Index Symbols | _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | X | Y | Z Symbols --additional-con rgpycrumbs-eon-plt-neb command line option --align-type rgpycrumbs-eon-con-splitter command line option --api-key rgpycrumbs-prefix-delete-packages command line option --arrow-head-length rgpycrumbs-eon-plt-neb command line option --arrow-head-width rgpycrumbs-eon-plt-neb command line option --arrow-tail-width rgpycrumbs-eon-plt-neb command line option --ase-rotation rgpycrumbs-eon-plt-neb command line option --aspect-ratio rgpycrumbs-eon-plt-neb command line option --box-diagonal rgpycrumbs-eon-con-splitter command line option --cache-file rgpycrumbs-eon-plt-neb 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 --cmap-landscape rgpycrumbs-eon-plt-neb command line option --cmap-profile rgpycrumbs-eon-plt-neb command line option --con-file rgpycrumbs-eon-plt-neb command line option --config rgpycrumbs-eon-generate-nwchem-input command line option --dpi rgpycrumbs-eon-plt-neb command line option --draw-product rgpycrumbs-eon-plt-neb command line option --draw-reactant rgpycrumbs-eon-plt-neb command line option --draw-saddle rgpycrumbs-eon-plt-neb command line option --dry-run rgpycrumbs-prefix-delete-packages command line option --end rgpycrumbs-eon-plt-neb command line option --facecolor rgpycrumbs-eon-plt-neb command line option --fig-height rgpycrumbs-eon-plt-neb command line option --figsize rgpycrumbs-eon-plt-neb command line option --fontsize-base rgpycrumbs-eon-plt-neb command line option --force-recompute rgpycrumbs-eon-plt-neb command line option --highlight-last rgpycrumbs-eon-plt-neb command line option --images-per-path rgpycrumbs-eon-con-splitter command line option --input-dat-pattern rgpycrumbs-eon-plt-neb command line option --input-path-pattern rgpycrumbs-eon-plt-neb command line option --ira-kmax rgpycrumbs-eon-con-splitter command line option rgpycrumbs-eon-plt-neb command line option --landscape-mode rgpycrumbs-eon-plt-neb command line option --landscape-path rgpycrumbs-eon-plt-neb 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 --no-highlight-last rgpycrumbs-eon-plt-neb command line option --no-show-pts rgpycrumbs-eon-plt-neb command line option --normalize-rc rgpycrumbs-eon-plt-neb 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 --output-file rgpycrumbs-eon-plt-neb 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 --plot-mode rgpycrumbs-eon-plt-neb command line option --plot-structures rgpycrumbs-eon-plt-neb command line option --plot-type rgpycrumbs-eon-plt-neb command line option --pos-file rgpycrumbs-eon-generate-nwchem-input command line option --radius-type rgpycrumbs-geom-detect-fragments-geometric command line option --rbf-smoothing rgpycrumbs-eon-plt-neb command line option --rc-mode rgpycrumbs-eon-plt-neb command line option --rounding rgpycrumbs-eon-plt-neb command line option --savgol-order rgpycrumbs-eon-plt-neb command line option --savgol-window rgpycrumbs-eon-plt-neb command line option --show-legend rgpycrumbs-eon-plt-neb command line option --show-pts rgpycrumbs-eon-plt-neb command line option --spline-method rgpycrumbs-eon-plt-neb command line option --start rgpycrumbs-eon-plt-neb command line option --structure-type rgpycrumbs-eon-ptmdisp command line option --surface-type rgpycrumbs-eon-plt-neb command line option --theme rgpycrumbs-eon-plt-neb command line option --threshold rgpycrumbs-geom-detect-fragments-bond-order command line option --title rgpycrumbs-eon-plt-neb 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 --xlabel rgpycrumbs-eon-plt-neb command line option --ylabel rgpycrumbs-eon-plt-neb command line option --zoom-ratio rgpycrumbs-eon-plt-neb command line option -o rgpycrumbs-eon-plt-neb command line option -s rgpycrumbs-eon-ptmdisp command line option -v rgpycrumbs-eon-ptmdisp command line option _ _aggregate_all_paths() (in module rgpycrumbs.eon.plt_neb) _apply_ira_alignment() (in module rgpycrumbs.geom.api.alignment) _calculate_fes_1d() (in module rgpycrumbs.plumed.direct_reconstruction) _calculate_fes_2d() (in module rgpycrumbs.plumed.direct_reconstruction) _determine_figsize() (in module rgpycrumbs.eon.plt_neb) _dispatch() (in module rgpycrumbs.cli) _get_profile_labels() (in module rgpycrumbs.eon.plt_neb) _get_scripts_in_folder() (in module rgpycrumbs.cli) _import_from_parent_env() (in module rgpycrumbs._aux) _load_or_compute_data() (in module rgpycrumbs.eon.plt_neb) _load_structures() (in module rgpycrumbs.eon.plt_neb) _NUM (in module rgpycrumbs.parsers.common) _plot_landscape() (in module rgpycrumbs.eon.plt_neb) _plot_profile() (in module rgpycrumbs.eon.plt_neb) _run_command_live() (in module rgpycrumbs.run.jupyter) _run_dependency_checks() (in module rgpycrumbs.eon.plt_neb) _setup_theme() (in module rgpycrumbs.eon.plt_neb) _validate_data_atoms_match() (in module rgpycrumbs.eon.plt_neb) A 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) apply_plot_theme() (in module rgpycrumbs.eon.plt_neb) ASE_PROCRUSTES (rgpycrumbs.geom.api.alignment.AlignmentMethod attribute) atoms (rgpycrumbs.geom.api.alignment.AlignmentResult attribute) B BASE_URL (in module rgpycrumbs.prefix.delete_packages) batch() (in module rgpycrumbs.geom.detect_fragments) BATLOW_THEME (in module rgpycrumbs.eon.plt_neb) BCC (rgpycrumbs.eon.ptmdisp.CrystalStructure attribute) BLESS_LOG (in module rgpycrumbs.parsers.bless) BLESS_TIME (in module rgpycrumbs.parsers.bless) BOND_ORDER (rgpycrumbs.geom.detect_fragments.DetectionMethod attribute) bond_order() (in module rgpycrumbs.geom.detect_fragments) build_cmap() (in module rgpycrumbs.eon.plt_neb) build_graph_and_find_components() (in module rgpycrumbs.geom.detect_fragments) C calculate_fes_from_hills() (in module rgpycrumbs.plumed.direct_reconstruction) calculate_landscape_coords() (in module rgpycrumbs.eon.plt_neb) calculate_rmsd_from_ref() (in module rgpycrumbs.eon.plt_neb) cmap_landscape (rgpycrumbs.eon.plt_neb.PlotTheme attribute) cmap_name (in module rgpycrumbs.geom.detect_fragments) cmap_profile (rgpycrumbs.eon.plt_neb.PlotTheme attribute) con_splitter() (in module rgpycrumbs.eon.con_splitter) CONSOLE (in module rgpycrumbs.eon.con_splitter) CrystalStructure (class in rgpycrumbs.eon.ptmdisp) CUH2_MIN (in module rgpycrumbs.xts.saddle.cuh2) D DEFAULT_BOND_MULTIPLIER (in module rgpycrumbs.geom.detect_fragments) DEFAULT_BOND_ORDER_THRESHOLD (in module rgpycrumbs.geom.detect_fragments) DEFAULT_INPUT_PATTERN (in module rgpycrumbs.eon.plt_neb) DEFAULT_PATH_PATTERN (in module rgpycrumbs.eon.plt_neb) delete_package() (in module rgpycrumbs.prefix.delete_packages) DetectionMethod (class in rgpycrumbs.geom.detect_fragments) DIRECTORY rgpycrumbs-geom-detect-fragments-batch command line option E edgecolor (rgpycrumbs.eon.plt_neb.PlotTheme attribute) EIGENVALUE (rgpycrumbs.eon.plt_neb.PlotMode attribute) enabled (rgpycrumbs.geom.api.alignment.IRAConfig attribute) ENDPOINTS (rgpycrumbs.eon.con_splitter.AlignMode attribute) ENERGY (rgpycrumbs.eon.plt_neb.PlotMode attribute) eon_config (in module rgpycrumbs.eon._mlflow.log_params) F facecolor (rgpycrumbs.eon.plt_neb.PlotTheme attribute) 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_fes_minima() (in module rgpycrumbs.plumed.direct_reconstruction) find_fragments_bond_order() (in module rgpycrumbs.geom.detect_fragments) find_fragments_geometric() (in module rgpycrumbs.geom.detect_fragments) find_mismatch_indices() (in module rgpycrumbs.eon.ptmdisp) FLEX (rgpycrumbs.eon.con_splitter.SplitMode attribute) font_family (rgpycrumbs.eon.plt_neb.PlotTheme attribute) font_size (rgpycrumbs.eon.plt_neb.PlotTheme attribute) G generate_nwchem_input() (in module rgpycrumbs.eon.generate_nwchem_input) GEOMETRIC (rgpycrumbs.geom.detect_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) getstrform() (in module rgpycrumbs._aux) gridcolor (rgpycrumbs.eon.plt_neb.PlotTheme attribute) H hausdorff_dist (rgpycrumbs.geom.api.alignment.IRAMatchResults attribute) HCP (rgpycrumbs.eon.ptmdisp.CrystalStructure attribute) helpers module HERMITE (rgpycrumbs.eon.plt_neb.SplineMethod attribute) highlight_color (rgpycrumbs.eon.plt_neb.PlotTheme attribute) HILLS_FILENAME (in module rgpycrumbs.plumed.direct_reconstruction) I ICO (rgpycrumbs.eon.ptmdisp.CrystalStructure attribute) INDEX (rgpycrumbs.eon.plt_neb.RCMode attribute) InsetImagePos (class in rgpycrumbs.eon.plt_neb) IRA_KMAX_DEFAULT (in module rgpycrumbs.eon.plt_neb) ira_mod (in module rgpycrumbs.eon.con_splitter) (in module rgpycrumbs.eon.plt_neb) (in module rgpycrumbs.geom.api.alignment) IRA_PERMUTATION (rgpycrumbs.geom.api.alignment.AlignmentMethod attribute) IRAConfig (class in rgpycrumbs.geom.api.alignment) IRAMatchInputs (class in rgpycrumbs.geom.api.alignment) IRAMatchResults (class in rgpycrumbs.geom.api.alignment) K kmax (rgpycrumbs.geom.api.alignment.IRAConfig attribute) (rgpycrumbs.geom.api.alignment.IRAMatchInputs attribute) L LANDSCAPE (rgpycrumbs.eon.plt_neb.PlotType attribute) load_paths() (in module rgpycrumbs.eon.plt_neb) log (in module rgpycrumbs.eon.plt_neb) (in module rgpycrumbs.eon.ptmdisp) (in module rgpycrumbs.prefix.delete_packages) log_config_ini() (in module rgpycrumbs.eon._mlflow.log_params) M main() (in module rgpycrumbs.cli) (in module rgpycrumbs.eon.generate_nwchem_input) (in module rgpycrumbs.eon.plt_neb) (in module rgpycrumbs.eon.ptmdisp) (in module rgpycrumbs.geom.detect_fragments) (in module rgpycrumbs.prefix.delete_packages) merge_fragments_by_distance() (in module rgpycrumbs.geom.detect_fragments) method (rgpycrumbs.geom.api.alignment.AlignmentResult attribute) MIN_DIST_ATM (in module rgpycrumbs.geom.detect_fragments) MIN_PATH_LENGTH (in module rgpycrumbs.eon.plt_neb) mobile_count (rgpycrumbs.geom.api.alignment.IRAMatchInputs attribute) mobile_numbers (rgpycrumbs.geom.api.alignment.IRAMatchInputs attribute) mobile_positions (rgpycrumbs.geom.api.alignment.IRAMatchInputs attribute) module helpers rgpycrumbs rgpycrumbs._aux rgpycrumbs.cli rgpycrumbs.eon rgpycrumbs.eon._mlflow rgpycrumbs.eon._mlflow.log_params rgpycrumbs.eon.con_splitter rgpycrumbs.eon.generate_nwchem_input rgpycrumbs.eon.helpers rgpycrumbs.eon.plt_neb rgpycrumbs.eon.ptmdisp rgpycrumbs.func rgpycrumbs.func.muller_brown rgpycrumbs.geom rgpycrumbs.geom.api rgpycrumbs.geom.api.alignment rgpycrumbs.geom.detect_fragments 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.xts rgpycrumbs.xts.cuh2 rgpycrumbs.xts.cuh2.datgen rgpycrumbs.xts.saddle rgpycrumbs.xts.saddle.cuh2 rgpycrumbs.xts.saddle.mb muller_brown() (in module rgpycrumbs.func.muller_brown) muller_brown_gradient() (in module rgpycrumbs.func.muller_brown) N name (rgpycrumbs.eon.plt_neb.PlotTheme attribute) NEB (rgpycrumbs.eon.con_splitter.SplitMode attribute) NEB_TRAJECTORY_FILE rgpycrumbs-eon-con-splitter command line option NONE (rgpycrumbs.eon.con_splitter.AlignMode attribute) (rgpycrumbs.geom.api.alignment.AlignmentMethod attribute) O one_day_tdelta() (in module helpers) OTHER (rgpycrumbs.eon.ptmdisp.CrystalStructure attribute) P PACKAGE_ROOT (in module rgpycrumbs.cli) parser (in module rgpycrumbs.xts.saddle.cuh2) (in module rgpycrumbs.xts.saddle.mb) PATH (rgpycrumbs.eon.plt_neb.RCMode attribute) permutation (rgpycrumbs.geom.api.alignment.IRAMatchResults attribute) PLATFORMS (in module rgpycrumbs.prefix.delete_packages) plot_band() (in module rgpycrumbs.xts.saddle.cuh2) plot_eigenvalue_path() (in module rgpycrumbs.eon.plt_neb) plot_energy_path() (in module rgpycrumbs.eon.plt_neb) plot_interpolated_grid() (in module rgpycrumbs.eon.plt_neb) plot_interpolated_rbf() (in module rgpycrumbs.eon.plt_neb) plot_landscape_path() (in module rgpycrumbs.eon.plt_neb) plot_single_inset() (in module rgpycrumbs.eon.plt_neb) plot_structure_insets() (in module rgpycrumbs.eon.plt_neb) plot_structure_strip() (in module rgpycrumbs.eon.plt_neb) PlotMode (class in rgpycrumbs.eon.plt_neb) PlotTheme (class in rgpycrumbs.eon.plt_neb) PlotType (class in rgpycrumbs.eon.plt_neb) polyorder (rgpycrumbs.eon.plt_neb.SmoothingParams attribute) print_results() (in module rgpycrumbs.geom.detect_fragments) PROFILE (rgpycrumbs.eon.plt_neb.PlotType attribute) R rad (rgpycrumbs.eon.plt_neb.InsetImagePos attribute) RCMode (class in rgpycrumbs.eon.plt_neb) ref_count (rgpycrumbs.geom.api.alignment.IRAMatchInputs attribute) ref_numbers (rgpycrumbs.geom.api.alignment.IRAMatchInputs attribute) ref_positions (rgpycrumbs.geom.api.alignment.IRAMatchInputs attribute) 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 rgpycrumbs-eon-plt-neb command line option --additional-con --arrow-head-length --arrow-head-width --arrow-tail-width --ase-rotation --aspect-ratio --cache-file --cmap-landscape --cmap-profile --con-file --dpi --draw-product --draw-reactant --draw-saddle --end --facecolor --fig-height --figsize --fontsize-base --force-recompute --highlight-last --input-dat-pattern --input-path-pattern --ira-kmax --landscape-mode --landscape-path --no-highlight-last --no-show-pts --normalize-rc --output-file --plot-mode --plot-structures --plot-type --rbf-smoothing --rc-mode --rounding --savgol-order --savgol-window --show-legend --show-pts --spline-method --start --surface-type --theme --title --xlabel --ylabel --zoom-ratio -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.cli module rgpycrumbs.eon module rgpycrumbs.eon._mlflow module rgpycrumbs.eon._mlflow.log_params module rgpycrumbs.eon.con_splitter module rgpycrumbs.eon.generate_nwchem_input module rgpycrumbs.eon.helpers module rgpycrumbs.eon.plt_neb module rgpycrumbs.eon.ptmdisp module rgpycrumbs.func module rgpycrumbs.func.muller_brown module rgpycrumbs.geom module rgpycrumbs.geom.api module rgpycrumbs.geom.api.alignment module rgpycrumbs.geom.detect_fragments 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.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 RMSD (rgpycrumbs.eon.plt_neb.RCMode attribute) rotation (rgpycrumbs.geom.api.alignment.IRAMatchResults attribute) ROUNDING_DF (in module rgpycrumbs.eon.plt_neb) RUHI_COLORS (in module rgpycrumbs.eon.plt_neb) RUHI_THEME (in module rgpycrumbs.eon.plt_neb) run_command_or_exit() (in module rgpycrumbs.run.jupyter) S SCALAR_BAR_ARGS (in module rgpycrumbs.geom.detect_fragments) setup_global_theme() (in module rgpycrumbs.eon.plt_neb) setup_plot_aesthetics() (in module rgpycrumbs.eon.plt_neb) SmoothingParams (class in rgpycrumbs.eon.plt_neb) SPLINE (rgpycrumbs.eon.plt_neb.SplineMethod attribute) SplineMethod (class in rgpycrumbs.eon.plt_neb) SplitMode (class in rgpycrumbs.eon.con_splitter) STRUCTURE_TYPE_MAP (in module rgpycrumbs.eon.ptmdisp) switchdir() (in module rgpycrumbs._aux) T tbliteinterface (in module rgpycrumbs.geom.detect_fragments) textcolor (rgpycrumbs.eon.plt_neb.PlotTheme attribute) THEMES (in module rgpycrumbs.eon.plt_neb) translation (rgpycrumbs.geom.api.alignment.IRAMatchResults attribute) TRUE_E_DAT (in module rgpycrumbs.xts.saddle.cuh2) U used_ira (rgpycrumbs.geom.api.alignment.AlignmentResult property) V visualize_with_pyvista() (in module rgpycrumbs.geom.detect_fragments) W window_length (rgpycrumbs.eon.plt_neb.SmoothingParams attribute) write_eon_config() (in module rgpycrumbs.eon.helpers) X x (in module rgpycrumbs.xts.saddle.mb) (rgpycrumbs.eon.plt_neb.InsetImagePos attribute) Y y (in module rgpycrumbs.xts.saddle.mb) (rgpycrumbs.eon.plt_neb.InsetImagePos attribute) Z Z (in module rgpycrumbs.xts.saddle.mb)
