Index Symbols | _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y Symbols --align-type rgpycrumbs-eon-con-splitter command line option --api-key rgpycrumbs-prefix-delete-packages command line option --box-diagonal rgpycrumbs-eon-con-splitter command line option --center rgpycrumbs-eon-con-splitter command line option --channel rgpycrumbs-prefix-delete-packages command line option --charge rgpycrumbs-geom-detect-fragments-bond-order command line option --config rgpycrumbs-eon-generate-nwchem-input command line option --dry-run rgpycrumbs-prefix-delete-packages command line option --images-per-path rgpycrumbs-eon-con-splitter command line option --ira-kmax rgpycrumbs-eon-con-splitter command line option --method rgpycrumbs-geom-detect-fragments-batch command line option rgpycrumbs-geom-detect-fragments-bond-order command line option --min-dist rgpycrumbs-geom-detect-fragments-batch command line option rgpycrumbs-geom-detect-fragments-bond-order command line option rgpycrumbs-geom-detect-fragments-geometric command line option --mode rgpycrumbs-eon-con-splitter command line option --multiplicity rgpycrumbs-geom-detect-fragments-bond-order command line option --multiplier rgpycrumbs-geom-detect-fragments-geometric command line option --no-center rgpycrumbs-eon-con-splitter command line option --no-fcc-vacancy rgpycrumbs-eon-ptmdisp command line option --output rgpycrumbs-eon-generate-nwchem-input command line option rgpycrumbs-geom-detect-fragments-batch command line option --output-dir rgpycrumbs-eon-con-splitter command line option --package-name rgpycrumbs-prefix-delete-packages command line option --path-index rgpycrumbs-eon-con-splitter command line option --path-list-filename rgpycrumbs-eon-con-splitter command line option --pattern rgpycrumbs-geom-detect-fragments-batch command line option --pos-file rgpycrumbs-eon-generate-nwchem-input command line option --radius-type rgpycrumbs-geom-detect-fragments-geometric command line option --structure-type rgpycrumbs-eon-ptmdisp command line option --threshold rgpycrumbs-geom-detect-fragments-bond-order command line option --use-ira rgpycrumbs-eon-con-splitter command line option --verbose rgpycrumbs-eon-ptmdisp command line option --version-regex rgpycrumbs-prefix-delete-packages command line option --visualize rgpycrumbs-geom-detect-fragments-bond-order command line option rgpycrumbs-geom-detect-fragments-geometric command line option -o rgpycrumbs-eon-generate-nwchem-input command line option -s rgpycrumbs-eon-ptmdisp command line option -v rgpycrumbs-eon-ptmdisp command line option _ __all__ (in module rgpycrumbs.eon) __call__() (rgpycrumbs.surfaces._base.BaseGradientSurface method) (rgpycrumbs.surfaces._base.BaseSurface method) (rgpycrumbs.surfaces.standard.FastTPS method) __getattr__() (in module rgpycrumbs) (in module rgpycrumbs.eon) (rgpycrumbs._aux._LazyModule method) __repr__() (rgpycrumbs._aux._LazyModule method) __version__ (in module rgpycrumbs) _apply() (in module rgpycrumbs.eon._render_cli) _apply_frame_energy() (in module rgpycrumbs.eon.con_splitter) _apply_ira_alignment() (in module rgpycrumbs.geom.api.alignment) _as_bool() (in module rgpycrumbs.config) _coerce_value() (in module rgpycrumbs.eon.plot_config) _COLUMN_ALIASES (in module rgpycrumbs.eon.plt_kmc) _COMMANDS (in module rgpycrumbs.eon) _CON_SUFFIXES (in module rgpycrumbs.eon.con_splitter) _CPU_OVERRIDES (in module rgpycrumbs._aux) _cuda_available (in module rgpycrumbs._aux) _cuh2_min() (in module rgpycrumbs.xts.saddle.cuh2) _DEFAULT_ORDER (in module rgpycrumbs.eon.plt_kmc) _DEPENDENCY_MAP (in module rgpycrumbs._aux) _dimer_config_sections() (in module rgpycrumbs.eon.seed_dimers) _dispatch() (in module rgpycrumbs.cli) _DISPLACE_MAGNITUDE (in module rgpycrumbs.eon.seed_dimers) _energy_from_atoms() (in module rgpycrumbs.eon.con_splitter) _env_flag() (in module rgpycrumbs.cli) _env_flag_any() (in module rgpycrumbs.config) _EXPECTED_COORD_COLS (in module rgpycrumbs.chemgp.match_atoms) _extract_dispatch() (in module rgpycrumbs.config) _file_stems (in module rgpycrumbs.cli) _find_editable_source() (in module rgpycrumbs.cli) _first_env() (in module rgpycrumbs.config) _fit() (rgpycrumbs.surfaces._base.BaseGradientSurface method) (rgpycrumbs.surfaces._base.BaseSurface method) (rgpycrumbs.surfaces.gradient_imq.GradientIMQ method) (rgpycrumbs.surfaces.gradient_matern.GradientMatern method) (rgpycrumbs.surfaces.gradient_nystrom.NystromGradientIMQ method) (rgpycrumbs.surfaces.gradient_rq.GradientRQ method) (rgpycrumbs.surfaces.gradient_se.GradientSE method) (rgpycrumbs.surfaces.standard.FastIMQ method) (rgpycrumbs.surfaces.standard.FastMatern method) _flatten_section() (in module rgpycrumbs.eon.plot_config) _get_dep_cache_dir() (in module rgpycrumbs._aux) _get_scripts_in_folder() (in module rgpycrumbs.cli) _grad_imq_predict() (in module rgpycrumbs.surfaces.gradient_imq) _grad_imq_solve() (in module rgpycrumbs.surfaces.gradient_imq) _grad_imq_var() (in module rgpycrumbs.surfaces.gradient_imq) _grad_matern_predict() (in module rgpycrumbs.surfaces.gradient_matern) _grad_matern_solve() (in module rgpycrumbs.surfaces.gradient_matern) _grad_matern_var() (in module rgpycrumbs.surfaces.gradient_matern) _grad_rq_predict() (in module rgpycrumbs.surfaces.gradient_rq) _grad_rq_solve() (in module rgpycrumbs.surfaces.gradient_rq) _grad_rq_var() (in module rgpycrumbs.surfaces.gradient_rq) _grad_se_predict() (in module rgpycrumbs.surfaces.gradient_se) _grad_se_solve() (in module rgpycrumbs.surfaces.gradient_se) _grad_se_var() (in module rgpycrumbs.surfaces.gradient_se) _has_cuda() (in module rgpycrumbs._aux) _image_energies() (in module rgpycrumbs.eon.seed_dimers) _import_from_parent_env() (in module rgpycrumbs._aux) _imq_kernel_matrix() (in module rgpycrumbs.surfaces._kernels) _imq_predict() (in module rgpycrumbs.surfaces.standard) _imq_solve() (in module rgpycrumbs.surfaces.standard) _imq_var() (in module rgpycrumbs.surfaces.standard) _IN_ENV_STACK_MODULES (in module rgpycrumbs.cli) _in_env_stack_ready() (in module rgpycrumbs.cli) _is_con_path() (in module rgpycrumbs.eon.con_splitter) _is_file() (in module rgpycrumbs.config) _LazyModule (class in rgpycrumbs._aux) _LIST_PATH_KEYS (in module rgpycrumbs.eon.plot_config) _load_lock_pins_or_exit() (in module rgpycrumbs.cli) _load_toml_file() (in module rgpycrumbs.config) _log_via_eon_config_fallback() (in module rgpycrumbs.eon._mlflow.log_params) _log_via_eon_schema() (in module rgpycrumbs.eon._mlflow.log_params) _make_script_command() (in module rgpycrumbs.cli) _match_eon_mode() (in module rgpycrumbs.eon.seed_dimers) _matern_kernel_matrix() (in module rgpycrumbs.surfaces._kernels) _matern_predict() (in module rgpycrumbs.surfaces.standard) _matern_solve() (in module rgpycrumbs.surfaces.standard) _matern_var() (in module rgpycrumbs.surfaces.standard) _merge_section() (in module rgpycrumbs.config) _neb_tangent() (in module rgpycrumbs.eon.seed_dimers) _noise_per_obs (rgpycrumbs.surfaces._base.BaseGradientSurface attribute) _normalize_dist_name() (in module rgpycrumbs.cli) _normalize_packages() (in module rgpycrumbs.config) _NUM (in module rgpycrumbs.parsers.common) _nystrom_grad_imq_predict() (in module rgpycrumbs.surfaces.gradient_nystrom) _nystrom_grad_imq_var() (in module rgpycrumbs.surfaces.gradient_nystrom) _parse_override() (in module rgpycrumbs.eon.plt_neb_stitch) _parse_segment() (in module rgpycrumbs.eon.plt_neb_stitch) _PATH_KEYS (in module rgpycrumbs.eon.plot_config) _perform_ira_match() (in module rgpycrumbs.geom.ira) _pin_from_purl() (in module rgpycrumbs.locks) _plot_convergence() (in module rgpycrumbs.eon.plt_min) (in module rgpycrumbs.eon.plt_saddle) _plot_landscape() (in module rgpycrumbs.eon.plt_min) (in module rgpycrumbs.eon.plt_saddle) _plot_mode_evolution() (in module rgpycrumbs.eon.plt_saddle) _plot_profile() (in module rgpycrumbs.eon.plt_min) (in module rgpycrumbs.eon.plt_saddle) _predict_chunk() (rgpycrumbs.surfaces._base.BaseGradientSurface method) (rgpycrumbs.surfaces._base.BaseSurface method) (rgpycrumbs.surfaces.gradient_imq.GradientIMQ method) (rgpycrumbs.surfaces.gradient_matern.GradientMatern method) (rgpycrumbs.surfaces.gradient_nystrom.NystromGradientIMQ method) (rgpycrumbs.surfaces.gradient_rq.GradientRQ method) (rgpycrumbs.surfaces.gradient_se.GradientSE method) (rgpycrumbs.surfaces.standard.FastIMQ method) (rgpycrumbs.surfaces.standard.FastMatern method) _prefer_in_env_interpreter() (in module rgpycrumbs.cli) _PYLOCK_NAME (in module rgpycrumbs.locks) _pyproject_project_name() (in module rgpycrumbs.cli) _RANDOM_SEED (in module rgpycrumbs.eon.seed_dimers) _read_trajectory_frames() (in module rgpycrumbs.eon.con_splitter) _require_tomllib() (in module rgpycrumbs.locks) _resolve() (rgpycrumbs._aux._LazyModule method) _resolve_path() (in module rgpycrumbs.config) _resolve_pip_spec() (in module rgpycrumbs._aux) _rmsd_single() (in module rgpycrumbs.geom.api.alignment) _run_command_live() (in module rgpycrumbs.run.jupyter) _run_plt_neb() (in module rgpycrumbs.eon.plt_neb_stitch) _solve() (rgpycrumbs.surfaces._base.BaseGradientSurface method) (rgpycrumbs.surfaces._base.BaseSurface method) (rgpycrumbs.surfaces.gradient_imq.GradientIMQ method) (rgpycrumbs.surfaces.gradient_matern.GradientMatern method) (rgpycrumbs.surfaces.gradient_nystrom.NystromGradientIMQ method) (rgpycrumbs.surfaces.gradient_rq.GradientRQ method) (rgpycrumbs.surfaces.gradient_se.GradientSE method) (rgpycrumbs.surfaces.standard.FastIMQ method) (rgpycrumbs.surfaces.standard.FastMatern method) _stable_nystrom_grad_imq_solve() (in module rgpycrumbs.surfaces.gradient_nystrom) _surface_grid() (in module rgpycrumbs.xts.saddle.mb) _tps_kernel_matrix() (in module rgpycrumbs.surfaces._kernels) _tps_predict() (in module rgpycrumbs.surfaces.standard) _tps_solve() (in module rgpycrumbs.surfaces.standard) _tps_var() (in module rgpycrumbs.surfaces.standard) _true_e_dat() (in module rgpycrumbs.xts.saddle.cuh2) _uv_editable_sources() (in module rgpycrumbs.cli) _uv_install() (in module rgpycrumbs._aux) _valid_groups (in module rgpycrumbs.cli) _var_chunk() (rgpycrumbs.surfaces._base.BaseGradientSurface method) (rgpycrumbs.surfaces._base.BaseSurface method) (rgpycrumbs.surfaces.gradient_imq.GradientIMQ method) (rgpycrumbs.surfaces.gradient_matern.GradientMatern method) (rgpycrumbs.surfaces.gradient_nystrom.NystromGradientIMQ method) (rgpycrumbs.surfaces.gradient_rq.GradientRQ method) (rgpycrumbs.surfaces.gradient_se.GradientSE method) (rgpycrumbs.surfaces.standard.FastIMQ method) (rgpycrumbs.surfaces.standard.FastMatern method) _VERSION_OPS (in module rgpycrumbs.locks) _write_con_atoms() (in module rgpycrumbs.eon.con_splitter) _write_con_frame() (in module rgpycrumbs.eon.con_splitter) _write_dimer_config() (in module rgpycrumbs.eon.seed_dimers) _xdg_config_home() (in module rgpycrumbs.config) A adapt_plot_source() (in module rgpycrumbs.eon.plot_dispatch) add_config_option() (in module rgpycrumbs.eon._render_cli) add_render_options() (in module rgpycrumbs.eon._render_cli) adjust_text() (in module rgpycrumbs.eon.plt_neb) align_path() (in module rgpycrumbs.eon.con_splitter) align_structure_robust() (in module rgpycrumbs.geom.api.alignment) AlignmentMethod (class in rgpycrumbs.geom.api.alignment) AlignmentResult (class in rgpycrumbs.geom.api.alignment) AlignMode (class in rgpycrumbs.eon.con_splitter) ALL (rgpycrumbs.eon.con_splitter.AlignMode attribute) analyze_structure() (in module rgpycrumbs.geom.analysis) apply_pin_to_spec() (in module rgpycrumbs.api) (in module rgpycrumbs.locks) (in module rgpycrumbs.sbom) arc_dist (rgpycrumbs.basetypes.nebpath attribute) ASE_PROCRUSTES (rgpycrumbs.geom.api.alignment.AlignmentMethod attribute) atoms (rgpycrumbs.geom.api.alignment.AlignmentResult attribute) auto_deps (rgpycrumbs.config.RgpycrumbsConfig attribute) AUTO_DEPS_ENVS (in module rgpycrumbs.config) B barrier (rgpycrumbs.basetypes.SaddleMeasure attribute) (rgpycrumbs.eon.plt_kmc.DynamicsStep attribute) BASE_URL (in module rgpycrumbs.prefix.delete_packages) BaseGradientSurface (class in rgpycrumbs.surfaces._base) BaseSurface (class in rgpycrumbs.surfaces._base) batch() (in module rgpycrumbs.chemgp.plot_gp) (in module rgpycrumbs.geom.detect_fragments) BCC (rgpycrumbs.eon.ptmdisp.CrystalStructure attribute) BLESS_LOG (in module rgpycrumbs.parsers.bless) BLESS_TIME() (in module rgpycrumbs.parsers.bless) BOND_ORDER (rgpycrumbs.geom.fragments.DetectionMethod attribute) bond_order() (in module rgpycrumbs.geom.detect_fragments) build_graph_and_find_components() (in module rgpycrumbs.geom.fragments) C calculate_rmsd() (in module rgpycrumbs.geom.ira) calculate_rmsd_from_ref() (in module rgpycrumbs.geom.api.alignment) cli() (in module rgpycrumbs.chemgp.plot_gp) click_nondefault_overrides() (in module rgpycrumbs.eon.plot_config) cmap_name (in module rgpycrumbs.geom.fragment_visualization) collect_kmc_n2_timeline() (in module rgpycrumbs.eon.plt_kmc) COMMAND_DEFAULTS (in module rgpycrumbs.eon.plot_config) common_options() (in module rgpycrumbs.chemgp.plot_gp) compute_projection_basis (in module rgpycrumbs.eon.plt_neb) con_splitter() (in module rgpycrumbs.eon.con_splitter) config_cmd() (in module rgpycrumbs.cli) CONFIG_HELP (in module rgpycrumbs.eon._render_cli) CONFIG_PATH_ENV (in module rgpycrumbs.api) (in module rgpycrumbs.config) CONFIG_PATH_ENV_LEGACY (in module rgpycrumbs.config) CONSOLE (in module rgpycrumbs.eon.con_splitter) (in module rgpycrumbs.eon.to_mlflow) convergence() (in module rgpycrumbs.chemgp.plot_gp) count_ejected_n2() (in module rgpycrumbs.eon.plt_kmc) CrystalStructure (class in rgpycrumbs.eon.ptmdisp) cuh2_potential() (in module rgpycrumbs.xts.saddle.cuh2) cumulative_n2 (rgpycrumbs.eon.plt_kmc.KmcTimeline attribute) CYCLONEDX (rgpycrumbs.locks.LockFormat attribute) D D_plus_1 (rgpycrumbs.surfaces._base.BaseGradientSurface attribute) DEFAULT_BOND_MULTIPLIER (in module rgpycrumbs.geom.fragments) DEFAULT_BOND_ORDER_THRESHOLD (in module rgpycrumbs.geom.fragments) DEFAULT_INPUT_PATTERN (in module rgpycrumbs.eon.plt_neb) default_output_path() (in module rgpycrumbs.eon._single_ended_cli) DEFAULT_PATH_PATTERN (in module rgpycrumbs.eon.plt_neb) DEFAULT_TARGET_COORDS (in module rgpycrumbs.chemgp.match_atoms) delete_package() (in module rgpycrumbs.prefix.delete_packages) detect_lock_format() (in module rgpycrumbs.locks) DetectionMethod (class in rgpycrumbs.geom.fragments) DEV_ENVS (in module rgpycrumbs.config) dimer_rot (rgpycrumbs.basetypes.SaddleMeasure attribute) DIMER_STEP_RE (in module rgpycrumbs.eon.to_mlflow) dimer_trans (rgpycrumbs.basetypes.SaddleMeasure attribute) DimerOpt (class in rgpycrumbs.basetypes) DIRECTORY rgpycrumbs-geom-detect-fragments-batch command line option do_ira() (in module rgpycrumbs.geom.ira) DynamicsStep (class in rgpycrumbs.eon.plt_kmc) E e_mean (rgpycrumbs.surfaces._base.BaseGradientSurface attribute) enable_library_auto_deps() (in module rgpycrumbs._aux) enabled (rgpycrumbs.geom.api.alignment.IRAConfig attribute) ENDPOINTS (rgpycrumbs.eon.con_splitter.AlignMode attribute) energies (rgpycrumbs.eon.plt_kmc.KmcTimeline attribute) energy (rgpycrumbs.basetypes.MolGeom attribute) (rgpycrumbs.basetypes.nebpath attribute) (rgpycrumbs.eon.plt_kmc.DynamicsStep attribute) (rgpycrumbs.eon.seed_dimers.PeakSeed attribute) energy_vs_reactant (rgpycrumbs.eon.seed_dimers.PeakSeed attribute) ensure_import (in module rgpycrumbs.eon.plt_neb) ensure_import() (in module rgpycrumbs._aux) (in module rgpycrumbs.api) extract_config_layers() (in module rgpycrumbs.eon.plot_config) F F (in module rgpycrumbs.eon._render_cli) FastIMQ (class in rgpycrumbs.surfaces.standard) FastMatern (class in rgpycrumbs.surfaces.standard) FastTPS (class in rgpycrumbs.surfaces.standard) FCC (rgpycrumbs.eon.ptmdisp.CrystalStructure attribute) FILENAME rgpycrumbs-eon-ptmdisp command line option rgpycrumbs-geom-detect-fragments-bond-order command line option rgpycrumbs-geom-detect-fragments-geometric command line option find_fragments_bond_order() (in module rgpycrumbs.geom.fragments) find_fragments_geometric() (in module rgpycrumbs.geom.fragments) find_mismatch_indices() (in module rgpycrumbs.eon.ptmdisp) find_neb_peaks() (in module rgpycrumbs.eon.seed_dimers) find_project_config() (in module rgpycrumbs.config) FLEX (rgpycrumbs.eon.con_splitter.SplitMode attribute) force_uv (rgpycrumbs.config.RgpycrumbsConfig attribute) FORCE_UV_ENVS (in module rgpycrumbs.config) forces (rgpycrumbs.basetypes.MolGeom attribute) fps() (in module rgpycrumbs.chemgp.plot_gp) full_covariance_imq() (in module rgpycrumbs.surfaces._kernels) full_covariance_matern() (in module rgpycrumbs.surfaces._kernels) full_covariance_rq() (in module rgpycrumbs.surfaces._kernels) full_covariance_se() (in module rgpycrumbs.surfaces._kernels) G generate_orca_input module generic_negative_mll() (in module rgpycrumbs.surfaces._base) GEOMETRIC (rgpycrumbs.geom.fragments.DetectionMethod attribute) geometric() (in module rgpycrumbs.geom.detect_fragments) get_from_gitroot_con() (in module rgpycrumbs.xts.cuh2.datgen) get_gitroot() (in module rgpycrumbs._aux) get_packages_to_delete() (in module rgpycrumbs.prefix.delete_packages) get_surface_model() (in module rgpycrumbs.surfaces) getstrform() (in module rgpycrumbs._aux) GradientIMQ (class in rgpycrumbs.surfaces.gradient_imq) GradientMatern (class in rgpycrumbs.surfaces.gradient_matern) GradientRQ (class in rgpycrumbs.surfaces.gradient_rq) GradientSE (class in rgpycrumbs.surfaces.gradient_se) H hausdorff_dist (rgpycrumbs.geom.api.alignment.IRAMatchResults attribute) HCP (rgpycrumbs.eon.ptmdisp.CrystalStructure attribute) hd (rgpycrumbs.geom.ira.IRAComp attribute) helpers module HILLS_FILENAME (in module rgpycrumbs.plumed.direct_reconstruction) I ICO (rgpycrumbs.eon.ptmdisp.CrystalStructure attribute) IDIMER_ROT_RE (in module rgpycrumbs.eon.to_mlflow) image_index (rgpycrumbs.eon.seed_dimers.PeakSeed attribute) imq_kernel_elem() (in module rgpycrumbs.surfaces._kernels) IncomparableStructuresError init_energy (rgpycrumbs.basetypes.SaddleMeasure attribute) IRA_KMAX_DEFAULT (in module rgpycrumbs.eon.plt_min) (in module rgpycrumbs.eon.plt_neb) (in module rgpycrumbs.eon.plt_saddle) ira_mod (in module rgpycrumbs.eon.con_splitter) (in module rgpycrumbs.geom.api.alignment) IRA_PERMUTATION (rgpycrumbs.geom.api.alignment.AlignmentMethod attribute) IRAComp (class in rgpycrumbs.geom.ira) IRAConfig (class in rgpycrumbs.geom.api.alignment) IRAMatchInputs (class in rgpycrumbs.geom.api.alignment) IRAMatchResults (class in rgpycrumbs.geom.api.alignment) is_ira_pair() (in module rgpycrumbs.geom.ira) iter_steps (rgpycrumbs.basetypes.SaddleMeasure attribute) iteration (rgpycrumbs.basetypes.nebiter attribute) K k_matrix_imq_grad_map (in module rgpycrumbs.surfaces._kernels) k_matrix_matern_grad_map (in module rgpycrumbs.surfaces._kernels) k_matrix_rq_grad_map (in module rgpycrumbs.surfaces._kernels) k_matrix_se_grad_map (in module rgpycrumbs.surfaces._kernels) kmax (rgpycrumbs.geom.api.alignment.IRAConfig attribute) (rgpycrumbs.geom.api.alignment.IRAMatchInputs attribute) KmcTimeline (class in rgpycrumbs.eon.plt_kmc) L lazy_import() (in module rgpycrumbs._aux) (in module rgpycrumbs.api) library_plot() (in module rgpycrumbs.eon.plot_config) load_config() (in module rgpycrumbs.api) (in module rgpycrumbs.config) load_cyclonedx() (in module rgpycrumbs.locks) (in module rgpycrumbs.sbom) load_plot_config() (in module rgpycrumbs.eon.plot_config) load_pypi_pins() (in module rgpycrumbs.api) (in module rgpycrumbs.locks) (in module rgpycrumbs.sbom) load_toml_lock() (in module rgpycrumbs.locks) load_trajectories() (in module rgpycrumbs.eon._single_ended_cli) lock_path (rgpycrumbs.config.RgpycrumbsConfig attribute) LOCK_PATH_ENV (in module rgpycrumbs.api) (in module rgpycrumbs.locks) LOCK_PATH_ENV_LEGACY (in module rgpycrumbs.locks) LOCK_PATH_ENVS (in module rgpycrumbs.config) LockFormat (class in rgpycrumbs.locks) log (in module rgpycrumbs.chemgp.match_atoms) (in module rgpycrumbs.chemgp.plot_gp) (in module rgpycrumbs.eon.plt_kmc) (in module rgpycrumbs.eon.plt_min) (in module rgpycrumbs.eon.plt_neb) (in module rgpycrumbs.eon.plt_neb_stitch) (in module rgpycrumbs.eon.plt_saddle) (in module rgpycrumbs.eon.ptmdisp) (in module rgpycrumbs.eon.seed_dimers) (in module rgpycrumbs.eon.to_mlflow) (in module rgpycrumbs.prefix.delete_packages) log_config_ini() (in module rgpycrumbs.eon._mlflow.log_params) logger (in module rgpycrumbs._aux) M main() (in module generate_orca_input) (in module rgpycrumbs.chemgp.match_atoms) (in module rgpycrumbs.chemgp.plot_gp) (in module rgpycrumbs.cli) (in module rgpycrumbs.eon.gen_dimer) (in module rgpycrumbs.eon.generate_nwchem_input) (in module rgpycrumbs.eon.plt_kmc) (in module rgpycrumbs.eon.plt_min) (in module rgpycrumbs.eon.plt_neb) (in module rgpycrumbs.eon.plt_neb_stitch) (in module rgpycrumbs.eon.plt_saddle) (in module rgpycrumbs.eon.ptmdisp) (in module rgpycrumbs.eon.to_mlflow) (in module rgpycrumbs.geom.detect_fragments) (in module rgpycrumbs.prefix.delete_packages) match_atoms() (in module rgpycrumbs.chemgp.match_atoms) matern_kernel_elem() (in module rgpycrumbs.surfaces._kernels) merge_fragments_by_distance() (in module rgpycrumbs.geom.fragments) merge_plot_settings() (in module rgpycrumbs.eon.plot_config) merged_package_pins_normalized() (rgpycrumbs.config.RgpycrumbsConfig method) method (rgpycrumbs.basetypes.SaddleMeasure attribute) (rgpycrumbs.geom.api.alignment.AlignmentResult attribute) MIN_DIST_ATM (in module rgpycrumbs.geom.fragment_visualization) MINIMAL_CONFIG_EXAMPLE (in module rgpycrumbs.eon.plot_config) mobile_count (rgpycrumbs.geom.api.alignment.IRAMatchInputs attribute) mobile_numbers (rgpycrumbs.geom.api.alignment.IRAMatchInputs attribute) mobile_positions (rgpycrumbs.geom.api.alignment.IRAMatchInputs attribute) mode_source (rgpycrumbs.eon.seed_dimers.PeakSeed attribute) module generate_orca_input helpers rgpycrumbs rgpycrumbs._aux rgpycrumbs.api rgpycrumbs.basetypes rgpycrumbs.chemgp rgpycrumbs.chemgp.match_atoms rgpycrumbs.chemgp.plot_gp rgpycrumbs.cli rgpycrumbs.config rgpycrumbs.eon rgpycrumbs.eon._mlflow rgpycrumbs.eon._mlflow.log_params rgpycrumbs.eon._render_cli rgpycrumbs.eon._single_ended_cli rgpycrumbs.eon._single_ended_plot rgpycrumbs.eon.con_splitter rgpycrumbs.eon.gen_dimer rgpycrumbs.eon.generate_nwchem_input rgpycrumbs.eon.helpers rgpycrumbs.eon.plot_config rgpycrumbs.eon.plot_dispatch rgpycrumbs.eon.plt_kmc rgpycrumbs.eon.plt_min rgpycrumbs.eon.plt_neb rgpycrumbs.eon.plt_neb_stitch rgpycrumbs.eon.plt_saddle rgpycrumbs.eon.ptmdisp rgpycrumbs.eon.seed_dimers rgpycrumbs.eon.to_mlflow rgpycrumbs.func rgpycrumbs.func.muller_brown rgpycrumbs.geom rgpycrumbs.geom.analysis rgpycrumbs.geom.api rgpycrumbs.geom.api.alignment rgpycrumbs.geom.detect_fragments rgpycrumbs.geom.fragment_visualization rgpycrumbs.geom.fragments rgpycrumbs.geom.ira rgpycrumbs.interpolation rgpycrumbs.locks rgpycrumbs.parsers rgpycrumbs.parsers.bless rgpycrumbs.parsers.common rgpycrumbs.plumed rgpycrumbs.plumed.direct_reconstruction rgpycrumbs.prefix rgpycrumbs.prefix.delete_packages rgpycrumbs.run rgpycrumbs.run.jupyter rgpycrumbs.sbom rgpycrumbs.surfaces rgpycrumbs.surfaces._base rgpycrumbs.surfaces._kernels rgpycrumbs.surfaces.gradient_imq rgpycrumbs.surfaces.gradient_matern rgpycrumbs.surfaces.gradient_nystrom rgpycrumbs.surfaces.gradient_rq rgpycrumbs.surfaces.gradient_se rgpycrumbs.surfaces.standard rgpycrumbs.xts rgpycrumbs.xts.cuh2 rgpycrumbs.xts.cuh2.datgen rgpycrumbs.xts.saddle rgpycrumbs.xts.saddle.cuh2 rgpycrumbs.xts.saddle.mb mol_id (rgpycrumbs.basetypes.SaddleMeasure attribute) (rgpycrumbs.basetypes.SpinID attribute) MolGeom (class in rgpycrumbs.basetypes) msg (in module rgpycrumbs.eon.plot_config) muller_brown() (in module rgpycrumbs.func.muller_brown) muller_brown_gradient() (in module rgpycrumbs.func.muller_brown) N n_inducing (rgpycrumbs.surfaces.gradient_nystrom.NystromGradientIMQ attribute) NEB (rgpycrumbs.eon.con_splitter.SplitMode attribute) NEB_ITER_RE (in module rgpycrumbs.eon.to_mlflow) NEB_LANDSCAPE_STRIP_MAX_COLS (in module rgpycrumbs.eon.plt_neb) NEB_LANDSCAPE_STRIP_ZOOM_MULT (in module rgpycrumbs.eon.plt_neb) NEB_PROFILE_MAIN_HEIGHT_IN (in module rgpycrumbs.eon.plt_neb) NEB_PROFILE_STRIP_HEIGHT_IN (in module rgpycrumbs.eon.plt_neb) NEB_PROFILE_STRIP_ZOOM_MULT (in module rgpycrumbs.eon.plt_neb) NEB_TRAJECTORY_FILE rgpycrumbs-eon-con-splitter command line option nebiter (class in rgpycrumbs.basetypes) nebpath (class in rgpycrumbs.basetypes) (rgpycrumbs.basetypes.nebiter attribute) negative_mll_imq_grad() (in module rgpycrumbs.surfaces.gradient_imq) negative_mll_imq_map() (in module rgpycrumbs.surfaces.gradient_imq) negative_mll_imq_std() (in module rgpycrumbs.surfaces.standard) negative_mll_matern_grad() (in module rgpycrumbs.surfaces.gradient_matern) negative_mll_matern_std() (in module rgpycrumbs.surfaces.standard) negative_mll_rq_map() (in module rgpycrumbs.surfaces.gradient_rq) negative_mll_se_grad() (in module rgpycrumbs.surfaces.gradient_se) negative_mll_tps() (in module rgpycrumbs.surfaces.standard) nimags (rgpycrumbs.surfaces.gradient_nystrom.NystromGradientIMQ attribute) nll() (in module rgpycrumbs.chemgp.plot_gp) NONE (rgpycrumbs.eon.con_splitter.AlignMode attribute) (rgpycrumbs.geom.api.alignment.AlignmentMethod attribute) norm_dist (rgpycrumbs.basetypes.nebpath attribute) normalize_pypi_name() (in module rgpycrumbs.api) (in module rgpycrumbs.locks) (in module rgpycrumbs.sbom) NYSTROM_N_INDUCING_DEFAULT (in module rgpycrumbs.surfaces) nystrom_paths_needed() (in module rgpycrumbs.surfaces) NYSTROM_THRESHOLD (in module rgpycrumbs.surfaces) NystromGradientIMQ (class in rgpycrumbs.surfaces.gradient_nystrom) O one_day_tdelta() (in module helpers) OTHER (rgpycrumbs.eon.ptmdisp.CrystalStructure attribute) overlay_labels() (in module rgpycrumbs.eon._single_ended_cli) P package_name_from_spec() (in module rgpycrumbs.locks) (in module rgpycrumbs.sbom) package_pins (rgpycrumbs.config.RgpycrumbsConfig attribute) PACKAGE_ROOT (in module rgpycrumbs.cli) parse_and_log_metrics() (in module rgpycrumbs.eon.to_mlflow) parse_dynamics() (in module rgpycrumbs.eon.plt_kmc) parse_target_coords() (in module rgpycrumbs.chemgp.match_atoms) parser (in module rgpycrumbs.xts.saddle.cuh2) (in module rgpycrumbs.xts.saddle.mb) peak_index (rgpycrumbs.eon.seed_dimers.PeakSeed attribute) PeakSeed (class in rgpycrumbs.eon.seed_dimers) perm (rgpycrumbs.geom.ira.IRAComp attribute) permutation (rgpycrumbs.geom.api.alignment.IRAMatchResults attribute) pes_calls (rgpycrumbs.basetypes.SaddleMeasure attribute) PINS_ENV (in module rgpycrumbs.locks) PINS_ENV_LEGACY (in module rgpycrumbs.locks) pins_from_env() (in module rgpycrumbs.api) (in module rgpycrumbs.locks) (in module rgpycrumbs.sbom) pins_to_constraint_lines() (in module rgpycrumbs.api) (in module rgpycrumbs.locks) (in module rgpycrumbs.sbom) PLATFORMS (in module rgpycrumbs.prefix.delete_packages) plot() (in module rgpycrumbs.eon.plot_dispatch) plot_band() (in module rgpycrumbs.xts.saddle.cuh2) plot_convergence (in module rgpycrumbs.chemgp) plot_fps (in module rgpycrumbs.chemgp) plot_gp_quality (in module rgpycrumbs.chemgp) plot_kmc_timeline() (in module rgpycrumbs.eon.plt_kmc) plot_min (in module rgpycrumbs.eon.plt_min) plot_min_from_settings() (in module rgpycrumbs.eon.plt_min) plot_neb (in module rgpycrumbs.eon.plt_neb) plot_neb_from_settings() (in module rgpycrumbs.eon.plt_neb) plot_nll (in module rgpycrumbs.chemgp) plot_profile (in module rgpycrumbs.chemgp) plot_rff (in module rgpycrumbs.chemgp) plot_saddle (in module rgpycrumbs.eon.plt_saddle) plot_saddle_from_settings() (in module rgpycrumbs.eon.plt_saddle) plot_sensitivity (in module rgpycrumbs.chemgp) plot_structure_evolution() (in module rgpycrumbs.eon.to_mlflow) plot_surface (in module rgpycrumbs.chemgp) plot_trust (in module rgpycrumbs.chemgp) plot_variance (in module rgpycrumbs.chemgp) PLT_NEB (in module rgpycrumbs.eon.plt_neb_stitch) pos (rgpycrumbs.basetypes.MolGeom attribute) POSCON_FILENAME (in module rgpycrumbs.chemgp.match_atoms) POT_CALLS_RE (in module rgpycrumbs.eon.to_mlflow) predict_var() (rgpycrumbs.surfaces._base.BaseGradientSurface method) (rgpycrumbs.surfaces._base.BaseSurface method) (rgpycrumbs.surfaces.standard.FastTPS method) print_results() (in module rgpycrumbs.geom.detect_fragments) process_id (rgpycrumbs.eon.plt_kmc.DynamicsStep attribute) product_id (rgpycrumbs.eon.plt_kmc.DynamicsStep attribute) profile() (in module rgpycrumbs.chemgp.plot_gp) PROJECT_CONFIG_NAMES (in module rgpycrumbs.config) PYLOCK (rgpycrumbs.locks.LockFormat attribute) pypi_pins_from_cyclonedx() (in module rgpycrumbs.locks) (in module rgpycrumbs.sbom) pypi_pins_from_pylock() (in module rgpycrumbs.locks) pypi_pins_from_uv_lock() (in module rgpycrumbs.locks) Q quality() (in module rgpycrumbs.chemgp.plot_gp) R rate (rgpycrumbs.eon.plt_kmc.DynamicsStep attribute) reactant_id (rgpycrumbs.eon.plt_kmc.DynamicsStep attribute) ref_count (rgpycrumbs.geom.api.alignment.IRAMatchInputs attribute) ref_numbers (rgpycrumbs.geom.api.alignment.IRAMatchInputs attribute) ref_positions (rgpycrumbs.geom.api.alignment.IRAMatchInputs attribute) RENDERER_CHOICES (in module rgpycrumbs.eon._render_cli) resolve_auto_deps_default() (in module rgpycrumbs.api) (in module rgpycrumbs.config) resolve_force_uv() (in module rgpycrumbs.api) (in module rgpycrumbs.config) resolve_from_click() (in module rgpycrumbs.eon.plot_config) resolve_lock_path_layered() (in module rgpycrumbs.api) (in module rgpycrumbs.config) rff() (in module rgpycrumbs.chemgp.plot_gp) rgpycrumbs module rgpycrumbs-eon-con-splitter command line option --align-type --box-diagonal --center --images-per-path --ira-kmax --mode --no-center --output-dir --path-index --path-list-filename --use-ira NEB_TRAJECTORY_FILE rgpycrumbs-eon-generate-nwchem-input command line option --config --output --pos-file -o rgpycrumbs-eon-ptmdisp command line option --no-fcc-vacancy --structure-type --verbose -s -v FILENAME rgpycrumbs-geom-detect-fragments-batch command line option --method --min-dist --output --pattern DIRECTORY rgpycrumbs-geom-detect-fragments-bond-order command line option --charge --method --min-dist --multiplicity --threshold --visualize FILENAME rgpycrumbs-geom-detect-fragments-geometric command line option --min-dist --multiplier --radius-type --visualize FILENAME rgpycrumbs-prefix-delete-packages command line option --api-key --channel --dry-run --package-name --version-regex rgpycrumbs._aux module rgpycrumbs.api module rgpycrumbs.basetypes module rgpycrumbs.chemgp module rgpycrumbs.chemgp.match_atoms module rgpycrumbs.chemgp.plot_gp module rgpycrumbs.cli module rgpycrumbs.config module rgpycrumbs.eon module rgpycrumbs.eon._mlflow module rgpycrumbs.eon._mlflow.log_params module rgpycrumbs.eon._render_cli module rgpycrumbs.eon._single_ended_cli module rgpycrumbs.eon._single_ended_plot module rgpycrumbs.eon.con_splitter module rgpycrumbs.eon.gen_dimer module rgpycrumbs.eon.generate_nwchem_input module rgpycrumbs.eon.helpers module rgpycrumbs.eon.plot_config module rgpycrumbs.eon.plot_dispatch module rgpycrumbs.eon.plt_kmc module rgpycrumbs.eon.plt_min module rgpycrumbs.eon.plt_neb module rgpycrumbs.eon.plt_neb_stitch module rgpycrumbs.eon.plt_saddle module rgpycrumbs.eon.ptmdisp module rgpycrumbs.eon.seed_dimers module rgpycrumbs.eon.to_mlflow module rgpycrumbs.func module rgpycrumbs.func.muller_brown module rgpycrumbs.geom module rgpycrumbs.geom.analysis module rgpycrumbs.geom.api module rgpycrumbs.geom.api.alignment module rgpycrumbs.geom.detect_fragments module rgpycrumbs.geom.fragment_visualization module rgpycrumbs.geom.fragments module rgpycrumbs.geom.ira module rgpycrumbs.interpolation module rgpycrumbs.locks module rgpycrumbs.parsers module rgpycrumbs.parsers.bless module rgpycrumbs.parsers.common module rgpycrumbs.plumed module rgpycrumbs.plumed.direct_reconstruction module rgpycrumbs.prefix module rgpycrumbs.prefix.delete_packages module rgpycrumbs.run module rgpycrumbs.run.jupyter module rgpycrumbs.sbom module rgpycrumbs.surfaces module rgpycrumbs.surfaces._base module rgpycrumbs.surfaces._kernels module rgpycrumbs.surfaces.gradient_imq module rgpycrumbs.surfaces.gradient_matern module rgpycrumbs.surfaces.gradient_nystrom module rgpycrumbs.surfaces.gradient_rq module rgpycrumbs.surfaces.gradient_se module rgpycrumbs.surfaces.standard module rgpycrumbs.xts module rgpycrumbs.xts.cuh2 module rgpycrumbs.xts.cuh2.datgen module rgpycrumbs.xts.saddle module rgpycrumbs.xts.saddle.cuh2 module rgpycrumbs.xts.saddle.mb module RgpycrumbsConfig (class in rgpycrumbs.config) rot (rgpycrumbs.basetypes.DimerOpt attribute) (rgpycrumbs.geom.ira.IRAComp attribute) rotation (rgpycrumbs.geom.api.alignment.IRAMatchResults attribute) rq_kernel_base() (in module rgpycrumbs.surfaces._kernels) rq_kernel_elem() (in module rgpycrumbs.surfaces._kernels) run_command_or_exit() (in module rgpycrumbs.run.jupyter) run_from_click() (in module rgpycrumbs.eon.plot_config) run_plot() (in module rgpycrumbs.eon.plot_config) S saddle (rgpycrumbs.basetypes.DimerOpt attribute) saddle_energy (rgpycrumbs.basetypes.SaddleMeasure attribute) saddle_fmax (rgpycrumbs.basetypes.SaddleMeasure attribute) SaddleMeasure (class in rgpycrumbs.basetypes) safe_cholesky_solve() (in module rgpycrumbs.surfaces._base) SBOM_PATH_ENV (in module rgpycrumbs.locks) (in module rgpycrumbs.sbom) SBOM_PINS_ENV (in module rgpycrumbs.locks) (in module rgpycrumbs.sbom) SCALAR_BAR_ARGS (in module rgpycrumbs.geom.fragment_visualization) scf (rgpycrumbs.basetypes.SaddleMeasure attribute) se_kernel_elem() (in module rgpycrumbs.surfaces._kernels) seed_dimers_from_peaks() (in module rgpycrumbs.eon.seed_dimers) seed_dir (rgpycrumbs.eon.seed_dimers.PeakSeed attribute) sensitivity() (in module rgpycrumbs.chemgp.plot_gp) SHARED_DEFAULTS (in module rgpycrumbs.eon.plot_config) SHARED_KEYS (in module rgpycrumbs.eon.plot_config) sources (rgpycrumbs.config.RgpycrumbsConfig attribute) spin (rgpycrumbs.basetypes.SaddleMeasure attribute) (rgpycrumbs.basetypes.SpinID attribute) SpinID (class in rgpycrumbs.basetypes) spline_interp() (in module rgpycrumbs.interpolation) SplitMode (class in rgpycrumbs.eon.con_splitter) state_ids (rgpycrumbs.eon.plt_kmc.KmcTimeline attribute) step (rgpycrumbs.eon.plt_kmc.DynamicsStep attribute) step_time (rgpycrumbs.eon.plt_kmc.DynamicsStep attribute) StrEnum (class in rgpycrumbs.eon.ptmdisp) (class in rgpycrumbs.geom.fragments) STRUCTURE_TYPE_MAP (in module rgpycrumbs.eon.ptmdisp) success (rgpycrumbs.basetypes.SaddleMeasure attribute) surface() (in module rgpycrumbs.chemgp.plot_gp) switchdir() (in module rgpycrumbs._aux) T T (in module rgpycrumbs.eon._single_ended_cli) tbliteinterface (in module rgpycrumbs.geom.fragments) termination_status (rgpycrumbs.basetypes.SaddleMeasure attribute) times (rgpycrumbs.eon.plt_kmc.KmcTimeline attribute) tomllib (in module rgpycrumbs.config) (in module rgpycrumbs.locks) tool_tables (rgpycrumbs.config.RgpycrumbsConfig attribute) tot_time (rgpycrumbs.basetypes.SaddleMeasure attribute) total_time (rgpycrumbs.eon.plt_kmc.DynamicsStep attribute) trans (rgpycrumbs.basetypes.DimerOpt attribute) (rgpycrumbs.geom.ira.IRAComp attribute) translation (rgpycrumbs.geom.api.alignment.IRAMatchResults attribute) trust() (in module rgpycrumbs.chemgp.plot_gp) U UNKNOWN (rgpycrumbs.locks.LockFormat attribute) used_ira (rgpycrumbs.geom.api.alignment.AlignmentResult property) USER_CONFIG_LEGACY_REL (in module rgpycrumbs.config) user_config_path() (in module rgpycrumbs.api) (in module rgpycrumbs.config) user_config_path_legacy() (in module rgpycrumbs.config) USER_CONFIG_REL (in module rgpycrumbs.config) UV_LOCK (rgpycrumbs.locks.LockFormat attribute) V variance() (in module rgpycrumbs.chemgp.plot_gp) visited_state_sequence() (in module rgpycrumbs.eon.plt_kmc) visualize_with_pyvista() (in module rgpycrumbs.geom.fragment_visualization) W warn_on_direct_script_import (in module rgpycrumbs.eon.gen_dimer) (in module rgpycrumbs.eon.plt_kmc) (in module rgpycrumbs.eon.plt_min) (in module rgpycrumbs.eon.plt_neb_stitch) (in module rgpycrumbs.eon.plt_saddle) warn_on_direct_script_import() (in module rgpycrumbs._aux) write_eon_config() (in module rgpycrumbs.eon.helpers) X x (rgpycrumbs.surfaces._base.BaseGradientSurface attribute) x_obs (rgpycrumbs.surfaces._base.BaseSurface attribute) (rgpycrumbs.surfaces.standard.FastTPS attribute) Y y_centered (rgpycrumbs.surfaces._base.BaseSurface attribute) y_flat (rgpycrumbs.surfaces._base.BaseGradientSurface attribute) y_full (rgpycrumbs.surfaces._base.BaseGradientSurface attribute) y_mean (rgpycrumbs.surfaces._base.BaseSurface attribute) (rgpycrumbs.surfaces.standard.FastTPS attribute) y_obs (rgpycrumbs.surfaces._base.BaseSurface attribute) (rgpycrumbs.surfaces.standard.FastTPS attribute)
