initial test case for Siesta

02c598c0 · Ask Hjorth Larsen · 1c7fa1cb · 02c598c0 · 02c598c0 · 02c598c0
Commit 02c598c0 authored 8 years ago by Ask Hjorth Larsen
--- a/H2O/0_NORMAL_EXIT
+++ b/H2O/0_NORMAL_EXIT
--- a/H2O/BASIS_ENTHALPY
+++ b/H2O/BASIS_ENTHALPY
+  -466.41494320905912     
+ The above number is the electronic (free)energy:  -466.96802127519641     
+ Plus the pressure :    1.3595453680289311E-005  (   0.20000000000000001       GPa)
+      times the orbital volume (in Bohr**3):    2989.9825130944155     
--- a/H2O/BASIS_HARRIS_ENTHALPY
+++ b/H2O/BASIS_HARRIS_ENTHALPY
+  -466.41494320989051     
+ The above number is the electronic (free) harris energy:  -466.96802127602780     
+ Plus the pressure :    1.3595453680289311E-005  (   0.20000000000000001       GPa)
+      times the orbital volume (in Bohr**3):    2989.9825130944155     
--- a/H2O/CLOCK
+++ b/H2O/CLOCK
+Start of run             0.000
+-------------- end of scf step             1.974
+-------------- end of scf step             2.079
+-------------- end of scf step             2.184
+-------------- end of scf step             2.289
+-------------- end of scf step             2.394
+-------------- end of scf step             2.498
+-------------- end of scf step             2.603
+-------------- end of scf step             2.708
+-------------- end of scf step             2.813
+-------------- end of scf step             2.918
+-------------- end of scf step             3.025
+-------------- end of scf step             3.130
+-------------- end of scf step             3.235
+-------------- end of scf step             3.339
+-------------- end of scf step             3.443
+-------------- end of scf step             3.548
+-------------- end of scf step             3.653
+-------------- end of scf step             3.759
+-------------- end of scf step             3.864
+-------------- end of scf step             3.971
+-------------- end of scf step             4.076
+--- end of geometry step             4.250
+End of run             4.252
--- a/H2O/FORCE_STRESS
+++ b/H2O/FORCE_STRESS
+                -34.3212469149
+         -0.000047631       0.000000000       0.000000000
+          0.000000000      -0.000025120      -0.000000000
+         -0.000000000       0.000000000      -0.000003624
+           3
+  1     8       0.000000000      -0.031546532       0.000000000  O
+  2     1       0.025540252       0.016408570      -0.000000000  H
+  2     1      -0.025540252       0.016408570      -0.000000000  H
--- a/H2O/H.ion
+++ b/H2O/H.ion
--- a/H2O/H.ion.xml
+++ b/H2O/H.ion.xml
--- a/H2O/H.psf
+++ b/H2O/H.psf
--- a/H2O/INPUT_TMP.95611
+++ b/H2O/INPUT_TMP.95611
+SystemName          Water molecule
+SystemLabel         h2o
+NumberOfAtoms       3
+NumberOfSpecies     2
+%block ChemicalSpeciesLabel
+ 1  8  O      # Species index, atomic number, species label
+ 2  1  H
+%endblock ChemicalSpeciesLabel
+AtomicCoordinatesFormat  Ang
+%block AtomicCoordinatesAndAtomicSpecies
+ 0.000  0.000  0.000  1
+ 0.757  0.586  0.000  2
+-0.757  0.586  0.000  2
+%endblock AtomicCoordinatesAndAtomicSpecies
+xc.functional                   GGA
+xc.authors                      PBE
--- a/H2O/NON_TRIMMED_KP_LIST
+++ b/H2O/NON_TRIMMED_KP_LIST
+     1
+     1    0.000000    0.000000    0.000000       1.000000
--- a/H2O/O.ion
+++ b/H2O/O.ion
--- a/H2O/O.ion.xml
+++ b/H2O/O.ion.xml
--- a/H2O/O.psf
+++ b/H2O/O.psf
--- a/H2O/fdf-95611.log
+++ b/H2O/fdf-95611.log
+SystemName     Water molecule                                                                  
+SystemLabel     h2o                                                                             
+XML.Write              T     # default value
+XML.AbortOnErrors              F     # default value
+XML.AbortOnWarnings              F     # default value
+timer_report_threshold          0.000000000         # default value
+UseTreeTimer              F     # default value
+alloc_report_level         0     # default value
+alloc_report_threshold          0.000000000         # default value
+xc.functional     GGA                                                                             
+xc.authors     PBE                                                                             
+MM.Cutoff          30.00000000     Bohr     # default value
+MM.UnitsEnergy     eV     # default value
+MM.UnitsDistance     Ang     # default value
+WriteIonPlotFiles              F     # default value
+Atom.Debug.KB.Generation              F     # default value
+KB.New.Reference.Orbitals              F     # default value
+user-basis              F     # default value
+user-basis-netcdf              F     # default value
+ReparametrizePseudos              F     # default value
+Restricted.Radial.Grid              T     # default value
+Rmax.Radial.Grid          0.000000000         # default value
+PAO.BasisSize     standard            # default value
+PAO.BasisType     split          # default value
+PAO.SoftDefault              F     # default value
+PAO.SoftInnerRadius         0.9000000000         # default value
+PAO.SoftPotential          40.00000000         # default value
+PAO.SplitNorm         0.1500000000         # default value
+PAO.SplitNormH         -1.000000000         # default value
+Number_of_species              2
+%block Chemical_species_label
+  1  8  O      # Species index, atomic number, species label
+  2  1  H
+%endblock Chemical_species_label
+FilterCutoff          0.000000000     Ry     # default value
+FilterTol          0.000000000     Ry     # default value
+KB.Rmax          6.000000000     Bohr     # default value
+PAO.EnergyShift         0.2000000000E-01 Ry     # default value
+PAO.SplitTailNorm              F     # default value
+PAO.FixSplitTable              F     # default value
+PAO.NewSplitCode              F     # default value
+PAO.Filter              F     # default value
+PAO.Keep.Findp.Bug              F     # default value
+PAO.Filter              F     # default value
+PAO.Filter              F     # default value
+PAO.Filter              F     # default value
+PAO.OldStylePolorbs              T     # default value
+PAO.SplitTailNorm              F     # default value
+PAO.FixSplitTable              F     # default value
+PAO.NewSplitCode              F     # default value
+PAO.Filter              F     # default value
+Vna.Filter              F     # default value
+FilterCutoff          0.000000000     Ry     # default value
+FilterTol          0.000000000     Ry     # default value
+KB.Rmax          6.000000000     Bohr     # default value
+PAO.EnergyShift         0.2000000000E-01 Ry     # default value
+PAO.SplitTailNorm              F     # default value
+PAO.FixSplitTable              F     # default value
+PAO.NewSplitCode              F     # default value
+PAO.Filter              F     # default value
+PAO.Filter              F     # default value
+PAO.OldStylePolorbs              T     # default value
+PAO.SplitTailNorm              F     # default value
+PAO.FixSplitTable              F     # default value
+PAO.NewSplitCode              F     # default value
+PAO.Filter              F     # default value
+Vna.Filter              F     # default value
+PAO.BasisType     split          # default value
+Atom-Setup-Only              F     # default value
+UseStructFile              F     # default value
+MD.UseStructFile              F     # default value
+LatticeConstant          0.000000000     Bohr     # default value
+AtomicCoordinatesFormat     Ang                                                                             
+NumberOfAtoms              3
+ZM.UnitsLength     Bohr           # default value
+ZM.UnitsAngle     rad            # default value
+ZM.ForceTolLength         0.1555740000E-02 Ry/Bohr     # default value
+ZM.ForceTolAngle         0.3565490000E-02 Ry/rad     # default value
+ZM.MaxDisplLength         0.2000000000     Bohr     # default value
+ZM.MaxDisplAngle         0.3000000000E-02 rad     # default value
+ZM.CalcAllForces              F     # default value
+%block AtomicCoordinatesAndAtomicSpecies
+  0.000  0.000  0.000  1
+  0.757  0.586  0.000  2
+ -0.757  0.586  0.000  2
+UseSaveData              F     # default value
+MD.UseSaveXV              F     # default value
+MD.UseSaveZM              F     # default value
+WriteCoorInitial              T     # default value
+MD.TypeOfRun     none     # default value
+NetCharge          0.000000000         # default value
+MaxBondDistance          6.000000000     Bohr     # default value
+Output-Structure-Only              F     # default value
+WriteCoorXmol              F     # default value
+SpinPolarized              F     # default value
+NonCollinearSpin              F     # default value
+HSetupOnly              F     # default value
+LongOutput              F     # default value
+WriteDenchar              F     # default value
+WriteMullikenPop         0     # default value
+WriteHirshfeldPop              F     # default value
+WriteVoronoiPop              F     # default value
+PartialChargesAtEveryGeometry              F     # default value
+PartialChargesAtEveryScfStep              F     # default value
+MeshCutoff          100.0000000     Ry     # default value
+NetCharge          0.000000000         # default value
+MinSCFIterations         0     # default value
+MaxSCFIterations        50     # default value
+SCFMustConverge              F     # default value
+MixHamiltonian              F     # default value
+TS.MixH              F     # default value
+MixCharge              F     # default value
+Compat-pre-v4-DM-H              F     # default value
+SCF.MixAfterConvergence              F     # default value
+SCF.Recompute-H-After-Scf              F     # default value
+DM.NumberPulay         0     # default value
+DM.NumberBroyden         0     # default value
+DM.FIRE.Mixing              F     # default value
+DM.MixSCF1              F     # default value
+DM.PulayOnFile              F     # default value
+DM.Pulay.Avoid.First.After.Kick              F     # default value
+DM.MixingWeight         0.2500000000         # default value
+DM.OccupancyTolerance         0.1000000000E-11     # default value
+DM.NumberKick         0     # default value
+DM.KickMixingWeight         0.5000000000         # default value
+DM.Tolerance         0.1000000000E-03     # default value
+DM.RequireEnergyConvergence              F     # default value
+DM.EnergyTolerance         0.7349806700E-06 Ry     # default value
+DM.RequireHarrisConvergence              F     # default value
+DM.HarrisTolerance         0.7349806700E-06 Ry     # default value
+MonitorForcesInSCF              F     # default value
+UseSaveData              F     # default value
+DM.UseSaveDM              F     # default value
+NeglNonOverlapInt              F     # default value
+SolutionMethod     diagon     # default value
+Diag.DivideAndConquer              T     # default value
+Diag.Memory          1.000000000         # default value
+ElectronicTemperature         0.1900000000E-02 Ry     # default value
+FixSpin              F     # default value
+ON.MaxNumIter      1000     # default value
+ON.etol         0.1000000000E-07     # default value
+ON.eta          0.000000000     Ry     # default value
+ON.eta_alpha          0.000000000     Ry     # default value
+ON.eta_beta          0.000000000     Ry     # default value
+On.RcLWF          9.500000000     Bohr     # default value
+ON.UseSaveLWF              F     # default value
+ON.functional     kim     # default value
+ON.ChemicalPotentialUse              F     # default value
+ON.ChemicalPotential              F     # default value
+ON.ChemicalPotentialRc          9.500000000     Bohr     # default value
+ON.ChemicalPotentialTemperature         0.5000000000E-01 Ry     # default value
+ON.ChemicalPotentialOrder       100     # default value
+MD.VariableCell              F     # default value
+compat-pre-v4-dynamics              F     # default value
+MD.TypeOfRun     cg     # default value
+MD.UseSaveCG              F     # default value
+Optim.Broyden              F     # default value
+MD.NumCGsteps         0     # default value
+MD.MaxCGDispl         0.2000000000     Bohr     # default value
+MD.MaxForceTol         0.1555740000E-02 Ry/Bohr     # default value
+MD.MaxStressTol         0.6797730000E-04 Ry/Bohr**3     # default value
+MD.InitialTimeStep         1     # default value
+MD.FinalTimeStep         1     # default value
+MD.LengthTimeStep          1.000000000     fs     # default value
+MD.Quench              F     # default value
+MD.FireQuench              F     # default value
+MD.InitialTemperature          0.000000000     K     # default value
+MD.TargetTemperature          0.000000000     K     # default value
+MD.TargetPressure          0.000000000     Ry/Bohr**3     # default value
+MD.NoseMass          100.0000000     Ry*fs**2     # default value
+MD.ParrinelloRahmanMass          100.0000000     Ry*fs**2     # default value
+MD.AnnealOption     TemperatureAndPressure     # default value
+MD.TauRelax          100.0000000     fs     # default value
+MD.BulkModulus         0.6797730000E-02 Ry/Bohr**3     # default value
+MD.FCDispl         0.4000000000E-01 Bohr     # default value
+MD.FCfirst         1     # default value
+MD.FClast         3     # default value
+UseSpatialDecomposition              F     # default value
+UseDomainDecomposition              F     # default value
+Harris_functional              F     # default value
+WriteKpoints              F     # default value
+WriteForces              F     # default value
+WriteDM              T     # default value
+WriteDM.NetCDF              F     # default value
+WriteDM.History.NetCDF              F     # default value
+WriteDMHS.NetCDF              F     # default value
+WriteDMHS.History.NetCDF              F     # default value
+SCF.Read.Charge.NetCDF              F     # default value
+SCF.Read.Deformation.Charge.NetCDF              F     # default value
+SaveInitialChargeDensity              F     # default value
+UseNewDiagk              F     # default value
+WriteBands              F     # default value
+WriteKbands              F     # default value
+WriteEigenvalues              F     # default value
+WriteCoorStep              F     # default value
+WriteMDhistory              F     # default value
+WriteMDXmol              T     # default value
+UseSaveData              F     # default value
+SaveHS              F     # default value
+FixAuxiliaryCell              F     # default value
+NaiveAuxiliaryCell              F     # default value
+ReInitialiseDM              T     # default value
+DM.AllowReuse              T     # default value
+DM.AllowExtrapolation              T     # default value
+DM.NormalizationTolerance         0.1000000000E-04     # default value
+DM.NormalizeDuringSCF              T     # default value
+MullikenInSCF              F     # default value
+WarningMinimumAtomicDistance          1.000000000     Bohr     # default value
+BornCharge              F     # default value
+ChangeKgridInMD              F     # default value
+Diag.ParallelOverK              F     # default value
+MD.RelaxCellOnly              F     # default value
+MD.RemoveIntraMolecularPressure              F     # default value
+COOP.Write              F     # default value
+SaveRho              F     # default value
+SaveDeltaRho              F     # default value
+SaveRhoXC              F     # default value
+SaveElectrostaticPotential              F     # default value
+SaveNeutralAtomPotential              F     # default value
+SaveTotalPotential              F     # default value
+SaveIonicCharge              F     # default value
+SaveBaderCharge              F     # default value
+SaveTotalCharge              F     # default value
+Siesta2Wannier90.WriteMmn              F     # default value
+Siesta2Wannier90.WriteUnk              F     # default value
+Siesta2Wannier90.WriteAmn              F     # default value
+Siesta2Wannier90.WriteEig              F     # default value
+Siesta2Wannier90.NumberOfBandsUp         0     # default value
+Siesta2Wannier90.NumberOfBandsDown         0     # default value
+Siesta2Wannier90.NumberOfBands         0     # default value
+RcSpatial          0.000000000     Bohr     # default value
+ProcessorGridX         1     # default value
+ProcessorGridY         1     # default value
+ProcessorGridZ         1     # default value
+NumberOfEigenStates        23     # default value
+TimeReversalSymmetryForKpoints              T     # default value
+kgrid_cutoff          0.000000000     Bohr     # default value
+LongOutput              F     # default value
+WriteWaveFunctions              F     # default value
+ForceAuxCell              F     # default value
+AtomicCoordinatesFormat     Ang                                                                             
+AtomCoorFormatOut     Ang                        # default value
+LatticeConstant          0.000000000     Bohr     # default value
+SCF.Pulay.Damping         -1.000000000         # default value
+SCF.MixingWeightAfterPulay         0.5000000000         # default value
+SCF.PulayMinimumHistory         2     # default value
+SCF.PulayDmaxRegion          1000.000000         # default value
+SCF.LinearMixingAfterPulay              F     # default value
+SCF.Pulay.UseSVD              F     # default value
+SCF.Pulay.DebugSVD              T     # default value
+SCF.Pulay.RcondSVD         0.1000000000E-07     # default value
+MeshSubDivisions         2     # default value
+LatticeConstant          0.000000000     Bohr     # default value
+DirectPhi              F     # default value
+SimulateDoping              F     # default value
+LatticeConstant          0.000000000     Bohr     # default value
+Diag.AllInOne              F     # default value
+Diag.DivideAndConquer              T     # default value
+Diag.NoExpert              F     # default value
+Diag.PreRotate              F     # default value
+Diag.Use2D              T     # default value
+SingleExcitation              F     # default value
+OccupationFunction     FD     # default value
+OccupationFunction     FD     # default value
+SCF.Want.Variational.EKS              F     # default value
+DM.FormattedFiles              F     # default value
+DM.FormattedInput              F     # default value
+DM.FormattedOutput              F     # default value
+SCF.Want.Variational.EKS              F     # default value
+SCF.Want.Variational.EKS              F     # default value
+SCF.Want.Variational.EKS              F     # default value
+SCF.Want.Variational.EKS              F     # default value
+SCF.Want.Variational.EKS              F     # default value
+SCF.Want.Variational.EKS              F     # default value
+SCF.Want.Variational.EKS              F     # default value
+SCF.Want.Variational.EKS              F     # default value
+SCF.Want.Variational.EKS              F     # default value
+SCF.Want.Variational.EKS              F     # default value
+SCF.Want.Variational.EKS              F     # default value
+SCF.Want.Variational.EKS              F     # default value
+SCF.Want.Variational.EKS              F     # default value
+SCF.Want.Variational.EKS              F     # default value
+SCF.Want.Variational.EKS              F     # default value
+SCF.Want.Variational.EKS              F     # default value
+SCF.Want.Variational.EKS              F     # default value
+SCF.Want.Variational.EKS              F     # default value
+SCF.Want.Variational.EKS              F     # default value
+SCF.Want.Variational.EKS              F     # default value
+WriteCoorXmol              F     # default value
+WriteCoorCerius              F     # default value
+BasisPressure         0.2000000000     GPa     # default value
+OpticalCalculation              F     # default value
--- a/H2O/h2o.BONDS
+++ b/H2O/h2o.BONDS
+Neighbors of:     1 O at:   0.0000  0.0000  0.0000
+    2 H                     0.9573  Ang. Really at:   1.4305  1.1074  0.0000
+    3 H                     0.9573  Ang. Really at:  -1.4305  1.1074  0.0000
+Neighbors of:     2 H at:   1.4305  1.1074  0.0000
+    1 O                     0.9573  Ang. Really at:   0.0000 -0.0000  0.0000
+    3 H                     1.5140  Ang. Really at:  -1.4305  1.1074  0.0000
+Neighbors of:     3 H at:  -1.4305  1.1074  0.0000
+    1 O                     0.9573  Ang. Really at:  -0.0000 -0.0000  0.0000
+    2 H                     1.5140  Ang. Really at:   1.4305  1.1074  0.0000
--- a/H2O/h2o.BONDS_FINAL
+++ b/H2O/h2o.BONDS_FINAL
+Neighbors of:     1 O at:   0.0000  0.0000  0.0000
+    2 H                     0.9573  Ang. Really at:   1.4305  1.1074  0.0000
+    3 H                     0.9573  Ang. Really at:  -1.4305  1.1074  0.0000
+Neighbors of:     2 H at:   1.4305  1.1074  0.0000
+    1 O                     0.9573  Ang. Really at:   0.0000 -0.0000  0.0000
+    3 H                     1.5140  Ang. Really at:  -1.4305  1.1074  0.0000
+Neighbors of:     3 H at:  -1.4305  1.1074  0.0000
+    1 O                     0.9573  Ang. Really at:  -0.0000 -0.0000  0.0000
+    2 H                     1.5140  Ang. Really at:   1.4305  1.1074  0.0000
--- a/H2O/h2o.DM
+++ b/H2O/h2o.DM
--- a/H2O/h2o.EIG
+++ b/H2O/h2o.EIG
+       -2.0182
+    23     1     1
+    1   -24.64690   -12.55426    -8.30268    -6.23845     2.03638     4.29524    10.61346    12.21265    13.04017    14.12931
+         15.66423    22.67140    25.54859    27.91666    28.52815    32.59313    44.50452    44.54666    46.99399    50.04076
+         51.70242    71.89650    96.49247
--- a/H2O/h2o.FA
+++ b/H2O/h2o.FA
+     3
+     1    0.000000   -0.811101    0.000000
+     2    0.656672    0.421885   -0.000000
+     3   -0.656672    0.421885   -0.000000
--- a/H2O/h2o.KP
+++ b/H2O/h2o.KP
+     1
+     1    0.000000    0.000000    0.000000       1.000000