Index

A

AIREBO (class in kvazar.core.airebo), [1]

B

BoxCell (class in kvazar.boxcell)

build_cells() (kvazar.boxcell.BoxCell method)

C

calc_neighbours() (kvazar.boxcell.BoxCell method) check_pbc() (kvazar.diesel.Diesel method) compare_topology_with() (kvazar.core.structure.Structure method) compare_with() (kvazar.core.structure.Structure method) compute() (kvazar.core.mm.MM method) (kvazar.core.tb.TB method)

compute_ebond() (kvazar.core.tb.TB method) compute_erep() (kvazar.core.tb.TB method) compute_i() (kvazar.core.mm.MM method) compute_ij() (kvazar.core.mm.MM method) copy() (kvazar.core.structure.Structure method)

D

Diesel (class in kvazar.diesel)

dissipative_step() (kvazar.diesel.Diesel method)

E

ensure_forces() (kvazar.core.tb.TB method)

F

FileManager (class in kvazar.fileman)

G

get_forces() (kvazar.diesel.Diesel method) get_full_links() (kvazar.core.structure.Structure method) get_neighbours() (kvazar.core.structure.Structure method)

get_tors_sequences() (kvazar.core.structure.Structure method) getsubstr() (kvazar.core.structure.Structure method)

I

init_cutoff() (kvazar.core.airebo.AIREBO method), [1] (kvazar.core.martini.MARTINI method) (kvazar.diesel.Diesel method)

K

kvazar.boxcell (module) kvazar.core.airebo (module), [1] kvazar.core.martini (module) kvazar.core.mm (module) kvazar.core.structure (module)

kvazar.core.tb (module) kvazar.diesel (module) kvazar.fileman (module) kvazar.record (module)

L

leapfrog_berendsen_step() (kvazar.diesel.Diesel method) leapfrog_nosehoover_step() (kvazar.diesel.Diesel method) leapfrog_step() (kvazar.diesel.Diesel method) load_force_function() (kvazar.core.tb.TB method)

load_tb_functions() (kvazar.core.tb.TB method) loadForceFunction() (kvazar.core.mm.MM method) loadMMFunctions() (kvazar.core.mm.MM method)

M

MARTINI (class in kvazar.core.martini)

MM (class in kvazar.core.mm)

P

preprocessing() (kvazar.core.airebo.AIREBO method), [1] (kvazar.core.martini.MARTINI method) (kvazar.core.mm.MM method) (kvazar.core.tb.TB method)

R

Record (class in kvazar.record)

run() (kvazar.diesel.Diesel method)

S

simulation() (kvazar.diesel.Diesel method)

Structure (class in kvazar.core.structure)

T

TB (class in kvazar.core.tb) time_to_update() (kvazar.boxcell.BoxCell method)

tors_dfs() (kvazar.core.structure.Structure method)

U

update_cutoff() (kvazar.core.airebo.AIREBO method), [1] (kvazar.core.martini.MARTINI method) update_neighbours() (kvazar.core.structure.Structure method) update_prev_coords() (kvazar.boxcell.BoxCell method)

update_tb_links() (kvazar.core.tb.TB method) use_pbc() (kvazar.diesel.Diesel method)

V

velocity_verlet_step() (kvazar.diesel.Diesel method)

verlet_step() (kvazar.diesel.Diesel method)