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mod_structures

Lines: 533 | Visibility: private

Implementation of types to store structure data. author: Knut Nikolas Lausch

Dependencies

Uses

module~~mod_structures~~UsesGraph module~mod_structures mod_structures module~mod_array_helpers mod_array_helpers module~mod_structures->module~mod_array_helpers module~mod_constants mod_constants module~mod_structures->module~mod_constants module~mod_linalg mod_linalg module~mod_structures->module~mod_linalg module~mod_mpi mod_mpi module~mod_structures->module~mod_mpi module~mod_periodic_table mod_periodic_table module~mod_structures->module~mod_periodic_table module~mod_precision mod_precision module~mod_structures->module~mod_precision module~mod_structures_helper mod_structures_helper module~mod_structures->module~mod_structures_helper module~mod_throw mod_throw 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_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_mpi->module~mod_precision mpi_f08 mpi_f08 module~mod_mpi->mpi_f08 module~mod_periodic_table->module~mod_array_helpers module~mod_periodic_table->module~mod_constants module~mod_periodic_table->module~mod_precision module~mod_periodic_table->module~mod_throw module~mod_io mod_io module~mod_periodic_table->module~mod_io module~mod_precision->iso_c_binding iso_fortran_env iso_fortran_env module~mod_precision->iso_fortran_env 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_precision module~mod_throw->iso_c_binding module~mod_throw->iso_fortran_env module~mod_throw->module~mod_io module~mod_sort mod_sort module~mod_throw->module~mod_sort module~cublas_wrapper->iso_c_binding module~cublas_wrapper->module~mod_settings module~mod_io->module~mod_precision module~mod_io->iso_fortran_env module~mod_optional_args mod_optional_args module~mod_io->module~mod_optional_args module~mod_settings->module~mod_constants module~mod_settings->module~mod_periodic_table module~mod_settings->module~mod_precision module~mod_settings->module~mod_throw module~mod_settings->module~mod_io module~mod_cpu_vendor mod_cpu_vendor module~mod_settings->module~mod_cpu_vendor module~mod_sort->module~mod_precision module~mod_cpu_vendor->iso_c_binding

Used By

module~~mod_structures~~UsedByGraph module~mod_structures mod_structures module~mod_abstract_angular_symmetry_function mod_abstract_angular_symmetry_function module~mod_abstract_angular_symmetry_function->module~mod_structures module~mod_abstract_symmetry_function mod_abstract_symmetry_function module~mod_abstract_angular_symmetry_function->module~mod_abstract_symmetry_function module~mod_feature_map_neighborlist mod_feature_map_neighborlist module~mod_abstract_angular_symmetry_function->module~mod_feature_map_neighborlist module~mod_abstract_charge_equilibration mod_abstract_charge_equilibration module~mod_abstract_charge_equilibration->module~mod_structures module~mod_abstract_electrostatics mod_abstract_electrostatics module~mod_abstract_charge_equilibration->module~mod_abstract_electrostatics module~mod_abstract_electrostatics->module~mod_structures module~mod_abstract_radial_symmetry_function mod_abstract_radial_symmetry_function module~mod_abstract_radial_symmetry_function->module~mod_structures module~mod_abstract_radial_symmetry_function->module~mod_abstract_symmetry_function module~mod_abstract_radial_symmetry_function->module~mod_feature_map_neighborlist module~mod_abstract_structure_data_file mod_abstract_structure_data_file module~mod_abstract_structure_data_file->module~mod_structures module~mod_abstract_symmetry_function->module~mod_structures module~mod_feature_map mod_feature_map module~mod_abstract_symmetry_function->module~mod_feature_map module~mod_abstract_symmetry_function->module~mod_feature_map_neighborlist module~mod_electric_field_prefactor mod_electric_field_prefactor module~mod_abstract_symmetry_function->module~mod_electric_field_prefactor module~mod_spin_prefactor mod_spin_prefactor module~mod_abstract_symmetry_function->module~mod_spin_prefactor module~mod_analyse_a_prime_matrix_eigenvalues mod_analyse_a_prime_matrix_eigenvalues module~mod_analyse_a_prime_matrix_eigenvalues->module~mod_structures module~mod_analyse_a_prime_matrix_eigenvalues->module~mod_abstract_electrostatics module~mod_direct_charge_equilibration mod_direct_charge_equilibration module~mod_analyse_a_prime_matrix_eigenvalues->module~mod_direct_charge_equilibration module~mod_pair_electrostatics mod_pair_electrostatics module~mod_analyse_a_prime_matrix_eigenvalues->module~mod_pair_electrostatics module~mod_angular_symmetry_function_3 mod_angular_symmetry_function_3 module~mod_angular_symmetry_function_3->module~mod_structures module~mod_angular_symmetry_function_3->module~mod_abstract_angular_symmetry_function module~mod_angular_symmetry_function_3->module~mod_abstract_symmetry_function module~mod_angular_symmetry_function_3->module~mod_feature_map module~mod_angular_symmetry_function_3->module~mod_feature_map_neighborlist module~mod_angular_symmetry_function_8 mod_angular_symmetry_function_8 module~mod_angular_symmetry_function_8->module~mod_structures module~mod_angular_symmetry_function_8->module~mod_abstract_angular_symmetry_function module~mod_angular_symmetry_function_8->module~mod_abstract_symmetry_function module~mod_angular_symmetry_function_8->module~mod_feature_map module~mod_angular_symmetry_function_8->module~mod_feature_map_neighborlist module~mod_angular_symmetry_function_9 mod_angular_symmetry_function_9 module~mod_angular_symmetry_function_9->module~mod_structures module~mod_angular_symmetry_function_9->module~mod_abstract_angular_symmetry_function module~mod_angular_symmetry_function_9->module~mod_abstract_symmetry_function module~mod_angular_symmetry_function_9->module~mod_feature_map module~mod_angular_symmetry_function_9->module~mod_feature_map_neighborlist module~mod_atomic_descriptor mod_atomic_descriptor module~mod_atomic_descriptor->module~mod_structures module~mod_element mod_element module~mod_atomic_descriptor->module~mod_element module~mod_calc_screening mod_calc_screening module~mod_calc_screening->module~mod_structures module~mod_calc_screening->module~mod_feature_map_neighborlist module~mod_dataloader_file mod_dataloader_file module~mod_dataloader_file->module~mod_structures module~mod_dataloader_file->module~mod_abstract_structure_data_file module~mod_feature_calculator mod_feature_calculator module~mod_dataloader_file->module~mod_feature_calculator module~mod_dataloader_file->module~mod_feature_map_neighborlist module~mod_memory_estimation mod_memory_estimation module~mod_dataloader_file->module~mod_memory_estimation module~mod_dataset_statistics mod_dataset_statistics module~mod_dataset_statistics->module~mod_structures module~mod_dataset_statistics->module~mod_dataloader_file module~mod_dataset_statistics->module~mod_feature_calculator module~mod_training_charge_equilibration mod_training_charge_equilibration module~mod_dataset_statistics->module~mod_training_charge_equilibration module~mod_ee4g_feature_calculator mod_ee4g_feature_calculator module~mod_ee4g_feature_calculator->module~mod_structures module~mod_ee4g_feature_calculator->module~mod_feature_map_neighborlist module~mod_global_feature_calculator mod_global_feature_calculator module~mod_ee4g_feature_calculator->module~mod_global_feature_calculator module~mod_evaluate_4g_single_structure mod_evaluate_4g_single_structure module~mod_evaluate_4g_single_structure->module~mod_structures module~mod_evaluate_4g_single_structure->module~mod_abstract_charge_equilibration module~mod_evaluate_4g_single_structure->module~mod_ee4g_feature_calculator module~mod_evaluate_4g_single_structure->module~mod_feature_calculator module~mod_evaluate_4g_single_structure->module~mod_feature_map_neighborlist module~mod_chain_features mod_chain_features module~mod_evaluate_4g_single_structure->module~mod_chain_features module~mod_feature_calculator->module~mod_structures module~mod_feature_calculator->module~mod_angular_symmetry_function_3 module~mod_feature_calculator->module~mod_angular_symmetry_function_8 module~mod_feature_calculator->module~mod_angular_symmetry_function_9 module~mod_feature_calculator->module~mod_atomic_descriptor module~mod_feature_calculator->module~mod_feature_map module~mod_feature_calculator->module~mod_feature_map_neighborlist module~mod_overlap_matrix mod_overlap_matrix module~mod_feature_calculator->module~mod_overlap_matrix module~mod_radial_symmetry_function_1 mod_radial_symmetry_function_1 module~mod_feature_calculator->module~mod_radial_symmetry_function_1 module~mod_radial_symmetry_function_2 mod_radial_symmetry_function_2 module~mod_feature_calculator->module~mod_radial_symmetry_function_2 module~mod_feature_calculator->module~mod_element module~mod_feature_calculator_statistics mod_feature_calculator_statistics module~mod_feature_calculator_statistics->module~mod_structures module~mod_feature_calculator_statistics->module~mod_feature_calculator module~mod_feature_calculator_statistics->module~mod_feature_map_neighborlist module~mod_scalingdata mod_scalingdata module~mod_feature_calculator_statistics->module~mod_scalingdata module~mod_feature_map->module~mod_structures module~mod_feature_map->module~mod_feature_map_neighborlist module~mod_feature_map_neighborlist->module~mod_structures module~mod_neighborlist mod_neighborlist module~mod_feature_map_neighborlist->module~mod_neighborlist module~mod_feature_map_scaling_all_chunks mod_feature_map_scaling_all_chunks module~mod_feature_map_scaling_all_chunks->module~mod_structures module~mod_feature_map_scaling_all_chunks->module~mod_dataloader_file module~mod_feature_map_scaling_all_chunks->module~mod_ee4g_feature_calculator module~mod_feature_map_scaling_all_chunks->module~mod_feature_calculator module~mod_feature_map_scaling_all_chunks->module~mod_feature_calculator_statistics module~mod_feature_map_scaling_all_chunks->module~mod_global_feature_calculator module~mod_prediction_statistics mod_prediction_statistics module~mod_feature_map_scaling_all_chunks->module~mod_prediction_statistics module~mod_qeq_feature_calculator mod_qeq_feature_calculator module~mod_feature_map_scaling_all_chunks->module~mod_qeq_feature_calculator module~mod_structure_batch_iterator mod_structure_batch_iterator module~mod_feature_map_scaling_all_chunks->module~mod_structure_batch_iterator 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_generic_interface mod_generic_interface module~mod_generic_interface->module~mod_structures module~mod_generic_interface->module~mod_feature_map_neighborlist module~mod_predict_single_structure mod_predict_single_structure module~mod_generic_interface->module~mod_predict_single_structure module~mod_runner_interface mod_runner_interface module~mod_generic_interface->module~mod_runner_interface module~mod_global_feature_calculator->module~mod_structures module~mod_global_feature_calculator->module~mod_training_charge_equilibration module~mod_global_features_helper mod_global_features_helper module~mod_global_features_helper->module~mod_structures module~mod_global_features_helper->module~mod_feature_calculator module~mod_global_features_helper->module~mod_global_feature_calculator module~mod_inputdata mod_inputdata module~mod_inputdata->module~mod_structures module~mod_inputdata->module~mod_abstract_structure_data_file module~mod_lammps_interface mod_lammps_interface module~mod_lammps_interface->module~mod_structures module~mod_lammps_interface->module~mod_feature_map_neighborlist module~mod_lammps_interface->module~mod_runner_interface module~mod_runner_interface_bindings mod_runner_interface_bindings module~mod_lammps_interface->module~mod_runner_interface_bindings module~mod_memory_estimation->module~mod_structures module~mod_memory_estimation->module~mod_feature_calculator module~mod_memory_estimation->module~mod_feature_map_neighborlist module~mod_neighborlist->module~mod_structures module~mod_overlap_matrix->module~mod_structures module~mod_overlap_matrix->module~mod_feature_map module~mod_overlap_matrix->module~mod_feature_map_neighborlist module~mod_post_processing_2g_single_structure mod_post_processing_2g_single_structure module~mod_post_processing_2g_single_structure->module~mod_structures module~mod_post_processing_2g_single_structure->module~mod_feature_calculator module~mod_post_processing_2g_single_structure->module~mod_feature_map_neighborlist module~mod_post_processing_2g_single_structure->module~mod_chain_features module~mod_post_processing_3g_single_structure mod_post_processing_3g_single_structure module~mod_post_processing_3g_single_structure->module~mod_structures module~mod_post_processing_3g_single_structure->module~mod_abstract_electrostatics module~mod_post_processing_3g_single_structure->module~mod_calc_screening module~mod_post_processing_3g_single_structure->module~mod_feature_calculator module~mod_post_processing_3g_single_structure->module~mod_feature_map_neighborlist module~mod_evaluate_electrostatics_3g_single_structure mod_evaluate_electrostatics_3g_single_structure module~mod_post_processing_3g_single_structure->module~mod_evaluate_electrostatics_3g_single_structure module~mod_post_processing_4g_single_structure mod_post_processing_4g_single_structure module~mod_post_processing_4g_single_structure->module~mod_structures module~mod_post_processing_4g_single_structure->module~mod_abstract_charge_equilibration module~mod_post_processing_4g_single_structure->module~mod_calc_screening module~mod_post_processing_4g_single_structure->module~mod_ee4g_feature_calculator module~mod_post_processing_4g_single_structure->module~mod_evaluate_4g_single_structure module~mod_post_processing_4g_single_structure->module~mod_feature_calculator module~mod_post_processing_4g_single_structure->module~mod_feature_map_neighborlist module~mod_post_processing_wrapper_single_structure mod_post_processing_wrapper_single_structure module~mod_post_processing_wrapper_single_structure->module~mod_structures module~mod_post_processing_wrapper_single_structure->module~mod_abstract_charge_equilibration module~mod_post_processing_wrapper_single_structure->module~mod_abstract_electrostatics module~mod_post_processing_wrapper_single_structure->module~mod_ee4g_feature_calculator module~mod_post_processing_wrapper_single_structure->module~mod_evaluate_4g_single_structure module~mod_post_processing_wrapper_single_structure->module~mod_feature_calculator module~mod_post_processing_wrapper_single_structure->module~mod_feature_map_neighborlist module~mod_post_processing_wrapper_single_structure->module~mod_global_features_helper module~mod_post_processing_wrapper_single_structure->module~mod_post_processing_2g_single_structure module~mod_post_processing_wrapper_single_structure->module~mod_post_processing_3g_single_structure module~mod_post_processing_wrapper_single_structure->module~mod_post_processing_4g_single_structure module~mod_store_atomic_property_single_structure mod_store_atomic_property_single_structure module~mod_post_processing_wrapper_single_structure->module~mod_store_atomic_property_single_structure module~mod_two_body mod_two_body module~mod_post_processing_wrapper_single_structure->module~mod_two_body module~mod_calc_atomic_properties mod_calc_atomic_properties module~mod_post_processing_wrapper_single_structure->module~mod_calc_atomic_properties module~mod_hirshfeld_vdw mod_hirshfeld_vdw module~mod_post_processing_wrapper_single_structure->module~mod_hirshfeld_vdw module~mod_post_processing_vdw_hirshfeld_single_structure mod_post_processing_vdw_hirshfeld_single_structure module~mod_post_processing_wrapper_single_structure->module~mod_post_processing_vdw_hirshfeld_single_structure module~mod_precompute_features_all_chunks mod_precompute_features_all_chunks module~mod_precompute_features_all_chunks->module~mod_structures module~mod_precompute_features_all_chunks->module~mod_dataloader_file module~mod_precompute_features_all_chunks->module~mod_feature_calculator module~mod_precompute_features_all_chunks->module~mod_feature_calculator_statistics module~mod_featuredata mod_featuredata module~mod_precompute_features_all_chunks->module~mod_featuredata module~mod_predict_4g_charges_training_qeq_multiple_structures mod_predict_4g_charges_training_qeq_multiple_structures module~mod_predict_4g_charges_training_qeq_multiple_structures->module~mod_structures module~mod_predict_4g_charges_training_qeq_multiple_structures->module~mod_feature_calculator module~mod_predict_4g_charges_training_qeq_multiple_structures->module~mod_feature_map_neighborlist module~mod_predict_4g_charges_training_qeq_multiple_structures->module~mod_structure_batch_iterator module~mod_predict_4g_charges_training_qeq_multiple_structures->module~mod_training_charge_equilibration module~mod_predict_4g_no_force_trick_single_structure mod_predict_4g_no_force_trick_single_structure module~mod_predict_4g_no_force_trick_single_structure->module~mod_structures module~mod_predict_4g_no_force_trick_single_structure->module~mod_feature_calculator module~mod_predict_4g_no_force_trick_single_structure->module~mod_feature_map_neighborlist module~mod_predict_4g_no_force_trick_single_structure->module~mod_global_feature_calculator module~mod_predict_4g_no_force_trick_single_structure->module~mod_global_features_helper module~mod_predict_4g_short_range_training_qeq_single_structure mod_predict_4g_short_range_training_qeq_single_structure module~mod_predict_4g_no_force_trick_single_structure->module~mod_predict_4g_short_range_training_qeq_single_structure module~mod_predict_qeq_feature_calculator_single_structure mod_predict_qeq_feature_calculator_single_structure module~mod_predict_4g_no_force_trick_single_structure->module~mod_predict_qeq_feature_calculator_single_structure module~mod_predict_4g_no_force_trick_single_structure->module~mod_qeq_feature_calculator module~mod_predict_4g_no_force_trick_single_structure->module~mod_calc_atomic_properties module~mod_predict_4g_short_range_training_qeq_multiple_structures mod_predict_4g_short_range_training_qeq_multiple_structures module~mod_predict_4g_short_range_training_qeq_multiple_structures->module~mod_structures module~mod_predict_4g_short_range_training_qeq_multiple_structures->module~mod_feature_calculator module~mod_predict_4g_short_range_training_qeq_multiple_structures->module~mod_feature_map_neighborlist module~mod_predict_4g_short_range_training_qeq_multiple_structures->module~mod_global_feature_calculator module~mod_predict_4g_short_range_training_qeq_multiple_structures->module~mod_global_features_helper module~mod_predict_4g_short_range_training_qeq_multiple_structures->module~mod_predict_4g_short_range_training_qeq_single_structure module~mod_predict_4g_short_range_training_qeq_multiple_structures->module~mod_structure_batch_iterator module~mod_predict_4g_short_range_training_qeq_single_structure->module~mod_structures module~mod_predict_4g_short_range_training_qeq_single_structure->module~mod_feature_calculator module~mod_predict_4g_short_range_training_qeq_single_structure->module~mod_feature_map_neighborlist module~mod_predict_4g_short_range_training_qeq_single_structure->module~mod_global_feature_calculator module~mod_predict_4g_short_range_training_qeq_single_structure->module~mod_post_processing_2g_single_structure module~mod_predict_ee4g_feature_calculator_multiple_structures mod_predict_ee4g_feature_calculator_multiple_structures module~mod_predict_ee4g_feature_calculator_multiple_structures->module~mod_structures module~mod_predict_ee4g_feature_calculator_multiple_structures->module~mod_dataloader_file module~mod_predict_ee4g_feature_calculator_multiple_structures->module~mod_ee4g_feature_calculator module~mod_predict_ee4g_feature_calculator_multiple_structures->module~mod_feature_calculator module~mod_predict_ee4g_feature_calculator_multiple_structures->module~mod_feature_map_neighborlist module~mod_predict_ee4g_feature_calculator_multiple_structures->module~mod_qeq_feature_calculator module~mod_predict_multiple_structures mod_predict_multiple_structures module~mod_predict_multiple_structures->module~mod_structures module~mod_predict_multiple_structures->module~mod_abstract_charge_equilibration module~mod_predict_multiple_structures->module~mod_abstract_electrostatics module~mod_predict_multiple_structures->module~mod_ee4g_feature_calculator module~mod_predict_multiple_structures->module~mod_feature_calculator module~mod_predict_multiple_structures->module~mod_feature_map_neighborlist module~mod_predict_multiple_structures->module~mod_post_processing_wrapper_single_structure module~mod_predict_multiple_structures->module~mod_store_atomic_property_single_structure module~mod_predict_multiple_structures->module~mod_structure_batch_iterator module~mod_predict_multiple_structures->module~mod_two_body module~mod_predict_multiple_structures->module~mod_hirshfeld_vdw module~mod_predict_multiple_structures->module~mod_pair_electrostatics module~mod_predict_qeq_feature_calculator_multiple_structures mod_predict_qeq_feature_calculator_multiple_structures module~mod_predict_qeq_feature_calculator_multiple_structures->module~mod_structures module~mod_predict_qeq_feature_calculator_multiple_structures->module~mod_dataloader_file module~mod_predict_qeq_feature_calculator_multiple_structures->module~mod_feature_calculator module~mod_predict_qeq_feature_calculator_multiple_structures->module~mod_feature_map_neighborlist module~mod_predict_qeq_feature_calculator_multiple_structures->module~mod_predict_qeq_feature_calculator_single_structure module~mod_predict_qeq_feature_calculator_multiple_structures->module~mod_qeq_feature_calculator module~mod_predict_qeq_feature_calculator_multiple_structures->module~mod_structure_batch_iterator module~mod_predict_qeq_feature_calculator_single_structure->module~mod_structures module~mod_predict_qeq_feature_calculator_single_structure->module~mod_calc_screening module~mod_predict_qeq_feature_calculator_single_structure->module~mod_feature_calculator module~mod_predict_qeq_feature_calculator_single_structure->module~mod_feature_map_neighborlist module~mod_predict_qeq_feature_calculator_single_structure->module~mod_qeq_feature_calculator module~mod_predict_qeq_feature_calculator_single_structure->module~mod_training_charge_equilibration module~mod_predict_qeq_feature_calculator_single_structure->module~mod_chain_features module~mod_predict_single_structure->module~mod_structures module~mod_predict_single_structure->module~mod_abstract_charge_equilibration module~mod_predict_single_structure->module~mod_abstract_electrostatics module~mod_predict_single_structure->module~mod_ee4g_feature_calculator module~mod_predict_single_structure->module~mod_feature_calculator module~mod_predict_single_structure->module~mod_feature_map_neighborlist module~mod_predict_single_structure->module~mod_post_processing_wrapper_single_structure module~mod_predict_single_structure->module~mod_two_body module~mod_predict_single_structure->module~mod_calc_atomic_properties module~mod_predict_single_structure->module~mod_hirshfeld_vdw module~mod_prediction_statistics->module~mod_structures module~mod_prediction_statistics->module~mod_feature_calculator module~mod_prediction_statistics->module~mod_feature_map_neighborlist module~mod_prediction_statistics->module~mod_calc_atomic_properties module~mod_qeq_feature_calculator->module~mod_structures module~mod_qeq_feature_calculator->module~mod_global_feature_calculator module~mod_qeq_feature_calculator->module~mod_training_charge_equilibration module~mod_radial_symmetry_function_1->module~mod_structures module~mod_radial_symmetry_function_1->module~mod_abstract_radial_symmetry_function module~mod_radial_symmetry_function_1->module~mod_feature_map module~mod_radial_symmetry_function_1->module~mod_feature_map_neighborlist module~mod_radial_symmetry_function_2->module~mod_structures module~mod_radial_symmetry_function_2->module~mod_abstract_radial_symmetry_function module~mod_radial_symmetry_function_2->module~mod_abstract_symmetry_function module~mod_radial_symmetry_function_2->module~mod_feature_map module~mod_radial_symmetry_function_2->module~mod_feature_map_neighborlist module~mod_runner_interface->module~mod_structures module~mod_runner_interface->module~mod_abstract_charge_equilibration module~mod_runner_interface->module~mod_abstract_electrostatics module~mod_runner_interface->module~mod_ee4g_feature_calculator module~mod_runner_interface->module~mod_feature_calculator module~mod_runner_interface->module~mod_feature_map_neighborlist module~mod_runner_interface->module~mod_two_body module~mod_runner_interface->module~mod_hirshfeld_vdw module~mod_store_atomic_property_single_structure->module~mod_structures module~mod_structure_batch_iterator->module~mod_structures module~mod_structure_batch_iterator->module~mod_feature_calculator module~mod_structure_batch_iterator->module~mod_feature_map_neighborlist module~mod_structure_batch_iterator->module~mod_global_feature_calculator module~mod_structure_batch_iterator->module~mod_global_features_helper module~mod_structure_batch_iterator->module~mod_calc_atomic_properties module~mod_train_atomic_property_multiple_atoms mod_train_atomic_property_multiple_atoms module~mod_train_atomic_property_multiple_atoms->module~mod_structures module~mod_train_atomic_property_multiple_atoms->module~mod_feature_calculator module~mod_train_energy_multiple_structures mod_train_energy_multiple_structures module~mod_train_energy_multiple_structures->module~mod_structures module~mod_initialize mod_initialize module~mod_train_energy_multiple_structures->module~mod_initialize module~mod_train_forces_multiple_structures mod_train_forces_multiple_structures module~mod_train_forces_multiple_structures->module~mod_structures module~mod_train_forces_multiple_structures->module~mod_train_energy_multiple_structures module~mod_train_forces_multiple_structures->module~mod_initialize module~mod_train_loop_4g_charges mod_train_loop_4g_charges module~mod_train_loop_4g_charges->module~mod_structures module~mod_train_loop_4g_charges->module~mod_dataloader_file module~mod_train_loop_4g_charges->module~mod_feature_calculator module~mod_train_loop_4g_charges->module~mod_training_charge_equilibration module~mod_cost_calculator mod_cost_calculator module~mod_train_loop_4g_charges->module~mod_cost_calculator module~mod_train_loop_4g_charges->module~mod_initialize module~mod_output_files_and_cost_4g_charges mod_output_files_and_cost_4g_charges module~mod_train_loop_4g_charges->module~mod_output_files_and_cost_4g_charges module~mod_train_4g_atomic_charges_structure_batch mod_train_4g_atomic_charges_structure_batch module~mod_train_loop_4g_charges->module~mod_train_4g_atomic_charges_structure_batch module~mod_train_loop_atomic_property mod_train_loop_atomic_property module~mod_train_loop_atomic_property->module~mod_structures module~mod_train_loop_atomic_property->module~mod_dataloader_file module~mod_train_loop_atomic_property->module~mod_feature_calculator module~mod_train_loop_atomic_property->module~mod_train_atomic_property_multiple_atoms module~mod_train_loop_atomic_property->module~mod_cost_calculator module~mod_train_loop_atomic_property->module~mod_initialize module~mod_output_files_and_cost mod_output_files_and_cost module~mod_train_loop_atomic_property->module~mod_output_files_and_cost module~mod_train_loop_short_range mod_train_loop_short_range module~mod_train_loop_short_range->module~mod_structures module~mod_train_loop_short_range->module~mod_abstract_charge_equilibration module~mod_train_loop_short_range->module~mod_abstract_electrostatics module~mod_train_loop_short_range->module~mod_dataloader_file module~mod_train_loop_short_range->module~mod_ee4g_feature_calculator module~mod_train_loop_short_range->module~mod_feature_calculator module~mod_train_loop_short_range->module~mod_global_feature_calculator module~mod_train_loop_short_range->module~mod_global_features_helper 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_qeq_feature_calculator module~mod_train_loop_short_range->module~mod_train_energy_multiple_structures module~mod_train_loop_short_range->module~mod_train_forces_multiple_structures module~mod_train_loop_short_range->module~mod_cost_calculator module~mod_train_loop_short_range->module~mod_initialize module~mod_train_loop_short_range->module~mod_output_files_and_cost module~mod_output_files_and_cost_4g_short_range mod_output_files_and_cost_4g_short_range module~mod_train_loop_short_range->module~mod_output_files_and_cost_4g_short_range module~mod_training_charge_equilibration->module~mod_structures module~mod_training_charge_equilibration->module~mod_abstract_electrostatics module~mod_ewald_summation mod_ewald_summation module~mod_training_charge_equilibration->module~mod_ewald_summation module~mod_training_charge_equilibration->module~mod_pair_electrostatics module~mod_two_body->module~mod_structures module~mod_two_body->module~mod_dataloader_file module~mod_two_body->module~mod_feature_map_neighborlist module~mod_abstract_iterative_charge_equilibration mod_abstract_iterative_charge_equilibration module~mod_abstract_iterative_charge_equilibration->module~mod_abstract_charge_equilibration module~mod_abstract_iterative_charge_equilibration->module~mod_abstract_electrostatics module~mod_abstract_iterative_charge_equilibration->module~mod_pair_electrostatics module~mod_calc_atomic_properties->module~mod_feature_calculator module~mod_calc_atomic_properties->module~mod_feature_map_neighborlist module~mod_calculate_coulomb_matrix mod_calculate_coulomb_matrix module~mod_calculate_coulomb_matrix->module~mod_dataloader_file module~mod_calculate_coulomb_matrix->module~mod_training_charge_equilibration module~mod_chain_features->module~mod_feature_calculator module~mod_chain_features->module~mod_feature_map_neighborlist 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_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_dataset_statistics_chi_all_chunks->module~mod_feature_calculator module~mod_dataset_statistics_chi_all_chunks->module~mod_training_charge_equilibration module~mod_direct_charge_equilibration->module~mod_abstract_charge_equilibration module~mod_direct_charge_equilibration->module~mod_abstract_electrostatics module~mod_electric_field_prefactor->module~mod_feature_map_neighborlist module~mod_element->module~mod_angular_symmetry_function_3 module~mod_element->module~mod_angular_symmetry_function_9 module~mod_element->module~mod_feature_map module~mod_element->module~mod_radial_symmetry_function_2 module~mod_enforce_reading mod_enforce_reading module~mod_enforce_reading->module~mod_feature_calculator module~mod_enforce_reading->module~mod_global_feature_calculator module~mod_evaluate_electrostatics_3g_single_structure->module~mod_abstract_electrostatics module~mod_evaluate_electrostatics_3g_single_structure->module~mod_feature_calculator module~mod_evaluate_electrostatics_3g_single_structure->module~mod_feature_map_neighborlist module~mod_evaluate_electrostatics_3g_single_structure->module~mod_chain_features module~mod_ewald_summation->module~mod_abstract_electrostatics module~mod_ewald_summation->module~mod_pair_electrostatics module~mod_feature_calc_interface mod_feature_calc_interface module~mod_feature_calc_interface->module~mod_generic_interface module~mod_feature_calc_interface->module~mod_runner_interface module~mod_featuredata->module~mod_feature_calculator module~mod_featuredata->module~mod_element module~mod_hirshfeld_vdw->module~mod_feature_map_neighborlist module~mod_initialize->module~mod_abstract_charge_equilibration module~mod_initialize->module~mod_abstract_electrostatics module~mod_initialize->module~mod_ee4g_feature_calculator module~mod_initialize->module~mod_feature_calculator module~mod_initialize->module~mod_qeq_feature_calculator module~mod_initialize->module~mod_two_body module~mod_initialize->module~mod_direct_charge_equilibration module~mod_initialize->module~mod_element module~mod_initialize->module~mod_ewald_summation module~mod_initialize->module~mod_hirshfeld_vdw module~mod_initialize->module~mod_pair_electrostatics module~mod_pppm mod_pppm module~mod_initialize->module~mod_pppm module~mod_pw mod_pw module~mod_initialize->module~mod_pw module~mod_iterative_charge_equilibration_cg mod_iterative_charge_equilibration_cg module~mod_initialize->module~mod_iterative_charge_equilibration_cg module~mod_iterative_charge_equilibration_sqnm mod_iterative_charge_equilibration_sqnm module~mod_initialize->module~mod_iterative_charge_equilibration_sqnm module~mod_output_files_and_cost->module~mod_abstract_charge_equilibration module~mod_output_files_and_cost->module~mod_abstract_electrostatics module~mod_output_files_and_cost->module~mod_dataloader_file module~mod_output_files_and_cost->module~mod_ee4g_feature_calculator module~mod_output_files_and_cost->module~mod_feature_calculator module~mod_output_files_and_cost->module~mod_predict_multiple_structures module~mod_output_files_and_cost->module~mod_cost_calculator module~mod_output_files_and_cost_4g_charges->module~mod_dataloader_file module~mod_output_files_and_cost_4g_charges->module~mod_feature_calculator module~mod_output_files_and_cost_4g_charges->module~mod_predict_4g_charges_training_qeq_multiple_structures module~mod_output_files_and_cost_4g_charges->module~mod_training_charge_equilibration module~mod_output_files_and_cost_4g_charges->module~mod_cost_calculator module~mod_output_files_and_cost_4g_short_range->module~mod_dataloader_file module~mod_output_files_and_cost_4g_short_range->module~mod_feature_calculator module~mod_output_files_and_cost_4g_short_range->module~mod_global_feature_calculator module~mod_output_files_and_cost_4g_short_range->module~mod_predict_4g_short_range_training_qeq_multiple_structures module~mod_output_files_and_cost_4g_short_range->module~mod_predict_qeq_feature_calculator_multiple_structures module~mod_output_files_and_cost_4g_short_range->module~mod_cost_calculator module~mod_pair_electrostatics->module~mod_abstract_electrostatics module~mod_post_processing_vdw_hirshfeld_single_structure->module~mod_feature_calculator module~mod_post_processing_vdw_hirshfeld_single_structure->module~mod_feature_map_neighborlist module~mod_post_processing_vdw_hirshfeld_single_structure->module~mod_chain_features module~mod_post_processing_vdw_hirshfeld_single_structure->module~mod_hirshfeld_vdw module~mod_pppm->module~mod_abstract_electrostatics module~mod_pppm->module~mod_ewald_summation module~mod_pppm->module~mod_pair_electrostatics module~mod_pppm->module~mod_pw 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_coulomb_matrix_all_chunks->module~mod_feature_calculator module~mod_precalc_coulomb_matrix_all_chunks->module~mod_predict_4g_charges_training_qeq_multiple_structures module~mod_precalc_coulomb_matrix_all_chunks->module~mod_training_charge_equilibration module~mod_precalc_nl_deriv_features_single_chunk->module~mod_dataloader_file module~mod_precalc_nl_deriv_features_single_chunk->module~mod_feature_calculator module~mod_precalc_nl_deriv_features_single_chunk->module~mod_memory_estimation 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_precompute_global_features_all_chunks->module~mod_ee4g_feature_calculator module~mod_precompute_global_features_all_chunks->module~mod_feature_calculator module~mod_precompute_global_features_all_chunks->module~mod_feature_calculator_statistics 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_precompute_global_features_all_chunks->module~mod_qeq_feature_calculator module~mod_predict_all_chunks mod_predict_all_chunks module~mod_predict_all_chunks->module~mod_abstract_charge_equilibration module~mod_predict_all_chunks->module~mod_abstract_electrostatics module~mod_predict_all_chunks->module~mod_dataloader_file module~mod_predict_all_chunks->module~mod_feature_calculator module~mod_predict_all_chunks->module~mod_predict_multiple_structures module~mod_predict_all_chunks->module~mod_two_body module~mod_predict_all_chunks->module~mod_hirshfeld_vdw module~mod_predict_mode mod_predict_mode module~mod_predict_mode->module~mod_abstract_charge_equilibration module~mod_predict_mode->module~mod_abstract_electrostatics module~mod_predict_mode->module~mod_dataloader_file module~mod_predict_mode->module~mod_ee4g_feature_calculator module~mod_predict_mode->module~mod_feature_calculator module~mod_predict_mode->module~mod_feature_calculator_statistics module~mod_predict_mode->module~mod_predict_multiple_structures module~mod_predict_mode->module~mod_qeq_feature_calculator module~mod_predict_mode->module~mod_two_body module~mod_predict_mode->module~mod_enforce_reading module~mod_predict_mode->module~mod_hirshfeld_vdw module~mod_predict_mode->module~mod_initialize module~mod_write_outfiles mod_write_outfiles module~mod_predict_mode->module~mod_write_outfiles module~mod_pw->module~mod_abstract_electrostatics module~mod_runner_interface_bindings->module~mod_calc_screening module~mod_runner_interface_bindings->module~mod_evaluate_4g_single_structure module~mod_runner_interface_bindings->module~mod_feature_calculator module~mod_runner_interface_bindings->module~mod_feature_calculator_statistics module~mod_runner_interface_bindings->module~mod_global_features_helper module~mod_runner_interface_bindings->module~mod_post_processing_2g_single_structure module~mod_runner_interface_bindings->module~mod_qeq_feature_calculator module~mod_runner_interface_bindings->module~mod_runner_interface module~mod_runner_interface_bindings->module~mod_two_body module~mod_runner_interface_bindings->module~mod_calc_atomic_properties module~mod_runner_interface_bindings->module~mod_enforce_reading module~mod_runner_interface_bindings->module~mod_evaluate_electrostatics_3g_single_structure module~mod_runner_interface_bindings->module~mod_hirshfeld_vdw module~mod_runner_interface_bindings->module~mod_initialize module~mod_runner_interface_bindings->module~mod_post_processing_vdw_hirshfeld_single_structure module~mod_scalingdata->module~mod_feature_calculator module~mod_scalingdata->module~mod_element module~mod_spin_prefactor->module~mod_feature_map_neighborlist module~mod_train_4g_atomic_charges_structure_batch->module~mod_dataloader_file module~mod_train_4g_atomic_charges_structure_batch->module~mod_feature_calculator module~mod_train_4g_atomic_charges_structure_batch->module~mod_training_charge_equilibration module~mod_train_mode mod_train_mode module~mod_train_mode->module~mod_abstract_charge_equilibration module~mod_train_mode->module~mod_abstract_electrostatics module~mod_train_mode->module~mod_dataloader_file module~mod_train_mode->module~mod_dataset_statistics module~mod_train_mode->module~mod_ee4g_feature_calculator module~mod_train_mode->module~mod_feature_calculator module~mod_train_mode->module~mod_feature_calculator_statistics module~mod_train_mode->module~mod_feature_map_scaling_all_chunks module~mod_train_mode->module~mod_global_feature_calculator module~mod_train_mode->module~mod_predict_4g_charges_training_qeq_multiple_structures 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_qeq_feature_calculator 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_training_charge_equilibration module~mod_train_mode->module~mod_two_body module~mod_train_mode->module~mod_dataset_statistics_chi_all_chunks module~mod_train_mode->module~mod_initialize 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_write_outfiles_training module~smod_atom_overlap smod_atom_overlap module~smod_atom_overlap->module~mod_overlap_matrix module~smod_cache smod_cache module~smod_cache->module~mod_overlap_matrix module~smod_constructor smod_constructor module~smod_constructor->module~mod_overlap_matrix module~smod_eigenval_and_vectors smod_eigenval_and_vectors module~smod_eigenval_and_vectors->module~mod_overlap_matrix module~smod_first_derivative smod_first_derivative module~smod_first_derivative->module~mod_overlap_matrix module~smod_original smod_original module~smod_original->module~mod_overlap_matrix module~smod_smooth smod_smooth module~smod_smooth->module~mod_overlap_matrix program~runner RuNNer program~runner->module~mod_abstract_charge_equilibration program~runner->module~mod_abstract_electrostatics program~runner->module~mod_dataloader_file program~runner->module~mod_ee4g_feature_calculator program~runner->module~mod_feature_calculator program~runner->module~mod_inputdata program~runner->module~mod_precompute_features_all_chunks program~runner->module~mod_qeq_feature_calculator program~runner->module~mod_two_body program~runner->module~mod_calculate_coulomb_matrix program~runner->module~mod_hirshfeld_vdw program~runner->module~mod_initialize program~runner->module~mod_precompute_global_features_all_chunks program~runner->module~mod_predict_mode program~runner->module~mod_train_mode module~mod_iterative_charge_equilibration_cg->module~mod_abstract_iterative_charge_equilibration module~mod_iterative_charge_equilibration_sqnm->module~mod_abstract_iterative_charge_equilibration module~mod_write_outfiles->module~mod_initialize module~mod_write_outfiles_training->module~mod_write_outfiles

Derived Types Summary

Name Description
Structure Type collecting data of all atoms of a structure.

Procedures Summary

Name Type Description
constructor_without_positions Function Initialize a new objects of type Structure. Initializes variables and arrays to 0.0_DP or...
constructor_with_positions_and_atomic_numbers Function
constructor_with_positions_and_symbols Function
get_relative_positions Function
get_volume Function
calc_recip_lattice Function Calculate the reciprocal lattice from the real-space lattice.
stress_to_lattice_gradients Function computes the postive gradient, dE/dlat(i,j) from the stress tensor
get_stress_from_lattice_derivatives Function computes stress tensor from dE/dlat(i,j)
elemental_property_to_atomic_property Function Convert an elemental property to an atomic property. author: Moritz Gubler
atomic_to_elemental_property Function Convert an atomic property to an elemental property. This assumes that the elemental...
get_id_on_process_atoms Function Indexes the ids on process of the atoms in ascending order.
get_id_on_process_across_chunks_atoms Function Indexes the ids on process of the atoms in ascending order.
get_id_on_process_across_chunks_non_continuous_atoms Function Indexes the ids on process of the atoms in ascending order.
get_id_on_process_local_atoms Function Indexes the ids on process of the local atoms in ascending order.
get_id_atoms Function Indexes the ids of the atoms in ascending order.
get_id_local_atoms Function Indexes the ids of the local atoms in ascending order.
sum_atomic_energies Function Remove atom energies author: Alea Tokita, Moritz R. Schaefer, Alexander Knoll
reset_structure Subroutine Reset the structure to a blank state.
trim_structure Subroutine Decrease the size of the internal arrays to exactly fit self%num_atoms. This is used during...
move_atoms_into_cell Subroutine Wrapping of atoms outside of box over periodic boundary conditions for periodic structuctures.
update_positions_and_lattice Subroutine
set_relative_positions Subroutine
distribute Subroutine Distributes a single structure from root to process specified by destination (rank + 1) using...
make_supercell Subroutine
set_all_ids_to_value Subroutine
concatenate_atom_id_on_process_without_mapping Subroutine Build continuous arrays of the ids on process and atomic numbers for a given list of structures.
concatenate_atom_id_on_process_across_chunks Subroutine Build continuous arrays of the ids on process and atomic numbers for a given list of structures.
concatenate_atom_id_on_process_with_mapping Subroutine Build continuous arrays of the ids on process and atomic numbers for a given list of structures.
concatenate_atom_id_on_process_with_double_mapping Subroutine Build continuous arrays of the ids on process and atomic numbers for a given list of structures.

Derived Types Details

type Structure

Type collecting data of all atoms of a structure.

Components

  • id_on_process : integer– The index of the structure on the MPI process within the current chunk.
  • id : integer– The index of the structure in the loaded dataset.
  • id_in_file : integer– The position of the structure in the input.data file. Due to thresholds, this may be different from `id`.
  • id_on_process_across_chunks : integer– The index of the structure on the MPI process over all chunks.
  • id_on_process_across_chunks_non_continuous : integer– The index of the structure on the MPI process over all chunks. This is the same as `id_on_process_across_chunks` on all MPI processes except rank 0. On rank 0, it is non-continuous, so we can index into the correct slice of results for each chunk of structures.
  • current_id_in_batch : integer– The index of the structure in the current active batch of structures. Only set during training not during prediction.
  • atom_offset : integer– Number of atoms in all structures loaded from the input file up to this structure (see `id` vs `id_in_file`). Marks the start of this structures' atom indices in a continuous list of structures loaded from file.
  • atom_offset_in_file : integer– Number of atoms in all structures in the input file up to this structure (see `id` vs `id_in_file`). Marks the start of this structures' atom indices in a continuous list of structures read from file.
  • atom_offset_on_process : integer– Same as `id_on_process`, but marks the start of the atom indices.
  • atom_offset_on_process_across_chunks : integer– Same as `id_on_process_across_chunks`, but marks the start of the atom indices.
  • atom_offset_on_process_across_chunks_non_continuous : integer– Same as `id_on_process_across_chunks_non_continuous`, but marks the start of the atom indices.
  • atomic_numbers : integer (dim: (:))
  • xyz : real(DP) (dim: (:,:))
  • atomic_spin : real(DP) (dim: (:))
  • num_atoms : integer– The total number of atoms in the structure (`len(atoms)`).
  • num_atoms_element : integer (dim: (MAX_ELEM_NUM))– The number of atoms per element in the structure.
  • num_local_atoms : integer– The number of true atoms that reside on this process. When interfacing with MD codes, we often also have ghost atoms in the list of atoms. Ghost atoms are required for the calculation of neighbor lists, but their contributions to energy, forces, stress, etc. are computed on other MPI processes.
  • lattice : real(DP) (dim: (3,3))– lattice(:, i) is the ith lattice vector.
  • total_charge : real(DP)– The total charge of the structure
  • efield_vec : real(DP) (dim: (3))– The electric field vector acting on the structure.
  • lperiodic : logical
  • lefield_vec : logical

Type-Bound Procedures

Name Attributes Binding
reset public ⇒ reset_structure
trim public ⇒ trim_structure
move_atoms_into_cell public ⇒ move_atoms_into_cell
update_positions_and_lattice public ⇒ update_positions_and_lattice
get_relative_positions public ⇒ get_relative_positions
set_relative_positions public ⇒ set_relative_positions
get_volume public ⇒ get_volume
distribute public ⇒ distribute
make_supercell public ⇒ make_supercell
calc_recip_lattice public ⇒ calc_recip_lattice
stress_to_lattice_gradients public ⇒ stress_to_lattice_gradients
get_stress_from_lattice_derivatives public ⇒ get_stress_from_lattice_derivatives
elemental_property_to_atomic_property public ⇒ elemental_property_to_atomic_property
atomic_to_elemental_property public ⇒ atomic_to_elemental_property
sum_atomic_energies public ⇒ sum_atomic_energies
get_id_on_process_atoms public ⇒ get_id_on_process_atoms
get_id_on_process_local_atoms public ⇒ get_id_on_process_local_atoms
get_id_on_process_across_chunks_atoms public ⇒ get_id_on_process_across_chunks_atoms
get_id_on_process_across_chunks_non_continuous_atoms public ⇒ get_id_on_process_across_chunks_non_continuous_atoms
get_id_atoms public ⇒ get_id_atoms
get_id_local_atoms public ⇒ get_id_local_atoms
set_all_ids_to_value public ⇒ set_all_ids_to_value

Inherited By

type~~structure~~InheritedByGraph type~structure Structure type~atomicdescriptor AtomicDescriptor type~atomicdescriptor->type~structure structure_ptr type~filedataloader FileDataLoader type~filedataloader->type~structure structures type~runnerinterface RuNNerInterface type~runnerinterface->type~structure struct type~featurecalculator FeatureCalculator type~runnerinterface->type~featurecalculator feature_calculators type~featurecalculator->type~atomicdescriptor atomic_list

Interface Details

interface Structure

interface concatenate_atom_id_on_process

Procedure Details

function constructor_without_positions

function constructor_without_positions( &
    num_atoms &
)

Initialize a new objects of type Structure.

Initializes variables and arrays to 0.0_DP or .false. Needs number of atoms and number of elements as arguments to allocate the atom and element list.

Arguments

  • num_atoms : integer [in]

Called By

proc~~constructor_without_positions~~CalledByGraph proc~constructor_without_positions mod_structures::constructor_without_positions interface~structure mod_structures::Structure interface~structure->proc~constructor_without_positions proc~constructor_with_positions_and_atomic_numbers mod_structures::constructor_with_positions_and_atomic_numbers interface~structure->proc~constructor_with_positions_and_atomic_numbers proc~constructor_with_positions_and_atomic_numbers->proc~constructor_without_positions

function constructor_with_positions_and_atomic_numbers

function constructor_with_positions_and_atomic_numbers( &
    num_atoms, &
    positions, &
    atomic_numbers, &
    lattice, &
    total_charge &
)

Arguments

  • num_atoms : integer [in]
  • positions : real(DP) (dim: (3,num_atoms)) [in]
  • atomic_numbers : integer (dim: (num_atoms)) [in]
  • lattice : real(DP) (dim: (3,3)) [in]
  • total_charge : real(DP) [in]

Called By

proc~~constructor_with_positions_and_atomic_numbers~~CalledByGraph proc~constructor_with_positions_and_atomic_numbers mod_structures::constructor_with_positions_and_atomic_numbers interface~structure mod_structures::Structure interface~structure->proc~constructor_with_positions_and_atomic_numbers

function constructor_with_positions_and_symbols

function constructor_with_positions_and_symbols( &
    num_atoms, &
    positions, &
    elements, &
    lattice, &
    total_charge &
)

Arguments

  • num_atoms : integer [in]
  • positions : real(DP) (dim: (3,num_atoms)) [in]
  • elements : character (dim: (num_atoms)) [in]
  • lattice : real(DP) (dim: (3,3)) [in]
  • total_charge : real(DP) [in]

Called By

proc~~constructor_with_positions_and_symbols~~CalledByGraph proc~constructor_with_positions_and_symbols mod_structures::constructor_with_positions_and_symbols interface~structure mod_structures::Structure interface~structure->proc~constructor_with_positions_and_symbols

function get_relative_positions

function get_relative_positions( &
    self &
)

Arguments

Called By

proc~~get_relative_positions~~CalledByGraph proc~get_relative_positions mod_structures::Structure%get_relative_positions proc~move_atoms_into_cell mod_structures::Structure%move_atoms_into_cell proc~move_atoms_into_cell->proc~get_relative_positions proc~numerical_stress_electrostatic mod_abstract_electrostatics::AbstractElectrostaticsCalculator%numerical_stress_electrostatic proc~numerical_stress_electrostatic->proc~get_relative_positions proc~build_structure_neighborlists_feature_calculators mod_generic_interface::build_structure_neighborlists_feature_calculators proc~build_structure_neighborlists_feature_calculators->proc~move_atoms_into_cell proc~count_structures_and_atoms_inputdata mod_inputdata::InputData%count_structures_and_atoms_inputdata proc~count_structures_and_atoms_inputdata->proc~move_atoms_into_cell proc~read_next_structure_inputdata mod_inputdata::InputData%read_next_structure_inputdata proc~read_next_structure_inputdata->proc~move_atoms_into_cell proc~constructor~3 mod_inputdata::constructor proc~constructor~3->proc~count_structures_and_atoms_inputdata proc~predict_structure_interface mod_generic_interface::predict_structure_interface proc~predict_structure_interface->proc~build_structure_neighborlists_feature_calculators proc~prepare_feature_calculator_get_neighbor_list_info mod_feature_calc_interface::prepare_feature_calculator_get_neighbor_list_info proc~prepare_feature_calculator_get_neighbor_list_info->proc~build_structure_neighborlists_feature_calculators proc~read_structures_inputdata mod_inputdata::InputData%read_structures_inputdata proc~read_structures_inputdata->proc~read_next_structure_inputdata interface~inputdata mod_inputdata::InputData interface~inputdata->proc~constructor~3

function get_volume

function get_volume( &
    self &
)

Arguments

Called By

proc~~get_volume~~CalledByGraph proc~get_volume mod_structures::Structure%get_volume proc~post_processing_3g_single_structure_electrostatics mod_post_processing_3g_single_structure::post_processing_3g_single_structure_electrostatics proc~post_processing_3g_single_structure_electrostatics->proc~get_volume proc~post_processing_wrapper_single_structure mod_post_processing_wrapper_single_structure::post_processing_wrapper_single_structure proc~post_processing_wrapper_single_structure->proc~get_volume proc~post_processing_wrapper_single_structure->proc~post_processing_3g_single_structure_electrostatics proc~store_meta_information_single_structure mod_store_atomic_property_single_structure::store_meta_information_single_structure proc~post_processing_wrapper_single_structure->proc~store_meta_information_single_structure proc~store_meta_information_single_structure->proc~get_volume proc~stress_to_lattice_gradients mod_structures::Structure%stress_to_lattice_gradients proc~stress_to_lattice_gradients->proc~get_volume proc~predict_multiple_structures mod_predict_multiple_structures::predict_multiple_structures proc~predict_multiple_structures->proc~post_processing_wrapper_single_structure proc~predict_multiple_structures->proc~store_meta_information_single_structure proc~predict_single_structure mod_predict_single_structure::predict_single_structure proc~predict_single_structure->proc~post_processing_wrapper_single_structure proc~output_files_and_cost mod_output_files_and_cost::output_files_and_cost proc~output_files_and_cost->proc~predict_multiple_structures proc~predict_all_chunks mod_predict_all_chunks::predict_all_chunks proc~predict_all_chunks->proc~predict_multiple_structures proc~predict_mode mod_predict_mode::predict_mode proc~predict_mode->proc~predict_multiple_structures proc~predict_structure_interface mod_generic_interface::predict_structure_interface proc~predict_structure_interface->proc~predict_single_structure proc~train_loop_atomic_property mod_train_loop_atomic_property::train_loop_atomic_property proc~train_loop_atomic_property->proc~output_files_and_cost proc~train_loop_short_range mod_train_loop_short_range::train_loop_short_range proc~train_loop_short_range->proc~output_files_and_cost proc~train_mode mod_train_mode::train_mode proc~train_mode->proc~predict_all_chunks proc~train_mode->proc~train_loop_atomic_property proc~train_mode->proc~train_loop_short_range program~runner RuNNer program~runner->proc~predict_mode program~runner->proc~train_mode

function calc_recip_lattice

function calc_recip_lattice( &
    self &
)

Calculate the reciprocal lattice from the real-space lattice.

Arguments

function stress_to_lattice_gradients

function stress_to_lattice_gradients( &
    self, &
    stress &
)

computes the postive gradient, dE/dlat(i,j) from the stress tensor

Arguments

  • self : class(Structure) [in]
  • stress : real(DP) (dim: (3,3)) [in]

function get_stress_from_lattice_derivatives

function get_stress_from_lattice_derivatives( &
    self, &
    dedlat &
)

computes stress tensor from dE/dlat(i,j)

Arguments

  • self : class(Structure) [in]
  • dedlat : real(DP) (dim: (3,3)) [in]

Called By

proc~~get_stress_from_lattice_derivatives~~CalledByGraph proc~get_stress_from_lattice_derivatives mod_structures::Structure%get_stress_from_lattice_derivatives proc~numerical_stress_electrostatic mod_abstract_electrostatics::AbstractElectrostaticsCalculator%numerical_stress_electrostatic proc~numerical_stress_electrostatic->proc~get_stress_from_lattice_derivatives

function elemental_property_to_atomic_property

function elemental_property_to_atomic_property( &
    self, &
    elemental_property &
)

Convert an elemental property to an atomic property. author: Moritz Gubler

Arguments

  • self : class(Structure) [in]
  • elemental_property : real(DP) (dim: (MAX_ELEM_NUM)) [in]

Called By

proc~~elemental_property_to_atomic_property~~CalledByGraph proc~elemental_property_to_atomic_property mod_structures::Structure%elemental_property_to_atomic_property proc~predict_4g_no_force_trick_single_structure mod_predict_4g_no_force_trick_single_structure::predict_4g_no_force_trick_single_structure proc~predict_4g_no_force_trick_single_structure->proc~elemental_property_to_atomic_property proc~runner_interface_calc_screening mod_runner_interface_bindings::runner_interface_calc_screening proc~runner_interface_calc_screening->proc~elemental_property_to_atomic_property

function atomic_to_elemental_property

function atomic_to_elemental_property( &
    self, &
    atomic_property &
)

Convert an atomic property to an elemental property.

This assumes that the elemental information is the same for all atoms of that element. Warning: Not all elements will be set, since the information is not there author: Moritz Gubler

Arguments

  • self : class(Structure) [in]
  • atomic_property : real(DP) (dim: (self%num_atoms)) [in]– Atomic property that should be transformed to elemental property

function get_id_on_process_atoms

function get_id_on_process_atoms( &
    self &
)

Indexes the ids on process of the atoms in ascending order.

Arguments

function get_id_on_process_across_chunks_atoms

function get_id_on_process_across_chunks_atoms( &
    self &
)

Indexes the ids on process of the atoms in ascending order.

Arguments

function get_id_on_process_across_chunks_non_continuous_atoms

function get_id_on_process_across_chunks_non_continuous_atoms( &
    self &
)

Indexes the ids on process of the atoms in ascending order.

Arguments

function get_id_on_process_local_atoms

function get_id_on_process_local_atoms( &
    self &
)

Indexes the ids on process of the local atoms in ascending order.

Arguments

Called By

proc~~get_id_on_process_local_atoms~~CalledByGraph proc~get_id_on_process_local_atoms mod_structures::Structure%get_id_on_process_local_atoms proc~post_processing_wrapper_single_structure mod_post_processing_wrapper_single_structure::post_processing_wrapper_single_structure proc~post_processing_wrapper_single_structure->proc~get_id_on_process_local_atoms proc~predict_4g_no_force_trick_single_structure mod_predict_4g_no_force_trick_single_structure::predict_4g_no_force_trick_single_structure proc~predict_4g_no_force_trick_single_structure->proc~get_id_on_process_local_atoms proc~predict_single_structure mod_predict_single_structure::predict_single_structure proc~predict_single_structure->proc~get_id_on_process_local_atoms proc~predict_single_structure->proc~post_processing_wrapper_single_structure proc~predict_multiple_structures mod_predict_multiple_structures::predict_multiple_structures proc~predict_multiple_structures->proc~post_processing_wrapper_single_structure proc~predict_structure_interface mod_generic_interface::predict_structure_interface proc~predict_structure_interface->proc~predict_single_structure proc~output_files_and_cost mod_output_files_and_cost::output_files_and_cost proc~output_files_and_cost->proc~predict_multiple_structures proc~predict_all_chunks mod_predict_all_chunks::predict_all_chunks proc~predict_all_chunks->proc~predict_multiple_structures proc~predict_mode mod_predict_mode::predict_mode proc~predict_mode->proc~predict_multiple_structures proc~train_loop_atomic_property mod_train_loop_atomic_property::train_loop_atomic_property proc~train_loop_atomic_property->proc~output_files_and_cost proc~train_loop_short_range mod_train_loop_short_range::train_loop_short_range proc~train_loop_short_range->proc~output_files_and_cost proc~train_mode mod_train_mode::train_mode proc~train_mode->proc~predict_all_chunks proc~train_mode->proc~train_loop_atomic_property proc~train_mode->proc~train_loop_short_range program~runner RuNNer program~runner->proc~predict_mode program~runner->proc~train_mode

function get_id_atoms

function get_id_atoms( &
    self &
)

Indexes the ids of the atoms in ascending order.

Arguments

Called By

proc~~get_id_atoms~~CalledByGraph proc~get_id_atoms mod_structures::Structure%get_id_atoms proc~store_meta_information_single_structure mod_store_atomic_property_single_structure::store_meta_information_single_structure proc~store_meta_information_single_structure->proc~get_id_atoms proc~post_processing_wrapper_single_structure mod_post_processing_wrapper_single_structure::post_processing_wrapper_single_structure proc~post_processing_wrapper_single_structure->proc~store_meta_information_single_structure proc~predict_multiple_structures mod_predict_multiple_structures::predict_multiple_structures proc~predict_multiple_structures->proc~store_meta_information_single_structure proc~predict_multiple_structures->proc~post_processing_wrapper_single_structure proc~output_files_and_cost mod_output_files_and_cost::output_files_and_cost proc~output_files_and_cost->proc~predict_multiple_structures proc~predict_all_chunks mod_predict_all_chunks::predict_all_chunks proc~predict_all_chunks->proc~predict_multiple_structures proc~predict_mode mod_predict_mode::predict_mode proc~predict_mode->proc~predict_multiple_structures proc~predict_single_structure mod_predict_single_structure::predict_single_structure proc~predict_single_structure->proc~post_processing_wrapper_single_structure proc~predict_structure_interface mod_generic_interface::predict_structure_interface proc~predict_structure_interface->proc~predict_single_structure proc~train_loop_atomic_property mod_train_loop_atomic_property::train_loop_atomic_property proc~train_loop_atomic_property->proc~output_files_and_cost proc~train_loop_short_range mod_train_loop_short_range::train_loop_short_range proc~train_loop_short_range->proc~output_files_and_cost proc~train_mode mod_train_mode::train_mode proc~train_mode->proc~predict_all_chunks proc~train_mode->proc~train_loop_atomic_property proc~train_mode->proc~train_loop_short_range program~runner RuNNer program~runner->proc~predict_mode program~runner->proc~train_mode

function get_id_local_atoms

function get_id_local_atoms( &
    self &
)

Indexes the ids of the local atoms in ascending order.

Arguments

function sum_atomic_energies

function sum_atomic_energies( &
    self, &
    atom_energies &
)

Remove atom energies author: Alea Tokita, Moritz R. Schaefer, Alexander Knoll

Arguments

  • self : class(Structure) [in]
  • atom_energies : real(DP) (dim: (MAX_ELEM_NUM)) [in]

subroutine reset_structure

subroutine reset_structure( &
    self &
)

Reset the structure to a blank state.

Arguments

Called By

proc~~reset_structure~~CalledByGraph proc~reset_structure mod_structures::Structure%reset_structure proc~constructor_without_positions mod_structures::constructor_without_positions proc~constructor_without_positions->proc~reset_structure interface~structure mod_structures::Structure interface~structure->proc~constructor_without_positions proc~constructor_with_positions_and_atomic_numbers mod_structures::constructor_with_positions_and_atomic_numbers interface~structure->proc~constructor_with_positions_and_atomic_numbers proc~constructor_with_positions_and_atomic_numbers->proc~constructor_without_positions

subroutine trim_structure

subroutine trim_structure( &
    self &
)

Decrease the size of the internal arrays to exactly fit self%num_atoms.

This is used during parsing from a file, where we first allocate a Structure object to max_num_atoms_in_file, fill it up line by line, and finally trim it down to the correct size so we do not waste memory.

Arguments

subroutine move_atoms_into_cell

subroutine move_atoms_into_cell( &
    self &
)

Wrapping of atoms outside of box over periodic boundary conditions for periodic structuctures.

Arguments

Called By

proc~~move_atoms_into_cell~~CalledByGraph proc~move_atoms_into_cell mod_structures::Structure%move_atoms_into_cell proc~build_structure_neighborlists_feature_calculators mod_generic_interface::build_structure_neighborlists_feature_calculators proc~build_structure_neighborlists_feature_calculators->proc~move_atoms_into_cell proc~count_structures_and_atoms_inputdata mod_inputdata::InputData%count_structures_and_atoms_inputdata proc~count_structures_and_atoms_inputdata->proc~move_atoms_into_cell proc~read_next_structure_inputdata mod_inputdata::InputData%read_next_structure_inputdata proc~read_next_structure_inputdata->proc~move_atoms_into_cell proc~constructor~3 mod_inputdata::constructor proc~constructor~3->proc~count_structures_and_atoms_inputdata proc~predict_structure_interface mod_generic_interface::predict_structure_interface proc~predict_structure_interface->proc~build_structure_neighborlists_feature_calculators proc~prepare_feature_calculator_get_neighbor_list_info mod_feature_calc_interface::prepare_feature_calculator_get_neighbor_list_info proc~prepare_feature_calculator_get_neighbor_list_info->proc~build_structure_neighborlists_feature_calculators proc~read_structures_inputdata mod_inputdata::InputData%read_structures_inputdata proc~read_structures_inputdata->proc~read_next_structure_inputdata interface~inputdata mod_inputdata::InputData interface~inputdata->proc~constructor~3

subroutine update_positions_and_lattice

subroutine update_positions_and_lattice( &
    self, &
    positions, &
    atomic_numbers, &
    num_local_atoms, &
    lperiodic, &
    cflength, &
    lattice &
)

Arguments

  • self : class(Structure) [inout]
  • positions : real(DP) (dim: (3,self%num_atoms)) [in]
  • atomic_numbers : integer (dim: (self%num_atoms)) [in]
  • num_local_atoms : integer [in]
  • lperiodic : logical [in]
  • cflength : real(DP) [in]
  • lattice : real(DP) (dim: (3,3)) [in]

Called By

proc~~update_positions_and_lattice~~CalledByGraph proc~update_positions_and_lattice mod_structures::Structure%update_positions_and_lattice proc~runner_lammps_interface_transfer_atoms_and_neighbor_lists mod_lammps_interface::runner_lammps_interface_transfer_atoms_and_neighbor_lists proc~runner_lammps_interface_transfer_atoms_and_neighbor_lists->proc~update_positions_and_lattice

subroutine set_relative_positions

subroutine set_relative_positions( &
    self, &
    rel_positions &
)

Arguments

  • self : class(Structure) [inout]
  • rel_positions : real(DP) (dim: (3,self%num_atoms)) [in]

Called By

proc~~set_relative_positions~~CalledByGraph proc~set_relative_positions mod_structures::Structure%set_relative_positions proc~move_atoms_into_cell mod_structures::Structure%move_atoms_into_cell proc~move_atoms_into_cell->proc~set_relative_positions proc~numerical_stress_electrostatic mod_abstract_electrostatics::AbstractElectrostaticsCalculator%numerical_stress_electrostatic proc~numerical_stress_electrostatic->proc~set_relative_positions proc~build_structure_neighborlists_feature_calculators mod_generic_interface::build_structure_neighborlists_feature_calculators proc~build_structure_neighborlists_feature_calculators->proc~move_atoms_into_cell proc~count_structures_and_atoms_inputdata mod_inputdata::InputData%count_structures_and_atoms_inputdata proc~count_structures_and_atoms_inputdata->proc~move_atoms_into_cell proc~read_next_structure_inputdata mod_inputdata::InputData%read_next_structure_inputdata proc~read_next_structure_inputdata->proc~move_atoms_into_cell proc~constructor~3 mod_inputdata::constructor proc~constructor~3->proc~count_structures_and_atoms_inputdata proc~predict_structure_interface mod_generic_interface::predict_structure_interface proc~predict_structure_interface->proc~build_structure_neighborlists_feature_calculators proc~prepare_feature_calculator_get_neighbor_list_info mod_feature_calc_interface::prepare_feature_calculator_get_neighbor_list_info proc~prepare_feature_calculator_get_neighbor_list_info->proc~build_structure_neighborlists_feature_calculators proc~read_structures_inputdata mod_inputdata::InputData%read_structures_inputdata proc~read_structures_inputdata->proc~read_next_structure_inputdata interface~inputdata mod_inputdata::InputData interface~inputdata->proc~constructor~3

subroutine distribute

subroutine distribute( &
    self, &
    destination &
)

Distributes a single structure from root to process specified by destination (rank + 1) using mpi.

This subroutine needs information read from input.nn. So, it needs to be called after finishing the initialization of input.nn.

Arguments

  • self : class(Structure) [inout]
  • destination : integer [in]

Called By

proc~~distribute~~CalledByGraph proc~distribute mod_structures::Structure%distribute proc~load_next_chunk mod_dataloader_file::FileDataLoader%load_next_chunk proc~load_next_chunk->proc~distribute proc~dataset_statistics_chi_all_chunks mod_dataset_statistics_chi_all_chunks::dataset_statistics_chi_all_chunks proc~dataset_statistics_chi_all_chunks->proc~load_next_chunk proc~determine_scaling_factor_and_centering_subtrahend_all_chunks~3 mod_feature_map_scaling_all_chunks::determine_scaling_factor_and_centering_subtrahend_all_chunks proc~determine_scaling_factor_and_centering_subtrahend_all_chunks~3->proc~load_next_chunk proc~output_files_and_cost mod_output_files_and_cost::output_files_and_cost proc~output_files_and_cost->proc~load_next_chunk proc~output_files_and_cost_4g_charges mod_output_files_and_cost_4g_charges::output_files_and_cost_4g_charges proc~output_files_and_cost_4g_charges->proc~load_next_chunk proc~output_files_and_cost_4g_short_range mod_output_files_and_cost_4g_short_range::output_files_and_cost_4g_short_range proc~output_files_and_cost_4g_short_range->proc~load_next_chunk proc~precalc_coulomb_matrix_all_chunks mod_precalc_coulomb_matrix_all_chunks::precalc_coulomb_matrix_all_chunks proc~precalc_coulomb_matrix_all_chunks->proc~load_next_chunk proc~precalc_nl_deriv_features_single_chunk mod_precalc_nl_deriv_features_single_chunk::precalc_nl_deriv_features_single_chunk proc~precalc_nl_deriv_features_single_chunk->proc~load_next_chunk proc~precompute_coulomb_matrix_all_chunks mod_calculate_coulomb_matrix::precompute_coulomb_matrix_all_chunks proc~precompute_coulomb_matrix_all_chunks->proc~load_next_chunk proc~create_chunks mod_dataloader_file::FileDataLoader%create_chunks proc~precompute_coulomb_matrix_all_chunks->proc~create_chunks proc~precompute_features_all_chunks mod_precompute_features_all_chunks::precompute_features_all_chunks proc~precompute_features_all_chunks->proc~load_next_chunk proc~precompute_features_all_chunks->proc~create_chunks proc~precompute_global_features_all_chunks mod_precompute_global_features_all_chunks::precompute_global_features_all_chunks proc~precompute_global_features_all_chunks->proc~load_next_chunk proc~precompute_global_features_all_chunks->proc~create_chunks proc~predict_all_chunks mod_predict_all_chunks::predict_all_chunks proc~predict_all_chunks->proc~load_next_chunk proc~predict_ee4g_feature_calculator_multiple_structures_all_chunks mod_predict_ee4g_feature_calculator_multiple_structures::predict_ee4g_feature_calculator_multiple_structures_all_chunks proc~predict_ee4g_feature_calculator_multiple_structures_all_chunks->proc~load_next_chunk proc~predict_mode mod_predict_mode::predict_mode proc~predict_mode->proc~load_next_chunk proc~predict_mode->proc~create_chunks proc~predict_two_body_all_chunks mod_two_body::TwoBodyCalculator%predict_two_body_all_chunks proc~predict_two_body_all_chunks->proc~load_next_chunk proc~prediction_statistics_all_chunks mod_feature_map_scaling_all_chunks::prediction_statistics_all_chunks proc~prediction_statistics_all_chunks->proc~load_next_chunk proc~read_global_features_all_chunks mod_train_mode::read_global_features_all_chunks proc~read_global_features_all_chunks->proc~load_next_chunk proc~set_num_structures_in_chunk_per_process mod_dataloader_file::FileDataLoader%set_num_structures_in_chunk_per_process proc~set_num_structures_in_chunk_per_process->proc~load_next_chunk proc~train_loop_4g_charges mod_train_loop_4g_charges::train_loop_4g_charges proc~train_loop_4g_charges->proc~load_next_chunk proc~train_loop_4g_charges->proc~output_files_and_cost_4g_charges proc~train_loop_atomic_property mod_train_loop_atomic_property::train_loop_atomic_property proc~train_loop_atomic_property->proc~load_next_chunk proc~train_loop_atomic_property->proc~output_files_and_cost proc~train_loop_short_range mod_train_loop_short_range::train_loop_short_range proc~train_loop_short_range->proc~load_next_chunk proc~train_loop_short_range->proc~output_files_and_cost proc~train_loop_short_range->proc~output_files_and_cost_4g_short_range proc~create_chunks->proc~set_num_structures_in_chunk_per_process proc~feature_scaling_and_prediction_statistics_all_chunks mod_feature_map_scaling_all_chunks::feature_scaling_and_prediction_statistics_all_chunks proc~feature_scaling_and_prediction_statistics_all_chunks->proc~determine_scaling_factor_and_centering_subtrahend_all_chunks~3 proc~feature_scaling_and_prediction_statistics_all_chunks->proc~prediction_statistics_all_chunks proc~train_mode mod_train_mode::train_mode proc~train_mode->proc~dataset_statistics_chi_all_chunks proc~train_mode->proc~precalc_coulomb_matrix_all_chunks proc~train_mode->proc~precalc_nl_deriv_features_single_chunk proc~train_mode->proc~predict_all_chunks proc~train_mode->proc~predict_ee4g_feature_calculator_multiple_structures_all_chunks proc~train_mode->proc~predict_two_body_all_chunks proc~train_mode->proc~read_global_features_all_chunks proc~train_mode->proc~train_loop_4g_charges proc~train_mode->proc~train_loop_atomic_property proc~train_mode->proc~train_loop_short_range proc~train_mode->proc~create_chunks proc~train_mode->proc~feature_scaling_and_prediction_statistics_all_chunks program~runner RuNNer program~runner->proc~precompute_coulomb_matrix_all_chunks program~runner->proc~precompute_features_all_chunks program~runner->proc~precompute_global_features_all_chunks program~runner->proc~predict_mode program~runner->proc~train_mode

subroutine make_supercell

subroutine make_supercell( &
    self, &
    nx, &
    ny, &
    nz, &
    supercell &
)

Arguments

  • self : class(Structure) [in]
  • nx : integer [in]
  • ny : integer [in]
  • nz : integer [in]
  • supercell : type(Structure) [out]

subroutine set_all_ids_to_value

subroutine set_all_ids_to_value( &
    self, &
    val &
)

Arguments

  • self : class(Structure) [inout]
  • val : integer [in]

Called By

proc~~set_all_ids_to_value~~CalledByGraph proc~set_all_ids_to_value mod_structures::Structure%set_all_ids_to_value proc~build_structure_neighborlists_feature_calculators mod_generic_interface::build_structure_neighborlists_feature_calculators proc~build_structure_neighborlists_feature_calculators->proc~set_all_ids_to_value proc~predict_structure_interface mod_generic_interface::predict_structure_interface proc~predict_structure_interface->proc~build_structure_neighborlists_feature_calculators proc~prepare_feature_calculator_get_neighbor_list_info mod_feature_calc_interface::prepare_feature_calculator_get_neighbor_list_info proc~prepare_feature_calculator_get_neighbor_list_info->proc~build_structure_neighborlists_feature_calculators

subroutine concatenate_atom_id_on_process_without_mapping

subroutine concatenate_atom_id_on_process_without_mapping( &
    structures, &
    id_on_process_strucs, &
    id_on_process_atoms &
)

Build continuous arrays of the ids on process and atomic numbers for a given list of structures.

Arguments

  • structures : type(Structure) (dim: (:)) [in]
  • id_on_process_strucs : integer (dim: (:)) [in]
  • id_on_process_atoms : integer (dim: (:)) [out]

Called By

proc~~concatenate_atom_id_on_process_without_mapping~~CalledByGraph proc~concatenate_atom_id_on_process_without_mapping mod_structures::concatenate_atom_id_on_process_without_mapping interface~concatenate_atom_id_on_process mod_structures::concatenate_atom_id_on_process interface~concatenate_atom_id_on_process->proc~concatenate_atom_id_on_process_without_mapping proc~determine_scaling_factor_and_centering_subtrahend_all_chunks~3 mod_feature_map_scaling_all_chunks::determine_scaling_factor_and_centering_subtrahend_all_chunks proc~determine_scaling_factor_and_centering_subtrahend_all_chunks~3->interface~concatenate_atom_id_on_process proc~precompute_features_all_chunks mod_precompute_features_all_chunks::precompute_features_all_chunks proc~precompute_features_all_chunks->interface~concatenate_atom_id_on_process proc~predict_structure_batch mod_structure_batch_iterator::StructureBatchIterator%predict_structure_batch proc~predict_structure_batch->interface~concatenate_atom_id_on_process proc~train_loop_4g_charges mod_train_loop_4g_charges::train_loop_4g_charges proc~train_loop_4g_charges->interface~concatenate_atom_id_on_process proc~output_files_and_cost_4g_charges mod_output_files_and_cost_4g_charges::output_files_and_cost_4g_charges proc~train_loop_4g_charges->proc~output_files_and_cost_4g_charges proc~train_loop_atomic_property mod_train_loop_atomic_property::train_loop_atomic_property proc~train_loop_atomic_property->interface~concatenate_atom_id_on_process proc~output_files_and_cost mod_output_files_and_cost::output_files_and_cost proc~train_loop_atomic_property->proc~output_files_and_cost proc~train_loop_short_range mod_train_loop_short_range::train_loop_short_range proc~train_loop_short_range->interface~concatenate_atom_id_on_process proc~predict_qeq_feature_calculator_multiple_structures mod_predict_qeq_feature_calculator_multiple_structures::predict_qeq_feature_calculator_multiple_structures proc~train_loop_short_range->proc~predict_qeq_feature_calculator_multiple_structures proc~train_loop_short_range->proc~output_files_and_cost proc~output_files_and_cost_4g_short_range mod_output_files_and_cost_4g_short_range::output_files_and_cost_4g_short_range proc~train_loop_short_range->proc~output_files_and_cost_4g_short_range proc~update_prediction_statistics_multiple_structures mod_prediction_statistics::update_prediction_statistics_multiple_structures proc~update_prediction_statistics_multiple_structures->interface~concatenate_atom_id_on_process proc~feature_scaling_and_prediction_statistics_all_chunks mod_feature_map_scaling_all_chunks::feature_scaling_and_prediction_statistics_all_chunks proc~feature_scaling_and_prediction_statistics_all_chunks->proc~determine_scaling_factor_and_centering_subtrahend_all_chunks~3 proc~prediction_statistics_all_chunks mod_feature_map_scaling_all_chunks::prediction_statistics_all_chunks proc~feature_scaling_and_prediction_statistics_all_chunks->proc~prediction_statistics_all_chunks proc~predict_4g_charges_training_qeq_multiple_structures mod_predict_4g_charges_training_qeq_multiple_structures::predict_4g_charges_training_qeq_multiple_structures proc~predict_4g_charges_training_qeq_multiple_structures->proc~predict_structure_batch proc~predict_4g_short_range_training_qeq_multiple_structures mod_predict_4g_short_range_training_qeq_multiple_structures::predict_4g_short_range_training_qeq_multiple_structures proc~predict_4g_short_range_training_qeq_multiple_structures->proc~predict_structure_batch proc~predict_multiple_structures mod_predict_multiple_structures::predict_multiple_structures proc~predict_multiple_structures->proc~predict_structure_batch proc~predict_qeq_feature_calculator_multiple_structures->proc~predict_structure_batch proc~prediction_statistics_all_chunks->proc~predict_structure_batch proc~train_mode mod_train_mode::train_mode proc~train_mode->proc~train_loop_4g_charges proc~train_mode->proc~train_loop_atomic_property proc~train_mode->proc~train_loop_short_range proc~train_mode->proc~feature_scaling_and_prediction_statistics_all_chunks proc~train_mode->proc~predict_qeq_feature_calculator_multiple_structures proc~predict_all_chunks mod_predict_all_chunks::predict_all_chunks proc~train_mode->proc~predict_all_chunks program~runner RuNNer program~runner->proc~precompute_features_all_chunks program~runner->proc~train_mode proc~precompute_global_features_all_chunks mod_precompute_global_features_all_chunks::precompute_global_features_all_chunks program~runner->proc~precompute_global_features_all_chunks proc~predict_mode mod_predict_mode::predict_mode program~runner->proc~predict_mode proc~output_files_and_cost->proc~predict_multiple_structures proc~output_files_and_cost_4g_charges->proc~predict_4g_charges_training_qeq_multiple_structures proc~output_files_and_cost_4g_short_range->proc~predict_4g_short_range_training_qeq_multiple_structures proc~precompute_global_features_all_chunks->proc~predict_qeq_feature_calculator_multiple_structures proc~predict_all_chunks->proc~predict_multiple_structures proc~predict_mode->proc~predict_multiple_structures

subroutine concatenate_atom_id_on_process_across_chunks

subroutine concatenate_atom_id_on_process_across_chunks( &
    structures, &
    id_on_process_strucs, &
    id_on_process_across_chunks_atoms &
)

Build continuous arrays of the ids on process and atomic numbers for a given list of structures.

Arguments

  • structures : type(Structure) (dim: (:)) [in]
  • id_on_process_strucs : integer (dim: (:)) [in]
  • id_on_process_across_chunks_atoms : integer (dim: (:)) [out]

Called By

proc~~concatenate_atom_id_on_process_across_chunks~~CalledByGraph proc~concatenate_atom_id_on_process_across_chunks mod_structures::concatenate_atom_id_on_process_across_chunks proc~train_loop_atomic_property mod_train_loop_atomic_property::train_loop_atomic_property proc~train_loop_atomic_property->proc~concatenate_atom_id_on_process_across_chunks proc~train_mode mod_train_mode::train_mode proc~train_mode->proc~train_loop_atomic_property program~runner RuNNer program~runner->proc~train_mode

subroutine concatenate_atom_id_on_process_with_mapping

subroutine concatenate_atom_id_on_process_with_mapping( &
    structures, &
    id_on_process_strucs, &
    id_on_process_atoms, &
    map_atom_to_target_structure, &
    atomic_numbers &
)

Build continuous arrays of the ids on process and atomic numbers for a given list of structures.

Arguments

  • structures : type(Structure) (dim: (:)) [in]
  • id_on_process_strucs : integer (dim: (:)) [in]
  • id_on_process_atoms : integer (dim: (:)) [out]
  • map_atom_to_target_structure : integer (dim: (:,:)) [out]
  • atomic_numbers : integer (dim: (:)) [out]

Called By

proc~~concatenate_atom_id_on_process_with_mapping~~CalledByGraph proc~concatenate_atom_id_on_process_with_mapping mod_structures::concatenate_atom_id_on_process_with_mapping interface~concatenate_atom_id_on_process mod_structures::concatenate_atom_id_on_process interface~concatenate_atom_id_on_process->proc~concatenate_atom_id_on_process_with_mapping proc~determine_scaling_factor_and_centering_subtrahend_all_chunks~3 mod_feature_map_scaling_all_chunks::determine_scaling_factor_and_centering_subtrahend_all_chunks proc~determine_scaling_factor_and_centering_subtrahend_all_chunks~3->interface~concatenate_atom_id_on_process proc~precompute_features_all_chunks mod_precompute_features_all_chunks::precompute_features_all_chunks proc~precompute_features_all_chunks->interface~concatenate_atom_id_on_process proc~predict_structure_batch mod_structure_batch_iterator::StructureBatchIterator%predict_structure_batch proc~predict_structure_batch->interface~concatenate_atom_id_on_process proc~train_loop_4g_charges mod_train_loop_4g_charges::train_loop_4g_charges proc~train_loop_4g_charges->interface~concatenate_atom_id_on_process proc~output_files_and_cost_4g_charges mod_output_files_and_cost_4g_charges::output_files_and_cost_4g_charges proc~train_loop_4g_charges->proc~output_files_and_cost_4g_charges proc~train_loop_atomic_property mod_train_loop_atomic_property::train_loop_atomic_property proc~train_loop_atomic_property->interface~concatenate_atom_id_on_process proc~output_files_and_cost mod_output_files_and_cost::output_files_and_cost proc~train_loop_atomic_property->proc~output_files_and_cost proc~train_loop_short_range mod_train_loop_short_range::train_loop_short_range proc~train_loop_short_range->interface~concatenate_atom_id_on_process proc~predict_qeq_feature_calculator_multiple_structures mod_predict_qeq_feature_calculator_multiple_structures::predict_qeq_feature_calculator_multiple_structures proc~train_loop_short_range->proc~predict_qeq_feature_calculator_multiple_structures proc~train_loop_short_range->proc~output_files_and_cost proc~output_files_and_cost_4g_short_range mod_output_files_and_cost_4g_short_range::output_files_and_cost_4g_short_range proc~train_loop_short_range->proc~output_files_and_cost_4g_short_range proc~update_prediction_statistics_multiple_structures mod_prediction_statistics::update_prediction_statistics_multiple_structures proc~update_prediction_statistics_multiple_structures->interface~concatenate_atom_id_on_process proc~feature_scaling_and_prediction_statistics_all_chunks mod_feature_map_scaling_all_chunks::feature_scaling_and_prediction_statistics_all_chunks proc~feature_scaling_and_prediction_statistics_all_chunks->proc~determine_scaling_factor_and_centering_subtrahend_all_chunks~3 proc~prediction_statistics_all_chunks mod_feature_map_scaling_all_chunks::prediction_statistics_all_chunks proc~feature_scaling_and_prediction_statistics_all_chunks->proc~prediction_statistics_all_chunks proc~predict_4g_charges_training_qeq_multiple_structures mod_predict_4g_charges_training_qeq_multiple_structures::predict_4g_charges_training_qeq_multiple_structures proc~predict_4g_charges_training_qeq_multiple_structures->proc~predict_structure_batch proc~predict_4g_short_range_training_qeq_multiple_structures mod_predict_4g_short_range_training_qeq_multiple_structures::predict_4g_short_range_training_qeq_multiple_structures proc~predict_4g_short_range_training_qeq_multiple_structures->proc~predict_structure_batch proc~predict_multiple_structures mod_predict_multiple_structures::predict_multiple_structures proc~predict_multiple_structures->proc~predict_structure_batch proc~predict_qeq_feature_calculator_multiple_structures->proc~predict_structure_batch proc~prediction_statistics_all_chunks->proc~predict_structure_batch proc~train_mode mod_train_mode::train_mode proc~train_mode->proc~train_loop_4g_charges proc~train_mode->proc~train_loop_atomic_property proc~train_mode->proc~train_loop_short_range proc~train_mode->proc~feature_scaling_and_prediction_statistics_all_chunks proc~train_mode->proc~predict_qeq_feature_calculator_multiple_structures proc~predict_all_chunks mod_predict_all_chunks::predict_all_chunks proc~train_mode->proc~predict_all_chunks program~runner RuNNer program~runner->proc~precompute_features_all_chunks program~runner->proc~train_mode proc~precompute_global_features_all_chunks mod_precompute_global_features_all_chunks::precompute_global_features_all_chunks program~runner->proc~precompute_global_features_all_chunks proc~predict_mode mod_predict_mode::predict_mode program~runner->proc~predict_mode proc~output_files_and_cost->proc~predict_multiple_structures proc~output_files_and_cost_4g_charges->proc~predict_4g_charges_training_qeq_multiple_structures proc~output_files_and_cost_4g_short_range->proc~predict_4g_short_range_training_qeq_multiple_structures proc~precompute_global_features_all_chunks->proc~predict_qeq_feature_calculator_multiple_structures proc~predict_all_chunks->proc~predict_multiple_structures proc~predict_mode->proc~predict_multiple_structures

subroutine concatenate_atom_id_on_process_with_double_mapping

subroutine concatenate_atom_id_on_process_with_double_mapping( &
    structures, &
    id_on_process_strucs, &
    id_on_process_atoms, &
    id_in_struc_atoms, &
    map_atom_to_target_structure, &
    map_target_structure_to_atom, &
    atomic_numbers &
)

Build continuous arrays of the ids on process and atomic numbers for a given list of structures.

Arguments

  • structures : type(Structure) (dim: (:)) [in]
  • id_on_process_strucs : integer (dim: (:)) [in]
  • id_on_process_atoms : integer (dim: (:)) [out]
  • id_in_struc_atoms : integer (dim: (:)) [out]
  • map_atom_to_target_structure : integer (dim: (:,:)) [out]
  • map_target_structure_to_atom : integer (dim: (:)) [out]
  • atomic_numbers : integer (dim: (:)) [out]

Called By

proc~~concatenate_atom_id_on_process_with_double_mapping~~CalledByGraph proc~concatenate_atom_id_on_process_with_double_mapping mod_structures::concatenate_atom_id_on_process_with_double_mapping interface~concatenate_atom_id_on_process mod_structures::concatenate_atom_id_on_process interface~concatenate_atom_id_on_process->proc~concatenate_atom_id_on_process_with_double_mapping proc~determine_scaling_factor_and_centering_subtrahend_all_chunks~3 mod_feature_map_scaling_all_chunks::determine_scaling_factor_and_centering_subtrahend_all_chunks proc~determine_scaling_factor_and_centering_subtrahend_all_chunks~3->interface~concatenate_atom_id_on_process proc~precompute_features_all_chunks mod_precompute_features_all_chunks::precompute_features_all_chunks proc~precompute_features_all_chunks->interface~concatenate_atom_id_on_process proc~predict_structure_batch mod_structure_batch_iterator::StructureBatchIterator%predict_structure_batch proc~predict_structure_batch->interface~concatenate_atom_id_on_process proc~train_loop_4g_charges mod_train_loop_4g_charges::train_loop_4g_charges proc~train_loop_4g_charges->interface~concatenate_atom_id_on_process proc~output_files_and_cost_4g_charges mod_output_files_and_cost_4g_charges::output_files_and_cost_4g_charges proc~train_loop_4g_charges->proc~output_files_and_cost_4g_charges proc~train_loop_atomic_property mod_train_loop_atomic_property::train_loop_atomic_property proc~train_loop_atomic_property->interface~concatenate_atom_id_on_process proc~output_files_and_cost mod_output_files_and_cost::output_files_and_cost proc~train_loop_atomic_property->proc~output_files_and_cost proc~train_loop_short_range mod_train_loop_short_range::train_loop_short_range proc~train_loop_short_range->interface~concatenate_atom_id_on_process proc~predict_qeq_feature_calculator_multiple_structures mod_predict_qeq_feature_calculator_multiple_structures::predict_qeq_feature_calculator_multiple_structures proc~train_loop_short_range->proc~predict_qeq_feature_calculator_multiple_structures proc~train_loop_short_range->proc~output_files_and_cost proc~output_files_and_cost_4g_short_range mod_output_files_and_cost_4g_short_range::output_files_and_cost_4g_short_range proc~train_loop_short_range->proc~output_files_and_cost_4g_short_range proc~update_prediction_statistics_multiple_structures mod_prediction_statistics::update_prediction_statistics_multiple_structures proc~update_prediction_statistics_multiple_structures->interface~concatenate_atom_id_on_process proc~feature_scaling_and_prediction_statistics_all_chunks mod_feature_map_scaling_all_chunks::feature_scaling_and_prediction_statistics_all_chunks proc~feature_scaling_and_prediction_statistics_all_chunks->proc~determine_scaling_factor_and_centering_subtrahend_all_chunks~3 proc~prediction_statistics_all_chunks mod_feature_map_scaling_all_chunks::prediction_statistics_all_chunks proc~feature_scaling_and_prediction_statistics_all_chunks->proc~prediction_statistics_all_chunks proc~predict_4g_charges_training_qeq_multiple_structures mod_predict_4g_charges_training_qeq_multiple_structures::predict_4g_charges_training_qeq_multiple_structures proc~predict_4g_charges_training_qeq_multiple_structures->proc~predict_structure_batch proc~predict_4g_short_range_training_qeq_multiple_structures mod_predict_4g_short_range_training_qeq_multiple_structures::predict_4g_short_range_training_qeq_multiple_structures proc~predict_4g_short_range_training_qeq_multiple_structures->proc~predict_structure_batch proc~predict_multiple_structures mod_predict_multiple_structures::predict_multiple_structures proc~predict_multiple_structures->proc~predict_structure_batch proc~predict_qeq_feature_calculator_multiple_structures->proc~predict_structure_batch proc~prediction_statistics_all_chunks->proc~predict_structure_batch proc~train_mode mod_train_mode::train_mode proc~train_mode->proc~train_loop_4g_charges proc~train_mode->proc~train_loop_atomic_property proc~train_mode->proc~train_loop_short_range proc~train_mode->proc~feature_scaling_and_prediction_statistics_all_chunks proc~train_mode->proc~predict_qeq_feature_calculator_multiple_structures proc~predict_all_chunks mod_predict_all_chunks::predict_all_chunks proc~train_mode->proc~predict_all_chunks program~runner RuNNer program~runner->proc~precompute_features_all_chunks program~runner->proc~train_mode proc~precompute_global_features_all_chunks mod_precompute_global_features_all_chunks::precompute_global_features_all_chunks program~runner->proc~precompute_global_features_all_chunks proc~predict_mode mod_predict_mode::predict_mode program~runner->proc~predict_mode proc~output_files_and_cost->proc~predict_multiple_structures proc~output_files_and_cost_4g_charges->proc~predict_4g_charges_training_qeq_multiple_structures proc~output_files_and_cost_4g_short_range->proc~predict_4g_short_range_training_qeq_multiple_structures proc~precompute_global_features_all_chunks->proc~predict_qeq_feature_calculator_multiple_structures proc~predict_all_chunks->proc~predict_multiple_structures proc~predict_mode->proc~predict_multiple_structures