From 9ed043f6752eb18450c25ca3b5c7485bdd4ab356 Mon Sep 17 00:00:00 2001
From: Ask Hjorth Larsen <asklarsen@gmail.com>
Date: Fri, 16 Sep 2016 19:00:48 +0200
Subject: [PATCH] better handling of upper/lowercase. Remove duplicate files
in tests
---
parser/parser-siesta/main.py | 153 +++++---
test/examples/Al-slab/fdf-95205.log | 504 --------------------------
test/examples/H2O-relax/fdf-47305.log | 426 ----------------------
test/examples/H2O-relax/fdf-55244.log | 426 ----------------------
4 files changed, 112 insertions(+), 1397 deletions(-)
delete mode 100644 test/examples/Al-slab/fdf-95205.log
delete mode 100644 test/examples/H2O-relax/fdf-47305.log
delete mode 100644 test/examples/H2O-relax/fdf-55244.log
diff --git a/parser/parser-siesta/main.py b/parser/parser-siesta/main.py
index b7cb512..e3b973b 100644
--- a/parser/parser-siesta/main.py
+++ b/parser/parser-siesta/main.py
@@ -48,10 +48,16 @@ def get_input_metadata(inputvars_file, use_new_format):
varset = set(varlist)
+ lower_vars = {}
+ for var in varlist:
+ lower_vars[var.lower()] = var
+
def addvar(tokens):
name = tokens[0]
val = ' '.join(tokens[1:])
- if name in varset:
+ name = name.lower()
+ if name in lower_vars:
+ name = lower_vars[name]
inputvars[name] = val
currentblock = None
@@ -119,12 +125,12 @@ class SiestaContext(object):
self.files = None # Dict of files
self.blocks = None # Dict of input blocks (coords, cell, etc.)
- self._is_last_configuration = False # XXX
self.data = {}
self.special_input_vars = {}
self.system_meta = {}
self.section_refs = {} # {name: gindex, ...}
+ self.simulation_type = None
def adhoc_format_new(self, parser):
assert self.format is None
@@ -156,51 +162,57 @@ class SiestaContext(object):
# what else? We already get force/stress/positions from stdout.
if self.format == 'new':
inplogfiles = glob('%s/fdf-*.log' % dirname)
+ assert len(inplogfiles) == 1
if inplogfiles:
inplogfiles.sort()
- files['inputlog'] = inplogfiles[-1]
+ files['inputlog'] = inplogfiles[0]
else:
assert self.format == 'old', self.format
files['inputlog'] = os.path.join(dirname, 'out.fdf')
self.files = files
+ def adhoc_set_simulation_type(self, parser):
+ line = parser.fIn.readline()
+
+ if self.simulation_type is not None:
+ return
+
+ line = line.strip()
+
+ if line.startswith('Single-point'):
+ self.simulation_type = 'singlepoint'
+ elif 'opt' in line or 'move' in line:
+ self.simulation_type = 'optimization'
+ else:
+ raise ValueError('Todo: recognize simulation type "%s"' % line)
+
def startedParsing(self, fname, parser):
self.fname = fname
path = os.path.abspath(fname)
self.dirname, _ = os.path.split(path)
#self.parser = parser
- def onClose_x_siesta_section_xc_authors(self, backend, gindex, section):
- authors = section['x_siesta_xc_authors']
- if authors is None:
- raise ValueError('XC authors not found!')
+ #def onClose_x_siesta_section_xc_authors(self, backend, gindex, section):
- assert len(authors) == 1
- authors = authors[0]
+ def onClose_section_frame_sequence(self, backend, gindex, section):
+ backend.addValue('frame_sequence_to_sampling_ref',
+ self.section_refs['sampling_method'])
- mapping = {'CA': ('LDA_X', 'LDA_C_PZ'),
- 'PZ': ('LDA_X', 'LDA_C_PZ'),
- 'PW92': ('LDA_X', 'LDA_C_PW'),
- #'PW91': '',
- 'PBE': ('GGA_X_PBE', 'GGA_C_PBE'),
- 'revPBE': ('GGA_X_PBE_R', 'GGA_C_PBE'),
- 'RPBE': ('GGA_X_RPBE', 'GGA_C_PBE'),
- #'WC': ('GGA_X_WC', ),
- # Siesta does not mention which correlation is used with
- # the WC functional. Is it just the PBE one?
- 'AM05': ('GGA_X_AM05', 'GGA_C_AM05'),
- 'PBEsol': ('GGA_X_PBE_SOL', 'GGA_C_PBE_SOL'),
- 'BLYP': ('GGA_X_B88 + GGA_C_LYP')}
- xc = mapping.get(authors)
+ def onOpen_section_sampling_method(self, backend, gindex, section):
+ self.section_refs['sampling_method'] = gindex
- if xc is None:
- raise ValueError('XC functional %s unsupported by parser'
- % authors)
+ def onOpen_section_frame_sequence(self, backend, gindex, section):
+ self.section_refs['frame_sequence'] = gindex
- for funcname in xc:
- gid = backend.openSection('section_XC_functionals')
- backend.addValue('XC_functional_name', funcname)
- backend.closeSection('section_XC_functionals', gid)
+ def onClose_section_sampling_method(self, backend, gindex, section):
+ simtype = self.simulation_type
+ assert simtype is not None
+ if simtype == 'optimization':
+ backend.addValue('sampling_method', 'geometry_optimization')
+ elif simtype == 'singlepoint':
+ pass
+ else:
+ raise ValueError('XXX: %s' % simtype)
def onClose_section_eigenvalues(self, backend, gindex, section):
self.read_eigenvalues(backend)
@@ -208,6 +220,18 @@ class SiestaContext(object):
def onOpen_section_method(self, backend, gindex, section):
self.section_refs['method'] = gindex
+ def onClose_section_method(self, backend, gindex, section):
+ temp = self.special_input_vars['ElectronicTemperature']
+ temp, unit = temp.split()
+ assert unit == 'Ry' # Siesta always converts to Ry here I think
+ temp = float(temp)
+ temp = convert_unit(temp, 'rydberg')
+ backend.addValue('smearing_width', temp)
+
+ #simtype = self.special_input_vars['MD.TypeOfRun']
+ #print('SIMTYPE', simtype)
+ #sdfsdf
+
def onOpen_section_system(self, backend, gindex, section):
self.section_refs['system'] = gindex
@@ -308,7 +332,7 @@ class SiestaContext(object):
def onClose_x_siesta_section_input(self, backend, gindex, section):
inputvars_file = self.files.get('inputlog')
if inputvars_file is None:
- return
+ raise ValueError('no input logfile!')
inputvars, blocks = get_input_metadata(inputvars_file,
self.format == 'new')
@@ -317,11 +341,44 @@ class SiestaContext(object):
for special_name in ['LatticeConstant',
'AtomicCoordinatesFormat',
- 'AtomicCoordinatesFormatOut']:
+ 'AtomicCoordinatesFormatOut',
+ 'ElectronicTemperature']:
self.special_input_vars[special_name] = inputvars.get(special_name)
self.blocks = blocks
+ authors = section['x_siesta_xc_authors']
+ if authors is None:
+ raise ValueError('XC authors not found!')
+
+ assert len(authors) == 1
+ authors = authors[0]
+
+ # XXX Case sensitive?
+ mapping = {'CA': ('LDA_X', 'LDA_C_PZ'),
+ 'PZ': ('LDA_X', 'LDA_C_PZ'),
+ 'PW92': ('LDA_X', 'LDA_C_PW'),
+ #'PW91': '',
+ 'PBE': ('GGA_X_PBE', 'GGA_C_PBE'),
+ 'revPBE': ('GGA_X_PBE_R', 'GGA_C_PBE'),
+ 'RPBE': ('GGA_X_RPBE', 'GGA_C_PBE'),
+ #'WC': ('GGA_X_WC', ),
+ # Siesta does not mention which correlation is used with
+ # the WC functional. Is it just the PBE one?
+ 'AM05': ('GGA_X_AM05', 'GGA_C_AM05'),
+ 'PBEsol': ('GGA_X_PBE_SOL', 'GGA_C_PBE_SOL'),
+ 'BLYP': ('GGA_X_B88 + GGA_C_LYP')}
+ xc = mapping.get(authors)
+
+ if xc is None:
+ raise ValueError('XC functional %s unsupported by parser'
+ % authors)
+
+ for funcname in xc:
+ gid = backend.openSection('section_XC_functionals')
+ backend.addValue('XC_functional_name', funcname)
+ backend.closeSection('section_XC_functionals', gid)
+
def read_eigenvalues(self, backend):
eigfile = self.files.get('EIG')
if eigfile is None:
@@ -448,35 +505,47 @@ def get_header_matcher():
return m
+def anycase(string):
+ tokens = []
+ for letter in list(string):
+ if letter.isalpha():
+ tokens.append('[%s%s]' % (letter.upper(),
+ letter.lower()))
+ else:
+ tokens.append(letter)
+ return ''.join(tokens)
+
welcome_pattern = r'\s*\*\s*WELCOME TO SIESTA\s*\*'
def get_input_matcher():
m = SM(welcome_pattern,
name='welcome',
- sections=['section_method'],
+ sections=['section_method', 'x_siesta_section_input'],
+ fixedStartValues={'electronic_structure_method': 'DFT',
+ 'smearing_kind': 'fermi'},
subFlags=SM.SubFlags.Unordered,
subMatchers=[
SM(r'NumberOfAtoms\s*(?P<number_of_atoms>\d+)',
name='natoms'),
context.multi_sm('block_species_label',
- r'%block ChemicalSpeciesLabel',
+ anycase(r'%block ChemicalSpeciesLabel'),
r'\s*\d+\s*\d+\s*(\S+)',
conflict='keep'),
context.multi_sm('block_coords_and_species',
- r'%block AtomicCoordinatesAndAtomicSpecies',
+ anycase(r'%block AtomicCoordinatesAndAtomicSpecies'),
r'\s*(\S+)\s*(\S+)\s*(\S+)\s*(\d+)'),
context.multi_sm('block_lattice_vectors',
- r'%block LatticeVectors',
+ anycase(r'%block LatticeVectors'),
r'(?!%)\s*(\S+)\s*(\S+)\s*(\S+)'),
- SM(r'xc.authors\s*(?P<x_siesta_xc_authors>\S+)',
+ SM(r'%s\s*(?P<x_siesta_xc_authors>\S+)' % anycase('xc\.authors'),
name='xc authors',
- fixedStartValues={'x_siesta_xc_authors': 'CA'},
- sections=['section_method', 'x_siesta_section_xc_authors']),
+ fixedStartValues={'x_siesta_xc_authors': 'CA'}),
+ #SM(r'MD.TypeOfRun\s*(?P<x_siesta_typeofrun>\S+)',
+ # fixedStartValues={'x_siesta_typeofrun': 'none'}),
SM(r'reinit: System Name:\s*(?P<system_name>.+)',
name='sysname'),
SM(r'reinit: System Label:\s*(?P<x_siesta_system_label>\S+)',
name='syslabel', forwardMatch=True,
- sections=['x_siesta_section_input'],
adHoc=context.adhoc_set_label),
context.multi_sm('coords_and_species',
r'siesta: Atomic coordinates \(Bohr\) and species',
@@ -495,6 +564,8 @@ step_pattern = r'\s*(Single-point calculation|Begin[^=]+=\s*\d+)'
def get_step_matcher():
m = SM(step_pattern,
name='step',
+ forwardMatch=True,
+ adHoc=context.adhoc_set_simulation_type,
sections=['section_single_configuration_calculation'],
subFlags=SM.SubFlags.Unordered,
subMatchers=[
@@ -547,7 +618,7 @@ mainFileDescription = SM(
forwardMatch=True,
repeats=True,
required=True,
- sections=['section_system'],
+ sections=['section_system', 'section_frame_sequence', 'section_sampling_method'],
subMatchers=[
get_input_matcher(),
get_step_matcher(),
diff --git a/test/examples/Al-slab/fdf-95205.log b/test/examples/Al-slab/fdf-95205.log
deleted file mode 100644
index 31f6313..0000000
--- a/test/examples/Al-slab/fdf-95205.log
+++ /dev/null
@@ -1,504 +0,0 @@
-SystemName Al_slab
-SystemLabel Al_slab
-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 LDA
-xc.authors CA
-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 1
-%block Chemical_species_label
- 1 13 Al
-%endblock Chemical_species_label
-%block PAO.Basis
- Al 3 # Species label, number of l-shells
- n=3 0 2 # n, l, Nzeta
- 5.859 4.513
- 1.000 1.000
- n=3 1 2 # n, l, Nzeta
- 6.809 5.09
- 1.000 1.000
- n=3 2 1 # n, l, Nzeta
- 5.176
- 1.000
-%endblock PAO.Basis
-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.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
-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 1.889726878 Bohr
-# above item originally: LatticeConstant 1.000000000 Ang
-%block LatticeVectors
-%block LatticeVectors
- 4.457602528 0.0 0.0
- 0.0 3.152000000 0.0
- 0.0 0.0 30
-AtomicCoordinatesFormat Ang
-NumberOfAtoms 12
-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
- 2.228801000 3.152000000 0.0 1
- 4.457606000 1.576024000 0.0 1
- 1.485868000 1.576024000 2.414 1
- 3.714668000 3.152000000 2.414 1
- 2.971741000 1.576024000 4.828 1
- 5.200541000 3.152000000 4.828 1
- 2.228801000 3.152000000 7.242 1
- 4.457606000 1.576024000 7.242 1
- 1.485868000 1.576024000 9.656 1
- 3.714668000 3.152000000 9.656 1
- 2.971741000 1.576024000 12.07 1
- 5.200541000 3.152000000 12.07 1
-UseSaveData F # default value
-MD.UseSaveXV F # default value
-MD.UseSaveZM F # default value
-WriteCoorInitial T # default value
-MD.TypeOfRun none # 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 400.0000000 Ry
-# above item originally: MeshCutoff 400.0000000 Ry
-NetCharge 0.000000000 # default value
-MinSCFIterations 0 # default value
-MaxSCFIterations 10000
-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 5
-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 0.1000000000E-02
-DM.OccupancyTolerance 0.1000000000E-11 # default value
-DM.NumberKick 0 # default value
-DM.KickMixingWeight 0.5000000000 # default value
-DM.Tolerance 0.1000000000E-03
-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 T
-NeglNonOverlapInt F # default value
-SolutionMethod diagon
-Diag.DivideAndConquer T # default value
-Diag.Memory 1.000000000 # default value
-ElectronicTemperature 0.1900069269E-02 Ry
-# above item originally: ElectronicTemperature 300.0000000 K
-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 12 # 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
-processorY 2 # default value
-blocksize 20 # default value
-NumberOfEigenStates 156 # default value
-TimeReversalSymmetryForKpoints T # default value
-%block kgrid_Monkhorst_Pack
- 8 0 0 0.0
- 0 8 0 0.0
- 0 0 1 0.0
-LongOutput F # default value
-WriteWaveFunctions F # default value
-ForceAuxCell F # default value
-AtomicCoordinatesFormat Ang
-AtomCoorFormatOut Ang # default value
-LatticeConstant 1.889726878 Bohr
-# above item originally: LatticeConstant 1.000000000 Ang
-DM.FormattedFiles F # default value
-DM.FormattedInput F # default value
-DM.FormattedOutput F # 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 1.889726878 Bohr
-# above item originally: LatticeConstant 1.000000000 Ang
-%block LatticeVectors
-%block LatticeVectors
- 4.457602528 0.0 0.0
- 0.0 3.152000000 0.0
- 0.0 0.0 30
-PROCS_PER_NODE 4 # default value
-PROCS_PER_NODE 4 # default value
-DirectPhi F # default value
-SimulateDoping F # default value
-SlabDipoleCorrection F # default value
-Diag.ParallelOverK F # default value
-LatticeConstant 1.889726878 Bohr
-# above item originally: LatticeConstant 1.000000000 Ang
-%block LatticeVectors
-%block LatticeVectors
- 4.457602528 0.0 0.0
- 0.0 3.152000000 0.0
- 0.0 0.0 30
-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
-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
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diff --git a/test/examples/H2O-relax/fdf-47305.log b/test/examples/H2O-relax/fdf-47305.log
deleted file mode 100644
index 8744e57..0000000
--- a/test/examples/H2O-relax/fdf-47305.log
+++ /dev/null
@@ -1,426 +0,0 @@
-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
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-PAO.Filter F # default value
-PAO.Filter F # default value
-PAO.Filter F # default value
-PAO.OldStylePolorbs T # default value
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-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
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-PAO.Filter F # default value
-PAO.OldStylePolorbs T # default value
-PAO.SplitTailNorm F # default value
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-Vna.Filter F # default value
-PAO.BasisType split # default value
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-UseStructFile F # default value
-MD.UseStructFile F # default value
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-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 0.600 0.000 2
- -0.757 0.600 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
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-SpinPolarized F # default value
-NonCollinearSpin F # default value
-HSetupOnly F # default value
-LongOutput F # default value
-WriteDenchar F # default value
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-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
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-SCF.MixAfterConvergence F # default value
-SCF.Recompute-H-After-Scf F # default value
-DM.NumberPulay 0 # default value
-DM.NumberBroyden 0 # default value
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-DM.MixingWeight 0.2500000000 # default value
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-DM.NumberKick 0 # default value
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-DM.HarrisTolerance 0.7349806700E-06 Ry # default value
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-ON.eta_beta 0.000000000 Ry # default value
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-MD.MaxCGDispl 0.2000000000 Bohr # default value
-MD.MaxForceTol 0.1555739508E-02 Ry/Bohr
-# above item originally: MD.MaxForceTol 0.4000000000E-01 eV/Ang
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-MD.InitialTimeStep 1 # default value
-MD.FinalTimeStep 1 # default value
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-SaveElectrostaticPotential F # default value
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-SaveIonicCharge F # default value
-SaveBaderCharge F # default value
-SaveTotalCharge F # default value
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-Siesta2Wannier90.WriteUnk F # default value
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-Siesta2Wannier90.NumberOfBandsUp 0 # default value
-Siesta2Wannier90.NumberOfBandsDown 0 # default value
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-ProcessorGridX 1 # default value
-ProcessorGridY 1 # default value
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-processorY 1 # default value
-blocksize 12 # default value
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-PROCS_PER_NODE 4 # default value
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-SCF.Want.Variational.EKS F # default value
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-SCF.Pulay.UseSVD F # default value
-SCF.Pulay.DebugSVD T # default value
-SCF.Pulay.RcondSVD 0.1000000000E-07 # default value
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-SCF.Want.Variational.EKS F # default value
-SCF.Want.Variational.EKS F # default value
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-DM.AllowExtrapolation F # default value
-SCF.Pulay.Damping -1.000000000 # default value
-SCF.MixingWeightAfterPulay 0.5000000000 # default value
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-SCF.PulayDmaxRegion 1000.000000 # default value
-SCF.LinearMixingAfterPulay F # default value
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-PROCS_PER_NODE 4 # default value
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-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
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-SCF.Want.Variational.EKS F # default value
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-SCF.Pulay.DebugSVD T # default value
-SCF.Pulay.RcondSVD 0.1000000000E-07 # default value
-PROCS_PER_NODE 4 # default value
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-SCF.Want.Variational.EKS F # default value
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-WriteCoorXmol F # default value
-WriteCoorCerius F # default value
-BasisPressure 0.2000000000 GPa # default value
-OpticalCalculation F # default value
diff --git a/test/examples/H2O-relax/fdf-55244.log b/test/examples/H2O-relax/fdf-55244.log
deleted file mode 100644
index 1f96dd0..0000000
--- a/test/examples/H2O-relax/fdf-55244.log
+++ /dev/null
@@ -1,426 +0,0 @@
-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
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-xc.functional GGA
-xc.authors PBE
-MM.Cutoff 30.00000000 Bohr # default value
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-KB.New.Reference.Orbitals F # default value
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-user-basis-netcdf F # default value
-ReparametrizePseudos F # default value
-Restricted.Radial.Grid T # default value
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-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
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-KB.Rmax 6.000000000 Bohr # default value
-PAO.EnergyShift 0.2000000000E-01 Ry # default value
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-Vna.Filter F # default value
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-KB.Rmax 6.000000000 Bohr # default value
-PAO.EnergyShift 0.2000000000E-01 Ry # default value
-PAO.SplitTailNorm F # default value
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-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 0.600 0.000 2
- -0.757 0.600 0.000 2
-UseSaveData F # default value
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-MD.UseSaveZM F # default value
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-MD.TypeOfRun none # default value
-NetCharge 0.000000000 # default value
-MaxBondDistance 6.000000000 Bohr # default value
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-NonCollinearSpin F # default value
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-WriteDenchar F # default value
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-PartialChargesAtEveryScfStep F # default value
-MeshCutoff 100.0000000 Ry # default value
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-SCF.MixAfterConvergence F # default value
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-MD.MaxCGDispl 0.2000000000 Bohr # default value
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-OpticalCalculation F # default value
--
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