Index

A

A (pibronic.server.server.ServerExecutionParameters attribute) (pibronic.vibronic.vibronic_model_keys.VibronicModelKeys attribute) add_harmonic_contribution() (in module pibronic.stats.stats) advance() (pibronic.vibronic.electronic_structure.VibronExecutionClass method) analytic_of_original_coupled_model() (in module pibronic.julia_wrapper)

analytic_of_sampling_model() (in module pibronic.julia_wrapper) analytic_results (in module pibronic.data.file_name) analytic_wrapper() (in module pibronic.julia_wrapper) annotate_intensity_grid() (pibronic.plotting.grid_plots.plotGrids method) assert_partition_exists() (in module pibronic.server.job_boss)

B

base_func() (in module pibronic.julia_wrapper) beads (pibronic.pimc.pimc.BoxData attribute) beta (pibronic.pimc.pimc.BoxData attribute) (pibronic.server.server.ServerExecutionParameters attribute) beta() (in module pibronic.constants) beta_minus (pibronic.pimc.pimc.BoxDataPM attribute) (pibronic.pimc.pimc.ModelVibronicPM attribute) beta_plus (pibronic.pimc.pimc.BoxDataPM attribute) (pibronic.pimc.pimc.ModelVibronicPM attribute) BlkS (pibronic.server.server.ServerExecutionParameters attribute)

block_compute() (in module pibronic.pimc.pimc) block_compute_pm() (in module pibronic.pimc.pimc) block_size (pibronic.pimc.pimc.BoxData attribute) blocks (pibronic.pimc.pimc.BoxData attribute) BoxData (class in pibronic.pimc.pimc) BoxDataPM (class in pibronic.pimc.pimc) BoxResult (class in pibronic.pimc.pimc) BoxResultPM (class in pibronic.pimc.pimc) build() (pibronic.pimc.pimc.BoxData class method) build_SKSM_and_identity() (in module pibronic.vibronic.orthonormal.sequences)

C

calculate_alpha_jackknife_terms() (in module pibronic.stats.jackknife) calculate_alpha_terms() (in module pibronic.stats.stats) calculate_basic_property_terms() (in module pibronic.stats.stats) calculate_jackknife_term() (in module pibronic.stats.jackknife) calculate_jackknife_terms() (in module pibronic.stats.jackknife) calculate_vibronic_model() (pibronic.vibronic.electronic_structure.VibronExecutionClass method) calculate_vibronic_model_wrapper_one() (in module pibronic.vibronic.electronic_structure) calculations_list (in module pibronic.vibronic.electronic_structure) change_rho() (pibronic.data.file_structure.FileStructure method) check_acct_state() (in module pibronic.server.job_boss) check_minimum_length_of_sequence() (in module pibronic.vibronic.orthonormal.sequences) check_running_state() (in module pibronic.server.job_boss) check_slurm_output() (in module pibronic.server.job_boss) compute() (in module pibronic.julia_wrapper) compute_linear_displacement() (pibronic.pimc.pimc.ModelSampling method) (pibronic.pimc.pimc.ModelVibronic method) compute_path_to_file() (pibronic.pimc.pimc.BoxResult method) compute_sampling_constants() (pibronic.pimc.pimc.ModelSampling method) compute_weight_for_each_state() (pibronic.pimc.pimc.ModelSampling method) (pibronic.pimc.pimc.ModelVibronic method) confirm_symmetry_in_modes() (in module pibronic.vibronic.model_auto)

confirm_symmetry_in_surfaces() (in module pibronic.vibronic.model_auto) construct_command_dictionary() (in module pibronic.julia_wrapper) construct_job_command() (pibronic.server.job_boss.SubmissionClass method) convert_keys() (in module pibronic.julia_wrapper) copyInput() (in module pibronic.everything) coupled_model (in module pibronic.data.file_name) create_basic_diagonal_model() (in module pibronic.vibronic.vibronic_model_io) create_coupling_from_h_file() (in module pibronic.vibronic.vibronic_model_io) create_coupling_from_op_file() (in module pibronic.vibronic.vibronic_model_io) create_coupling_from_op_hyperlink() (in module pibronic.vibronic.vibronic_model_io) create_diagonal_model_hash() (in module pibronic.vibronic.vibronic_model_io) create_fake_coupled_model() (in module pibronic.vibronic.vibronic_model_io) create_harmonic_model() (in module pibronic.vibronic.vibronic_model_io) create_model_hash() (in module pibronic.vibronic.vibronic_model_io) create_orthonormal_matrix_lambda_close_to_identity() (in module pibronic.vibronic.orthonormal.create) (in module pibronic.vibronic.vibronic_model_io) create_random_diagonal_model() (in module pibronic.vibronic.vibronic_model_io) create_random_model() (in module pibronic.vibronic.vibronic_model_io) create_random_orthonormal_matrix() (in module pibronic.vibronic.vibronic_model_io) cubic (pibronic.pimc.pimc.ModelClass attribute) cubic_couplings (pibronic.vibronic.vibronic_model_keys.VibronicModelKeys attribute)

D

D (pibronic.server.server.ServerExecutionParameters attribute) dB (pibronic.server.server.ServerExecutionParameters attribute) debugging_matrix_checking_function() (in module pibronic.vibronic.orthonormal.sequences) delta_beta (pibronic.pimc.pimc.BoxData attribute) (pibronic.pimc.pimc.BoxDataPM attribute) (pibronic.pimc.pimc.ModelVibronicPM attribute)

diagonal_model_shape_dict() (in module pibronic.vibronic.vibronic_model_io) diagonal_model_zeros_template_json_dict() (in module pibronic.vibronic.vibronic_model_io) difference_function() (in module pibronic.vibronic.orthonormal.sequences) dir_list (pibronic.data.file_structure.FileStructure attribute) directories_exist() (pibronic.data.file_structure.FileStructure method) draw_sample() (pibronic.pimc.pimc.BoxData method) (pibronic.pimc.pimc.ModelSampling method)

E

E (pibronic.vibronic.vibronic_model_keys.VibronicModelKeys attribute) encode_self() (pibronic.pimc.pimc.BoxData method) energies (pibronic.vibronic.vibronic_model_keys.VibronicModelKeys attribute) energy (pibronic.pimc.pimc.ModelClass attribute) estimate_basic_properties() (in module pibronic.stats.stats) estimate_jackknife() (in module pibronic.stats.jackknife) execute() (in module pibronic.everything) execution_output() (in module pibronic.data.file_name) extract_basis_value_from_sos_file_path() (in module pibronic.data.postprocessing) extract_bead_paramater_list() (in module pibronic.data.postprocessing) extract_bead_value_from_pimc_file_path() (in module pibronic.data.postprocessing) extract_bead_value_from_thermo_file_path() (in module pibronic.data.postprocessing) extract_bead_value_from_trotter_file_path() (in module pibronic.data.postprocessing) extract_bicubic_couplings() (in module pibronic.vibronic.model_op) extract_biquartic_couplings() (in module pibronic.vibronic.model_op) extract_cubic_couplings() (in module pibronic.vibronic.model_h) (in module pibronic.vibronic.model_op) extract_dimensions_of_diagonal_model() (in module pibronic.vibronic.vibronic_model_io) extract_dimensions_of_model() (in module pibronic.vibronic.vibronic_model_io) extract_energies() (in module pibronic.vibronic.model_h) (in module pibronic.vibronic.model_op)

extract_id_job_from_output() (in module pibronic.server.job_boss) extract_jackknife_parameters() (in module pibronic.data.postprocessing) extract_job_value_from_pimc_file_path() (in module pibronic.data.postprocessing) extract_linear_couplings() (in module pibronic.vibronic.model_h) (in module pibronic.vibronic.model_op) extract_normal_mode_frequencies() (in module pibronic.vibronic.model_h) (in module pibronic.vibronic.model_op) extract_offdiag_quadratic_couplings() (in module pibronic.vibronic.model_h) extract_parameter_lists() (in module pibronic.data.postprocessing) extract_pimc_parameters() (in module pibronic.data.postprocessing) extract_quadratic_couplings() (in module pibronic.vibronic.model_h) (in module pibronic.vibronic.model_op) extract_quartic_couplings() (in module pibronic.vibronic.model_h) (in module pibronic.vibronic.model_op) extract_sample_value_from_thermo_file_path() (in module pibronic.data.postprocessing) extract_sos_basis_paramater_list() (in module pibronic.data.postprocessing) extract_T_from_beta() (in module pibronic.constants) extract_temperature_paramater_list() (in module pibronic.data.postprocessing) extract_temperature_value_from_pimc_file_path() (in module pibronic.data.postprocessing) extract_temperature_value_from_thermo_file_path() (in module pibronic.data.postprocessing) extract_trotter_paramater_list() (in module pibronic.data.postprocessing)

F

file_in (pibronic.vibronic.electronic_structure.VibronExecutionClass attribute) file_out (pibronic.vibronic.electronic_structure.VibronExecutionClass attribute) FileStructure (class in pibronic.data.file_structure) fill_in_diagonal_quadratic_couplings() (in module pibronic.vibronic.model_auto) fill_in_excitation_energies() (in module pibronic.vibronic.model_auto) fill_in_linear_couplings() (in module pibronic.vibronic.model_auto) fill_in_offdiagonal_quadratic_couplings() (in module pibronic.vibronic.model_auto) fill_offdiagonal_of_model_with_zeros() (in module pibronic.vibronic.vibronic_model_io) find_first_turn_around_point() (in module pibronic.vibronic.orthonormal.sequences) find_string_in_file() (in module pibronic.helper) (in module pibronic.vibronic.electronic_structure)

finish_folding_in_terms() (pibronic.pimc.pimc.ModelSampling method) (pibronic.pimc.pimc.ModelVibronic method) FINISHED (pibronic.vibronic.electronic_structure.State attribute) flow() (pibronic.log_conf.MyLogger method) frequencies (pibronic.vibronic.vibronic_model_keys.VibronicModelKeys attribute) from_boxdata() (pibronic.data.file_structure.FileStructure class method) from_FileStructure() (pibronic.pimc.pimc.BoxData class method) from_json_file() (pibronic.pimc.pimc.BoxData class method) (pibronic.pimc.pimc.ModelClass class method) from_json_string() (pibronic.pimc.pimc.BoxData class method)

G

G1 (pibronic.vibronic.vibronic_model_keys.VibronicModelKeys attribute) G2 (pibronic.vibronic.vibronic_model_keys.VibronicModelKeys attribute) G3 (pibronic.vibronic.vibronic_model_keys.VibronicModelKeys attribute) G4 (pibronic.vibronic.vibronic_model_keys.VibronicModelKeys attribute) generate_analytical_results() (in module pibronic.everything) generate_and_save_x_pairs() (in module pibronic.vibronic.orthonormal.sequences) generate_file_lists() (pibronic.plotting.plotting.plot_original_Z_test method) (pibronic.plotting.plotting.plot_Z_multiple_FS method) (pibronic.plotting.plotting.plot_Z_test method) (pibronic.plotting.virtual.plotVirtual method) generate_full_monotonic_sequence() (in module pibronic.vibronic.orthonormal.sequences) generate_full_monotonic_sequence_for_plotting() (in module pibronic.vibronic.orthonormal.sequences) generate_model_hashes() (pibronic.data.file_structure.FileStructure method) generate_monotonic_sequence_to_first_turn_around() (in module pibronic.vibronic.orthonormal.sequences) generate_parameter_lists() (pibronic.plotting.plotting.plot_original_Z_test method) (pibronic.plotting.plotting.plot_Z_multiple_FS method) (pibronic.plotting.plotting.plot_Z_test method) (pibronic.plotting.virtual.plotVirtual method)

generate_random_R_values() (pibronic.pimc.pimc.BoxData method) generate_sequences_for_plotting() (in module pibronic.vibronic.orthonormal.sequences) generate_sign_array() (pibronic.plotting.grid_plots.plotGrids method) generate_tau_values() (in module pibronic.plotting.plotting) (pibronic.plotting.plotting.plot_original_Z_test method) (pibronic.plotting.plotting.plot_original_Z_vs_diagonal_test method) (pibronic.plotting.plotting.plot_rectangle method) generate_turning_point_sequence_for_plotting() (in module pibronic.vibronic.orthonormal.sequences) generate_vibronic_model_data() (in module pibronic.vibronic.vibronic_model_io) geom() (pibronic.vibronic.electronic_structure.VibronExecutionClass method) geometry_optimization() (in module pibronic.vibronic.electronic_structure) get() (pibronic.vibronic.electronic_structure.ZmatClass method) get_hostname() (in module pibronic.server.job_boss) get_integer_from_user() (in module pibronic.vibronic.electronic_structure) get_number_of_electronic_states() (in module pibronic.vibronic.model_h) get_number_of_normal_modes() (in module pibronic.vibronic.model_h) get_path_of_job_boss_directory() (in module pibronic.server.job_boss) get_path_to_python_executable() (in module pibronic.server.job_boss) get_yes_no_from_user() (in module pibronic.vibronic.electronic_structure)

H

harmonic_model (in module pibronic.data.file_name) hartree_fock_calculation() (in module pibronic.vibronic.electronic_structure) hash_rho (pibronic.pimc.pimc.BoxData attribute) (pibronic.pimc.pimc.BoxResult attribute)

hash_vib (pibronic.pimc.pimc.BoxData attribute) (pibronic.pimc.pimc.BoxResult attribute) hf() (pibronic.vibronic.electronic_structure.VibronExecutionClass method)

I

id_data (pibronic.pimc.pimc.BoxData attribute) id_job (pibronic.pimc.pimc.BoxResult attribute) id_rho (pibronic.pimc.pimc.BoxData attribute) initialize_arrays() (pibronic.pimc.pimc.BoxResult method) (pibronic.pimc.pimc.BoxResultPM method) initialize_models() (pibronic.pimc.pimc.BoxData method) (pibronic.pimc.pimc.BoxDataPM method) initialize_TDP_object() (pibronic.pimc.pimc.ModelSampling method) (pibronic.pimc.pimc.ModelVibronic method) (pibronic.pimc.pimc.ModelVibronicPM method)

ip_calc() (pibronic.vibronic.electronic_structure.VibronExecutionClass method) ip_calculation() (in module pibronic.vibronic.electronic_structure) IPEOMCC (pibronic.vibronic.electronic_structure.State attribute) iterate_method() (in module pibronic.julia_wrapper) iterative_matrix (in module pibronic.data.file_name) iterative_model (in module pibronic.data.file_name)

J

jackknife() (in module pibronic.data.file_name)

json_serialize() (pibronic.pimc.pimc.BoxData class method)

K

key_list (pibronic.pimc.pimc.BoxResult attribute) (pibronic.pimc.pimc.BoxResultPM attribute)

kind (pibronic.vibronic.electronic_structure.ZmatClass attribute)

L

linear (pibronic.pimc.pimc.ModelClass attribute) linear_couplings (pibronic.vibronic.vibronic_model_keys.VibronicModelKeys attribute) list_of_turning_points() (in module pibronic.vibronic.orthonormal.sequences) load_analytic_data() (in module pibronic.data.postprocessing) load_analytical_data() (pibronic.plotting.plotting.plot_original_Z_test method) (pibronic.plotting.plotting.plot_original_Z_vs_diagonal_test method) load_analytical_original() (in module pibronic.plotting.plotting) load_analytical_sampling() (in module pibronic.plotting.plotting) load_coupled_models() (pibronic.plotting.grid_plots.plotGrids method) load_data() (pibronic.plotting.grid_plots.plotGrids method) (pibronic.plotting.plotting.plot_Z_multiple_FS method) (pibronic.plotting.plotting.plot_Z_test method) (pibronic.plotting.plotting.plot_original_Z_test method) (pibronic.plotting.plotting.plot_original_Z_vs_diagonal_test method) (pibronic.plotting.plotting.plot_rectangle method) (pibronic.plotting.plotting.plot_sos_Z_vs_rho_n method) load_diagonal_model_from_JSON() (in module pibronic.vibronic.vibronic_model_io) load_json_string() (pibronic.pimc.pimc.BoxData method)

load_latex_module_on_server() (in module pibronic.plotting) (in module pibronic.plotting.prepare) load_model() (pibronic.pimc.pimc.ModelClass method) (pibronic.pimc.pimc.ModelSampling method) load_model_from_JSON() (in module pibronic.vibronic.vibronic_model_io) load_multiple_results() (pibronic.pimc.pimc.BoxResult method) (pibronic.pimc.pimc.BoxResultPM method) load_original_models() (pibronic.plotting.grid_plots.plotGrids method) load_pimc_data() (in module pibronic.data.postprocessing) (pibronic.plotting.plotting.plot_Z_multiple_FS method) (pibronic.plotting.plotting.plot_original_Z_test method) load_results() (pibronic.pimc.pimc.BoxResult method) (pibronic.pimc.pimc.BoxResultPM method) load_rho_sos_data() (in module pibronic.data.postprocessing) load_sequence() (in module pibronic.vibronic.orthonormal.sequences) load_sos() (in module pibronic.plotting.plotting) load_trotter_coupled() (in module pibronic.plotting.plotting) lock() (pibronic.log_conf.MyLogger method)

M

main() (in module pibronic.julia_wrapper) (in module pibronic.vibronic.electronic_structure) (in module pibronic.vibronic.orthonormal.create) (in module pibronic.vibronic.orthonormal.sequences) (in module pibronic.vibronic.vibronic_model_io) make_directories() (pibronic.data.file_structure.FileStructure method) make_rho_directories() (pibronic.data.file_structure.FileStructure method) MAX_SAMPLES_PER_JOB (pibronic.server.job_boss.PimcSubmissionClass attribute) (pibronic.server.job_boss.SubmissionClass attribute) model_parameters_are_symmetric_in_modes() (in module pibronic.vibronic.vibronic_model_io)

model_parameters_are_symmetric_in_surfaces() (in module pibronic.vibronic.vibronic_model_io) model_shape_dict() (in module pibronic.vibronic.vibronic_model_io) model_zeros_template_json_dict() (in module pibronic.vibronic.vibronic_model_io) ModelClass (class in pibronic.pimc.pimc) ModelSampling (class in pibronic.pimc.pimc) ModelVibronic (class in pibronic.pimc.pimc) ModelVibronicPM (class in pibronic.pimc.pimc) modes (pibronic.pimc.pimc.BoxData attribute) (pibronic.pimc.pimc.ModelClass attribute) MyLogger (class in pibronic.log_conf)

N

N (pibronic.server.server.ServerExecutionParameters attribute) (pibronic.vibronic.vibronic_model_keys.VibronicModelKeys attribute) name (pibronic.vibronic.electronic_structure.VibronExecutionClass attribute) nBlk (pibronic.server.server.ServerExecutionParameters attribute)

NIP (pibronic.vibronic.electronic_structure.State attribute) node_dict (pibronic.server.job_boss.SubmissionClass attribute) number_of_modes (pibronic.vibronic.vibronic_model_keys.VibronicModelKeys attribute) number_of_surfaces (pibronic.vibronic.vibronic_model_keys.VibronicModelKeys attribute)

O

omega (pibronic.pimc.pimc.ModelClass attribute) OPT (pibronic.vibronic.electronic_structure.State attribute) optimize_energy() (pibronic.pimc.pimc.ModelSampling method) (pibronic.pimc.pimc.ModelVibronic method)

original_analytic_results (in module pibronic.data.file_name) original_model (in module pibronic.data.file_name)

P

P (pibronic.server.server.ServerExecutionParameters attribute) Pair (in module pibronic.vibronic.orthonormal.sequences) pairwise() (in module pibronic.vibronic.electronic_structure) param_dict (pibronic.server.job_boss.PimcSubmissionClass attribute) (pibronic.server.job_boss.SubmissionClass attribute) parameter_dictionary (pibronic.vibronic.electronic_structure.VibronExecutionClass attribute) parse_hartree_fock_output() (in module pibronic.vibronic.electronic_structure) parse_input_parameters() (in module pibronic.vibronic.electronic_structure) (pibronic.vibronic.electronic_structure.VibronExecutionClass method) parse_ip_output() (in module pibronic.vibronic.electronic_structure) parse_opt_output() (in module pibronic.vibronic.electronic_structure) parse_ouput() (in module pibronic.julia_wrapper) parse_prepVibron_output() (in module pibronic.vibronic.electronic_structure) parse_vibron_output() (in module pibronic.vibronic.electronic_structure) path_rho_model (pibronic.pimc.pimc.BoxData attribute) path_root (pibronic.vibronic.electronic_structure.VibronExecutionClass attribute) path_to_sequence_file() (in module pibronic.vibronic.orthonormal.sequences) path_to_x_pair_file() (in module pibronic.vibronic.orthonormal.sequences) path_vib_model (pibronic.pimc.pimc.BoxData attribute) pibronic (module) pibronic.constants (module) pibronic.data (module) pibronic.data.file_name (module) pibronic.data.file_structure (module) pibronic.data.postprocessing (module) pibronic.everything (module) pibronic.helper (module) pibronic.julia_wrapper (module) pibronic.log_conf (module) pibronic.pimc (module) pibronic.pimc.pimc (module) pibronic.plotting (module) pibronic.plotting.grid_plots (module) pibronic.plotting.plotting (module) pibronic.plotting.prepare (module) pibronic.plotting.virtual (module) pibronic.server (module) pibronic.server.job_boss (module) pibronic.server.server (module) pibronic.stats (module) pibronic.stats.jackknife (module) pibronic.stats.stats (module) pibronic.vibronic (module) pibronic.vibronic.electronic_structure (module) pibronic.vibronic.model_auto (module) pibronic.vibronic.model_h (module) pibronic.vibronic.model_op (module) pibronic.vibronic.orthonormal (module) pibronic.vibronic.orthonormal.create (module) pibronic.vibronic.orthonormal.sequences (module) pibronic.vibronic.vibronic_model_io (module) pibronic.vibronic.vibronic_model_keys (module) pimc() (in module pibronic.data.file_name) PimcSubmissionClass (class in pibronic.server.job_boss) plot() (pibronic.plotting.plotting.plot_original_Z_test method) (pibronic.plotting.plotting.plot_Z_test method) (pibronic.plotting.plotting.plot_original_Z_vs_diagonal_test method) (pibronic.plotting.plotting.plot_rectangle method) (pibronic.plotting.plotting.plot_sos_Z_vs_rho_n method)

plot_coupled_energy_grid() (pibronic.plotting.grid_plots.plotGrids method) plot_coupled_linear_grids() (pibronic.plotting.grid_plots.plotGrids method) plot_coupled_quadratic_grids() (pibronic.plotting.grid_plots.plotGrids method) plot_Cv() (pibronic.plotting.plotting.plot_Z_test method) plot_E() (pibronic.plotting.plotting.plot_Z_test method) plot_energy() (pibronic.plotting.grid_plots.plotGrids method) plot_linear_coupling() (pibronic.plotting.grid_plots.plotGrids method) plot_original_energy_grid() (pibronic.plotting.grid_plots.plotGrids method) plot_original_linear_grids() (pibronic.plotting.grid_plots.plotGrids method) plot_original_quadratic_grids() (pibronic.plotting.grid_plots.plotGrids method) plot_original_Z_test (class in pibronic.plotting.plotting) plot_original_Z_vs_diagonal_test (class in pibronic.plotting.plotting) plot_quadratic_coupling() (pibronic.plotting.grid_plots.plotGrids method) plot_rectangle (class in pibronic.plotting.plotting) plot_single_energy_grid() (pibronic.plotting.grid_plots.plotGrids method) plot_single_linear_grid() (pibronic.plotting.grid_plots.plotGrids method) plot_single_quadratic_grid() (pibronic.plotting.grid_plots.plotGrids method) plot_sos_Z_vs_rho_n (class in pibronic.plotting.plotting) plot_Z() (pibronic.plotting.plotting.plot_original_Z_test method) (pibronic.plotting.plotting.plot_Z_test method) (pibronic.plotting.plotting.plot_original_Z_vs_diagonal_test method) (pibronic.plotting.plotting.plot_rectangle method) (pibronic.plotting.plotting.plot_sos_Z_vs_rho_n method) plot_Z_multiple_FS (class in pibronic.plotting.plotting) plot_Z_test (class in pibronic.plotting.plotting) plotGrids (class in pibronic.plotting.grid_plots) plotVirtual (class in pibronic.plotting.virtual) precompute() (pibronic.pimc.pimc.ModelSampling method) (pibronic.pimc.pimc.ModelVibronic method) (pibronic.pimc.pimc.ModelVibronicPM method) prepare_data() (pibronic.plotting.grid_plots.plotGrids method) (pibronic.plotting.plotting.plot_original_Z_test method) (pibronic.plotting.plotting.plot_original_Z_vs_diagonal_test method) (pibronic.plotting.plotting.plot_rectangle method) (pibronic.plotting.plotting.plot_sos_Z_vs_rho_n method) prepare_job_compute_canada() (in module pibronic.server.job_boss) prepare_job_feynman() (in module pibronic.server.job_boss) prepare_job_graham() (in module pibronic.server.job_boss) prepare_job_nlogn() (in module pibronic.server.job_boss) prepare_job_orca() (in module pibronic.server.job_boss) prepare_julia() (in module pibronic.julia_wrapper) prepare_mpl_rc_file() (in module pibronic.plotting) (in module pibronic.plotting.prepare) prepare_paths() (pibronic.server.job_boss.PimcSubmissionClass method) (pibronic.server.job_boss.SubmissionClass method) preprocess() (pibronic.pimc.pimc.BoxData method) (pibronic.pimc.pimc.BoxDataPM method) PREPVIB (pibronic.vibronic.electronic_structure.State attribute) prepVibron() (pibronic.vibronic.electronic_structure.VibronExecutionClass method) prepVibron_calculation() (in module pibronic.vibronic.electronic_structure) pretty_print_job_status() (in module pibronic.vibronic.electronic_structure) prune_results_using_hashes() (in module pibronic.data.postprocessing)

Q

quadratic (pibronic.pimc.pimc.ModelClass attribute) quadratic_couplings (pibronic.vibronic.vibronic_model_keys.VibronicModelKeys attribute)

quartic (pibronic.pimc.pimc.ModelClass attribute) quartic_couplings (pibronic.vibronic.vibronic_model_keys.VibronicModelKeys attribute)

R

R (pibronic.server.server.ServerExecutionParameters attribute) read_header() (in module pibronic.vibronic.model_auto) read_model_auto_file() (in module pibronic.vibronic.model_auto) (in module pibronic.vibronic.vibronic_model_io) read_model_h_file() (in module pibronic.vibronic.model_h) (in module pibronic.vibronic.vibronic_model_io) read_model_op_file() (in module pibronic.vibronic.model_op) (in module pibronic.vibronic.vibronic_model_io) read_number_of_samples() (pibronic.pimc.pimc.BoxResult class method) readlines() (in module pibronic.helper) recalculate_energy_values_of_diagonal_model() (in module pibronic.vibronic.vibronic_model_io) record_state() (pibronic.vibronic.electronic_structure.VibronExecutionClass method)

remove_coupling_from_model() (in module pibronic.vibronic.vibronic_model_io) result_keys_are_present_in() (pibronic.pimc.pimc.BoxResult class method) (pibronic.pimc.pimc.BoxResultPM class method) retrive_all_file_paths() (in module pibronic.data.postprocessing) retrive_file_paths_for_jackknife() (in module pibronic.data.postprocessing) retrive_jackknife_file_list() (in module pibronic.data.postprocessing) retrive_pimc_file_list() (in module pibronic.data.postprocessing) retrive_sos_coupled_file_list() (in module pibronic.data.postprocessing) retrive_sos_sampling_file_list() (in module pibronic.data.postprocessing) rfind_string_in_file() (in module pibronic.helper) (in module pibronic.vibronic.electronic_structure) rho (pibronic.pimc.pimc.BoxData attribute)

S

samples (pibronic.pimc.pimc.BoxData attribute) sampling_model (in module pibronic.data.file_name) save_diagonal_model_to_JSON() (in module pibronic.vibronic.vibronic_model_io) save_model_to_JSON() (in module pibronic.vibronic.vibronic_model_io) save_results() (pibronic.pimc.pimc.BoxResult method) (pibronic.pimc.pimc.BoxResultPM method) save_sequence() (in module pibronic.vibronic.orthonormal.sequences) select_pair() (in module pibronic.vibronic.orthonormal.sequences) serialize_BoxData_dictionary() (in module pibronic.server.job_boss) ServerExecutionParameters (class in pibronic.server.server) set() (pibronic.vibronic.electronic_structure.ZmatClass method) setup_blocks_and_jobs() (pibronic.server.job_boss.PimcSubmissionClass method) setup_zmat() (pibronic.vibronic.electronic_structure.VibronExecutionClass method) SIGUSR1_handle() (in module pibronic.server.job_boss) simple_single_point_energy_calculation() (in module pibronic.vibronic.vibronic_model_io) singles_cutoff (pibronic.vibronic.electronic_structure.VibronExecutionClass attribute) skip_back_lines() (in module pibronic.helper)

skip_back_n_lines() (in module pibronic.vibronic.electronic_structure) skip_forward_lines() (in module pibronic.helper) skip_forward_n_lines() (in module pibronic.vibronic.electronic_structure) sos() (in module pibronic.data.file_name) sos_of_coupled_model() (in module pibronic.julia_wrapper) sos_wrapper() (in module pibronic.julia_wrapper) State (class in pibronic.vibronic.electronic_structure) state (pibronic.vibronic.electronic_structure.VibronExecutionClass attribute) states (pibronic.pimc.pimc.BoxData attribute) (pibronic.pimc.pimc.ModelClass attribute) SubmissionClass (class in pibronic.server.job_boss) submit_job() (in module pibronic.server.job_boss) (in module pibronic.vibronic.electronic_structure) submit_job_array() (pibronic.server.job_boss.PimcSubmissionClass method) submit_jobs() (pibronic.server.job_boss.PimcSubmissionClass method) subprocess_run_wrapper() (in module pibronic.server.job_boss) subprocess_submit_asynch_wrapper() (in module pibronic.server.job_boss) synchronize_with_job() (in module pibronic.server.job_boss)

T

T (pibronic.server.server.ServerExecutionParameters attribute) tau (pibronic.pimc.pimc.BoxData attribute) (pibronic.server.server.ServerExecutionParameters attribute) tau_minus (pibronic.pimc.pimc.BoxDataPM attribute) (pibronic.pimc.pimc.ModelVibronicPM attribute) tau_plus (pibronic.pimc.pimc.BoxDataPM attribute) (pibronic.pimc.pimc.ModelVibronicPM attribute) temp_file_path() (in module pibronic.vibronic.electronic_structure) temperature (pibronic.pimc.pimc.BoxData attribute) template_rho (pibronic.data.file_structure.FileStructure attribute) template_rho_output (pibronic.data.file_structure.FileStructure attribute) template_rho_params (pibronic.data.file_structure.FileStructure attribute) template_rho_plots (pibronic.data.file_structure.FileStructure attribute) template_rho_results (pibronic.data.file_structure.FileStructure attribute)

template_vib (pibronic.data.file_structure.FileStructure attribute) template_vib_output (pibronic.data.file_structure.FileStructure attribute) template_vib_params (pibronic.data.file_structure.FileStructure attribute) template_vib_plots (pibronic.data.file_structure.FileStructure attribute) template_vib_results (pibronic.data.file_structure.FileStructure attribute) test_one() (in module pibronic.vibronic.electronic_structure) training_data_g_output() (in module pibronic.data.file_name) training_data_input() (in module pibronic.data.file_name) training_data_rho_output() (in module pibronic.data.file_name) transform_sampled_coordinates() (pibronic.pimc.pimc.BoxData method) triples_cutoff (pibronic.vibronic.electronic_structure.VibronExecutionClass attribute) trotter() (in module pibronic.data.file_name) trotter_of_coupled_model() (in module pibronic.julia_wrapper) trotter_wrapper() (in module pibronic.julia_wrapper)

V

valid_rho_hash() (pibronic.data.file_structure.FileStructure method) valid_vib_and_rho_hashes() (pibronic.data.file_structure.FileStructure method) valid_vib_hash() (pibronic.data.file_structure.FileStructure method) validate_data() (pibronic.plotting.virtual.plotVirtual method) validate_old_model_data() (in module pibronic.julia_wrapper) validate_old_rho_data() (in module pibronic.julia_wrapper) verify_aces2_completed() (in module pibronic.vibronic.electronic_structure) verify_diagonal_model_parameters() (in module pibronic.vibronic.vibronic_model_io) verify_directories_exists() (pibronic.data.file_structure.FileStructure method) verify_file_exists() (in module pibronic.helper) (in module pibronic.vibronic.electronic_structure) verify_hostname_is_valid() (pibronic.server.job_boss.SubmissionClass method) verify_ip_states() (in module pibronic.vibronic.electronic_structure)

verify_model_parameters() (in module pibronic.vibronic.vibronic_model_io) verify_result_keys_are_present() (pibronic.pimc.pimc.BoxResult class method) (pibronic.pimc.pimc.BoxResultPM class method) vib (pibronic.pimc.pimc.BoxData attribute) VIB (pibronic.vibronic.electronic_structure.State attribute) vib() (pibronic.vibronic.electronic_structure.VibronExecutionClass method) vibrational_frequency() (in module pibronic.vibronic.electronic_structure) VIBRON (pibronic.vibronic.electronic_structure.State attribute) vibron_calc() (pibronic.vibronic.electronic_structure.VibronExecutionClass method) vibron_calculation() (in module pibronic.vibronic.electronic_structure) VibronExecutionClass (class in pibronic.vibronic.electronic_structure) VibronicModelKeys (class in pibronic.vibronic.vibronic_model_keys) VMK (in module pibronic.vibronic)

W

w (pibronic.vibronic.vibronic_model_keys.VibronicModelKeys attribute)

wait_on_results() (in module pibronic.vibronic.electronic_structure)

X

X (pibronic.server.server.ServerExecutionParameters attribute)

Z

zmat (pibronic.vibronic.electronic_structure.VibronExecutionClass attribute)

ZmatClass (class in pibronic.vibronic.electronic_structure)