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mod_abstract_structure_data_file

Lines: 60 | Visibility: private

Implementation of an abstract base class for all files that provide chemical structures for training/prediction. author: Alexander Knoll

Dependencies

Uses

module~~mod_abstract_structure_data_file~~UsesGraph module~mod_abstract_structure_data_file mod_abstract_structure_data_file module~mod_dataset_storage mod_dataset_storage module~mod_abstract_structure_data_file->module~mod_dataset_storage module~mod_genericfile mod_genericfile module~mod_abstract_structure_data_file->module~mod_genericfile module~mod_mpi mod_mpi module~mod_abstract_structure_data_file->module~mod_mpi module~mod_periodic_table mod_periodic_table module~mod_abstract_structure_data_file->module~mod_periodic_table module~mod_structures mod_structures module~mod_abstract_structure_data_file->module~mod_structures module~mod_dataset_storage->module~mod_mpi mod_property_list mod_property_list module~mod_dataset_storage->mod_property_list module~mod_sort mod_sort module~mod_dataset_storage->module~mod_sort module~mod_storage_container mod_storage_container module~mod_dataset_storage->module~mod_storage_container module~mod_genericfile->module~mod_mpi module~mod_io mod_io module~mod_genericfile->module~mod_io module~mod_throw mod_throw module~mod_genericfile->module~mod_throw module~mod_precision mod_precision module~mod_mpi->module~mod_precision mpi_f08 mpi_f08 module~mod_mpi->mpi_f08 module~mod_array_helpers mod_array_helpers module~mod_periodic_table->module~mod_array_helpers module~mod_constants mod_constants module~mod_periodic_table->module~mod_constants module~mod_periodic_table->module~mod_io module~mod_periodic_table->module~mod_precision module~mod_periodic_table->module~mod_throw module~mod_structures->module~mod_mpi module~mod_structures->module~mod_periodic_table module~mod_structures->module~mod_array_helpers module~mod_structures->module~mod_constants module~mod_linalg mod_linalg module~mod_structures->module~mod_linalg module~mod_structures->module~mod_precision module~mod_structures_helper mod_structures_helper module~mod_structures->module~mod_structures_helper module~mod_structures->module~mod_throw module~mod_array_helpers->module~mod_precision module~mod_array_helpers->module~mod_throw module~mod_constants->module~mod_precision iso_c_binding iso_c_binding module~mod_constants->iso_c_binding module~mod_io->module~mod_precision iso_fortran_env iso_fortran_env module~mod_io->iso_fortran_env module~mod_optional_args mod_optional_args module~mod_io->module~mod_optional_args module~mod_linalg->module~mod_precision module~mod_linalg->module~mod_throw module~cublas_wrapper cublas_wrapper module~mod_linalg->module~cublas_wrapper module~mod_settings mod_settings module~mod_linalg->module~mod_settings module~mod_precision->iso_c_binding module~mod_precision->iso_fortran_env module~mod_sort->module~mod_precision module~mod_storage_container->module~mod_mpi module~mod_storage_container->mod_property_list module~mod_storage_container->module~mod_io module~mod_storage_container->module~mod_sort module~mod_abstract_property_list mod_abstract_property_list module~mod_storage_container->module~mod_abstract_property_list module~mod_dynamic_int_array mod_dynamic_int_array module~mod_storage_container->module~mod_dynamic_int_array module~mod_string mod_string module~mod_storage_container->module~mod_string module~mod_structures_helper->module~mod_linalg module~mod_structures_helper->module~mod_precision module~mod_throw->module~mod_mpi module~mod_throw->module~mod_io module~mod_throw->module~mod_precision module~mod_throw->module~mod_sort module~mod_throw->iso_c_binding module~mod_throw->iso_fortran_env module~cublas_wrapper->iso_c_binding module~cublas_wrapper->module~mod_settings module~mod_abstract_property_list->module~mod_mpi module~mod_abstract_property_list->module~mod_throw module~mod_abstract_property_list->module~mod_dynamic_int_array module~mod_abstract_property_list->module~mod_optional_args module~mod_abstract_property_list->module~mod_string module~mod_dynamic_int_array_2d mod_dynamic_int_array_2d module~mod_abstract_property_list->module~mod_dynamic_int_array_2d module~mod_dynamic_string_array mod_dynamic_string_array module~mod_abstract_property_list->module~mod_dynamic_string_array module~mod_settings->module~mod_periodic_table module~mod_settings->module~mod_constants module~mod_settings->module~mod_io module~mod_settings->module~mod_precision module~mod_settings->module~mod_throw module~mod_cpu_vendor mod_cpu_vendor module~mod_settings->module~mod_cpu_vendor module~mod_string->module~mod_precision module~mod_cpu_vendor->iso_c_binding module~mod_dynamic_int_array_2d->module~mod_mpi module~mod_dynamic_string_array->module~mod_string

Used By

module~~mod_abstract_structure_data_file~~UsedByGraph module~mod_abstract_structure_data_file mod_abstract_structure_data_file module~mod_dataloader_file mod_dataloader_file module~mod_dataloader_file->module~mod_abstract_structure_data_file module~mod_inputdata mod_inputdata module~mod_inputdata->module~mod_abstract_structure_data_file module~mod_calculate_coulomb_matrix mod_calculate_coulomb_matrix module~mod_calculate_coulomb_matrix->module~mod_dataloader_file module~mod_cost_calculator mod_cost_calculator module~mod_cost_calculator->module~mod_dataloader_file module~mod_write_outfiles_training mod_write_outfiles_training module~mod_cost_calculator->module~mod_write_outfiles_training module~mod_dataset_statistics mod_dataset_statistics module~mod_dataset_statistics->module~mod_dataloader_file module~mod_dataset_statistics_chi_all_chunks mod_dataset_statistics_chi_all_chunks module~mod_dataset_statistics_chi_all_chunks->module~mod_dataloader_file module~mod_dataset_statistics_chi_all_chunks->module~mod_dataset_statistics module~mod_feature_map_scaling_all_chunks mod_feature_map_scaling_all_chunks module~mod_feature_map_scaling_all_chunks->module~mod_dataloader_file module~mod_precalc_nl_deriv_features_single_chunk mod_precalc_nl_deriv_features_single_chunk module~mod_feature_map_scaling_all_chunks->module~mod_precalc_nl_deriv_features_single_chunk module~mod_output_files_and_cost mod_output_files_and_cost module~mod_output_files_and_cost->module~mod_dataloader_file module~mod_output_files_and_cost->module~mod_cost_calculator module~mod_predict_multiple_structures mod_predict_multiple_structures module~mod_output_files_and_cost->module~mod_predict_multiple_structures module~mod_output_files_and_cost_4g_charges mod_output_files_and_cost_4g_charges module~mod_output_files_and_cost_4g_charges->module~mod_dataloader_file module~mod_output_files_and_cost_4g_charges->module~mod_cost_calculator module~mod_output_files_and_cost_4g_short_range mod_output_files_and_cost_4g_short_range module~mod_output_files_and_cost_4g_short_range->module~mod_dataloader_file module~mod_output_files_and_cost_4g_short_range->module~mod_cost_calculator module~mod_predict_qeq_feature_calculator_multiple_structures mod_predict_qeq_feature_calculator_multiple_structures module~mod_output_files_and_cost_4g_short_range->module~mod_predict_qeq_feature_calculator_multiple_structures module~mod_precalc_coulomb_matrix_all_chunks mod_precalc_coulomb_matrix_all_chunks module~mod_precalc_coulomb_matrix_all_chunks->module~mod_dataloader_file module~mod_precalc_nl_deriv_features_single_chunk->module~mod_dataloader_file module~mod_precompute_features_all_chunks mod_precompute_features_all_chunks module~mod_precompute_features_all_chunks->module~mod_dataloader_file module~mod_precompute_global_features_all_chunks mod_precompute_global_features_all_chunks module~mod_precompute_global_features_all_chunks->module~mod_dataloader_file module~mod_predict_ee4g_feature_calculator_multiple_structures mod_predict_ee4g_feature_calculator_multiple_structures module~mod_precompute_global_features_all_chunks->module~mod_predict_ee4g_feature_calculator_multiple_structures module~mod_precompute_global_features_all_chunks->module~mod_predict_qeq_feature_calculator_multiple_structures module~mod_predict_all_chunks mod_predict_all_chunks module~mod_predict_all_chunks->module~mod_dataloader_file module~mod_two_body mod_two_body module~mod_predict_all_chunks->module~mod_two_body module~mod_predict_all_chunks->module~mod_predict_multiple_structures module~mod_predict_ee4g_feature_calculator_multiple_structures->module~mod_dataloader_file module~mod_predict_mode mod_predict_mode module~mod_predict_mode->module~mod_dataloader_file module~mod_predict_mode->module~mod_two_body module~mod_initialize mod_initialize module~mod_predict_mode->module~mod_initialize module~mod_predict_mode->module~mod_predict_multiple_structures module~mod_write_outfiles mod_write_outfiles module~mod_predict_mode->module~mod_write_outfiles module~mod_predict_qeq_feature_calculator_multiple_structures->module~mod_dataloader_file module~mod_train_4g_atomic_charges_structure_batch mod_train_4g_atomic_charges_structure_batch module~mod_train_4g_atomic_charges_structure_batch->module~mod_dataloader_file module~mod_train_loop_4g_charges mod_train_loop_4g_charges module~mod_train_loop_4g_charges->module~mod_dataloader_file module~mod_train_loop_4g_charges->module~mod_cost_calculator module~mod_train_loop_4g_charges->module~mod_output_files_and_cost_4g_charges module~mod_train_loop_4g_charges->module~mod_train_4g_atomic_charges_structure_batch module~mod_train_loop_4g_charges->module~mod_initialize module~mod_train_loop_atomic_property mod_train_loop_atomic_property module~mod_train_loop_atomic_property->module~mod_dataloader_file module~mod_train_loop_atomic_property->module~mod_cost_calculator module~mod_train_loop_atomic_property->module~mod_output_files_and_cost module~mod_train_loop_atomic_property->module~mod_initialize module~mod_train_loop_short_range mod_train_loop_short_range module~mod_train_loop_short_range->module~mod_dataloader_file module~mod_train_loop_short_range->module~mod_cost_calculator module~mod_train_loop_short_range->module~mod_output_files_and_cost module~mod_train_loop_short_range->module~mod_output_files_and_cost_4g_short_range module~mod_train_loop_short_range->module~mod_predict_ee4g_feature_calculator_multiple_structures module~mod_train_loop_short_range->module~mod_predict_qeq_feature_calculator_multiple_structures module~mod_train_loop_short_range->module~mod_initialize module~mod_train_energy_multiple_structures mod_train_energy_multiple_structures module~mod_train_loop_short_range->module~mod_train_energy_multiple_structures module~mod_train_forces_multiple_structures mod_train_forces_multiple_structures module~mod_train_loop_short_range->module~mod_train_forces_multiple_structures module~mod_train_mode mod_train_mode module~mod_train_mode->module~mod_dataloader_file module~mod_train_mode->module~mod_dataset_statistics module~mod_train_mode->module~mod_dataset_statistics_chi_all_chunks module~mod_train_mode->module~mod_feature_map_scaling_all_chunks module~mod_train_mode->module~mod_precalc_coulomb_matrix_all_chunks module~mod_train_mode->module~mod_precalc_nl_deriv_features_single_chunk module~mod_train_mode->module~mod_predict_all_chunks module~mod_train_mode->module~mod_predict_ee4g_feature_calculator_multiple_structures module~mod_train_mode->module~mod_predict_qeq_feature_calculator_multiple_structures module~mod_train_mode->module~mod_train_loop_4g_charges module~mod_train_mode->module~mod_train_loop_atomic_property module~mod_train_mode->module~mod_train_loop_short_range module~mod_train_mode->module~mod_two_body module~mod_train_mode->module~mod_initialize module~mod_train_mode->module~mod_write_outfiles_training module~mod_two_body->module~mod_dataloader_file program~runner RuNNer program~runner->module~mod_dataloader_file program~runner->module~mod_inputdata program~runner->module~mod_calculate_coulomb_matrix program~runner->module~mod_precompute_features_all_chunks program~runner->module~mod_precompute_global_features_all_chunks program~runner->module~mod_predict_mode program~runner->module~mod_train_mode program~runner->module~mod_two_body program~runner->module~mod_initialize module~mod_initialize->module~mod_two_body module~mod_post_processing_wrapper_single_structure mod_post_processing_wrapper_single_structure module~mod_post_processing_wrapper_single_structure->module~mod_two_body module~mod_predict_multiple_structures->module~mod_two_body module~mod_predict_multiple_structures->module~mod_post_processing_wrapper_single_structure module~mod_predict_single_structure mod_predict_single_structure module~mod_predict_single_structure->module~mod_two_body module~mod_predict_single_structure->module~mod_post_processing_wrapper_single_structure module~mod_runner_interface mod_runner_interface module~mod_runner_interface->module~mod_two_body module~mod_runner_interface_bindings mod_runner_interface_bindings module~mod_runner_interface_bindings->module~mod_two_body module~mod_runner_interface_bindings->module~mod_initialize module~mod_runner_interface_bindings->module~mod_runner_interface module~mod_feature_calc_interface mod_feature_calc_interface module~mod_feature_calc_interface->module~mod_runner_interface module~mod_generic_interface mod_generic_interface module~mod_feature_calc_interface->module~mod_generic_interface module~mod_generic_interface->module~mod_predict_single_structure module~mod_generic_interface->module~mod_runner_interface module~mod_lammps_interface mod_lammps_interface module~mod_lammps_interface->module~mod_runner_interface module~mod_lammps_interface->module~mod_runner_interface_bindings module~mod_train_energy_multiple_structures->module~mod_initialize module~mod_train_forces_multiple_structures->module~mod_initialize module~mod_train_forces_multiple_structures->module~mod_train_energy_multiple_structures module~mod_write_outfiles->module~mod_initialize module~mod_write_outfiles_training->module~mod_write_outfiles

Derived Types Summary

Name Description
AbstractStructureDataFile

Procedures Summary

Name Type Description
rewind Subroutine

Derived Types Details

type AbstractStructureDataFile

Components

  • name : character– The name of the file. – Inherited from GenericFile
  • path : character– The relative or absolute path to the file. – Inherited from GenericFile
  • iomsg : character– Inherited from GenericFile
  • fileunit : integer– Fortran file unit ID. -1 is the (invalid) default and has to be changed to an actual fileunit, preferably using new_unit in the intrinsic open() routine. – Inherited from GenericFile
  • ios : integer– I/O status. 0 is the default and indicates that no error has occurred. Any other value indicates an error. – Inherited from GenericFile
  • tot_num_structures : integer– Total number of structures in the file.
  • tot_num_atoms : integer– Total number of atoms in the file.
  • num_atoms_element : integer (dim: (MAX_ELEM_NUM))– Total number of atoms per element in the file.
  • max_num_atoms : integer– Maximum number of atoms in a single structure.
  • max_num_atoms_per_element : integer (dim: (MAX_ELEM_NUM))– Maximum number of atoms per element in a single structure.
  • mean_num_neighbors : real(DP)– The average number of neighbors per atom. Collected for statistical purposes.
  • num_parsed_atoms : integer– Total number of atoms that were seen while parsing the file.
  • num_used_atoms : integer– Total number of atoms that were parsed from the file. This may differ from `num_parsed_atoms` due to thresholds applied during parsing.
  • num_parsed_structures : integer– Total number of structures that were seen while parsing the file.
  • num_used_structures : integer– Total number of structures that were parsed from the file. This may differ from `num_parsed_structures` due to thresholds applied during parsing.
  • reference_properties : type(DatasetStorage)– Inherited from AbstractStructureDataFile

Type-Bound Procedures

Name Attributes Binding
open public ⇒ open_abstract_file
close public ⇒ close_abstract_file
check_ios public ⇒ check_ios
count_structures_and_atoms public ⇒ count_structures_and_atoms
read_next_structure public ⇒ read_next_structure
read_structures public ⇒ read_structures
read_reference_properties public ⇒ read_reference_properties
rewind public ⇒ rewind

Inherits

type~~abstractstructuredatafile~~InheritsGraph type~abstractstructuredatafile AbstractStructureDataFile type~datasetstorage DatasetStorage type~abstractstructuredatafile->type~datasetstorage reference_properties type~genericfile GenericFile type~abstractstructuredatafile->type~genericfile type~storagecontainer StorageContainer type~datasetstorage->type~storagecontainer structure, atom PropertyListInt PropertyListInt type~storagecontainer->PropertyListInt int PropertyListReal PropertyListReal type~storagecontainer->PropertyListReal real

Inherited By

type~~abstractstructuredatafile~~InheritedByGraph type~abstractstructuredatafile AbstractStructureDataFile type~filedataloader FileDataLoader type~filedataloader->type~abstractstructuredatafile data_src type~inputdata InputData type~inputdata->type~abstractstructuredatafile

Procedure Details

subroutine rewind

subroutine rewind( &
    self &
)

Arguments