Commit 0ea345af authored by Daniel Speckhard's avatar Daniel Speckhard
Browse files

Added Phonopy parser.

parent da8266a5
Pipeline #45120 failed with stages
in 27 minutes and 8 seconds
......@@ -73,3 +73,6 @@
[submodule "dependencies/parsers/phonopy"]
path = dependencies/parsers/phonopy
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-phonopy
[submodule "dependencies/parsers/phonopy-library"]
path = dependencies/parsers/phonopy-library
url = https://gitlab.mpcdf.mpg.de/nomad-lab/phonopy
Subproject commit dcc29f7418dd193c53e8815bdbe20a32ccaf37ea
......@@ -64,8 +64,14 @@ class RepositoryNormalizer(Normalizer):
continue
# Compare values from iterations.
diff_bool = new_val != val
# We can't compare numpy arrays of different lengths.
if val is None: # We also can't check the length of none-type objects.
diff_bool = True
elif len(new_val) != len(val):
diff_bool = False
else: # If the first value wasn't none and the lengths are the same.
diff_bool = new_val != val
if type(diff_bool) is bool:
if diff_bool and val is not None:
diff_flag = True
......
......@@ -292,7 +292,14 @@ parsers = [
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.
),
LegacyParser(
name='parsers/phonopy',
parser_class_name='phonopyparser.PhonopyParserWrapper',
mainfile_contents_re=r'', # Empty regex since this code calls other DFT codes.
mainfile_name_re=(r'.*/phonopy-FHI-aims-displacement-0*1/control\\.in$')
)
]
""" Instanciation and constructor based config of all parsers. """
......
{
"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
# control file used to get the finite displacements in the phonon calculations
xc pw-lda
relativistic atomic_zora scalar
k_grid 12 12 12
# Slightly overconverged kp, would need 10.05
sc_accuracy_rho 1E-6
sc_accuracy_eev 1E-4
sc_accuracy_etot 1E-6
sc_accuracy_forces 1E-4
sc_iter_limit 100
occupation_type gaussian 0.01
mixer pulay
n_max_pulay 10
charge_mix_param 0.4
phonon displacement 0.01
phonon supercell -1 1 1 1 -1 1 1 1 -1
phonon frequency_units cm^-1
# phonon cv 0 800 801 200
phonon dos 0 800 800 1 50
phonon free_energy 0 1200 1200 50
phonon band 0 0 0 0.00 0.25 0.25 100 Gamma Delta
phonon band 0.00 0.25 0.25 0 0.5 0.5 100 Delta X
phonon band 0 0.5 0.5 0.25 0.50 0.75 100 X W
phonon band 0.25 0.50 0.75 0.375 0.375 0.75 100 W K
phonon band 0.375 0.375 0.75 0 0 0 100 K Gamma
phonon band 0 0 0 0.25 0.25 0.25 100 Gamma Lambda
phonon band 0.25 0.25 0.25 0.5 0.5 0.5 100 Lambda L
################################################################################
#
# FHI-aims code project
# VB, Fritz-Haber Institut, 2009
#
# Suggested "light" defaults for Ge atom (to be pasted into control.in file)
# Be sure to double-check any results obtained with these settings for post-processing,
# e.g., with the "tight" defaults and larger basis sets.
#
################################################################################
species Ge
# global species definitions
nucleus 32
mass 72.64
#
l_hartree 4
#
cut_pot 3.5 1.5 1.0
basis_dep_cutoff 1e-4
#
radial_base 54 5.0
radial_multiplier 1
angular_grids specified
division 0.0947 110
division 0.1314 194
division 0.7746 302
# division 0.8710 434
# division 0.9770 590
# division 1.1356 770
# division 2.6430 974
# outer_grid 974
outer_grid 302
################################################################################
#
# Definition of "minimal" basis
#
################################################################################
# valence basis states
valence 4 s 2.
valence 4 p 2.
valence 3 d 10.
# ion occupancy
ion_occ 4 s 1.
ion_occ 4 p 1.
ion_occ 3 d 10.
################################################################################
#
# Suggested additional basis functions. For production calculations,
# uncomment them one after another (the most important basis functions are
# listed first).
#
# Constructed for dimers: 1.80 A, 2.00 A, 2.35 A, 3.00 A, 4.00 A
#
################################################################################
# "First tier" - improvements: -329.04 meV to -37.61 meV
hydro 2 p 1.4
hydro 3 d 4.3
# hydro 4 f 7.4
hydro 3 s 3.4
# "Second tier" - improvements: -13.91 meV to -1.23 meV
# hydro 5 g 10.8
# hydro 3 d 2.5
# hydro 3 p 3.3
# hydro 4 f 12
# hydro 6 h 15.6
# hydro 3 s 7.2
# "Third tier" - improvements: -1.47 meV to -0.40 meV
# hydro 3 d 5.8
# hydro 4 f 4.3
# hydro 5 g 11.6
# hydro 5 s 14.8
# hydro 4 p 3.9
# "Fourth tier" -improvements: -0.39 meV to -0.11 meV
# hydro 4 f 23.2
# hydro 2 s 6.2
# hydro 5 d 9.8
# hydro 5 p 6
# hydro 6 h 14.8
# Further functions - -0.13 meV and below
# hydro 5 f 9.6
lattice_vector 0 2.76360 2.76360
lattice_vector 2.76360 0 2.76360
lattice_vector 2.76360 2.76360 0
atom 0 0 0 Ge
atom 1.3818000000 1.3818000000 1.3818000000 Ge
### run in /bin/bash
#$ -S /bin/bash
### join stdout and stderr
#$ -j y
### change to current working dir
#$ -cwd
### send no mail
#$ -m n
### my email address
#$ -M my
### Parallel Environment
#$ -pe impi 16
### wallclock, e.g. 3600 seconds
#$ -l h_rt=80000
### virtual memory (45G is max. on AIMS)
#$ -l h_vmem=22G
module load impi
module load mkl
export LD_LIBRARY_PATH="/afs/@cell/common/soft/intel/Compiler/11.0/c/mkl/lib/em64t/"
binary='/u/abha/fhi-aims-13/bin/aims.012513.scalapack.mpi.x'
mpiexec -n $NSLOTS $binary > tmp.out
-catch_rsh /var/spool/SGE6/aims125/active_jobs/449118.1/pe_hostfile /afs/ipp/.cs/intel/impi/4.0.0
aims125
aims398
start_impi_sles11.sh: check for local mpd daemon (1 of 5)
start_impi_sles11.sh: check for local mpd daemon (2 of 5)
start_impi_sles11.sh: check for mpd daemons (1 of 5)
start_impi_sles11.sh: check for mpd daemons (2 of 5)
start_impi_sles11.sh: got all 2 of 2 nodes
-catch_rsh /afs/ipp/.cs/intel/impi/4.0.0
# control file used to get the finite displacements in the phonon calculations
xc pw-lda
relativistic atomic_zora scalar
k_grid 12 12 12
# Slightly overconverged kp, would need 10.05
sc_accuracy_rho 1E-6
sc_accuracy_eev 1E-4
sc_accuracy_etot 1E-6
sc_accuracy_forces 1E-4
</