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LLL
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abinitBag
aide
aide
check_float
combined_excel
count_poscars
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
scientific_to_readable
string2integer
tmp_file_handling
to_format
to_yaml
xyz2json
antar
ase_atoms
bond_length
bonds
c
cell
cell
Lattice_n_Pos_transform_ExtendSequize_adv
Lattice_n_Pos_transform_Supercell
check_bond_between_atoms_xyz
check_float
dat2xls_n_csv
datadotpy__move2_lattice_table__removing_atomic_data
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
bending_acb_centroid_vacuum_
bending_acb_centroid_vacuum_adv1
bending_acb_centroid_vacuum_adv2
bending_nanoribbon
boltzmann
calculate_rmsd
cartAndSpherical
charge_bader
circle_equation
circle_least_squares
compare_scalar
conjugate_gradient
conversion_factors
crystal_latticee
direction_index2str
distance_conformation
distance_matrix
distances_ase_esa
div_distance_adv
entropy_data
excel2latex_
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
local_sites_finder_around_atom_STABLE_BEST
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
surface_adsorbate_dist_lookup_table
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
greek
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
kappalBag
kspace
kspace
kgrid
kpath
lat2atm_obj
lib_xyz
lib_xyz
get_sdf_pubchem_database_molecules
get_xyz_pdb_jsonizsed_from_sdf
load_data
load_data_
xyz2json
xyz2json
Table of contents
xyz2json
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_advv
get_bands_kpts_band_gap_adv3
get_kohn_sham_energy
get_kpath_bandstr
get_output_qe
get_postprocessing_input_qe
get_xyz_from_qe_rlxout
neb_qe
neb_qe1
parse_cmdline
parse_pseudo
poscar_from_qe_input
poscar_from_qe_input0
poscar_from_qe_input1
poscar_from_qe_input2
poscar_from_qe_input3
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
ris2bib_adv
rmsd
rmsd
calculate_rmsd
see_markdown_mdutils
siestaBag
spaceGroup
spaceGroup
read_cif
transform
transform_adv
special_symbol
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
crystal_lattice_stable19072026
diameter_or_area_nanowire
get_kpath_bandstr
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
planarAverage
planarAverage
grid_data_reading
grid_data_reading_
input_data
isosurface
isosurface
atoms
isosurface
isosurface_
planar_average
planar_average_
test_planar_average_new
v0pt4_stable
v0pt4_stable
grid_data_reading
input_data
planar_average
v0pt6_this
v0pt6_this
grid_data_reading
input_data
planar_average
rotateAxisUnitCell
rotateAxisUnitCell
rotate_axis
rotate_axes
vaspin
xtbBag
xtbBag
hessian
xtb_calculator_for_EStA_21012025_v3
xyzdata
xyz2json
esta.lib_xyz.xyz2json
¶
read xyz and store the xyz data into json format
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