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parser-siesta
Commit 7505b8b1 authored by Daniel Speckhard's avatar Daniel Speckhard
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removing src.

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parser/parser-siesta/check.sh deleted 100755 → 0
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#!/bin/bash
python main.py test/H2O/out --annotate 2>&1 | tee test/H2O/json
python main.py test/H2O-relax/out --annotate 2>&1 | tee test/H2O-relax/json
python main.py test/Al-bulk/out --annotate 2>&1 | tee test/Al-bulk/json
python main.py test/Al-slab/out --annotate 2>&1 | tee test/Al-slab/json
python main.py test/MgO/out --annotate 2>&1 | tee test/MgO/json
python main.py test/smeagol-Au-leads/Au.out --annotate 2>&1 | tee test/smeagol-Au-leads/json
python main.py test/smeagol-Au-scregion/Au.out --annotate 2>&1 | tee test/smeagol-Au-scregion/json
parser/parser-siesta/inputvars.py deleted 100644 → 0
View file @ 63c52686
# Copyright 2016-2018 Ask Hjorth Larsen, Fawzi Mohamed
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# Main author and maintainer: Ask Hjorth Larsen <asklarsen@gmail.com>
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',
'DM.AllowReuse',
'DM.EnergyTolerance',
'DM.FIRE.Mixing',
'DM.FormattedFiles',
'DM.FormattedInput',
'DM.FormattedOutput',
'DM.HarrisTolerance',
'DM.KickMixingWeight',
'DM.MixSCF1',
'DM.MixingWeight',
'DM.NormalizationTolerance',
'DM.NormalizeDuringSCF',
'DM.NumberBroyden',
'DM.NumberKick',
'DM.NumberPulay',
'DM.OccupancyTolerance',
'DM.Pulay.Avoid.First.After.Kick',
'DM.PulayOnFile',
'DM.RequireEnergyConvergence',
'DM.RequireHarrisConvergence',
'DM.Tolerance',
'DM.UseSaveDM',
'Delta',
'DeltaWorkfunction',
'Diag.AllInOne',
'Diag.DivideAndConquer',
'Diag.Memory',
'Diag.NoExpert',
'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',
'MD.FireQuench',
'MD.InitialTemperature',
'MD.InitialTimeStep',
'MD.LengthTimeStep',
'MD.MaxCGDispl',
'MD.MaxForceTol',
'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',
'MD.VariableCell',
'MM.Cutoff',
'MM.UnitsDistance',
'MM.UnitsEnergy',
'MPSHAtomFirst',
'MPSHAtomLast',
'MPSHOrbFirst',
'MPSHOrbLast',
'MaxBondDistance',
'MaxSCFIterations',
'MeshCutoff',
'MeshSubDivisions',
'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',
'ON.ChemicalPotentialRc',
'ON.ChemicalPotentialTemperature',
'ON.ChemicalPotentialUse',
'ON.MaxNumIter',
'ON.UseSaveLWF',
'ON.eta',
'ON.eta_alpha',
'ON.eta_beta',
'ON.etol',
'ON.functional',
'OccupationFunction',
'On.RcLWF',
'OpticalCalculation',
'Optim.Broyden',
'Output-Structure-Only',
'PAO.BasisSize',
'PAO.BasisType',
'PAO.EnergyShift',
'PAO.Filter',
'PAO.FixSplitTable',
'PAO.Keep.Findp.Bug',
'PAO.NewSplitCode',
'PAO.OldStylePolorbs',
'PAO.SoftDefault',
'PAO.SoftInnerRadius',
'PAO.SoftPotential',
'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',
'SCF.Pulay.Damping',
'SCF.Pulay.DebugSVD',
'SCF.Pulay.RcondSVD',
'SCF.Pulay.UseSVD',
'SCF.PulayDmaxRegion',
'SCF.PulayMinimumHistory',
'SCF.Read.Charge.NetCDF',
'SCF.Read.Deformation.Charge.NetCDF',
'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',
'SaveHS',
'SaveInitialChargeDensity',
'SaveIonicCharge',
'SaveNeutralAtomPotential',
'SaveRho',
'SaveRhoXC',
'SaveTotalCharge',
'SaveTotalPotential',
'Scissor.Operator',
'SetBulkTransvCell',
'Siesta2Wannier90.NumberOfBands',
'Siesta2Wannier90.NumberOfBandsDown',
'Siesta2Wannier90.NumberOfBandsUp',
'Siesta2Wannier90.WriteAmn',
'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',
'WriteCoorCerius',
'WriteCoorInitial',
'WriteCoorStep',
'WriteCoorXmol',
'WriteDM',
'WriteDM.History.NetCDF',
'WriteDM.NetCDF',
'WriteDMHS.History.NetCDF',
'WriteDMHS.NetCDF',
'WriteDMT',
'WriteDenchar',
'WriteDiagdS',
'WriteEDM',
'WriteEigenvalues',
'WriteForces',
'WriteHSDeriv',
'WriteHamiltonPop',
'WriteHirshfeldPop',
'WriteIonPlotFiles',
'WriteKbands',
'WriteKpoints',
'WriteMDXmol',
'WriteMDhistory',
'WriteMullikenPop',
'WriteProjections',
'WriteSpinMulliken',
'WriteSpinSCF',
'WriteVNA',
'WriteVoronoiPop',
'WriteWaveFunctions',
'XML.AbortOnErrors',
'XML.AbortOnWarnings',
'XML.Write',
'ZBroadeningG',
'ZLeftVcte',
'ZM.CalcAllForces',
'ZM.ForceTolAngle',
'ZM.ForceTolLength',
'ZM.MaxDisplAngle',
'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',
'xc.authors',
'xc.functional',
]
parser/parser-siesta/main.py deleted 100644 → 0
View file @ 63c52686
# Copyright 2016-2018 Ask Hjorth Larsen, Fawzi Mohamed
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# Main author and maintainer: Ask Hjorth Larsen <asklarsen@gmail.com>
from __future__ import print_function
import os
import sys
import setup_paths
from glob import glob
import re
import numpy as np
from ase.data import chemical_symbols
from ase import Atoms
from nomadcore.simple_parser import (mainFunction, SimpleMatcher as SM,
AncillaryParser)
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
from nomadcore.unit_conversion.unit_conversion \
import register_userdefined_quantity, convert_unit
from inputvars import varlist
metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/siesta.nomadmetainfo.json"))
metaInfoEnv, warnings = loadJsonFile(filePath=metaInfoPath,
dependencyLoader=None,
extraArgsHandling=InfoKindEl.ADD_EXTRA_ARGS,
uri=None)
parser_info = {'name':'siesta-parser', 'version': '1.0'}
def siesta_energy(title, meta, **kwargs):
return SM(r'siesta:\s*%s\s*=\s*(?P<%s__eV>\S+)' % (title, meta),
name=meta, **kwargs)
def line_iter(fd, linepattern = re.compile(r'\s*([^#]+)')):
# Strip off comments and whitespace, return only non-empty strings
for line in fd:
match = linepattern.match(line)
if match:
line = match.group().rstrip()
if line:
yield line
def get_input_metadata(inputvars_file, use_new_format):
inputvars = {}
blocks = {}
varset = set(varlist)
lower_vars = {}
for var in varlist:
lower_vars[var.lower()] = var
def addvar(tokens):
name = tokens[0]
val = ' '.join(tokens[1:])
name = name.lower()
if name in lower_vars:
name = lower_vars[name]
inputvars[name] = val
currentblock = None
with open(inputvars_file) as fd:
lines = line_iter(fd)
for line in lines:
tokens = line.split()
assert len(tokens) > 0
if tokens[0].startswith('%'):
if tokens[0].lower() == '%block':
#assert currentblock == None
currentblock = []
blocks[tokens[1]] = currentblock
elif tokens[0].lower() == '%endblock':
currentblock = None
else:
raise ValueError('Unknown: %s' % tokens[0])
else:
if use_new_format:
if line.startswith(' '):
if currentblock is None:
continue # Ignore. Probably some warning
#assert currentblock is not None, line
currentblock.append(tokens)
else:
currentblock = None
addvar(tokens)
else:
if currentblock is not None:
currentblock.append(tokens)
else:
addvar(tokens)
return inputvars, blocks
"""
%block PAO.Basis # Define Basis set
O 2 # Species label, number of l-shells
n=2 0 2 # n, l, Nzeta
3.305 2.479
1.000 1.000
n=2 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
3.937 2.542
1.000 1.000
H 1 # Species label, number of l-shells
n=1 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
4.709 3.760
1.000 1.000
%endblock PAO.Basis
"""
class SiestaContext(object):
def __init__(self):
self.fname = None # The file that we are parsing
self.dirname = None # Base directory of calculations
#self.parser = None # The parser object
self.format = None # 'old' or 'new'; when parsing version
# label and things determined by label
self.label = None
self.files = None # Dict of files
self.blocks = None # Dict of input blocks (coords, cell, etc.)
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
self.format = 'new'
def adhoc_format_old(self, parser):
assert self.format is None
self.format = 'old'
def adhoc_set_label(self, parser):
# ASSUMPTION: the parser fIn is in the 'root' of whatever was uploaded.
# This may not be true. Figure out how to do this in general.
line = parser.fIn.readline()
assert line.startswith('reinit: System Label:')
self.label = label = line.split()[-1]
dirname = self.dirname
files = {}
for fileid in ['EIG', 'KP']:
path = os.path.join(dirname, '%s.%s' % (label, fileid))
if os.path.isfile(path):
files[fileid] = path
# Warn if files are not present?
#
# Also: input file
# input parser logfile
#
# 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[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):
def onClose_section_frame_sequence(self, backend, gindex, section):
backend.addValue('frame_sequence_to_sampling_ref',
self.section_refs['sampling_method'])
def onOpen_section_sampling_method(self, backend, gindex, section):
self.section_refs['sampling_method'] = gindex
def onOpen_section_frame_sequence(self, backend, gindex, section):
self.section_refs['frame_sequence'] = gindex
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)
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