Commit 04728a25 authored by Markus Scheidgen's avatar Markus Scheidgen
Browse files

Merged latest parsers.

parents 722fa8b9 7420b800
Pipeline #44560 failed with stages
in 25 minutes and 37 seconds
......@@ -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
......@@ -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",
......
Subproject commit 8957235e5ca6bbb3278790e2587a30323169610f
Subproject commit b232a5fdd11c344656ff1e6ec7a2ed6f787cf49f
Subproject commit b68bce7db5c02ac56b1cf892ae20458fffb23b65
Subproject commit 71f7a2ad0d77d376e30d3c1a8ae55920fc7d7e5c
Subproject commit b42810dee0ef7eb97cc5de41f4b5b110f21ab374
Subproject commit 5c7cf8add659c51d940960daa430927923720f7e
Subproject commit de6d49f89748010236baa9b683464b70bc8507a6
Subproject commit d7bfc62deebfd40d3033817c529d1f6f89c901e5
Subproject commit 4d2bc0250f9aa6183825b35fd3c6d88c0c3417ec
Subproject commit 248e14fd36539380eed6a4e2a41986d3317d9ac3
Subproject commit 83a4de4efa40731f7e192c795fc1e82f00f27fc8
Subproject commit 0d12af93c4db658e6d93afb4435e8518b973efbe
Subproject commit fcda3a9ab4a23ea0c7363955999943d9be6fa0fb
......@@ -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)
......
......@@ -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
......
......@@ -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,
......
{
"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
{
"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
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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
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