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EStA 3

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- esta
  esta
  - ._data.py__move2_lattice_table__removing_atomic_data
  - abinitBag
  - aide
    
    aide
    
    check_float
    
    combined_excel
    
    dat2xls_n_csv
    
    dict_to_xlsx
    
    dict_to_xlsx_csv
    
    dict_to_yaml
    
    get_cid
    
    get_docx
    
    get_match_count
    
    interval2Range
    
    interval2Range_adv
    
    list_of_dict_to_xlsx_csv
    
    path_length
    
    pretty_int
    
    save_and_read_data_HDF5
    
    string2integer
    
    to_format
    
    to_yaml
    
    xyz2json
  - antar
  - ase_atoms
  - bonds
  - c
  - check_bond_between_atoms_xyz
  - check_float
  - dat2xls_n_csv
  - dict_to_xlsx
  - dict_to_xlsx_csv
  - dict_to_yaml
  - element
  - element_data
  - element_property
  - externalBag
    
    externalBag
    
    external_atomic
    
    external_xyz_py
    
    geometry
    
    get_connection
    
    mathutil_nwchem
    
    rmsd
    
    spharmonic4mcartesiancoord
    
    timestamp
    
    tools_AICON2
    
    xtb_ase
    
    xtb_ase
    
    calculator
  - extract_data
  - fortran
  - gamessBag
  - gaussianBag
    
    gaussianBag
    
    input_gaussian
    
    input_gaussian1
    
    input_gaussian1_1Dec2023
    
    input_grrm_advv
    
    output_gaussian_adv
    
    output_gaussian_adv0
    
    xx__input_gaussian0
    
    xx__output_gaussian_adv0
    
    xx_input_grrm
    
    xxx__input_gaussian_TODO
  - general
    
    general
    
    ._toaxsf
    
    aadhaar
    
    add_const_to_dict
    
    add_vacuum_to_unit_cell
    
    adjust_vacuum
    
    affine
    
    angle
    
    atomic_Distance_Density
    
    average
    
    b
    
    bending_acb_centroid_vacuum
    
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    bending_acb_centroid_vacuum_adv1
    
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    bending_nanoribbon
    
    boltzmann
    
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    cartAndSpherical
    
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    circle_equation
    
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    compare_scalar
    
    conjugate_gradient
    
    conversion_factors
    
    crystal_latticee
    
    direction_index2str
    
    distance_conformation
    
    distance_matrix
    
    distances_ase_esa
    
    entropy_data
    
    filter_vib_freq
    
    finding_vacuum_region2
    
    finite_difference
    
    free_energy_ethane
    
    from_pos2xyz
    
    from_pos2xyz_adv
    
    functionalize
    
    get_ACF_bader
    
    get_com
    
    get_configs
    
    get_configs_btw2strs
    
    get_dihedral
    
    get_element_natomeach_xyz
    
    get_labelling_atoms
    
    get_merged_dict
    
    get_moved_atom_n_symb
    
    get_poscar_from_cxyz
    
    get_pystyle_integer
    
    get_range_from_intervals
    
    get_rotation_matrix
    
    get_similar_configuration0
    
    get_similar_configuration_advv
    
    integration1D_over_a_cutoff
    
    list_grouped_and_unique
    
    manipulate
    
    manipulate_adv
    
    manipulate_adv____add_split_and_resuffle_to__manipulate
    
    metric_tensor
    
    min_trans_rot
    
    neighbors
    
    niggli_reduce
    
    nnb_of_atom
    
    operation
    
    peak_position_and_average_1D
    
    pseudo_info
    
    quat2rotation
    
    rate_const_IS0_TS1
    
    read_force_constant
    
    read_jmol
    
    read_kappa
    
    read_xyz
    
    reciprocal_lattice
    
    rename
    
    rename_general
    
    reverse_array
    
    rodrigues
    
    rodrigues1
    
    rott
    
    shift
    
    shift0
    
    shift_atom_test_old
    
    shift_poscar
    
    shuffle_output_csv_file_data_adv
    
    stack
    
    substitute_atom
    
    sum_dictionaries
    
    supercell_frame
    
    superpose3D_se
    
    symbol_from_atm_number
    
    table_latex
    
    thermo
    
    thermo2
    
    toaxsf
    
    unique_array
    
    unique_id
    
    use_pbc_ASE
    
    vacuum_level
    
    xsf
    
    xsf2cube
    
    xtb_calculator_for_EStA_21012025_v2
    
    xtb_calculator_for_EStA_21012025_v3
    
    xyz
    
    xyz_grouped
    
    xyz_images
    
    xyz_sanity
  - geometry__ASE_tosee
  - get_dihedral
  - get_docx
  - grrmBag
    
    grrmBag
    
    LUPINP
    
    a
    
    com2xyz
    
    get_IRC_path
    
    get_LUP
    
    get_LUPINP
    
    get_LUP_profile_advv
    
    get_nTS_nEQ_nPT
    
    get_xyz_grrm_IRC_step_advv
    
    input_grrm
    
    input_grrm_advv
    
    input_grrm_advvv
    
    output_grrm
    
    output_grrm_EQ
    
    output_grrm_ITR_adv
    
    output_grrm_ITR_adv1
    
    output_grrm_ITR_adv2
    
    output_grrm_ITR_adv3
    
    output_grrm_ITR_adv4
    
    output_grrm_ITR_adv5
    
    output_grrm_PT
    
    output_grrm_RxnMap6
    
    output_grrm_TS
    
    output_grrm_init
    
    plot_strs_energy
    
    reenergy_grrm
    
    search_structure2
    
    search_structure2_mod
    
    search_structure3
    
    to_location
    
    to_location_adv
    
    write_xyz
    
    x
  - innout
    
    innout
    
    get_docx
  - interval2Range
  - interval2Range_adv
  - kspace
    
    kspace
    
    kgrid
    
    kpath
  - lib_xyz
    
    lib_xyz
    
    load_data
    
    load_data_
  - list_of_dict_to_xlsx_csv
  - log
  - measure
    
    measure
    
    atomic_units
    
    conversion_factors
  - mlBag
  - neighbor
  - orcaBag
    
    orcaBag
    
    input_orca
    
    output_orca
  - pbc
  - ped
    
    ped
    
    afir
    
    dpe
  - phonon
    
    phonon
    
    atm_displacements
    
    atm_displacements_selective
    
    atm_displacements_selective_general_disp
    
    atm_displacements_selective_general_disp_adv
    
    fc_and_freq_selected_atoms
    
    fc_and_freq_selected_atoms_02112024
    
    fc_and_freq_selected_atoms_05112024
    
    fc_and_freq_selected_atoms_06112024
    
    force_constant_and_frequencies_selective_subspace_
    
    force_constant_and_frequencies_selective_subspace_general
    
    force_constant_and_frequencies_selective_subspace_general_adv
    
    forces
    
    forces_selective
    
    normal_mode_analysis__project_out_Trans_n_rotations_EXPLORE_also_read_gaussian_notes_IT_TODO
    
    sum_freq_and_zpe
    
    x_error_force_constant_and_frequencies_selective_subspace
    
    yaml_read_band
  - phononBag
    
    phononBag
    
    atom_projected_phDOS
    
    atom_projected_phDOS_over_mesh_adv
    
    eigen_vector_adv
    
    get_dynG
    
    intensity
    
    ir_intensity
    
    phono3py
    
    phono3py
    
    get_phono3py_data_n_plot
    
    plot_kappa_multiple_systems
    
    read_kappa
    
    phonopy
    
    phonopy
    
    eigen_vector
    
    eigenvector
    
    get_phonon_disp_with_phdos
    
    gruneisen
    
    phonon_dispersion
    
    projected_phonon_dos
    
    read_force_constant
    
    read_force_constant
    
    read_force_constant_stable
  - plot
    
    plot
    
    atomic_Distance_Density
    
    atomic_distance_density_class2
    
    broken_axis_plot__most_done_only_axis_allignmnet_left
    
    charge_bader
    
    free_energy_2
    
    get_plot_potential_energy
    
    multiplot
    
    plot1d
    
    plot2D
    
    plot_2Ddata_NEB
    
    plot_2Ddata_NEB_adv
    
    plot_bar_chart_bader
    
    plot_free_energy_vs_reaction_coordinate_adv
    
    plot_pdos_Natoms_contribution_adv_both_spin_possible
    
    plot_pdos_with_atoms_contribution_2plots_qe
    
    plot_xanes_
    
    plotxy
    
    plotxy0
    
    plotxy1
    
    plotxy_adv
    
    plotxy_advv
    
    polar_plot
    
    py3dmol_view_smiles_and_xyz_TODO_close
    
    tex_demo
  - pointGroup
  - pretty_int
  - printlog
  - pymatgenBag
  - qeBag
    
    qeBag
    
    23
    
    band_gap_xml
    
    bands_kpts_band_gap
    
    critic2_qe_input
    
    gen_qeinput
    
    gen_qeinput2
    
    gen_qeinput_adv
    
    gen_qeinput_adv0
    
    gen_qeinput_advv
    
    get_bands_kpts_band_gap_adv3
    
    get_kohn_sham_energy
    
    get_output_qe
    
    get_postprocessing_input_qe
    
    get_xyz_from_qe_rlxout
    
    neb_qe
    
    neb_qe1
    
    parse_cmdline parse_cmdline
    Table of contents
    
    parse_cmdline
    
    parse_cml_args
    
    parse_pseudo
    
    pspot_core_states
    
    qe_comment
    
    rate_const_adv
    
    read_dynmat_adv
    
    read_write
    
    read_write_0
    
    read_write_adv
    
    read_write_x
    
    replace_pseudo_UPF
    
    sum_pdos_atom
    
    xbands_kpts_band_gap
    
    xml_cml
    
    xml_qe
    
    xml_qe_adv
    
    xml_qe_advv
    
    xml_qe_advvv
    
    zpe
  - rmsd
    
    rmsd
    
    calculate_rmsd
  - siestaBag
  - spaceGroup
    
    spaceGroup
    
    read_cif
    
    transform
    
    transform_adv
  - string2integer
  - super_using_inheritance
  - surfReact
    
    surfReact
    
    conformer
  - to_format
  - to_yaml
  - transitionState
    
    transitionState
    
    associated_legendre
    
    neb
    
    optimizer
    
    potential_2D
  - turbomoleBag
  - vaspBag
    
    vaspBag
    
    add_vacuum_to_unit_cell
    
    band_gap
    
    inout
    
    inout
    
    cartesian2crystal
    
    crystal2cartesian
    
    crystal_lattice
    
    diameter_or_area_nanowire
    
    get_labelling_atoms
    
    lattice
    
    old_reciprocal_lattice
    
    read_eigenval
    
    read_eigenval_file
    
    read_outcar
    
    read_outcar_file
    
    read_poscar
    
    reciprocal_lattice
    
    shift_to_origin
    
    xml_vasp
    
    xml_vasp_ASE
    
    xml_vasp_adv
    
    xml_vasp_hse
    
    postproc
    
    postproc
    
    band_gap
    
    rotateAxisUnitCell
    
    rotateAxisUnitCell
    
    rotate_axis
    
    vaspin
  - xtbBag
    
    xtbBag
    
    hessian
    
    xtb_calculator_for_EStA_21012025_v3
  - xyzdata

Table of contents

parse_cmdline
- parse_cml_args

parse_cmdline

`esta.qeBag.parse_cmdline` ¶

`parse_cml_args(cml)` ¶

command line argument parsering .... TODO ...!!

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