Index

A

angle() (in module mdgo.util) angle_array() (mdgo.core.MdRun method) angular_dist_of_neighbor() (in module mdgo.coordination)

assign_name() (in module mdgo.util) assign_resname() (in module mdgo.util) atom_vec() (in module mdgo.util) autocorr_fft() (in module mdgo.conductivity)

C

calc_acf() (in module mdgo.residence_time) calc_cond_msd() (in module mdgo.conductivity) calc_neigh_corr() (in module mdgo.residence_time) check_contiguous_steps() (in module mdgo.coordination) choose_cond_fit_region() (mdgo.core.MdRun method) choose_msd_fitting_region() (in module mdgo.conductivity) cluster_coordinates() (in module mdgo.coordination) concat_coord_array() (in module mdgo.coordination)

concentration_matcher() (in module mdgo.util) conductivity_calculator() (in module mdgo.conductivity) coord_num_array_multi_species() (mdgo.core.MdRun method) coord_num_array_single_species() (mdgo.core.MdRun method) coord_num_array_specific() (mdgo.core.MdRun method) coord_type_array() (mdgo.core.MdRun method) coordination() (mdgo.core.MdRun method) coordination_specific() (mdgo.core.MdRun method) coordination_type() (mdgo.core.MdRun method)

D

dsq() (in module mdgo.volume)

E

exponential_func() (in module mdgo.residence_time)

extract_atom_from_ion() (in module mdgo.util) extract_atom_from_molecule() (in module mdgo.util)

F

ff_parser() (in module mdgo.util) fill_volume_matrix() (in module mdgo.volume) find_in_n_out() (in module mdgo.coordination) find_nearest() (in module mdgo.coordination) find_nearest_free_only() (in module mdgo.coordination)

fit_residence_time() (in module mdgo.residence_time) from_dict() (mdgo.core.MdJob class method) from_lammps() (mdgo.core.MdRun class method) from_recipe() (mdgo.core.MdJob class method) full_solvation_structure() (in module mdgo.coordination)

G

get_beta() (in module mdgo.conductivity) get_cluster_distance() (mdgo.core.MdRun method) get_cond_array() (mdgo.core.MdRun method) get_conductivity() (mdgo.core.MdRun method) get_d() (mdgo.core.MdRun method) get_dimensions() (in module mdgo.volume) get_equilibrium_dimension() (mdgo.core.MdRun method) get_full_coords() (in module mdgo.coordination) get_heat_map() (mdgo.core.MdRun method) get_hopping_freq_dist() (mdgo.core.MdRun method)

get_init_dimension() (mdgo.core.MdRun method) get_max_dimensions() (in module mdgo.volume) get_msd_all() (mdgo.core.MdRun method) get_msd_partial() (mdgo.core.MdRun method) get_neighbor_corr() (mdgo.core.MdRun method) get_neighbor_trj() (mdgo.core.MdRun method) get_nvt_dimension() (mdgo.core.MdRun method) get_occupied_volume() (in module mdgo.volume) get_radii() (in module mdgo.volume) get_residence_time() (mdgo.core.MdRun method) get_unoccupied_volume() (in module mdgo.volume)

H

heat_map() (in module mdgo.coordination)

L

lmp_mass_to_name() (in module mdgo.util)

M

make_matrix() (in module mdgo.volume) mass_to_name() (in module mdgo.util) mdgo module mdgo.conductivity module mdgo.coordination module mdgo.core module mdgo.msd module mdgo.residence_time module mdgo.util module

mdgo.volume module MdJob (class in mdgo.core) MdRun (class in mdgo.core) module mdgo mdgo.conductivity mdgo.coordination mdgo.core mdgo.msd mdgo.residence_time mdgo.util mdgo.volume molecular_volume() (in module mdgo.volume) msd_fft() (in module mdgo.conductivity) msd_from_frags() (in module mdgo.msd)

N

neighbor_distance() (in module mdgo.coordination) neighbors_one_atom() (in module mdgo.residence_time)

num_of_neighbor() (in module mdgo.coordination) num_of_neighbor_simple() (in module mdgo.coordination) num_of_neighbor_specific() (in module mdgo.coordination)

P

parse_command_line() (in module mdgo.volume) partial_msd() (in module mdgo.msd)

plot_cond_array() (mdgo.core.MdRun method) position_vec() (in module mdgo.util) process_evol() (in module mdgo.coordination)

R

rdf_integral() (mdgo.core.MdRun method) res_dict_from_datafile() (in module mdgo.util)

res_dict_from_lammpsdata() (in module mdgo.util) res_dict_from_select_dict() (in module mdgo.util) round_dimensions() (in module mdgo.volume)

S

sdf_to_pdb() (in module mdgo.util) select_dict_from_resname() (in module mdgo.util) select_shell() (in module mdgo.coordination)

set_max_dimensions() (in module mdgo.volume) shell_evolution() (mdgo.core.MdRun method) states_coord_array() (in module mdgo.msd) strip_zeros() (in module mdgo.util)

T

total_msd() (in module mdgo.msd)

W

write_out() (in module mdgo.coordination)

write_solvation_structure() (mdgo.core.MdRun method)