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Commit e82738ab authored by Daniel Speckhard's avatar Daniel Speckhard
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Added octopus parser.

parent 400cf5bf
Pipeline #44454 failed with stages
in 58 minutes and 10 seconds
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.gitmodules
View file @ e82738ab
......@@ -67,3 +67,6 @@
[submodule "dependencies/parsers/lib-atoms"]
path = dependencies/parsers/lib-atoms
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-lib-atoms
[submodule "dependencies/parsers/octopus"]
path = dependencies/parsers/octopus
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-octopus
.vscode/launch.json
View file @ e82738ab
......@@ -187,6 +187,16 @@
"-sv", "tests/test_normalizing.py::test_normalizer[parsers/lib-atoms-tests/data/parsers/lib-atoms/gp.xml]"
]
},
{
"name": "Octopus Normalizer",
"type": "python",
"request": "launch",
"cwd": "${workspaceFolder}",
"program": "${workspaceFolder}/.pyenv/bin/pytest",
"args": [
"-sv", "tests/test_normalizing.py::test_normalizer[parsers/octopus-tests/data/parsers/octopus/stdout.txt]"
]
},
{
"name": "Python: Current File",
"type": "python",
......
lib-atoms @ d7bfc62d
Compare b3f6f3a8...d7bfc62d
Subproject commit b3f6f3a8ffffea0f0f4c52ebc04a241b2ead29a5
Subproject commit d7bfc62deebfd40d3033817c529d1f6f89c901e5
octopus @ 4d2bc025
Subproject commit 4d2bc0250f9aa6183825b35fd3c6d88c0c3417ec
nomad/parsing/__init__.py
View file @ e82738ab
......@@ -284,10 +284,14 @@ parsers = [
name='parsers/lib-atoms',
parser_class_name='libatomsparser.LibAtomsParserWrapper',
mainfile_contents_re=(r'\s*<GAP_params\s')
),
LegacyParser(
name='parsers/octopus',
parser_class_name='octopusparser.OctopusParserWrapper',
mainfile_contents_re=(r'\*{32} Grid \*{32}Simulation Box:')
)
]
""" Instanciation and constructor based config of all parsers. """
parser_dict = {parser.name: parser for parser in parsers} # type: ignore
......
test_file_name_parsing.json 0 → 100644
View file @ e82738ab
{
"section_run": {
"_name": "section_run",
"_gIndex": 0,
"program_name": "Octopus",
"program_basis_set_type": "Real-space grid",
"x_octopus_input_Units": "ev_angstrom",
"x_octopus_input_PeriodicDimensions": "0",
"x_octopus_input_Output": "density + wfs + potential + forces",
"x_octopus_input_OutputFormat": "xcrysden",
"x_octopus_input_FromScratch": true,
"x_octopus_input_RestartWrite": false,
"x_octopus_input_stdout": "'stdout.txt'",
"x_octopus_input_SCFCalculateDipole": true,
"x_octopus_input_Coordinates": "[[\"'O'\", 0.0, 0.0, 0.119262], [\"'H'\", 0.0, 0.763239, -0.477047], [\"'H'\", 0.0, -0.763239, -0.477047]]",
"x_octopus_parserlog_ExperimentalFeatures": true,
"x_octopus_parserlog_Debug": "0",
"x_octopus_parserlog_ReportMemory": true,
"x_octopus_parserlog_CalculationMode": "1",
"x_octopus_parserlog_stdout": "\"stdout.txt\"",
"x_octopus_parserlog_stderr": "\"-\"",
"x_octopus_parserlog_WorkDir": "\".\"",
"x_octopus_parserlog_FlushMessages": true,
"x_octopus_parserlog_ProfilingMode": "0",
"x_octopus_parserlog_FFTOptimize": true,
"x_octopus_parserlog_FFTPreparePlan": "0",
"x_octopus_parserlog_Units": "1",
"x_octopus_parserlog_UnitsXYZFiles": "0",
"x_octopus_parserlog_DisableOpenCL": true,
"x_octopus_parserlog_Dimensions": "3",
"x_octopus_parserlog_PseudopotentialSet": "1",
"x_octopus_parserlog_SpinComponents": "1",
"x_octopus_parserlog_SpeciesProjectorSphereThreshold": 0.001,
"x_octopus_parserlog_Splines": "1",
"x_octopus_parserlog_SpeciesTimeDependent": true,
"x_octopus_parserlog_PeriodicDimensions": "0",
"x_octopus_parserlog_BoxShape": "3",
"x_octopus_parserlog_Radius": -0.529177,
"x_octopus_parserlog_SymmetriesCompute": true,
"x_octopus_parserlog_KPointsUseSymmetries": true,
"x_octopus_parserlog_KPointsUseTimeReversal": true,
"x_octopus_parserlog_ExcessCharge": 0.0,
"x_octopus_parserlog_CalcEigenvalues": true,
"x_octopus_parserlog_TotalStates": "0",
"x_octopus_parserlog_ExtraStates": "0",
"x_octopus_parserlog_StatesBlockSize": "4",
"x_octopus_parserlog_ComplexScaling": "0",
"x_octopus_parserlog_ComplexScalingRotateSpectrum": 0.0,
"x_octopus_parserlog_ComplexScalingPenalizationFactor": 2.0,
"x_octopus_parserlog_ComplexScalingLocalizedStates": "0",
"x_octopus_parserlog_ComplexScalingLocalizationThreshold": 1.0,
"x_octopus_parserlog_ComplexScalingAlpha": 0.0,
"x_octopus_parserlog_ComplexScalingAlphaLeft": 0.0,
"x_octopus_parserlog_ComplexScalingLocalizationRadius": 0.0,
"x_octopus_parserlog_OnlyUserDefinedInitialStates": true,
"x_octopus_parserlog_RestartFixedOccupations": true,
"x_octopus_parserlog_SmearingFunction": "1",
"x_octopus_parserlog_NParticleModelmb": "0",
"x_octopus_parserlog_SymmetrizeDensity": true,
"x_octopus_parserlog_UseFineMesh": true,
"x_octopus_parserlog_Spacing": -0.529177,
"x_octopus_parserlog_CurvMethod": "1",
"x_octopus_parserlog_DerivativesStencil": "1",
"x_octopus_parserlog_DerivativesOrder": "4",
"x_octopus_parserlog_ParallelizationOfDerivatives": "2",
"x_octopus_parserlog_DoubleGrid": true,
"x_octopus_parserlog_DoubleGridOrder": "9",
"x_octopus_parserlog_ParDomains": "-1",
"x_octopus_parserlog_ParStates": "0",
"x_octopus_parserlog_ParKPoints": "0",
"x_octopus_parserlog_ParOther": "0",
"x_octopus_parserlog_ParallelizationNumberSlaves": "0",
"x_octopus_parserlog_ScaLAPACKCompatible": true,
"x_octopus_parserlog_MeshOrder": "1",
"x_octopus_parserlog_MeshPartitionDir": "\"restart/partition\"",
"x_octopus_parserlog_MeshPartitionRead": true,
"x_octopus_parserlog_MeshPartitionVirtualSize": "4",
"x_octopus_parserlog_MeshPartitionPackage": "1",
"x_octopus_parserlog_MeshPartitionStencil": "1",
"x_octopus_parserlog_MeshPartition": "1",
"x_octopus_parserlog_MeshPartitionWrite": true,
"x_octopus_parserlog_MeshUseTopology": true,
"x_octopus_parserlog_PartitionPrint": true,
"x_octopus_parserlog_OperateDouble": "1",
"x_octopus_parserlog_OperateComplex": "1",
"x_octopus_parserlog_OperateSingle": "0",
"x_octopus_parserlog_OperateComplexSingle": "0",
"x_octopus_parserlog_NLOperatorCompactBoundaries": true,
"x_octopus_parserlog_Output": "262151",
"x_octopus_parserlog_OutputWfsNumber": "\"1-4\"",
"x_octopus_parserlog_OutputInterval": "50",
"x_octopus_parserlog_OutputDuringSCF": true,
"x_octopus_parserlog_OutputIterDir": "\"output_iter\"",
"x_octopus_parserlog_RestartWriteInterval": "50",
"x_octopus_parserlog_OutputFormat": "1024",
"x_octopus_parserlog_StatesPack": true,
"x_octopus_parserlog_StatesOrthogonalization": "1",
"x_octopus_parserlog_StatesCLDeviceMemory": -512.0,
"x_octopus_parserlog_ELFWithCurrentTerm": true,
"x_octopus_parserlog_ParallelizationPoissonAllNodes": true,
"x_octopus_parserlog_PoissonSolver": "8",
"x_octopus_parserlog_PoissonSolverNodes": "0",
"x_octopus_parserlog_XCFunctional": "10001",
"x_octopus_parserlog_XCKernel": "10001",
"x_octopus_parserlog_XCKernelLRCAlpha": 0.0,
"x_octopus_parserlog_XCDensityCorrection": "0",
"x_octopus_parserlog_XCParallel": true,
"x_octopus_parserlog_TheoryLevel": "4",
"x_octopus_parserlog_SICCorrection": "1",
"x_octopus_parserlog_CurrentDensity": "2",
"x_octopus_parserlog_VDWCorrection": "0",
"x_octopus_parserlog_ParticleMass": 1.0,
"x_octopus_parserlog_RashbaSpinOrbitCoupling": 0.0,
"x_octopus_parserlog_FilterPotentials": "2",
"x_octopus_parserlog_TDDeltaKickTime": 0.0,
"x_octopus_parserlog_TDDeltaStrength": 0.0,
"x_octopus_parserlog_GyromagneticRatio": 2.00232,
"x_octopus_parserlog_RelativisticCorrection": "0",
"x_octopus_parserlog_IgnoreExternalIons": true,
"x_octopus_parserlog_ForceTotalEnforce": true,
"x_octopus_parserlog_EwaldAlpha": 0.21,
"x_octopus_parserlog_CalculateSelfInducedMagneticField": true,
"x_octopus_parserlog_AbsorbingBoundaries": "0",
"x_octopus_parserlog_PCMCalculation": true,
"x_octopus_parserlog_SCDM_EXX": true,
"x_octopus_parserlog_TimeZero": true,
"x_octopus_parserlog_FromScratch": true,
"x_octopus_parserlog_ForceComplex": true,
"x_octopus_parserlog_MaximumIter": "200",
"x_octopus_parserlog_ConvEnergy": 0.0,
"x_octopus_parserlog_ConvAbsDens": 0.0,
"x_octopus_parserlog_ConvRelDens": 1e-05,
"x_octopus_parserlog_ConvAbsEv": 0.0,
"x_octopus_parserlog_ConvRelEv": 0.0,
"x_octopus_parserlog_ConvForce": 0.0,
"x_octopus_parserlog_ConvEigenError": true,
"x_octopus_parserlog_MixField": "1",
"x_octopus_parserlog_MixingScheme": "2",
"x_octopus_parserlog_Mixing": 0.3,
"x_octopus_parserlog_MixNumberSteps": "3",
"x_octopus_parserlog_Eigensolver": "5",
"x_octopus_parserlog_EigensolverTolerance": 1e-06,
"x_octopus_parserlog_EigensolverMaxIter": "25",
"x_octopus_parserlog_Preconditioner": "1",
"x_octopus_parserlog_PreconditionerFilterFactor": 0.5,
"x_octopus_parserlog_SubspaceDiagonalization": "1",
"x_octopus_parserlog_SCFinLCAO": true,
"x_octopus_parserlog_SCFCalculateForces": true,
"x_octopus_parserlog_SCFCalculateDipole": true,
"x_octopus_parserlog_SCFCalculatePartialCharges": true,
"x_octopus_parserlog_LocalMagneticMomentsSphereRadius": 0.484283,
"x_octopus_parserlog_LCAOStart": "3",
"x_octopus_parserlog_LCAOAlternative": true,
"x_octopus_parserlog_LCAOScaleFactor": 1.0,
"x_octopus_parserlog_LCAOMaximumOrbitalRadius": 10.5835,
"x_octopus_parserlog_LCAODimension": "0",
"x_octopus_parserlog_RestartWrite": true,
"program_version": "mimus",
"x_octopus_log_svn_revision": 15432,
"section_basis_set_cell_dependent": {
"_name": "section_basis_set_cell_dependent",
"_gIndex": 0,
"basis_set_cell_dependent_kind": "realspace_grids"
},
"section_system": {
"_name": "section_system",
"_gIndex": 0,
"configuration_periodic_dimensions": [
false,
false,
false
],
"atom_labels": [
"O",
"H",
"H"
],
"atom_positions": [
[
0.0,
0.0,
1.192620000239253e-11
],
[
0.0,
7.632390001531143e-11,
-4.77047000095701e-11
],
[
0.0,
-7.632390001531143e-11,
-4.77047000095701e-11
]
]
},
"section_single_configuration_calculation": {
"_name": "section_single_configuration_calculation",
"_gIndex": 0,
"single_configuration_calculation_to_system_ref": 0,
"single_configuration_to_calculation_method_ref": 0,
"atom_forces_free_raw": [
[
-0.0,
0.0,
1.6064126847453203e-19
],
[
-0.0,
1.4491029821472702e-19,
-1.35811377483204e-19
],
[
-0.0,
-1.4491029821472702e-19,
-1.35811377483204e-19
]
],
"section_eigenvalues": {
"_name": "section_eigenvalues",
"_gIndex": 0,
"eigenvalues_kind": "normal",
"number_of_eigenvalues_kpoints": 1,
"eigenvalues_kpoints": [
[
0.0,
0.0,
0.0
]
],
"eigenvalues_values": [
[
[
-4.093476759664522e-18,
-2.109261075868369e-18,
-1.5179821533485e-18,
-1.172209226614815e-18
]
]
],
"eigenvalues_occupation": [
[
[
2.0,
2.0,
2.0,
2.0
]
]
]
}
},
"section_method": {
"_name": "section_method",
"_gIndex": 0,
"smearing_kind": "empty",
"number_of_spin_channels": 1,
"total_charge": 0.0,
"electronic_structure_method": "DFT",
"section_method_basis_set": [
{
"_name": "section_method_basis_set",
"_gIndex": 0,
"method_basis_set_kind": "density",
"mapping_section_method_basis_set_cell_associated": 0
},
{
"_name": "section_method_basis_set",
"_gIndex": 1,
"method_basis_set_kind": "wavefunction",
"mapping_section_method_basis_set_cell_associated": 0
}
],
"section_XC_functionals": [
{
"_name": "section_XC_functionals",
"_gIndex": 0,
"XC_functional_name": "LDA_X"
},
{
"_name": "section_XC_functionals",
"_gIndex": 1,
"XC_functional_name": "LDA_C_PZ_MOD"
}
]
}
},
"section_calculation_info": [
],
"section_repository_info": [
]
}
\ No newline at end of file
test_file_name_repository.json 0 → 100644
View file @ e82738ab
{
"section_run": {
"_name": "section_run",
"_gIndex": 0,
"program_name": "VASP",
"program_version": "4.6.35 3Apr08 complex parallel LinuxIFC",
"program_basis_set_type": "plane waves",
"section_method": {
"_name": "section_method",
"_gIndex": 0,
"electronic_structure_method": "DFT",
"section_XC_functionals": {
"_name": "section_XC_functionals",
"_gIndex": 0,
"XC_functional_name": "GGA_X_PBE"
}
},
"section_system": {
"_name": "section_system",
"_gIndex": 0,
"atom_species": [
35,
19,
14,
14
],
"chemical_composition": "BrKSiSi",
"chemical_composition_reduced": "BrKSi2",
"chemical_composition_bulk_reduced": "BrKSi2",
"configuration_raw_gid": "sTZqOzYKfxJbI5jmm8xVLp4OcGhdj",
"system_type": "Unknown",
"configuration_periodic_dimensions": [
true,
true,
true
],
"atom_positions": [
[
true,
false,
true
],
[
true,
false,
true
],
[
true,
false,
true
],
[
true,
true,
false
]
],
"atom_labels": [
"Br",
"K",
"Si",
"Si"
]
},
"section_single_configuration_calculation": {
"_name": "section_single_configuration_calculation",
"_gIndex": 0,
"single_configuration_calculation_to_system_ref": 0,
"single_configuration_to_calculation_method_ref": 0,
"energy_free": -1.5936767191492225e-18,
"energy_total": -1.5935696296699573e-18,
"energy_total_T0": -3.2126683561907e-22
},
"section_sampling_method": {
"_name": "section_sampling_method",
"_gIndex": 0,
"sampling_method": "geometry_optimization"
},
"section_frame_sequence": {
"_name": "section_frame_sequence",
"_gIndex": 0,
"frame_sequence_to_sampling_ref": 0,
"frame_sequence_local_frames_ref": [
0
]
}
},
"section_calculation_info": {
"_name": "section_calculation_info",
"_gIndex": 0,
"upload_id": "test_upload_id",
"calc_id": "test_calc_id",
"calc_hash": "test_calc_hash",
"main_file": "test/mainfile.txt",
"parser_name": "testParser"
},
"section_repository_info": [
]
}
\ No newline at end of file
tests/data/parsers/octopus/exec/messages 0 → 100644
View file @ e82738ab
warnings = 1
experimental = 0
tests/data/parsers/octopus/exec/parser.log 0 → 100644
View file @ e82738ab
# Octopus parser started
ExperimentalFeatures = 0 # default
Debug = 0 # default
ReportMemory = 0 # default
CalculationMode = 1 # default
stdout = "stdout.txt"
stderr = "-" # default
WorkDir = "." # default
FlushMessages = 0 # default
ProfilingMode = 0 # default
FFTOptimize = 1 # default
FFTPreparePlan = 0 # default
Units = 1
UnitsXYZFiles = 0 # default
DisableOpenCL = 1 # default
Dimensions = 3 # default
Opened block 'Coordinates'
Coordinates (0, 0) = "O"
Coordinates (0, 1) = 0
Coordinates (0, 2) = 0
Coordinates (0, 3) = 0.119262
Coordinates (1, 0) = "H"
Coordinates (1, 1) = 0
Coordinates (1, 2) = 0.763239
Coordinates (1, 3) = -0.477047
Coordinates (2, 0) = "H"
Coordinates (2, 1) = 0
Coordinates (2, 2) = -0.763239
Coordinates (2, 3) = -0.477047
Closed block 'Coordinates'
PseudopotentialSet = 1 # default
SpinComponents = 1 # default
SpeciesProjectorSphereThreshold = 0.001 # default
Splines = 1 # default
SpeciesProjectorSphereThreshold = 0.001 # default
SpeciesTimeDependent = 0 # default
PeriodicDimensions = 0
BoxShape = 3 # default
radius = -0.529177 # default
SymmetriesCompute = 1 # default
KPointsUseSymmetries = 0 # default
KPointsUseTimeReversal = 1 # default
SpinComponents = 1 # default
ExcessCharge = 0 # default
CalcEigenvalues = 1 # default
TotalStates = 0 # default
ExtraStates = 0 # default
StatesBlockSize = 4 # default
ComplexScaling = 0 # default
ComplexScalingRotateSpectrum = 0 # default
ComplexScalingPenalizationFactor = 2 # default
ComplexScalingLocalizedStates = 0 # default
ComplexScalingLocalizationThreshold = 1 # default
ComplexScalingAlpha = 0 # default
ComplexScalingAlphaLeft = 0 # default
ComplexScalingLocalizationRadius = 0 # default
OnlyUserDefinedInitialStates = 0 # default
RestartFixedOccupations = 0 # default
SmearingFunction = 1 # default
NParticleModelmb = 0 # default
SymmetrizeDensity = 0 # default
UseFineMesh = 0 # default
Spacing = -0.529177 # default
CurvMethod = 1 # default
DerivativesStencil = 1 # default
DerivativesOrder = 4 # default
ParallelizationOfDerivatives = 2 # default
DoubleGrid = 0 # default
DoubleGridOrder = 9 # default
ParDomains = -1 # default
ParStates = 0 # default
ParKPoints = 0 # default
ParOther = 0 # default
ParallelizationNumberSlaves = 0 # default
ScaLAPACKCompatible = 1 # default
MeshOrder = 1 # default
MeshPartitionDir = "restart/partition" # default
MeshPartitionRead = 1 # default
MeshPartitionVirtualSize = 4 # default
MeshPartitionPackage = 1 # default
MeshPartitionStencil = 1 # default
MeshPartition = 1 # default
MeshPartitionWrite = 0 # default
MeshUseTopology = 0 # default
PartitionPrint = 1 # default
OperateDouble = 1 # default
OperateComplex = 1 # default
OperateSingle = 0 # default
OperateComplexSingle = 0 # default
NLOperatorCompactBoundaries = 0 # default
Output = 262151
OutputWfsNumber = "1-4" # default
OutputInterval = 50 # default
OutputDuringSCF = 0 # default
OutputIterDir = "output_iter" # default
RestartWriteInterval = 50 # default
OutputFormat = 1024
StatesPack = 0 # default
StatesOrthogonalization = 1 # default
StatesCLDeviceMemory = -512 # default
ELFWithCurrentTerm = 1 # default
ParallelizationPoissonAllNodes = 1 # default
PoissonSolver = 8 # default
PoissonSolverNodes = 0 # default
XCFunctional = 10001 # default
XCKernel = 10001 # default
XCKernelLRCAlpha = 0 # default
XCDensityCorrection = 0 # default
XCParallel = 0 # default
TheoryLevel = 4 # default
SICCorrection = 1 # default
CurrentDensity = 2 # default
VDWCorrection = 0 # default
ParticleMass = 1 # default
RashbaSpinOrbitCoupling = 0 # default
FilterPotentials = 2 # default
TDDeltaKickTime = 0 # default
TDDeltaStrength = 0 # default
GyromagneticRatio = 2.00232 # default
RelativisticCorrection = 0 # default
IgnoreExternalIons = 0 # default
ForceTotalEnforce = 0 # default
EwaldAlpha = 0.21 # default
CalculateSelfInducedMagneticField = 0 # default
AbsorbingBoundaries = 0 # default
StatesPack = 1 # default
PCMCalculation = 0 # default
scdm_EXX = 0 # default
TimeZero = 0 # default
FromScratch = 1
ForceComplex = 0 # default
MaximumIter = 200 # default
ConvEnergy = 0 # default
ConvAbsDens = 0 # default
ConvRelDens = 1e-05 # default
ConvAbsEv = 0 # default
ConvRelEv = 0 # default
ConvForce = 0 # default
ConvEigenError = 0 # default
MixField = 1 # default
MixingScheme = 2 # default
MixingPreconditioner = 0 # default
Mixing = 0.3 # default
MixNumberSteps = 3 # default
MixInterval = 1 # default
Eigensolver = 5 # default
EigensolverTolerance = 1e-06 # default
EigensolverMaxIter = 25 # default
Preconditioner = 1 # default
PreconditionerFilterFactor = 0.5 # default
SubspaceDiagonalization = 1 # default
SCFinLCAO = 0 # default
SCFCalculateForces = 1 # default
SCFCalculateDipole = 1
SCFCalculatePartialCharges = 0 # default
LocalMagneticMomentsSphereRadius = 0.484283 # default
LCAOStart = 3 # default
LCAOAlternative = 0 # default
LCAOScaleFactor = 1 # default
LCAOMaximumOrbitalRadius = 10.5835 # default
LCAODimension = 0 # default
RestartWrite = 0