def setUp(self):
# create a temporary directories
self.main_folder = tempfile.mkdtemp()
configs = set_configs(main_folder=self.main_folder)
self.configs = configs
ase_db_file_binaries = get_data_filename(
'data/db_ase/binaries_lowest_energy_ghiringhelli2015.json')
results_binaries_lasso = get_data_filename(
'data/viewer_files/l1_l0_dim2_for_viewer.csv')
results_metal_non_metal = get_data_filename(
'data/viewer_files/tutorial_metal_non_metal_2017.csv')
results_topological_ins = get_data_filename(
'data/viewer_files/tutorial_topological_insulators_2017.csv')
control_file_binaries = get_data_filename(
'data/viewer_files/binaries_control.json')
self.ase_atoms_binaries = read_ase_db(db_path=ase_db_file_binaries)
self.results_binaries_lasso = results_binaries_lasso
self.results_metal_non_metal = results_metal_non_metal
self.control_file_binaries = control_file_binaries
self.results_topological_ins = results_topological_ins
'/home/ziletti/Documents/calc_xray/2d_nature_comm/db_ase/elemental_solids_ncomms_1e-3_1e-6_166.db',
'/home/ziletti/Documents/calc_xray/2d_nature_comm/db_ase/elemental_solids_ncomms_1e-3_1e-6_194.db',
'/home/ziletti/Documents/calc_xray/2d_nature_comm/db_ase/elemental_solids_ncomms_1e-3_1e-6_1e-9_221.db',
'/home/ziletti/Documents/calc_xray/2d_nature_comm/db_ase/elemental_solids_ncomms_1e-3_1e-6_1e-9_225.db',
'/home/ziletti/Documents/calc_xray/2d_nature_comm/db_ase/elemental_solids_ncomms_1e-3_1e-6_1e-9_227.db',
'/home/ziletti/Documents/calc_xray/2d_nature_comm/db_ase/elemental_solids_ncomms_1e-3_1e-6_1e-9_229.db'
]
# ase_db_file_vac20 = '/home/ziletti/Documents/calc_xray/2d_nature_comm/db_ase/elemental_solids_ncomms_1e-3_1e-6_1e-9_vac0.2.db'
# ase_db_file_pristine = '/home/ziletti/Documents/calc_xray/2d_nature_comm/db_ase/elemental_solids_ncomms_7_classes.db'
# ase_db_file_vac20 = '/home/ziletti/Documents/calc_xray/2d_nature_comm/db_ase/elemental_solids_ncomms_1e-3_1e-6_1e-9_vac0.2.db'
# ase_atoms_list_vac20 = read_ase_db(db_path=ase_dpb_file_vac20)
ase_atoms_list_pristine = []
for db_path in ase_db_file_pristine:
ase_atoms_list_pristine.extend(read_ase_db(db_path=db_path))
symprec = 1.e-9
angle_tolerance = -1.0
y_true = []
for idx, ase_atom_pristine in enumerate(ase_atoms_list_pristine):
if idx % (int(len(ase_atoms_list_pristine) / 10) + 1) == 0:
logger.debug("Reading ASE atom structure: file {0}/{1}".format(
idx + 1, len(ase_atoms_list_pristine)))
y_true.extend(
get_spacegroup(ase_atom_pristine,
symprec=symprec,
angle_tolerance=angle_tolerance))
true_labels_filename = 'y_true_list' + '_symprec' + str(
symprec) + '_angletol' + str(angle_tolerance)
random_rotation=False,
random_rotation_before=True,
cell_type='standard_no_symmetries',
optimal_supercell=False))]
# =============================================================================
# Descriptor calculation
# =============================================================================
# desc_file_name = 'desc_calc_trial'
desc_file_name = 'try1'
# ase_db_file = '/home/ziletti/Documents/calc_xray/2d_nature_comm/db_ase/elemental_solids_ncomms_1e-3_1e-6_1e-9_139.db'
ase_db_file = '/home/ziletti/Documents/calc_xray/2d_nature_comm/db_ase/elemental_solids_ncomms_7_classes.db'
# ase_db_file = '/home/ziletti/Documents/calc_xray/2d_nature_comm/db_ase/elemental_solids_ncomms_1e-3_1e-6_pristine.db'
ase_atoms_list = read_ase_db(db_path=ase_db_file)
desc_file_path = calc_descriptor(
descriptor=descriptor,
configs=configs,
ase_atoms_list=ase_atoms_list,
tmp_folder=tmp_folder,
desc_folder=desc_folder,
desc_info_file=desc_info_file,
desc_file=str(desc_file_name) + '.tar.gz',
format_geometry='aims',
operations_on_structure=operations_on_structure_list[1],
nb_jobs=-1)
desc_file_path = '/home/ziletti/Documents/nomadml_docs/desc_folder/try1.tar.gz'
target_list, structure_list = load_descriptor(desc_files=desc_file_path,
def setUp(self):
ase_db_file_binaries = get_data_filename(
'data/db_ase/binaries_ghiringhelli2015.json')
self.ase_atoms_binaries = read_ase_db(db_path=ase_db_file_binaries)
# sys.exit(1)
# setup folder and files
main_folder = '/home/ziletti/Documents/nomadml_docs/'
tmp_folder = os.path.abspath(
os.path.normpath(os.path.join(main_folder, 'tmp')))
desc_folder = os.path.abspath(
os.path.normpath(os.path.join(main_folder, 'desc_folder')))
desc_info_file = os.path.abspath(
os.path.normpath(os.path.join(desc_folder, 'desc_info.json.info')))
descriptor = PRDF(configs=configs)
desc_file_name = 'prdf_binaries'
ase_db_file_binaries = '/home/ziletti/PycharmProjects/ai4materials/ai4materials/data/db_ase/binaries_ghiringhelli2015.db'
ase_atoms_list = read_ase_db(db_path=ase_db_file_binaries)
desc_file_path = calc_descriptor(descriptor=descriptor,
configs=configs,
ase_atoms_list=ase_atoms_list,
tmp_folder=tmp_folder,
desc_folder=desc_folder,
desc_info_file=desc_info_file,
desc_file=str(desc_file_name) + '.tar.gz',
format_geometry='aims',
nb_jobs=-1)
desc_file_path = '/home/ziletti/Documents/nomadml_docs/desc_folder/prdf_binaries.tar.gz'
target_list, structure_list = load_descriptor(desc_files=desc_file_path,
configs=configs)
# write an ase db to file for each spacegroup
# ase_db_file = write_ase_db(ase_atoms, main_folder, db_name=proto_names[idx_proto], overwrite=True,
# folder_name='db_ase_prototypes')
# ase_db_files.append(ase_db_file)
# for ase_db_file in ase_db_files:
# ase_atoms_list = read_ase_db(db_path=ase_db_file)
# print(ase_db_file, len(ase_atoms_list))
# =============================================================================
# Descriptor calculation
# =============================================================================
for idx_db, db_proto in enumerate(db_protos):
ase_atoms_list = read_ase_db(db_path=ase_db_files[idx_db])[:]
print('{} structures for prototype {}'.format(len(ase_atoms_list),
db_proto[0]))
for idx_rot in range(nb_rotations):
desc_file_path = calc_descriptor_in_memory(
descriptor=descriptor,
configs=configs,
ase_atoms_list=ase_atoms_list,
tmp_folder=configs['io']['tmp_folder'],
desc_folder=configs['io']['desc_folder'],
# desc_file='try1.tar.gz',
desc_file='{0}_target_nb_atoms{1}_rotid{2}_disp0002.tar.gz'.
format(db_proto[0], target_nb_atoms, idx_rot),