _________________________________________________________________________
===============================================================================
H Z= 1 Mass= 1.0100 Charge= 0.17977+309
Lmxo=0 Lmxkb= 2 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=1
i=1 nzeta=2 polorb=1 (1s)
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
===============================================================================
atom: Called for H (Z = 1)
read_vps: Pseudopotential generation method:
read_vps: ATM3 Troullier-Martins
Valence charge for ps generation: 1.00000
xc_check: Exchange-correlation functional:
xc_check: Ceperley-Alder
V l=0 = -2*Zval/r beyond r= 1.2343
V l=1 = -2*Zval/r beyond r= 1.2189
V l=2 = -2*Zval/r beyond r= 1.2189
All V_l potentials equal beyond r= 1.2343
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r= 1.2343
VLOCAL1: 99.0% of the norm of Vloc inside 28.493 Ry
VLOCAL1: 99.9% of the norm of Vloc inside 64.935 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.45251
atom: Maximum radius for r*vlocal+2*Zval: 1.21892
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= 1.364359 el= -0.467325 Ekb= -2.005361 kbcos= -0.336422
l= 1 rc= 1.434438 el= 0.001430 Ekb= -0.501708 kbcos= -0.021697
l= 2 rc= 1.470814 el= 0.002365 Ekb= -0.190555 kbcos= -0.002281
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 = 4.828263
energy = -0.449375
kinetic = 0.929372
potential(screened) = -1.378747
potential(ionic) = -1.915047
izeta = 2
rmatch = 3.854947
splitnorm = 0.150000
energy = -0.336153
kinetic = 1.505294
potential(screened) = -1.841447
potential(ionic) = -2.413582
POLgen: Perturbative polarization orbital with L= 1
POLgen: Polarization orbital for state 1s
izeta = 1
rc = 4.828263
energy = 0.706972
kinetic = 1.396397
potential(screened) = -0.689424
potential(ionic) = -1.169792
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: 4.828263
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 2.510
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
4.828 3.855
1.000 1.000
%endblock PAO.Basis
prinput: ----------------------------------------------------------------------
Dumping basis to NetCDF file O.ion.nc
Dumping basis to NetCDF file H.ion.nc
coor: Atomic-coordinates input format = Cartesian coordinates
coor: (in Angstroms)
siesta: WARNING: XV file not found
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: 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: 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 = 2
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 = 1000
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 = F
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 = Verlet MD run
redata: Initial MD time step = 1
redata: Final MD time step = 20
redata: Length of MD time step = 0.2000 fs
redata: Initial Temperature of MD run = 600.0000 K
redata: Perform a MD quench = F
mix.SCF: Pulay mixing = Pulay
mix.SCF: Variant = stable
mix.SCF: History steps = 2
mix.SCF: Linear mixing weight = 0.250000
mix.SCF: Mixing weight = 0.250000
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 0.2500
weight.linear 0.2500
history 2
%endblock SCF.Mixer.Pulay
Size of DM history Fstack: 1
Total number of electrons: 8.000000
Total ionic charge: 8.000000
* ProcessorY, Blocksize: 2 3
* Orbital distribution balance (max,min): 3 2
Kpoints in: 1 . Kpoints trimmed: 1
siesta: k-grid: Number of k-points = 1
siesta: k-grid: Cutoff (effective) = 3.200 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 = 3
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
ts: **************************************************************
ts: Save H and S matrices = F
ts: Save DM and EDM matrices = F
ts: Only save the overlap matrix S = F
ts: **************************************************************
************************ Begin: TS CHECKS AND WARNINGS ************************
************************ End: TS CHECKS AND WARNINGS **************************
====================================
Begin MD step = 1
====================================
outcoor: Atomic coordinates (Ang):
0.00000000 0.00000000 0.00000000 1 1 O
0.75700000 0.58600000 0.00000000 2 2 H
-0.75700000 0.58600000 0.00000000 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 1
Initializing Density Matrix...
DM filled with atomic data:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 8
3 1: 9 7: 25 8: 20
4 11: 25 1: 6 9: 20
5 10: 25 7: 25 1: 7
6 1: 10 1: 6 9: 20
7 10: 25 7: 25 8: 20
8 1: 10 1: 6 1: 8
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5165
stepf: Fermi-Dirac step function
siesta: Program's energy decomposition (eV):
siesta: Ebs = -82.119669
siesta: Eions = 815.854478
siesta: Ena = 175.155695
siesta: Ekin = 377.531314
siesta: Enl = -69.272321
siesta: Eso = 0.000000
siesta: Edftu = 0.000000
siesta: DEna = -17.548253
siesta: DUscf = 2.107478
siesta: DUext = 0.000000
siesta: Exc = -117.110096
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
siesta: Emolmec = 0.000000
siesta: Ekinion = 0.000000
siesta: Eharris = -466.820729
siesta: Etot = -464.990661
siesta: FreeEng = -464.990661
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -466.820729 -464.990661 -464.990661 1.433758 -4.421566 7.362816
timer: Routine,Calls,Time,% = IterSCF 1 0.021 1.60
scf: 2 -466.222677 -465.720515 -465.720515 0.059267 -3.209848 2.873260
scf: 3 -465.834534 -465.817252 -465.817252 0.028397 -2.390871 0.344099
scf: 4 -465.822842 -465.820237 -465.820237 0.010402 -2.315513 0.265656
scf: 5 -465.822394 -465.821750 -465.821750 0.021596 -2.104162 0.064327
scf: 6 -465.821894 -465.821832 -465.821832 0.000473 -2.074057 0.029944
scf: 7 -465.821907 -465.821875 -465.821875 0.000931 -2.076615 0.020268
scf: 8 -465.821906 -465.821892 -465.821892 0.000897 -2.081282 0.012963
scf: 9 -465.821896 -465.821895 -465.821895 0.000620 -2.087336 0.005007
scf: 10 -465.821894 -465.821895 -465.821895 0.000099 -2.089924 0.002495
scf: 11 -465.821895 -465.821895 -465.821895 0.000039 -2.090352 0.001641
scf: 12 -465.821895 -465.821895 -465.821895 0.000042 -2.090515 0.000723
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000415343
max |H_out - H_in| (eV) : 0.0007228882
SCF cycle converged after 12 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: 3 23
siesta: E_KS(eV) = -465.8219
siesta: E_KS - E_eggbox = -465.8219
siesta: Atomic forces (eV/Ang):
1 0.000000 -0.692488 0.000000
2 0.665998 0.319146 -0.000000
3 -0.665998 0.319146 -0.000000
----------------------------------------
Tot -0.000000 -0.054197 0.000000
----------------------------------------
Max 0.692488
Res 0.417713 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.692488 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -4.36 -2.33 -1.07 -0.00 0.08 0.36
(Free)E + p*V (eV/cell) -465.1609
Target enthalpy (eV/cell) -465.8219
siesta: Stress tensor (static) (eV/Ang**3):
-0.002568 0.000000 0.000000
-0.000000 -0.001104 0.000000
-0.000000 0.000000 -0.000417
siesta: Pressure (static): 2.18394413 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.002718 0.000223 0.000048
0.000223 -0.001456 -0.000003
0.000048 -0.000003 -0.000667
siesta: Pressure (total): 2.58550296 kBar
siesta: Temp_ion = 600.000 K
====================================
Begin MD step = 2
====================================
outcoor: Atomic coordinates (Ang):
0.00019082 -0.00042428 0.00038907 1 1 O
0.75258336 0.59326734 -0.00010629 2 2 H
-0.75560632 0.58544359 -0.00605717 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 2
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 8
3 1: 9 7: 25 8: 20
4 11: 25 1: 6 9: 20
5 10: 25 7: 25 1: 7
6 1: 10 1: 6 9: 20
7 10: 25 7: 25 8: 20
8 1: 10 1: 6 1: 8
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5155
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.816427 -465.820181 -465.820181 0.005385 -2.111993 0.037620
scf: 2 -465.820026 -465.820165 -465.820165 0.001400 -2.135079 0.054200
scf: 3 -465.820268 -465.820241 -465.820241 0.000823 -2.121472 0.003760
scf: 4 -465.820243 -465.820242 -465.820242 0.000040 -2.121462 0.002010
scf: 5 -465.820243 -465.820243 -465.820243 0.000061 -2.121522 0.000704
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000609123
max |H_out - H_in| (eV) : 0.0007043356
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: 3 23
siesta: E_KS(eV) = -465.8202
siesta: Atomic forces (eV/Ang):
1 0.095186 -0.645321 -0.005307
2 0.653330 0.267011 0.001260
3 -0.751421 0.332279 -0.006813
----------------------------------------
Tot -0.002905 -0.046031 -0.010861
----------------------------------------
Max 0.751421
Res 0.421473 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.751421 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -4.57 -2.24 -1.07 0.01 0.06 0.56
(Free)E + p*V (eV/cell) -465.1489
Target enthalpy (eV/cell) -465.8202
siesta: Stress tensor (static) (eV/Ang**3):
-0.002699 0.000124 -0.000011
0.000124 -0.001048 0.000006
-0.000013 0.000006 -0.000417
siesta: Pressure (static): 2.22442332 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.002850 0.000348 0.000037
0.000347 -0.001400 0.000003
0.000035 0.000004 -0.000667
siesta: Pressure (total): 2.62598215 kBar
siesta: Temp_ion = 593.670 K
====================================
Begin MD step = 3
====================================
outcoor: Atomic coordinates (Ang):
0.00038393 -0.00086401 0.00077801 1 1 O
0.74841457 0.60063598 -0.00021211 2 2 H
-0.75449770 0.58501324 -0.01211693 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 3
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 8
3 1: 9 7: 25 8: 20
4 11: 25 1: 6 9: 20
5 10: 25 7: 25 1: 7
6 1: 10 1: 6 9: 20
7 10: 25 7: 25 8: 20
8 1: 10 1: 6 1: 8
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5157
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.818370 -465.818576 -465.818576 0.005419 -2.142786 0.042838
scf: 2 -465.818357 -465.818545 -465.818545 0.001629 -2.169296 0.063249
scf: 3 -465.818677 -465.818642 -465.818642 0.000965 -2.153498 0.004086
scf: 4 -465.818645 -465.818643 -465.818643 0.000042 -2.153554 0.002206
scf: 5 -465.818645 -465.818644 -465.818644 0.000063 -2.153702 0.000661
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000633661
max |H_out - H_in| (eV) : 0.0006609259
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: 3 23
siesta: E_KS(eV) = -465.8186
siesta: Atomic forces (eV/Ang):
1 0.188648 -0.577837 -0.010141
2 0.627572 0.205217 0.002848
3 -0.821685 0.335052 -0.013557
----------------------------------------
Tot -0.005465 -0.037568 -0.020851
----------------------------------------
Max 0.821685
Res 0.420735 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.821685 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -4.66 -2.12 -1.07 0.02 0.02 0.74
(Free)E + p*V (eV/cell) -465.1497
Target enthalpy (eV/cell) -465.8186
siesta: Stress tensor (static) (eV/Ang**3):
-0.002778 0.000247 -0.000025
0.000247 -0.000960 0.000012
-0.000026 0.000012 -0.000417
siesta: Pressure (static): 2.21917654 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.002910 0.000460 0.000013
0.000460 -0.001323 0.000015
0.000012 0.000015 -0.000667
siesta: Pressure (total): 2.61649890 kBar
siesta: Temp_ion = 587.525 K
====================================
Begin MD step = 4
====================================
outcoor: Atomic coordinates (Ang):
0.00058155 -0.00131758 0.00116671 1 1 O
0.74448386 0.60808247 -0.00031684 2 2 H
-0.75370080 0.58471000 -0.01818183 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 4
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 8
3 1: 9 7: 25 8: 20
4 11: 25 1: 6 9: 20
5 10: 25 7: 25 1: 7
6 1: 10 1: 6 9: 20
7 10: 25 7: 25 8: 20
8 1: 10 1: 6 1: 8
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5142
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.820425 -465.817046 -465.817046 0.005478 -2.174308 0.048300
scf: 2 -465.816746 -465.816994 -465.816994 0.001854 -2.204200 0.072884
scf: 3 -465.817162 -465.817118 -465.817118 0.001108 -2.186186 0.004326
scf: 4 -465.817121 -465.817120 -465.817120 0.000043 -2.186298 0.002361
scf: 5 -465.817121 -465.817121 -465.817121 0.000066 -2.186524 0.000657
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000661789
max |H_out - H_in| (eV) : 0.0006574628
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: 3 23
siesta: E_KS(eV) = -465.8171
siesta: Atomic forces (eV/Ang):
1 0.277221 -0.489565 -0.015329
2 0.589580 0.134809 0.005051
3 -0.874471 0.326442 -0.020353
----------------------------------------
Tot -0.007671 -0.028314 -0.030632
----------------------------------------
Max 0.874471
Res 0.415564 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.874471 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -4.67 -1.94 -1.07 0.04 -0.02 0.91
(Free)E + p*V (eV/cell) -465.1625
Target enthalpy (eV/cell) -465.8171
siesta: Stress tensor (static) (eV/Ang**3):
-0.002802 0.000365 -0.000039
0.000365 -0.000840 0.000017
-0.000041 0.000018 -0.000417
siesta: Pressure (static): 2.16755911 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.002916 0.000568 -0.000013
0.000567 -0.001212 0.000026
-0.000015 0.000026 -0.000667
siesta: Pressure (total): 2.56076871 kBar
siesta: Temp_ion = 581.660 K
====================================
Begin MD step = 5
====================================
outcoor: Atomic coordinates (Ang):
0.00078581 -0.00178287 0.00155504 1 1 O
0.74077682 0.61558010 -0.00041966 2 2 H
-0.75323565 0.58453060 -0.02425445 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 5
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 8
3 1: 9 7: 25 8: 20
4 11: 25 1: 6 9: 20
5 10: 25 7: 25 1: 7
6 1: 10 1: 6 9: 20
7 10: 25 7: 25 8: 20
8 1: 10 1: 6 1: 8
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5148
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.822505 -465.815584 -465.815584 0.005536 -2.206361 0.053481
scf: 2 -465.815190 -465.815505 -465.815505 0.002068 -2.239444 0.082159
scf: 3 -465.815719 -465.815664 -465.815664 0.001246 -2.219332 0.004454
scf: 4 -465.815667 -465.815666 -465.815666 0.000044 -2.219493 0.002451
scf: 5 -465.815667 -465.815667 -465.815667 0.000069 -2.219790 0.000667
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000685652
max |H_out - H_in| (eV) : 0.0006665344
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: 3 23
siesta: E_KS(eV) = -465.8157
siesta: Atomic forces (eV/Ang):
1 0.357351 -0.381728 -0.021336
2 0.541476 0.056758 0.007843
3 -0.908865 0.305859 -0.026716
----------------------------------------
Tot -0.010038 -0.019110 -0.040209
----------------------------------------
Max 0.908865
Res 0.406974 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.908865 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -4.61 -1.71 -1.07 0.06 -0.07 1.07
(Free)E + p*V (eV/cell) -465.1862
Target enthalpy (eV/cell) -465.8157
siesta: Stress tensor (static) (eV/Ang**3):
-0.002776 0.000473 -0.000055
0.000473 -0.000689 0.000022
-0.000057 0.000022 -0.000417
siesta: Pressure (static): 2.07290364 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.002875 0.000666 -0.000041
0.000666 -0.001067 0.000035
-0.000043 0.000036 -0.000668
siesta: Pressure (total): 2.46218793 kBar
siesta: Temp_ion = 576.057 K
====================================
Begin MD step = 6
====================================
outcoor: Atomic coordinates (Ang):
0.00099863 -0.00225730 0.00194286 1 1 O
0.73727520 0.62309927 -0.00051950 2 2 H
-0.75311530 0.58446723 -0.03033721 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 6
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 8
3 1: 9 7: 25 8: 20
4 11: 25 1: 6 9: 20
5 10: 25 7: 25 1: 7
6 1: 10 1: 6 9: 20
7 10: 25 7: 25 8: 20
8 1: 10 1: 6 1: 8
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5157
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.824488 -465.814152 -465.814152 0.005593 -2.238780 0.058254
scf: 2 -465.813675 -465.814061 -465.814061 0.002266 -2.274780 0.090906
scf: 3 -465.814305 -465.814240 -465.814240 0.001374 -2.252739 0.004488
scf: 4 -465.814242 -465.814241 -465.814241 0.000044 -2.252940 0.002485
scf: 5 -465.814243 -465.814242 -465.814242 0.000071 -2.253301 0.000685
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000707186
max |H_out - H_in| (eV) : 0.0006854927
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: 3 23
siesta: E_KS(eV) = -465.8142
siesta: Atomic forces (eV/Ang):
1 0.427546 -0.255523 -0.028495
2 0.485153 -0.027808 0.011183
3 -0.924359 0.273262 -0.032175
----------------------------------------
Tot -0.011660 -0.010069 -0.049487
----------------------------------------
Max 0.924359
Res 0.396557 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.924359 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -4.46 -1.43 -1.07 0.07 -0.11 1.21
(Free)E + p*V (eV/cell) -465.2211
Target enthalpy (eV/cell) -465.8142
siesta: Stress tensor (static) (eV/Ang**3):
-0.002698 0.000570 -0.000071
0.000570 -0.000507 0.000024
-0.000073 0.000024 -0.000418
siesta: Pressure (static): 1.93467501 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.002786 0.000754 -0.000070
0.000753 -0.000890 0.000043
-0.000072 0.000043 -0.000669
siesta: Pressure (total): 2.32020994 kBar
siesta: Temp_ion = 570.578 K
====================================
Begin MD step = 7
====================================
outcoor: Atomic coordinates (Ang):
0.00122168 -0.00273785 0.00233000 1 1 O
0.73395763 0.63060788 -0.00061510 2 2 H
-0.75334561 0.58450753 -0.03643217 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 7
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 8
3 1: 9 7: 25 8: 20
4 11: 25 1: 6 9: 20
5 10: 25 7: 25 1: 7
6 1: 10 1: 6 9: 20
7 10: 25 7: 25 8: 20
8 1: 10 1: 6 1: 8
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5159
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.826246 -465.812696 -465.812696 0.005646 -2.271391 0.062517
scf: 2 -465.812123 -465.812581 -465.812581 0.002445 -2.309972 0.098920
scf: 3 -465.812867 -465.812791 -465.812791 0.001491 -2.286210 0.004446
scf: 4 -465.812793 -465.812792 -465.812792 0.000045 -2.286444 0.002473
scf: 5 -465.812794 -465.812793 -465.812793 0.000073 -2.286860 0.000720
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000727731
max |H_out - H_in| (eV) : 0.0007199451
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: 3 23
siesta: E_KS(eV) = -465.8128
siesta: Atomic forces (eV/Ang):
1 0.484837 -0.112395 -0.037547
2 0.422663 -0.117614 0.015030
3 -0.921334 0.228886 -0.036337
----------------------------------------
Tot -0.013834 -0.001123 -0.058854
----------------------------------------
Max 0.921334
Res 0.386491 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.921334 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -4.26 -1.09 -1.07 0.08 -0.16 1.32
(Free)E + p*V (eV/cell) -465.2652
Target enthalpy (eV/cell) -465.8128
siesta: Stress tensor (static) (eV/Ang**3):
-0.002578 0.000653 -0.000085
0.000653 -0.000299 0.000024
-0.000087 0.000024 -0.000419
siesta: Pressure (static): 1.75998393 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.002657 0.000827 -0.000098
0.000827 -0.000683 0.000047
-0.000100 0.000047 -0.000671
siesta: Pressure (total): 2.14185153 kBar
siesta: Temp_ion = 564.978 K
====================================
Begin MD step = 8
====================================
outcoor: Atomic coordinates (Ang):
0.00145635 -0.00322110 0.00271624 1 1 O
0.73080041 0.63807188 -0.00070500 2 2 H
-0.75392545 0.58463466 -0.04254092 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 8
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 8
3 1: 9 7: 25 8: 20
4 11: 25 1: 6 9: 20
5 10: 25 7: 25 1: 7
6 1: 10 1: 6 9: 20
7 10: 25 7: 25 8: 20
8 1: 10 1: 6 1: 8
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5148
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.827623 -465.811135 -465.811135 0.005697 -2.304019 0.066179
scf: 2 -465.810470 -465.810996 -465.810996 0.002600 -2.344794 0.106018
scf: 3 -465.811323 -465.811236 -465.811236 0.001593 -2.319551 0.004336
scf: 4 -465.811238 -465.811237 -465.811237 0.000046 -2.319812 0.002420
scf: 5 -465.811239 -465.811238 -465.811238 0.000075 -2.320274 0.000746
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000748213
max |H_out - H_in| (eV) : 0.0007455693
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: 3 23
siesta: E_KS(eV) = -465.8112
siesta: Atomic forces (eV/Ang):
1 0.528754 0.044583 -0.048470
2 0.355975 -0.211275 0.019307
3 -0.900191 0.173350 -0.038840
----------------------------------------
Tot -0.015462 0.006657 -0.068003
----------------------------------------
Max 0.900191
Res 0.379700 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.900191 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.99 -0.72 -1.08 0.08 -0.20 1.42
(Free)E + p*V (eV/cell) -465.3180
Target enthalpy (eV/cell) -465.8112
siesta: Stress tensor (static) (eV/Ang**3):
-0.002418 0.000719 -0.000098
0.000719 -0.000067 0.000022
-0.000100 0.000022 -0.000420
siesta: Pressure (static): 1.55127875 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.002491 0.000886 -0.000125
0.000885 -0.000449 0.000048
-0.000127 0.000049 -0.000673
siesta: Pressure (total): 1.92939855 kBar
siesta: Temp_ion = 558.944 K
====================================
Begin MD step = 9
====================================
outcoor: Atomic coordinates (Ang):
0.00170368 -0.00370328 0.00310132 1 1 O
0.72777823 0.64545572 -0.00078757 2 2 H
-0.75484680 0.58482756 -0.04866440 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 9
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 8
3 1: 9 7: 25 8: 20
4 11: 25 1: 6 9: 20
5 10: 25 7: 25 1: 7
6 1: 10 1: 6 9: 20
7 10: 25 7: 25 8: 20
8 1: 10 1: 6 1: 8
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5156
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.828465 -465.809378 -465.809378 0.005743 -2.336487 0.069145
scf: 2 -465.808628 -465.809217 -465.809217 0.002728 -2.379010 0.112021
scf: 3 -465.809581 -465.809484 -465.809484 0.001679 -2.352565 0.004172
scf: 4 -465.809487 -465.809486 -465.809486 0.000046 -2.352846 0.002335
scf: 5 -465.809487 -465.809486 -465.809486 0.000077 -2.353345 0.000762
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000769218
max |H_out - H_in| (eV) : 0.0007618424
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: 3 23
siesta: E_KS(eV) = -465.8095
siesta: Atomic forces (eV/Ang):
1 0.557694 0.213138 -0.061641
2 0.287744 -0.307150 0.023970
3 -0.861960 0.107623 -0.039323
----------------------------------------
Tot -0.016522 0.013611 -0.076993
----------------------------------------
Max 0.861960
Res 0.379190 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.861960 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.68 -0.31 -1.08 0.07 -0.24 1.48
(Free)E + p*V (eV/cell) -465.3777
Target enthalpy (eV/cell) -465.8095
siesta: Stress tensor (static) (eV/Ang**3):
-0.002227 0.000767 -0.000108
0.000767 0.000185 0.000016
-0.000110 0.000016 -0.000420
siesta: Pressure (static): 1.31503237 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.002297 0.000926 -0.000148
0.000926 -0.000191 0.000045
-0.000150 0.000045 -0.000674
siesta: Pressure (total): 1.68911367 kBar
siesta: Temp_ion = 552.124 K
====================================
Begin MD step = 10
====================================
outcoor: Atomic coordinates (Ang):
0.00196437 -0.00418035 0.00348492 1 1 O
0.72486521 0.65272304 -0.00086105 2 2 H
-0.75609514 0.58506128 -0.05480281 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 10
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 8
3 1: 9 7: 25 8: 20
4 11: 25 1: 6 9: 20
5 10: 25 7: 25 1: 7
6 1: 10 1: 6 9: 20
7 10: 25 7: 25 8: 20
8 1: 10 1: 6 1: 8
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5160
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.828612 -465.807322 -465.807322 0.005784 -2.368610 0.071337
scf: 2 -465.806501 -465.807142 -465.807142 0.002825 -2.412395 0.116778
scf: 3 -465.807536 -465.807432 -465.807432 0.001746 -2.385053 0.003963
scf: 4 -465.807434 -465.807433 -465.807433 0.000047 -2.385347 0.002222
scf: 5 -465.807435 -465.807434 -465.807434 0.000079 -2.385875 0.000768
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000790960
max |H_out - H_in| (eV) : 0.0007684553
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: 3 23
siesta: E_KS(eV) = -465.8074
siesta: Atomic forces (eV/Ang):
1 0.572288 0.390264 -0.077252
2 0.218588 -0.403542 0.028940
3 -0.808529 0.033082 -0.037612
----------------------------------------
Tot -0.017653 0.019804 -0.085924
----------------------------------------
Max 0.808529
Res 0.387797 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.808529 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.33 0.14 -1.08 0.06 -0.27 1.52
(Free)E + p*V (eV/cell) -465.4437
Target enthalpy (eV/cell) -465.8074
siesta: Stress tensor (static) (eV/Ang**3):
-0.002006 0.000797 -0.000115
0.000797 0.000454 0.000006
-0.000117 0.000006 -0.000421
siesta: Pressure (static): 1.05343383 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.002076 0.000950 -0.000169
0.000949 0.000088 0.000037
-0.000171 0.000037 -0.000676
siesta: Pressure (total): 1.42295126 kBar
siesta: Temp_ion = 544.184 K
====================================
Begin MD step = 11
====================================
outcoor: Atomic coordinates (Ang):
0.00223876 -0.00464808 0.00386667 1 1 O
0.72203511 0.65983728 -0.00092356 2 2 H
-0.75765021 0.58530755 -0.06095548 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 11
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 8
3 1: 9 7: 25 8: 20
4 11: 25 1: 6 9: 20
5 10: 25 7: 25 1: 7
6 1: 10 1: 6 9: 20
7 10: 25 7: 25 8: 20
8 1: 10 1: 6 1: 8
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5160
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.827955 -465.804903 -465.804903 0.005820 -2.400206 0.072693
scf: 2 -465.804027 -465.804708 -465.804708 0.002887 -2.444730 0.120153
scf: 3 -465.805125 -465.805015 -465.805015 0.001792 -2.416822 0.003718
scf: 4 -465.805017 -465.805016 -465.805016 0.000048 -2.417122 0.002087
scf: 5 -465.805017 -465.805017 -465.805017 0.000081 -2.417670 0.000765
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000813554
max |H_out - H_in| (eV) : 0.0007652749
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: 3 23
siesta: E_KS(eV) = -465.8050
siesta: Atomic forces (eV/Ang):
1 0.572260 0.572324 -0.095260
2 0.150856 -0.498730 0.034146
3 -0.741443 -0.048750 -0.033528
----------------------------------------
Tot -0.018327 0.024844 -0.094642
----------------------------------------
Max 0.741443
Res 0.406886 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.741443 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -2.94 0.61 -1.08 0.04 -0.30 1.53
(Free)E + p*V (eV/cell) -465.5142
Target enthalpy (eV/cell) -465.8050
siesta: Stress tensor (static) (eV/Ang**3):
-0.001763 0.000808 -0.000119
0.000808 0.000735 -0.000008
-0.000120 -0.000008 -0.000420
siesta: Pressure (static): 0.77347879 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.001835 0.000955 -0.000185
0.000955 0.000382 0.000023
-0.000187 0.000023 -0.000677
siesta: Pressure (total): 1.13768208 kBar
siesta: Temp_ion = 534.844 K
====================================
Begin MD step = 12
====================================
outcoor: Atomic coordinates (Ang):
0.00252685 -0.00510210 0.00424614 1 1 O
0.71926225 0.66676230 -0.00097310 2 2 H
-0.75948657 0.58553533 -0.06712086 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 12
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 8
3 1: 9 7: 25 8: 20
4 11: 25 1: 6 9: 20
5 10: 25 7: 25 1: 7
6 1: 10 1: 6 9: 20
7 10: 25 7: 25 8: 20
8 1: 10 1: 6 1: 8
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5162
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.826408 -465.802068 -465.802068 0.005850 -2.431079 0.073161
scf: 2 -465.801165 -465.801868 -465.801868 0.002914 -2.475795 0.122029
scf: 3 -465.802293 -465.802179 -465.802179 0.001815 -2.447669 0.003446
scf: 4 -465.802182 -465.802181 -465.802181 0.000048 -2.447971 0.001936
scf: 5 -465.802182 -465.802181 -465.802181 0.000084 -2.448529 0.000752
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000836940
max |H_out - H_in| (eV) : 0.0007523455
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: 3 23
siesta: E_KS(eV) = -465.8022
siesta: Atomic forces (eV/Ang):
1 0.558659 0.756315 -0.115186
2 0.085976 -0.591018 0.039513
3 -0.662915 -0.136258 -0.027047
----------------------------------------
Tot -0.018280 0.029038 -0.102720
----------------------------------------
Max 0.756315
Res 0.436449 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.756315 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -2.53 1.10 -1.08 0.01 -0.32 1.51
(Free)E + p*V (eV/cell) -465.5882
Target enthalpy (eV/cell) -465.8022
siesta: Stress tensor (static) (eV/Ang**3):
-0.001499 0.000801 -0.000118
0.000801 0.001022 -0.000025
-0.000119 -0.000025 -0.000419
siesta: Pressure (static): 0.47908955 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.001576 0.000942 -0.000196
0.000942 0.000685 0.000005
-0.000198 0.000005 -0.000676
siesta: Pressure (total): 0.83704156 kBar
siesta: Temp_ion = 523.909 K
====================================
Begin MD step = 13
====================================
outcoor: Atomic coordinates (Ang):
0.00282832 -0.00553801 0.00462286 1 1 O
0.71652200 0.67346312 -0.00100766 2 2 H
-0.76157441 0.58571142 -0.07329651 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 13
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 10: 25 7: 25 1: 8
2 1: 9 7: 25 1: 7
3 11: 25 1: 6 9: 20
4 11: 25 1: 6 1: 8
5 1: 10 1: 6 9: 20
6 1: 10 1: 6 1: 8
7 10: 25 7: 25 9: 20
8 1: 9 7: 25 8: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5158
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.823934 -465.798801 -465.798801 0.005874 -2.461036 0.072715
scf: 2 -465.797889 -465.798598 -465.798598 0.002902 -2.505386 0.122330
scf: 3 -465.799030 -465.798917 -465.798917 0.001815 -2.477399 0.003155
scf: 4 -465.798919 -465.798918 -465.798918 0.000049 -2.477697 0.001774
scf: 5 -465.798919 -465.798918 -465.798918 0.000086 -2.478257 0.000730
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000860883
max |H_out - H_in| (eV) : 0.0007303893
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: 3 23
siesta: E_KS(eV) = -465.7989
siesta: Atomic forces (eV/Ang):
1 0.531276 0.938771 -0.137353
2 0.025241 -0.678896 0.044988
3 -0.575759 -0.227602 -0.018238
----------------------------------------
Tot -0.019242 0.032272 -0.110603
----------------------------------------
Max 0.938771
Res 0.474881 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.938771 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -2.11 1.59 -1.08 -0.03 -0.33 1.46
(Free)E + p*V (eV/cell) -465.6630
Target enthalpy (eV/cell) -465.7989
siesta: Stress tensor (static) (eV/Ang**3):
-0.001232 0.000776 -0.000113
0.000776 0.001310 -0.000045
-0.000114 -0.000045 -0.000417
siesta: Pressure (static): 0.18102095 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.001314 0.000911 -0.000202
0.000911 0.000993 -0.000018
-0.000204 -0.000018 -0.000674
siesta: Pressure (total): 0.53165483 kBar
siesta: Temp_ion = 511.306 K
====================================
Begin MD step = 14
====================================
outcoor: Atomic coordinates (Ang):
0.00314252 -0.00595143 0.00499628 1 1 O
0.71379133 0.67990638 -0.00102515 2 2 H
-0.76388068 0.58580116 -0.07947908 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 14
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 10: 25 7: 25 1: 8
2 1: 9 7: 25 1: 7
3 11: 25 1: 6 9: 20
4 11: 25 1: 6 1: 8
5 1: 10 1: 6 9: 20
6 1: 10 1: 6 1: 8
7 10: 25 7: 25 9: 20
8 1: 9 7: 25 8: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5158
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.820558 -465.795135 -465.795135 0.005891 -2.489876 0.071339
scf: 2 -465.794227 -465.794922 -465.794922 0.002851 -2.533297 0.120993
scf: 3 -465.795351 -465.795240 -465.795240 0.001789 -2.505813 0.003006
scf: 4 -465.795242 -465.795241 -465.795241 0.000050 -2.506101 0.001746
scf: 5 -465.795242 -465.795242 -465.795242 0.000088 -2.506652 0.000700
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000884347
max |H_out - H_in| (eV) : 0.0006997261
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: 3 23
siesta: E_KS(eV) = -465.7952
siesta: Atomic forces (eV/Ang):
1 0.492001 1.116680 -0.161843
2 -0.030291 -0.760960 0.050512
3 -0.481563 -0.321035 -0.007178
----------------------------------------
Tot -0.019853 0.034685 -0.118509
----------------------------------------
Max 1.116680
Res 0.519912 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 1.116680 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -1.68 2.08 -1.08 -0.08 -0.33 1.38
(Free)E + p*V (eV/cell) -465.7378
Target enthalpy (eV/cell) -465.7952
siesta: Stress tensor (static) (eV/Ang**3):
-0.000959 0.000734 -0.000103
0.000734 0.001593 -0.000070
-0.000105 -0.000070 -0.000414
siesta: Pressure (static): -0.11733489 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.001048 0.000864 -0.000202
0.000863 0.001299 -0.000047
-0.000204 -0.000047 -0.000672
siesta: Pressure (total): 0.22486389 kBar
siesta: Temp_ion = 497.089 K
====================================
Begin MD step = 15
====================================
outcoor: Atomic coordinates (Ang):
0.00346850 -0.00633812 0.00536583 1 1 O
0.71104917 0.68606096 -0.00102348 2 2 H
-0.76636963 0.58576911 -0.08566438 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 15
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 10: 25 7: 25 1: 8
2 1: 9 7: 25 1: 7
3 11: 25 1: 6 1: 12
4 11: 25 1: 6 13: 20
5 1: 10 1: 6 9: 20
6 1: 10 1: 6 1: 8
7 10: 25 7: 25 9: 20
8 1: 9 7: 25 8: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5154
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.816314 -465.791102 -465.791102 0.005900 -2.517391 0.069033
scf: 2 -465.790246 -465.790909 -465.790909 0.002759 -2.559326 0.117979
scf: 3 -465.791306 -465.791201 -465.791201 0.001738 -2.532710 0.002962
scf: 4 -465.791202 -465.791202 -465.791202 0.000051 -2.532983 0.001759
scf: 5 -465.791203 -465.791202 -465.791202 0.000091 -2.533516 0.000662
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000907306
max |H_out - H_in| (eV) : 0.0006619509
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: 3 23
siesta: E_KS(eV) = -465.7912
siesta: Atomic forces (eV/Ang):
1 0.441830 1.287286 -0.188179
2 -0.079310 -0.835948 0.056041
3 -0.383245 -0.414763 0.005803
----------------------------------------
Tot -0.020724 0.036575 -0.126335
----------------------------------------
Max 1.287286
Res 0.569103 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 1.287286 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -1.26 2.56 -1.07 -0.13 -0.32 1.28
(Free)E + p*V (eV/cell) -465.8105
Target enthalpy (eV/cell) -465.7912
siesta: Stress tensor (static) (eV/Ang**3):
-0.000692 0.000676 -0.000090
0.000676 0.001866 -0.000097
-0.000092 -0.000097 -0.000410
siesta: Pressure (static): -0.40809477 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.000787 0.000799 -0.000197
0.000799 0.001596 -0.000081
-0.000199 -0.000081 -0.000669
siesta: Pressure (total): -0.07541061 kBar
siesta: Temp_ion = 481.452 K
====================================
Begin MD step = 16
====================================
outcoor: Atomic coordinates (Ang):
0.00380505 -0.00669398 0.00573087 1 1 O
0.70827692 0.69189841 -0.00100055 2 2 H
-0.76900398 0.58557972 -0.09184747 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 16
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 10: 25 7: 25 1: 9
2 1: 9 7: 25 1: 7
3 11: 25 1: 6 1: 12
4 11: 25 1: 6 13: 20
5 1: 10 1: 6 9: 20
6 1: 10 1: 6 1: 8
7 10: 25 7: 25 10: 20
8 1: 9 7: 25 8: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5150
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.811301 -465.786787 -465.786787 0.005905 -2.543370 0.065815
scf: 2 -465.785995 -465.786608 -465.786608 0.002629 -2.583279 0.113293
scf: 3 -465.786974 -465.786877 -465.786877 0.001662 -2.557886 0.002915
scf: 4 -465.786878 -465.786878 -465.786878 0.000051 -2.558141 0.001769
scf: 5 -465.786879 -465.786878 -465.786878 0.000093 -2.558646 0.000618
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000928756
max |H_out - H_in| (eV) : 0.0006183721
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: 3 23
siesta: E_KS(eV) = -465.7869
siesta: Atomic forces (eV/Ang):
1 0.383104 1.447635 -0.215601
2 -0.121575 -0.902798 0.061472
3 -0.282922 -0.507135 0.020484
----------------------------------------
Tot -0.021394 0.037702 -0.133645
----------------------------------------
Max 1.447635
Res 0.620050 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 1.447635 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -0.85 3.01 -1.06 -0.19 -0.30 1.16
(Free)E + p*V (eV/cell) -465.8802
Target enthalpy (eV/cell) -465.7869
siesta: Stress tensor (static) (eV/Ang**3):
-0.000431 0.000605 -0.000074
0.000605 0.002124 -0.000127
-0.000076 -0.000127 -0.000406
siesta: Pressure (static): -0.68729157 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.000533 0.000721 -0.000187
0.000721 0.001880 -0.000118
-0.000189 -0.000118 -0.000664
siesta: Pressure (total): -0.36507305 kBar
siesta: Temp_ion = 464.721 K
====================================
Begin MD step = 17
====================================
outcoor: Atomic coordinates (Ang):
0.00415079 -0.00701517 0.00609075 1 1 O
0.70545855 0.69739337 -0.00095429 2 2 H
-0.77174566 0.58519793 -0.09802279 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 17
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 10: 25 7: 25 1: 9
2 1: 9 7: 25 1: 7
3 11: 25 1: 6 1: 12
4 11: 25 1: 6 13: 20
5 1: 10 1: 6 9: 20
6 1: 10 1: 6 1: 8
7 10: 25 7: 25 10: 20
8 1: 9 7: 25 8: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5157
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.805658 -465.782304 -465.782304 0.005902 -2.567614 0.061722
scf: 2 -465.781591 -465.782138 -465.782138 0.002460 -2.604980 0.106968
scf: 3 -465.782470 -465.782384 -465.782384 0.001560 -2.581151 0.002864
scf: 4 -465.782385 -465.782385 -465.782385 0.000052 -2.581384 0.001776
scf: 5 -465.782386 -465.782385 -465.782385 0.000095 -2.581854 0.000571
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000947792
max |H_out - H_in| (eV) : 0.0005705775
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: 3 23
siesta: E_KS(eV) = -465.7824
siesta: Atomic forces (eV/Ang):
1 0.316990 1.595820 -0.244320
2 -0.156118 -0.960644 0.066821
3 -0.182932 -0.596518 0.036395
----------------------------------------
Tot -0.022060 0.038658 -0.141104
----------------------------------------
Max 1.595820
Res 0.670747 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 1.595820 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -0.47 3.44 -1.06 -0.25 -0.28 1.01
(Free)E + p*V (eV/cell) -465.9455
Target enthalpy (eV/cell) -465.7824
siesta: Stress tensor (static) (eV/Ang**3):
-0.000185 0.000523 -0.000055
0.000523 0.002364 -0.000158
-0.000056 -0.000158 -0.000402
siesta: Pressure (static): -0.94922559 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.000293 0.000631 -0.000173
0.000631 0.002147 -0.000158
-0.000175 -0.000158 -0.000659
siesta: Pressure (total): -0.63820445 kBar
siesta: Temp_ion = 447.340 K
====================================
Begin MD step = 18
====================================
outcoor: Atomic coordinates (Ang):
0.00450411 -0.00729815 0.00644477 1 1 O
0.70258095 0.70252389 -0.00088269 2 2 H
-0.77455674 0.58458985 -0.10418430 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 18
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 12
3 11: 25 1: 6 13: 20
4 10: 25 7: 25 12: 20
5 10: 25 7: 25 1: 11
6 1: 10 1: 6 9: 20
7 1: 9 7: 25 8: 20
8 1: 10 1: 6 1: 8
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5152
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.799542 -465.777779 -465.777779 0.005893 -2.589914 0.056799
scf: 2 -465.777167 -465.777637 -465.777637 0.002254 -2.624252 0.099058
scf: 3 -465.777921 -465.777848 -465.777848 0.001435 -2.602313 0.002811
scf: 4 -465.777849 -465.777848 -465.777848 0.000052 -2.602521 0.001779
scf: 5 -465.777849 -465.777849 -465.777849 0.000096 -2.602948 0.000520
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000963363
max |H_out - H_in| (eV) : 0.0005203030
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: 3 23
siesta: E_KS(eV) = -465.7778
siesta: Atomic forces (eV/Ang):
1 0.244244 1.730244 -0.274173
2 -0.182636 -1.008848 0.072004
3 -0.084690 -0.681752 0.053367
----------------------------------------
Tot -0.023082 0.039645 -0.148802
----------------------------------------
Max 1.730244
Res 0.719544 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 1.730244 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -0.11 3.83 -1.04 -0.32 -0.25 0.85
(Free)E + p*V (eV/cell) -466.0066
Target enthalpy (eV/cell) -465.7778
siesta: Stress tensor (static) (eV/Ang**3):
0.000047 0.000429 -0.000032
0.000429 0.002583 -0.000191
-0.000033 -0.000191 -0.000394
siesta: Pressure (static): -1.19398292 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.000066 0.000527 -0.000153
0.000527 0.002392 -0.000202
-0.000154 -0.000202 -0.000651
siesta: Pressure (total): -0.89459372 kBar
siesta: Temp_ion = 429.838 K
====================================
Begin MD step = 19
====================================
outcoor: Atomic coordinates (Ang):
0.00486329 -0.00753969 0.00679223 1 1 O
0.69963406 0.70727168 -0.00078377 2 2 H
-0.77739994 0.58372313 -0.11032556 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 19
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 12
3 11: 25 1: 6 13: 20
4 10: 25 7: 25 13: 20
5 10: 25 7: 25 1: 12
6 1: 10 1: 6 9: 20
7 1: 9 7: 25 8: 20
8 1: 10 1: 6 1: 8
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5141
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.793155 -465.773378 -465.773378 0.005878 -2.610080 0.051107
scf: 2 -465.772876 -465.773261 -465.773261 0.002014 -2.640942 0.089660
scf: 3 -465.773495 -465.773435 -465.773435 0.001287 -2.621195 0.002754
scf: 4 -465.773436 -465.773435 -465.773435 0.000053 -2.621374 0.001778
scf: 5 -465.773436 -465.773436 -465.773436 0.000097 -2.621749 0.000469
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000974537
max |H_out - H_in| (eV) : 0.0004688341
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: 3 23
siesta: E_KS(eV) = -465.7734
siesta: Atomic forces (eV/Ang):
1 0.167116 1.848366 -0.304309
2 -0.200929 -1.046859 0.077013
3 0.009704 -0.761478 0.070813
----------------------------------------
Tot -0.024108 0.040029 -0.156483
----------------------------------------
Max 1.848366
Res 0.764792 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 1.848366 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 0.23 4.18 -1.03 -0.40 -0.21 0.67
(Free)E + p*V (eV/cell) -466.0612
Target enthalpy (eV/cell) -465.7734
siesta: Stress tensor (static) (eV/Ang**3):
0.000259 0.000328 -0.000007
0.000328 0.002774 -0.000226
-0.000008 -0.000226 -0.000387
siesta: Pressure (static): -1.41337462 kBar
siesta: Stress tensor (total) (eV/Ang**3):
0.000141 0.000416 -0.000129
0.000416 0.002608 -0.000248
-0.000130 -0.000248 -0.000641
siesta: Pressure (total): -1.12569938 kBar
siesta: Temp_ion = 412.798 K
====================================
Begin MD step = 20
====================================
outcoor: Atomic coordinates (Ang):
0.00522646 -0.00773696 0.00713241 1 1 O
0.69661095 0.71162233 -0.00065564 2 2 H
-0.78023947 0.58256753 -0.11643997 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 20
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 12
3 11: 25 1: 6 13: 20
4 10: 25 7: 25 13: 20
5 10: 25 7: 25 1: 12
6 1: 10 1: 6 9: 20
7 1: 9 7: 25 8: 20
8 1: 10 1: 6 1: 8
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5133
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.786693 -465.769250 -465.769250 0.005859 -2.627921 0.044728
scf: 2 -465.768862 -465.769160 -465.769160 0.001744 -2.654910 0.078906
scf: 3 -465.769342 -465.769295 -465.769295 0.001118 -2.637624 0.002694
scf: 4 -465.769296 -465.769296 -465.769296 0.000053 -2.637772 0.001772
scf: 5 -465.769296 -465.769296 -465.769296 0.000098 -2.638089 0.000418
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000980020
max |H_out - H_in| (eV) : 0.0004175824
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: 3 23
siesta: E_KS(eV) = -465.7693
siesta: Atomic forces (eV/Ang):
1 0.086676 1.948808 -0.334338
2 -0.210727 -1.074325 0.081824
3 0.099157 -0.834697 0.088436
----------------------------------------
Tot -0.024894 0.039786 -0.164078
----------------------------------------
Max 1.948808
Res 0.805315 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 1.948808 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 0.52 4.47 -1.01 -0.47 -0.17 0.47
(Free)E + p*V (eV/cell) -466.1091
Target enthalpy (eV/cell) -465.7693
siesta: Stress tensor (static) (eV/Ang**3):
0.000449 0.000220 0.000020
0.000220 0.002936 -0.000260
0.000019 -0.000260 -0.000379
siesta: Pressure (static): -1.60544029 kBar
siesta: Stress tensor (total) (eV/Ang**3):
0.000327 0.000296 -0.000102
0.000296 0.002792 -0.000295
-0.000103 -0.000295 -0.000631
siesta: Pressure (total): -1.32916947 kBar
siesta: Temp_ion = 396.830 K
siesta: Program's energy decomposition (eV):
siesta: Ebs = -102.634166
siesta: Eions = 815.854478
siesta: Ena = 174.892324
siesta: Ekin = 349.711175
siesta: Enl = -60.959680
siesta: Eso = 0.000000
siesta: Edftu = 0.000000
siesta: DEna = -1.911074
siesta: DUscf = 0.725809
siesta: DUext = 0.000000
siesta: Exc = -112.373371
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
siesta: Emolmec = 0.000000
siesta: Ekinion = 0.102584
siesta: Eharris = -465.666712
siesta: Etot = -465.666712
siesta: FreeEng = -465.666712
siesta: Final energy (eV):
siesta: Band Struct. = -102.634166
siesta: Kinetic = 349.711175
siesta: Hartree = 411.788122
siesta: Edftu = 0.000000
siesta: Eso = 0.000000
siesta: Ext. field = 0.000000
siesta: Exch.-corr. = -112.373371
siesta: Ion-electron = -1128.692329
siesta: Ion-ion = 13.797108
siesta: Ekinion = 0.102584
siesta: Total = -465.666712
siesta: Fermi = -2.638089
siesta: Atomic forces (eV/Ang):
siesta: 1 0.086676 1.948808 -0.334338
siesta: 2 -0.210727 -1.074325 0.081824
siesta: 3 0.099157 -0.834697 0.088436
siesta: ----------------------------------------
siesta: Tot -0.024894 0.039786 -0.164078
siesta: Stress tensor (static) (eV/Ang**3):
siesta: 0.000449 0.000220 0.000020
siesta: 0.000220 0.002936 -0.000260
siesta: 0.000019 -0.000260 -0.000379
siesta: Cell volume = 409.600000 Ang**3
siesta: Pressure (static):
siesta: Solid Molecule Units
siesta: -0.00001091 0.00000261 Ry/Bohr**3
siesta: -0.00100203 0.00023986 eV/Ang**3
siesta: -1.60544029 0.38430011 kBar
(Free)E+ p_basis*V_orbitals = -465.184129
(Free)Eharris+ p_basis*V_orbitals = -465.184129
siesta: Electric dipole (a.u.) = -0.042630 0.591839 -0.059918
siesta: Electric dipole (Debye) = -0.108354 1.504305 -0.152297
cite: Please see "h2o.bib" for an exhaustive BiBTeX file.
cite: Please clearly indicate Siesta version in published work: v4.1-b4-351
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: 22-JAN-2021 23:12:45
Job completed
Siesta Version : v4.1-b4-351
Architecture : x86_64-linux-n-62-26-19
Compiler version: GNU Fortran (GCC) 9.3.0
Compiler flags : mpifort -m64 -fPIC -O3 -march=native -ftree-vectorize -fexpensive-optimizatioons -funroll-loops -fprefetch-loop-arrays -fno-second-underscore -flto
PP flags : -I/dtu/sw/dcc/SL73/2020-aug/generic/build-tools/1.0/include -I/dtu/sw/dcc/SL773/2020-aug/generic/gcc/9.3.0/include -I/dtu/sw/dcc/SL73/2020-aug/generic/gcc/9.3.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/zlib/1.2.11/include -I/dtu/sw/dcc/SL73/2020-aug/generic/numactl/2.0.12/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/libxml2/2.9.10/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/hwloc/2.2.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/knem/1.1.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/ucx/1.8.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/openmpi/4.0.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/szip/2.1.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/hdf5/1.12.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/pnetcdf/1.12.1/include -I/dtu/sw/dcc/SL73/2020-aug/generic/gen-zlib/1.2.11/include -I/dtu/sw/dcc/SL73/2020-aug/generic/openssl/1.1.1/include -I/dtu/sw/dcc/SL73/2020-aug/generic/libssh2/1.8.2/include -I/dtu/sw/dcc/SL73/2020-aug/generic/curl/7.65.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/netcdf/4.7.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/fftw/3.3.8/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/parmetis/4.0.3/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/scalapack/2.1.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/lapack/3.9.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/blis/0.7.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/scotch/6.0.9/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/mumps/5.3.3/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/elpa/2020.05.001/include -DSIESTA__ELPA -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DCDF4 -DSIESTA__FLOOK -DNCDF -DNCDF_4 -DNCDF_PARALLEL -DTS_NOCHECKS -DSIESTA__METIS -DSIESTA__MUMPS -DSIESTA__MRRR -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/elpa/2020.05.001/include/elpa
Libraries : libncdf.a libfdict.a -lnetcdff -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lz -lzmuumps -lmumps_common -lesmumps -lscotch -lscotcherr -lpord -lparmetis -lmetis -lelpa -lscalapack -llapack -lblis -L/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/lib -Wl,-rpath=/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/lib -lflookall -ldl -flto -fuse-linker-plugin -lmetis
PARALLEL version
NetCDF support
NetCDF-4 support
NetCDF-4 MPI-IO support
METIS ordering support
Lua support
* Running on 8 nodes in parallel
>> Start of run: 22-JAN-2021 23:12:46
***********************
* WELCOME TO SIESTA *
***********************
reinit: Reading from standard input
reinit: Dumped input in INPUT_TMP.98208
************************** Dump of input data file ****************************
SystemName Water molecule -- md verlet
SystemLabel h2o
NumberOfAtoms 3
NumberOfSpecies 2
MeshCutoff 100 Ry
%block ChemicalSpeciesLabel
1 8 O # Species index, atomic number, species label
2 1 H
%endblock ChemicalSpeciesLabel
LatticeConstant 8.0 Ang
%block LatticeVectors
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 0.8
%endblock LatticeVectors
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
Solution.Method diagon
MeshCutoff 100 Ry
WriteCoorStep .true.
WriteForces .true.
WriteMDHistory .true.
MD.UseSaveXV T
MD.TypeOfRun Verlet
MD.InitialTemperature 600 K
MD.Initial.Time.Step 1
MD.Final.Time.Step 20
MD.Length.Time.Step 0.2 fs
************************** End of input data file *****************************
reinit: -----------------------------------------------------------------------
reinit: System Name: Water molecule -- md verlet
reinit: -----------------------------------------------------------------------
reinit: System Label: h2o
reinit: -----------------------------------------------------------------------
initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Species number: 1 Atomic number: 8 Label: O
Species number: 2 Atomic number: 1 Label: H
Ground state valence configuration: 2s02 2p04
Reading pseudopotential information in formatted form from O.psf
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
Valence configuration for pseudopotential generation:
1s( 1.00) rc: 1.25
2p( 0.00) rc: 1.25
3d( 0.00) rc: 1.25
4f( 0.00) rc: 1.25
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.
===============================================================================
O Z= 8 Mass= 16.000 Charge= 0.17977+309
Lmxo=1 Lmxkb= 3 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=2
i=1 nzeta=2 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 0.0000
lambdas: 1.0000 1.0000
L=1 Nsemic=0 Cnfigmx=2
i=1 nzeta=2 polorb=1 (2p)
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
===============================================================================
atom: Called for O (Z = 8)
read_vps: Pseudopotential generation method:
read_vps: ATM3 Troullier-Martins
Valence charge for ps generation: 6.00000
xc_check: Exchange-correlation functional:
xc_check: Ceperley-Alder
V l=0 = -2*Zval/r beyond r= 1.1278
V l=1 = -2*Zval/r beyond r= 1.1278
V l=2 = -2*Zval/r beyond r= 1.1278
V l=3 = -2*Zval/r beyond r= 1.1138
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= 1.1278
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= 1.294105 el= -1.742414 Ekb= 9.135903 kbcos= 0.326910
l= 1 rc= 1.294105 el= -0.676589 Ekb= -8.124878 kbcos= -0.395047
l= 2 rc= 1.448233 el= 0.002386 Ekb= -2.039267 kbcos= -0.003484
l= 3 rc= 1.561052 el= 0.003508 Ekb= -0.799141 kbcos= -0.000344
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 = -1.723766
kinetic = 1.614911
potential(screened) = -3.338677
potential(ionic) = -11.304675
izeta = 2
rmatch = 2.510382
splitnorm = 0.150000
energy = -1.471299
kinetic = 2.446434
potential(screened) = -3.917732
potential(ionic) = -12.476133
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 = -0.658841
kinetic = 5.005986
potential(screened) = -5.664827
potential(ionic) = -13.452360
izeta = 2
rmatch = 2.541963
splitnorm = 0.150000
energy = -0.367441
kinetic = 7.530509
potential(screened) = -7.897949
potential(ionic) = -16.611953
POLgen: Perturbative polarization orbital with L= 2
POLgen: Polarization orbital for state 2p
izeta = 1
rc = 3.937239
energy = 2.398520
kinetic = 4.716729
potential(screened) = -2.318209
potential(ionic) = -8.603170
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: _________________________________________________________________________
===============================================================================
H Z= 1 Mass= 1.0100 Charge= 0.17977+309
Lmxo=0 Lmxkb= 2 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=1
i=1 nzeta=2 polorb=1 (1s)
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
===============================================================================
atom: Called for H (Z = 1)
read_vps: Pseudopotential generation method:
read_vps: ATM3 Troullier-Martins
Valence charge for ps generation: 1.00000
xc_check: Exchange-correlation functional:
xc_check: Ceperley-Alder
V l=0 = -2*Zval/r beyond r= 1.2343
V l=1 = -2*Zval/r beyond r= 1.2189
V l=2 = -2*Zval/r beyond r= 1.2189
All V_l potentials equal beyond r= 1.2343
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r= 1.2343
VLOCAL1: 99.0% of the norm of Vloc inside 28.493 Ry
VLOCAL1: 99.9% of the norm of Vloc inside 64.935 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.45251
atom: Maximum radius for r*vlocal+2*Zval: 1.21892
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= 1.364359 el= -0.467325 Ekb= -2.005361 kbcos= -0.336422
l= 1 rc= 1.434438 el= 0.001430 Ekb= -0.501708 kbcos= -0.021697
l= 2 rc= 1.470814 el= 0.002365 Ekb= -0.190555 kbcos= -0.002281
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 = 4.828263
energy = -0.449375
kinetic = 0.929372
potential(screened) = -1.378747
potential(ionic) = -1.915047
izeta = 2
rmatch = 3.854947
splitnorm = 0.150000
energy = -0.336153
kinetic = 1.505294
potential(screened) = -1.841447
potential(ionic) = -2.413582
POLgen: Perturbative polarization orbital with L= 1
POLgen: Polarization orbital for state 1s
izeta = 1
rc = 4.828263
energy = 0.706972
kinetic = 1.396397
potential(screened) = -0.689424
potential(ionic) = -1.169792
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: 4.828263
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 2.510
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
4.828 3.855
1.000 1.000
%endblock PAO.Basis
prinput: ----------------------------------------------------------------------
Dumping basis to NetCDF file O.ion.nc
Dumping basis to NetCDF file H.ion.nc
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
WARNING: h2o.VERLET_RESTART not found--reading only XV file and moving back 1 time step using Euler
siesta: Atomic coordinates (Bohr) and species
siesta: 0.00988 -0.01458 0.01347 1 1
siesta: 1.31633 1.34439 -0.00121 2 2
siesta: -1.47440 1.10059 -0.22001 2 3
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: 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 = 2
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 = 1000
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 = F
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 = Verlet MD run
redata: Initial MD time step = 1
redata: Final MD time step = 20
redata: Length of MD time step = 0.2000 fs
redata: Initial Temperature of MD run = 600.0000 K
redata: Perform a MD quench = F
mix.SCF: Pulay mixing = Pulay
mix.SCF: Variant = stable
mix.SCF: History steps = 2
mix.SCF: Linear mixing weight = 0.250000
mix.SCF: Mixing weight = 0.250000
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 0.2500
weight.linear 0.2500
history 2
%endblock SCF.Mixer.Pulay
Size of DM history Fstack: 1
Total number of electrons: 8.000000
Total ionic charge: 8.000000
* ProcessorY, Blocksize: 2 3
* Orbital distribution balance (max,min): 3 2
Kpoints in: 1 . Kpoints trimmed: 1
siesta: k-grid: Number of k-points = 1
siesta: k-grid: Cutoff (effective) = 3.200 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 = 3
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
ts: **************************************************************
ts: Save H and S matrices = F
ts: Save DM and EDM matrices = F
ts: Only save the overlap matrix S = F
ts: **************************************************************
************************ Begin: TS CHECKS AND WARNINGS ************************
************************ End: TS CHECKS AND WARNINGS **************************
====================================
Begin MD step = 1
====================================
outcoor: Atomic coordinates (Ang):
0.00522750 -0.00771363 0.00712840 1 1 O
0.69657098 0.71141855 -0.00064012 2 2 H
-0.78022066 0.58240920 -0.11642319 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 1
Initializing Density Matrix...
DM filled with atomic data:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 12
3 11: 25 1: 6 13: 20
4 10: 25 7: 25 13: 20
5 10: 25 7: 25 1: 12
6 1: 10 1: 6 9: 20
7 1: 9 7: 25 8: 20
8 1: 10 1: 6 1: 8
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5133
stepf: Fermi-Dirac step function
siesta: Program's energy decomposition (eV):
siesta: Ebs = -82.264876
siesta: Eions = 815.854478
siesta: Ena = 174.893053
siesta: Ekin = 371.577802
siesta: Enl = -66.805890
siesta: Eso = 0.000000
siesta: Edftu = 0.000000
siesta: DEna = -14.792749
siesta: DUscf = 1.911589
siesta: DUext = 0.000000
siesta: Exc = -115.961161
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
siesta: Emolmec = 0.000000
siesta: Ekinion = 0.000000
siesta: Eharris = -467.439257
siesta: Etot = -465.031834
siesta: FreeEng = -465.031834
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -467.439257 -465.031834 -465.031834 1.369148 -4.721235 6.832340
timer: Routine,Calls,Time,% = IterSCF 1 0.020 1.51
scf: 2 -466.126578 -465.691169 -465.691169 0.055536 -3.619916 2.524245
scf: 3 -465.778310 -465.765100 -465.765100 0.023489 -2.942223 0.377120
scf: 4 -465.770671 -465.768050 -465.768050 0.011237 -2.860531 0.279514
scf: 5 -465.770185 -465.769517 -465.769517 0.023829 -2.632443 0.051459
scf: 6 -465.769763 -465.769654 -465.769654 0.001677 -2.627348 0.032581
scf: 7 -465.769727 -465.769693 -465.769693 0.001027 -2.627075 0.017074
scf: 8 -465.769713 -465.769704 -465.769704 0.000590 -2.629402 0.011344
scf: 9 -465.769708 -465.769706 -465.769706 0.000518 -2.633348 0.004456
scf: 10 -465.769706 -465.769706 -465.769706 0.000094 -2.635292 0.002214
scf: 11 -465.769707 -465.769706 -465.769706 0.000023 -2.636738 0.001692
scf: 12 -465.769707 -465.769706 -465.769706 0.000020 -2.637047 0.000980
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000198530
max |H_out - H_in| (eV) : 0.0009803347
SCF cycle converged after 12 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: 3 23
siesta: E_KS(eV) = -465.7697
siesta: E_KS - E_eggbox = -465.7697
siesta: Atomic forces (eV/Ang):
1 0.085359 1.939331 -0.333528
2 -0.205938 -1.068491 0.081347
3 0.095667 -0.831304 0.088205
----------------------------------------
Tot -0.024911 0.039535 -0.163976
----------------------------------------
Max 1.939331
Res 0.801265 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 1.939331 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 0.50 4.48 -1.01 -0.49 -0.16 0.45
(Free)E + p*V (eV/cell) -466.1080
Target enthalpy (eV/cell) -465.7697
siesta: Stress tensor (static) (eV/Ang**3):
0.000434 0.000216 0.000019
0.000216 0.002919 -0.000259
0.000019 -0.000259 -0.000379
siesta: Pressure (static): -1.58880755 kBar
siesta: Stress tensor (total) (eV/Ang**3):
0.000310 0.000280 -0.000100
0.000280 0.002795 -0.000308
-0.000100 -0.000308 -0.000628
siesta: Pressure (total): -1.32322336 kBar
siesta: Temp_ion = 396.830 K
====================================
Begin MD step = 2
====================================
outcoor: Atomic coordinates (Ang):
0.00559273 -0.00786435 0.00746058 1 1 O
0.69346884 0.71536274 -0.00048103 2 2 H
-0.78302323 0.58093758 -0.12250409 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 2
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 12
3 11: 25 1: 6 13: 20
4 10: 25 7: 25 13: 20
5 10: 25 7: 25 1: 12
6 1: 10 1: 6 9: 20
7 1: 9 7: 25 8: 20
8 1: 10 1: 6 1: 8
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5134
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.780804 -465.765983 -465.765983 0.005855 -2.641986 0.037703
scf: 2 -465.765704 -465.765920 -465.765920 0.001429 -2.664523 0.066994
scf: 3 -465.766051 -465.766017 -465.766017 0.000922 -2.650051 0.002585
scf: 4 -465.766018 -465.766018 -465.766018 0.000053 -2.650149 0.001774
scf: 5 -465.766019 -465.766018 -465.766018 0.000098 -2.650379 0.000383
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000983573
max |H_out - H_in| (eV) : 0.0003832012
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: 3 23
siesta: E_KS(eV) = -465.7660
siesta: Atomic forces (eV/Ang):
1 0.002634 2.022374 -0.363266
2 -0.207316 -1.085304 0.086256
3 0.178986 -0.897309 0.105279
----------------------------------------
Tot -0.025697 0.039761 -0.171730
----------------------------------------
Max 2.022374
Res 0.836564 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 2.022374 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 0.77 4.69 -0.99 -0.55 -0.12 0.27
(Free)E + p*V (eV/cell) -466.1465
Target enthalpy (eV/cell) -465.7660
siesta: Stress tensor (static) (eV/Ang**3):
0.000602 0.000103 0.000047
0.000102 0.003052 -0.000293
0.000046 -0.000293 -0.000370
siesta: Pressure (static): -1.75381269 kBar
siesta: Stress tensor (total) (eV/Ang**3):
0.000478 0.000166 -0.000073
0.000166 0.002928 -0.000342
-0.000074 -0.000342 -0.000619
siesta: Pressure (total): -1.48822850 kBar
siesta: Temp_ion = 382.582 K
====================================
Begin MD step = 3
====================================
outcoor: Atomic coordinates (Ang):
0.00595803 -0.00796664 0.00778406 1 1 O
0.69028804 0.71889520 -0.00028922 2 2 H
-0.78575790 0.57912556 -0.12854505 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 3
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 12
3 11: 25 1: 6 13: 20
4 10: 25 7: 25 13: 20
5 10: 25 7: 25 1: 12
6 1: 10 1: 6 9: 20
7 1: 9 7: 25 8: 20
8 1: 10 1: 6 1: 8
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5135
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.774824 -465.762869 -465.762869 0.005807 -2.654538 0.030291
scf: 2 -465.762691 -465.762830 -465.762830 0.001129 -2.672812 0.054010
scf: 3 -465.762916 -465.762894 -465.762894 0.000729 -2.661122 0.002538
scf: 4 -465.762895 -465.762894 -465.762894 0.000053 -2.661197 0.001733
scf: 5 -465.762895 -465.762895 -465.762895 0.000096 -2.661379 0.000380
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000963897
max |H_out - H_in| (eV) : 0.0003802018
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: 3 23
siesta: E_KS(eV) = -465.7629
siesta: Atomic forces (eV/Ang):
1 -0.081429 2.085796 -0.392353
2 -0.199878 -1.091016 0.090576
3 0.254160 -0.955127 0.122050
----------------------------------------
Tot -0.027147 0.039653 -0.179726
----------------------------------------
Max 2.085796
Res 0.865470 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 2.085796 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 0.98 4.87 -0.97 -0.62 -0.07 0.06
(Free)E + p*V (eV/cell) -466.1791
Target enthalpy (eV/cell) -465.7629
siesta: Stress tensor (static) (eV/Ang**3):
0.000737 -0.000016 0.000075
-0.000016 0.003151 -0.000326
0.000074 -0.000326 -0.000360
siesta: Pressure (static): -1.88404385 kBar
siesta: Stress tensor (total) (eV/Ang**3):
0.000611 0.000035 -0.000041
0.000035 0.003043 -0.000389
-0.000042 -0.000389 -0.000606
siesta: Pressure (total): -1.62799507 kBar
siesta: Temp_ion = 370.519 K
====================================
Begin MD step = 4
====================================
outcoor: Atomic coordinates (Ang):
0.00632138 -0.00801898 0.00809814 1 1 O
0.68703142 0.72201377 -0.00006305 2 2 H
-0.78839614 0.57695119 -0.13453970 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 4
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 7: 25 1: 5 1: 6
3 7: 25 1: 5 7: 20
4 1: 6 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 6 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 12
3 1: 9 7: 25 8: 20
4 11: 25 1: 6 13: 20
5 10: 25 7: 25 1: 13
6 1: 10 1: 6 9: 20
7 1: 10 1: 6 1: 8
8 10: 25 7: 25 14: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5136
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.769327 -465.760436 -465.760436 0.005777 -2.664480 0.022417
scf: 2 -465.760340 -465.760417 -465.760417 0.000831 -2.678021 0.040226
scf: 3 -465.760465 -465.760453 -465.760453 0.000534 -2.669398 0.002392
scf: 4 -465.760454 -465.760453 -465.760453 0.000052 -2.669429 0.001680
scf: 5 -465.760454 -465.760454 -465.760454 0.000093 -2.669534 0.000377
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000927473
max |H_out - H_in| (eV) : 0.0003766835
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: 3 23
siesta: E_KS(eV) = -465.7605
siesta: Atomic forces (eV/Ang):
1 -0.165410 2.129459 -0.420043
2 -0.184118 -1.085775 0.094632
3 0.321210 -1.004325 0.138049
----------------------------------------
Tot -0.028318 0.039359 -0.187362
----------------------------------------
Max 2.129459
Res 0.887635 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 2.129459 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 1.15 5.00 -0.95 -0.70 -0.01 -0.16
(Free)E + p*V (eV/cell) -466.2038
Target enthalpy (eV/cell) -465.7605
siesta: Stress tensor (static) (eV/Ang**3):
0.000845 -0.000136 0.000103
-0.000136 0.003216 -0.000357
0.000101 -0.000357 -0.000350
siesta: Pressure (static): -1.98208068 kBar
siesta: Stress tensor (total) (eV/Ang**3):
0.000720 -0.000099 -0.000008
-0.000099 0.003119 -0.000436
-0.000009 -0.000436 -0.000592
siesta: Pressure (total): -1.73410538 kBar
siesta: Temp_ion = 361.109 K
====================================
Begin MD step = 5
====================================
outcoor: Atomic coordinates (Ang):
0.00668077 -0.00802032 0.00840216 1 1 O
0.68370495 0.72472043 0.00019902 2 2 H
-0.79091253 0.57439581 -0.14048198 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 5
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 7 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 12
3 1: 9 7: 25 8: 20
4 11: 25 1: 6 13: 20
5 10: 25 7: 25 1: 13
6 1: 10 1: 6 9: 20
7 1: 10 1: 6 1: 8
8 10: 25 7: 25 14: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5131
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.764464 -465.758782 -465.758782 0.005745 -2.671563 0.014858
scf: 2 -465.758748 -465.758778 -465.758778 0.000579 -2.680189 0.025802
scf: 3 -465.758799 -465.758794 -465.758794 0.000331 -2.674774 0.002213
scf: 4 -465.758794 -465.758794 -465.758794 0.000049 -2.674749 0.001550
scf: 5 -465.758795 -465.758794 -465.758794 0.000083 -2.674766 0.000371
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000827890
max |H_out - H_in| (eV) : 0.0003710915
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: 3 23
siesta: E_KS(eV) = -465.7588
siesta: Atomic forces (eV/Ang):
1 -0.248805 2.153510 -0.446209
2 -0.159365 -1.069405 0.098435
3 0.379227 -1.044491 0.152970
----------------------------------------
Tot -0.028943 0.039614 -0.194804
----------------------------------------
Max 2.153510
Res 0.902804 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 2.153510 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 1.28 5.06 -0.92 -0.77 0.04 -0.38
(Free)E + p*V (eV/cell) -466.2198
Target enthalpy (eV/cell) -465.7588
siesta: Stress tensor (static) (eV/Ang**3):
0.000921 -0.000259 0.000129
-0.000259 0.003247 -0.000386
0.000128 -0.000386 -0.000340
siesta: Pressure (static): -2.04494868 kBar
siesta: Stress tensor (total) (eV/Ang**3):
0.000796 -0.000236 0.000025
-0.000236 0.003157 -0.000480
0.000024 -0.000480 -0.000577
siesta: Pressure (total): -1.80327115 kBar
siesta: Temp_ion = 354.716 K
====================================
Begin MD step = 6
====================================
outcoor: Atomic coordinates (Ang):
0.00703420 -0.00797009 0.00869550 1 1 O
0.68031802 0.72702139 0.00049843 2 2 H
-0.79328506 0.57144419 -0.14636624 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 6
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 7 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 12
3 1: 9 7: 25 8: 20
4 11: 25 1: 6 13: 20
5 10: 25 7: 25 1: 13
6 1: 10 1: 6 9: 20
7 1: 10 1: 6 1: 8
8 10: 25 7: 25 14: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5122
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.760349 -465.757967 -465.757967 0.005712 -2.675708 0.010053
scf: 2 -465.757972 -465.757977 -465.757977 0.000562 -2.679296 0.010948
scf: 3 -465.757983 -465.757981 -465.757981 0.000218 -2.677167 0.001650
scf: 4 -465.757981 -465.757981 -465.757981 0.000035 -2.677074 0.001138
scf: 5 -465.757981 -465.757981 -465.757981 0.000052 -2.677020 0.000341
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000515139
max |H_out - H_in| (eV) : 0.0003408861
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: 3 23
siesta: E_KS(eV) = -465.7580
siesta: Atomic forces (eV/Ang):
1 -0.331172 2.156705 -0.470740
2 -0.126950 -1.042201 0.101920
3 0.427411 -1.075341 0.166664
----------------------------------------
Tot -0.030711 0.039163 -0.202155
----------------------------------------
Max 2.156705
Res 0.910564 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 2.156705 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 1.35 5.05 -0.90 -0.84 0.09 -0.60
(Free)E + p*V (eV/cell) -466.2271
Target enthalpy (eV/cell) -465.7580
siesta: Stress tensor (static) (eV/Ang**3):
0.000969 -0.000382 0.000154
-0.000382 0.003241 -0.000413
0.000153 -0.000413 -0.000329
siesta: Pressure (static): -2.07224449 kBar
siesta: Stress tensor (total) (eV/Ang**3):
0.000846 -0.000372 0.000057
-0.000373 0.003152 -0.000522
0.000056 -0.000522 -0.000562
siesta: Pressure (total): -1.83484591 kBar
siesta: Temp_ion = 351.583 K
====================================
Begin MD step = 7
====================================
outcoor: Atomic coordinates (Ang):
0.00737969 -0.00786822 0.00897757 1 1 O
0.67688293 0.72892697 0.00083651 2 2 H
-0.79549544 0.56808461 -0.15218726 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 7
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 7 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 12
3 1: 9 7: 25 8: 20
4 11: 25 1: 6 13: 20
5 10: 25 7: 25 1: 13
6 1: 10 1: 6 9: 20
7 1: 10 1: 6 1: 8
8 10: 25 7: 25 14: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5107
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.757083 -465.758033 -465.758033 0.005681 -2.676866 0.010052
scf: 2 -465.758039 -465.758039 -465.758039 0.000542 -2.675360 0.006013
scf: 3 -465.758042 -465.758041 -465.758041 0.000169 -2.676196 0.001181
scf: 4 -465.758041 -465.758041 -465.758041 0.000021 -2.676268 0.000841
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000205560
max |H_out - H_in| (eV) : 0.0008407716
SCF cycle converged after 4 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: 3 23
siesta: E_KS(eV) = -465.7580
siesta: Atomic forces (eV/Ang):
1 -0.409533 2.138843 -0.492447
2 -0.086969 -1.004243 0.105501
3 0.466050 -1.096827 0.178280
----------------------------------------
Tot -0.030452 0.037773 -0.208666
----------------------------------------
Max 2.138843
Res 0.910682 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 2.138843 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 1.38 4.97 -0.88 -0.90 0.13 -0.81
(Free)E + p*V (eV/cell) -466.2248
Target enthalpy (eV/cell) -465.7580
siesta: Stress tensor (static) (eV/Ang**3):
0.000981 -0.000502 0.000176
-0.000503 0.003198 -0.000436
0.000173 -0.000435 -0.000320
siesta: Pressure (static): -2.06096253 kBar
siesta: Stress tensor (total) (eV/Ang**3):
0.000861 -0.000505 0.000087
-0.000506 0.003105 -0.000560
0.000084 -0.000560 -0.000548
siesta: Pressure (total): -1.82566041 kBar
siesta: Temp_ion = 351.835 K
====================================
Begin MD step = 8
====================================
outcoor: Atomic coordinates (Ang):
0.00771538 -0.00771512 0.00924784 1 1 O
0.67341485 0.73045158 0.00121461 2 2 H
-0.79752901 0.56430894 -0.15794065 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 8
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 7 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 12
3 1: 9 7: 25 8: 20
4 11: 25 1: 6 13: 20
5 10: 25 7: 25 1: 13
6 1: 10 1: 6 9: 20
7 1: 10 1: 6 1: 8
8 10: 25 7: 25 14: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5099
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.754697 -465.758960 -465.758960 0.005614 -2.675017 0.011672
scf: 2 -465.758943 -465.758960 -465.758960 0.000641 -2.668420 0.019340
scf: 3 -465.758973 -465.758970 -465.758970 0.000360 -2.672491 0.002014
scf: 4 -465.758970 -465.758970 -465.758970 0.000045 -2.672540 0.001401
scf: 5 -465.758970 -465.758970 -465.758970 0.000073 -2.672556 0.000353
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000734859
max |H_out - H_in| (eV) : 0.0003526076
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: 3 23
siesta: E_KS(eV) = -465.7590
siesta: Atomic forces (eV/Ang):
1 -0.485248 2.100666 -0.512272
2 -0.039845 -0.956079 0.108094
3 0.494085 -1.108416 0.189496
----------------------------------------
Tot -0.031007 0.036171 -0.214682
----------------------------------------
Max 2.100666
Res 0.903491 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 2.100666 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 1.36 4.83 -0.85 -0.95 0.18 -1.02
(Free)E + p*V (eV/cell) -466.2141
Target enthalpy (eV/cell) -465.7590
siesta: Stress tensor (static) (eV/Ang**3):
0.000965 -0.000619 0.000195
-0.000619 0.003119 -0.000455
0.000194 -0.000455 -0.000310
siesta: Pressure (static): -2.01595119 kBar
siesta: Stress tensor (total) (eV/Ang**3):
0.000849 -0.000634 0.000115
-0.000634 0.003018 -0.000594
0.000114 -0.000594 -0.000533
siesta: Pressure (total): -1.78048075 kBar
siesta: Temp_ion = 355.436 K
====================================
Begin MD step = 9
====================================
outcoor: Atomic coordinates (Ang):
0.00803945 -0.00751172 0.00950584 1 1 O
0.66993165 0.73161348 0.00163372 2 2 H
-0.79937514 0.56011276 -0.16362215 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 9
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 7 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 12
3 1: 9 7: 25 8: 20
4 11: 25 1: 6 13: 20
5 10: 25 7: 25 1: 13
6 1: 10 1: 6 9: 20
7 1: 10 1: 6 1: 8
8 10: 25 7: 25 14: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5093
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.753205 -465.760706 -465.760706 0.005610 -2.670056 0.018970
scf: 2 -465.760644 -465.760695 -465.760695 0.000972 -2.658784 0.032965
scf: 3 -465.760728 -465.760720 -465.760720 0.000579 -2.665911 0.002247
scf: 4 -465.760721 -465.760720 -465.760720 0.000050 -2.665896 0.001584
scf: 5 -465.760721 -465.760721 -465.760721 0.000088 -2.665823 0.000358
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000879326
max |H_out - H_in| (eV) : 0.0003575688
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: 3 23
siesta: E_KS(eV) = -465.7607
siesta: Atomic forces (eV/Ang):
1 -0.556615 2.043030 -0.529167
2 0.013924 -0.897853 0.110719
3 0.511365 -1.110715 0.198123
----------------------------------------
Tot -0.031326 0.034461 -0.220325
----------------------------------------
Max 2.043030
Res 0.889247 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 2.043030 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 1.29 4.63 -0.83 -1.00 0.22 -1.21
(Free)E + p*V (eV/cell) -466.1949
Target enthalpy (eV/cell) -465.7607
siesta: Stress tensor (static) (eV/Ang**3):
0.000919 -0.000732 0.000210
-0.000732 0.003008 -0.000470
0.000209 -0.000470 -0.000301
siesta: Pressure (static): -1.93632173 kBar
siesta: Stress tensor (total) (eV/Ang**3):
0.000807 -0.000758 0.000139
-0.000758 0.002891 -0.000624
0.000138 -0.000624 -0.000518
siesta: Pressure (total): -1.69844067 kBar
siesta: Temp_ion = 362.224 K
====================================
Begin MD step = 10
====================================
outcoor: Atomic coordinates (Ang):
0.00835019 -0.00725939 0.00975117 1 1 O
0.66645374 0.73243476 0.00209483 2 2 H
-0.80102728 0.55549522 -0.16922850 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 10
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 7 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 12
3 1: 9 7: 25 8: 20
4 11: 25 1: 6 13: 20
5 10: 25 7: 25 1: 13
6 1: 10 1: 6 9: 20
7 1: 10 1: 6 1: 8
8 10: 25 7: 25 14: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5101
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.752595 -465.763205 -465.763205 0.005574 -2.662237 0.026902
scf: 2 -465.763070 -465.763176 -465.763176 0.001307 -2.646130 0.047025
scf: 3 -465.763242 -465.763225 -465.763225 0.000795 -2.656398 0.002435
scf: 4 -465.763226 -465.763226 -465.763226 0.000051 -2.656333 0.001638
scf: 5 -465.763226 -465.763226 -465.763226 0.000092 -2.656178 0.000357
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000923641
max |H_out - H_in| (eV) : 0.0003566734
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: 3 23
siesta: E_KS(eV) = -465.7632
siesta: Atomic forces (eV/Ang):
1 -0.623931 1.965534 -0.542832
2 0.073970 -0.830063 0.113077
3 0.517897 -1.103604 0.204606
----------------------------------------
Tot -0.032064 0.031867 -0.225150
----------------------------------------
Max 1.965534
Res 0.868112 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 1.965534 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 1.17 4.37 -0.81 -1.04 0.25 -1.41
(Free)E + p*V (eV/cell) -466.1665
Target enthalpy (eV/cell) -465.7632
siesta: Stress tensor (static) (eV/Ang**3):
0.000839 -0.000842 0.000221
-0.000842 0.002862 -0.000481
0.000220 -0.000481 -0.000294
siesta: Pressure (static): -1.81973287 kBar
siesta: Stress tensor (total) (eV/Ang**3):
0.000732 -0.000877 0.000160
-0.000877 0.002726 -0.000648
0.000158 -0.000649 -0.000505
siesta: Pressure (total): -1.57730944 kBar
siesta: Temp_ion = 371.921 K
====================================
Begin MD step = 11
====================================
outcoor: Atomic coordinates (Ang):
0.00864599 -0.00696000 0.00998350 1 1 O
0.66300388 0.73294114 0.00259884 2 2 H
-0.80248295 0.55045901 -0.17475722 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 11
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 7 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 12
3 1: 9 7: 25 8: 20
4 11: 25 1: 6 13: 20
5 10: 25 7: 25 1: 13
6 1: 10 1: 6 9: 20
7 1: 10 1: 6 1: 8
8 10: 25 7: 25 14: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5094
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.752825 -465.766359 -465.766359 0.005537 -2.651523 0.034507
scf: 2 -465.766133 -465.766309 -465.766309 0.001623 -2.630803 0.060277
scf: 3 -465.766416 -465.766389 -465.766389 0.000996 -2.644045 0.002529
scf: 4 -465.766390 -465.766389 -465.766389 0.000050 -2.643939 0.001652
scf: 5 -465.766390 -465.766390 -465.766390 0.000093 -2.643710 0.000358
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000932700
max |H_out - H_in| (eV) : 0.0003581336
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: 3 23
siesta: E_KS(eV) = -465.7664
siesta: Atomic forces (eV/Ang):
1 -0.685280 1.870618 -0.553041
2 0.139091 -0.753585 0.115098
3 0.513484 -1.087257 0.208667
----------------------------------------
Tot -0.032705 0.029775 -0.229276
----------------------------------------
Max 1.870618
Res 0.840932 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 1.870618 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 1.01 4.05 -0.79 -1.07 0.28 -1.58
(Free)E + p*V (eV/cell) -466.1306
Target enthalpy (eV/cell) -465.7664
siesta: Stress tensor (static) (eV/Ang**3):
0.000731 -0.000945 0.000227
-0.000946 0.002689 -0.000487
0.000226 -0.000487 -0.000286
siesta: Pressure (static): -1.67353522 kBar
siesta: Stress tensor (total) (eV/Ang**3):
0.000630 -0.000987 0.000175
-0.000987 0.002529 -0.000667
0.000174 -0.000667 -0.000492
siesta: Pressure (total): -1.42462137 kBar
siesta: Temp_ion = 384.139 K
====================================
Begin MD step = 12
====================================
outcoor: Atomic coordinates (Ang):
0.00892538 -0.00661580 0.01020259 1 1 O
0.65960680 0.73316164 0.00314652 2 2 H
-0.80374381 0.54501032 -0.18020678 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 12
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 7 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 9 7: 25 1: 7
2 11: 25 1: 6 1: 12
3 1: 9 7: 25 8: 20
4 11: 25 1: 6 13: 20
5 10: 25 7: 25 1: 13
6 1: 10 1: 6 9: 20
7 1: 10 1: 6 1: 8
8 10: 25 7: 25 14: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5088
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.753811 -465.770036 -465.770036 0.005500 -2.638003 0.041618
scf: 2 -465.769706 -465.769960 -465.769960 0.001915 -2.612949 0.072547
scf: 3 -465.770115 -465.770075 -465.770075 0.001180 -2.628967 0.002590
scf: 4 -465.770076 -465.770076 -465.770076 0.000050 -2.628825 0.001650
scf: 5 -465.770077 -465.770076 -465.770076 0.000093 -2.628528 0.000411
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000926868
max |H_out - H_in| (eV) : 0.0004112516
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: 3 23
siesta: E_KS(eV) = -465.7701
siesta: Atomic forces (eV/Ang):
1 -0.740025 1.758480 -0.559487
2 0.208613 -0.668991 0.116822
3 0.498431 -1.061770 0.210123
----------------------------------------
Tot -0.032981 0.027719 -0.232543
----------------------------------------
Max 1.758480
Res 0.808123 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 1.758480 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 0.80 3.68 -0.77 -1.09 0.30 -1.74
(Free)E + p*V (eV/cell) -466.0870
Target enthalpy (eV/cell) -465.7701
siesta: Stress tensor (static) (eV/Ang**3):
0.000596 -0.001041 0.000229
-0.001042 0.002487 -0.000487
0.000228 -0.000488 -0.000280
siesta: Pressure (static): -1.49658939 kBar
siesta: Stress tensor (total) (eV/Ang**3):
0.000501 -0.001088 0.000186
-0.001089 0.002300 -0.000680
0.000185 -0.000680 -0.000480
siesta: Pressure (total): -1.23949878 kBar
siesta: Temp_ion = 398.399 K
====================================
Begin MD step = 13
====================================
outcoor: Atomic coordinates (Ang):
0.00918705 -0.00622950 0.01040828 1 1 O
0.65628885 0.73312834 0.00373851 2 2 H
-0.80481559 0.53915884 -0.18557662 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 13
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 7 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 10 7: 25 1: 7
2 11: 25 1: 6 1: 12
3 1: 10 7: 25 8: 20
4 11: 25 1: 6 13: 20
5 11: 25 7: 25 1: 13
6 1: 10 1: 6 9: 20
7 1: 10 1: 6 1: 8
8 11: 25 7: 25 14: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5091
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.755476 -465.774106 -465.774106 0.005539 -2.621797 0.048150
scf: 2 -465.773666 -465.774005 -465.774005 0.002180 -2.592735 0.083670
scf: 3 -465.774210 -465.774157 -465.774157 0.001345 -2.611302 0.002637
scf: 4 -465.774158 -465.774158 -465.774158 0.000049 -2.611126 0.001641
scf: 5 -465.774158 -465.774158 -465.774158 0.000091 -2.610770 0.000465
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000912736
max |H_out - H_in| (eV) : 0.0004652322
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: 3 23
siesta: E_KS(eV) = -465.7742
siesta: Atomic forces (eV/Ang):
1 -0.787740 1.629352 -0.562264
2 0.281093 -0.577686 0.118204
3 0.472696 -1.027533 0.208741
----------------------------------------
Tot -0.033952 0.024134 -0.235319
----------------------------------------
Max 1.629352
Res 0.770354 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 1.629352 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 0.56 3.27 -0.75 -1.10 0.30 -1.89
(Free)E + p*V (eV/cell) -466.0359
Target enthalpy (eV/cell) -465.7742
siesta: Stress tensor (static) (eV/Ang**3):
0.000436 -0.001129 0.000225
-0.001129 0.002257 -0.000484
0.000223 -0.000484 -0.000276
siesta: Pressure (static): -1.29064200 kBar
siesta: Stress tensor (total) (eV/Ang**3):
0.000348 -0.001179 0.000191
-0.001180 0.002040 -0.000687
0.000189 -0.000687 -0.000470
siesta: Pressure (total): -1.02400730 kBar
siesta: Temp_ion = 414.164 K
====================================
Begin MD step = 14
====================================
outcoor: Atomic coordinates (Ang):
0.00942985 -0.00580418 0.01060050 1 1 O
0.65307754 0.73287589 0.00437535 2 2 H
-0.80570804 0.53291754 -0.19086728 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 14
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 7 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 10 7: 25 1: 7
2 12: 25 1: 6 1: 12
3 1: 10 7: 25 8: 20
4 12: 25 1: 6 13: 20
5 11: 25 7: 25 1: 13
6 1: 11 1: 6 9: 20
7 1: 11 1: 6 1: 8
8 11: 25 7: 25 14: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5083
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.757697 -465.778401 -465.778401 0.006016 -2.603030 0.054013
scf: 2 -465.777852 -465.778274 -465.778274 0.002414 -2.570343 0.093494
scf: 3 -465.778530 -465.778463 -465.778463 0.001490 -2.591198 0.002679
scf: 4 -465.778465 -465.778464 -465.778464 0.000048 -2.590992 0.001629
scf: 5 -465.778465 -465.778465 -465.778465 0.000090 -2.590584 0.000519
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000901545
max |H_out - H_in| (eV) : 0.0005189689
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: 3 23
siesta: E_KS(eV) = -465.7785
siesta: Atomic forces (eV/Ang):
1 -0.827155 1.485565 -0.561191
2 0.355579 -0.480705 0.119253
3 0.436559 -0.984928 0.204190
----------------------------------------
Tot -0.035017 0.019932 -0.237747
----------------------------------------
Max 1.485565
Res 0.728783 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 1.485565 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 0.27 2.81 -0.74 -1.10 0.30 -2.02
(Free)E + p*V (eV/cell) -465.9783
Target enthalpy (eV/cell) -465.7785
siesta: Stress tensor (static) (eV/Ang**3):
0.000252 -0.001208 0.000214
-0.001208 0.002005 -0.000475
0.000212 -0.000475 -0.000274
siesta: Pressure (static): -1.05880929 kBar
siesta: Stress tensor (total) (eV/Ang**3):
0.000171 -0.001259 0.000188
-0.001259 0.001755 -0.000688
0.000186 -0.000688 -0.000462
siesta: Pressure (total): -0.78162372 kBar
siesta: Temp_ion = 430.868 K
====================================
Begin MD step = 15
====================================
outcoor: Atomic coordinates (Ang):
0.00965284 -0.00534328 0.01077929 1 1 O
0.65000113 0.73244108 0.00505743 2 2 H
-0.80643488 0.52630259 -0.19608047 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 15
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 7 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 10 7: 25 1: 7
2 1: 14 1: 6 1: 8
3 1: 10 7: 25 8: 20
4 1: 14 1: 6 9: 20
5 11: 25 7: 25 1: 13
6 15: 25 1: 6 1: 12
7 15: 25 1: 6 13: 20
8 11: 25 7: 25 14: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5075
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.760392 -465.782798 -465.782798 0.006435 -2.581865 0.059135
scf: 2 -465.782152 -465.782652 -465.782652 0.002615 -2.545973 0.101923
scf: 3 -465.782956 -465.782877 -465.782877 0.001612 -2.568832 0.002718
scf: 4 -465.782878 -465.782878 -465.782878 0.000052 -2.568598 0.001616
scf: 5 -465.782879 -465.782878 -465.782878 0.000096 -2.568144 0.000571
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000959361
max |H_out - H_in| (eV) : 0.0005709931
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: 3 23
siesta: E_KS(eV) = -465.7829
siesta: Atomic forces (eV/Ang):
1 -0.857230 1.329066 -0.555941
2 0.430659 -0.379421 0.119955
3 0.390456 -0.934322 0.196379
----------------------------------------
Tot -0.036115 0.015323 -0.239607
----------------------------------------
Max 1.329066
Res 0.684602 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 1.329066 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -0.04 2.32 -0.73 -1.09 0.28 -2.12
(Free)E + p*V (eV/cell) -465.9150
Target enthalpy (eV/cell) -465.7829
siesta: Stress tensor (static) (eV/Ang**3):
0.000047 -0.001274 0.000196
-0.001274 0.001735 -0.000460
0.000195 -0.000460 -0.000274
siesta: Pressure (static): -0.80530745 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.000026 -0.001324 0.000178
-0.001325 0.001450 -0.000683
0.000177 -0.000683 -0.000456
siesta: Pressure (total): -0.51694296 kBar
siesta: Temp_ion = 447.943 K
====================================
Begin MD step = 16
====================================
outcoor: Atomic coordinates (Ang):
0.00985531 -0.00485055 0.01094476 1 1 O
0.64708810 0.73186232 0.00578501 2 2 H
-0.80701358 0.51933319 -0.20121916 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 16
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 7: 20
5 1: 6 6: 25 1: 6
6 1: 7 1: 5 1: 6
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 10 7: 25 1: 7
2 1: 14 1: 6 1: 8
3 1: 10 7: 25 8: 20
4 1: 14 1: 6 9: 20
5 11: 25 7: 25 1: 13
6 15: 25 1: 6 1: 12
7 15: 25 1: 6 13: 20
8 11: 25 7: 25 14: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5082
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.763468 -465.787164 -465.787164 0.006792 -2.558459 0.063454
scf: 2 -465.786423 -465.786993 -465.786993 0.002781 -2.519827 0.108829
scf: 3 -465.787338 -465.787248 -465.787248 0.001711 -2.544377 0.002754
scf: 4 -465.787250 -465.787249 -465.787249 0.000055 -2.544118 0.001603
scf: 5 -465.787250 -465.787249 -465.787249 0.000100 -2.543627 0.000620
scf: 6 -465.787249 -465.787249 -465.787249 0.000010 -2.543563 0.000376
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000101023
max |H_out - H_in| (eV) : 0.0003762859
SCF cycle converged after 6 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: 3 23
siesta: E_KS(eV) = -465.7872
siesta: Atomic forces (eV/Ang):
1 -0.877478 1.162683 -0.546609
2 0.505008 -0.275313 0.120104
3 0.334784 -0.876204 0.185205
----------------------------------------
Tot -0.037686 0.011166 -0.241300
----------------------------------------
Max 1.162683
Res 0.639440 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 1.162683 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -0.39 1.82 -0.73 -1.08 0.26 -2.21
(Free)E + p*V (eV/cell) -465.8474
Target enthalpy (eV/cell) -465.7872
siesta: Stress tensor (static) (eV/Ang**3):
-0.000176 -0.001329 0.000173
-0.001329 0.001454 -0.000441
0.000172 -0.000441 -0.000276
siesta: Pressure (static): -0.53524507 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.000241 -0.001377 0.000161
-0.001377 0.001135 -0.000671
0.000160 -0.000671 -0.000453
siesta: Pressure (total): -0.23545233 kBar
siesta: Temp_ion = 464.855 K
====================================
Begin MD step = 17
====================================
outcoor: Atomic coordinates (Ang):
0.01003676 -0.00432998 0.01109714 1 1 O
0.64436664 0.73117912 0.00655816 2 2 H
-0.80746529 0.51203138 -0.20628759 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 17
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 6 6: 25 1: 6
6 1: 7 1: 5 1: 7
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 10 7: 25 1: 7
2 1: 15 1: 6 1: 8
3 1: 10 7: 25 8: 20
4 1: 15 1: 6 9: 20
5 11: 25 7: 25 1: 13
6 16: 25 1: 6 1: 12
7 16: 25 1: 6 13: 20
8 11: 25 7: 25 14: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5072
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.766816 -465.791360 -465.791360 0.007092 -2.532993 0.066918
scf: 2 -465.790548 -465.791173 -465.791173 0.002910 -2.492123 0.114104
scf: 3 -465.791552 -465.791453 -465.791453 0.001787 -2.518029 0.002785
scf: 4 -465.791454 -465.791454 -465.791454 0.000057 -2.517749 0.001604
scf: 5 -465.791455 -465.791454 -465.791454 0.000104 -2.517225 0.000662
scf: 6 -465.791454 -465.791454 -465.791454 0.000011 -2.517158 0.000404
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000108125
max |H_out - H_in| (eV) : 0.0004040267
SCF cycle converged after 6 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: 3 23
siesta: E_KS(eV) = -465.7915
siesta: Atomic forces (eV/Ang):
1 -0.886508 0.988341 -0.532947
2 0.576942 -0.170251 0.120007
3 0.270849 -0.811550 0.170356
----------------------------------------
Tot -0.038716 0.006540 -0.242585
----------------------------------------
Max 0.988341
Res 0.594791 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.988341 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -0.75 1.30 -0.72 -1.05 0.22 -2.27
(Free)E + p*V (eV/cell) -465.7766
Target enthalpy (eV/cell) -465.7915
siesta: Stress tensor (static) (eV/Ang**3):
-0.000411 -0.001370 0.000143
-0.001370 0.001164 -0.000416
0.000142 -0.000416 -0.000280
siesta: Pressure (static): -0.25295775 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.000467 -0.001415 0.000136
-0.001415 0.000810 -0.000654
0.000135 -0.000654 -0.000452
siesta: Pressure (total): 0.05815301 kBar
siesta: Temp_ion = 481.130 K
====================================
Begin MD step = 18
====================================
outcoor: Atomic coordinates (Ang):
0.01019698 -0.00378574 0.01123676 1 1 O
0.64186407 0.73043133 0.00737683 2 2 H
-0.80781424 0.50442170 -0.21129140 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 18
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 6 6: 25 1: 6
6 1: 7 1: 5 1: 7
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 10 7: 25 1: 7
2 1: 15 1: 6 1: 8
3 1: 10 7: 25 8: 20
4 1: 15 1: 6 9: 20
5 11: 25 7: 25 1: 13
6 16: 25 1: 6 1: 12
7 16: 25 1: 6 13: 20
8 11: 25 7: 25 14: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5077
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.770371 -465.795295 -465.795295 0.007309 -2.505645 0.069492
scf: 2 -465.794433 -465.795097 -465.795097 0.003001 -2.463057 0.117795
scf: 3 -465.795500 -465.795395 -465.795395 0.001838 -2.489979 0.002818
scf: 4 -465.795397 -465.795396 -465.795396 0.000059 -2.489682 0.001623
scf: 5 -465.795397 -465.795396 -465.795396 0.000106 -2.489137 0.000700
scf: 6 -465.795396 -465.795396 -465.795396 0.000011 -2.489067 0.000430
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000114006
max |H_out - H_in| (eV) : 0.0004296090
SCF cycle converged after 6 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: 3 23
siesta: E_KS(eV) = -465.7954
siesta: Atomic forces (eV/Ang):
1 -0.883531 0.809407 -0.515391
2 0.644696 -0.066204 0.119423
3 0.199077 -0.741155 0.151826
----------------------------------------
Tot -0.039757 0.002048 -0.244142
----------------------------------------
Max 0.883531
Res 0.552536 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.883531 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -1.12 0.78 -0.73 -1.01 0.17 -2.30
(Free)E + p*V (eV/cell) -465.7041
Target enthalpy (eV/cell) -465.7954
siesta: Stress tensor (static) (eV/Ang**3):
-0.000654 -0.001396 0.000106
-0.001396 0.000874 -0.000388
0.000105 -0.000388 -0.000285
siesta: Pressure (static): 0.03516456 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.000702 -0.001436 0.000104
-0.001436 0.000486 -0.000632
0.000103 -0.000632 -0.000453
siesta: Pressure (total): 0.35716809 kBar
siesta: Temp_ion = 496.396 K
====================================
Begin MD step = 19
====================================
outcoor: Atomic coordinates (Ang):
0.01033604 -0.00322212 0.01136404 1 1 O
0.63960607 0.72965843 0.00824081 2 2 H
-0.80808767 0.49653085 -0.21623760 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 19
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 6 6: 25 1: 6
6 1: 7 1: 5 1: 7
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 10 7: 25 1: 7
2 1: 15 1: 6 1: 8
3 1: 10 7: 25 8: 20
4 1: 15 1: 6 9: 20
5 11: 25 7: 25 1: 13
6 16: 25 1: 6 1: 12
7 16: 25 1: 6 13: 20
8 11: 25 7: 25 14: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5066
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.774085 -465.798906 -465.798906 0.007449 -2.476615 0.071155
scf: 2 -465.798019 -465.798704 -465.798704 0.003054 -2.432852 0.119856
scf: 3 -465.799121 -465.799012 -465.799012 0.001865 -2.460436 0.003028
scf: 4 -465.799014 -465.799013 -465.799013 0.000060 -2.460127 0.001715
scf: 5 -465.799014 -465.799013 -465.799013 0.000107 -2.459570 0.000730
scf: 6 -465.799013 -465.799013 -465.799013 0.000012 -2.459499 0.000451
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000118276
max |H_out - H_in| (eV) : 0.0004507566
SCF cycle converged after 6 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: 3 23
siesta: E_KS(eV) = -465.7990
siesta: Atomic forces (eV/Ang):
1 -0.867705 0.629342 -0.493670
2 0.706410 0.034763 0.118302
3 0.120983 -0.666262 0.129897
----------------------------------------
Tot -0.040312 -0.002156 -0.245472
----------------------------------------
Max 0.867705
Res 0.514493 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.867705 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -1.51 0.27 -0.73 -0.97 0.10 -2.31
(Free)E + p*V (eV/cell) -465.6315
Target enthalpy (eV/cell) -465.7990
siesta: Stress tensor (static) (eV/Ang**3):
-0.000901 -0.001404 0.000065
-0.001404 0.000589 -0.000355
0.000064 -0.000355 -0.000294
siesta: Pressure (static): 0.32307975 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.000940 -0.001439 0.000066
-0.001439 0.000171 -0.000604
0.000065 -0.000604 -0.000458
siesta: Pressure (total): 0.65530025 kBar
siesta: Temp_ion = 510.391 K
====================================
Begin MD step = 20
====================================
outcoor: Atomic coordinates (Ang):
0.01045433 -0.00264342 0.01147949 1 1 O
0.63761606 0.72889872 0.00914967 2 2 H
-0.80831520 0.48838724 -0.22113453 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 20
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 6 6: 25 1: 6
6 1: 7 1: 5 1: 7
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 10 7: 25 1: 7
2 1: 15 1: 6 1: 8
3 1: 10 7: 25 8: 20
4 1: 15 1: 6 9: 20
5 11: 25 7: 25 1: 13
6 16: 25 1: 6 1: 12
7 16: 25 1: 6 13: 20
8 11: 25 7: 25 14: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5058
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.777915 -465.802147 -465.802147 0.007511 -2.446110 0.071911
scf: 2 -465.801252 -465.801940 -465.801940 0.003071 -2.401716 0.120324
scf: 3 -465.802366 -465.802255 -465.802255 0.001869 -2.429610 0.003243
scf: 4 -465.802258 -465.802257 -465.802257 0.000061 -2.429294 0.001834
scf: 5 -465.802258 -465.802257 -465.802257 0.000107 -2.428733 0.000752
scf: 6 -465.802257 -465.802257 -465.802257 0.000012 -2.428662 0.000467
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000120733
max |H_out - H_in| (eV) : 0.0004665857
SCF cycle converged after 6 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: 3 23
siesta: E_KS(eV) = -465.8023
siesta: Atomic forces (eV/Ang):
1 -0.839479 0.449243 -0.467943
2 0.760536 0.130640 0.116668
3 0.037601 -0.588004 0.104776
----------------------------------------
Tot -0.041341 -0.008121 -0.246499
----------------------------------------
Max 0.839479
Res 0.482211 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.839479 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -1.89 -0.22 -0.75 -0.92 0.03 -2.29
(Free)E + p*V (eV/cell) -465.5590
Target enthalpy (eV/cell) -465.8023
siesta: Stress tensor (static) (eV/Ang**3):
-0.001148 -0.001397 0.000017
-0.001397 0.000310 -0.000317
0.000016 -0.000317 -0.000304
siesta: Pressure (static): 0.60974711 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.001178 -0.001427 0.000020
-0.001428 -0.000138 -0.000572
0.000019 -0.000572 -0.000465
siesta: Pressure (total): 0.95133354 kBar
siesta: Temp_ion = 522.973 K
siesta: Program's energy decomposition (eV):
siesta: Ebs = -103.597105
siesta: Eions = 815.854478
siesta: Ena = 175.020443
siesta: Ekin = 351.850237
siesta: Enl = -62.028573
siesta: Eso = 0.000000
siesta: Edftu = 0.000000
siesta: DEna = -2.686492
siesta: DUscf = 0.738051
siesta: DUext = 0.000000
siesta: Exc = -112.841446
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
siesta: Emolmec = 0.000000
siesta: Ekinion = 0.135194
siesta: Eharris = -465.667064
siesta: Etot = -465.667064
siesta: FreeEng = -465.667064
siesta: Final energy (eV):
siesta: Band Struct. = -103.597105
siesta: Kinetic = 351.850237
siesta: Hartree = 414.775787
siesta: Edftu = 0.000000
siesta: Eso = 0.000000
siesta: Ext. field = 0.000000
siesta: Exch.-corr. = -112.841446
siesta: Ion-electron = -1137.151829
siesta: Ion-ion = 17.564994
siesta: Ekinion = 0.135194
siesta: Total = -465.667064
siesta: Fermi = -2.428662
siesta: Atomic forces (eV/Ang):
siesta: 1 -0.839479 0.449243 -0.467943
siesta: 2 0.760536 0.130640 0.116668
siesta: 3 0.037601 -0.588004 0.104776
siesta: ----------------------------------------
siesta: Tot -0.041341 -0.008121 -0.246499
siesta: Stress tensor (static) (eV/Ang**3):
siesta: -0.001148 -0.001397 0.000017
siesta: -0.001397 0.000310 -0.000317
siesta: 0.000016 -0.000317 -0.000304
siesta: Cell volume = 409.600000 Ang**3
siesta: Pressure (static):
siesta: Solid Molecule Units
siesta: 0.00000414 0.00000229 Ry/Bohr**3
siesta: 0.00038057 0.00020987 eV/Ang**3
siesta: 0.60974711 0.33625591 kBar
(Free)E+ p_basis*V_orbitals = -465.217090
(Free)Eharris+ p_basis*V_orbitals = -465.217090
siesta: Electric dipole (a.u.) = -0.088042 0.562278 -0.109158
siesta: Electric dipole (Debye) = -0.223780 1.429170 -0.277451
cite: Please see "h2o.bib" for an exhaustive BiBTeX file.
cite: Please clearly indicate Siesta version in published work: v4.1-b4-351
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: 22-JAN-2021 23:12:50
Job completed
Siesta Version : v4.1-b4-351
Architecture : x86_64-linux-n-62-26-19
Compiler version: GNU Fortran (GCC) 9.3.0
Compiler flags : mpifort -m64 -fPIC -O3 -march=native -ftree-vectorize -fexpensive-optimizatioons -funroll-loops -fprefetch-loop-arrays -fno-second-underscore -flto
PP flags : -I/dtu/sw/dcc/SL73/2020-aug/generic/build-tools/1.0/include -I/dtu/sw/dcc/SL773/2020-aug/generic/gcc/9.3.0/include -I/dtu/sw/dcc/SL73/2020-aug/generic/gcc/9.3.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/zlib/1.2.11/include -I/dtu/sw/dcc/SL73/2020-aug/generic/numactl/2.0.12/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/libxml2/2.9.10/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/hwloc/2.2.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/knem/1.1.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/ucx/1.8.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/openmpi/4.0.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/szip/2.1.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/hdf5/1.12.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/pnetcdf/1.12.1/include -I/dtu/sw/dcc/SL73/2020-aug/generic/gen-zlib/1.2.11/include -I/dtu/sw/dcc/SL73/2020-aug/generic/openssl/1.1.1/include -I/dtu/sw/dcc/SL73/2020-aug/generic/libssh2/1.8.2/include -I/dtu/sw/dcc/SL73/2020-aug/generic/curl/7.65.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/netcdf/4.7.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/fftw/3.3.8/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/parmetis/4.0.3/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/scalapack/2.1.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/lapack/3.9.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/blis/0.7.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/scotch/6.0.9/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/mumps/5.3.3/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/elpa/2020.05.001/include -DSIESTA__ELPA -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DCDF4 -DSIESTA__FLOOK -DNCDF -DNCDF_4 -DNCDF_PARALLEL -DTS_NOCHECKS -DSIESTA__METIS -DSIESTA__MUMPS -DSIESTA__MRRR -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/elpa/2020.05.001/include/elpa
Libraries : libncdf.a libfdict.a -lnetcdff -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lz -lzmuumps -lmumps_common -lesmumps -lscotch -lscotcherr -lpord -lparmetis -lmetis -lelpa -lscalapack -llapack -lblis -L/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/lib -Wl,-rpath=/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/lib -lflookall -ldl -flto -fuse-linker-plugin -lmetis
PARALLEL version
NetCDF support
NetCDF-4 support
NetCDF-4 MPI-IO support
METIS ordering support
Lua support
* Running on 8 nodes in parallel
>> Start of run: 22-JAN-2021 23:12:51
***********************
* WELCOME TO SIESTA *
***********************
reinit: Reading from standard input
reinit: Dumped input in INPUT_TMP.03479
************************** Dump of input data file ****************************
SystemName Water molecule -- md verlet
SystemLabel h2o
NumberOfAtoms 3
NumberOfSpecies 2
MeshCutoff 100 Ry
%block ChemicalSpeciesLabel
1 8 O # Species index, atomic number, species label
2 1 H
%endblock ChemicalSpeciesLabel
LatticeConstant 8.0 Ang
%block LatticeVectors
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 0.8
%endblock LatticeVectors
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
Solution.Method diagon
MeshCutoff 100 Ry
WriteCoorStep .true.
WriteForces .true.
WriteMDHistory .true.
MD.UseSaveXV T
MD.TypeOfRun Verlet
MD.InitialTemperature 600 K
MD.Initial.Time.Step 1
MD.Final.Time.Step 20
MD.Length.Time.Step 0.2 fs
************************** End of input data file *****************************
reinit: -----------------------------------------------------------------------
reinit: System Name: Water molecule -- md verlet
reinit: -----------------------------------------------------------------------
reinit: System Label: h2o
reinit: -----------------------------------------------------------------------
initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Species number: 1 Atomic number: 8 Label: O
Species number: 2 Atomic number: 1 Label: H
Ground state valence configuration: 2s02 2p04
Reading pseudopotential information in formatted form from O.psf
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
Valence configuration for pseudopotential generation:
1s( 1.00) rc: 1.25
2p( 0.00) rc: 1.25
3d( 0.00) rc: 1.25
4f( 0.00) rc: 1.25
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.
===============================================================================
O Z= 8 Mass= 16.000 Charge= 0.17977+309
Lmxo=1 Lmxkb= 3 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=2
i=1 nzeta=2 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 0.0000
lambdas: 1.0000 1.0000
L=1 Nsemic=0 Cnfigmx=2
i=1 nzeta=2 polorb=1 (2p)
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
===============================================================================
atom: Called for O (Z = 8)
read_vps: Pseudopotential generation method:
read_vps: ATM3 Troullier-Martins
Valence charge for ps generation: 6.00000
xc_check: Exchange-correlation functional:
xc_check: Ceperley-Alder
V l=0 = -2*Zval/r beyond r= 1.1278
V l=1 = -2*Zval/r beyond r= 1.1278
V l=2 = -2*Zval/r beyond r= 1.1278
V l=3 = -2*Zval/r beyond r= 1.1138
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= 1.1278
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= 1.294105 el= -1.742414 Ekb= 9.135903 kbcos= 0.326910
l= 1 rc= 1.294105 el= -0.676589 Ekb= -8.124878 kbcos= -0.395047
l= 2 rc= 1.448233 el= 0.002386 Ekb= -2.039267 kbcos= -0.003484
l= 3 rc= 1.561052 el= 0.003508 Ekb= -0.799141 kbcos= -0.000344
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 = -1.723766
kinetic = 1.614911
potential(screened) = -3.338677
potential(ionic) = -11.304675
izeta = 2
rmatch = 2.510382
splitnorm = 0.150000
energy = -1.471299
kinetic = 2.446434
potential(screened) = -3.917732
potential(ionic) = -12.476133
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 = -0.658841
kinetic = 5.005986
potential(screened) = -5.664827
potential(ionic) = -13.452360
izeta = 2
rmatch = 2.541963
splitnorm = 0.150000
energy = -0.367441
kinetic = 7.530509
potential(screened) = -7.897949
potential(ionic) = -16.611953
POLgen: Perturbative polarization orbital with L= 2
POLgen: Polarization orbital for state 2p
izeta = 1
rc = 3.937239
energy = 2.398520
kinetic = 4.716729
potential(screened) = -2.318209
potential(ionic) = -8.603170
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: _________________________________________________________________________
===============================================================================
H Z= 1 Mass= 1.0100 Charge= 0.17977+309
Lmxo=0 Lmxkb= 2 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=1
i=1 nzeta=2 polorb=1 (1s)
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
===============================================================================
atom: Called for H (Z = 1)
read_vps: Pseudopotential generation method:
read_vps: ATM3 Troullier-Martins
Valence charge for ps generation: 1.00000
xc_check: Exchange-correlation functional:
xc_check: Ceperley-Alder
V l=0 = -2*Zval/r beyond r= 1.2343
V l=1 = -2*Zval/r beyond r= 1.2189
V l=2 = -2*Zval/r beyond r= 1.2189
All V_l potentials equal beyond r= 1.2343
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r= 1.2343
VLOCAL1: 99.0% of the norm of Vloc inside 28.493 Ry
VLOCAL1: 99.9% of the norm of Vloc inside 64.935 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.45251
atom: Maximum radius for r*vlocal+2*Zval: 1.21892
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= 1.364359 el= -0.467325 Ekb= -2.005361 kbcos= -0.336422
l= 1 rc= 1.434438 el= 0.001430 Ekb= -0.501708 kbcos= -0.021697
l= 2 rc= 1.470814 el= 0.002365 Ekb= -0.190555 kbcos= -0.002281
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 = 4.828263
energy = -0.449375
kinetic = 0.929372
potential(screened) = -1.378747
potential(ionic) = -1.915047
izeta = 2
rmatch = 3.854947
splitnorm = 0.150000
energy = -0.336153
kinetic = 1.505294
potential(screened) = -1.841447
potential(ionic) = -2.413582
POLgen: Perturbative polarization orbital with L= 1
POLgen: Polarization orbital for state 1s
izeta = 1
rc = 4.828263
energy = 0.706972
kinetic = 1.396397
potential(screened) = -0.689424
potential(ionic) = -1.169792
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: 4.828263
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 2.510
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
4.828 3.855
1.000 1.000
%endblock PAO.Basis
prinput: ----------------------------------------------------------------------
Dumping basis to NetCDF file O.ion.nc
Dumping basis to NetCDF file H.ion.nc
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
WARNING: h2o.VERLET_RESTART not found--reading only XV file and moving back 1 time step using Euler
siesta: Atomic coordinates (Bohr) and species
siesta: 0.01974 -0.00499 0.02168 1 1
siesta: 1.20519 1.37747 0.01733 2 2
siesta: -1.52748 0.92271 -0.41785 2 3
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: 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 = 2
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 = 1000
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 = F
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 = Verlet MD run
redata: Initial MD time step = 1
redata: Final MD time step = 20
redata: Length of MD time step = 0.2000 fs
redata: Initial Temperature of MD run = 600.0000 K
redata: Perform a MD quench = F
mix.SCF: Pulay mixing = Pulay
mix.SCF: Variant = stable
mix.SCF: History steps = 2
mix.SCF: Linear mixing weight = 0.250000
mix.SCF: Mixing weight = 0.250000
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 0.2500
weight.linear 0.2500
history 2
%endblock SCF.Mixer.Pulay
Size of DM history Fstack: 1
Total number of electrons: 8.000000
Total ionic charge: 8.000000
* ProcessorY, Blocksize: 2 3
* Orbital distribution balance (max,min): 3 2
Kpoints in: 1 . Kpoints trimmed: 1
siesta: k-grid: Number of k-points = 1
siesta: k-grid: Cutoff (effective) = 3.200 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 = 3
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
ts: **************************************************************
ts: Save H and S matrices = F
ts: Save DM and EDM matrices = F
ts: Only save the overlap matrix S = F
ts: **************************************************************
************************ Begin: TS CHECKS AND WARNINGS ************************
************************ End: TS CHECKS AND WARNINGS **************************
====================================
Begin MD step = 1
====================================
outcoor: Atomic coordinates (Ang):
0.01044428 -0.00263804 0.01147389 1 1 O
0.63776032 0.72892350 0.00917180 2 2 H
-0.80830806 0.48827571 -0.22111466 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 1
Initializing Density Matrix...
DM filled with atomic data:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 6 6: 25 1: 6
6 1: 7 1: 5 1: 7
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 10 7: 25 1: 7
2 1: 15 1: 6 1: 8
3 1: 10 7: 25 8: 20
4 1: 15 1: 6 9: 20
5 11: 25 7: 25 1: 13
6 16: 25 1: 6 1: 12
7 16: 25 1: 6 13: 20
8 11: 25 7: 25 14: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5058
stepf: Fermi-Dirac step function
siesta: Program's energy decomposition (eV):
siesta: Ebs = -82.376595
siesta: Eions = 815.854478
siesta: Ena = 175.020263
siesta: Ekin = 374.722329
siesta: Enl = -68.070849
siesta: Eso = 0.000000
siesta: Edftu = 0.000000
siesta: DEna = -16.250328
siesta: DUscf = 2.005479
siesta: DUext = 0.000000
siesta: Exc = -116.590183
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
siesta: Emolmec = 0.000000
siesta: Ekinion = 0.000000
siesta: Eharris = -467.090534
siesta: Etot = -465.017768
siesta: FreeEng = -465.017768
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -467.090534 -465.017768 -465.017768 1.395154 -4.640241 7.085923
timer: Routine,Calls,Time,% = IterSCF 1 0.020 1.52
scf: 2 -466.182135 -465.712932 -465.712932 0.055425 -3.483389 2.692412
scf: 3 -465.812595 -465.797866 -465.797866 0.025484 -2.732741 0.355489
scf: 4 -465.803388 -465.800803 -465.800803 0.010180 -2.653238 0.269178
scf: 5 -465.802922 -465.802288 -465.802288 0.021748 -2.427259 0.054044
scf: 6 -465.802494 -465.802405 -465.802405 0.000936 -2.414545 0.028503
scf: 7 -465.802462 -465.802435 -465.802435 0.000734 -2.414720 0.020220
scf: 8 -465.802460 -465.802448 -465.802448 0.000575 -2.417268 0.015366
scf: 9 -465.802456 -465.802453 -465.802453 0.000699 -2.423133 0.006370
scf: 10 -465.802453 -465.802453 -465.802453 0.000167 -2.426319 0.002887
scf: 11 -465.802453 -465.802453 -465.802453 0.000018 -2.427633 0.002170
scf: 12 -465.802454 -465.802453 -465.802453 0.000026 -2.428060 0.001203
scf: 13 -465.802454 -465.802453 -465.802453 0.000024 -2.428116 0.000684
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000243222
max |H_out - H_in| (eV) : 0.0006838238
SCF cycle converged after 13 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: 3 23
siesta: E_KS(eV) = -465.8025
siesta: E_KS - E_eggbox = -465.8025
siesta: Atomic forces (eV/Ang):
1 -0.832186 0.450317 -0.466715
2 0.755644 0.126677 0.116118
3 0.035264 -0.585172 0.104218
----------------------------------------
Tot -0.041278 -0.008178 -0.246379
----------------------------------------
Max 0.832186
Res 0.479375 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.832186 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -1.87 -0.26 -0.74 -0.92 0.03 -2.26
(Free)E + p*V (eV/cell) -465.5579
Target enthalpy (eV/cell) -465.8025
siesta: Stress tensor (static) (eV/Ang**3):
-0.001145 -0.001385 0.000016
-0.001385 0.000313 -0.000316
0.000016 -0.000316 -0.000304
siesta: Pressure (static): 0.60673177 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.001168 -0.001412 0.000019
-0.001412 -0.000160 -0.000575
0.000019 -0.000575 -0.000463
siesta: Pressure (total): 0.95673889 kBar
siesta: Temp_ion = 522.973 K
====================================
Begin MD step = 2
====================================
outcoor: Atomic coordinates (Ang):
0.01054254 -0.00204858 0.01157815 1 1 O
0.63605790 0.72821259 0.01012482 2 2 H
-0.80852177 0.47990957 -0.22597194 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 2
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 6 6: 25 1: 6
6 1: 7 1: 5 1: 7
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 1: 10 7: 25 1: 7
2 1: 15 1: 6 1: 8
3 1: 10 7: 25 8: 20
4 1: 15 1: 6 9: 20
5 11: 25 7: 25 1: 13
6 16: 25 1: 6 1: 12
7 16: 25 1: 6 13: 20
8 11: 25 7: 25 14: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5059
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.782042 -465.805202 -465.805202 0.007552 -2.413549 0.071837
scf: 2 -465.804335 -465.805008 -465.805008 0.003062 -2.368945 0.119240
scf: 3 -465.805420 -465.805312 -465.805312 0.001856 -2.396861 0.003393
scf: 4 -465.805314 -465.805313 -465.805313 0.000061 -2.396535 0.001917
scf: 5 -465.805314 -465.805314 -465.805314 0.000107 -2.395965 0.000757
scf: 6 -465.805314 -465.805314 -465.805314 0.000012 -2.395897 0.000470
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000120979
max |H_out - H_in| (eV) : 0.0004699475
SCF cycle converged after 6 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: 3 23
siesta: E_KS(eV) = -465.8053
siesta: Atomic forces (eV/Ang):
1 -0.790493 0.274698 -0.437709
2 0.800346 0.215122 0.114158
3 -0.051357 -0.505073 0.076149
----------------------------------------
Tot -0.041504 -0.015253 -0.247402
----------------------------------------
Max 0.800346
Res 0.454035 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.800346 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -2.25 -0.68 -0.76 -0.86 -0.05 -2.22
(Free)E + p*V (eV/cell) -465.4900
Target enthalpy (eV/cell) -465.8053
siesta: Stress tensor (static) (eV/Ang**3):
-0.001383 -0.001360 -0.000035
-0.001360 0.000046 -0.000277
-0.000036 -0.000277 -0.000317
siesta: Pressure (static): 0.88346206 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.001406 -0.001386 -0.000032
-0.001387 -0.000427 -0.000536
-0.000034 -0.000536 -0.000476
siesta: Pressure (total): 1.23346918 kBar
siesta: Temp_ion = 534.092 K
====================================
Begin MD step = 3
====================================
outcoor: Atomic coordinates (Ang):
0.01062188 -0.00145253 0.01167193 1 1 O
0.63465911 0.72758329 0.01112114 2 2 H
-0.80875496 0.47135182 -0.23080034 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 3
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 8: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 7 6: 25 1: 6
6 1: 7 1: 5 1: 7
7 8: 25 6: 25 7: 20
8 1: 7 6: 25 7: 20
New grid distribution: 3
1 1: 10 7: 25 1: 7
2 1: 15 1: 6 1: 8
3 1: 10 7: 25 8: 20
4 1: 15 1: 6 9: 20
5 11: 25 7: 25 1: 13
6 16: 25 1: 6 1: 12
7 16: 25 1: 6 13: 20
8 11: 25 7: 25 14: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 50 x 52 x 38 = 98800
PhiOnMesh: Number of (b)points on node 0 = 2160
PhiOnMesh: nlist on node 0 = 4789
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.786090 -465.807720 -465.807720 0.007400 -2.380661 0.070749
scf: 2 -465.806894 -465.807538 -465.807538 0.002998 -2.336633 0.116685
scf: 3 -465.807933 -465.807828 -465.807828 0.001812 -2.364106 0.003585
scf: 4 -465.807831 -465.807830 -465.807830 0.000060 -2.363792 0.002022
scf: 5 -465.807831 -465.807830 -465.807830 0.000102 -2.363249 0.000766
scf: 6 -465.807831 -465.807830 -465.807830 0.000012 -2.363182 0.000479
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000119887
max |H_out - H_in| (eV) : 0.0004791759
SCF cycle converged after 6 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: 3 23
siesta: E_KS(eV) = -465.8078
siesta: Atomic forces (eV/Ang):
1 -0.735503 0.106082 -0.405779
2 0.834401 0.295038 0.111141
3 -0.139871 -0.423626 0.046220
----------------------------------------
Tot -0.040972 -0.022506 -0.248417
----------------------------------------
Max 0.834401
Res 0.436356 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.834401 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -2.61 -1.12 -0.78 -0.80 -0.14 -2.15
(Free)E + p*V (eV/cell) -465.4238
Target enthalpy (eV/cell) -465.8078
siesta: Stress tensor (static) (eV/Ang**3):
-0.001610 -0.001315 -0.000091
-0.001315 -0.000201 -0.000235
-0.000092 -0.000235 -0.000332
siesta: Pressure (static): 1.14482937 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.001627 -0.001339 -0.000089
-0.001339 -0.000697 -0.000499
-0.000090 -0.000499 -0.000489
siesta: Pressure (total): 1.50227851 kBar
siesta: Temp_ion = 543.854 K
====================================
Begin MD step = 4
====================================
outcoor: Atomic coordinates (Ang):
0.01068360 -0.00085395 0.01175600 1 1 O
0.63357686 0.72706592 0.01215963 2 2 H
-0.80904122 0.46263336 -0.23561120 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 4
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 8: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 7 6: 25 1: 6
6 1: 7 1: 5 1: 7
7 8: 25 6: 25 7: 20
8 1: 7 6: 25 7: 20
New grid distribution: 3
1 1: 11 7: 25 1: 7
2 1: 15 1: 6 1: 8
3 1: 11 7: 25 8: 20
4 1: 15 1: 6 9: 20
5 12: 25 7: 25 1: 14
6 16: 25 1: 6 1: 12
7 16: 25 1: 6 13: 20
8 12: 25 7: 25 15: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 50 x 52 x 38 = 98800
PhiOnMesh: Number of (b)points on node 0 = 2160
PhiOnMesh: nlist on node 0 = 4776
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.790275 -465.809934 -465.809934 0.007227 -2.347015 0.068905
scf: 2 -465.809169 -465.809768 -465.809768 0.002913 -2.303953 0.112764
scf: 3 -465.810138 -465.810040 -465.810040 0.001753 -2.330721 0.003704
scf: 4 -465.810042 -465.810041 -465.810041 0.000058 -2.330417 0.002084
scf: 5 -465.810042 -465.810042 -465.810042 0.000098 -2.329896 0.000759
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000984379
max |H_out - H_in| (eV) : 0.0007586657
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: 3 23
siesta: E_KS(eV) = -465.8100
siesta: Atomic forces (eV/Ang):
1 -0.669505 -0.052839 -0.370949
2 0.856184 0.364253 0.107508
3 -0.228022 -0.342421 0.014463
----------------------------------------
Tot -0.041342 -0.031007 -0.248978
----------------------------------------
Max 0.856184
Res 0.426273 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.856184 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -2.93 -1.51 -0.81 -0.73 -0.24 -2.05
(Free)E + p*V (eV/cell) -465.3628
Target enthalpy (eV/cell) -465.8100
siesta: Stress tensor (static) (eV/Ang**3):
-0.001818 -0.001255 -0.000148
-0.001256 -0.000427 -0.000191
-0.000150 -0.000191 -0.000349
siesta: Pressure (static): 1.38543320 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.001829 -0.001278 -0.000149
-0.001279 -0.000942 -0.000459
-0.000150 -0.000459 -0.000505
siesta: Pressure (total): 1.74941550 kBar
siesta: Temp_ion = 552.427 K
====================================
Begin MD step = 5
====================================
outcoor: Atomic coordinates (Ang):
0.01072929 -0.00025663 0.01183118 1 1 O
0.63281943 0.72668674 0.01323890 2 2 H
-0.80941398 0.45378499 -0.24041658 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 5
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 8: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 7 6: 25 1: 6
6 1: 7 1: 5 1: 7
7 8: 25 6: 25 7: 20
8 1: 7 6: 25 7: 20
New grid distribution: 3
1 14: 25 7: 25 1: 14
2 1: 15 1: 6 1: 8
3 1: 15 1: 6 9: 20
4 14: 25 7: 25 15: 20
5 1: 13 7: 25 1: 7
6 16: 25 1: 6 1: 12
7 1: 13 7: 25 8: 20
8 16: 25 1: 6 13: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 50 x 52 x 38 = 98800
PhiOnMesh: Number of (b)points on node 0 = 2160
PhiOnMesh: nlist on node 0 = 4788
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.794602 -465.811891 -465.811891 0.006967 -2.312735 0.066254
scf: 2 -465.811201 -465.811745 -465.811745 0.002796 -2.271142 0.107583
scf: 3 -465.812082 -465.811992 -465.811992 0.001675 -2.296891 0.003782
scf: 4 -465.811995 -465.811994 -465.811994 0.000055 -2.296605 0.002123
scf: 5 -465.811995 -465.811995 -465.811995 0.000093 -2.296116 0.000741
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000929810
max |H_out - H_in| (eV) : 0.0007405902
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: 3 23
siesta: E_KS(eV) = -465.8120
siesta: Atomic forces (eV/Ang):
1 -0.591481 -0.197774 -0.333876
2 0.864589 0.421390 0.102842
3 -0.313630 -0.262236 -0.017983
----------------------------------------
Tot -0.040521 -0.038620 -0.249017
----------------------------------------
Max 0.864589
Res 0.422105 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.864589 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.22 -1.85 -0.84 -0.67 -0.34 -1.92
(Free)E + p*V (eV/cell) -465.3093
Target enthalpy (eV/cell) -465.8120
siesta: Stress tensor (static) (eV/Ang**3):
-0.002000 -0.001176 -0.000206
-0.001176 -0.000623 -0.000145
-0.000208 -0.000145 -0.000366
siesta: Pressure (static): 1.59650352 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.002007 -0.001200 -0.000210
-0.001201 -0.001153 -0.000417
-0.000212 -0.000417 -0.000522
siesta: Pressure (total): 1.96622328 kBar
siesta: Temp_ion = 560.046 K
====================================
Begin MD step = 6
====================================
outcoor: Atomic coordinates (Ang):
0.01076082 0.00033595 0.01189836 1 1 O
0.63238999 0.72646742 0.01435719 2 2 H
-0.80990572 0.44483715 -0.24522877 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 6
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 8: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 7 6: 25 1: 6
6 1: 7 1: 5 1: 7
7 8: 25 6: 25 7: 20
8 1: 7 6: 25 7: 20
New grid distribution: 3
1 14: 25 7: 25 1: 14
2 1: 15 1: 6 1: 8
3 1: 15 1: 6 9: 20
4 14: 25 7: 25 15: 20
5 1: 13 7: 25 1: 7
6 16: 25 1: 6 1: 12
7 1: 13 7: 25 8: 20
8 16: 25 1: 6 13: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 50 x 52 x 38 = 98800
PhiOnMesh: Number of (b)points on node 0 = 2160
PhiOnMesh: nlist on node 0 = 4782
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.799108 -465.813675 -465.813675 0.006655 -2.278061 0.062918
scf: 2 -465.813069 -465.813550 -465.813550 0.002655 -2.238381 0.101272
scf: 3 -465.813850 -465.813770 -465.813770 0.001583 -2.262834 0.003808
scf: 4 -465.813772 -465.813771 -465.813771 0.000052 -2.262570 0.002131
scf: 5 -465.813773 -465.813772 -465.813772 0.000087 -2.262121 0.000714
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000869943
max |H_out - H_in| (eV) : 0.0007138576
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: 3 23
siesta: E_KS(eV) = -465.8138
siesta: Atomic forces (eV/Ang):
1 -0.504964 -0.329041 -0.295609
2 0.858696 0.465253 0.097221
3 -0.394532 -0.184402 -0.050708
----------------------------------------
Tot -0.040800 -0.048191 -0.249096
----------------------------------------
Max 0.858696
Res 0.422446 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.858696 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.46 -2.14 -0.87 -0.60 -0.44 -1.78
(Free)E + p*V (eV/cell) -465.2626
Target enthalpy (eV/cell) -465.8138
siesta: Stress tensor (static) (eV/Ang**3):
-0.002155 -0.001083 -0.000263
-0.001084 -0.000794 -0.000099
-0.000265 -0.000099 -0.000386
siesta: Pressure (static): 1.78098040 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.002158 -0.001111 -0.000272
-0.001112 -0.001337 -0.000375
-0.000274 -0.000375 -0.000541
siesta: Pressure (total): 2.15579946 kBar
siesta: Temp_ion = 566.971 K
====================================
Begin MD step = 7
====================================
outcoor: Atomic coordinates (Ang):
0.01078025 0.00092065 0.01195847 1 1 O
0.63228631 0.72642460 0.01551236 2 2 H
-0.81054713 0.43581934 -0.25006021 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 7
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 8: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 7 6: 25 1: 6
6 1: 7 1: 5 1: 7
7 8: 25 6: 25 7: 20
8 1: 7 6: 25 7: 20
New grid distribution: 3
1 16: 25 7: 25 1: 14
2 1: 15 1: 6 1: 8
3 1: 15 1: 6 9: 20
4 16: 25 7: 25 15: 20
5 1: 15 7: 25 1: 7
6 16: 25 1: 6 1: 12
7 1: 15 7: 25 8: 20
8 16: 25 1: 6 13: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 50 x 52 x 38 = 98800
PhiOnMesh: Number of (b)points on node 0 = 2160
PhiOnMesh: nlist on node 0 = 4795
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.803801 -465.815353 -465.815353 0.006286 -2.243205 0.058957
scf: 2 -465.814837 -465.815251 -465.815251 0.002492 -2.205844 0.094019
scf: 3 -465.815511 -465.815441 -465.815441 0.001477 -2.228751 0.003780
scf: 4 -465.815444 -465.815443 -465.815443 0.000048 -2.228515 0.002108
scf: 5 -465.815444 -465.815443 -465.815443 0.000080 -2.228114 0.000678
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000800792
max |H_out - H_in| (eV) : 0.0006782753
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: 3 23
siesta: E_KS(eV) = -465.8154
siesta: Atomic forces (eV/Ang):
1 -0.411081 -0.442575 -0.256968
2 0.838103 0.495115 0.090562
3 -0.468119 -0.109904 -0.082908
----------------------------------------
Tot -0.041097 -0.057363 -0.249314
----------------------------------------
Max 0.838103
Res 0.424884 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.838103 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.64 -2.38 -0.90 -0.54 -0.54 -1.62
(Free)E + p*V (eV/cell) -465.2256
Target enthalpy (eV/cell) -465.8154
siesta: Stress tensor (static) (eV/Ang**3):
-0.002271 -0.000978 -0.000317
-0.000978 -0.000933 -0.000055
-0.000319 -0.000055 -0.000405
siesta: Pressure (static): 1.92759023 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.002274 -0.001012 -0.000333
-0.001012 -0.001484 -0.000334
-0.000335 -0.000334 -0.000562
siesta: Pressure (total): 2.30704361 kBar
siesta: Temp_ion = 573.458 K
====================================
Begin MD step = 8
====================================
outcoor: Atomic coordinates (Ang):
0.01078984 0.00149476 0.01201242 1 1 O
0.63250058 0.72656962 0.01670189 2 2 H
-0.81136613 0.42675984 -0.25492309 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 8
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 8: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 7 6: 25 1: 6
6 1: 7 1: 5 1: 7
7 8: 25 6: 25 7: 20
8 1: 7 6: 25 7: 20
New grid distribution: 3
1 16: 25 7: 25 1: 14
2 1: 15 1: 6 1: 8
3 1: 15 1: 6 9: 20
4 16: 25 7: 25 15: 20
5 1: 15 7: 25 1: 7
6 16: 25 1: 6 1: 12
7 1: 15 7: 25 8: 20
8 16: 25 1: 6 13: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 50 x 52 x 38 = 98800
PhiOnMesh: Number of (b)points on node 0 = 2160
PhiOnMesh: nlist on node 0 = 4785
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.808660 -465.816970 -465.816970 0.005866 -2.208394 0.054464
scf: 2 -465.816545 -465.816891 -465.816891 0.002309 -2.173705 0.085976
scf: 3 -465.817109 -465.817051 -465.817051 0.001360 -2.194849 0.003693
scf: 4 -465.817053 -465.817052 -465.817052 0.000044 -2.194648 0.002104
scf: 5 -465.817054 -465.817053 -465.817053 0.000072 -2.194302 0.000634
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000722752
max |H_out - H_in| (eV) : 0.0006342515
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: 3 23
siesta: E_KS(eV) = -465.8171
siesta: Atomic forces (eV/Ang):
1 -0.311252 -0.537192 -0.218841
2 0.802759 0.510695 0.082794
3 -0.532378 -0.039750 -0.113778
----------------------------------------
Tot -0.040870 -0.066247 -0.249825
----------------------------------------
Max 0.802759
Res 0.427315 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.802759 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.77 -2.55 -0.93 -0.47 -0.63 -1.44
(Free)E + p*V (eV/cell) -465.1986
Target enthalpy (eV/cell) -465.8171
siesta: Stress tensor (static) (eV/Ang**3):
-0.002349 -0.000858 -0.000367
-0.000858 -0.001038 -0.000011
-0.000369 -0.000011 -0.000424
siesta: Pressure (static): 2.03530453 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.002352 -0.000901 -0.000390
-0.000901 -0.001594 -0.000295
-0.000392 -0.000295 -0.000584
siesta: Pressure (total): 2.41909964 kBar
siesta: Temp_ion = 579.728 K
====================================
Begin MD step = 9
====================================
outcoor: Atomic coordinates (Ang):
0.01079198 0.00205600 0.01206113 1 1 O
0.63301939 0.72690837 0.01792282 2 2 H
-0.81238710 0.41768526 -0.25982915 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 9
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 8: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 7 6: 25 1: 6
6 1: 7 1: 5 1: 7
7 8: 25 6: 25 7: 20
8 1: 7 6: 25 7: 20
New grid distribution: 3
1 16: 25 7: 25 1: 14
2 1: 15 1: 6 1: 8
3 1: 15 1: 6 9: 20
4 16: 25 7: 25 15: 20
5 1: 15 7: 25 1: 7
6 16: 25 1: 6 1: 12
7 1: 15 7: 25 8: 20
8 16: 25 1: 6 13: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 50 x 52 x 38 = 98800
PhiOnMesh: Number of (b)points on node 0 = 2160
PhiOnMesh: nlist on node 0 = 4784
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.813653 -465.818566 -465.818566 0.005696 -2.173858 0.049540
scf: 2 -465.818229 -465.818508 -465.818508 0.002111 -2.142132 0.077307
scf: 3 -465.818687 -465.818639 -465.818639 0.001233 -2.161334 0.003540
scf: 4 -465.818642 -465.818640 -465.818640 0.000043 -2.161175 0.002129
scf: 5 -465.818642 -465.818641 -465.818641 0.000070 -2.160892 0.000617
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000695000
max |H_out - H_in| (eV) : 0.0006165140
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: 3 23
siesta: E_KS(eV) = -465.8186
siesta: Atomic forces (eV/Ang):
1 -0.208954 -0.611822 -0.181604
2 0.752982 0.512119 0.073839
3 -0.584800 0.025257 -0.142331
----------------------------------------
Tot -0.040773 -0.074446 -0.250096
----------------------------------------
Max 0.752982
Res 0.427987 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.752982 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.83 -2.67 -0.97 -0.41 -0.71 -1.26
(Free)E + p*V (eV/cell) -465.1825
Target enthalpy (eV/cell) -465.8186
siesta: Stress tensor (static) (eV/Ang**3):
-0.002383 -0.000729 -0.000411
-0.000729 -0.001108 0.000031
-0.000413 0.000031 -0.000442
siesta: Pressure (static): 2.10053430 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.002389 -0.000783 -0.000442
-0.000784 -0.001666 -0.000257
-0.000444 -0.000257 -0.000604
siesta: Pressure (total): 2.48852579 kBar
siesta: Temp_ion = 585.931 K
====================================
Begin MD step = 10
====================================
outcoor: Atomic coordinates (Ang):
0.01078911 0.00260258 0.01210549 1 1 O
0.63382386 0.72744140 0.01917177 2 2 H
-0.81362992 0.40862027 -0.26478919 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 10
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 8: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 7 6: 25 1: 6
6 1: 7 1: 5 1: 7
7 8: 25 6: 25 7: 20
8 1: 7 6: 25 7: 20
New grid distribution: 3
1 16: 25 7: 25 1: 14
2 1: 15 1: 6 1: 8
3 1: 15 1: 6 9: 20
4 16: 25 7: 25 15: 20
5 1: 15 7: 25 1: 7
6 16: 25 1: 6 1: 12
7 1: 15 7: 25 8: 20
8 16: 25 1: 6 13: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 50 x 52 x 38 = 98800
PhiOnMesh: Number of (b)points on node 0 = 2160
PhiOnMesh: nlist on node 0 = 4778
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.818726 -465.820165 -465.820165 0.005797 -2.139839 0.044288
scf: 2 -465.819910 -465.820127 -465.820127 0.001902 -2.111303 0.068182
scf: 3 -465.820269 -465.820230 -465.820230 0.001100 -2.128425 0.003367
scf: 4 -465.820233 -465.820232 -465.820232 0.000042 -2.128314 0.002128
scf: 5 -465.820233 -465.820233 -465.820233 0.000068 -2.128102 0.000665
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000676877
max |H_out - H_in| (eV) : 0.0006654102
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: 3 23
siesta: E_KS(eV) = -465.8202
siesta: Atomic forces (eV/Ang):
1 -0.106819 -0.666521 -0.146575
2 0.689437 0.499940 0.063678
3 -0.623453 0.084330 -0.167656
----------------------------------------
Tot -0.040835 -0.082251 -0.250553
----------------------------------------
Max 0.689437
Res 0.425621 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.689437 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.81 -2.73 -1.00 -0.36 -0.78 -1.06
(Free)E + p*V (eV/cell) -465.1776
Target enthalpy (eV/cell) -465.8202
siesta: Stress tensor (static) (eV/Ang**3):
-0.002368 -0.000591 -0.000445
-0.000592 -0.001146 0.000070
-0.000447 0.000070 -0.000459
siesta: Pressure (static): 2.12172738 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.002379 -0.000659 -0.000486
-0.000659 -0.001704 -0.000222
-0.000488 -0.000222 -0.000624
siesta: Pressure (total): 2.51387010 kBar
siesta: Temp_ion = 592.122 K
====================================
Begin MD step = 11
====================================
outcoor: Atomic coordinates (Ang):
0.01078368 0.00313321 0.01214634 1 1 O
0.63488988 0.72816410 0.02044487 2 2 H
-0.81510926 0.39958726 -0.26981284 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 11
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 8: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 7 6: 25 1: 6
6 1: 7 1: 5 1: 7
7 8: 25 6: 25 7: 20
8 1: 7 6: 25 7: 20
New grid distribution: 3
1 16: 25 7: 25 1: 14
2 1: 14 1: 6 1: 8
3 1: 14 1: 6 9: 20
4 16: 25 7: 25 15: 20
5 1: 15 7: 25 1: 7
6 15: 25 1: 6 1: 12
7 1: 15 7: 25 8: 20
8 15: 25 1: 6 13: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 50 x 52 x 38 = 98800
PhiOnMesh: Number of (b)points on node 0 = 2160
PhiOnMesh: nlist on node 0 = 4774
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.823785 -465.821750 -465.821750 0.005898 -2.106581 0.038829
scf: 2 -465.821568 -465.821729 -465.821729 0.001685 -2.081386 0.058799
scf: 3 -465.821838 -465.821808 -465.821808 0.000963 -2.096335 0.003325
scf: 4 -465.821811 -465.821809 -465.821809 0.000040 -2.096279 0.002093
scf: 5 -465.821811 -465.821810 -465.821810 0.000065 -2.096144 0.000706
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000651193
max |H_out - H_in| (eV) : 0.0007060195
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: 3 23
siesta: E_KS(eV) = -465.8218
siesta: Atomic forces (eV/Ang):
1 -0.008113 -0.701184 -0.114951
2 0.613268 0.475154 0.052240
3 -0.646536 0.136775 -0.188833
----------------------------------------
Tot -0.041380 -0.089254 -0.251543
----------------------------------------
Max 0.701184
Res 0.419247 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.701184 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.72 -2.73 -1.03 -0.31 -0.84 -0.85
(Free)E + p*V (eV/cell) -465.1843
Target enthalpy (eV/cell) -465.8218
siesta: Stress tensor (static) (eV/Ang**3):
-0.002303 -0.000450 -0.000469
-0.000451 -0.001152 0.000105
-0.000471 0.000105 -0.000473
siesta: Pressure (static): 2.09746629 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.002320 -0.000532 -0.000520
-0.000533 -0.001707 -0.000191
-0.000522 -0.000191 -0.000643
siesta: Pressure (total): 2.49375255 kBar
siesta: Temp_ion = 598.254 K
====================================
Begin MD step = 12
====================================
outcoor: Atomic coordinates (Ang):
0.01077806 0.00364704 0.01218444 1 1 O
0.63618856 0.72906706 0.02173780 2 2 H
-0.81683388 0.39060615 -0.27490813 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 12
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 8: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 7 6: 25 1: 6
6 1: 7 1: 5 1: 7
7 8: 25 6: 25 7: 20
8 1: 7 6: 25 7: 20
New grid distribution: 3
1 16: 25 7: 25 1: 14
2 1: 14 1: 6 1: 8
3 1: 14 1: 6 9: 20
4 16: 25 7: 25 15: 20
5 1: 15 7: 25 1: 7
6 15: 25 1: 6 1: 12
7 1: 15 7: 25 8: 20
8 15: 25 1: 6 13: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 50 x 52 x 38 = 98800
PhiOnMesh: Number of (b)points on node 0 = 2160
PhiOnMesh: nlist on node 0 = 4765
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.828716 -465.823283 -465.823283 0.005994 -2.074326 0.033277
scf: 2 -465.823163 -465.823277 -465.823277 0.001467 -2.052552 0.049336
scf: 3 -465.823358 -465.823335 -465.823335 0.000823 -2.065280 0.003217
scf: 4 -465.823337 -465.823336 -465.823336 0.000040 -2.065284 0.002020
scf: 5 -465.823338 -465.823337 -465.823337 0.000062 -2.065233 0.000733
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000616151
max |H_out - H_in| (eV) : 0.0007334626
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: 3 23
siesta: E_KS(eV) = -465.8233
siesta: Atomic forces (eV/Ang):
1 0.084619 -0.717414 -0.086730
2 0.525933 0.439030 0.039570
3 -0.652934 0.182009 -0.205123
----------------------------------------
Tot -0.042381 -0.096375 -0.252283
----------------------------------------
Max 0.717414
Res 0.408495 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.717414 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.55 -2.69 -1.06 -0.26 -0.87 -0.65
(Free)E + p*V (eV/cell) -465.2018
Target enthalpy (eV/cell) -465.8233
siesta: Stress tensor (static) (eV/Ang**3):
-0.002188 -0.000307 -0.000483
-0.000307 -0.001129 0.000137
-0.000484 0.000137 -0.000485
siesta: Pressure (static): 2.03078758 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.002214 -0.000405 -0.000544
-0.000405 -0.001679 -0.000163
-0.000546 -0.000163 -0.000659
siesta: Pressure (total): 2.43117794 kBar
siesta: Temp_ion = 604.177 K
====================================
Begin MD step = 13
====================================
outcoor: Atomic coordinates (Ang):
0.01077447 0.00414370 0.01222047 1 1 O
0.63768675 0.73013656 0.02304573 2 2 H
-0.81880620 0.38169408 -0.28008124 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 13
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 8: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 7 6: 25 1: 6
6 1: 7 1: 5 1: 7
7 8: 25 6: 25 7: 20
8 1: 7 6: 25 7: 20
New grid distribution: 3
1 16: 25 7: 25 1: 14
2 1: 13 1: 6 1: 8
3 1: 13 1: 6 9: 20
4 16: 25 7: 25 15: 20
5 1: 15 7: 25 1: 7
6 14: 25 1: 6 1: 12
7 1: 15 7: 25 8: 20
8 14: 25 1: 6 13: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 50 x 52 x 38 = 98800
PhiOnMesh: Number of (b)points on node 0 = 2160
PhiOnMesh: nlist on node 0 = 4776
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.833367 -465.824691 -465.824691 0.006085 -2.043330 0.027742
scf: 2 -465.824620 -465.824696 -465.824696 0.001249 -2.024982 0.039972
scf: 3 -465.824754 -465.824738 -465.824738 0.000684 -2.035487 0.003022
scf: 4 -465.824740 -465.824739 -465.824739 0.000039 -2.035558 0.001902
scf: 5 -465.824740 -465.824739 -465.824739 0.000057 -2.035592 0.000741
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000569961
max |H_out - H_in| (eV) : 0.0007407038
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: 3 23
siesta: E_KS(eV) = -465.8247
siesta: Atomic forces (eV/Ang):
1 0.169232 -0.715752 -0.062969
2 0.429213 0.393252 0.025706
3 -0.641418 0.219803 -0.215794
----------------------------------------
Tot -0.042973 -0.102697 -0.253058
----------------------------------------
Max 0.715752
Res 0.393098 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.715752 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.30 -2.60 -1.08 -0.22 -0.89 -0.44
(Free)E + p*V (eV/cell) -465.2306
Target enthalpy (eV/cell) -465.8247
siesta: Stress tensor (static) (eV/Ang**3):
-0.002023 -0.000162 -0.000482
-0.000163 -0.001079 0.000166
-0.000484 0.000166 -0.000493
siesta: Pressure (static): 1.91970226 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.002057 -0.000276 -0.000554
-0.000277 -0.001623 -0.000137
-0.000556 -0.000138 -0.000672
siesta: Pressure (total): 2.32405650 kBar
siesta: Temp_ion = 609.642 K
====================================
Begin MD step = 14
====================================
outcoor: Atomic coordinates (Ang):
0.01077492 0.00462321 0.01225498 1 1 O
0.63934778 0.73135526 0.02436342 2 2 H
-0.82102185 0.37286540 -0.28533621 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 14
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 6 6: 25 1: 6
6 1: 7 1: 5 1: 7
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 16: 25 7: 25 1: 14
2 1: 13 1: 6 1: 8
3 1: 13 1: 6 9: 20
4 16: 25 7: 25 15: 20
5 1: 15 7: 25 1: 7
6 14: 25 1: 6 1: 12
7 1: 15 7: 25 8: 20
8 14: 25 1: 6 13: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5054
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.837598 -465.825903 -465.825903 0.006167 -2.013832 0.022343
scf: 2 -465.825870 -465.825916 -465.825916 0.001038 -1.998839 0.030890
scf: 3 -465.825957 -465.825945 -465.825945 0.000549 -2.007174 0.002720
scf: 4 -465.825947 -465.825946 -465.825946 0.000036 -2.007313 0.001749
scf: 5 -465.825947 -465.825946 -465.825946 0.000056 -2.007434 0.000716
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000555895
max |H_out - H_in| (eV) : 0.0007155612
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: 3 23
siesta: E_KS(eV) = -465.8259
siesta: Atomic forces (eV/Ang):
1 0.242968 -0.698503 -0.044341
2 0.325142 0.339673 0.010671
3 -0.611658 0.250116 -0.220433
----------------------------------------
Tot -0.043548 -0.108714 -0.254102
----------------------------------------
Max 0.698503
Res 0.373480 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.698503 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -2.97 -2.47 -1.09 -0.19 -0.88 -0.24
(Free)E + p*V (eV/cell) -465.2693
Target enthalpy (eV/cell) -465.8259
siesta: Stress tensor (static) (eV/Ang**3):
-0.001809 -0.000020 -0.000467
-0.000021 -0.001008 0.000191
-0.000469 0.000191 -0.000496
siesta: Pressure (static): 1.76922027 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.001853 -0.000150 -0.000550
-0.000151 -0.001543 -0.000116
-0.000552 -0.000116 -0.000681
siesta: Pressure (total): 2.17723247 kBar
siesta: Temp_ion = 614.322 K
====================================
Begin MD step = 15
====================================
outcoor: Atomic coordinates (Ang):
0.01078120 0.00508600 0.01228843 1 1 O
0.64113215 0.73270282 0.02568515 2 2 H
-0.82346954 0.36413160 -0.29067480 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 15
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 6 6: 25 1: 6
6 1: 7 1: 5 1: 7
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 7: 20
New grid distribution: 3
1 16: 25 7: 25 1: 14
2 1: 14 1: 6 1: 8
3 1: 14 1: 6 9: 20
4 16: 25 7: 25 15: 20
5 1: 15 7: 25 1: 7
6 15: 25 1: 6 1: 12
7 1: 15 7: 25 8: 20
8 15: 25 1: 6 13: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5052
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.841237 -465.826810 -465.826810 0.006237 -1.986072 0.017184
scf: 2 -465.826804 -465.826829 -465.826829 0.000836 -1.974295 0.022256
scf: 3 -465.826858 -465.826849 -465.826849 0.000421 -1.980569 0.002325
scf: 4 -465.826850 -465.826849 -465.826849 0.000032 -1.980768 0.001601
scf: 5 -465.826850 -465.826850 -465.826850 0.000059 -1.980971 0.000633
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000589885
max |H_out - H_in| (eV) : 0.0006327504
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: 3 23
siesta: E_KS(eV) = -465.8268
siesta: Atomic forces (eV/Ang):
1 0.304117 -0.667010 -0.031479
2 0.215452 0.280127 -0.005444
3 -0.563201 0.273301 -0.218581
----------------------------------------
Tot -0.043632 -0.113582 -0.255505
----------------------------------------
Max 0.667010
Res 0.350074 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.667010 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -2.56 -2.31 -1.10 -0.16 -0.85 -0.04
(Free)E + p*V (eV/cell) -465.3184
Target enthalpy (eV/cell) -465.8268
siesta: Stress tensor (static) (eV/Ang**3):
-0.001546 0.000119 -0.000436
0.000118 -0.000914 0.000211
-0.000438 0.000211 -0.000494
siesta: Pressure (static): 1.57765995 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.001600 -0.000026 -0.000530
-0.000027 -0.001440 -0.000098
-0.000531 -0.000098 -0.000685
siesta: Pressure (total): 1.98880380 kBar
siesta: Temp_ion = 617.823 K
====================================
Begin MD step = 16
====================================
outcoor: Atomic coordinates (Ang):
0.01079476 0.00553281 0.01232113 1 1 O
0.64299827 0.73415664 0.02700482 2 2 H
-0.82613090 0.35550149 -0.29609632 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 16
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 6 6: 25 1: 7
6 1: 7 1: 5 1: 7
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 8: 20
New grid distribution: 3
1 16: 25 7: 25 1: 14
2 11: 25 1: 6 1: 13
3 1: 10 1: 6 9: 20
4 11: 25 1: 6 14: 20
5 1: 15 7: 25 1: 7
6 1: 10 1: 6 1: 8
7 1: 15 7: 25 8: 20
8 16: 25 7: 25 15: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5042
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.844124 -465.827311 -465.827311 0.006292 -1.960265 0.016630
scf: 2 -465.827321 -465.827334 -465.827334 0.000733 -1.951499 0.014241
scf: 3 -465.827354 -465.827347 -465.827347 0.000304 -1.955893 0.002141
scf: 4 -465.827348 -465.827348 -465.827348 0.000034 -1.956124 0.001537
scf: 5 -465.827348 -465.827348 -465.827348 0.000064 -1.956404 0.000434
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000638905
max |H_out - H_in| (eV) : 0.0004342194
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: 3 23
siesta: E_KS(eV) = -465.8273
siesta: Atomic forces (eV/Ang):
1 0.350923 -0.625263 -0.024160
2 0.102587 0.216661 -0.022457
3 -0.497173 0.289684 -0.210267
----------------------------------------
Tot -0.043663 -0.118918 -0.256884
----------------------------------------
Max 0.625263
Res 0.324545 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.625263 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -2.09 -2.12 -1.10 -0.13 -0.79 0.14
(Free)E + p*V (eV/cell) -465.3748
Target enthalpy (eV/cell) -465.8273
siesta: Stress tensor (static) (eV/Ang**3):
-0.001244 0.000249 -0.000391
0.000249 -0.000809 0.000228
-0.000392 0.000228 -0.000488
siesta: Pressure (static): 1.35660445 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.001307 0.000091 -0.000495
0.000090 -0.001324 -0.000084
-0.000496 -0.000084 -0.000684
siesta: Pressure (total): 1.77009150 kBar
siesta: Temp_ion = 619.727 K
====================================
Begin MD step = 17
====================================
outcoor: Atomic coordinates (Ang):
0.01081672 0.00596465 0.01235325 1 1 O
0.64490329 0.73569266 0.02831597 2 2 H
-0.82898087 0.34698127 -0.30159760 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 17
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 6 6: 25 1: 7
6 1: 7 1: 5 1: 7
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 8: 20
New grid distribution: 3
1 16: 25 7: 25 1: 14
2 11: 25 1: 6 1: 13
3 1: 10 1: 6 9: 20
4 11: 25 1: 6 14: 20
5 1: 15 7: 25 1: 7
6 1: 10 1: 6 1: 8
7 1: 15 7: 25 8: 20
8 16: 25 7: 25 15: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5016
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.846085 -465.827280 -465.827280 0.006331 -1.936594 0.017059
scf: 2 -465.827299 -465.827304 -465.827304 0.000644 -1.930565 0.012305
scf: 3 -465.827320 -465.827314 -465.827314 0.000232 -1.933331 0.002532
scf: 4 -465.827315 -465.827314 -465.827314 0.000034 -1.933540 0.001696
scf: 5 -465.827315 -465.827315 -465.827315 0.000072 -1.933888 0.000244
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000723844
max |H_out - H_in| (eV) : 0.0002441246
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: 3 23
siesta: E_KS(eV) = -465.8273
siesta: Atomic forces (eV/Ang):
1 0.383005 -0.575405 -0.022361
2 -0.011816 0.151067 -0.040367
3 -0.413761 0.300392 -0.195161
----------------------------------------
Tot -0.042571 -0.123946 -0.257888
----------------------------------------
Max 0.575405
Res 0.298589 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.575405 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -1.56 -1.92 -1.08 -0.11 -0.71 0.33
(Free)E + p*V (eV/cell) -465.4386
Target enthalpy (eV/cell) -465.8273
siesta: Stress tensor (static) (eV/Ang**3):
-0.000901 0.000374 -0.000331
0.000373 -0.000694 0.000242
-0.000331 0.000242 -0.000475
siesta: Pressure (static): 1.10576037 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.000973 0.000204 -0.000443
0.000204 -0.001197 -0.000071
-0.000443 -0.000071 -0.000677
siesta: Pressure (total): 1.52052170 kBar
siesta: Temp_ion = 619.611 K
====================================
Begin MD step = 18
====================================
outcoor: Atomic coordinates (Ang):
0.01084786 0.00638271 0.01238483 1 1 O
0.64680384 0.73728600 0.02961181 2 2 H
-0.83198780 0.33857501 -0.30717293 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 18
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 6 6: 25 1: 7
6 1: 7 1: 5 1: 7
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 8: 20
New grid distribution: 3
1 16: 25 7: 25 1: 14
2 11: 25 1: 6 1: 13
3 1: 10 1: 6 9: 20
4 11: 25 1: 6 14: 20
5 1: 15 7: 25 1: 7
6 1: 10 1: 6 1: 8
7 1: 15 7: 25 8: 20
8 16: 25 7: 25 15: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5012
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.846995 -465.826630 -465.826630 0.006349 -1.915218 0.017264
scf: 2 -465.826650 -465.826652 -465.826652 0.000570 -1.911529 0.010773
scf: 3 -465.826667 -465.826661 -465.826661 0.000221 -1.912993 0.002633
scf: 4 -465.826662 -465.826662 -465.826662 0.000034 -1.913126 0.001755
scf: 5 -465.826662 -465.826662 -465.826662 0.000076 -1.913465 0.000247
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000764012
max |H_out - H_in| (eV) : 0.0002474815
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: 3 23
siesta: E_KS(eV) = -465.8267
siesta: Atomic forces (eV/Ang):
1 0.400136 -0.519994 -0.026241
2 -0.125422 0.085150 -0.058824
3 -0.315154 0.306493 -0.173320
----------------------------------------
Tot -0.040440 -0.128351 -0.258385
----------------------------------------
Max 0.519994
Res 0.275062 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.519994 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -0.97 -1.71 -1.07 -0.10 -0.60 0.50
(Free)E + p*V (eV/cell) -465.5073
Target enthalpy (eV/cell) -465.8267
siesta: Stress tensor (static) (eV/Ang**3):
-0.000530 0.000490 -0.000257
0.000489 -0.000574 0.000252
-0.000257 0.000252 -0.000458
siesta: Pressure (static): 0.83439447 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.000608 0.000311 -0.000376
0.000311 -0.001065 -0.000062
-0.000377 -0.000062 -0.000665
siesta: Pressure (total): 1.24907795 kBar
siesta: Temp_ion = 617.075 K
====================================
Begin MD step = 19
====================================
outcoor: Atomic coordinates (Ang):
0.01088858 0.00678832 0.01241579 1 1 O
0.64865680 0.73891163 0.03088533 2 2 H
-0.83511429 0.33028503 -0.31281400 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 19
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 6 6: 25 1: 7
6 1: 7 1: 5 1: 7
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 8: 20
New grid distribution: 3
1 16: 25 7: 25 1: 14
2 11: 25 1: 6 1: 13
3 1: 10 1: 6 9: 20
4 11: 25 1: 6 14: 20
5 1: 15 7: 25 1: 7
6 1: 10 1: 6 1: 8
7 1: 15 7: 25 8: 20
8 16: 25 7: 25 15: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5004
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.846731 -465.825265 -465.825265 0.006357 -1.896262 0.017292
scf: 2 -465.825284 -465.825287 -465.825287 0.000553 -1.894372 0.010917
scf: 3 -465.825301 -465.825296 -465.825296 0.000217 -1.894889 0.002528
scf: 4 -465.825296 -465.825296 -465.825296 0.000035 -1.894937 0.001749
scf: 5 -465.825296 -465.825296 -465.825296 0.000069 -1.895181 0.000339
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000685594
max |H_out - H_in| (eV) : 0.0003387599
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: 3 23
siesta: E_KS(eV) = -465.8253
siesta: Atomic forces (eV/Ang):
1 0.401690 -0.461465 -0.035129
2 -0.236458 0.020504 -0.077641
3 -0.203646 0.309543 -0.144731
----------------------------------------
Tot -0.038414 -0.131419 -0.257501
----------------------------------------
Max 0.461465
Res 0.257366 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.461465 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -0.35 -1.49 -1.04 -0.09 -0.47 0.66
(Free)E + p*V (eV/cell) -465.5804
Target enthalpy (eV/cell) -465.8253
siesta: Stress tensor (static) (eV/Ang**3):
-0.000133 0.000595 -0.000170
0.000595 -0.000451 0.000260
-0.000170 0.000260 -0.000436
siesta: Pressure (static): 0.54509316 kBar
siesta: Stress tensor (total) (eV/Ang**3):
-0.000216 0.000411 -0.000295
0.000410 -0.000930 -0.000054
-0.000296 -0.000054 -0.000648
siesta: Pressure (total): 0.95807977 kBar
siesta: Temp_ion = 611.788 K
====================================
Begin MD step = 20
====================================
outcoor: Atomic coordinates (Ang):
0.01093891 0.00718287 0.01244591 1 1 O
0.65042006 0.74054504 0.03212940 2 2 H
-0.83831804 0.32211247 -0.31850999 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 20
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 6 6: 25 1: 7
6 1: 7 1: 5 1: 7
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 8: 20
New grid distribution: 3
1 16: 25 7: 25 1: 14
2 11: 25 1: 6 1: 13
3 1: 10 1: 6 9: 20
4 11: 25 1: 6 14: 20
5 1: 15 7: 25 1: 7
6 1: 10 1: 6 1: 8
7 1: 15 7: 25 8: 20
8 16: 25 7: 25 15: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5008
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.845218 -465.823129 -465.823129 0.006364 -1.879680 0.017263
scf: 2 -465.823144 -465.823148 -465.823148 0.000541 -1.879275 0.010996
scf: 3 -465.823163 -465.823158 -465.823158 0.000217 -1.879019 0.002336
scf: 4 -465.823158 -465.823158 -465.823158 0.000035 -1.878992 0.001702
scf: 5 -465.823158 -465.823158 -465.823158 0.000059 -1.879144 0.000499
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000591572
max |H_out - H_in| (eV) : 0.0004987894
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: 3 23
siesta: E_KS(eV) = -465.8232
siesta: Atomic forces (eV/Ang):
1 0.390093 -0.403259 -0.048481
2 -0.343009 -0.041021 -0.096604
3 -0.082914 0.310139 -0.110030
----------------------------------------
Tot -0.035830 -0.134141 -0.255115
----------------------------------------
Max 0.403259
Res 0.249662 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.403259 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 0.31 -1.28 -1.00 -0.07 -0.32 0.81
(Free)E + p*V (eV/cell) -465.6550
Target enthalpy (eV/cell) -465.8232
siesta: Stress tensor (static) (eV/Ang**3):
0.000276 0.000691 -0.000071
0.000691 -0.000332 0.000266
-0.000072 0.000266 -0.000409
siesta: Pressure (static): 0.24824066 kBar
siesta: Stress tensor (total) (eV/Ang**3):
0.000191 0.000504 -0.000200
0.000504 -0.000798 -0.000046
-0.000201 -0.000046 -0.000624
siesta: Pressure (total): 0.65768849 kBar
siesta: Temp_ion = 603.530 K
siesta: Program's energy decomposition (eV):
siesta: Ebs = -103.241556
siesta: Eions = 815.854478
siesta: Ena = 175.088041
siesta: Ekin = 352.894003
siesta: Enl = -62.841393
siesta: Eso = 0.000000
siesta: Edftu = 0.000000
siesta: DEna = -2.947026
siesta: DUscf = 0.766537
siesta: DUext = 0.000000
siesta: Exc = -112.928841
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
siesta: Emolmec = 0.000000
siesta: Ekinion = 0.156019
siesta: Eharris = -465.667140
siesta: Etot = -465.667139
siesta: FreeEng = -465.667139
siesta: Final energy (eV):
siesta: Band Struct. = -103.241556
siesta: Kinetic = 352.894003
siesta: Hartree = 415.380290
siesta: Edftu = 0.000000
siesta: Eso = 0.000000
siesta: Ext. field = 0.000000
siesta: Exch.-corr. = -112.928841
siesta: Ion-electron = -1138.933270
siesta: Ion-ion = 17.764660
siesta: Ekinion = 0.156019
siesta: Total = -465.667139
siesta: Fermi = -1.879144
siesta: Atomic forces (eV/Ang):
siesta: 1 0.390093 -0.403259 -0.048481
siesta: 2 -0.343009 -0.041021 -0.096604
siesta: 3 -0.082914 0.310139 -0.110030
siesta: ----------------------------------------
siesta: Tot -0.035830 -0.134141 -0.255115
siesta: Stress tensor (static) (eV/Ang**3):
siesta: 0.000276 0.000691 -0.000071
siesta: 0.000691 -0.000332 0.000266
siesta: -0.000072 0.000266 -0.000409
siesta: Cell volume = 409.600000 Ang**3
siesta: Pressure (static):
siesta: Solid Molecule Units
siesta: 0.00000169 0.00000194 Ry/Bohr**3
siesta: 0.00015494 0.00017848 eV/Ang**3
siesta: 0.24824066 0.28596547 kBar
(Free)E+ p_basis*V_orbitals = -465.237991
(Free)Eharris+ p_basis*V_orbitals = -465.237991
siesta: Electric dipole (a.u.) = -0.098717 0.493917 -0.147951
siesta: Electric dipole (Debye) = -0.250913 1.255413 -0.376055
cite: Please see "h2o.bib" for an exhaustive BiBTeX file.
cite: Please clearly indicate Siesta version in published work: v4.1-b4-351
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: 22-JAN-2021 23:12:56
Job completed
Siesta Version : v4.1-b4-351
Architecture : x86_64-linux-n-62-26-19
Compiler version: GNU Fortran (GCC) 9.3.0
Compiler flags : mpifort -m64 -fPIC -O3 -march=native -ftree-vectorize -fexpensive-optimizatioons -funroll-loops -fprefetch-loop-arrays -fno-second-underscore -flto
PP flags : -I/dtu/sw/dcc/SL73/2020-aug/generic/build-tools/1.0/include -I/dtu/sw/dcc/SL773/2020-aug/generic/gcc/9.3.0/include -I/dtu/sw/dcc/SL73/2020-aug/generic/gcc/9.3.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/zlib/1.2.11/include -I/dtu/sw/dcc/SL73/2020-aug/generic/numactl/2.0.12/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/libxml2/2.9.10/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/hwloc/2.2.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/knem/1.1.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/ucx/1.8.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/openmpi/4.0.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/szip/2.1.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/hdf5/1.12.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/pnetcdf/1.12.1/include -I/dtu/sw/dcc/SL73/2020-aug/generic/gen-zlib/1.2.11/include -I/dtu/sw/dcc/SL73/2020-aug/generic/openssl/1.1.1/include -I/dtu/sw/dcc/SL73/2020-aug/generic/libssh2/1.8.2/include -I/dtu/sw/dcc/SL73/2020-aug/generic/curl/7.65.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/netcdf/4.7.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/fftw/3.3.8/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/parmetis/4.0.3/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/scalapack/2.1.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/lapack/3.9.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/blis/0.7.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/scotch/6.0.9/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/mumps/5.3.3/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/elpa/2020.05.001/include -DSIESTA__ELPA -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DCDF4 -DSIESTA__FLOOK -DNCDF -DNCDF_4 -DNCDF_PARALLEL -DTS_NOCHECKS -DSIESTA__METIS -DSIESTA__MUMPS -DSIESTA__MRRR -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/elpa/2020.05.001/include/elpa
Libraries : libncdf.a libfdict.a -lnetcdff -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lz -lzmuumps -lmumps_common -lesmumps -lscotch -lscotcherr -lpord -lparmetis -lmetis -lelpa -lscalapack -llapack -lblis -L/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/lib -Wl,-rpath=/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/lib -lflookall -ldl -flto -fuse-linker-plugin -lmetis
PARALLEL version
NetCDF support
NetCDF-4 support
NetCDF-4 MPI-IO support
METIS ordering support
Lua support
* Running on 8 nodes in parallel
>> Start of run: 22-JAN-2021 23:12:57
***********************
* WELCOME TO SIESTA *
***********************
reinit: Reading from standard input
reinit: Dumped input in INPUT_TMP.08870
************************** Dump of input data file ****************************
SystemName Water molecule -- md verlet
SystemLabel h2o
NumberOfAtoms 3
NumberOfSpecies 2
MeshCutoff 100 Ry
%block ChemicalSpeciesLabel
1 8 O # Species index, atomic number, species label
2 1 H
%endblock ChemicalSpeciesLabel
LatticeConstant 8.0 Ang
%block LatticeVectors
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 0.8
%endblock LatticeVectors
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
Solution.Method diagon
MeshCutoff 100 Ry
WriteCoorStep .true.
WriteForces .true.
WriteMDHistory .true.
MD.UseSaveXV T
MD.TypeOfRun Verlet
MD.InitialTemperature 600 K
MD.Initial.Time.Step 1
MD.Final.Time.Step 20
MD.Length.Time.Step 0.2 fs
************************** End of input data file *****************************
reinit: -----------------------------------------------------------------------
reinit: System Name: Water molecule -- md verlet
reinit: -----------------------------------------------------------------------
reinit: System Label: h2o
reinit: -----------------------------------------------------------------------
initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Species number: 1 Atomic number: 8 Label: O
Species number: 2 Atomic number: 1 Label: H
Ground state valence configuration: 2s02 2p04
Reading pseudopotential information in formatted form from O.psf
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
Valence configuration for pseudopotential generation:
1s( 1.00) rc: 1.25
2p( 0.00) rc: 1.25
3d( 0.00) rc: 1.25
4f( 0.00) rc: 1.25
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.
===============================================================================
O Z= 8 Mass= 16.000 Charge= 0.17977+309
Lmxo=1 Lmxkb= 3 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=2
i=1 nzeta=2 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 0.0000
lambdas: 1.0000 1.0000
L=1 Nsemic=0 Cnfigmx=2
i=1 nzeta=2 polorb=1 (2p)
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
===============================================================================
atom: Called for O (Z = 8)
read_vps: Pseudopotential generation method:
read_vps: ATM3 Troullier-Martins
Valence charge for ps generation: 6.00000
xc_check: Exchange-correlation functional:
xc_check: Ceperley-Alder
V l=0 = -2*Zval/r beyond r= 1.1278
V l=1 = -2*Zval/r beyond r= 1.1278
V l=2 = -2*Zval/r beyond r= 1.1278
V l=3 = -2*Zval/r beyond r= 1.1138
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= 1.1278
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= 1.294105 el= -1.742414 Ekb= 9.135903 kbcos= 0.326910
l= 1 rc= 1.294105 el= -0.676589 Ekb= -8.124878 kbcos= -0.395047
l= 2 rc= 1.448233 el= 0.002386 Ekb= -2.039267 kbcos= -0.003484
l= 3 rc= 1.561052 el= 0.003508 Ekb= -0.799141 kbcos= -0.000344
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 = -1.723766
kinetic = 1.614911
potential(screened) = -3.338677
potential(ionic) = -11.304675
izeta = 2
rmatch = 2.510382
splitnorm = 0.150000
energy = -1.471299
kinetic = 2.446434
potential(screened) = -3.917732
potential(ionic) = -12.476133
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 = -0.658841
kinetic = 5.005986
potential(screened) = -5.664827
potential(ionic) = -13.452360
izeta = 2
rmatch = 2.541963
splitnorm = 0.150000
energy = -0.367441
kinetic = 7.530509
potential(screened) = -7.897949
potential(ionic) = -16.611953
POLgen: Perturbative polarization orbital with L= 2
POLgen: Polarization orbital for state 2p
izeta = 1
rc = 3.937239
energy = 2.398520
kinetic = 4.716729
potential(screened) = -2.318209
potential(ionic) = -8.603170
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: _________________________________________________________________________
===============================================================================
H Z= 1 Mass= 1.0100 Charge= 0.17977+309
Lmxo=0 Lmxkb= 2 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=1
i=1 nzeta=2 polorb=1 (1s)
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
===============================================================================
atom: Called for H (Z = 1)
read_vps: Pseudopotential generation method:
read_vps: ATM3 Troullier-Martins
Valence charge for ps generation: 1.00000
xc_check: Exchange-correlation functional:
xc_check: Ceperley-Alder
V l=0 = -2*Zval/r beyond r= 1.2343
V l=1 = -2*Zval/r beyond r= 1.2189
V l=2 = -2*Zval/r beyond r= 1.2189
All V_l potentials equal beyond r= 1.2343
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r= 1.2343
VLOCAL1: 99.0% of the norm of Vloc inside 28.493 Ry
VLOCAL1: 99.9% of the norm of Vloc inside 64.935 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.45251
atom: Maximum radius for r*vlocal+2*Zval: 1.21892
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= 1.364359 el= -0.467325 Ekb= -2.005361 kbcos= -0.336422
l= 1 rc= 1.434438 el= 0.001430 Ekb= -0.501708 kbcos= -0.021697
l= 2 rc= 1.470814 el= 0.002365 Ekb= -0.190555 kbcos= -0.002281
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 = 4.828263
energy = -0.449375
kinetic = 0.929372
potential(screened) = -1.378747
potential(ionic) = -1.915047
izeta = 2
rmatch = 3.854947
splitnorm = 0.150000
energy = -0.336153
kinetic = 1.505294
potential(screened) = -1.841447
potential(ionic) = -2.413582
POLgen: Perturbative polarization orbital with L= 1
POLgen: Polarization orbital for state 1s
izeta = 1
rc = 4.828263
energy = 0.706972
kinetic = 1.396397
potential(screened) = -0.689424
potential(ionic) = -1.169792
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: 4.828263
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 2.510
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
4.828 3.855
1.000 1.000
%endblock PAO.Basis
prinput: ----------------------------------------------------------------------
Dumping basis to NetCDF file O.ion.nc
Dumping basis to NetCDF file H.ion.nc
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
WARNING: h2o.VERLET_RESTART not found--reading only XV file and moving back 1 time step using Euler
siesta: Atomic coordinates (Bohr) and species
siesta: 0.02068 0.01356 0.02352 1 1
siesta: 1.22899 1.39941 0.06068 2 2
siesta: -1.58422 0.60882 -0.60194 2 3
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: 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 = 2
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 = 1000
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 = F
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 = Verlet MD run
redata: Initial MD time step = 1
redata: Final MD time step = 20
redata: Length of MD time step = 0.2000 fs
redata: Initial Temperature of MD run = 600.0000 K
redata: Perform a MD quench = F
mix.SCF: Pulay mixing = Pulay
mix.SCF: Variant = stable
mix.SCF: History steps = 2
mix.SCF: Linear mixing weight = 0.250000
mix.SCF: Mixing weight = 0.250000
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 0.2500
weight.linear 0.2500
history 2
%endblock SCF.Mixer.Pulay
Size of DM history Fstack: 1
Total number of electrons: 8.000000
Total ionic charge: 8.000000
* ProcessorY, Blocksize: 2 3
* Orbital distribution balance (max,min): 3 2
Kpoints in: 1 . Kpoints trimmed: 1
siesta: k-grid: Number of k-points = 1
siesta: k-grid: Cutoff (effective) = 3.200 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 = 3
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
ts: **************************************************************
ts: Save H and S matrices = F
ts: Save DM and EDM matrices = F
ts: Only save the overlap matrix S = F
ts: **************************************************************
************************ Begin: TS CHECKS AND WARNINGS ************************
************************ End: TS CHECKS AND WARNINGS **************************
====================================
Begin MD step = 1
====================================
outcoor: Atomic coordinates (Ang):
0.01094358 0.00717805 0.01244532 1 1 O
0.65035500 0.74053726 0.03211107 2 2 H
-0.83833377 0.32217130 -0.31853086 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 1
Initializing Density Matrix...
DM filled with atomic data:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 6 6: 25 1: 7
6 1: 7 1: 5 1: 7
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 8: 20
New grid distribution: 3
1 16: 25 7: 25 1: 14
2 11: 25 1: 6 1: 13
3 1: 10 1: 6 9: 20
4 11: 25 1: 6 14: 20
5 1: 15 7: 25 1: 7
6 1: 10 1: 6 1: 8
7 1: 15 7: 25 8: 20
8 16: 25 7: 25 15: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5008
stepf: Fermi-Dirac step function
siesta: Program's energy decomposition (eV):
siesta: Ebs = -81.381907
siesta: Eions = 815.854478
siesta: Ena = 175.088001
siesta: Ekin = 376.395689
siesta: Enl = -68.955909
siesta: Eso = 0.000000
siesta: Edftu = 0.000000
siesta: DEna = -16.972909
siesta: DUscf = 2.091072
siesta: DUext = 0.000000
siesta: Exc = -116.798708
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
siesta: Emolmec = 0.000000
siesta: Ekinion = 0.000000
siesta: Eharris = -467.075475
siesta: Etot = -465.007242
siesta: FreeEng = -465.007242
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -467.075475 -465.007242 -465.007242 1.455125 -4.169504 7.243025
timer: Routine,Calls,Time,% = IterSCF 1 0.021 1.55
scf: 2 -466.215583 -465.723676 -465.723676 0.055936 -2.969817 2.796687
scf: 3 -465.836758 -465.818463 -465.818463 0.026979 -2.172878 0.339013
scf: 4 -465.824200 -465.821519 -465.821519 0.009712 -2.100462 0.261222
scf: 5 -465.823786 -465.823073 -465.823073 0.019398 -1.903769 0.064105
scf: 6 -465.823188 -465.823137 -465.823137 0.000942 -1.867747 0.034743
scf: 7 -465.823223 -465.823183 -465.823183 0.000825 -1.867782 0.022292
scf: 8 -465.823220 -465.823203 -465.823203 0.000704 -1.870317 0.013852
scf: 9 -465.823211 -465.823208 -465.823208 0.000504 -1.874663 0.006731
scf: 10 -465.823207 -465.823207 -465.823207 0.000198 -1.877969 0.002483
scf: 11 -465.823208 -465.823208 -465.823208 0.000012 -1.879156 0.001992
scf: 12 -465.823208 -465.823208 -465.823208 0.000014 -1.879747 0.001087
scf: 13 -465.823208 -465.823208 -465.823208 0.000015 -1.879834 0.000547
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000154296
max |H_out - H_in| (eV) : 0.0005471635
SCF cycle converged after 13 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: 3 23
siesta: E_KS(eV) = -465.8232
siesta: E_KS - E_eggbox = -465.8232
siesta: Atomic forces (eV/Ang):
1 0.386384 -0.404584 -0.049337
2 -0.340970 -0.039044 -0.096727
3 -0.081249 0.309517 -0.109022
----------------------------------------
Tot -0.035835 -0.134111 -0.255086
----------------------------------------
Max 0.404584
Res 0.248740 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.404584 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 0.31 -1.26 -1.00 -0.07 -0.32 0.80
(Free)E + p*V (eV/cell) -465.6562
Target enthalpy (eV/cell) -465.8232
siesta: Stress tensor (static) (eV/Ang**3):
0.000276 0.000687 -0.000070
0.000687 -0.000335 0.000266
-0.000070 0.000266 -0.000408
siesta: Pressure (static): 0.24937643 kBar
siesta: Stress tensor (total) (eV/Ang**3):
0.000192 0.000500 -0.000201
0.000500 -0.000788 -0.000045
-0.000201 -0.000045 -0.000627
siesta: Pressure (total): 0.65329788 kBar
siesta: Temp_ion = 603.530 K
====================================
Begin MD step = 2
====================================
outcoor: Atomic coordinates (Ang):
0.01100322 0.00756293 0.01247427 1 1 O
0.65198852 0.74215549 0.03331847 2 2 H
-0.84156866 0.31411629 -0.32426839 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 2
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 6 6: 25 1: 7
6 1: 7 1: 5 1: 7
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 8: 20
New grid distribution: 3
1 16: 25 7: 25 1: 14
2 11: 25 1: 6 1: 13
3 1: 10 1: 6 9: 20
4 11: 25 1: 6 14: 20
5 1: 15 7: 25 1: 7
6 1: 10 1: 6 1: 8
7 1: 15 7: 25 8: 20
8 16: 25 7: 25 15: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 5002
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.842499 -465.820263 -465.820263 0.006362 -1.865504 0.017321
scf: 2 -465.820273 -465.820281 -465.820281 0.000546 -1.866573 0.011691
scf: 3 -465.820297 -465.820291 -465.820291 0.000221 -1.865524 0.002103
scf: 4 -465.820292 -465.820291 -465.820291 0.000037 -1.865429 0.001632
scf: 5 -465.820292 -465.820292 -465.820292 0.000055 -1.865509 0.000702
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000545059
max |H_out - H_in| (eV) : 0.0007019773
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: 3 23
siesta: E_KS(eV) = -465.8203
siesta: Atomic forces (eV/Ang):
1 0.362047 -0.347728 -0.067031
2 -0.441616 -0.096418 -0.115472
3 0.045485 0.307194 -0.070202
----------------------------------------
Tot -0.034084 -0.136952 -0.252706
----------------------------------------
Max 0.441616
Res 0.252874 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.441616 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 0.97 -1.08 -0.95 -0.07 -0.15 0.94
(Free)E + p*V (eV/cell) -465.7300
Target enthalpy (eV/cell) -465.8203
siesta: Stress tensor (static) (eV/Ang**3):
0.000693 0.000772 0.000037
0.000772 -0.000221 0.000269
0.000036 0.000269 -0.000377
siesta: Pressure (static): -0.05081471 kBar
siesta: Stress tensor (total) (eV/Ang**3):
0.000608 0.000586 -0.000094
0.000585 -0.000674 -0.000041
-0.000095 -0.000041 -0.000595
siesta: Pressure (total): 0.35310675 kBar
siesta: Temp_ion = 592.276 K
====================================
Begin MD step = 3
====================================
outcoor: Atomic coordinates (Ang):
0.01107152 0.00793949 0.01250161 1 1 O
0.65345451 0.74373714 0.03448205 2 2 H
-0.84478630 0.30617781 -0.33003255 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 3
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 25 1: 13 1: 5
2 1: 25 1: 13 6: 10
3 1: 25 1: 13 11: 15
4 1: 25 1: 13 16: 20
5 1: 25 14: 25 1: 5
6 1: 25 14: 25 6: 10
7 1: 25 14: 25 11: 15
8 1: 25 14: 25 16: 20
InitMesh: MESH = 50 x 50 x 40 = 100000
InitMesh: (bp) = 25 x 25 x 20 = 12500
InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry
ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905
New grid distribution: 2
1 7: 25 6: 25 1: 6
2 8: 25 1: 5 1: 6
3 8: 25 1: 5 7: 20
4 1: 7 1: 5 8: 20
5 1: 6 6: 25 1: 7
6 1: 7 1: 5 1: 7
7 7: 25 6: 25 7: 20
8 1: 6 6: 25 8: 20
New grid distribution: 3
1 16: 25 7: 25 1: 14
2 11: 25 1: 6 1: 13
3 1: 10 1: 6 9: 20
4 11: 25 1: 6 14: 20
5 1: 15 7: 25 1: 7
6 1: 10 1: 6 1: 8
7 1: 15 7: 25 8: 20
8 16: 25 7: 25 15: 20
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776
PhiOnMesh: Number of (b)points on node 0 = 2280
PhiOnMesh: nlist on node 0 = 4997
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -465.838524 -465.816610 -465.816610 0.006340 -1.853636 0.016751
scf: 2 -465.816617 -465.816626 -465.816626 0.000592 -1.855394 0.013035
scf: 3 -465.816641 -465.816636 -465.816636 0.000229 -1.853999 0.001967
scf: 4 -465.816637 -465.816636 -465.816636 0.000037 -1.853888 0.001560
scf: 5 -465.816637 -465.816636 -465.816636 0.000053 -1.853948 0.000719
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000530949
max |H_out - H_in| (eV) : 0.0007191727
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: 3 23
siesta: E_KS(eV) = -465.8166
siesta: Atomic forces (eV/Ang):
1 0.326271 -0.296594 -0.087647
2 -0.535300 -0.148109 -0.134590
3 0.175303 0.303412 -0.028311
----------------------------------------
Tot -0.033726 -0.141291 -0.250549
----------------------------------------
Max 0.535300
Res 0.269215 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.535300 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 1.64 -0.89 -0.90 -0.05 0.03 1.06
(Free)E + p*V (eV/cell) -465.8040
Target enthalpy (eV/cell) -465.8166
siesta: Stress tensor (static) (eV/Ang**3):
0.001109 0.000848 0.000151
0.000847 -0.000118 0.000273
0.000150 0.000273 -0.000342
siesta: Pressure (static): -0.34678193 kBar
siesta: Stress tensor (total) (eV/Ang**3):
0.001026 0.000665 0.000021
0.000664 -0.000557 -0.000034
0.000020 -0.000034 -0.000562
siesta: Pressure (total): 0.04960744 kBar
siesta: Temp_ion = 578.181 K
====================================
Begin MD step = 4
====================================
outcoor: Atomic coordinates (Ang):
0.01114764 0.00830894 0.01252685 1 1 O
0.65471741 0.74526260 0.03559458 2 2 H
-0.84793742 0.29835444 -0.33580746 2 3 H
outcell: Unit cell vectors (Ang):
8.000000 0.000000 0.000000
0.000000 8.000000 0.000000
0.000000 0.000000 6.400000
outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 409.6000
refcount: 1>
new_DM -- step: 4
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
1 1.00000
New DM after history re-use: