Python Module Index

i


	i
	`ichor`
	`ichor.cli`
	`ichor.cli.completers`
	`ichor.cli.completers.tab_completer`
	`ichor.cli.console_menu`
	`ichor.cli.global_menu_variables`
	`ichor.cli.main_menu`
	`ichor.cli.main_menu_submenus`
	`ichor.cli.main_menu_submenus.analysis_menu`
	`ichor.cli.main_menu_submenus.analysis_menu.analysis_menu`
	`ichor.cli.main_menu_submenus.database_menu`
	`ichor.cli.main_menu_submenus.database_menu.submit_csvs_from_database`
	`ichor.cli.main_menu_submenus.molecular_dynamics_menu`
	`ichor.cli.main_menu_submenus.molecular_dynamics_menu.molecular_dynamics_menu`
	`ichor.cli.main_menu_submenus.molecular_dynamics_menu.molecular_dynamics_submenus`
	`ichor.cli.main_menu_submenus.molecular_dynamics_menu.molecular_dynamics_submenus.amber_submenu`
	`ichor.cli.main_menu_submenus.molecular_dynamics_menu.molecular_dynamics_submenus.cp2k_submenu`
	`ichor.cli.main_menu_submenus.points_directory_menu`
	`ichor.cli.main_menu_submenus.points_directory_menu.points_directory_menu`
	`ichor.cli.main_menu_submenus.points_directory_menu.points_directory_submenus`
	`ichor.cli.main_menu_submenus.points_directory_menu.points_directory_submenus.submit_aimall_menu`
	`ichor.cli.main_menu_submenus.points_directory_menu.points_directory_submenus.submit_database_menu`
	`ichor.cli.main_menu_submenus.points_directory_menu.points_directory_submenus.submit_gaussian_menu`
	`ichor.cli.main_menu_submenus.tools_menu`
	`ichor.cli.main_menu_submenus.tools_menu.tools_menu`
	`ichor.cli.main_menu_submenus.trajectory_menu`
	`ichor.cli.main_menu_submenus.trajectory_menu.trajectory_menu`
	`ichor.cli.menu_description`
	`ichor.cli.menu_options`
	`ichor.cli.useful_functions`
	`ichor.cli.useful_functions.user_input`
	`ichor.core`
	`ichor.core.analysis`
	`ichor.core.analysis.dlpoly`
	`ichor.core.analysis.dlpoly.dlpoly_analysis`
	`ichor.core.analysis.dlpoly.dlpoly_files`
	`ichor.core.analysis.dlpoly.mae_forces`
	`ichor.core.analysis.dlpoly.plot_energy`
	`ichor.core.analysis.dlpoly.true_vs_predicted`
	`ichor.core.analysis.predictions`
	`ichor.core.analysis.s_curves`
	`ichor.core.analysis.s_curves.compact_s_curves`
	`ichor.core.analysis.s_curves.s_curves`
	`ichor.core.analysis.trajectory_analysis`
	`ichor.core.atoms`
	`ichor.core.atoms.alf`
	`ichor.core.atoms.atom`
	`ichor.core.atoms.atoms`
	`ichor.core.atoms.atoms_not_found_exception`
	`ichor.core.atoms.list_of_atoms`
	`ichor.core.atoms.list_of_atoms_atom_view`
	`ichor.core.calculators`
	`ichor.core.calculators.alf`
	`ichor.core.calculators.alf.cahn_ingold_prelog_alf_calculator`
	`ichor.core.calculators.alf.sequence_alf_calculator`
	`ichor.core.calculators.alf_features_to_coordinates_calculator`
	`ichor.core.calculators.c_matrix_calculator`
	`ichor.core.calculators.connectivity`
	`ichor.core.calculators.connectivity.distance_connectivity_calculator`
	`ichor.core.calculators.connectivity.valence_connectivity_calculator`
	`ichor.core.calculators.features`
	`ichor.core.calculators.features.alf_features_calculator`
	`ichor.core.calculators.geometry_calculator`
	`ichor.core.calculators.spherical_to_cartesian_calculator`
	`ichor.core.common`
	`ichor.core.common.arith`
	`ichor.core.common.bool`
	`ichor.core.common.constants`
	`ichor.core.common.conversion`
	`ichor.core.common.dict`
	`ichor.core.common.excel`
	`ichor.core.common.float`
	`ichor.core.common.formatting`
	`ichor.core.common.functools`
	`ichor.core.common.functools.functools`
	`ichor.core.common.int`
	`ichor.core.common.io`
	`ichor.core.common.itertools`
	`ichor.core.common.linalg`
	`ichor.core.common.np`
	`ichor.core.common.obj`
	`ichor.core.common.os`
	`ichor.core.common.pairwise`
	`ichor.core.common.patterns`
	`ichor.core.common.search`
	`ichor.core.common.sorting`
	`ichor.core.common.str`
	`ichor.core.common.types`
	`ichor.core.common.types.bool_toggle`
	`ichor.core.common.types.class_dict`
	`ichor.core.common.types.coordinates`
	`ichor.core.common.types.dict_list`
	`ichor.core.common.types.enum`
	`ichor.core.common.types.file_tree`
	`ichor.core.common.types.itypes`
	`ichor.core.common.types.multipole_moments`
	`ichor.core.common.types.mutable_value`
	`ichor.core.common.types.no_str`
	`ichor.core.common.types.range_dict`
	`ichor.core.common.types.var_repr`
	`ichor.core.common.types.version`
	`ichor.core.common.units`
	`ichor.core.database`
	`ichor.core.database.json`
	`ichor.core.database.json.add_to_database`
	`ichor.core.database.json.query_database`
	`ichor.core.database.query_database`
	`ichor.core.database.sql`
	`ichor.core.database.sql.add_to_database`
	`ichor.core.database.sql.database`
	`ichor.core.database.sql.query_database`
	`ichor.core.files`
	`ichor.core.files.aimall`
	`ichor.core.files.aimall.ab_int`
	`ichor.core.files.aimall.aim`
	`ichor.core.files.aimall.int`
	`ichor.core.files.aimall.ints`
	`ichor.core.files.directory`
	`ichor.core.files.dl_poly`
	`ichor.core.files.dl_poly.dl_poly_config`
	`ichor.core.files.dl_poly.dl_poly_control`
	`ichor.core.files.dl_poly.dl_poly_fflux`
	`ichor.core.files.dl_poly.dl_poly_field`
	`ichor.core.files.dl_poly.dl_poly_history`
	`ichor.core.files.dl_poly.dl_poly_iqa_energies`
	`ichor.core.files.dl_poly.dl_poly_iqa_forces`
	`ichor.core.files.dl_poly.fflux_directory`
	`ichor.core.files.file`
	`ichor.core.files.file_data`
	`ichor.core.files.gaussian`
	`ichor.core.files.gaussian.gaussian_output`
	`ichor.core.files.gaussian.gjf`
	`ichor.core.files.gaussian.wfn`
	`ichor.core.files.gaussian.wfx`
	`ichor.core.files.mol2`
	`ichor.core.files.optional_content`
	`ichor.core.files.orca`
	`ichor.core.files.orca.orca_engrad`
	`ichor.core.files.orca.orca_input`
	`ichor.core.files.orca.orca_output`
	`ichor.core.files.pandora`
	`ichor.core.files.pandora.morfi_output`
	`ichor.core.files.pandora.mout`
	`ichor.core.files.pandora.pandora_directory`
	`ichor.core.files.pandora.pandora_input`
	`ichor.core.files.pandora.pyscf_output`
	`ichor.core.files.path_object`
	`ichor.core.files.point_directory`
	`ichor.core.files.points_directory`
	`ichor.core.files.points_directory_parent`
	`ichor.core.files.qcp`
	`ichor.core.files.xyz`
	`ichor.core.files.xyz.trajectory`
	`ichor.core.files.xyz.xyz`
	`ichor.core.models`
	`ichor.core.models.calculate_fflux_derivatives`
	`ichor.core.models.create_datasets`
	`ichor.core.models.fflux_derivative_helper_functions`
	`ichor.core.models.gaussian_energy_derivative_wrt_features`
	`ichor.core.models.kernels`
	`ichor.core.models.kernels.constant`
	`ichor.core.models.kernels.distance`
	`ichor.core.models.kernels.interpreter`
	`ichor.core.models.kernels.interpreter.ast`
	`ichor.core.models.kernels.interpreter.interpreter`
	`ichor.core.models.kernels.interpreter.lexer`
	`ichor.core.models.kernels.interpreter.parser`
	`ichor.core.models.kernels.interpreter.token`
	`ichor.core.models.kernels.interpreter.token_type`
	`ichor.core.models.kernels.kernel`
	`ichor.core.models.kernels.mixed_kernel_with_derivatives`
	`ichor.core.models.kernels.periodic_kernel`
	`ichor.core.models.kernels.rbf`
	`ichor.core.models.kernels.rbf_cyclic`
	`ichor.core.models.mean`
	`ichor.core.models.mean.constant`
	`ichor.core.models.mean.linear`
	`ichor.core.models.mean.mean`
	`ichor.core.models.mean.quadratic`
	`ichor.core.models.mean.zero`
	`ichor.core.models.model`
	`ichor.core.models.model_with_gradient`
	`ichor.core.models.models`
	`ichor.core.models.predict_forces_for_all_atoms`
	`ichor.core.molecular_dynamics`
	`ichor.core.molecular_dynamics.amber`
	`ichor.core.molecular_dynamics.cp2k`
	`ichor.core.multipoles`
	`ichor.core.multipoles.dipole`
	`ichor.core.multipoles.hexadecapole`
	`ichor.core.multipoles.octupole`
	`ichor.core.multipoles.quadrupole`
	`ichor.core.processing`
	`ichor.core.processing.callables`
	`ichor.core.processing.callables.gaussian_processing_callables`
	`ichor.core.processing.callables.int_processing_callables`
	`ichor.core.processing.callables.no_processing_callables`
	`ichor.core.processing.check_functions`
	`ichor.core.processing.point_directory_processing`
	`ichor.core.useful_functions`
	`ichor.core.useful_functions.check_aimall_completed`
	`ichor.core.useful_functions.check_points_dir_suffix`
	`ichor.core.useful_functions.debugging`
	`ichor.core.useful_functions.get_atoms`
	`ichor.hpc`
	`ichor.hpc.batch_system`
	`ichor.hpc.batch_system.batch_system`
	`ichor.hpc.batch_system.jobs`
	`ichor.hpc.batch_system.local`
	`ichor.hpc.batch_system.node`
	`ichor.hpc.batch_system.parallel_environment`
	`ichor.hpc.batch_system.sge`
	`ichor.hpc.batch_system.slurm`
	`ichor.hpc.batch_system.utils`
	`ichor.hpc.global_variables`
	`ichor.hpc.log`
	`ichor.hpc.main`
	`ichor.hpc.main.aimall`
	`ichor.hpc.main.check_for_missing_files`
	`ichor.hpc.main.database`
	`ichor.hpc.main.gaussian`
	`ichor.hpc.main.orca`
	`ichor.hpc.main.trajectory`
	`ichor.hpc.molecular_dynamics`
	`ichor.hpc.molecular_dynamics.amber`
	`ichor.hpc.molecular_dynamics.cp2k`
	`ichor.hpc.submission_command`
	`ichor.hpc.submission_commands`
	`ichor.hpc.submission_commands.aimall_command`
	`ichor.hpc.submission_commands.amber_command`
	`ichor.hpc.submission_commands.cp2k_command`
	`ichor.hpc.submission_commands.dlpoly_command`
	`ichor.hpc.submission_commands.free_flow_python_command`
	`ichor.hpc.submission_commands.gaussian_command`
	`ichor.hpc.submission_commands.orca_command`
	`ichor.hpc.submission_commands.python_command`
	`ichor.hpc.submission_commands.tyche_command`
	`ichor.hpc.submission_script`
	`ichor.hpc.submission_script.command_group`
	`ichor.hpc.submission_script.script_names`
	`ichor.hpc.submission_script.submission_script`
	`ichor.hpc.uid`
	`ichor.hpc.useful_functions`
	`ichor.hpc.useful_functions.get_machine`
	`ichor.hpc.useful_functions.get_python_environment`
	`ichor.hpc.useful_functions.submit_free_flow_python_on_compute`