Lines: 701 |
Visibility: private
Implementation of type to store neighbor information.
author: Gunnar Schmitz based on old neighbor list by Jonas Finkler and Knut
Nikolas Lausch. Use of symmetry and improved grid based approach by
Moritz R. Schäfer.
Dependencies
Uses
module~~mod_neighborlist~~UsesGraph
module~mod_neighborlist
mod_neighborlist
module~mod_dynamic_double_array
mod_dynamic_double_array
module~mod_neighborlist->module~mod_dynamic_double_array
module~mod_dynamic_int_array
mod_dynamic_int_array
module~mod_neighborlist->module~mod_dynamic_int_array
module~mod_io
mod_io
module~mod_neighborlist->module~mod_io
module~mod_mpi
mod_mpi
module~mod_neighborlist->module~mod_mpi
module~mod_neighbor_grid
mod_neighbor_grid
module~mod_neighborlist->module~mod_neighbor_grid
module~mod_neighborlist_helper
mod_neighborlist_helper
module~mod_neighborlist->module~mod_neighborlist_helper
module~mod_precision
mod_precision
module~mod_neighborlist->module~mod_precision
module~mod_settings
mod_settings
module~mod_neighborlist->module~mod_settings
module~mod_structures
mod_structures
module~mod_neighborlist->module~mod_structures
module~mod_throw
mod_throw
module~mod_neighborlist->module~mod_throw
module~mod_dynamic_double_array->module~mod_precision
module~mod_dynamic_double_array->module~mod_throw
module~mod_io->module~mod_precision
iso_fortran_env
iso_fortran_env
module~mod_io->iso_fortran_env
module~mod_optional_args
mod_optional_args
module~mod_io->module~mod_optional_args
module~mod_mpi->module~mod_precision
mpi_f08
mpi_f08
module~mod_mpi->mpi_f08
module~mod_neighbor_grid->module~mod_dynamic_int_array
module~mod_neighbor_grid->module~mod_mpi
module~mod_neighbor_grid->module~mod_neighborlist_helper
module~mod_neighbor_grid->module~mod_precision
module~mod_structures_helper
mod_structures_helper
module~mod_neighbor_grid->module~mod_structures_helper
module~mod_neighborlist_helper->module~mod_mpi
module~mod_neighborlist_helper->module~mod_precision
module~mod_linalg
mod_linalg
module~mod_neighborlist_helper->module~mod_linalg
iso_c_binding
iso_c_binding
module~mod_precision->iso_c_binding
module~mod_precision->iso_fortran_env
module~mod_settings->module~mod_io
module~mod_settings->module~mod_precision
module~mod_settings->module~mod_throw
module~mod_constants
mod_constants
module~mod_settings->module~mod_constants
module~mod_cpu_vendor
mod_cpu_vendor
module~mod_settings->module~mod_cpu_vendor
module~mod_periodic_table
mod_periodic_table
module~mod_settings->module~mod_periodic_table
module~mod_structures->module~mod_mpi
module~mod_structures->module~mod_precision
module~mod_structures->module~mod_throw
module~mod_array_helpers
mod_array_helpers
module~mod_structures->module~mod_array_helpers
module~mod_structures->module~mod_constants
module~mod_structures->module~mod_linalg
module~mod_structures->module~mod_periodic_table
module~mod_structures->module~mod_structures_helper
module~mod_throw->module~mod_io
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_sort
mod_sort
module~mod_throw->module~mod_sort
module~mod_array_helpers->module~mod_precision
module~mod_array_helpers->module~mod_throw
module~mod_constants->module~mod_precision
module~mod_constants->iso_c_binding
module~mod_cpu_vendor->iso_c_binding
module~mod_linalg->module~mod_precision
module~mod_linalg->module~mod_settings
module~mod_linalg->module~mod_throw
module~cublas_wrapper
cublas_wrapper
module~mod_linalg->module~cublas_wrapper
module~mod_periodic_table->module~mod_io
module~mod_periodic_table->module~mod_precision
module~mod_periodic_table->module~mod_throw
module~mod_periodic_table->module~mod_array_helpers
module~mod_periodic_table->module~mod_constants
module~mod_sort->module~mod_precision
module~mod_structures_helper->module~mod_precision
module~mod_structures_helper->module~mod_linalg
module~cublas_wrapper->module~mod_settings
module~cublas_wrapper->iso_c_binding
Nodes of different colours represent the following:
Graph Key
Module
Module
Submodule
Submodule
Subroutine
Subroutine
Function
Function
Program
Program
This Page's Entity
This Page's Entity
Solid arrows point from a submodule to the (sub)module which it is
descended from. Dashed arrows point from a module or program unit to
modules which it uses.
Where possible, edges connecting nodes are
given different colours to make them easier to distinguish in
large graphs.
Used By
module~~mod_neighborlist~~UsedByGraph
module~mod_neighborlist
mod_neighborlist
module~mod_feature_map_neighborlist
mod_feature_map_neighborlist
module~mod_feature_map_neighborlist->module~mod_neighborlist
module~mod_abstract_angular_symmetry_function
mod_abstract_angular_symmetry_function
module~mod_abstract_angular_symmetry_function->module~mod_feature_map_neighborlist
module~mod_abstract_symmetry_function
mod_abstract_symmetry_function
module~mod_abstract_angular_symmetry_function->module~mod_abstract_symmetry_function
module~mod_abstract_radial_symmetry_function
mod_abstract_radial_symmetry_function
module~mod_abstract_radial_symmetry_function->module~mod_feature_map_neighborlist
module~mod_abstract_radial_symmetry_function->module~mod_abstract_symmetry_function
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_feature_map
mod_feature_map
module~mod_abstract_symmetry_function->module~mod_feature_map
module~mod_spin_prefactor
mod_spin_prefactor
module~mod_abstract_symmetry_function->module~mod_spin_prefactor
module~mod_angular_symmetry_function_3
mod_angular_symmetry_function_3
module~mod_angular_symmetry_function_3->module~mod_feature_map_neighborlist
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_8
mod_angular_symmetry_function_8
module~mod_angular_symmetry_function_8->module~mod_feature_map_neighborlist
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_9
mod_angular_symmetry_function_9
module~mod_angular_symmetry_function_9->module~mod_feature_map_neighborlist
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_calc_atomic_properties
mod_calc_atomic_properties
module~mod_calc_atomic_properties->module~mod_feature_map_neighborlist
module~mod_feature_calculator
mod_feature_calculator
module~mod_calc_atomic_properties->module~mod_feature_calculator
module~mod_calc_screening
mod_calc_screening
module~mod_calc_screening->module~mod_feature_map_neighborlist
module~mod_chain_features
mod_chain_features
module~mod_chain_features->module~mod_feature_map_neighborlist
module~mod_chain_features->module~mod_feature_calculator
module~mod_dataloader_file
mod_dataloader_file
module~mod_dataloader_file->module~mod_feature_map_neighborlist
module~mod_dataloader_file->module~mod_feature_calculator
module~mod_memory_estimation
mod_memory_estimation
module~mod_dataloader_file->module~mod_memory_estimation
module~mod_ee4g_feature_calculator
mod_ee4g_feature_calculator
module~mod_ee4g_feature_calculator->module~mod_feature_map_neighborlist
module~mod_electric_field_prefactor->module~mod_feature_map_neighborlist
module~mod_evaluate_4g_single_structure
mod_evaluate_4g_single_structure
module~mod_evaluate_4g_single_structure->module~mod_feature_map_neighborlist
module~mod_evaluate_4g_single_structure->module~mod_chain_features
module~mod_evaluate_4g_single_structure->module~mod_ee4g_feature_calculator
module~mod_evaluate_4g_single_structure->module~mod_feature_calculator
module~mod_evaluate_electrostatics_3g_single_structure
mod_evaluate_electrostatics_3g_single_structure
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_evaluate_electrostatics_3g_single_structure->module~mod_feature_calculator
module~mod_feature_calculator->module~mod_feature_map_neighborlist
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_feature_map
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_element
mod_element
module~mod_feature_calculator->module~mod_element
module~mod_atomic_descriptor
mod_atomic_descriptor
module~mod_feature_calculator->module~mod_atomic_descriptor
module~mod_feature_calculator_statistics
mod_feature_calculator_statistics
module~mod_feature_calculator_statistics->module~mod_feature_map_neighborlist
module~mod_feature_calculator_statistics->module~mod_feature_calculator
module~mod_scalingdata
mod_scalingdata
module~mod_feature_calculator_statistics->module~mod_scalingdata
module~mod_feature_map->module~mod_feature_map_neighborlist
module~mod_generic_interface
mod_generic_interface
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_hirshfeld_vdw
mod_hirshfeld_vdw
module~mod_hirshfeld_vdw->module~mod_feature_map_neighborlist
module~mod_lammps_interface
mod_lammps_interface
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_feature_map_neighborlist
module~mod_memory_estimation->module~mod_feature_calculator
module~mod_overlap_matrix->module~mod_feature_map_neighborlist
module~mod_overlap_matrix->module~mod_feature_map
module~mod_post_processing_2g_single_structure
mod_post_processing_2g_single_structure
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_2g_single_structure->module~mod_feature_calculator
module~mod_post_processing_3g_single_structure
mod_post_processing_3g_single_structure
module~mod_post_processing_3g_single_structure->module~mod_feature_map_neighborlist
module~mod_post_processing_3g_single_structure->module~mod_calc_screening
module~mod_post_processing_3g_single_structure->module~mod_evaluate_electrostatics_3g_single_structure
module~mod_post_processing_3g_single_structure->module~mod_feature_calculator
module~mod_post_processing_4g_single_structure
mod_post_processing_4g_single_structure
module~mod_post_processing_4g_single_structure->module~mod_feature_map_neighborlist
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_vdw_hirshfeld_single_structure
mod_post_processing_vdw_hirshfeld_single_structure
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_feature_calculator
module~mod_post_processing_vdw_hirshfeld_single_structure->module~mod_hirshfeld_vdw
module~mod_post_processing_wrapper_single_structure
mod_post_processing_wrapper_single_structure
module~mod_post_processing_wrapper_single_structure->module~mod_feature_map_neighborlist
module~mod_post_processing_wrapper_single_structure->module~mod_calc_atomic_properties
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_hirshfeld_vdw
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_post_processing_wrapper_single_structure->module~mod_post_processing_vdw_hirshfeld_single_structure
module~mod_two_body
mod_two_body
module~mod_post_processing_wrapper_single_structure->module~mod_two_body
module~mod_global_features_helper
mod_global_features_helper
module~mod_post_processing_wrapper_single_structure->module~mod_global_features_helper
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_feature_map_neighborlist
module~mod_predict_4g_charges_training_qeq_multiple_structures->module~mod_feature_calculator
module~mod_structure_batch_iterator
mod_structure_batch_iterator
module~mod_predict_4g_charges_training_qeq_multiple_structures->module~mod_structure_batch_iterator
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_feature_map_neighborlist
module~mod_predict_4g_no_force_trick_single_structure->module~mod_calc_atomic_properties
module~mod_predict_4g_no_force_trick_single_structure->module~mod_feature_calculator
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_global_features_helper
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_feature_map_neighborlist
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_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_multiple_structures->module~mod_global_features_helper
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_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_feature_map_neighborlist
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_multiple_structures
mod_predict_multiple_structures
module~mod_predict_multiple_structures->module~mod_feature_map_neighborlist
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_hirshfeld_vdw
module~mod_predict_multiple_structures->module~mod_post_processing_wrapper_single_structure
module~mod_predict_multiple_structures->module~mod_structure_batch_iterator
module~mod_predict_multiple_structures->module~mod_two_body
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_feature_map_neighborlist
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_predict_qeq_feature_calculator_single_structure
module~mod_predict_qeq_feature_calculator_multiple_structures->module~mod_structure_batch_iterator
module~mod_predict_qeq_feature_calculator_single_structure->module~mod_feature_map_neighborlist
module~mod_predict_qeq_feature_calculator_single_structure->module~mod_calc_screening
module~mod_predict_qeq_feature_calculator_single_structure->module~mod_chain_features
module~mod_predict_qeq_feature_calculator_single_structure->module~mod_feature_calculator
module~mod_predict_single_structure->module~mod_feature_map_neighborlist
module~mod_predict_single_structure->module~mod_calc_atomic_properties
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_hirshfeld_vdw
module~mod_predict_single_structure->module~mod_post_processing_wrapper_single_structure
module~mod_predict_single_structure->module~mod_two_body
module~mod_prediction_statistics
mod_prediction_statistics
module~mod_prediction_statistics->module~mod_feature_map_neighborlist
module~mod_prediction_statistics->module~mod_calc_atomic_properties
module~mod_prediction_statistics->module~mod_feature_calculator
module~mod_radial_symmetry_function_1->module~mod_feature_map_neighborlist
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_2->module~mod_feature_map_neighborlist
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_runner_interface->module~mod_feature_map_neighborlist
module~mod_runner_interface->module~mod_ee4g_feature_calculator
module~mod_runner_interface->module~mod_feature_calculator
module~mod_runner_interface->module~mod_hirshfeld_vdw
module~mod_runner_interface->module~mod_two_body
module~mod_spin_prefactor->module~mod_feature_map_neighborlist
module~mod_structure_batch_iterator->module~mod_feature_map_neighborlist
module~mod_structure_batch_iterator->module~mod_calc_atomic_properties
module~mod_structure_batch_iterator->module~mod_feature_calculator
module~mod_structure_batch_iterator->module~mod_global_features_helper
module~mod_two_body->module~mod_feature_map_neighborlist
module~mod_two_body->module~mod_dataloader_file
module~mod_calculate_coulomb_matrix
mod_calculate_coulomb_matrix
module~mod_calculate_coulomb_matrix->module~mod_dataloader_file
module~mod_cost_calculator
mod_cost_calculator
module~mod_cost_calculator->module~mod_dataloader_file
module~mod_write_outfiles_training
mod_write_outfiles_training
module~mod_cost_calculator->module~mod_write_outfiles_training
module~mod_dataset_statistics
mod_dataset_statistics
module~mod_dataset_statistics->module~mod_dataloader_file
module~mod_dataset_statistics->module~mod_feature_calculator
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_feature_calculator
module~mod_dataset_statistics_chi_all_chunks->module~mod_dataset_statistics
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_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_feature_map_scaling_all_chunks
mod_feature_map_scaling_all_chunks
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_prediction_statistics
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_featuredata
mod_featuredata
module~mod_featuredata->module~mod_feature_calculator
module~mod_featuredata->module~mod_element
module~mod_global_features_helper->module~mod_feature_calculator
module~mod_initialize
mod_initialize
module~mod_initialize->module~mod_ee4g_feature_calculator
module~mod_initialize->module~mod_feature_calculator
module~mod_initialize->module~mod_hirshfeld_vdw
module~mod_initialize->module~mod_two_body
module~mod_initialize->module~mod_element
module~mod_output_files_and_cost
mod_output_files_and_cost
module~mod_output_files_and_cost->module~mod_dataloader_file
module~mod_output_files_and_cost->module~mod_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
mod_output_files_and_cost_4g_charges
module~mod_output_files_and_cost_4g_charges->module~mod_dataloader_file
module~mod_output_files_and_cost_4g_charges->module~mod_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_cost_calculator
module~mod_output_files_and_cost_4g_short_range
mod_output_files_and_cost_4g_short_range
module~mod_output_files_and_cost_4g_short_range->module~mod_dataloader_file
module~mod_output_files_and_cost_4g_short_range->module~mod_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_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_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_features_all_chunks
mod_precompute_features_all_chunks
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_precompute_features_all_chunks->module~mod_featuredata
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_predict_all_chunks
mod_predict_all_chunks
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_hirshfeld_vdw
module~mod_predict_all_chunks->module~mod_predict_multiple_structures
module~mod_predict_all_chunks->module~mod_two_body
module~mod_predict_mode
mod_predict_mode
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_hirshfeld_vdw
module~mod_predict_mode->module~mod_predict_multiple_structures
module~mod_predict_mode->module~mod_two_body
module~mod_predict_mode->module~mod_enforce_reading
module~mod_predict_mode->module~mod_initialize
module~mod_write_outfiles
mod_write_outfiles
module~mod_predict_mode->module~mod_write_outfiles
module~mod_runner_interface_bindings->module~mod_calc_atomic_properties
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_evaluate_electrostatics_3g_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_hirshfeld_vdw
module~mod_runner_interface_bindings->module~mod_post_processing_2g_single_structure
module~mod_runner_interface_bindings->module~mod_post_processing_vdw_hirshfeld_single_structure
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_enforce_reading
module~mod_runner_interface_bindings->module~mod_global_features_helper
module~mod_runner_interface_bindings->module~mod_initialize
module~mod_scalingdata->module~mod_feature_calculator
module~mod_scalingdata->module~mod_element
module~mod_train_4g_atomic_charges_structure_batch
mod_train_4g_atomic_charges_structure_batch
module~mod_train_4g_atomic_charges_structure_batch->module~mod_dataloader_file
module~mod_train_4g_atomic_charges_structure_batch->module~mod_feature_calculator
module~mod_train_atomic_property_multiple_atoms
mod_train_atomic_property_multiple_atoms
module~mod_train_atomic_property_multiple_atoms->module~mod_feature_calculator
module~mod_train_loop_4g_charges
mod_train_loop_4g_charges
module~mod_train_loop_4g_charges->module~mod_dataloader_file
module~mod_train_loop_4g_charges->module~mod_feature_calculator
module~mod_train_loop_4g_charges->module~mod_cost_calculator
module~mod_train_loop_4g_charges->module~mod_initialize
module~mod_train_loop_4g_charges->module~mod_output_files_and_cost_4g_charges
module~mod_train_loop_4g_charges->module~mod_train_4g_atomic_charges_structure_batch
module~mod_train_loop_atomic_property
mod_train_loop_atomic_property
module~mod_train_loop_atomic_property->module~mod_dataloader_file
module~mod_train_loop_atomic_property->module~mod_feature_calculator
module~mod_train_loop_atomic_property->module~mod_cost_calculator
module~mod_train_loop_atomic_property->module~mod_initialize
module~mod_train_loop_atomic_property->module~mod_output_files_and_cost
module~mod_train_loop_atomic_property->module~mod_train_atomic_property_multiple_atoms
module~mod_train_loop_short_range
mod_train_loop_short_range
module~mod_train_loop_short_range->module~mod_dataloader_file
module~mod_train_loop_short_range->module~mod_ee4g_feature_calculator
module~mod_train_loop_short_range->module~mod_feature_calculator
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_cost_calculator
module~mod_train_loop_short_range->module~mod_global_features_helper
module~mod_train_loop_short_range->module~mod_initialize
module~mod_train_loop_short_range->module~mod_output_files_and_cost
module~mod_train_loop_short_range->module~mod_output_files_and_cost_4g_short_range
module~mod_train_energy_multiple_structures
mod_train_energy_multiple_structures
module~mod_train_loop_short_range->module~mod_train_energy_multiple_structures
module~mod_train_forces_multiple_structures
mod_train_forces_multiple_structures
module~mod_train_loop_short_range->module~mod_train_forces_multiple_structures
module~mod_train_mode
mod_train_mode
module~mod_train_mode->module~mod_dataloader_file
module~mod_train_mode->module~mod_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_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_two_body
module~mod_train_mode->module~mod_dataset_statistics
module~mod_train_mode->module~mod_dataset_statistics_chi_all_chunks
module~mod_train_mode->module~mod_feature_map_scaling_all_chunks
module~mod_train_mode->module~mod_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_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_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_dataloader_file
program~runner->module~mod_ee4g_feature_calculator
program~runner->module~mod_feature_calculator
program~runner->module~mod_hirshfeld_vdw
program~runner->module~mod_two_body
program~runner->module~mod_calculate_coulomb_matrix
program~runner->module~mod_initialize
program~runner->module~mod_precompute_features_all_chunks
program~runner->module~mod_precompute_global_features_all_chunks
program~runner->module~mod_predict_mode
program~runner->module~mod_train_mode
module~mod_atomic_descriptor->module~mod_element
module~mod_train_energy_multiple_structures->module~mod_initialize
module~mod_train_forces_multiple_structures->module~mod_initialize
module~mod_train_forces_multiple_structures->module~mod_train_energy_multiple_structures
module~mod_write_outfiles->module~mod_initialize
module~mod_write_outfiles_training->module~mod_write_outfiles
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large graphs.
Module Variables
INITIAL_NUM_NEIGHBORS :
integer – The initial guess for the number of neighbors of each atom.
The internal storage of each neighbor list will first be allocated to
this value and then dynamically grows. In other words, this
saves the first iterations of deallocation and allocation.
UPPER_BOUND_NUM_ATOMS_PAIRWISE :
integer – All structures that have fewer atoms than this number will be calculated
using the pairwise neighbor approach.
LOWER_BOUND_NUM_GRIDPOINTS_PAIRWISE :
integer – If the number of gridpoints for a structure is larger than this number
its neighborlist will be constructed using the pairwise approach.
Derived Types Summary
Name
Description
NeighborListType for book keeping of neighbors.
Procedures Summary
Derived Types Details
type NeighborListType for book keeping of neighbors.
Components
num_atoms :
integer – Inherited from NeighborList
num_neighbors :
integer (dim: (:))– array contraining the number of numbers for a given atom.
neighbors :
integer (dim: (:))– flat array containing the global neighbor atom indices
id_in_struct :
integer (dim: (:))– flat array containing all ids in structure of neighbors
xyz_rel :
real (DP) (dim: (:,:))– coordinates of the neighbors.
distance :
real (DP) (dim: (:))– interatomic distance between central atom and neighbor.
info :
integer (dim: (:,:))– start and end index for the neighbors of each atom.
inv_neighbors :
integer (dim: (:))– local index of the reverse edge (opposite periodic image)
atomic_number :
integer (dim: (:))– Atomic number of all neighbors.
cutoff :
real (DP)– save used cutoff
bond_threshold :
real (DP)– Inherited from NeighborList
storage_size :
integer – Inherited from NeighborList
max_storage_size :
integer – Inherited from NeighborList
Type-Bound Procedures
Name
Attributes
Binding
clear
public
⇒ clear
get_distance
public
⇒ get_distance
get_relative_position
public
⇒ get_relative_position
get_id_in_struct
public
⇒ get_id_in_struct
get_atomic_number
public
⇒ get_atomic_number
count_and_allocate
public
⇒ count_and_allocate
generate_neighborlist_single_structure
private
⇒ generate_neighborlist_single_structure
generate_neighborlist_structure_list
private
⇒ generate_neighborlist_structure_list
generate_neighborlist
public
⇒ generate_neighborlist_structure_list⇒ generate_neighborlist_single_structure
resize_storage
public
⇒ resize_storage
add_data_to_storage
public
⇒ add_data_to_storage
allocate_memory
public
⇒ allocate_memory
allocate_memory_exact
public
⇒ allocate_memory_exact
allocate_and_generate
public
⇒ allocate_and_generate_single_structure⇒ allocate_and_generate_structure_list
allocate_and_generate_single_structure
private
⇒ allocate_and_generate_single_structure
allocate_and_generate_structure_list
private
⇒ allocate_and_generate_structure_list
allocate_and_generate_adaptive
public
⇒ allocate_and_generate_single_structure⇒ allocate_and_generate_structure_list
trim
public
⇒ trim
count_neighbors_single_structure
private
⇒ count_neighbors_single_structure
count_neighbors_structure_list
private
⇒ count_neighbors_structure_list
count_neighbors
public
⇒ count_neighbors_single_structure⇒ count_neighbors_structure_list
flatten_nl
private
⇒ flatten_nl
reallocate
private
⇒ reallocate
Inherited By
type~~neighborlist~~InheritedByGraph
type~neighborlist
NeighborList
type~featuremapneighborlist
FeatureMapNeighborList
type~featuremapneighborlist->type~neighborlist
type~filedataloader
FileDataLoader
type~filedataloader->type~featuremapneighborlist
neighbor_lists
type~runnerinterface
RuNNerInterface
type~runnerinterface->type~featuremapneighborlist
neighbor_lists
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Interface Details
interface NeighborListProcedure Details
function constructor_empty_list
function constructor_empty_list ( &)
Construct an empty neighbor list with expected size.
Arguments
num_atoms :
integer [in]
bond_threshold :
real (DP) [in]
mean_num_neighbors :
integer [in]
Called By
proc~~constructor_empty_list~~CalledByGraph
proc~constructor_empty_list
mod_neighborlist::constructor_empty_list
interface~neighborlist
mod_neighborlist::NeighborList
interface~neighborlist->proc~constructor_empty_list
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function constructor_single_structure
function constructor_single_structure ( &)
constructor for a given structure and cutoff.
Arguments
struct :
type (Structure ) [in]
cutoff :
real (DP) [in]
enforce_grid :
logical [in]
bond_threshold :
real (DP) [in]
mean_num_neighbors :
integer [in]
Called By
proc~~constructor_single_structure~2~~CalledByGraph
proc~constructor_single_structure~2
mod_neighborlist::constructor_single_structure
interface~neighborlist
mod_neighborlist::NeighborList
interface~neighborlist->proc~constructor_single_structure~2
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function constructor_structure_list
function constructor_structure_list ( &)
Constructor for a list of structures and a single cutoff.
Arguments
structures :
type (Structure ) (dim: (:)) [in]
cutoff :
real (DP) [in]
enforce_grid :
logical [in]
bond_threshold :
real (DP) [in]
mean_num_neighbors :
integer [in]
Called By
proc~~constructor_structure_list~2~~CalledByGraph
proc~constructor_structure_list~2
mod_neighborlist::constructor_structure_list
interface~neighborlist
mod_neighborlist::NeighborList
interface~neighborlist->proc~constructor_structure_list~2
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function get_distance
function get_distance ( &)
Returns the distance between atom iat and its neighbor ineigh.
Arguments
self :
class (NeighborList ) [in]
iat :
integer [in]
ineigh :
integer [in]
function get_relative_position
function get_relative_position ( &)
Returns the position of neighbor ineigh of atom iat.
Arguments
self :
class (NeighborList ) [in]
iat :
integer [in]
ineigh :
integer [in]
function get_id_in_struct
function get_id_in_struct ( &)
Returns the id in structure of neighbor ineigh of atom iat.
Arguments
self :
class (NeighborList ) [in]
iat :
integer [in]
ineigh :
integer [in]
function get_atomic_number
function get_atomic_number ( &)
Returns the atomic_number of neighbor ineigh of atom iat.
Arguments
self :
class (NeighborList ) [in]
iat :
integer [in]
ineigh :
integer [in]
subroutine allocate_memory
subroutine allocate_memory ( &)
Allocate memory for neighborlist to fit a given number of atoms.
For all arrays that store flat information for the neighbors of all atoms,
an initial guess is made based on INITIAL_NUM_NEIGHBORS.
Arguments
self :
class (NeighborList ) [inout]
num_atoms :
integer [in]
mean_num_neighbors :
integer [in]
Called By
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subroutine allocate_memory_exact
subroutine allocate_memory_exact ( &)
Allocate memory for neighborlist with exact storage size.
This version allocates the flat arrays with the exact storage size
determined from a statistics run, avoiding dynamic resizing.
Arguments
self :
class (NeighborList ) [inout]
num_atoms :
integer [in]
exact_storage_size :
integer [in]
Called By
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subroutine count_and_allocate
subroutine count_and_allocate ( &)
Count the number of atoms in a list of structures and allocate the
internal storage accordingly.
Arguments
self :
class (NeighborList ) [inout]
structures :
type (Structure ) (dim: (:)) [in]
cutoff :
real (DP) [in]
mean_num_neighbors :
integer [in]
Called By
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subroutine generate_neighborlist_structure_list
subroutine generate_neighborlist_structure_list ( &)
Create a flat neighbor list for all given structures.
Arguments
self :
class (NeighborList ) [inout]
structures :
type (Structure ) (dim: (:)) [in]
cutoff :
real (DP) [in]
enforce_grid :
logical [in]
Called By
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subroutine generate_neighborlist_single_structure
subroutine generate_neighborlist_single_structure ( &)
Create a flat neighbor list for all given structures.
Arguments
self :
class (NeighborList ) [inout]
struct :
type (Structure ) [in]
cutoff :
real (DP) [in]
enforce_grid :
logical [in]
Called By
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subroutine clear
subroutine clear ( &)
Free all internal storage and reset all type-bound variables.
Arguments
subroutine find_neighbors_grid
subroutine find_neighbors_grid ( &)
Compute neighborlist using a grid based method. O(n)
Moves atoms back to cell.
Arguments
Called By
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subroutine find_neighbors_pairwise
subroutine find_neighbors_pairwise ( &)
Finds neighbors in a structure given a cutoff. Scales as O(n^2).
Arguments
Called By
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subroutine check_and_add_pair
subroutine check_and_add_pair ( &)
Arguments
iat :
integer [in]
iat_local :
integer [in]
jat :
integer [in]
struct :
type (Structure ) [in]
xyz_relative :
real (DP) (dim: (3)) [in]
tmp_neighbors :
type (DynamicIntArray ) (dim: (struct%num_atoms)) [inout]
tmp_neighbor_id_in_struct :
type (DynamicIntArray ) (dim: (struct%num_atoms)) [inout]
tmp_neighbor_positions :
type (DynamicDoubleArray ) (dim: (struct%num_atoms)) [inout]
tmp_distance :
type (DynamicDoubleArray ) (dim: (struct%num_atoms)) [inout]
tmp_inv_neighbors :
type (DynamicIntArray ) (dim: (struct%num_atoms)) [inout]
cutoff2 :
real (DP) [in]
bond_threshold :
real (DP) [in]
Called By
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subroutine check_and_count_pair
subroutine check_and_count_pair ( &)
Arguments
iat :
integer [in]
iat_local :
integer [in]
jat :
integer [in]
struct :
type (Structure ) [in]
xyz_relative :
real (DP) (dim: (3)) [in]
cutoff2 :
real (DP) [in]
bond_threshold :
real (DP) [in]
num_neighbors :
integer (dim: (:)) [inout]
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subroutine flatten_nl
subroutine flatten_nl ( &)
Arguments
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subroutine resize_storage
subroutine resize_storage ( &)
Arguments
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subroutine add_data_to_storage
subroutine add_data_to_storage ( &)
Append data concerning a neighbor of central atom iat.
Important: This assumes that the storage has the correct size.
Arguments
self :
class (NeighborList ) [inout]
struct :
type (Structure ) [in]
iat :
integer [in]– id_in_struct of the central atom.
jat :
integer [in]– id_in_struct of the neighbor atom.
ineigh :
integer [in]– Index of `neighbor` in the neighbor list of the central atom.
`ioff` + `ineigh` determine the global location of the
neighbor across the entire flat arrays.
ioff :
integer [in]– Start of the central atom's section in the flat neighbor arrays.
neighbor :
integer [in]– id_on_process of the neighbor atom.
xyz :
real (DP) (dim: (3)) [in]– Coordinates of the `neighbor` atom.
inv_neighbor :
integer [in]– Index of the central atom in the neighbor list of the neighbor atom.
distance :
real (DP) [in]– Distance from the central atom to the `neighbor` atom.
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Solid arrows point from a procedure to one which it calls. Dashed
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subroutine trim
subroutine trim ( &)
Arguments
subroutine count_neighbors_structure_list
subroutine count_neighbors_structure_list ( &)
Count neighbors for a list of structures without populating storage.
This fills self%num_neighbors and self%info and sets self%storage_size
and self%max_storage_size to the exact required size. No neighbor entries
are stored.
Arguments
self :
class (NeighborList ) [inout]
structures :
type (Structure ) (dim: (:)) [in]
cutoff :
real (DP) [in]
enforce_grid :
logical [in]
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subroutine count_neighbors_single_structure
subroutine count_neighbors_single_structure ( &)
Count neighbors for a single structure without populating storage.
Arguments
self :
class (NeighborList ) [inout]
struct :
type (Structure ) [in]
cutoff :
real (DP) [in]
enforce_grid :
logical [in]
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subroutine count_neighbors_grid
subroutine count_neighbors_grid ( &)
Grid-based counting pass
Arguments
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Solid arrows point from a procedure to one which it calls. Dashed
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subroutine count_neighbors_pairwise
subroutine count_neighbors_pairwise ( &)
Pairwise counting pass
Arguments
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subroutine reallocate
subroutine reallocate ( &)
Arguments
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subroutine allocate_and_generate_single_structure
subroutine allocate_and_generate_single_structure ( &)
Adaptively allocate and generate neighborlist for a single structure.
This uses either the two-pass statistics approach (if enabled globally)
or the original estimate-and-grow approach.
Arguments
self :
class (NeighborList ) [inout]
struct :
type (Structure ) [in]
cutoff :
real (DP) [in]
enforce_grid :
logical [in]
mean_num_neighbors :
integer [in]
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Solid arrows point from a procedure to one which it calls. Dashed
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Where possible, edges connecting nodes are
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subroutine allocate_and_generate_structure_list
subroutine allocate_and_generate_structure_list ( &)
Adaptively allocate and generate neighborlist for a list of structures.
This uses either the two-pass statistics approach (if enabled globally)
or the original estimate-and-grow approach.
Arguments
self :
class (NeighborList ) [inout]
structures :
type (Structure ) (dim: (:)) [in]
cutoff :
real (DP) [in]
enforce_grid :
logical [in]
mean_num_neighbors :
integer [in]
Called By
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Solid arrows point from a procedure to one which it calls. Dashed
arrows point from an interface to procedures which implement that interface.
This could include the module procedures in a generic interface or the
implementation in a submodule of an interface in a parent module.
Where possible, edges connecting nodes are
given different colours to make them easier to distinguish in
large graphs.