diff --git a/parser/parser-siesta/main.py b/parser/parser-siesta/main.py index b7cb512391fc4f7ae0cd6bd4bff440cd053b0727..e3b973b97c100adf3aa53e61f5cbec9ff032ab0c 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 31f63136ed58fa2dcc0db61100b4c6ecf65f27ad..0000000000000000000000000000000000000000 --- 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 -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 # 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