Index

A

acf module acf_mat() (in module libra_py.acf) acf_vec() (in module libra_py.acf) add_atom_to_system() (in module libra_py.build) add_atoms_to_system() (in module libra_py.build) adjust_SD_probabilities() (in module libra_py.workflows.nbra.lz) amplitudes2denmat() (in module libra_py.tsh_stat) apply_normalization() (in module libra_py.workflows.nbra.step3) apply_orthonormalization_general() (in module libra_py.workflows.nbra.step3)

apply_phase_correction() (in module libra_py.workflows.nbra.step3) apply_phase_correction_general() (in module libra_py.workflows.nbra.step3) apply_state_reordering() (in module libra_py.workflows.nbra.step3) apply_state_reordering_general() (in module libra_py.workflows.nbra.step3) autoconnect module autoconnect() (in module libra_py.autoconnect) avarage_populations() (in module libra_py.tsh_stat) ave_en() (in module libra_py.tsh_stat) ave_pop() (in module libra_py.tsh_stat)

B

Belyaev_Lebedev() (in module libra_py.workflows.nbra.lz) bin2list() (in module libra_py.data_outs) Boltz_cl_prob() (in module libra_py.probabilities) Boltz_cl_prob_up() (in module libra_py.probabilities) Boltz_corr_Ham() (in module libra_py.tsh)

boltz_factor() (in module libra_py.tsh) Boltz_quant_prob() (in module libra_py.probabilities) bootstrapping() (in module libra_py.data_stat) build module build_SD_basis() (in module libra_py.workflows.nbra.step3)

C

chain_potential() (in module libra_py.models.Tully) cmat_distrib() (in module libra_py.data_stat) cmat_stat() (in module libra_py.data_stat) cmat_stat2() (in module libra_py.data_stat) collapse() (in module libra_py.tsh) compute_all() (in module libra_py.influence_spectrum) compute_ci_energies_midpoint() (in module libra_py.workflows.nbra.step3) compute_cov() (in module libra_py.normal_modes) compute_cov1() (in module libra_py.normal_modes) compute_cov2() (in module libra_py.normal_modes) compute_cube_ks_overlaps() (in module libra_py.workflows.nbra.step2_many_body) compute_density() (in module libra_py.data_stat) compute_dm() (in module libra_py.tsh_stat) compute_dynmat() (in module libra_py.LAMMPS_methods) (in module libra_py.normal_modes) compute_etot() (in module libra_py.tsh_stat) compute_etot_tsh() (in module libra_py.tsh_stat) compute_freqs() (in module libra_py.workflows.nbra.qsh) compute_hprime module compute_hprime_dia() (in module libra_py.workflows.nbra.compute_hprime) compute_Hvib() (in module libra_py.namd) (in module libra_py.workflows.nbra.step3) compute_Hvib_sd() (in module libra_py.namd)

compute_mat_elt() (in module libra_py.influence_spectrum) compute_oscillator_strengths() (in module libra_py.workflows.nbra.step2_analysis) compute_properties_onekpt() (in module libra_py.workflows.nbra.compute_properties) compute_qs_Hvib() (in module libra_py.workflows.nbra.qsh) compute_sh_statistics() (in module libra_py.tsh_stat) compute_spectrum() (in module libra_py.workflows.nbra.step2_analysis) convert_Landry_Subotnik2model1() (in module libra_py.models.Libra) convolve() (in module libra_py.pdos) convolve_cp2k_pdos() (in module libra_py.pdos) coords2xyz() (in module libra_py.scan) covariance_matrix() (in module libra_py.normal_modes) cp2k_distribute() (in module libra_py.CP2K_methods) CP2K_input_static() (in module libra_py.CP2K_methods) CP2K_methods module crop_sphere_xyz() (in module libra_py.build) crop_sphere_xyz2() (in module libra_py.build) crop_sphere_xyz3() (in module libra_py.build) cryst2cart() (in module libra_py.QE_methods) cube_file_methods module cube_file_names_cp2k() (in module libra_py.CP2K_methods) cube_generator_dftbplus() (in module libra_py.DFTB_methods) cube_generator_gaussian() (in module libra_py.Gaussian_methods) curr_and_final_step_job() (in module libra_py.workflows.nbra.step2_many_body)

D

data_conv module data_outs module data_read module data_stat module decoherence_times module decoherence_times() (in module libra_py.workflows.nbra.decoherence_times) decoherence_times2rates() (in module libra_py.workflows.nbra.decoherence_times)

decoherence_times_ave() (in module libra_py.workflows.nbra.decoherence_times) denmat2prob() (in module libra_py.tsh_stat) dftb_distribute() (in module libra_py.DFTB_methods) DFTB_methods module dish_py() (in module libra_py.tsh) distribute() (in module libra_py.hpc_utils) do_ovlp() (in module libra_py.workflows.nbra.step2_dftb) (in module libra_py.workflows.nbra.step2_ergoscf) do_phase_corr() (in module libra_py.workflows.nbra.step3) do_step() (in module libra_py.workflows.nbra.step2_dftb) (in module libra_py.workflows.nbra.step2_ergoscf)

E

energies() (in module libra_py.ERGO_methods) energy_arb() (in module libra_py.workflows.nbra.mapping) energy_gaps() (in module libra_py.workflows.nbra.decoherence_times)

energy_gaps_ave() (in module libra_py.workflows.nbra.decoherence_times) energy_mat_arb() (in module libra_py.workflows.nbra.mapping) ERGO_methods module

F

Faist_Levine() (in module libra_py.models.Faist_Levine) fgr_py module find_last_file() (in module libra_py.ERGO_methods) find_maxima() (in module libra_py.data_stat) find_undercoordinated_atoms() (in module libra_py.autoconnect) fit module fit_exp() (in module libra_py.fit)

fit_gau() (in module libra_py.fit) fix_motion module form_block_matrix() (in module libra_py.data_conv) form_Hvib_real() (in module libra_py.workflows.nbra.step2_many_body) ft module ft() (in module libra_py.ft) ft2() (in module libra_py.ft)

G

gaussian_distribute() (in module libra_py.Gaussian_methods) gaussian_input() (in module libra_py.Gaussian_methods) Gaussian_methods module generate_replicas_xyz() (in module libra_py.build) generate_replicas_xyz2() (in module libra_py.build) get_data() (in module libra_py.data_read) get_data_from_file() (in module libra_py.data_read) get_data_from_file2() (in module libra_py.data_read) get_data_sets() (in module libra_py.data_read) get_dftb_ks_energies() (in module libra_py.DFTB_methods) get_dftb_matrices() (in module libra_py.DFTB_methods) get_energy_forces() (in module libra_py.DFTB_methods) get_excitation_analysis_output() (in module libra_py.workflows.nbra.step2_many_body) get_Faist_Levine_LiI() (in module libra_py.models.Faist_Levine) get_Faist_Levine_NaI() (in module libra_py.models.Faist_Levine) get_Holstein_set1() (in module libra_py.models.Holstein) get_Hvib() (in module libra_py.workflows.nbra.step4)

get_Hvib2() (in module libra_py.workflows.nbra.step4) get_Landry_Subotnik_set1() (in module libra_py.models.Libra) get_Landry_Subotnik_set2() (in module libra_py.models.Libra) get_Lowdin() (in module libra_py.workflows.nbra.step3) get_Lowdin_general() (in module libra_py.workflows.nbra.step3) get_LVC_set1() (in module libra_py.models.LVC) get_LVC_set1b() (in module libra_py.models.LVC) get_LVC_set2() (in module libra_py.models.LVC) get_LVC_set3() (in module libra_py.models.LVC) get_matrix() (in module libra_py.data_read) get_mtx_matrices() (in module libra_py.ERGO_methods) get_QE_normal_modes() (in module libra_py.QE_methods) get_reordering() (in module libra_py.unavoided) get_step2_data() (in module libra_py.workflows.nbra.step3) get_step2_mb_sp_properties() (in module libra_py.workflows.nbra.step2_analysis) get_value() (in module libra_py.QE_utils) get_xyz() (in module libra_py.normal_modes) get_xyz2() (in module libra_py.normal_modes) grid_volume() (in module libra_py.cube_file_methods)

H

Henon_Heiles() (in module libra_py.models.Henon_Heiles) HO_prob() (in module libra_py.probabilities) HO_prob_E_up() (in module libra_py.probabilities) HO_prob_up() (in module libra_py.probabilities) Holstein2() (in module libra_py.models.Holstein) Holstein3() (in module libra_py.models.Holstein) Holstein4() (in module libra_py.models.Holstein)

Holstein5() (in module libra_py.models.Holstein) Holstein_uncoupled() (in module libra_py.models.Holstein) hop_py() (in module libra_py.tsh) hopping() (in module libra_py.tsh) hpc_utils module hprime_py() (in module libra_py.workflows.nbra.compute_hprime)

I

ida_py() (in module libra_py.tsh) influence_spectrum module init_ensembles module init_ext_hamiltonians() (in module libra_py.init_ensembles) init_mm_Hamiltonians() (in module libra_py.init_ensembles) init_mols() (in module libra_py.init_ensembles)

init_system module init_system() (in module libra_py.init_system) init_systems() (in module libra_py.init_ensembles) init_systems2() (in module libra_py.init_ensembles) init_therms() (in module libra_py.init_ensembles) integrate_cube() (in module libra_py.cube_file_methods) integrate_cube_set() (in module libra_py.workflows.nbra.step2_many_body)

J

job() (in module libra_py.hpc_utils)

L

LAMMPS_methods module length_converter() (in module libra_py.units) libra_pdos() (in module libra_py.pdos) libra_py.acf module libra_py.autoconnect module libra_py.build module libra_py.CP2K_methods module libra_py.cube_file_methods module libra_py.data_conv module libra_py.data_outs module libra_py.data_read module libra_py.data_stat module libra_py.DFTB_methods module libra_py.dynamics.exact.save module libra_py.dynamics.heom.plot module libra_py.ERGO_methods module libra_py.fgr_py module libra_py.fit module libra_py.fix_motion module libra_py.ft module libra_py.Gaussian_methods module libra_py.hpc_utils module libra_py.hungarian module libra_py.influence_spectrum module libra_py.init_ensembles module libra_py.init_system module libra_py.LAMMPS_methods module libra_py.LoadGAFF module libra_py.LoadMMFF94 module libra_py.LoadMolecule module libra_py.LoadPT module libra_py.LoadTRIPOS module libra_py.LoadUFF module libra_py.models.Faist_Levine module libra_py.models.Henon_Heiles module libra_py.models.Holstein module libra_py.models.Libra module

libra_py.models.LVC module libra_py.models.Martens module libra_py.models.SSY module libra_py.models.Tully module libra_py.namd module libra_py.normal_modes module libra_py.nve_md module libra_py.parse_gamess module libra_py.pdos module libra_py.probabilities module libra_py.QE_methods module libra_py.QE_utils module libra_py.regexlib module libra_py.scan module libra_py.scf module libra_py.tsh module libra_py.tsh_stat module libra_py.unavoided module libra_py.units module libra_py.vesta2qe module libra_py.workflows.nbra.compute_hprime module libra_py.workflows.nbra.compute_properties module libra_py.workflows.nbra.decoherence_times module libra_py.workflows.nbra.lz module libra_py.workflows.nbra.mapping module libra_py.workflows.nbra.qsh module libra_py.workflows.nbra.step2 module libra_py.workflows.nbra.step2_analysis module libra_py.workflows.nbra.step2_dftb module libra_py.workflows.nbra.step2_ergoscf module libra_py.workflows.nbra.step2_many_body module libra_py.workflows.nbra.step3 module libra_py.workflows.nbra.step4 module list2bin() (in module libra_py.data_outs) list2MATRIX() (in module libra_py.data_conv) Load_Molecule() (in module libra_py.LoadMolecule) LoadMolecule module LVC() (in module libra_py.models.LVC)

M

make_cost_mat() (in module libra_py.workflows.nbra.step3) make_dftb_input() (in module libra_py.DFTB_methods) make_list() (in module libra_py.data_conv) make_path_xyz() (in module libra_py.scan) make_path_xyz2() (in module libra_py.scan) make_submit() (in module libra_py.hpc_utils) make_system() (in module libra_py.build) make_T_matricies() (in module libra_py.workflows.nbra.step3) make_xyz() (in module libra_py.build) make_xyz_mat() (in module libra_py.build) mapping module mat_average() (in module libra_py.data_stat) mat_center_data() (in module libra_py.data_stat) mat_stat() (in module libra_py.data_stat) matrix2list() (in module libra_py.data_conv) MATRIX2nparray() (in module libra_py.data_conv) maximize() (in module libra_py.hungarian) measure() (in module libra_py.fix_motion) measure2() (in module libra_py.fix_motion) merge_orbitals() (in module libra_py.QE_utils) model1() (in module libra_py.models.Libra) (in module libra_py.models.Martens) model1a() (in module libra_py.models.Libra) model2() (in module libra_py.models.Libra) (in module libra_py.models.Martens) model2a() (in module libra_py.models.Libra) model3() (in module libra_py.models.Libra) model3a() (in module libra_py.models.Libra) model4() (in module libra_py.models.Libra) model4a() (in module libra_py.models.Libra) model5() (in module libra_py.models.Libra) model6() (in module libra_py.models.Libra) model7() (in module libra_py.models.Libra) models_Faist_Levine module models_Henon_Heiles module models_Holstein module models_Libra module models_LVC module models_Martens module models_SSY module models_Tully module module acf autoconnect build compute_hprime CP2K_methods cube_file_methods data_conv data_outs data_read data_stat decoherence_times DFTB_methods ERGO_methods fgr_py fit fix_motion ft Gaussian_methods hpc_utils influence_spectrum init_ensembles init_system LAMMPS_methods libra_py.acf libra_py.autoconnect libra_py.build libra_py.CP2K_methods libra_py.cube_file_methods libra_py.data_conv libra_py.data_outs libra_py.data_read libra_py.data_stat libra_py.DFTB_methods libra_py.dynamics.exact.save libra_py.dynamics.heom.plot libra_py.ERGO_methods libra_py.fgr_py libra_py.fit libra_py.fix_motion libra_py.ft libra_py.Gaussian_methods libra_py.hpc_utils libra_py.hungarian libra_py.influence_spectrum libra_py.init_ensembles libra_py.init_system libra_py.LAMMPS_methods libra_py.LoadGAFF libra_py.LoadMMFF94 libra_py.LoadMolecule libra_py.LoadPT libra_py.LoadTRIPOS libra_py.LoadUFF libra_py.models.Faist_Levine libra_py.models.Henon_Heiles libra_py.models.Holstein libra_py.models.Libra libra_py.models.LVC libra_py.models.Martens libra_py.models.SSY libra_py.models.Tully libra_py.namd libra_py.normal_modes libra_py.nve_md libra_py.parse_gamess libra_py.pdos libra_py.probabilities libra_py.QE_methods libra_py.QE_utils libra_py.regexlib libra_py.scan libra_py.scf libra_py.tsh libra_py.tsh_stat libra_py.unavoided libra_py.units libra_py.vesta2qe libra_py.workflows.nbra.compute_hprime libra_py.workflows.nbra.compute_properties libra_py.workflows.nbra.decoherence_times libra_py.workflows.nbra.lz libra_py.workflows.nbra.mapping libra_py.workflows.nbra.qsh libra_py.workflows.nbra.step2 libra_py.workflows.nbra.step2_analysis libra_py.workflows.nbra.step2_dftb libra_py.workflows.nbra.step2_ergoscf libra_py.workflows.nbra.step2_many_body libra_py.workflows.nbra.step3 libra_py.workflows.nbra.step4 LoadMolecule mapping models_Faist_Levine models_Henon_Heiles models_Holstein models_Libra models_LVC models_Martens models_SSY models_Tully namd nve_md pdos probabilities QE_methods qsh scan step2 step2_analysis step2_dftb step2_ergoscf step2_many_body tsh tsh_stat units

N

namd module name2no() (in module libra_py.parse_gamess) ndigits() (in module libra_py.CP2K_methods) normalize_ci_coefficients() (in module libra_py.workflows.nbra.step2_many_body)

nparray2CMATRIX() (in module libra_py.data_conv) nparray2MATRIX() (in module libra_py.data_conv) nve_md module nve_md_init() (in module libra_py.nve_md) nve_md_step() (in module libra_py.nve_md)

O

optimize_syst() (in module libra_py.nve_md) orbs2spinorbs() (in module libra_py.workflows.nbra.mapping) orthogonalize_orbitals() (in module libra_py.QE_utils) orthogonalize_orbitals2() (in module libra_py.QE_utils) out2inp() (in module libra_py.QE_methods)

out2pdb() (in module libra_py.QE_methods) out2xyz() (in module libra_py.QE_methods) output_sorted_Hvibs() (in module libra_py.workflows.nbra.step3) ovlp_arb() (in module libra_py.workflows.nbra.mapping) ovlp_mat_arb() (in module libra_py.workflows.nbra.mapping)

P

parse_gamess_basis() (in module libra_py.parse_gamess) parse_vesta() (in module libra_py.vesta2qe) pdos module permutation() (in module libra_py.fix_motion) permutation1() (in module libra_py.fix_motion) permutation2() (in module libra_py.fix_motion) plot_cubes() (in module libra_py.cube_file_methods) pops2denmat() (in module libra_py.tsh_stat) post_process() (in module libra_py.QE_utils) print_orbitals() (in module libra_py.scf)

print_pdos() (in module libra_py.scf) print_SD_basis() (in module libra_py.workflows.nbra.step3) printout() (in module libra_py.data_outs) (in module libra_py.workflows.nbra.step4) probabilities module probabilities_1D_scattering() (in module libra_py.tsh_stat) process_xyz() (in module libra_py.fix_motion) project_out() (in module libra_py.tsh) py_cft() (in module libra_py.ft) pyxaid2libra() (in module libra_py.workflows.nbra.step3)

Q

QE_methods module

QE_pdos() (in module libra_py.pdos) qsh module

R

read_2D_grid() (in module libra_py.data_read) read_all() (in module libra_py.QE_methods) read_cp2k_tddfpt_log_file() (in module libra_py.CP2K_methods) read_cube() (in module libra_py.cube_file_methods) read_dftb_output() (in module libra_py.DFTB_methods) read_dftbplus_TRA_file() (in module libra_py.DFTB_methods) read_energies_from_cp2k_log_file() (in module libra_py.CP2K_methods) read_energies_from_cp2k_md_log_file() (in module libra_py.CP2K_methods) read_energies_from_gaussian_log_file() (in module libra_py.Gaussian_methods) read_gaussian_tddft_log_file() (in module libra_py.Gaussian_methods) read_info() (in module libra_py.QE_methods) read_md_data() (in module libra_py.QE_methods) read_md_data_cell() (in module libra_py.QE_methods) read_md_data_xyz() (in module libra_py.QE_methods) read_md_data_xyz2() (in module libra_py.QE_methods) read_mo_restricted() (in module libra_py.ERGO_methods) read_mo_unrestricted() (in module libra_py.ERGO_methods) read_qe_index() (in module libra_py.QE_methods) read_qe_schema() (in module libra_py.QE_methods) read_qe_wfc() (in module libra_py.QE_methods) read_qe_wfc_grid() (in module libra_py.QE_methods) read_qe_wfc_info() (in module libra_py.QE_methods) read_spectrum_restricted() (in module libra_py.ERGO_methods) read_spectrum_unrestricted() (in module libra_py.ERGO_methods)

read_trajectory_xyz_file() (in module libra_py.CP2K_methods) read_trajectory_xyz_file_gaussian() (in module libra_py.Gaussian_methods) read_volumetric_data() (in module libra_py.cube_file_methods) read_wfc_grid() (in module libra_py.QE_methods) read_xyz() (in module libra_py.build) read_xyz_crystal() (in module libra_py.build) recipe1() (in module libra_py.influence_spectrum) Regression() (in module libra_py.fit) reindex_cp2k_sd_states() (in module libra_py.workflows.nbra.step2_many_body) remove_rotation() (in module libra_py.fix_motion) remove_translation() (in module libra_py.fix_motion) run() (in module libra_py.workflows.nbra.lz) (in module libra_py.workflows.nbra.qsh) (in module libra_py.workflows.nbra.step2) (in module libra_py.workflows.nbra.step3) (in module libra_py.workflows.nbra.step4) run_dftb_adi() (in module libra_py.DFTB_methods) run_NEFGRL_populations() (in module libra_py.fgr_py) run_NEFRG_acf() (in module libra_py.fgr_py) run_qe() (in module libra_py.QE_methods) run_step2() (in module libra_py.workflows.nbra.step2_dftb) (in module libra_py.workflows.nbra.step2_ergoscf) run_step2_lz() (in module libra_py.workflows.nbra.step2_dftb) run_step2_many_body() (in module libra_py.workflows.nbra.step2_many_body)

S

sac_matrices() (in module libra_py.workflows.nbra.step3) sample() (in module libra_py.tsh) scalar_stat() (in module libra_py.data_stat) scale_H_vib() (in module libra_py.workflows.nbra.step3) scale_NAC() (in module libra_py.data_conv) scale_NACs() (in module libra_py.data_conv) scan module scissor() (in module libra_py.data_conv) sd2indx() (in module libra_py.workflows.nbra.mapping) sdm_py() (in module libra_py.tsh) set_random_state() (in module libra_py.tsh) show_matrix_pyplot() (in module libra_py.data_outs) show_matrix_splot() (in module libra_py.data_outs) sort_SD_energies() (in module libra_py.workflows.nbra.step3) sort_unique_SD_basis() (in module libra_py.workflows.nbra.step3) spectrum() (in module libra_py.scf) split_orbitals_energies() (in module libra_py.QE_utils) SSY() (in module libra_py.models.SSY) state_num_cp2k() (in module libra_py.CP2K_methods)

step1() (in module libra_py.hungarian) step2 module step2() (in module libra_py.hungarian) step2_analysis module step2_dftb module step2_ergoscf module step2_many_body module step3() (in module libra_py.hungarian) step4() (in module libra_py.hungarian) step5() (in module libra_py.hungarian) step6() (in module libra_py.hungarian) substitute() (in module libra_py.hpc_utils) surface_hopping() (in module libra_py.tsh) surface_hopping_cpa() (in module libra_py.tsh) surface_hopping_cpa2() (in module libra_py.tsh) syst2xyz() (in module libra_py.nve_md)

T

test_1() (libra_py.autoconnect.TestAutoconnect method) (libra_py.influence_spectrum.TestDatautils method) test_2() (libra_py.autoconnect.TestAutoconnect method) (libra_py.influence_spectrum.TestDatautils method) test_3() (libra_py.influence_spectrum.TestDatautils method) test_4() (libra_py.influence_spectrum.TestDatautils method) test_maximize() (libra_py.hungarian.TestHungarian method) test_minimize() (libra_py.hungarian.TestHungarian method) test_reordering() (libra_py.unavoided.TestUnavoided method) TestAutoconnect (class in libra_py.autoconnect) TestDatautils (class in libra_py.influence_spectrum) TestHungarian (class in libra_py.hungarian)

TestUnavoided (class in libra_py.unavoided) traj_statistics() (in module libra_py.workflows.nbra.step4) traj_statistics2() (in module libra_py.workflows.nbra.step4) traj_statistics2_fast() (in module libra_py.workflows.nbra.step4) transform_data() (in module libra_py.data_conv) tsh module tsh_stat module Tully1() (in module libra_py.models.Tully) Tully1_py() (in module libra_py.models.Tully) Tully2() (in module libra_py.models.Tully) Tully3() (in module libra_py.models.Tully)

U

unit_conversion() (in module libra_py.data_conv) units module

unpack1() (in module libra_py.data_conv) unpack2() (in module libra_py.data_conv) update_sh_pop() (in module libra_py.tsh_stat)

V

vec_average() (in module libra_py.data_stat)

vec_center_data() (in module libra_py.data_stat) visualize_modes() (in module libra_py.normal_modes)

X

xyz2inp() (in module libra_py.QE_methods) xyz_traj2gen_ovlp() (in module libra_py.DFTB_methods) (in module libra_py.ERGO_methods)

xyz_traj2gen_sp() (in module libra_py.DFTB_methods) (in module libra_py.ERGO_methods)