Commit 0e98f1ad authored by Nick R. Papior's avatar Nick R. Papior
Browse files

Re-runned all tests and updated the reference tests

- I have re-runned all tests with the new defaults (mix hamiltonian
  and H converge as well.)

  A couple of the tests showed changes (see r554) which could
  be explained by a not fully converged system in the mix DM case.

  As such it seems these new defaults exhibit superior convergence
  and, hopefully, more consistent results as both the Hamiltonian and
  DM are converged.

  It would perhaps be interesting to also converge EDM?

- A couple of the tests was not added in the previous reference frame
  and they are now there.
  I haven't compared these against the old version.
  These tests are:
    anneal-cont.out
    carbon_nanoscroll.out
    dipole_correction.out
    fe_cohp.out
    fe_noncol_kp.out
    fen.out
    force_constants.out
    ge111.out
    h2o-rhog-mixing.out
    h2o_2.out
    pb_bulk.out
    si001.out
    sinw.out
    sinw_2.out
    
parent 130e1a6d
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Siesta Version: trunk-509
Architecture : x86_64-linux-gcc
Compiler flags: mpif90 -m64 -fPIC -O3 -ftree-vectorize -fexpensive-optimizations -funroll-loops -fprefetch-loop-arrays -fgraphite -fipa-icf -fipa-pure-const -march=native -fschedule-fusion -fselective-scheduling -fipa-sra -fipa-cp -Warray-temporaries -fcheck=array-temps -fno-second-underscore -I/opt/zlib/1.2.8/gnu-6.1.0/include -I/opt/hdf5/1.8.16/gnu-6.1.0/include -I/opt/pnetcdf/1.7.0/gnu-6.1.0/include -I/opt/netcdf/4.4.0/gnu-6.1.0/include -I/opt/openmpi/1.10.2/gnu-6.1.0/include -I/opt/mumps/5.0.1/gnu-6.1.0/include
PP flags : -DSIESTA__FLOOK -DSIESTA__METIS -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DGRID_DP -DMPI_TIMING -DTRANSIESTA_TIMING -DTBTRANS_TIMING -DSIESTA__MUMPS -DNCDF_PARALLEL -DNCDF -DNCDF_4 -DSCALAPACK_DEBUG
Libraries : -lzmumps -lmumps_common -lpord -lparmetis -lmetis -L/opt/scalapack/204/gnu-6.1.0/lib -Wl,-rpath=/opt/scalapack/204/gnu-6.1.0/lib -lscalapack -L/opt/openblas/0.2.17/gnu-6.1.0/lib -Wl,-rpath=/opt/openblas/0.2.17/gnu-6.1.0/lib -lopenblas -L/home/nicpa/phd/esl/flook -lflookall -ldl -lnetcdff -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lz
PARALLEL version
NetCDF support
NetCDF-4 support
NetCDF-4 MPI-IO support
METIS ordering support
* Running on 2 nodes in parallel
>> Start of run: 5-JUN-2016 12:07:24
***********************
* WELCOME TO SIESTA *
***********************
reinit: Reading from standard input
************************** Dump of input data file ****************************
#
# System which gives problems with split
# To see them, uncomment the PAO.FixSplitTable directive
#
SystemName Ag test
SystemLabel ag
NumberOfAtoms 1
NumberOfSpecies 1
Reparametrize.Pseudos T # Options for more accuracy
Restricted.Radial.Grid F
XC.functional GGA
XC.authors PBE
Meshcutoff 100 Ry
%block ChemicalSpeciesLabel
1 47 Ag
%endblock ChemicalSpeciesLabel
# Full template for Basis parameters
#
Basis.Pressure 0.02 GPa # As in Anglada et al
PAO.FixSplitTable T
#PAO.SoftDefault T # Global soft-confinement options
#PAO.SoftPotential $Global_Vsoft Ry
#PAO.SoftInnerRadius $Global_Soft_Radius
#
PAO.BasisType split
%block PAO.Basis # Define Basis set
Ag 3 0.0700000
n=5 0 2 S 0.1500000 E 4.5000000 -0.9000000
4.9700000 0.000000
1.00000 1.000000
n=5 1 1 E 2.9200000 -0.5000000
5.0100000
1.00000
n=4 2 2 S 0.1500000 E 4.9400000 -0.5000000
5.1200000 0.000000
1.00000 1.000000
%endblock PAO.Basis
LatticeConstant 4.09 Ang
%block LatticeVectors
0.500 0.500 0.000
0.500 0.000 0.500
0.000 0.500 0.500
%endblock LatticeVectors
%block AtomicCoordinatesAndAtomicSpecies
0.000000 0.0000 0.0000 1
%endblock AtomicCoordinatesAndAtomicSpecies
************************** End of input data file *****************************
reinit: Reading from ../ag.fdf
reinit: -----------------------------------------------------------------------
reinit: System Name: Ag test
reinit: -----------------------------------------------------------------------
reinit: System Label: ag
reinit: System Label: ag
reinit: -----------------------------------------------------------------------
Siesta Version: trunk-554
Architecture : x86_64-linux-gcc
Compiler flags: mpif90 -m64 -fPIC -O3 -ftree-vectorize -fexpensive-optimizations -funroll-loops -fprefetch-loop-arrays -fgraphite -fipa-icf -fipa-pure-const -march=native -fschedule-fusion -fselective-scheduling -fipa-sra -fipa-cp -fno-second-underscore -I/opt/zlib/1.2.8/gnu-6.1.0/include -I/opt/hdf5/1.8.16/gnu-6.1.0/include -I/opt/pnetcdf/1.7.0/gnu-6.1.0/include -I/opt/netcdf/4.4.0/gnu-6.1.0/include -I/opt/openmpi/1.10.2/gnu-6.1.0/include -I/opt/mumps/5.0.1/gnu-6.1.0/include
PP flags : -DSIESTA__FLOOK -DSIESTA__METIS -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DGRID_DP -DMPI_TIMING -DTRANSIESTA_TIMING -DTBTRANS_TIMING -DSIESTA__MUMPS -DNCDF_PARALLEL -DNCDF -DNCDF_4 -DSCALAPACK_DEBUG
Libraries : -lzmumps -lmumps_common -lpord -lparmetis -lmetis -L/opt/scalapack/204/gnu-6.1.0/lib -Wl,-rpath=/opt/scalapack/204/gnu-6.1.0/lib -lscalapack -L/opt/openblas/0.2.17/gnu-6.1.0/lib -Wl,-rpath=/opt/openblas/0.2.17/gnu-6.1.0/lib -lopenblas -L/home/nicpa/phd/esl/flook -lflookall -ldl -lnetcdff -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lz -m64 -fPIC -O3 -ftree-vectorize -fexpensive-optimizations -funroll-loops -fprefetch-loop-arrays -fgraphite -fipa-icf -fipa-pure-const -march=native -fschedule-fusion -fselective-scheduling -fipa-sra -fipa-cp -fno-second-underscore -I/opt/zlib/1.2.8/gnu-6.1.0/include -I/opt/hdf5/1.8.16/gnu-6.1.0/include -I/opt/pnetcdf/1.7.0/gnu-6.1.0/include -I/opt/netcdf/4.4.0/gnu-6.1.0/include -I/opt/openmpi/1.10.2/gnu-6.1.0/include -I/opt/mumps/5.0.1/gnu-6.1.0/include
PARALLEL version
NetCDF support
NetCDF-4 support
NetCDF-4 MPI-IO support
METIS ordering support
* Running on 4 nodes in parallel
>> Start of run: 18-AUG-2016 7:57:13
initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Species number: 1 Atomic number: 47 Label: Ag
......@@ -285,7 +236,7 @@ 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 = non-polarized
redata: Spin configuration = none
redata: Number of spin components = 1
redata: Time-Reversal Symmetry = T
redata: Spin-spiral = F
......@@ -297,6 +248,7 @@ redata: Mesh Cutoff = 100.0000 Ry
redata: Net charge of the system = 0.0000 |e|
redata: Min. number of SCF Iter = 0
redata: Max. number of SCF Iter = 50
redata: 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
......@@ -306,13 +258,14 @@ redata: New DM Mixing Weight = 0.2500
redata: New DM Occupancy tolerance = 0.000000000001
redata: No kicks to SCF
redata: DM Mixing Weight for Kicks = 0.5000
redata: DM Tolerance for SCF = 0.000100
redata: Require H convergence for SCF = F
redata: Hamiltonian Tolerance in SCF = 0.000100 Ry
redata: Require (free) Energy convergence in SCF = F
redata: DM (free)Energy tolerance for SCF = 0.000010 eV
redata: Require Harris convergence for SCF = F
redata: DM Harris energy tolerance for SCF = 0.000010 eV
redata: Harris energy tolerance for SCF = 0.000100 eV
redata: Require DM convergence for SCF = T
redata: DM tolerance for SCF = 0.000100
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
......@@ -325,19 +278,39 @@ mix.SCF: Pulay mixing = Pulay
mix.SCF: Variant = stable
mix.SCF: History steps = 2
mix.SCF: Linear mixing weight = 0.250000
mix.SCF: Damping = 0.250000
mix.SCF: Mixing weight = 0.250000
mix.SCF: SVD condition = 0.1000E-07
redata: Save data in SIESTA.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
restart 0
restart.save 1
# Continuation options
%endblock SCF.Mixer.Pulay
DM_history_depth set to one: no extrapolation allowed by default for geometry relaxation
Size of DM history Fstack: 1
Total number of electrons: 11.000000
Total ionic charge: 11.000000
* ProcessorY, Blocksize: 1 8
* ProcessorY, Blocksize: 2 4
* Orbital distribution balance (max,min): 8 7
* Orbital distribution balance (max,min): 4 3
Kpoints in: 1 . Kpoints trimmed: 1
......@@ -364,75 +337,84 @@ outcell: Cell volume (Ang**3) : 17.1045
Folding of H and S is implicitly performed
<dSpData1D:S at geom step 0
<sparsity:sparsity for geom step 0
nrows_g=15 nrows=8 sparsity=.5333 nnzs=120, refcount: 7>
<dData1D:(new from dSpData1D) n=120, refcount: 1>
nrows_g=15 nrows=4 sparsity=.2667 nnzs=60, refcount: 7>
<dData1D:(new from dSpData1D) n=60, refcount: 1>
refcount: 1>
New_DM. Step: 1
Initializing Density Matrix...
DM after filling with atomic data:
<dSpData2D:(DM initialized from atoms)
<sparsity:sparsity for geom step 0
nrows_g=15 nrows=8 sparsity=.5333 nnzs=120, refcount: 8>
<dData2D:(DMatomic) n=120 m=1, refcount: 1>
nrows_g=15 nrows=4 sparsity=.2667 nnzs=60, refcount: 8>
<dData2D:(DMatomic) n=60 m=1, refcount: 1>
refcount: 1>
Note: For starting DM, Qtot, Tr[D*S] = 11.00000000 12.88354914
New grid distribution: 1
1 1: 8 1: 8 1: 4
2 1: 8 1: 8 5: 8
1 1: 8 1: 4 1: 4
2 1: 8 1: 4 5: 8
3 1: 8 5: 8 1: 4
4 1: 8 5: 8 5: 8
InitMesh: MESH = 16 x 16 x 16 = 4096
InitMesh: (bp) = 8 x 8 x 8 = 512
InitMesh: Mesh cutoff (required, used) = 100.000 126.887 Ry
ExtMesh (bp) on 0 = 48 x 48 x 44 = 101376
ExtMesh (bp) on 0 = 48 x 44 x 44 = 92928
New grid distribution: 2
1 1: 8 1: 8 1: 4
2 1: 8 1: 8 5: 8
1 1: 8 1: 4 1: 4
2 1: 8 1: 4 5: 8
3 1: 8 5: 8 1: 4
4 1: 8 5: 8 5: 8
New grid distribution: 3
1 1: 8 1: 8 1: 4
2 1: 8 1: 8 5: 8
1 1: 8 1: 4 1: 4
2 1: 8 1: 4 5: 8
3 1: 8 5: 8 1: 4
4 1: 8 5: 8 5: 8
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 48 x 48 x 44 = 101376
PhiOnMesh: Number of (b)points on node 0 = 256
PhiOnMesh: nlist on node 0 = 14865
rdiag-debug: Node=1, lwork= 368>= lworkq= 331, liwork= 123>= liworkq= 123
rdiag-debug: Node=0, lwork= 368>= lworkq= 361, liwork= 123>= liworkq= 123
ExtMesh (bp) on 0 = 48 x 44 x 44 = 92928
PhiOnMesh: Number of (b)points on node 0 = 128
PhiOnMesh: nlist on node 0 = 7079
rdiag-debug: Node=1, lwork= 233>= lworkq= 233, liwork= 139>= liworkq= 123
rdiag-debug: Node=3, lwork= 219>= lworkq= 219, liwork= 139>= liworkq= 123
rdiag-debug: Node=2, lwork= 233>= lworkq= 233, liwork= 139>= liworkq= 123
rdiag-debug: Node=0, lwork= 249>= lworkq= 249, liwork= 139>= liworkq= 123
stepf: Fermi-Dirac step function
siesta: Program's energy decomposition (eV):
siesta: Ebs = -106.410455
siesta: Ebs = -19.918577
siesta: Eions = 997.075652
siesta: Ena = 7.749557
siesta: Ekin = 793.398639
siesta: Enl = -647.930456
siesta: Ekin = 968.880024
siesta: Enl = -801.088164
siesta: Eso = 0.000000
siesta: Eldau = 0.000000
siesta: DEna = -7.119385
siesta: DUscf = 5.516928
siesta: DEna = 3.086469
siesta: DUscf = 0.569176
siesta: DUext = 0.000000
siesta: Exc = -237.603404
siesta: Exc = -259.395465
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
siesta: Emolmec = 0.000000
siesta: Ekinion = 0.000000
siesta: Eharris = -1084.975739
siesta: Etot = -1083.063775
siesta: FreeEng = -1083.100836
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmx(Ry)
scf: 1 -1084.9757 -1083.0638 -1083.1008 0.62740 -9.11928 -1.00000
timer: Routine,Calls,Time,% = IterSCF 1 0.024 1.58
scf: 2 -1083.9329 -1083.0556 -1083.1137 0.37967 -7.05794 -1.00000
scf: 3 -1083.9253 -1083.2969 -1083.3551 0.27093 -7.01785 -1.00000
scf: 4 -1083.9189 -1083.8934 -1083.9515 0.01435 -6.93911 -1.00000
scf: 5 -1083.9187 -1083.9040 -1083.9622 0.00870 -6.95419 -1.00000
scf: 6 -1083.9186 -1083.9192 -1083.9773 0.00201 -6.97630 -1.00000
scf: 7 -1083.9186 -1083.9191 -1083.9772 0.00153 -6.97651 -1.00000
scf: 8 -1083.9186 -1083.9187 -1083.9769 0.00009 -6.97695 -1.00000
SCF Convergence by dDmax criteria
max |DM_out - DM_in|: 0.00008847
siesta: Eharris = -1063.912959
siesta: Etot = -1077.274055
siesta: FreeEng = -1077.311116
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -1063.912959 -1077.274055 -1077.311116 0.627398 -9.119277 10.860663
timer: Routine,Calls,Time,% = IterSCF 1 0.060 2.87
scf: 2 -1086.498257 -1083.916868 -1083.975015 0.248326 -7.046938 0.249993
scf: 3 -1083.919030 -1083.918007 -1083.976155 0.006718 -7.009088 0.144806
scf: 4 -1083.918972 -1083.918598 -1083.976746 0.009329 -6.962443 0.050220
scf: 5 -1083.918606 -1083.918602 -1083.976750 0.001061 -6.965786 0.037195
scf: 6 -1083.918611 -1083.918607 -1083.976754 0.003112 -6.976038 0.001769
scf: 7 -1083.918607 -1083.918607 -1083.976755 0.000043 -6.976367 0.001043
scf: 8 -1083.918607 -1083.918607 -1083.976755 0.000060 -6.976786 0.000293
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000597504
max |H_out - H_in| (eV): 0.0002932544
SCF cycle converged after 8 iterations
Using DM_out to compute the final energy and forces
......@@ -443,29 +425,29 @@ siesta: E_KS - E_eggbox = -1083.9186
siesta: Atomic forces (eV/Ang):
----------------------------------------
Tot 0.000000 -0.000000 -0.000000
Tot 0.000000 0.000000 0.000000
----------------------------------------
Max 0.000000
Res 0.000000 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.000000 constrained
Stress-tensor-Voigt (kbar): 730.63 730.63 730.63 -2.48 -2.48 -2.48
Stress-tensor-Voigt (kbar): 730.62 730.62 730.62 -2.48 -2.48 -2.48
(Free)E + p*V (eV/cell) -1091.7767
Target enthalpy (eV/cell) -1083.9768
siesta: Program's energy decomposition (eV):
siesta: Ebs = -86.346183
siesta: Ebs = -86.344066
siesta: Eions = 997.075652
siesta: Ena = 7.749557
siesta: Ekin = 839.856355
siesta: Enl = -689.598465
siesta: Ekin = 839.852572
siesta: Enl = -689.595057
siesta: Eso = 0.000000
siesta: Eldau = 0.000000
siesta: DEna = -4.312353
siesta: DUscf = 2.535225
siesta: DEna = -4.312609
siesta: DUscf = 2.535416
siesta: DUext = 0.000000
siesta: Exc = -243.073274
siesta: Exc = -243.072832
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
......@@ -476,30 +458,31 @@ siesta: Etot = -1083.918607
siesta: FreeEng = -1083.976755
siesta: Final energy (eV):
siesta: Band Struct. = -86.346183
siesta: Kinetic = 839.856355
siesta: Hartree = 161.322245
siesta: Band Struct. = -86.344066
siesta: Kinetic = 839.852572
siesta: Hartree = 161.320662
siesta: Eldau = 0.000000
siesta: Eso = 0.000000
siesta: Ext. field = 0.000000
siesta: Exch.-corr. = -243.073274
siesta: Ion-electron = -1026.142040
siesta: Exch.-corr. = -243.072832
siesta: Ion-electron = -1026.137115
siesta: Ion-ion = -815.881894
siesta: Ekinion = 0.000000
siesta: Total = -1083.918607
siesta: Fermi = -6.976786
siesta: Stress tensor (static) (eV/Ang**3):
siesta: 0.456020 -0.001548 -0.001548
siesta: -0.001548 0.456020 -0.001548
siesta: -0.001548 -0.001548 0.456020
siesta: 0.456015 -0.001549 -0.001549
siesta: -0.001549 0.456015 -0.001549
siesta: -0.001549 -0.001549 0.456015
siesta: Cell volume = 17.104482 Ang**3
siesta: Pressure (static):
siesta: Solid Molecule Units
siesta: -0.00496664 -0.00496664 Ry/Bohr**3
siesta: -0.45602000 -0.45602000 eV/Ang**3
siesta: -730.63248199 -730.63248199 kBar
siesta: -0.00496658 -0.00496658 Ry/Bohr**3
siesta: -0.45601475 -0.45601475 eV/Ang**3
siesta: -730.62407931 -730.62407931 kBar
(Free)E+ p_basis*V_orbitals = -1083.936563
(Free)Eharris+ p_basis*V_orbitals = -1083.936563
>> End of run: 5-JUN-2016 12:07:25
>> End of run: 18-AUG-2016 7:57:16
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Siesta Version: trunk-509
Architecture : x86_64-linux-gcc
Compiler flags: mpif90 -m64 -fPIC -O3 -ftree-vectorize -fexpensive-optimizations -funroll-loops -fprefetch-loop-arrays -fgraphite -fipa-icf -fipa-pure-const -march=native -fschedule-fusion -fselective-scheduling -fipa-sra -fipa-cp -Warray-temporaries -fcheck=array-temps -fno-second-underscore -I/opt/zlib/1.2.8/gnu-6.1.0/include -I/opt/hdf5/1.8.16/gnu-6.1.0/include -I/opt/pnetcdf/1.7.0/gnu-6.1.0/include -I/opt/netcdf/4.4.0/gnu-6.1.0/include -I/opt/openmpi/1.10.2/gnu-6.1.0/include -I/opt/mumps/5.0.1/gnu-6.1.0/include
PP flags : -DSIESTA__FLOOK -DSIESTA__METIS -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DGRID_DP -DMPI_TIMING -DTRANSIESTA_TIMING -DTBTRANS_TIMING -DSIESTA__MUMPS -DNCDF_PARALLEL -DNCDF -DNCDF_4 -DSCALAPACK_DEBUG
Libraries : -lzmumps -lmumps_common -lpord -lparmetis -lmetis -L/opt/scalapack/204/gnu-6.1.0/lib -Wl,-rpath=/opt/scalapack/204/gnu-6.1.0/lib -lscalapack -L/opt/openblas/0.2.17/gnu-6.1.0/lib -Wl,-rpath=/opt/openblas/0.2.17/gnu-6.1.0/lib -lopenblas -L/home/nicpa/phd/esl/flook -lflookall -ldl -lnetcdff -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lz
PARALLEL version
NetCDF support
NetCDF-4 support
NetCDF-4 MPI-IO support
METIS ordering support
* Running on 2 nodes in parallel
>> Start of run: 5-JUN-2016 11:57:15
***********************
* WELCOME TO SIESTA *
***********************
reinit: Reading from standard input
************************** Dump of input data file ****************************
SystemName Water molecule with Bessel Orbitals
SystemLabel bessel
NumberOfAtoms 5
NumberOfSpecies 3
%block ChemicalSpeciesLabel
1 8 O # Species index, atomic number, species label
2 1 H
3 -100 Bessel
%endblock ChemicalSpeciesLabel
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.000 0.000 0.000 1
0.757 0.586 0.000 2
-0.757 0.586 0.000 2
0.3785 0.293 0.000 3
-0.3785 0.293 0.000 3
%endblock AtomicCoordinatesAndAtomicSpecies
%block PAO.Basis
Bessel 1
n=1 0 1
2.0
1.0
%endblock PAO.Basis
************************** End of input data file *****************************
reinit: Reading from ../bessel.fdf
reinit: -----------------------------------------------------------------------
reinit: System Name: Water molecule with Bessel Orbitals
reinit: -----------------------------------------------------------------------
reinit: System Label: bessel
reinit: System Label: bessel
reinit: -----------------------------------------------------------------------
Siesta Version: trunk-554
Architecture : x86_64-linux-gcc
Compiler flags: mpif90 -m64 -fPIC -O3 -ftree-vectorize -fexpensive-optimizations -funroll-loops -fprefetch-loop-arrays -fgraphite -fipa-icf -fipa-pure-const -march=native -fschedule-fusion -fselective-scheduling -fipa-sra -fipa-cp -fno-second-underscore -I/opt/zlib/1.2.8/gnu-6.1.0/include -I/opt/hdf5/1.8.16/gnu-6.1.0/include -I/opt/pnetcdf/1.7.0/gnu-6.1.0/include -I/opt/netcdf/4.4.0/gnu-6.1.0/include -I/opt/openmpi/1.10.2/gnu-6.1.0/include -I/opt/mumps/5.0.1/gnu-6.1.0/include
PP flags : -DSIESTA__FLOOK -DSIESTA__METIS -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DGRID_DP -DMPI_TIMING -DTRANSIESTA_TIMING -DTBTRANS_TIMING -DSIESTA__MUMPS -DNCDF_PARALLEL -DNCDF -DNCDF_4 -DSCALAPACK_DEBUG
Libraries : -lzmumps -lmumps_common -lpord -lparmetis -lmetis -L/opt/scalapack/204/gnu-6.1.0/lib -Wl,-rpath=/opt/scalapack/204/gnu-6.1.0/lib -lscalapack -L/opt/openblas/0.2.17/gnu-6.1.0/lib -Wl,-rpath=/opt/openblas/0.2.17/gnu-6.1.0/lib -lopenblas -L/home/nicpa/phd/esl/flook -lflookall -ldl -lnetcdff -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lz -m64 -fPIC -O3 -ftree-vectorize -fexpensive-optimizations -funroll-loops -fprefetch-loop-arrays -fgraphite -fipa-icf -fipa-pure-const -march=native -fschedule-fusion -fselective-scheduling -fipa-sra -fipa-cp -fno-second-underscore -I/opt/zlib/1.2.8/gnu-6.1.0/include -I/opt/hdf5/1.8.16/gnu-6.1.0/include -I/opt/pnetcdf/1.7.0/gnu-6.1.0/include -I/opt/netcdf/4.4.0/gnu-6.1.0/include -I/opt/openmpi/1.10.2/gnu-6.1.0/include -I/opt/mumps/5.0.1/gnu-6.1.0/include
PARALLEL version
NetCDF support
NetCDF-4 support
NetCDF-4 MPI-IO support
METIS ordering support
* Running on 4 nodes in parallel
>> Start of run: 18-AUG-2016 8:09:03
initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Species number: 1 Atomic number: 8 Label: O
......@@ -398,7 +373,7 @@ 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 = non-polarized
redata: Spin configuration = none
redata: Number of spin components = 1
redata: Time-Reversal Symmetry = T
redata: Spin-spiral = F
......@@ -410,6 +385,7 @@ redata: Mesh Cutoff = 100.0000 Ry
redata: Net charge of the system = 0.0000 |e|
redata: Min. number of SCF Iter = 0
redata: Max. number of SCF Iter = 50
redata: 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
......@@ -419,13 +395,14 @@ redata: New DM Mixing Weight = 0.2500
redata: New DM Occupancy tolerance = 0.000000000001
redata: No kicks to SCF
redata: DM Mixing Weight for Kicks = 0.5000
redata: DM Tolerance for SCF = 0.000100
redata: Require H convergence for SCF = F
redata: Hamiltonian Tolerance in SCF = 0.000100 Ry
redata: Require (free) Energy convergence in SCF = F
redata: DM (free)Energy tolerance for SCF = 0.000010 eV
redata: Require Harris convergence for SCF = F
redata: DM Harris energy tolerance for SCF = 0.000010 eV
redata: Harris energy tolerance for SCF = 0.000100 eV
redata: Require DM convergence for SCF = T
redata: DM tolerance for SCF = 0.000100
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
......@@ -438,19 +415,39 @@ mix.SCF: Pulay mixing = Pulay
mix.SCF: Variant = stable
mix.SCF: History steps = 2
mix.SCF: Linear mixing weight = 0.250000
mix.SCF: Damping = 0.250000
mix.SCF: Mixing weight = 0.250000
mix.SCF: SVD condition = 0.1000E-07
redata: Save data in SIESTA.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
restart 0
restart.save 1
# Continuation options
%endblock SCF.Mixer.Pulay
DM_history_depth set to one: no extrapolation allowed by default for geometry relaxation
Size of DM history Fstack: 1
Total number of electrons: 8.000000
Total ionic charge: 8.000000
* ProcessorY, Blocksize: 1 13
* ProcessorY, Blocksize: 2 7
* Orbital distribution balance (max,min): 13 12
* Orbital distribution balance (max,min): 7 4
Kpoints in: 1 . Kpoints trimmed: 1
......@@ -474,87 +471,90 @@ outcell: Unit cell vectors (Ang):
outcell: Cell vector modules (Ang) : 7.286412 5.746952 5.621012
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 235.3780
siesta: WARNING: Atoms 1 5 too close: rij = 0.478656 Ang
siesta: WARNING: Atoms 2 4 too close: rij = 0.478656 Ang
siesta: WARNING: Atoms 3 5 too close: rij = 0.478656 Ang
<dSpData1D:S at geom step 0
<sparsity:sparsity for geom step 0
nrows_g=25 nrows=13 sparsity=.5200 nnzs=325, refcount: 7>
<dData1D:(new from dSpData1D) n=325, refcount: 1>
nrows_g=25 nrows=7 sparsity=.2800 nnzs=175, refcount: 7>
<dData1D:(new from dSpData1D) n=175, refcount: 1>
refcount: 1>
New_DM. Step: 1
Initializing Density Matrix...
DM after filling with atomic data:
<dSpData2D:(DM initialized from atoms)
<sparsity:sparsity for geom step 0
nrows_g=25 nrows=13 sparsity=.5200 nnzs=325, refcount: 8>
<dData2D:(DMatomic) n=325 m=1, refcount: 1>
nrows_g=25 nrows=7 sparsity=.2800 nnzs=175, refcount: 8>
<dData2D:(DMatomic) n=175 m=1, refcount: 1>
refcount: 1>
New grid distribution: 1
1 1: 24 1: 18 1: 9
2 1: 24 1: 18 10: 18
1 1: 24 1: 9 1: 9
2 1: 24 1: 9 10: 18
3 1: 24 10: 18 1: 9
4 1: 24 10: 18 10: 18
InitMesh: MESH = 48 x 36 x 36 = 62208
InitMesh: (bp) = 24 x 18 x 18 = 7776
InitMesh: Mesh cutoff (required, used) = 100.000 108.450 Ry
ExtMesh (bp) on 0 = 60 x 54 x 45 = 145800
ExtMesh (bp) on 0 = 60 x 45 x 45 = 121500
New grid distribution: 2
1 7: 24 1: 18 1: 18
2 1: 6 1: 18 1: 18
1 7: 24 1: 18 1: 6
2 7: 24 1: 18 7: 18
3 1: 6 1: 18 1: 6
4 1: 6 1: 18 7: 18
New grid distribution: 3
1 11: 24 1: 18 1: 18
2 1: 10 1: 18 1: 18
1 11: 24 1: 18 1: 8
2 11: 24 1: 18 9: 18
3 1: 10 1: 18 1: 8
4 1: 10 1: 18 9: 18
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 54 x 54 x 54 = 157464
PhiOnMesh: Number of (b)points on node 0 = 5832
PhiOnMesh: nlist on node 0 = 21590
rdiag-debug: Node=1, lwork= 988>= lworkq= 801, liwork= 193>= liworkq= 193
rdiag-debug: Node=0, lwork= 988>= lworkq= 851, liwork= 193>= liworkq= 193
ExtMesh (bp) on 0 = 54 x 54 x 42 = 122472
PhiOnMesh: Number of (b)points on node 0 = 1944
PhiOnMesh: nlist on node 0 = 10363
rdiag-debug: Node=0, lwork= 593>= lworkq= 593, liwork= 209>= liworkq= 193