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SODA documentation

Getting started

  • Installation guide
  • Output analysis

SODA basics

  • Overview
  • Preparing a run
  • Parallel execution
  • Monitoring and outputs
  • Restarting a run

Workflows

  • APE
    • First exploration with EAM
    • Exploration with MACE
    • APE settings
    • Analyzing APE output
  • EZGA
    • FCC argon with Lennard–Jones
    • EZGA settings
    • Preparing custom factories for SODA–EZGA
    • Analyzing EZGA output
  • NEBScape
    • Surface reactions with MACE
    • NEBScape settings
    • Analyzing NEBScape output
  • AKMC
    • First diffusion run with EAM
    • AKMC with GAP
    • AKMC with MACE
    • AKMC settings
    • Analyzing AKMC output

Reference

  • API reference
    • Opening databases
      • soda_lib_class
        • analyze_process_product_states
        • check_ape_cluster_member_distances
        • check_duplicate_processes
        • check_duplicate_states
        • check_nebscape_minhop_history_equivalence
        • close
        • compare_nebscape_fairchem_native_outputs
        • compare_nebscape_native_downstream_outputs
        • compare_nebscape_optimize_only_native_outputs
        • detect_workflow
        • get_final_results
        • get_nebscape_workflow_progress_diagnostics
        • read_dynamics
        • read_environmentlib
        • read_ezga
        • read_meta
        • read_nebscape
        • read_process_product_states
        • read_state
        • read_statelist
        • summarize_descriptor_registry_provenance
        • summarize_descriptor_sampling_flags
        • summarize_nebscape_fairchem_hdf5_numeric_sanity
        • summarize_nebscape_fairchem_runtime
        • summarize_nebscape_geometry_pair_preparation_logs
        • summarize_nebscape_hpc_acceptance
        • summarize_nebscape_minhop_rejections
        • summarize_nebscape_minhop_run_modes
        • summarize_nebscape_workflow_progress
    • States and processes
      • read_state_struct_array
      • get_atomic_numbers_list
      • get_species_list
      • get_cell
      • get_fixed_list
      • get_pos
      • get_atoms
      • get_rsp_pos
      • get_rsp_atoms
      • get_barrier
      • get_barrier_list
      • get_prefactor
      • get_prefactor_list
      • get_rate
      • get_energy
      • get_process_product_states_table
      • get_process_table
      • get_state_id_list
      • get_state_process_id_list
      • structures_are_equivalent
      • process_class
        • get_atoms
        • get_barrier
        • get_barrier_list
        • get_cell
        • get_count
        • get_energies
        • get_energy
        • get_fixed_list
        • get_pos
        • get_prefactor
        • get_prefactor_list
        • get_rates
        • get_refst
        • get_rsp_atoms
        • get_rsp_count
        • get_rsp_pos
        • get_rsp_refst
        • get_species_list
        • get_stat_repeats
      • state_class
        • get_atoms
        • get_barrier_list
        • get_cell
        • get_energy
        • get_fixed_list
        • get_force_calls
        • get_pos
        • get_prefactor_list
        • get_proc_list
        • get_search_ids
        • get_species_list
        • get_stat_repeats_list
        • get_termination_ids
        • preload
        • soda_analyzer.state_class.atoms
        • soda_analyzer.state_class.barrier_list
        • soda_analyzer.state_class.cell
        • soda_analyzer.state_class.energy
        • soda_analyzer.state_class.fixed_list
        • soda_analyzer.state_class.force_calls
        • soda_analyzer.state_class.pos
        • soda_analyzer.state_class.prefactor_list
        • soda_analyzer.state_class.proc_num
        • soda_analyzer.state_class.search_id_list
        • soda_analyzer.state_class.search_stats
        • soda_analyzer.state_class.species_list
        • soda_analyzer.state_class.stat_repeats_list
        • soda_analyzer.state_class.termination_list
    • APE environments
      • get_descriptor_registries_table
      • get_full_descriptors_table
      • get_descriptor_embedding_operator
      • normalize_descriptor_embed_op_for_decaf
      • get_descriptor_bandwidths
      • get_descriptor_embedding_members
      • get_descriptor_clustering_members
      • get_descriptor_meta_dict
      • get_descriptor_full_id_from_registry_row
      • read_descriptor_model_from_h5
      • build_decaf_model_from_h5
      • environment_class
        • get_atom
        • get_atoms
        • get_embedded_descriptor
        • get_full_descriptor
        • get_registry_row
        • get_registry_table
        • soda_analyzer.environment_class.atom
        • soda_analyzer.environment_class.atoms
        • soda_analyzer.environment_class.embedded_descriptor
        • soda_analyzer.environment_class.full_descriptor
      • environment_lib_class
        • build_decaf_model
        • export_cluster_members
        • get_atom
        • get_atoms
        • get_atoms_by_trace
        • get_cluster_birth_cycle
        • get_cluster_birth_cycles
        • get_cluster_ids
        • get_cluster_member_count
        • get_cluster_member_traces
        • get_cluster_members
        • get_cluster_model_member_rows
        • get_clustering_member_rows
        • get_clusters_for_structure
        • get_embedded_descriptor
        • get_embedded_descriptors
        • get_embedded_descriptors_by_cluster
        • get_embedded_descriptors_by_registry_rows
        • get_embedding_member_rows
        • get_full_descriptor
        • get_full_descriptor_id
        • get_full_descriptor_ids_by_registry_rows
        • get_full_descriptors_by_cluster
        • get_full_descriptors_by_registry_rows
        • get_model_member_registry_rows
        • get_model_meta
        • get_model_payload
        • get_registry_members
        • get_registry_row
        • get_representative_environment
        • get_trace
        • group_cluster_members_by_structure
        • read_env
        • read_envlist
        • read_meta
        • summarize_clusters
    • EZGA populations and generations
      • ezga_generation_commit_class
        • to_dict
      • ezga_sage_structure_payload_class
        • to_dict
      • ezga_structure_class
        • to_dict
      • ezga_blob_class
        • to_dict
      • ezga_simulation_frame_class
        • get_structure
        • to_dict
      • ezga_reactivity_irc_path_class
        • get_endpoint_structures
        • get_frames
        • get_frames_by_kind
        • to_dict
      • ezga_lib_class
        • close
        • get_agent_ids
        • get_blobs
        • get_committed_table_prefix
        • get_complete_commits
        • get_generation_commits
        • get_generations
        • get_hise_stages
        • get_latest_complete_commit
        • get_population_memberships
        • get_reactivity_irc_paths
        • get_rejected_structures
        • get_row_dicts
        • get_rows
        • get_sage_structure_payloads
        • get_structures
        • get_table
        • read_agent_metadata
        • read_blob
        • read_reactivity_irc_path
        • read_sage_structure_payload
        • read_structure
        • summarize
        • validate_sage_structure_payloads
    • NEBScape structures and pathways
      • nebscape_molecule_class
      • nebscape_reaction_side_class
      • nebscape_reaction_class
      • nebscape_prepare_summary_class
      • nebscape_minhop_summary_class
      • nebscape_minhop_accepted_minimum_class
        • get_audit_record
      • nebscape_structure_class
        • get_lineage
        • get_lineage_summary
        • get_parent_structure
      • nebscape_geometry_pair_class
        • get_endpoint_summary
      • nebscape_band_class
        • get_endpoint_analysis
        • get_endpoint_summary
        • get_geometry_pair
        • get_images
        • get_neb_result_images
        • get_neb_sella_irc_frames
        • get_neb_sella_irc_info
        • get_neb_summary
      • nebscape_band_image_class
      • nebscape_neb_summary_class
        • get_result_images
        • get_sella_irc_frames
        • get_sella_irc_info
      • nebscape_neb_result_image_class
      • nebscape_sella_irc_info_class
        • get_frames
        • get_frames_by_kind
      • nebscape_sella_irc_frame_class
      • nebscape_lib_class
        • check_minhop_history_equivalence
        • close
        • export_native_nebscape_format
        • get_accepted_minhop_structures
        • get_aligned_fs_relaxation_summaries
        • get_band_endpoint_analysis
        • get_band_endpoint_summaries
        • get_band_ids_by_reaction
        • get_band_image_atoms
        • get_band_images
        • get_band_metadata
        • get_bands
        • get_bands_for_pair
        • get_downstream_work_diagnostics
        • get_dropped_bands
        • get_final_results
        • get_finalized_minhop_structures
        • get_geometry_pair_preparation_summaries
        • get_geometry_pairs
        • get_initial_selected_placements
        • get_initial_selected_structures
        • get_latest_workflow_checkpoint
        • get_loadrun_resume_diagnostics
        • get_minhop_accepted_minima
        • get_minhop_cost_diagnostics
        • get_minhop_decision_records
        • get_minhop_finalization_diagnostics
        • get_minhop_finalization_records
        • get_minhop_finalization_work_records
        • get_minhop_history_scope_diagnostics
        • get_minhop_invalidation_records
        • get_minhop_proposal_records
        • get_minhop_reference_records
        • get_minhop_repair_diagnostics
        • get_minhop_result_structures
        • get_minhop_run_mode_diagnostics
        • get_minhop_summaries
        • get_minima
        • get_neb_result_images
        • get_neb_sella_irc_frames
        • get_neb_summaries
        • get_partial_neb_result_diagnostics
        • get_phase_generation_diagnostics
        • get_prepare_summaries
        • get_reaction_lineage_trace
        • get_selected_bands
        • get_selected_placements
        • get_sorted_interpolation_table
        • get_structures
        • get_table_counts
        • get_uncheckpointed_row_diagnostics
        • get_workflow_checkpoints
        • get_workflow_progress_diagnostics
        • has_minhop_history_records
        • read_band
        • read_band_image
        • read_geometry_pair
        • read_minhop_accepted_minimum
        • read_minhop_summary
        • read_neb_result_image
        • read_neb_sella_irc_frame
        • read_neb_sella_irc_info
        • read_neb_summary
        • read_prepare_summary
        • read_reaction
        • read_structure
        • summarize_minhop_rejections
    • Run preparation and diagnostics
      • format_nebscape_setup_conversion_report
      • format_soda_run_check_report
      • check_soda_run_folder
      • format_soda_run_command_suggestion
      • suggest_soda_run_command
      • format_ezga_setup_conversion_report
      • check_nebscape_minhop_history_equivalence
      • summarize_nebscape_minhop_rejections
      • summarize_nebscape_minhop_run_modes
      • summarize_nebscape_minhop_finalization_timing
      • summarize_nebscape_workflow_progress
      • summarize_nebscape_hpc_acceptance
      • format_nebscape_hpc_acceptance_report
      • compare_nebscape_optimize_only_native_outputs
      • format_nebscape_optimize_only_native_comparison_report
      • compare_nebscape_native_downstream_outputs
      • format_nebscape_native_downstream_comparison_report
      • summarize_nebscape_fairchem_runtime
      • format_nebscape_fairchem_runtime_report
      • summarize_nebscape_fairchem_soda_config
      • compare_nebscape_fairchem_config_runtime
      • summarize_nebscape_fairchem_hdf5_numeric_sanity
      • format_nebscape_fairchem_hdf5_numeric_sanity_report
      • compare_nebscape_fairchem_native_outputs
      • format_nebscape_fairchem_native_comparison_report
      • summarize_nebscape_geometry_pair_preparation_logs
      • check_duplicate_states
      • check_duplicate_processes
      • check_ape_cluster_member_distances
      • analyze_process_product_states
      • summarize_descriptor_sampling_flags
      • summarize_descriptor_registry_provenance
      • format_duplicate_state_report
      • format_duplicate_process_report
      • format_ape_cluster_member_distance_report
      • format_process_product_state_report
      • format_descriptor_sampling_flags_report
      • format_descriptor_registry_provenance_report
    • Conversion and export
      • read_con
      • repair_con_file
      • flip_nebscape_soda_xyz_tags
      • convert_native_nebscape_xyz_to_soda
      • convert_soda_xyz_to_native_nebscape
      • convert_native_nebscape_calculator_to_soda_config
      • convert_native_nebscape_run_setup_to_soda
      • convert_ezga_soda_xyz_fixed_flags
      • convert_native_ezga_xyz_to_soda
      • convert_soda_xyz_to_native_ezga
      • convert_native_ezga_run_setup_to_soda
      • convert_native_ezga_multi_agent_run_setup_to_soda
      • convert_hdf5_to_current
      • export_nebscape_native_format
  • Citing SODA
  • Third-party notices
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