more comprehensive input vars. Better handling of case sensitivity

parser/parser-siesta/inputvars.py

 varlist = [
+    '%endblock',
     'Atom-Setup-Only',
     'Atom.Debug.KB.Generation',
     'AtomCoorFormatOut',
+    'AtomLeftVcte',
+    'AtomRightVcte',
     'AtomicCoordinatesFormat',
     'BasisPressure',
     'BornCharge',
+    'BuildSuperCell',
+    'BulkLead',
+    'BulkTransport',
+    'BulkTransvCellSize',
+    'BulkTransvCellSizeX',
+    'BulkTransvCellSizeY',
+    'BulkTransvCellSizeZ',
+    'CB.MaxKappa',
+    'CB.WriteComplexBands',
+    'CDFT',
+    'CDFT.MaxIter',
     'COOP.Write',
+    'CalcIETS',
+    'CalcMPSH',
     'ChangeKgridInMD',
     'Compat-pre-v4-DM-H',
     'DM.AllowExtrapolation',
@@ -31,6 +47,8 @@ varlist = [
     'DM.RequireHarrisConvergence',
     'DM.Tolerance',
     'DM.UseSaveDM',
+    'Delta',
+    'DeltaWorkfunction',
     'Diag.AllInOne',
     'Diag.DivideAndConquer',
     'Diag.Memory',
@@ -38,22 +56,63 @@ varlist = [
     'Diag.ParallelOverK',
     'Diag.PreRotate',
     'Diag.Use2D',
+    'DiagMemory',
+    'DiagScale',
     'DirectPhi',
+    'DivideAndConquer',
+    'EM.AddRhoGate',
+    'EM.AddVgIsolatedLocalCharges',
+    'EM.COOPCalculate',
+    'EM.COOPNumberOfBonds',
+    'EM.DebugRhoGate',
+    'EM.NetRhoGateCharge',
+    'EM.PrintLimits',
+    'EM.RhoGateLxMax',
+    'EM.RhoGateLxMin',
+    'EM.RhoGateLyMax',
+    'EM.RhoGateLyMin',
+    'EM.RhoGateLzMax',
+    'EM.RhoGateLzMin',
+    'EM.TRCAddVCDFT',
+    'EM.TimeReversal',
+    'EM.Timings',
+    'EM.addV',
+    'EMPDOSKSO',
+    'EMTransport',
     'ElectronicTemperature',
+    'EnergLowestBound',
     'FilterCutoff',
     'FilterTol',
+    'FinalTransmRange',
     'FixAuxiliaryCell',
+    'FixAuxillaryCell',
     'FixSpin',
     'ForceAuxCell',
+    'FullRamp',
     'HSetupOnly',
     'Harris_functional',
+    'HartreeLeadsBottom',
+    'HartreeLeadsLeft',
+    'HartreeLeadsRight',
+    'Ik_Select',
+    'InitTransmRange',
+    'InitTransport',
     'KB.New.Reference.Orbitals',
     'KB.Rmax',
+    'LDAU.units',
+    'LDAUForces',
+    'LDAU_METHOD',
     'LatticeConstant',
     'LongOutput',
     'MD.AnnealOption',
     'MD.BulkModulus',
+    'MD.FCAcousticSumRule',
+    'MD.FCAtomRestart',
+    'MD.FCAxisRestart',
     'MD.FCDispl',
+    'MD.FCEigenVectors',
+    'MD.FCIR',
+    'MD.FCRead',
     'MD.FCfirst',
     'MD.FClast',
     'MD.FinalTimeStep',
@@ -66,15 +125,20 @@ varlist = [
     'MD.MaxStressTol',
     'MD.NoseMass',
     'MD.NumCGsteps',
+    'MD.NumNEBsteps',
     'MD.ParrinelloRahmanMass',
     'MD.Quench',
     'MD.RelaxCellOnly',
     'MD.RemoveIntraMolecularPressure',
+    'MD.TRCSampling',
+    'MD.TRCSkip',
     'MD.TargetPressure',
     'MD.TargetTemperature',
     'MD.TauRelax',
+    'MD.Timing',
     'MD.TypeOfRun',
     'MD.UseSaveCG',
+    'MD.UseSaveNEB',
     'MD.UseSaveXV',
     'MD.UseSaveZM',
     'MD.UseStructFile',
@@ -82,6 +146,10 @@ varlist = [
     'MM.Cutoff',
     'MM.UnitsDistance',
     'MM.UnitsEnergy',
+    'MPSHAtomFirst',
+    'MPSHAtomLast',
+    'MPSHOrbFirst',
+    'MPSHOrbLast',
     'MaxBondDistance',
     'MaxSCFIterations',
     'MeshCutoff',
@@ -89,14 +157,28 @@ varlist = [
     'MinSCFIterations',
     'MixCharge',
     'MixHamiltonian',
+    'MixedParallel',
     'MonitorForcesInSCF',
     'MullikenInSCF',
+    'NC.OrbitalRotationEnd',
+    'NC.OrbitalRotationStart',
+    'NEB.SkipEdge',
+    'NEnergReal',
+    'NIVPoints',
+    'NPoles',
+    'NSlices',
+    'NTransmPoints',
     'NaiveAuxiliaryCell',
     'NeglNonOverlapInt',
+    'NenergImCircle',
+    'NenergImLine',
     'NetCharge',
     'NonCollinearSpin',
+    'NumSkipWriteDM',
+    'NumberLinearMix',
     'NumberOfAtoms',
     'NumberOfEigenStates',
+    'NumberOfSpecies',
     'Number_of_species',
     'ON.ChemicalPotential',
     'ON.ChemicalPotentialOrder',
@@ -129,16 +211,26 @@ varlist = [
     'PAO.SplitNorm',
     'PAO.SplitNormH',
     'PAO.SplitTailNorm',
+    'PS.SIC',
+    'ParallelOverK',
     'PartialChargesAtEveryGeometry',
     'PartialChargesAtEveryScfStep',
+    'PoissonMultigrid',
+    'Print_ldau',
     'ProcessorGridX',
     'ProcessorGridY',
     'ProcessorGridZ',
+    'ProjectionInSCF',
+    'ProjectionMethod',
     'RcSpatial',
     'ReInitialiseDM',
+    'ReadHamiltonian',
+    'ReadKPIN',
     'ReparametrizePseudos',
     'Restricted.Radial.Grid',
     'Rmax.Radial.Grid',
+    'RotateSpin.Phi',
+    'RotateSpin.Theta',
     'SCF.LinearMixingAfterPulay',
     'SCF.MixAfterConvergence',
     'SCF.MixingWeightAfterPulay',
@@ -153,6 +245,18 @@ varlist = [
     'SCF.Recompute-H-After-Scf',
     'SCF.Want.Variational.EKS',
     'SCFMustConverge',
+    'SIC.Flavour',
+    'SIC.Lambda',
+    'SIC.NoRelaxation',
+    'SIC.Npop',
+    'SIC.PopDMConv',
+    'SIC.PopKgridFactor',
+    'SIC.PopSmatSparsity',
+    'SIC.ProjectionMode',
+    'SIC.ProjectionType',
+    'SIC.Rot_Inv',
+    'STT.Calculation',
+    'STT.LinearResponse',
     'SaveBaderCharge',
     'SaveDeltaRho',
     'SaveElectrostaticPotential',
@@ -164,6 +268,8 @@ varlist = [
     'SaveRhoXC',
     'SaveTotalCharge',
     'SaveTotalPotential',
+    'Scissor.Operator',
+    'SetBulkTransvCell',
     'Siesta2Wannier90.NumberOfBands',
     'Siesta2Wannier90.NumberOfBandsDown',
     'Siesta2Wannier90.NumberOfBandsUp',
@@ -171,20 +277,32 @@ varlist = [
     'Siesta2Wannier90.WriteEig',
     'Siesta2Wannier90.WriteMmn',
     'Siesta2Wannier90.WriteUnk',
+    'Sigma.DSigmaDE',
+    'SignatureRecords',
     'SimulateDoping',
     'SingleExcitation',
+    'SkipLastIter',
+    'SlabDipoleCorrection',
     'SolutionMethod',
+    'SpinConfLeads',
+    'SpinOrbit',
     'SpinPolarized',
     'SystemLabel',
     'SystemName',
     'TS.MixH',
+    'TimeReversal',
     'TimeReversalSymmetryForKpoints',
+    'TrCoefficients',
+    'TryMemoryIncrease',
     'UseDomainDecomposition',
     'UseNewDiagk',
     'UseSaveData',
     'UseSpatialDecomposition',
     'UseStructFile',
     'UseTreeTimer',
+    'VFinal',
+    'VGate',
+    'VInitial',
     'Vna.Filter',
     'WarningMinimumAtomicDistance',
     'WriteBands',
@@ -197,9 +315,14 @@ varlist = [
     'WriteDM.NetCDF',
     'WriteDMHS.History.NetCDF',
     'WriteDMHS.NetCDF',
+    'WriteDMT',
     'WriteDenchar',
+    'WriteDiagdS',
+    'WriteEDM',
     'WriteEigenvalues',
     'WriteForces',
+    'WriteHSDeriv',
+    'WriteHamiltonPop',
     'WriteHirshfeldPop',
     'WriteIonPlotFiles',
     'WriteKbands',
@@ -207,11 +330,17 @@ varlist = [
     'WriteMDXmol',
     'WriteMDhistory',
     'WriteMullikenPop',
+    'WriteProjections',
+    'WriteSpinMulliken',
+    'WriteSpinSCF',
+    'WriteVNA',
     'WriteVoronoiPop',
     'WriteWaveFunctions',
     'XML.AbortOnErrors',
     'XML.AbortOnWarnings',
     'XML.Write',
+    'ZBroadeningG',
+    'ZLeftVcte',
     'ZM.CalcAllForces',
     'ZM.ForceTolAngle',
     'ZM.ForceTolLength',
@@ -219,10 +348,19 @@ varlist = [
     'ZM.MaxDisplLength',
     'ZM.UnitsAngle',
     'ZM.UnitsLength',
+    'ZRightVcte',
+    'ZVGateL',
+    'ZVGateR',
+    'ZeemanTermBx',
+    'ZeemanTermBy',
+    'ZeemanTermBz',
     'alloc_report_level',
     'alloc_report_threshold',
+    'blocksize',
     'compat-pre-v4-dynamics',
+    'fdf-debug',
     'kgrid_cutoff',
+    'processorY',
     'timer_report_threshold',
     'user-basis',
     'user-basis-netcdf',

parser/parser-siesta/mkjson.py

@@ -26,6 +26,13 @@ json_section_template = """{
       "description": "%(description)s",
       "kindStr": "type_abstract_document_content",
       "name": "%(name)s",
+      "superNames": [
+        "x_siesta_section_input"
+      ]
+    }, {
+      "description": "input section",
+      "kindStr": "type_section",
+      "name": "x_siesta_section_input",
       "superNames": [
         "section_run"
       ]
@@ -33,20 +40,47 @@ json_section_template = """{
 # END OF TEMPLATES FROM OCTOPUS
 
 import sys
-fname = sys.argv[1]
+#fname = sys.argv[1]
 
 inputvars_fd = open('inputvars.py', 'w')
-print('inputvars = [', file=inputvars_fd)
+print('varlist = [', file=inputvars_fd)
 
-with open(fname) as fd:
-    varnames = []
+def getlines():
+    fd = open('test/H2O/fdf-95611.log')
     for line in fd:
         if not line[:1].isalpha():  # Get rid of blocks
             continue
+        yield line
+
+    withinblock = False
+    fd = open('test/smeagol-Au-leads/out.fdf')
+    for line in fd:
+        if line.startswith('%block'):
+            withinblock = True
+        elif line.startswith('%endblock'):
+            withinblock = False
+        if withinblock:
+            continue
+        yield line
+
+seen = set()
+
+#with open(fname) as fd:
+#for line in getlines():
+if 1:
+    varnames = []
+    for line in getlines():
 
         # Get rid of comments
-        line = line.strip().rsplit('#', 1)[0]
+        line = line.strip().rsplit('#', 1)[0].strip()
+        if not line:
+            continue
         varname = line.split()[0]
+        lowervarname = varname.lower()
+        if lowervarname in seen:
+            continue  # Already registered
+
+        seen.add(lowervarname)
         varnames.append(varname)
     varnames = list(set(varnames))
     varnames.sort()