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nomad-lab
parser-siesta
Commits
7505b8b1
Commit
7505b8b1
authored
Mar 20, 2019
by
Daniel Speckhard
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removing src.
parent
63c52686
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parser/parser-siesta/check.sh
parser/parser-siesta/check.sh
+0
-9
parser/parser-siesta/inputvars.py
parser/parser-siesta/inputvars.py
+0
-386
parser/parser-siesta/main.py
parser/parser-siesta/main.py
+0
-672
parser/parser-siesta/mkjson.py
parser/parser-siesta/mkjson.py
+0
-123
parser/parser-siesta/nomad_meta_info
parser/parser-siesta/nomad_meta_info
+0
-1
parser/parser-siesta/pycheck.py
parser/parser-siesta/pycheck.py
+0
-35
parser/parser-siesta/setup_paths.py
parser/parser-siesta/setup_paths.py
+0
-23
parser/parser-siesta/test
parser/parser-siesta/test
+0
-1
No files found.
parser/parser-siesta/check.sh
deleted
100755 → 0
View file @
63c52686
#!/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
This diff is collapsed.
Click to expand it.
parser/parser-siesta/mkjson.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
# TEMPLATES TAKEN FROM OCTOPUS. KEEP SYNCHRONIZED.
json_header
=
"""{
"type": "nomad_meta_info_1_0",
"description": "autogenerated nomad meta info for %(parser)s parser. The file which generates this maintained in the parser's git repository.",
"dependencies": [ {
"relativePath": "common.nomadmetainfo.json"
}],
"metaInfos": [ %(info)s]
}"""
json_template
=
"""{
"description": "%(description)s",
"dtypeStr": "%(dtypeStr)s",
"name": "%(name)s",
"repeats": false,
"shape": [],
"superNames": [
"%(supername)s"
]
}"""
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_method"
]
}"""
# END OF TEMPLATES FROM OCTOPUS
import
sys
#fname = sys.argv[1]
inputvars_fd
=
open
(
'inputvars.py'
,
'w'
)
print
(
'varlist = ['
,
file
=
inputvars_fd
)
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
].
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
()
jsontokens
=
[]
for
var
in
varnames
:
print
(
" '%s',"
%
var
,
file
=
inputvars_fd
)
json
=
json_template
%
dict
(
description
=
r
'siesta input variable \"%s\"'
%
var
,
name
=
'x_siesta_input_%s'
%
var
,
dtypeStr
=
'C'
,
supername
=
'x_siesta_input'
)
jsontokens
.
append
(
json
)
section
=
json_section_template
%
dict
(
description
=
'siesta input '
'variables'
,
name
=
'x_siesta_input'
)
jsontokens
.
append
(
section
)
txt
=
json_header
%
dict
(
parser
=
'siesta'
,
info
=
', '
.
join
(
jsontokens
))
print
(
txt
)
print
(
']'
,
file
=
inputvars_fd
)
parser/parser-siesta/nomad_meta_info
deleted
120000 → 0
View file @
63c52686
../../../../nomad-meta-info/meta_info/nomad_meta_info
\ No newline at end of file
parser/parser-siesta/pycheck.py
deleted
100755 → 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
from
main
import
main
testdir
=
'../../test/examples'
dirnames
=
[
'H2O'
,
'H2O-relax'
,
'Al-slab'
,
'Al-uc'
,
'Fe'
,
'MgO'
]
for
dirname
in
dirnames
:
fname
=
os
.
path
.
join
(
testdir
,
dirname
,
'out'
)
with
open
(
'out.pycheck.%s.txt'
%
dirname
,
'w'
)
as
outfd
:
main
(
mainFile
=
fname
,
outF
=
outfd
)
parser/parser-siesta/setup_paths.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>
import
sys
,
os
,
os
.
path
baseDir
=
os
.
path
.
dirname
(
os
.
path
.
abspath
(
__file__
))
commonDir
=
os
.
path
.
normpath
(
os
.
path
.
join
(
baseDir
,
"../../../../python-common/common/python"
))
if
not
commonDir
in
sys
.
path
:
sys
.
path
.
insert
(
0
,
commonDir
)
parser/parser-siesta/test
deleted
120000 → 0
View file @
63c52686
../../test/examples
\ No newline at end of file
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