Index

_

__all__ (in module chemparseplot.parse.orca.neb) __getattr__() (in module chemparseplot.plot) __new__() (chemparseplot.parse.eon.saddle_search.EONSaddleStatus method) __repr__() (chemparseplot.plot.structs.TwoDimPlot method) _ALPHABET_SIZE (in module chemparseplot.parse.plumed) _apply_perspective_tilt() (in module chemparseplot.plot.neb) _augment_minima_points() (in module chemparseplot.plot.neb) _augment_with_gradients() (in module chemparseplot.plot.neb) _calculate_fes_1d() (in module chemparseplot.parse.plumed) _calculate_fes_2d() (in module chemparseplot.parse.plumed) _calculate_rmsd() (in module chemparseplot.parse.orca.neb.opi_parser) _check_xyzrender() (in module chemparseplot.plot.neb) _CLAMP_PRESETS (in module chemparseplot.plot.chemgp) _compute_synthetic_gradients() (in module chemparseplot.parse.orca.neb.opi_parser) _DOUBLET_MULT (in module chemparseplot.parse.eon.gprd) _ensure_ruhi_cmap() (in module chemparseplot.plot.chemgp) _EXPECTED_COORD_COLS (in module chemparseplot.util) _extract_initial_energy() (in module chemparseplot.parse.eon.saddle_search) _extract_saddle_info() (in module chemparseplot.parse.eon.saddle_search) _extract_total_time() (in module chemparseplot.parse.eon.saddle_search) _find_initial_structure() (in module chemparseplot.parse.eon.dimer_trajectory) _find_log_file() (in module chemparseplot.parse.eon.saddle_search)

_get_energy() (in module chemparseplot.parse.trajectory.neb) _get_methods() (in module chemparseplot.parse.eon.saddle_search) _get_opi_output() (in module chemparseplot.parse.orca.neb.opi_parser) _JOST_THEME (in module chemparseplot.plot.chemgp) _LABELS (in module chemparseplot.plot.optimization) _load_mode_dat() (in module chemparseplot.parse.eon.dimer_trajectory) _METHOD_PALETTE (in module chemparseplot.plot.chemgp) _MIN_BIN_SIZE (in module chemparseplot.parse.plumed) _MIN_COLS_1D (in module chemparseplot.parse.plumed) _MIN_COLS_2D (in module chemparseplot.parse.plumed) _opi_output (in module chemparseplot.parse.orca.neb.opi_parser) _parse_rotation_angles() (in module chemparseplot.plot.neb) _process_single_path_step() (in module chemparseplot.parse.eon.neb) _read_path_group() (in module chemparseplot.parse.trajectory.hdf5) _read_results_dat() (in module chemparseplot.parse.eon.saddle_search) _reconstruct_atoms() (in module chemparseplot.parse.trajectory.hdf5) _render_atoms() (in module chemparseplot.plot.neb) _render_ovito() (in module chemparseplot.plot.neb) _render_solvis() (in module chemparseplot.plot.neb) _render_xyzrender() (in module chemparseplot.plot.neb) _setup() (in module chemparseplot.plot.chemgp) _STROKE (in module chemparseplot.plot.chemgp) _validate_data_atoms_match() (in module chemparseplot.parse.eon.neb)

A

a_start (chemparseplot.parse.projection.ProjectionBasis attribute) add_data() (chemparseplot.plot.structs.TwoDimPlot method) add_title() (chemparseplot.plot.structs.BasePlotter method) aggregate_neb_landscape_data() (in module chemparseplot.parse.eon.neb)

apply_axis_theme() (in module chemparseplot.plot.theme) atoms (in module chemparseplot.util) atoms_list (chemparseplot.parse.eon.dimer_trajectory.DimerTrajectoryData attribute) (chemparseplot.parse.eon.min_trajectory.MinTrajectoryData attribute)

B

b_start (chemparseplot.parse.projection.ProjectionBasis attribute) BAD_HIGH_BARRIER (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) BAD_HIGH_ENERGY (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) BAD_MAX_CONCAVE_ITERATIONS (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) BAD_MAX_ITERATIONS (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) BAD_MD_TRAJECTORY_TOO_SHORT (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) BAD_MINIMA (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute)

BAD_NO_BARRIER (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) BAD_NO_CONVEX (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) BAD_NO_NEGATIVE_MODE_AT_SADDLE (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) BAD_NOT_CONNECTED (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) BAD_PREFACTOR (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) BasePlotter (class in chemparseplot.plot.structs) BATLOW_THEME (in module chemparseplot.plot.theme) build_cmap() (in module chemparseplot.plot.theme)

C

calculate() (chemparseplot.parse.eon.gprd.HDF5Calculator method) (chemparseplot.parse.eon.gprd.HDF5CalculatorDimerMidpoint method) calculate_fes_from_hills() (in module chemparseplot.parse.plumed) calculate_landscape_coords() (in module chemparseplot.parse.neb_utils) chemparseplot module chemparseplot.parse module chemparseplot.parse.chemgp_hdf5 module chemparseplot.parse.chemgp_jsonl module chemparseplot.parse.converter module chemparseplot.parse.eon module chemparseplot.parse.eon.dimer_trajectory module chemparseplot.parse.eon.gprd module chemparseplot.parse.eon.min_trajectory module chemparseplot.parse.eon.minimization module chemparseplot.parse.eon.neb module chemparseplot.parse.eon.saddle_search module chemparseplot.parse.file_ module chemparseplot.parse.neb_utils module chemparseplot.parse.orca module chemparseplot.parse.orca.geomscan module chemparseplot.parse.orca.neb module chemparseplot.parse.orca.neb.interp module chemparseplot.parse.orca.neb.opi_parser module chemparseplot.parse.patterns module

chemparseplot.parse.plumed module chemparseplot.parse.projection module chemparseplot.parse.trajectory module chemparseplot.parse.trajectory.hdf5 module chemparseplot.parse.trajectory.neb module chemparseplot.plot module chemparseplot.plot.chemgp module chemparseplot.plot.geomscan module chemparseplot.plot.neb module chemparseplot.plot.optimization module chemparseplot.plot.plumed module chemparseplot.plot.structs module chemparseplot.plot.theme module chemparseplot.units module chemparseplot.util module cmap_landscape (chemparseplot.plot.theme.PlotTheme attribute) cmap_profile (chemparseplot.plot.theme.PlotTheme attribute) ComparisonData (class in chemparseplot.parse.chemgp_jsonl) compute_cumulative_distance() (in module chemparseplot.parse.trajectory.neb) compute_profile_rmsd() (in module chemparseplot.parse.eon.neb) compute_projection_basis() (in module chemparseplot.parse.projection) compute_synthetic_gradients() (in module chemparseplot.parse.neb_utils) compute_tangent_force() (in module chemparseplot.parse.trajectory.neb) create_full_traj_from_hdf5() (in module chemparseplot.parse.eon.gprd) create_geom_traj_from_hdf5() (in module chemparseplot.parse.eon.gprd) create_landscape_dataframe() (in module chemparseplot.parse.neb_utils) create_multicol_pattern() (in module chemparseplot.parse.patterns) create_nwchem_trajectory() (in module chemparseplot.parse.eon.gprd)

D

d_rff_values (chemparseplot.parse.chemgp_jsonl.RFFQualityData attribute) dat_df (chemparseplot.parse.eon.dimer_trajectory.DimerTrajectoryData attribute) (chemparseplot.parse.eon.min_trajectory.MinTrajectoryData attribute)

detect_clamp() (in module chemparseplot.plot.chemgp) DIGIT (in module chemparseplot.parse.patterns) DimerTrajectoryData (class in chemparseplot.parse.eon.dimer_trajectory)

E

edgecolor (chemparseplot.plot.theme.PlotTheme attribute) energies (chemparseplot.parse.chemgp_jsonl.OptimizerTrace attribute) energy (chemparseplot.parse.chemgp_jsonl.StationaryPoint attribute) energy_mae_vs_gp (chemparseplot.parse.chemgp_jsonl.RFFQualityData attribute) energy_mae_vs_true (chemparseplot.parse.chemgp_jsonl.RFFQualityData attribute) EnergyPath (in module chemparseplot.plot.structs) EONSaddleStatus (class in chemparseplot.parse.eon.saddle_search)

estimate_rbf_smoothing() (in module chemparseplot.parse.eon.neb) exact_energy_mae (chemparseplot.parse.chemgp_jsonl.RFFQualityData attribute) exact_gradient_mae (chemparseplot.parse.chemgp_jsonl.RFFQualityData attribute) extract_energy_data() (in module chemparseplot.parse.orca.geomscan) extract_interp_points() (in module chemparseplot.parse.orca.neb.interp) extract_profile_data() (in module chemparseplot.parse.trajectory.neb) extract_saddle_gprd() (in module chemparseplot.parse.eon.saddle_search)

F

facecolor (chemparseplot.plot.theme.PlotTheme attribute) FAILED_PREFACTOR (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) final_atoms (chemparseplot.parse.eon.min_trajectory.MinTrajectoryData attribute) find_fes_minima() (in module chemparseplot.parse.plumed)

find_file_paths() (in module chemparseplot.parse.file_) font_family (chemparseplot.plot.theme.PlotTheme attribute) font_size (chemparseplot.plot.theme.PlotTheme attribute) forces (chemparseplot.parse.chemgp_jsonl.OptimizerTrace attribute) from_value() (chemparseplot.parse.eon.saddle_search.EONSaddleStatus class method)

G

get_atoms_from_hdf5() (in module chemparseplot.parse.eon.gprd) get_theme() (in module chemparseplot.plot.theme) GOOD (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) gp_e (chemparseplot.parse.chemgp_jsonl.GPQualityGrid attribute) gp_var (chemparseplot.parse.chemgp_jsonl.GPQualityGrid attribute)

GPQualityData (class in chemparseplot.parse.chemgp_jsonl) GPQualityGrid (class in chemparseplot.parse.chemgp_jsonl) gradient_mae_vs_gp (chemparseplot.parse.chemgp_jsonl.RFFQualityData attribute) gradient_mae_vs_true (chemparseplot.parse.chemgp_jsonl.RFFQualityData attribute) gridcolor (chemparseplot.plot.theme.PlotTheme attribute) grids (chemparseplot.parse.chemgp_jsonl.GPQualityData attribute)

H

HAS_OPI (in module chemparseplot.parse.orca.neb.opi_parser) HDF5Calculator (class in chemparseplot.parse.eon.gprd) HDF5CalculatorDimerMidpoint (class in chemparseplot.parse.eon.gprd)

highlight_color (chemparseplot.plot.theme.PlotTheme attribute) history_to_landscape_df() (in module chemparseplot.parse.trajectory.hdf5) history_to_profile_dats() (in module chemparseplot.parse.trajectory.hdf5)

I

id (chemparseplot.parse.chemgp_jsonl.StationaryPoint attribute) implemented_properties (chemparseplot.parse.eon.gprd.HDF5Calculator attribute) (chemparseplot.parse.eon.gprd.HDF5CalculatorDimerMidpoint attribute) INIT (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute)

initial_atoms (chemparseplot.parse.eon.dimer_trajectory.DimerTrajectoryData attribute) (chemparseplot.parse.eon.min_trajectory.MinTrajectoryData attribute) InsetImagePos (in module chemparseplot.plot.neb) INTERP_PAT (in module chemparseplot.parse.orca.neb.interp) inverse_sd_to_ab() (in module chemparseplot.parse.projection)

K

kind (chemparseplot.parse.chemgp_jsonl.StationaryPoint attribute)

L

load_augmenting_neb_data() (in module chemparseplot.parse.eon.neb) load_dimer_trajectory() (in module chemparseplot.parse.eon.dimer_trajectory) load_min_trajectory() (in module chemparseplot.parse.eon.min_trajectory) load_neb_history() (in module chemparseplot.parse.trajectory.hdf5) load_neb_result() (in module chemparseplot.parse.trajectory.hdf5) load_or_compute_data() (in module chemparseplot.parse.eon.neb) load_structures_and_calculate_additional_rmsd() (in module chemparseplot.parse.eon.neb) load_trajectory() (in module chemparseplot.parse.trajectory.neb) log (in module chemparseplot.parse.eon.dimer_trajectory) (in module chemparseplot.parse.eon.gprd) (in module chemparseplot.parse.eon.min_trajectory) (in module chemparseplot.parse.eon.neb) (in module chemparseplot.parse.eon.saddle_search) (in module chemparseplot.parse.file_) (in module chemparseplot.parse.neb_utils) (in module chemparseplot.parse.trajectory.hdf5) (in module chemparseplot.parse.trajectory.neb) (in module chemparseplot.plot.chemgp) (in module chemparseplot.plot.neb) (in module chemparseplot.plot.optimization) (in module chemparseplot.plot.theme) (in module chemparseplot.util)

M

meta (chemparseplot.parse.chemgp_jsonl.GPQualityData attribute) method (chemparseplot.parse.chemgp_jsonl.OptimizerTrace attribute) min_e_result() (in module chemparseplot.parse.eon.minimization) MIN_PATH_LENGTH (in module chemparseplot.plot.neb) MinTrajectoryData (class in chemparseplot.parse.eon.min_trajectory) mode_vector (chemparseplot.parse.eon.dimer_trajectory.DimerTrajectoryData attribute) module chemparseplot chemparseplot.parse chemparseplot.parse.chemgp_hdf5 chemparseplot.parse.chemgp_jsonl chemparseplot.parse.converter chemparseplot.parse.eon chemparseplot.parse.eon.dimer_trajectory chemparseplot.parse.eon.gprd chemparseplot.parse.eon.min_trajectory chemparseplot.parse.eon.minimization chemparseplot.parse.eon.neb chemparseplot.parse.eon.saddle_search chemparseplot.parse.file_ chemparseplot.parse.neb_utils chemparseplot.parse.orca chemparseplot.parse.orca.geomscan chemparseplot.parse.orca.neb chemparseplot.parse.orca.neb.interp chemparseplot.parse.orca.neb.opi_parser chemparseplot.parse.patterns chemparseplot.parse.plumed chemparseplot.parse.projection chemparseplot.parse.trajectory chemparseplot.parse.trajectory.hdf5 chemparseplot.parse.trajectory.neb chemparseplot.plot chemparseplot.plot.chemgp chemparseplot.plot.geomscan chemparseplot.plot.neb chemparseplot.plot.optimization chemparseplot.plot.plumed chemparseplot.plot.structs chemparseplot.plot.theme chemparseplot.units chemparseplot.util

N

n_train (chemparseplot.parse.chemgp_jsonl.GPQualityGrid attribute) name (chemparseplot.plot.theme.PlotTheme attribute) NEGATIVE_BARRIER (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) NONLOCAL_ABORT (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute)

NONNEGATIVE_ABORT (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) np_txt() (in module chemparseplot.parse.converter) nx (chemparseplot.parse.chemgp_jsonl.GPQualityGrid attribute) ny (chemparseplot.parse.chemgp_jsonl.GPQualityGrid attribute)

O

OPTIMIZER_ERROR (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute)

OptimizerTrace (class in chemparseplot.parse.chemgp_jsonl) oracle_calls (chemparseplot.parse.chemgp_jsonl.OptimizerTrace attribute)

P

parse_climb_con() (in module chemparseplot.parse.eon.dimer_trajectory) parse_climb_dat() (in module chemparseplot.parse.eon.dimer_trajectory) parse_comparison_jsonl() (in module chemparseplot.parse.chemgp_jsonl) parse_eon_saddle() (in module chemparseplot.parse.eon.saddle_search) parse_gp_quality_jsonl() (in module chemparseplot.parse.chemgp_jsonl) parse_min_con() (in module chemparseplot.parse.eon.min_trajectory) parse_min_dat() (in module chemparseplot.parse.eon.min_trajectory) parse_orca_neb() (in module chemparseplot.parse.orca.neb.opi_parser) parse_orca_neb_fallback() (in module chemparseplot.parse.orca.neb.opi_parser) parse_rff_quality_jsonl() (in module chemparseplot.parse.chemgp_jsonl) parse_target_coords() (in module chemparseplot.util) path_norm (chemparseplot.parse.projection.ProjectionBasis attribute) plot_convergence_curve() (in module chemparseplot.plot.chemgp) plot_convergence_panel() (in module chemparseplot.plot.optimization) plot_dimer_mode_evolution() (in module chemparseplot.plot.optimization) plot_eigenvalue_path() (in module chemparseplot.plot.neb) plot_energy_path() (in module chemparseplot.plot.neb) plot_energy_paths() (in module chemparseplot.plot.geomscan) plot_energy_profile() (in module chemparseplot.plot.chemgp) plot_fes_1d() (in module chemparseplot.plot.plumed) plot_fes_2d() (in module chemparseplot.plot.plumed) plot_fps_projection() (in module chemparseplot.plot.chemgp) plot_gp_progression() (in module chemparseplot.plot.chemgp)

plot_hyperparameter_sensitivity() (in module chemparseplot.plot.chemgp) plot_landscape_path_overlay() (in module chemparseplot.plot.neb) plot_landscape_surface() (in module chemparseplot.plot.neb) plot_mmf_peaks_overlay() (in module chemparseplot.plot.neb) plot_neb_evolution() (in module chemparseplot.plot.neb) plot_nll_landscape() (in module chemparseplot.plot.chemgp) plot_optimization_landscape() (in module chemparseplot.plot.optimization) plot_optimization_profile() (in module chemparseplot.plot.optimization) plot_orca_neb_energy_profile() (in module chemparseplot.plot.neb) plot_orca_neb_landscape() (in module chemparseplot.plot.neb) plot_orca_neb_profile() (in module chemparseplot.plot.neb) plot_rff_quality() (in module chemparseplot.plot.chemgp) plot_structure_inset() (in module chemparseplot.plot.neb) plot_structure_strip() (in module chemparseplot.plot.neb) plot_surface_contour() (in module chemparseplot.plot.chemgp) plot_trust_region() (in module chemparseplot.plot.chemgp) plot_variance_overlay() (in module chemparseplot.plot.chemgp) PlotTheme (class in chemparseplot.plot.theme) polyorder (chemparseplot.plot.neb.SmoothingParams attribute) POSCON_FILENAME (in module chemparseplot.util) POTENTIAL_FAILED (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) project_to_sd() (in module chemparseplot.parse.projection) ProjectionBasis (class in chemparseplot.parse.projection)

Q

Q_ (in module chemparseplot.units)

R

read_h5_grid() (in module chemparseplot.parse.chemgp_hdf5) read_h5_metadata() (in module chemparseplot.parse.chemgp_hdf5) read_h5_path() (in module chemparseplot.parse.chemgp_hdf5) read_h5_points() (in module chemparseplot.parse.chemgp_hdf5) read_h5_table() (in module chemparseplot.parse.chemgp_hdf5) redraw_plot() (chemparseplot.plot.structs.TwoDimPlot method)

render_structure_to_image() (in module chemparseplot.plot.neb) result_to_atoms_list() (in module chemparseplot.parse.trajectory.hdf5) result_to_profile_dat() (in module chemparseplot.parse.trajectory.hdf5) RFFQualityData (class in chemparseplot.parse.chemgp_jsonl) rmdat() (chemparseplot.plot.structs.TwoDimPlot method) RUHI_COLORS (in module chemparseplot.plot.theme) RUHI_THEME (in module chemparseplot.plot.theme)

S

saddle_atoms (chemparseplot.parse.eon.dimer_trajectory.DimerTrajectoryData attribute) safe_plot() (in module chemparseplot.plot.chemgp) save_plot() (in module chemparseplot.plot.chemgp) set_labels() (chemparseplot.plot.structs.TwoDimPlot method) set_units() (chemparseplot.plot.structs.TwoDimPlot method) setup_global_theme() (in module chemparseplot.plot.theme)

setup_publication_theme() (in module chemparseplot.plot.theme) SmoothingParams (class in chemparseplot.plot.neb) stationary (chemparseplot.parse.chemgp_jsonl.GPQualityData attribute) StationaryPoint (class in chemparseplot.parse.chemgp_jsonl) steps (chemparseplot.parse.chemgp_jsonl.OptimizerTrace attribute) summary (chemparseplot.parse.chemgp_jsonl.ComparisonData attribute)

T

target_coords (in module chemparseplot.util) target_coords_text (in module chemparseplot.util) textcolor (chemparseplot.plot.theme.PlotTheme attribute) THEMES (in module chemparseplot.plot.theme) THREE_COL_NUM (in module chemparseplot.parse.patterns) traces (chemparseplot.parse.chemgp_jsonl.ComparisonData attribute) train_e (chemparseplot.parse.chemgp_jsonl.GPQualityGrid attribute)

train_x (chemparseplot.parse.chemgp_jsonl.GPQualityGrid attribute) train_y (chemparseplot.parse.chemgp_jsonl.GPQualityGrid attribute) trajectory_to_landscape_df() (in module chemparseplot.parse.trajectory.neb) trajectory_to_profile_dat() (in module chemparseplot.parse.trajectory.neb) true_e (chemparseplot.parse.chemgp_jsonl.GPQualityGrid attribute) TWO_COL_NUM (in module chemparseplot.parse.patterns) TwoDimPlot (class in chemparseplot.plot.structs)

U

u_a (chemparseplot.parse.projection.ProjectionBasis attribute) u_b (chemparseplot.parse.projection.ProjectionBasis attribute)

UNKNOWN (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) update_labels() (chemparseplot.plot.structs.TwoDimPlot method) ureg (in module chemparseplot.units)

V

v_a (chemparseplot.parse.projection.ProjectionBasis attribute)

v_b (chemparseplot.parse.projection.ProjectionBasis attribute) validate_hdf5_structure() (in module chemparseplot.parse.chemgp_hdf5)

W

window_length (chemparseplot.plot.neb.SmoothingParams attribute)

X

x (chemparseplot.parse.chemgp_jsonl.GPQualityGrid attribute) (chemparseplot.parse.chemgp_jsonl.StationaryPoint attribute)

XYData (in module chemparseplot.plot.structs)

Y

y (chemparseplot.parse.chemgp_jsonl.GPQualityGrid attribute) (chemparseplot.parse.chemgp_jsonl.StationaryPoint attribute)

Z

ZEROMODE_ABORT (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute)