# Copyright The NOMAD Authors.
#
# This file is part of NOMAD. See https://nomad-lab.eu for further info.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
import sys
import json
import logging
from nomad.utils import configure_logging
from nomad.datamodel import EntryArchive
from phonopyparser import PhonopyParser
if __name__ == "__main__":
configure_logging(console_log_level=logging.DEBUG)
archive = EntryArchive()
PhonopyParser().parse(sys.argv[1], archive, logging)
json.dump(archive.m_to_dict(), sys.stdout, indent=2)
def parse(filepath):
"""Used to parse a file in the fiven filepath with the Crystal parser."""
archive = EntryArchive()
logger = None
parser.parse(filepath, archive, logger)
return archive
def parse(filename: str):
archive = EntryArchive()
QBallParser().run(filename, archive, logging)
json.dump(archive.m_to_dict(), sys.stdout, indent=2)
def test_md_edr(parser):
archive = EntryArchive()
parser.parse('tests/data/fe_test/mdrun.out', archive, None)
assert len(
archive.section_run[0].section_single_configuration_calculation) == 7
def silicon(parser):
archive = EntryArchive()
parser.parse('tests/data/Si_band_dos/aims_CC.out', archive, None)
return archive
def test_4(parser):
archive = EntryArchive()
parser.parse('tests/data/output.out', archive, None)
def test_scf(parser):
archive = EntryArchive()
parser.parse('tests/data/HO_scf/benchmark2.out', archive, None)
sec_run = archive.section_run[0]
assert sec_run.program_version == '5.2.1 (svn rev. 11920)'
assert sec_run.x_qe_input_filename == 'uspp1.in'
assert sec_run.time_run_date_start.magnitude == 1451140876.0
assert sec_run.x_qe_section_compile_options[0].x_qe_lmaxx == 3
assert sec_run.x_qe_section_parallel[0].x_qe_nproc == 4
assert sec_run.section_basis_set_cell_dependent[0].basis_set_cell_dependent_name == 'PW_25.0'
assert sec_run.section_basis_set_cell_dependent[1].basis_set_planewave_cutoff.magnitude == approx(2.17987236e-16,)
assert sec_run.section_sampling_method[0].sampling_method == 'geometry_optimization'
assert 'rdiaghg' in sec_run.x_qe_profile_function
assert sec_run.time_run_date_end.magnitude == 1451140881.0
assert sec_run.run_clean_end
sec_method = sec_run.section_method[0]
assert sec_method.x_qe_sticks_sum_G_smooth == 135043
assert 'NL pseudopotentials' in sec_method.x_qe_allocated_array_name
assert sec_method.x_qe_allocated_array_size[2] == 33554432.
assert sec_method.x_qe_temporary_array_dimensions[3] == '262144, 8'
assert sec_method.x_qe_per_process_mem == approx(2.84373811e+08)
assert sec_method.x_qe_potential_mixing_scheme == 'plain'
assert sec_method.x_qe_starting_charge == 7.99998
assert len(sec_method.section_XC_functionals) == 2
assert sec_method.x_qe_xc_igcc_name == 'pbc'
assert sec_method.section_XC_functionals[1].XC_functional_name == 'GGA_X_PBE'
sec_atoms = sec_method.section_method_atom_kind
assert len(sec_atoms) == 2
assert sec_atoms[1].method_atom_kind_label == 'H'
assert sec_atoms[0].x_qe_pp_md5sum == '7e325307d184e51bd80757047dcf04f9'
assert sec_atoms[1].x_qe_pp_ncoefficients == 8
assert sec_atoms[0].x_qe_kind_mass == 16.0
sec_system = sec_run.section_system[0]
assert sec_system.atom_labels == ['O', 'H', 'H']
assert sec_system.atom_positions[2][0].magnitude == approx(5.12015994e-10)
assert False not in sec_system.configuration_periodic_dimensions
assert sec_system.x_qe_reciprocal_cell[2][2].magnitude == approx(5.93674971e+09)
assert len(sec_system.x_qe_k_info_vec) == 1
assert sec_system.x_qe_cell_volume == approx(1.18547769e-27)
assert sec_system.x_qe_nsymm == 4
assert sec_system.x_qe_dense_FFT_grid[1] == 64
assert sec_system.number_of_electrons[0] == 8
sec_scc = sec_run.section_single_configuration_calculation[0]
assert sec_scc.energy_total.magnitude == approx(-7.49748432e-17)
assert 'ewald contribution' in sec_scc.x_qe_energy_decomposition_name
assert sec_scc.x_qe_energy_decomposition_value[1] == approx(7.42289975e-17)
assert sec_scc.atom_forces_raw[1][1].magnitude == approx(-3.57815176e-10)
assert sec_scc.stress_tensor[2][2].magnitude == approx(-1.68e+08)
assert np.shape(sec_scc.section_eigenvalues[0].eigenvalues_kpoints) == (1, 3)
assert np.shape(sec_scc.section_eigenvalues[0].eigenvalues_values) == (1, 1, 4)
assert sec_scc.section_eigenvalues[0].eigenvalues_values[0][0][2].magnitude == approx(-1.42427094e-18)
assert sec_scc.energy_reference_highest_occupied.magnitude == approx(-1.15444837e-18)
assert sec_scc.x_qe_output_datafile == 'pwscf.save'
sec_scfs = sec_scc.section_scf_iteration
assert len(sec_scfs) == 8
assert sec_scfs[4].energy_total_scf_iteration.magnitude == approx(-7.49748038e-17)
assert sec_scfs[1].x_qe_energy_total_accuracy_estimate_iteration == approx(1.15623477e-18)
assert sec_scfs[6].x_qe_iteration_ecutwfc == approx(5.4496809027589626e-17)
assert sec_scfs[0].time_scf_iteration_cpu1_end.magnitude == 1.2
assert sec_scfs[3].x_qe_iteration_charge_negative_up == 0.06614
def test_2(parser):
archive = EntryArchive()
parser.parse('tests/data/abinit_1.out', archive, None)
def test_3(parser):
archive = EntryArchive()
parser.parse('tests/data/libxc_101130.out', archive, None)
def test_1(parser):
archive = EntryArchive()
parser.parse('tests/data/periodic.out', archive, None)
def silicon_gw(parser):
archive = EntryArchive()
parser.parse('tests/data/Si_gw/INFO.OUT', archive, None)
return archive
def test_AlN(parser):
'''
Geometry optimization (atomic positions only) AlN test case.
'''
archive = EntryArchive()
parser.parse('tests/AlN_ionic_optimization/AlN.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) == 5
assert scc[0].energy_total.magnitude == approx(Ha_to_J(-25.194346653540))
assert scc[4].energy_total.magnitude == approx(Ha_to_J(-25.194358042252))
assert np.shape(scc[0].atom_forces) == (4, 3)
assert scc[0].atom_forces[0][2].magnitude == approx(HaB_to_N(0.00139))
assert scc[4].atom_forces[3][2].magnitude == approx(HaB_to_N(-0.00018))
scf = scc[0].section_scf_iteration
assert len(scf) == 21
scf[20].energy_sum_eigenvalues_scf_iteration == approx(
-3.4038353611878345e-17)
scf = scc[3].section_scf_iteration
assert len(scf) == 6
scf[5].energy_sum_eigenvalues_scf_iteration == approx(
-3.4038520917173614e-17)
method = run.section_method[0]
section_XC_functionals1 = method.section_XC_functionals[0]
section_XC_functionals2 = method.section_XC_functionals[1]
assert method.number_of_spin_channels == 1
assert method.electronic_structure_method == 'DFT'
assert method.smearing_width == approx(K_to_J(300))
assert section_XC_functionals1.XC_functional_name == 'GGA_C_PBE'
assert section_XC_functionals2.XC_functional_name == 'GGA_X_PBE'
assert method.scf_max_iteration == 100
assert method.scf_threshold_energy_change.magnitude == approx(
Ha_to_J(1e-7))
sampling_method = run.section_sampling_method
assert len(sampling_method) == 1
assert sampling_method[
0].geometry_optimization_method == "steepest_descent"
assert sampling_method[0].sampling_method == "geometry_optimization"
assert sampling_method[
0].geometry_optimization_threshold_force.magnitude == approx(
(0.0003 * units.hartree / units.bohr).to_base_units().magnitude)
assert len(run.section_system) == 5
system = run.section_system[0]
assert all([
a == b for a, b in zip(system.configuration_periodic_dimensions,
[True, True, True])
])
assert system.lattice_vectors[0][0].magnitude == approx(A_to_m(3.10997))
assert system.lattice_vectors[1][0].magnitude == approx(A_to_m(-1.55499))
assert len(system.atom_positions) == 4
assert system.atom_positions[0][0].magnitude == approx(A_to_m(1.55499))
assert system.atom_positions[3][2].magnitude == approx(A_to_m(4.39210))
assert len(system.atom_labels) == 4
assert system.atom_labels[3] == 'N'
system = run.section_system[0]
assert np.shape(system.velocities) == (4, 3)
assert system.velocities[0][0].magnitude == pytest.approx(0.0)
assert system.velocities[3][2].magnitude == pytest.approx(0.0)
system = run.section_system[3]
assert system.lattice_vectors[1][1].magnitude == approx(A_to_m(2.69331))
assert system.lattice_vectors[2][2].magnitude == approx(A_to_m(4.98010))
assert len(system.atom_positions) == 4
assert system.atom_positions[0][1].magnitude == approx(A_to_m(0.89807))
assert system.atom_positions[2][2].magnitude == approx(A_to_m(1.90030))
assert len(system.atom_labels) == 4
assert system.atom_labels[0] == 'Al'
system = run.section_system[4]
assert system.lattice_vectors[0][0].magnitude == approx(A_to_m(3.10997))
assert system.lattice_vectors[2][2].magnitude == approx(A_to_m(4.98010))
assert len(system.atom_positions) == 4
assert system.atom_positions[0][2].magnitude == approx(A_to_m(0.00253))
assert system.atom_positions[3][2].magnitude == approx(A_to_m(4.39015))
assert len(system.atom_labels) == 4
assert system.atom_labels[1] == 'Al'
eigenvalues = run.section_single_configuration_calculation[
-1].section_eigenvalues[0]
assert eigenvalues.eigenvalues_kind == 'normal'
assert eigenvalues.number_of_eigenvalues_kpoints == 74
assert np.shape(eigenvalues.eigenvalues_kpoints) == (74, 3)
assert eigenvalues.eigenvalues_kpoints[0][0] == approx(-0.42857)
assert eigenvalues.eigenvalues_kpoints[0][2] == approx(-0.33333)
assert eigenvalues.eigenvalues_kpoints[73][2] == pytest.approx(0.0)
assert eigenvalues.number_of_eigenvalues == 52
assert np.shape(eigenvalues.eigenvalues_values) == (1, 74, 52)
assert eigenvalues.eigenvalues_values[0, 0, 0].magnitude == approx(
Ha_to_J(-0.77128985545768))
assert eigenvalues.eigenvalues_values[0, 73, 51].magnitude == approx(
Ha_to_J(4.86822333092339))
def test_1(parser):
archive = EntryArchive()
parser.parse('tests/data/dhcp_gd/out', archive, None)
assert len(archive.section_run[0].section_system[0].atom_positions) == 4
def test_vasp(parser):
archive = EntryArchive()
parser.parse('tests/data/vasp/phonopy.yaml', archive, None)