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Commit 04728a25 authored by Markus Scheidgen's avatar Markus Scheidgen
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Merged latest parsers.

parents 722fa8b9 7420b800
Pipeline #44560 failed with stages
in 25 minutes and 37 seconds
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.gitmodules
View file @ 04728a25
......@@ -61,3 +61,12 @@
[submodule "dependencies/parsers/castep"]
path = dependencies/parsers/castep
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-castep
[submodule "dependencies/parsers/dl-poly"]
path = dependencies/parsers/dl-poly
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-dl-poly
[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 @ 04728a25
......@@ -167,6 +167,36 @@
"-sv", "tests/test_normalizing.py::test_normalizer[parsers/castep-tests/data/parsers/castep/BC2N-Pmm2-Raman.castep]"
]
},
{
"name": "DL-Poly Normalizer",
"type": "python",
"request": "launch",
"cwd": "${workspaceFolder}",
"program": "${workspaceFolder}/.pyenv/bin/pytest",
"args": [
"-sv", "tests/test_normalizing.py::test_normalizer[parsers/dl-poly-tests/data/parsers/dl-poly/OUTPUT]"
]
},
{
"name": "Lib Atoms Normalizer",
"type": "python",
"request": "launch",
"cwd": "${workspaceFolder}",
"program": "${workspaceFolder}/.pyenv/bin/pytest",
"args": [
"-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",
......
nomad-meta-info @ b232a5fd
Compare 8957235e...b232a5fd
Subproject commit 8957235e5ca6bbb3278790e2587a30323169610f
Subproject commit b232a5fdd11c344656ff1e6ec7a2ed6f787cf49f
band @ 71f7a2ad
Compare b68bce7d...71f7a2ad
Subproject commit b68bce7db5c02ac56b1cf892ae20458fffb23b65
Subproject commit 71f7a2ad0d77d376e30d3c1a8ae55920fc7d7e5c
castep @ 5c7cf8ad
Compare b42810de...5c7cf8ad
Subproject commit b42810dee0ef7eb97cc5de41f4b5b110f21ab374
Subproject commit 5c7cf8add659c51d940960daa430927923720f7e
dl-poly @ de6d49f8
Subproject commit de6d49f89748010236baa9b683464b70bc8507a6
lib-atoms @ d7bfc62d
Subproject commit d7bfc62deebfd40d3033817c529d1f6f89c901e5
octopus @ 4d2bc025
Subproject commit 4d2bc0250f9aa6183825b35fd3c6d88c0c3417ec
orca @ 83a4de4e
Compare 248e14fd...83a4de4e
Subproject commit 248e14fd36539380eed6a4e2a41986d3317d9ac3
Subproject commit 83a4de4efa40731f7e192c795fc1e82f00f27fc8
python_common @ fcda3a9a
Compare 0d12af93...fcda3a9a
Subproject commit 0d12af93c4db658e6d93afb4435e8518b973efbe
Subproject commit fcda3a9ab4a23ea0c7363955999943d9be6fa0fb
nomad/normalizing/system.py
View file @ 04728a25
......@@ -83,21 +83,23 @@ class SystemNormalizer(SystemBasedNormalizer):
except Exception as e:
self.logger.error(
'cannot build ase atoms from atom labels',
atom_labels=atom_labels, exc_info=e, error=str(e))
atom_labels=atom_labels[:10], exc_info=e, error=str(e))
return
chemical_symbols = list(atoms.get_chemical_symbols())
if atom_labels != chemical_symbols:
self.logger.error('atom labels are ambiguous', atom_labels=atom_labels)
self.logger.error('atom labels are ambiguous', atom_labels=atom_labels[:10])
return
if atom_species is None:
atom_species = atoms.get_atomic_numbers().tolist()
set_value('atom_species', atom_species)
else:
if not isinstance(atom_species, list):
atom_species = [atom_species]
if atom_species != atoms.get_atomic_numbers().tolist():
self.logger.warning(
'atom species do not match labels',
atom_labels=atom_labels, atom_species=atom_species)
atom_labels=atom_labels[:10], atom_species=atom_species[:10])
atom_species = atoms.get_atomic_numbers().tolist()
set_value('atom_species', atom_species)
......
nomad/parsing/__init__.py
View file @ 04728a25
......@@ -261,24 +261,39 @@ parsers = [
parser_class_name='abinitparser.AbinitParser',
mainfile_contents_re=(r'^\n\.Version\s*[0-9.]*\s*of ABINIT\s*')
),
# LegacyParser(
# name='parsers/orca',
# parser_class_name='orcaparser.OrcaParser',
# mainfile_contents_re=(
# r'\s+\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\**\s*'
# r'\s+\* O R C A \*\s*'
# r'\s+\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\**\s*'
# r'\s*'
# r'\s*--- An Ab Initio, DFT and Semiempirical electronic structure package ---\s*')
# ),
LegacyParser(
name='parsers/orca',
parser_class_name='orcaparser.OrcaParser',
mainfile_contents_re=(
r'\s+\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\**\s*'
r'\s+\* O R C A \*\s*'
r'\s+\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\**\s*'
r'\s*'
r'\s*--- An Ab Initio, DFT and Semiempirical electronic structure package ---\s*')
),
LegacyParser(
name='parsers/castep',
parser_class_name='castepparser.CastepParser',
mainfile_contents_re=(r'\s\|\s*CCC\s*AA\s*SSS\s*TTTTT\s*EEEEE\s*PPPP\s*\|\s*')
),
LegacyParser(
name='parsers/dl-poly',
parser_class_name='dlpolyparser.DlPolyParserWrapper',
mainfile_contents_re=(r'\*\* DL_POLY \*\*')
),
LegacyParser(
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'\|0\) ~ \(0\) \|')
# We decided to use the octopus eyes instead of
# r'\*{32} Grid \*{32}Simulation Box:' since it was so far down in the file.
)
]
""" Instanciation and constructor based config of all parsers. """
parser_dict = {parser.name: parser for parser in parsers} # type: ignore
......
setup.py
View file @ 04728a25
......@@ -12,7 +12,7 @@ reqs = [str(ir.req) for ir in install_reqs if 'sphinxcontrib.httpdomain' not in
setup(
name='nomad',
version='0.2.0',
version='0.4.0',
description='The nomad@FAIRDI infrastructure python package',
py_modules=['nomad'],
install_requires=reqs,
......
test_file_name_parsing.json 0 → 100644
View file @ 04728a25
{
"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 @ 04728a25
{
"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/dl-poly/CONFIG 0 → 100644
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tests/data/parsers/dl-poly/CONTROL 0 → 100644
View file @ 04728a25
SODIUM CHLORIDE WITH (27000 IONS)
restart scale
temperature 500.0
equilibration steps 200
steps 200
timestep 0.001
#scale 5
cutoff 12.0
rvdw 12.0
ewald precision 1d-6
#ensemble nvt hoover 0.02
ensemble nvt berendsen 0.01
print every 10
stats every 10
collect
job time 100
close time 10
finish
tests/data/parsers/dl-poly/HISTORY 0 → 100644
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tests/data/parsers/dl-poly/OUTPUT 0 → 100644
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tests/data/parsers/lib-atoms/gp.xml 0 → 100644
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