Index

Symbols

2D=[ T | F ], [1]

``apply_Z_wall=[T|F] ``, [1] ``keep_atoms_fixed=int ``, [1]

A

adjust_step_interval_times_fraction_killed=float, [1] Anti (rngstream.RngStream_InfoState attribute) ASE_calc_module=str, [1] atom_algorithm=[MC | MD | GMC], [1]

atom_traj_len=int, [1] atom_traj_len_cost_multiplier=int, [1] atom_velo_rej_free_fully_randomize=[T | F], [1] atom_velo_rej_free_perturb_angle=float, [1]

B

Bg (rngstream.RngStream_InfoState attribute)

break_up_atom_traj=[T | F], [1]

C

calc_nn_dis=[ T | F ], [1] calculate() (lammpslib.LAMMPSlib method) cell_shape_equil_steps=int, [1] Cg (rngstream.RngStream_InfoState attribute)

config_file_format=str, [1] converge_down_to_T=flot, [1] convert_cell() (in module lammpslib) create_stream() (rngstream.RngStream method)

D

debug() (in module stacktrace) debug=int, [1]

default_parameters (lammpslib.LAMMPSlib attribute) delta_random_seed=int, [1] do_good_load_balance=[T | F], [1]

E

energy_calculator= ( ASE | lammps | internal | fortran), [1]

F

float_uniform() (ns_rng.NsRng method) (ns_rng.NsRngInternal method) (ns_rng.NsRngNumpy method) (ns_rng.NsRngStream method)

float_uniform_01() (rngstream.RngStream method) FORTRAN_model=str, [1] FORTRAN_model_params=str, [1] full_auto_step_sizes=[T | F], [1]

G

get_state() (rngstream.RngStream method) GMC_adjust_max_rate=float, [1] GMC_adjust_min_rate=float, [1]

GMC_dir_perturb_angle=float, [1] GMC_dir_perturb_angle_during=float, [1] GMC_no_reverse=[T | F], [1]

I

Ig (rngstream.RngStream_InfoState attribute) implemented_properties (lammpslib.LAMMPSlib attribute) IncPrec (rngstream.RngStream_InfoState attribute) initial_walk_adjust_interval=int, [1] initial_walk_Emax_offset_per_atom=float, [1] initial_walk_N_walks=int, [1] initial_walk_only=[T | F], [1]

initialise_lammps() (lammpslib.LAMMPSlib method) initialized (lammpslib.LAMMPSlib attribute) int_uniform() (ns_rng.NsRng method) (ns_rng.NsRngInternal method) (ns_rng.NsRngNumpy method) (ns_rng.NsRngStream method) (rngstream.RngStream method) is_upper_triangular() (in module lammpslib)

K

kB=float, [1]

KEmax_max_T=float, [1]

L

LAMMPS_atom_types=str, [1] LAMMPS_fix_gmc=[T | F], [1] LAMMPS_header=str, [1] LAMMPS_header_extra=str, [1] LAMMPS_init_cmds=str, [1] LAMMPS_molecular_info=[ T | F ], [1]

LAMMPS_name=str, [1] LAMMPS_serial=[T | F], [1] lammpsbc() (lammpslib.LAMMPSlib method) lammpslib module LAMMPSlib (class in lammpslib) listen() (in module stacktrace)

M

max_volume_per_atom=float, [1] MC_adjust_max_rate=float, [1] MC_adjust_min_rate=float, [1] MC_adjust_step_factor=float, [1] MC_atom_Galilean=[T | F], [1] MC_atom_step_size=float, [1] MC_atom_step_size_max=float, [1] MC_atom_uniform_rv=[T | F], [1] MC_atom_velo_step_size=float, [1] MC_atom_velo_step_size_max=float, [1] MC_atom_velo_walk_rej_free=[T | F], [1] MC_atom_velocities=[T | F], [1] MC_atom_velocities_pre_perturb=[T | F], [1] MC_cell_flat_V_prior=[T | F], [1] MC_cell_min_aspect_ratio=float, [1] MC_cell_P=float, [1] MC_cell_shear_prob=float, [1] MC_cell_shear_step_size=float, [1] MC_cell_shear_step_size_max=float, [1] MC_cell_stretch_prob=float, [1] MC_cell_stretch_step_size=float, [1] MC_cell_stretch_step_size_max=float, [1]

MC_cell_volume_per_atom_prob=float, [1] MC_cell_volume_per_atom_step_size=float, [1] MC_cell_volume_per_atom_step_size_max=float, [1] MD_adjust_max_rate=float, [1] MD_adjust_min_rate=float, [1] MD_adjust_step_factor=float, [1] MD_atom_energy_fuzz=float, [1] MD_atom_reject_energy_violation=[ T | F ], [1] MD_atom_timestep=float, [1] MD_atom_timestep_max=float, [1] MD_atom_velo_flip_accept=[T | F], [1] MD_atom_velo_post_perturb=[T | F], [1] MD_atom_velo_pre_perturb=[T | F], [1] min_Emax=float, [1] min_nn_dis=float, [1] min_volume_per_atom=float, [1] module lammpslib ns_rng ns_run rngstream stacktrace monitor_step_interval_times_fraction_killed=float, [1]

mu1 [, Z2

``semi_grand_potentials=Z1, [1]

N

n_atom_steps=int, [1] n_cell_shear_steps=int, [1] n_cell_stretch_steps=int, [1] n_cell_volume_steps=int, [1] n_cull=int, [1] n_extra_data=int, [1] n_extra_walk_per_task=int, [1] n_iter_times_fraction_killed=int, [1] n_model_calls=int, [1] n_model_calls_expected=int, [1] n_semi_grand_steps=int, [1] n_swap_steps=int, [1] n_walkers=int, [1] name (rngstream.RngStream_InfoState attribute) no_extra_walks_at_all=[ T | F ], [1]

no_swap_velo_fix_mag_alt=[T | F], [1] normal() (ns_rng.NsRng method) (ns_rng.NsRngInternal method) (ns_rng.NsRngNumpy method) (ns_rng.NsRngStream method) normal_variate() (ns_rng.NsRngStream method) ns_rng module ns_run module ns_run_analyzers=string, [1] NsRng (class in ns_rng) NsRngInternal (class in ns_rng) NsRngNumpy (class in ns_rng) NsRngStream (class in ns_rng)

O

os_random_uint32() (in module ns_rng)

out_file_prefix=str, [1]

P

parse_angles() (lammpslib.LAMMPSlib method) parse_bonds() (lammpslib.LAMMPSlib method) parse_dihedrals() (lammpslib.LAMMPSlib method)

parse_impropers() (lammpslib.LAMMPSlib method) profile=rank_to_profile, [1] propagate() (lammpslib.LAMMPSlib method) python_MD=[ T | F ], [1]

R

random_energy_perturbation=float, [1] random_init_max_n_tries=int, [1] random_initialise_cell=[ T | F ], [1] random_initialise_pos=[ T | F ], [1] rebuild() (lammpslib.LAMMPSlib method) redo_atom_types() (lammpslib.LAMMPSlib method)

restart_file=path_to_file, [1] restart_lammps() (lammpslib.LAMMPSlib method) rng=( numpy | internal | rngstream ), [1] rngstream module RngStream (class in rngstream) RngStream_InfoState (class in rngstream)

S

seed_common() (ns_rng.NsRng method) seed_init() (ns_rng.NsRng method) seed_local() (ns_rng.NsRng method) set_angles() (lammpslib.LAMMPSlib method) set_bonds() (lammpslib.LAMMPSlib method) set_cell() (lammpslib.LAMMPSlib method) set_charges() (lammpslib.LAMMPSlib method) set_dihedrals() (lammpslib.LAMMPSlib method) set_impropers() (lammpslib.LAMMPSlib method) set_lammps_pos() (lammpslib.LAMMPSlib method) set_package_seed() (ns_rng.NsRngStream method) (rngstream.RngStream method) shuffle_in_place() (ns_rng.NsRng method) (ns_rng.NsRngInternal method) (ns_rng.NsRngNumpy method) (ns_rng.NsRngStream method) snapshot_clean=[ T | F ], [1] snapshot_interval=int, [1] snapshot_per_parallel_task=[ T | F ], [1]

snapshot_time=int, [1] stacktrace module start_config_file=str, [1] start_energy_ceiling=float, [1] start_energy_ceiling_per_atom=float, [1] start_lammps() (lammpslib.LAMMPSlib method) start_species=int int [ float ] [, int int [ float ] ... ], [1] started (lammpslib.LAMMPSlib attribute) swap_cluster_probability_increment=float, [1] swap_max_cluster=int, [1] swap_r_cut=float, [1] swap_velo=[T | F], [1] switch_to_common() (ns_rng.NsRngInternal method) (ns_rng.NsRngNumpy method) (ns_rng.NsRngStream method) switch_to_local() (ns_rng.NsRngInternal method) (ns_rng.NsRngNumpy method) (ns_rng.NsRngStream method)

T

T_estimate_finite_diff_lag=int, [1] track_configs=[ T | F ], [1]

track_configs_write=[ T | F ], [1] traj_interval=int, [1]

U

unit_convert() (in module lammpslib)

usage() (in module ns_run)

V

velo_traj_len=int, [1]

W

write_lammps_data() (in module lammpslib)

Z

Z_cell_axis=float, [1]