diff --git a/parser/parser-lib-atoms/libAtomsParser.py b/parser/parser-lib-atoms/libAtomsParser.py index d22a7228924109eb38af13858b4a0a32269e3dbf..afb198c38ec27588e541be5bbdc8236fc400eaa0 100644 --- a/parser/parser-lib-atoms/libAtomsParser.py +++ b/parser/parser-lib-atoms/libAtomsParser.py @@ -137,7 +137,8 @@ def parse(output_file_name): push_array_values(jbe, frame.virial, 'x_lib_atoms_virial_tensor') # Forces if frame.ase_config.has('forces'): - push_array_values(jbe, frame.ase_config.get_forces(), 'atom_forces') + with open_section(jbe, 'section_atom_forces') as fId: + push_array_values(jbe, frame.ase_config.get_forces(), 'atom_forces') # Type label if frame.has_config_type: push_value(jbe, frame.config_type, 'x_lib_atoms_config_type') @@ -147,24 +148,24 @@ def parse(output_file_name): with open_section(jbe, 'section_frame_sequence'): push_value(jbe, len(all_frames), 'number_of_frames_in_sequence') refs_config = np.array(refs_single_configuration) - push_array_values(jbe, refs_config, 'frame_sequence_local_frames_ref') + push_array_values(jbe, refs_config, 'frame_sequence_to_frames_ref') # GAP DESCRIPTION if gap.has_gap_data: with open_section(jbe, 'x_lib_atoms_section_gap') as gap_gid: push_array_values(jbe, np.array(refs_single_configuration), 'x_lib_atoms_training_config_refs') - push_value(jbe, gap['GAP_params.label'].As(), 'x_lib_atoms_GAP_params_label') - push_value(jbe, gap['GAP_params.svn_version'].As(), 'x_lib_atoms_GAP_params_svn_version') - push_value(jbe, gap['GAP_data.do_core'].As(), 'x_lib_atoms_GAP_data_do_core') - push_value(jbe, gap['GAP_data.e0'].As(float), 'x_lib_atoms_GAP_data_e0') + push_value(jbe, gap['GAP_params.label'].As(), 'x_lib_atoms_gap_params_label') + push_value(jbe, gap['GAP_params.svn_version'].As(), 'x_lib_atoms_gap_params_svn_version') + push_value(jbe, gap['GAP_data.do_core'].As(), 'x_lib_atoms_gap_data_do_core') + push_value(jbe, gap['GAP_data.e0'].As(float), 'x_lib_atoms_gap_data_e0') push_value(jbe, gap['command_line.command_line'].As(), 'x_lib_atoms_command_line_command_line') - push_value(jbe, gap['gpSparse.n_coordinate'].As(int), 'x_lib_atoms_gpSparse_n_coordinate') + push_value(jbe, gap['gpSparse.n_coordinate'].As(int), 'x_lib_atoms_gpsparse_n_coordinate') types = [int, int, int, str, float, float, float, str, str, float, str, int, int ] keys = ['n_sparseX', 'dimensions', 'n_permutations', 'sparsified', 'signal_variance', 'signal_mean', 'covariance_type', 'label', 'sparseX_filename', 'theta', 'descriptor', 'perm.permutation', 'perm.i'] for i,key in enumerate(keys): - push_value(jbe, gap['gpCoordinates.%s' % key].As(types[i]), 'x_lib_atoms_gpCoordinates_%s' % key.replace('.', '_')) + push_value(jbe, gap['gpCoordinates.%s' % key].As(types[i]), 'x_lib_atoms_gpcoordinates_%s' % key.replace('.', '_').lower()) for key in ['alpha', 'sparseX']: - push_array_values(jbe, gap['gpCoordinates.%s' % key].As(), 'x_lib_atoms_gpCoordinates_%s' % key.replace('.', '_')) + push_array_values(jbe, gap['gpCoordinates.%s' % key].As(), 'x_lib_atoms_gpcoordinates_%s' % key.replace('.', '_').lower()) jbe.finishedParsingSession("ParseSuccess", None) return diff --git a/src/main/scala/eu/nomad_lab/parsers/LibAtomsParser.scala b/src/main/scala/eu/nomad_lab/parsers/LibAtomsParser.scala index eb676dc83da0dfe049c047a7736379bc778b6024..19c99d10a13124e627660d12a07041ed43f0928b 100644 --- a/src/main/scala/eu/nomad_lab/parsers/LibAtomsParser.scala +++ b/src/main/scala/eu/nomad_lab/parsers/LibAtomsParser.scala @@ -47,7 +47,7 @@ object LibAtomsParser extends SimpleExternalParserGenerator( "parser-lib-atoms/setup_paths.py", "nomad_meta_info/public.nomadmetainfo.json", "nomad_meta_info/common.nomadmetainfo.json", - "nomad_meta_info/meta_types.nomadmetainfo.json", + "nomad_meta_info/meta.nomadmetainfo.json", "nomad_meta_info/lib_atoms.nomadmetainfo.json" ) ++ DefaultPythonInterpreter.commonFiles(), dirMap = Map(