Index

B

batch_mode() (in module ensemble_analyzer.cli.pickle_editor.cli)

boltzmann_distribution() (in module ensemble_analyzer.constants)

C

calc_damp() (in module ensemble_analyzer.rrho) calc_electronic_entropy() (in module ensemble_analyzer.rrho) calc_qRRHO_energy() (in module ensemble_analyzer.rrho) calc_rotational_energy() (in module ensemble_analyzer.rrho) calc_rotational_entropy() (in module ensemble_analyzer.rrho) calc_S_R_grimme() (in module ensemble_analyzer.rrho) calc_S_V_grimme() (in module ensemble_analyzer.rrho) calc_translational_energy() (in module ensemble_analyzer.rrho) calc_translational_entropy() (in module ensemble_analyzer.rrho) calc_vibrational_energy() (in module ensemble_analyzer.rrho) calc_vibrational_entropy() (in module ensemble_analyzer.rrho) calc_zpe() (in module ensemble_analyzer.rrho) calculate_population_vector() (in module ensemble_analyzer.cli.get_av_energy) calculate_weighted_average() (in module ensemble_analyzer.cli.get_av_energy) change_alpha_flow() (ensemble_analyzer.cli.pickle_editor.tui.InteractiveTUI method) change_colors_flow() (ensemble_analyzer.cli.pickle_editor.tui.InteractiveTUI method) change_line_alpha() (ensemble_analyzer.cli.pickle_editor.core.MatplotlibPickleEditor method) change_line_colors() (ensemble_analyzer.cli.pickle_editor.core.MatplotlibPickleEditor method) change_line_linestyle() (ensemble_analyzer.cli.pickle_editor.core.MatplotlibPickleEditor method)

change_line_linewidth() (ensemble_analyzer.cli.pickle_editor.core.MatplotlibPickleEditor method) change_line_visibility() (ensemble_analyzer.cli.pickle_editor.core.MatplotlibPickleEditor method) change_linestyle_flow() (ensemble_analyzer.cli.pickle_editor.tui.InteractiveTUI method) change_linewidth_flow() (ensemble_analyzer.cli.pickle_editor.tui.InteractiveTUI method) change_visibility_flow() (ensemble_analyzer.cli.pickle_editor.tui.InteractiveTUI method) check_gaussian() (in module ensemble_analyzer.cli.check_setup) check_mlip() (in module ensemble_analyzer.cli.check_setup) check_models_dir() (in module ensemble_analyzer.cli.check_setup) check_nwchem() (in module ensemble_analyzer.cli.check_setup) check_orca() (in module ensemble_analyzer.cli.check_setup) check_python_dependencies() (in module ensemble_analyzer.cli.check_setup) check_tblite() (in module ensemble_analyzer.cli.check_setup) ClusteringConfig (class in ensemble_analyzer._clustering.cluster_config) clusters (ensemble_analyzer._clustering.cluster_config.PCAResult attribute) ColoredFormatter (class in ensemble_analyzer._logger.formatter) colors (ensemble_analyzer._clustering.cluster_config.PCAResult attribute) COLORS (ensemble_analyzer._logger.formatter.ColoredFormatter attribute) ComparedGraph (class in ensemble_analyzer._spectral.compare) components (ensemble_analyzer._clustering.cluster_config.PCAResult attribute) compute_boltzmann_populations() (in module ensemble_analyzer.constants)

D

default() (ensemble_analyzer.io_utils.SerialiseEncoder method)

E

energies (ensemble_analyzer._clustering.cluster_config.PCAResult attribute) ensemble_analyzer._clustering.cluster_config module ensemble_analyzer._logger.formatter module ensemble_analyzer._spectral.compare module ensemble_analyzer._spectral.graph_default module ensemble_analyzer.cli.check_setup module ensemble_analyzer.cli.get_av_energy module ensemble_analyzer.cli.pickle_editor.cli module ensemble_analyzer.cli.pickle_editor.core module

ensemble_analyzer.cli.pickle_editor.tui module ensemble_analyzer.cli.protocol_wizard module ensemble_analyzer.cli.regraph module ensemble_analyzer.constants module ensemble_analyzer.io_utils module ensemble_analyzer.launch module ensemble_analyzer.rrho module eV_to_nm() (in module ensemble_analyzer.constants) experimental_file (ensemble_analyzer._spectral.compare.ComparedGraph attribute) explained_variance (ensemble_analyzer._clustering.cluster_config.PCAResult attribute)

F

format() (ensemble_analyzer._logger.formatter.ColoredFormatter method)

free_gibbs_energy() (in module ensemble_analyzer.rrho)

G

get_legend_labels() (ensemble_analyzer.cli.pickle_editor.core.MatplotlibPickleEditor method) get_line_colors() (ensemble_analyzer.cli.pickle_editor.core.MatplotlibPickleEditor method) get_models_dir() (in module ensemble_analyzer.constants)

get_thermo_data() (in module ensemble_analyzer.cli.get_av_energy) graph_type (ensemble_analyzer._spectral.compare.ComparedGraph attribute) (ensemble_analyzer._spectral.graph_default.GraphDefault attribute) GraphDefault (class in ensemble_analyzer._spectral.graph_default)

H

has_modifications() (ensemble_analyzer.cli.pickle_editor.core.MatplotlibPickleEditor method)

I

include_H (ensemble_analyzer._clustering.cluster_config.ClusteringConfig attribute)

InteractiveTUI (class in ensemble_analyzer.cli.pickle_editor.tui)

L

load() (ensemble_analyzer.cli.pickle_editor.core.MatplotlibPickleEditor method) log (ensemble_analyzer._spectral.compare.ComparedGraph attribute)

log_fail() (in module ensemble_analyzer.cli.check_setup) log_pass() (in module ensemble_analyzer.cli.check_setup) log_warn() (in module ensemble_analyzer.cli.check_setup)

M

main() (in module ensemble_analyzer.cli.check_setup) (in module ensemble_analyzer.cli.get_av_energy) (in module ensemble_analyzer.cli.pickle_editor.cli) (in module ensemble_analyzer.cli.regraph) (in module ensemble_analyzer.launch) MatplotlibPickleEditor (class in ensemble_analyzer.cli.pickle_editor.core) max_k (ensemble_analyzer._clustering.cluster_config.ClusteringConfig attribute) min_k (ensemble_analyzer._clustering.cluster_config.ClusteringConfig attribute) mkdir() (in module ensemble_analyzer.io_utils) module ensemble_analyzer._clustering.cluster_config ensemble_analyzer._logger.formatter ensemble_analyzer._spectral.compare ensemble_analyzer._spectral.graph_default ensemble_analyzer.cli.check_setup ensemble_analyzer.cli.get_av_energy ensemble_analyzer.cli.pickle_editor.cli ensemble_analyzer.cli.pickle_editor.core ensemble_analyzer.cli.pickle_editor.tui ensemble_analyzer.cli.protocol_wizard ensemble_analyzer.cli.regraph ensemble_analyzer.constants ensemble_analyzer.io_utils ensemble_analyzer.launch ensemble_analyzer.rrho

move_files() (in module ensemble_analyzer.io_utils)

N

n_clusters (ensemble_analyzer._clustering.cluster_config.ClusteringConfig attribute) (ensemble_analyzer._clustering.cluster_config.PCAResult attribute)

nm (ensemble_analyzer._spectral.compare.ComparedGraph attribute) numbers (ensemble_analyzer._clustering.cluster_config.PCAResult attribute)

O

ordinal() (in module ensemble_analyzer.constants)

original_features (ensemble_analyzer._clustering.cluster_config.PCAResult attribute)

P

parse_argument() (in module ensemble_analyzer.cli.regraph) parse_mapping_file() (in module ensemble_analyzer.cli.pickle_editor.cli) PCAResult (class in ensemble_analyzer._clustering.cluster_config) PickleSecurityError

plot() (ensemble_analyzer._spectral.compare.ComparedGraph method) preview() (ensemble_analyzer.cli.pickle_editor.core.MatplotlibPickleEditor method) print_panel() (ensemble_analyzer.cli.pickle_editor.tui.InteractiveTUI method) protocol_index (ensemble_analyzer._spectral.compare.ComparedGraph attribute)

R

random_state (ensemble_analyzer._clustering.cluster_config.ClusteringConfig attribute) rename_labels_flow() (ensemble_analyzer.cli.pickle_editor.tui.InteractiveTUI method)

rename_legend_labels() (ensemble_analyzer.cli.pickle_editor.core.MatplotlibPickleEditor method) RESET (ensemble_analyzer._logger.formatter.ColoredFormatter attribute) run() (ensemble_analyzer.cli.pickle_editor.tui.InteractiveTUI method)

S

save() (ensemble_analyzer.cli.pickle_editor.core.MatplotlibPickleEditor method) save_flow() (ensemble_analyzer.cli.pickle_editor.tui.InteractiveTUI method) scores (ensemble_analyzer._clustering.cluster_config.PCAResult attribute) SerialiseEncoder (class in ensemble_analyzer.io_utils)

set_cluster_attribute (ensemble_analyzer._clustering.cluster_config.ClusteringConfig attribute) set_limits_flow() (ensemble_analyzer.cli.pickle_editor.tui.InteractiveTUI method) set_xlim() (ensemble_analyzer.cli.pickle_editor.core.MatplotlibPickleEditor method) set_ylim() (ensemble_analyzer.cli.pickle_editor.core.MatplotlibPickleEditor method) show_current_state() (ensemble_analyzer.cli.pickle_editor.tui.InteractiveTUI method)

T

tail() (in module ensemble_analyzer.io_utils)

W

write_json() (in module ensemble_analyzer.io_utils)