def test_dos(parser):
archive = EntryArchive()
parser.parse('tests/data/NiO-dos.out', archive, None)
sec_dos = archive.section_run[0].section_single_configuration_calculation[
0].section_dos[0]
assert np.shape(sec_dos.dos_values) == (2, 158)
assert sec_dos.dos_energies[78].magnitude == approx(-8.6717613e-20)
assert sec_dos.dos_values[1][19] == approx(4.66493971e+14)
archive = EntryArchive()
parser.parse('tests/data/NiO-dos-restricted.out', archive, None)
sec_dos = archive.section_run[0].section_single_configuration_calculation[
0].section_dos[0]
assert np.shape(sec_dos.dos_values) == (1, 154)
def parse_exciting_results(directory: str):
"""
Parse all exciting outputs in 'directory' into a dictionary, via
NOMAD's exciting parser.
:param directory:
:return: dict
"""
archive = EntryArchive()
parser = ExcitingParser()
parser.parse(directory + '/INFO.OUT', archive, None)
data_as_json_str = archive.m_to_json()
data_as_dict = json.loads(data_as_json_str)['section_run'][0]
# dict_keys(['program_basis_set_type', 'program_name', 'program_version', 'section_frame_sequence', 'section_method', 'section_sampling_method', 'section_single_configuration_calculation', 'section_system'])
print(data_as_dict)
def test_relaxation(parser):
archive = EntryArchive()
parser.parse('tests/data/relaxation.nc', archive, None)
assert archive.section_workflow.workflow_type == 'geometry_optimization'
assert len(archive.section_run) == 1
sec_attrs = archive.section_run[0].section_method[
0].x_fhi_vibes_section_attributes[0]
assert sec_attrs.x_fhi_vibes_attributes_timestep.magnitude == approx(1e-15)
assert len(sec_attrs.x_fhi_vibes_section_attributes_atoms) == 1
sec_atoms = sec_attrs.x_fhi_vibes_section_attributes_atoms[0]
assert len(sec_atoms.x_fhi_vibes_atoms_symbols) == 2
assert sec_atoms.x_fhi_vibes_atoms_masses.magnitude == approx(
4.66362397e-26)
sec_metadata = sec_attrs.x_fhi_vibes_section_attributes_metadata[0]
sec_relaxation = sec_metadata.x_fhi_vibes_section_metadata_relaxation[0]
assert sec_relaxation.x_fhi_vibes_relaxation_maxstep == 0.2
assert not sec_relaxation.x_fhi_vibes_relaxation_hydrostatic_strain
assert sec_relaxation.x_fhi_vibes_relaxation_type == 'optimization'
sec_sccs = archive.section_run[0].section_single_configuration_calculation
assert len(sec_sccs) == 3
assert sec_sccs[2].x_fhi_vibes_volume.magnitude == approx(3.97721030e-29)
assert sec_sccs[0].section_energy_contribution[
1].energy_contribution_value.magnitude == approx(-2.52313962e-15)
def test_molecular_dynamics(parser):
archive = EntryArchive()
parser.parse('tests/data/molecular_dynamics.nc', archive, None)
assert archive.section_workflow.workflow_type == 'molecular_dynamics'
sec_attrs = archive.section_run[0].section_method[
0].x_fhi_vibes_section_attributes[0]
sec_md = sec_attrs.x_fhi_vibes_section_attributes_metadata[
0].x_fhi_vibes_section_metadata_MD[0]
assert sec_md.x_fhi_vibes_MD_md_type == 'Langevin'
assert sec_md.x_fhi_vibes_MD_friction == 0.02
sec_systems = archive.section_run[0].section_system
assert len(sec_systems) == 11
assert sec_systems[3].atom_positions[6][1].magnitude == approx(
1.39537854e-10)
assert sec_systems[7].atom_velocities[1][0].magnitude == approx(
-249.97586102)
assert sec_systems[2].lattice_vectors[0][2].magnitude == approx(
2.20004000e-21)
sec_sccs = archive.section_run[0].section_single_configuration_calculation
assert sec_sccs[4].x_fhi_vibes_heat_flux_0_harmonic[1].magnitude == approx(
1.40863863e+13)
assert sec_sccs[5].x_fhi_vibes_atom_forces_harmonic[3][
0].magnitude == approx(8.40976902e-10)
assert sec_sccs[6].x_fhi_vibes_momenta[7][2].magnitude == approx(
-1.18929315e-24)
def test_single_point(parser):
archive = EntryArchive()
parser.parse('tests/data/basic/ok.scf', archive, None)
sec_run = archive.section_run[0]
assert sec_run.program_version == '12.1 22/7/2012'
assert sec_run.time_run_date_start.magnitude == 1397313280.0
sec_method = archive.section_run[0].section_method[0]
assert sec_method.section_XC_functionals[1].XC_functional_name == 'GGA_C_PBE_SOL'
assert sec_method.x_wien2k_ifft[1] == 120
assert sec_method.x_wien2k_rkmax[2] == 4
assert sec_method.smearing_kind == 'tetrahedra'
assert sec_method.x_wien2k_in2_espermin == 0.50
sec_scc = archive.section_run[0].section_single_configuration_calculation[0]
assert sec_scc.energy_total.magnitude == approx(-8.09654094e-15)
assert np.shape(sec_scc.atom_forces) == (49, 3)
assert sec_scc.atom_forces[19][1].magnitude == approx(-2.76650574e-10)
assert sec_scc.energy_reference_fermi[0].magnitude == approx(-4.46784636e-19)
sec_scfs = sec_scc.section_scf_iteration
assert len(sec_scfs) == 40
assert sec_scfs[21].energy_total_scf_iteration.magnitude == approx(-8.09654095e-15)
assert sec_scfs[6].x_wien2k_noe == 196.000
assert sec_scfs[17].x_wien2k_tot_diff_charge[9] == approx(0.0001539)
sec_system = archive.section_run[0].section_system[0]
assert np.shape(sec_system.atom_positions) == (49, 3)
assert sec_system.atom_positions[18][1].magnitude == approx(9.94126646e-10)
assert sec_system.lattice_vectors[1][1].magnitude == approx(1.06500038e-09)
assert sec_system.atom_labels == ['C'] * 49
def test_scf(parser):
archive = EntryArchive()
parser.parse('tests/data/Si_scf/stdout.txt', archive, None)
sec_run = archive.section_run[0]
assert sec_run.program_version == 'wolfi'
assert sec_run.x_octopus_input_Spacing == approx(0.28345892)
assert sec_run.x_octopus_parserlog_SpeciesProjectorSphereThreshold == 0.001
sec_method = sec_run.section_method[0]
assert sec_method.smearing_kind == 'empty'
assert sec_method.electronic_structure_method == 'DFT'
assert sec_method.section_XC_functionals[0].XC_functional_name == 'LDA_C_PZ_MOD'
sec_system = sec_run.section_system[0]
assert False not in sec_system.configuration_periodic_dimensions
assert sec_system.atom_labels == ['Si', 'Si', 'Si', 'Si']
assert sec_system.atom_positions[1][0].magnitude == approx(1.91979671e-10)
sec_scc = sec_run.section_single_configuration_calculation[0]
assert sec_scc.energy_total.magnitude == approx(-6.91625667e-17)
assert sec_scc.energy_electrostatic.magnitude == approx(4.79087203e-18)
assert np.count_nonzero(sec_scc.atom_forces_free_raw) == 0
sec_eig = sec_scc.section_eigenvalues[0]
assert np.shape(sec_eig.eigenvalues_values) == (1, 18, 8)
assert sec_eig.eigenvalues_kpoints[11][2] == 0.25
assert sec_eig.eigenvalues_values[0][4][6].magnitude == approx(5.26639723e-19)
assert sec_eig.eigenvalues_occupation[0][16][1] == 2.0
sec_scf = sec_scc.section_scf_iteration
assert len(sec_scf) == 8
assert sec_scf[3].energy_total_scf_iteration.magnitude == approx(-6.91495422e-17)
assert sec_scf[7].time_scf_iteration.magnitude == 9.42
def test_gpw2(parser):
archive = EntryArchive()
parser.parse('tests/data/Si_pw.gpw2', archive, None)
assert archive.section_run[0].program_version == '1.1.1b1'
assert archive.section_run[0].program_basis_set_type == 'plane waves'
assert archive.section_run[0].section_basis_set_cell_dependent[
0].basis_set_planewave_cutoff.magnitude == approx(4.8065299e-17)
sec_method = archive.section_run[0].section_method[0]
assert sec_method.scf_threshold_energy_change.magnitude == approx(
8.01088317e-23)
assert sec_method.smearing_width == approx(1.60217663e-20)
assert not sec_method.x_gpaw_fix_density
assert sec_method.section_XC_functionals[0].XC_functional_name == 'LDA_X'
sec_system = archive.section_run[0].section_system[0]
assert sec_system.atom_labels == ['Si', 'Si']
assert sec_system.lattice_vectors[0][1].magnitude == approx(2.715e-10)
assert False not in sec_system.configuration_periodic_dimensions
assert sec_system.atom_positions[1][0].magnitude == approx(1.3575e-10)
sec_scc = archive.section_run[0].section_single_configuration_calculation[
0]
assert sec_scc.energy_XC.magnitude == approx(-2.19623851e-18)
assert sec_scc.energy_reference_fermi[0].magnitude == approx(
8.60653138e-19)
assert np.shape(sec_scc.section_eigenvalues[0].eigenvalues_values) == (1,
10,
8)
assert sec_scc.section_eigenvalues[0].eigenvalues_values[0][7][
4].magnitude == approx(9.50790908e-19)
assert sec_scc.section_eigenvalues[0].eigenvalues_occupation[0][0][
0] == 1.0
assert sec_scc.single_configuration_calculation_converged
def test_grad_statpt_dscf(parser):
archive = EntryArchive()
parser.parse('tests/data/acrolein_grad_statpt_dscf.out', archive, None)
assert archive.section_run[0].section_basis_set_atom_centered[
1].basis_set_atom_centered_short_name == 'def2-SVP'
sec_methods = archive.section_run[0].section_method
assert len(sec_methods) == 3
assert sec_methods[0].section_XC_functionals[
0].XC_functional_name == 'HYB_GGA_XC_B3LYP'
sec_systems = archive.section_run[0].section_system
assert len(sec_systems) == 3
assert sec_systems[1].atom_positions[5][1].magnitude == approx(
1.22377337e-10, )
sec_sccs = archive.section_run[0].section_single_configuration_calculation
assert sec_sccs[0].atom_forces_raw[6][0].magnitude == approx(
-4.2984543e-12)
sec_scfs = sec_sccs[2].section_scf_iteration
assert len(sec_scfs) == 3
assert sec_scfs[1].energy_total_scf_iteration.magnitude == approx(
-8.35592725e-16)
assert sec_scfs[0].x_turbomole_delta_eigenvalues.magnitude == approx(
2.92683961e-22)
assert sec_sccs[2].electronic_kinetic_energy.magnitude == approx(
8.27834082e-16)
sec_sampling = archive.section_run[0].section_sampling_method[0]
assert sec_sampling.x_turbomole_geometry_optimization_trustregion_min.magnitude == approx(
5.29177211e-14)
assert sec_sampling.geometry_optimization_method == 'BFGS'
assert sec_sampling.geometry_optimization_threshold_force.magnitude == approx(
8.2387235e-11)
def test_strucopt(parser):
archive = EntryArchive()
parser.parse('tests/data/GaO_strucopt/INFO.OUT', archive, None)
sec_systems = archive.section_run[0].section_system
assert len(sec_systems) == 15
assert sec_systems[0].atom_labels == [
'Ga', 'Ga', 'Ga', 'Ga', 'O', 'O', 'O', 'O', 'O', 'O'
]
assert sec_systems[0].x_exciting_gkmax.magnitude == approx(1.13383567e+11)
assert sec_systems[3].atom_positions[1][1].magnitude == approx(
3.07695918e-10)
assert sec_systems[10].atom_positions[-1][0].magnitude == approx(
3.67156876e-11)
assert sec_systems[1].lattice_vectors[2][1].magnitude == approx(
sec_systems[13].lattice_vectors[2][1].magnitude)
sec_sccs = archive.section_run[0].section_single_configuration_calculation
assert len(sec_sccs) == 15
assert len(sec_sccs[0].section_scf_iteration) == 19
assert sec_sccs[0].section_scf_iteration[
10].time_scf_iteration.magnitude == approx(431.84)
assert sec_sccs[0].section_scf_iteration[
18].x_exciting_effective_potential_convergence_scf_iteration[
0].magnitude == approx(4.62350928e-26)
assert sec_sccs[3].x_exciting_maximum_force_magnitude.magnitude == approx(
1.64771998e-10)
assert sec_sccs[6].energy_total.magnitude == approx(-3.58415586e-14)
assert sec_sccs[9].time_calculation.magnitude == approx(724.33)
assert len(sec_sccs[-1].x_exciting_section_MT_charge_atom) == 10
assert sec_sccs[-1].x_exciting_fermi_energy.magnitude == approx(
1.03200886e-18)
def test_metagga(parser):
archive = EntryArchive()
parser.parse('tests/data/hle17_vasprun.xml.gz', archive, None)
sec_xc_functional = archive.section_run[-1].section_method[
-1].section_XC_functionals[0]
assert sec_xc_functional.XC_functional_name == 'MGGA_XC_HLE17'
def test_hybrid(parser):
archive = EntryArchive()
parser.parse('tests/data/hybrid_vasprun.xml.gz', archive, None)
sec_xc_functional = archive.section_run[-1].section_method[
-1].section_XC_functionals[0]
assert sec_xc_functional.XC_functional_name == 'HYB_GGA_XC_HSE06'
def run(self, mainfile: str, archive: EntryArchive, logger):
# Log a hello world, just to get us started. TODO remove from an actual parser.
logger.info('Hello World')
# Use the previously defined parsers on the given mainfile
mainfile_parser.mainfile = mainfile
mainfile_parser.parse()
# Output all parsed data into the given archive.
run = archive.m_create(Run)
run.program_name = 'super_code'
run.program_version = str(mainfile_parser.get('program_version'))
date = datetime.datetime.strptime(
mainfile_parser.get('date'),
'%Y/%m/%d') - datetime.datetime(1970, 1, 1)
run.program_compilation_datetime = date.total_seconds()
for calculation in mainfile_parser.get('calculation'):
system = run.m_create(System)
system.lattice_vectors = calculation.get('lattice_vectors')
sites = calculation.get('sites')
system.atom_labels = [site[0] for site in sites]
system.atom_positions = [site[1] for site in sites]
scc = run.m_create(SCC)
scc.single_configuration_calculation_to_system_ref = system
scc.energy_total = calculation.get('energy') * units.eV
scc.single_configuration_calculation_to_system_ref = system
magic_source = calculation.get('magic_source')
if magic_source is not None:
scc.x_example_magic_value = magic_source
def test_scf_multirun(parser):
archive = EntryArchive()
parser.parse('tests/data/Al_multistep/m61b5.out', archive, None)
sec_runs = archive.section_run
assert len(sec_runs) == 2
assert len(sec_runs[0].section_single_configuration_calculation) == 6
assert len(sec_runs[1].section_single_configuration_calculation) == 1
assert len(sec_runs[0].section_single_configuration_calculation[2].
section_scf_iteration) == 11
assert len(sec_runs[1].section_single_configuration_calculation[0].
section_scf_iteration) == 1
assert len(sec_runs[0].section_system) == 6
assert len(sec_runs[1].section_system) == 1
assert len(sec_runs[0].section_method) == 1
assert len(sec_runs[1].section_method) == 1
sec_scc = sec_runs[0].section_single_configuration_calculation[4]
assert sec_scc.atom_forces_raw[0][2].magnitude == approx(-9.69697756e-14)
assert sec_scc.section_scf_iteration[
3].x_gaussian_delta_energy_total_scf_iteration.magnitude == approx(
-8.82412332e-27)
sec_thermo = sec_runs[1].x_gaussian_section_thermochem[0]
assert sec_thermo.x_gaussian_temperature == approx(298.15)
assert sec_thermo.x_gaussian_moments[1] == approx(8.59409221e-45)
assert sec_thermo.x_gaussian_thermal_correction_free_energy == approx(
-1.00274129e-19)
def test_scf(parser):
archive = EntryArchive()
parser.parse('tests/data/phenylrSmall-metagga.out', archive, None)
sec_run = archive.section_run[0]
assert sec_run.program_version == '70630 2018-11-24'
assert sec_run.time_run_date_start.magnitude == 1550053118.0
sec_method = archive.section_run[0].section_method[0]
assert sec_method.number_of_spin_channels == 2
assert sec_method.section_XC_functionals[
0].XC_functional_name == 'MGGA_XC_TPSS'
sec_system = archive.section_run[0].section_system[0]
assert sec_system.atom_positions[2][1].magnitude == approx(2.31103866e-10)
assert sec_system.lattice_vectors[0][0].magnitude == approx(8.72113987e-10)
assert sec_system.configuration_periodic_dimensions == [True, True, False]
sec_scc = archive.section_run[0].section_single_configuration_calculation[
0]
assert sec_scc.energy_total.magnitude == approx(-1.11415974e-17)
assert sec_scc.electronic_kinetic_energy.magnitude == approx(
1.11552116e-17)
assert sec_scc.energy_XC.magnitude == approx(-1.01588269e-17)
assert sec_scc.energy_electrostatic.magnitude == approx(-8.69562185e-18)
sec_scfs = sec_scc.section_scf_iteration
assert len(sec_scfs) == 20
assert sec_scfs[11].energy_change_scf_iteration.magnitude == approx(
2.1449944e-21)
def test_md_verbose(parser):
archive = EntryArchive()
parser.parse('tests/data/fe_test/md.log', archive, None)
sec_run = archive.section_run[0]
assert sec_run.program_version == '5.1.4'
sec_control = sec_run.x_gromacs_section_control_parameters[0]
assert sec_control.x_gromacs_inout_control_coulombtype == 'PME'
assert np.shape(sec_control.x_gromacs_inout_control_deform) == (3, 3)
sec_sampling = sec_run.section_sampling_method[0]
assert sec_sampling.ensemble_type == 'NPT'
assert sec_sampling.x_gromacs_integrator_dt.magnitude == 0.0005
assert sec_sampling.x_gromacs_barostat_target_pressure.magnitude == approx(
33333.33)
sec_sccs = sec_run.section_single_configuration_calculation
assert len(sec_sccs) == 7
assert sec_sccs[2].energy_total.magnitude == approx(
-3.2711290665182795e-17)
assert sec_sccs[5].pressure.magnitude == approx(-63926916.5)
assert sec_sccs[-2].section_energy_contribution[
1].energy_contribution_value.magnitude == approx(-4.15778738e-17)
assert sec_sccs[0].atom_forces[5][2].magnitude == approx(
-7.932968909721231e-10)
sec_systems = sec_run.section_system
assert len(sec_systems) == 2
assert np.shape(sec_systems[0].atom_positions) == (1516, 3)
assert sec_systems[1].atom_positions[800][1].magnitude == approx(
2.4609454e-09)
assert sec_systems[0].atom_velocities[500][0].magnitude == approx(869.4773)
assert sec_systems[1].lattice_vectors[2][2].magnitude == approx(
2.469158e-09)
def test_md(parser):
archive = EntryArchive()
parser.parse('tests/data/Si8-md-NPT.castep', archive, None)
sec_sampling = archive.section_run[0].section_sampling_method[0]
assert sec_sampling.sampling_method == 'molecular_dynamics'
assert sec_sampling.ensemble_type == 'NPT'
assert sec_sampling.x_castep_thermostat_type == 'Nose-Hoover chain thermostat'
assert sec_sampling.x_castep_frame_energy_tolerance.magnitude == approx(
1.60217663e-24)
sec_sccs = archive.section_run[0].section_single_configuration_calculation
assert len(sec_sccs) == 13
assert sec_sccs[2].energy_total.magnitude == approx(-1.37059981e-16)
assert sec_sccs[6].stress_tensor[2][1].magnitude == approx(4.06626e+09)
assert sec_sccs[9].pressure.magnitude == approx(1.111e+09)
assert sec_sccs[11].energy_total_T0.magnitude == approx(-1.37069057e-16)
assert len(sec_sccs[12].section_scf_iteration) == 7
assert sec_sccs[7].section_scf_iteration[
3].energy_change_scf_iteration.magnitude == approx(-1.90981043e-21)
sec_systems = archive.section_run[0].section_system
assert len(sec_systems) == 13
assert sec_systems[0].atom_positions[7][2].magnitude == approx(1.3575e-10)
assert sec_systems[1].atom_velocities[1][1].magnitude == approx(324.536)
assert sec_systems[12].lattice_vectors[2][2].magnitude == approx(
5.5475876e-10)
def test_pnoccsd(parser):
archive = EntryArchive()
parser.parse('tests/data/pnoccsd.out', archive, None)
assert np.shape(
archive.section_run[0].section_system[0].atom_positions) == (51, 3)
sec_methods = archive.section_run[0].section_method
assert len(sec_methods) == 4
assert sec_methods[0].electronic_structure_method == 'CCSD(T)'
assert sec_methods[1].electronic_structure_method == 'MP2'
assert sec_methods[2].electronic_structure_method == 'CCSD'
assert sec_methods[3].electronic_structure_method == 'CCSD(T0)'
sec_sccs = archive.section_run[0].section_single_configuration_calculation
assert len(sec_sccs) == 4
assert sec_sccs[0].energy_total.magnitude == approx(-5.63810959e-15)
assert sec_sccs[1].energy_total.magnitude == approx(-5.63669838e-15)
assert sec_sccs[2].energy_current.magnitude == approx(-2.19140251e-17)
assert sec_sccs[3].energy_total.magnitude == approx(-5.6380984e-15)
sec_scfs = sec_sccs[0].section_scf_iteration
assert len(sec_scfs) == 13
assert sec_scfs[6].energy_total_scf_iteration.magnitude == approx(
-5.63708622e-15)
def test_basic(parser):
archive = EntryArchive()
parser.parse('tests/data/n2_output.out', archive, None)
sec_run = archive.section_run[0]
assert sec_run.program_version == '1.8'
sec_method = sec_run.section_method[0]
assert sec_method.scf_max_iteration == 50
assert sec_method.number_of_spin_channels == 1
assert sec_method.section_XC_functionals[
0].XC_functional_name == 'LDA_XC_TETER93'
sec_system = sec_run.section_system[0]
assert sec_system.atom_positions[0][2].magnitude == approx(3.60977554e-10)
assert sec_system.lattice_vectors[2][2].magnitude == approx(8.3345e-10)
assert True not in sec_system.configuration_periodic_dimensions
sec_scc = sec_run.section_single_configuration_calculation[0]
assert sec_scc.energy_total.magnitude == approx(-8.66869132e-17)
assert sec_scc.atom_forces[0][2].magnitude == approx(4.67181276e-09)
sec_scfs = sec_scc.section_scf_iteration
assert len(sec_scfs) == 11
assert sec_scfs[3].energy_total_scf_iteration.magnitude == approx(
-8.66861188e-17)
assert sec_scfs[6].energy_XC_potential_scf_iteration.magnitude == approx(
-2.7272656e-17)
assert sec_scfs[
7].electronic_kinetic_energy_scf_iteration.magnitude == approx(
6.34717211e-17)
def test_xs_tddft(parser):
archive = EntryArchive()
parser.parse('tests/data/CSi_tddft/INFO_QMT001.OUT', archive, None)
sec_sccs = archive.section_run[0].section_single_configuration_calculation
assert len(sec_sccs) == 2
assert len(sec_sccs[1].x_exciting_xs_tddft_epsilon_energies) == 10001
assert np.shape(
sec_sccs[1].x_exciting_xs_tddft_dielectric_function_local_field) == (
2, 1, 3, 10001)
assert np.shape(
sec_sccs[1].x_exciting_xs_tddft_dielectric_function_no_local_field
) == (2, 1, 3, 10001)
assert np.shape(
sec_sccs[1].x_exciting_xs_tddft_loss_function_local_field) == (1, 3,
10001)
assert np.shape(
sec_sccs[1].x_exciting_xs_tddft_loss_function_no_local_field) == (
1, 3, 10001)
assert np.shape(
sec_sccs[1].x_exciting_xs_tddft_loss_function_no_local_field) == (
1, 3, 10001)
assert np.shape(
sec_sccs[1].x_exciting_xs_tddft_sigma_local_field) == (2, 1, 3, 10001)
assert np.shape(
sec_sccs[1].x_exciting_xs_tddft_sigma_no_local_field) == (2, 1, 3,
10001)
def test_dos_spinpol(parser):
archive = EntryArchive()
parser.parse('tests/data/CeO_dos/INFO.OUT', archive, None)
sec_scc = archive.section_run[0].section_single_configuration_calculation[
0]
assert len(sec_scc.section_dos) == 1
sec_doss = sec_scc.section_dos
assert np.shape(sec_doss[0].dos_values) == (2, 500)
assert sec_doss[0].dos_energies[79].magnitude == approx(-1.70772016e-18)
assert sec_doss[0].dos_values[0][126] == approx(1.8925127e-10)
assert sec_doss[0].dos_values[1][136] == approx(1.91606129e-11)
assert sec_doss[0].dos_energies[240].magnitude == approx(1.09995544e-18)
assert sec_doss[0].dos_values[0][220] == approx(5.63875821e-10)
assert sec_doss[0].dos_values[1][78] == approx(4.33359121e-10)
sec_pdoss = sec_scc.section_atom_projected_dos
assert len(sec_pdoss) == 1
assert np.shape(sec_pdoss[0].atom_projected_dos_values_lm) == (25, 2, 3,
500)
assert sec_doss[0].dos_energies[100].magnitude == approx(
sec_pdoss[0].atom_projected_dos_energies[100].magnitude)
assert sec_pdoss[0].atom_projected_dos_values_lm[1][0][1][116] == approx(
1.07677456e+16)
assert sec_pdoss[0].atom_projected_dos_values_lm[20][1][0][85] == approx(
7.81205293e+11)
def test_CrO2(parser):
'''
Single run of feromagnetic CrO2 using LDA+U
'''
archive = EntryArchive()
parser.parse('tests/CrO2_single_point/CrO2.out', archive, logging)
run = archive.section_run[0]
method = run.section_method[0]
assert method.number_of_spin_channels == 2
assert method.electronic_structure_method == 'DFT+U'
assert method.smearing_width == approx(K_to_J(500))
assert method.section_XC_functionals[0].XC_functional_name == 'LDA_X'
assert method.section_XC_functionals[1].XC_functional_name == 'LDA_C_PW'
assert method.scf_max_iteration == 40
assert method.scf_threshold_energy_change.magnitude == approx(
Ha_to_J(1e-7))
eigenvalues = run.section_single_configuration_calculation[
-1].section_eigenvalues[0]
assert eigenvalues.eigenvalues_kind == 'normal'
assert eigenvalues.number_of_eigenvalues_kpoints == 100
assert np.shape(eigenvalues.eigenvalues_kpoints) == (100, 3)
assert eigenvalues.eigenvalues_kpoints[39, 2] == approx(0.43750)
assert eigenvalues.number_of_eigenvalues == 90
assert np.shape(eigenvalues.eigenvalues_values) == (2, 100, 90)
assert eigenvalues.eigenvalues_values[0, 42, 8].magnitude == approx(
Ha_to_J(-0.92962144255459))
assert eigenvalues.eigenvalues_values[1, 99, 89].magnitude == approx(
Ha_to_J(13.66867939417960))
def test_band_spinpol(parser):
archive = EntryArchive()
parser.parse('tests/data/Fe_band_spinpol/Fe_band_structure_dos_spin.out', archive, None)
assert len(archive.section_run[0].section_single_configuration_calculation) == 1
sec_scc = archive.section_run[0].section_single_configuration_calculation[0]
sec_k_band = sec_scc.section_k_band[0]
assert len(sec_k_band.section_k_band_segment) == 3
assert np.shape(sec_k_band.section_k_band_segment[0].band_energies) == (2, 15, 19)
assert np.shape(sec_k_band.section_k_band_segment[1].band_k_points) == (15, 3)
assert np.shape(sec_k_band.section_k_band_segment[2].band_occupations) == (2, 15, 19)
assert sec_k_band.section_k_band_segment[0].band_occupations[1][9][2] == approx(1.0)
assert sec_k_band.section_k_band_segment[1].band_energies[0][3][5].magnitude == approx(-1.54722007e-17)
assert sec_k_band.section_k_band_segment[2].band_k_points[14][2] == approx(0.5)
sec_dos = sec_scc.section_dos[0]
assert np.shape(sec_dos.dos_energies) == (50,)
assert np.shape(sec_dos.dos_values) == (2, 50)
assert sec_dos.dos_energies[46].magnitude == approx(-1.1999976e-18)
assert sec_dos.dos_values[0][46] == approx(1.2418252951253564e-11)
assert sec_dos.dos_values[1][15] == approx(3.9151704709731774e-11)
sec_atom_dos = sec_scc.section_atom_projected_dos[0]
assert np.shape(sec_atom_dos.atom_projected_dos_energies) == (50,)
assert np.shape(sec_atom_dos.atom_projected_dos_values_lm) == (4, 2, 1, 50)
assert np.shape(sec_atom_dos.atom_projected_dos_values_total) == (2, 1, 50)
assert sec_atom_dos.atom_projected_dos_energies[49].magnitude == approx(-1.12152364e-18)
assert sec_atom_dos.atom_projected_dos_values_lm[2][1][0][22] == approx(6.61986474e+18)
assert sec_atom_dos.atom_projected_dos_values_lm[0][0][0][8] == approx(3.35029976e+17)
assert sec_atom_dos.atom_projected_dos_values_total[0][0][40] == approx(9.950877863070872e+17)
def test_1(parser):
archive = EntryArchive()
parser.parse('tests/data/test003.input.out', archive, None)
sec_sccs = archive.section_run[0].section_single_configuration_calculation
assert len(sec_sccs) == 61
assert sec_sccs[4].energy_total.magnitude == approx(-9.14252116e-15)
def test_2(parser):
archive = EntryArchive()
parser.parse('tests/data/GaAs/INFO.OUT', archive, None)
sec_system = archive.section_run[0].section_system[0]
assert sec_system.atom_labels == ['Ga', 'As']
assert sec_system.atom_positions[1][2].magnitude == approx(1.41382921e-10)
def test_example(parser):
archive = EntryArchive()
parser.parse('tests/Test1/metadata.json', archive, logging)
measurement = archive.section_measurement[0]
assert measurement.section_metadata[0].section_sample[0].sample_id is not None
assert measurement.section_metadata[0].section_experiment[0].method_name is not None
assert measurement.section_data[0].section_spectrum[0].n_values == 226
def test_example(parser):
archive = EntryArchive()
parser.run('tests/data/example.out', archive, logging)
run = archive.section_run[0]
assert len(run.section_system) == 2
assert len(run.section_single_configuration_calculation) == 2
assert run.section_single_configuration_calculation[0].x_example_magic_value == 42
def test_1(parser):
archive = EntryArchive()
parser.parse('tests/data/example18.got', archive, None)
sec_sccs = archive.section_run[0].section_single_configuration_calculation
assert len(sec_sccs) == 4
assert sec_sccs[2].energy_total.magnitude == approx(-2.10631951e-16)
def test_1(parser):
archive = EntryArchive()
parser.parse('tests/data/test08/ethene_relax.out', archive, None)
sec_sccs = archive.section_run[0].section_single_configuration_calculation
assert len(sec_sccs) == 33
assert sec_sccs[8].energy_total.magnitude == approx(-5.95750082e-17)
assert sec_sccs[2].atom_forces[5][1].magnitude == approx(-6.68217323e-10)
def test_C2N2(parser):
'''
Molecular dynamics using the Nose-Hover thermostat for simple N2H2 molecule
'''
archive = EntryArchive()
parser.parse('tests/C2H2_molecular_dynamics/C2H2.out', archive, logging)
run = archive.section_run[0]
assert run.program_version == '3.9.2'
assert run.program_basis_set_type == 'Numeric AOs'
assert run.run_clean_end
scc = run.section_single_configuration_calculation
assert len(scc) == 100
assert scc[0].temperature.magnitude == approx(300.0)
assert scc[99].temperature.magnitude == approx(46.053)
assert np.shape(scc[0].atom_forces) == (4, 3)
assert scc[0].atom_forces[0][0].magnitude == approx(HaB_to_N(0.10002))
assert scc[99].atom_forces[2][2].magnitude == approx(HaB_to_N(-0.00989))
assert len(run.section_system) == 100
method = run.section_method[0]
assert method.number_of_spin_channels == 1
assert method.electronic_structure_method == 'DFT'
assert method.smearing_width == approx(K_to_J(500))
assert method.section_XC_functionals[0].XC_functional_name == 'LDA_X'
assert method.section_XC_functionals[1].XC_functional_name == 'LDA_C_PZ'
sampling_method = run.section_sampling_method
assert len(sampling_method) == 1
assert sampling_method[0].sampling_method == "molecular_dynamics"
assert sampling_method[0].ensemble_type == "NVT"
system = run.section_system[0]
assert np.shape(system.velocities) == (4, 3)
assert system.velocities[0][0].magnitude == approx(396.15464)
assert system.velocities[3][2].magnitude == approx(2359.24208)
system = run.section_system[99]
assert system.velocities[0][1].magnitude == approx(-353.94304)
assert system.velocities[3][0].magnitude == approx(-315.74184)
eigenvalues = run.section_single_configuration_calculation[
-1].section_eigenvalues[0]
assert eigenvalues.eigenvalues_kind == 'normal'
assert eigenvalues.number_of_eigenvalues_kpoints == 1
assert np.shape(eigenvalues.eigenvalues_kpoints) == (1, 3)
assert all([
a == pytest.approx(b)
for a, b in zip(eigenvalues.eigenvalues_kpoints[0], [0, 0, 0])
])
assert eigenvalues.number_of_eigenvalues == 64
assert np.shape(eigenvalues.eigenvalues_values) == (1, 1, 64)
assert eigenvalues.eigenvalues_values[0, 0, 0].magnitude == approx(
Ha_to_J(-0.67352892393426))
assert eigenvalues.eigenvalues_values[0, 0, 63].magnitude == approx(
Ha_to_J(7.29352095903235))
def test_bfgs(parser):
archive = EntryArchive()
parser.parse('tests/data/Si2_opt.castep', archive, None)
assert archive.section_run[0].section_sampling_method[
0].sampling_method == 'geometry_optimization'
sec_sccs = archive.section_run[0].section_single_configuration_calculation
assert len(sec_sccs) == 9
sec_sccs[7].pressure.magnitude == approx(400000.0)