Index

A

AbstractAcceptor (class in transition_sampling.algo.acceptors) AbstractEngine (class in transition_sampling.engines.abstract_engine) accepted_states (transition_sampling.algo.aimless_shooting.AsyncAimlessShooting attribute) acceptor (transition_sampling.algo.aimless_shooting.AsyncAimlessShooting attribute) after (transition_sampling.engines.plumed.PlumedInputHandler attribute)

AimlessShootingDriver (class in transition_sampling.algo.aimless_shooting) AsyncAimlessShooting (class in transition_sampling.algo.aimless_shooting) atomic_symbols_to_mass() (in module transition_sampling.util.periodic_table) atoms (transition_sampling.engines.abstract_engine.AbstractEngine property) (transition_sampling.engines.cp2k.CP2K_engine.CP2KEngine property) (transition_sampling.engines.cp2k.CP2K_inputs.CP2KInputsHandler property)

B

base_acceptor (transition_sampling.algo.aimless_shooting.AimlessShootingDriver attribute) base_engine (transition_sampling.algo.aimless_shooting.AimlessShootingDriver attribute) base_logger (transition_sampling.algo.aimless_shooting.ResultsLogger attribute)

before (transition_sampling.engines.plumed.PlumedInputHandler attribute) box_size (transition_sampling.engines.abstract_engine.AbstractEngine property) (transition_sampling.engines.cp2k.CP2K_engine.CP2KEngine property) (transition_sampling.engines.cp2k.CP2K_inputs.CP2KInputsHandler property)

C

calc_p() (in module transition_sampling.likelihood.optimization) calc_r() (in module transition_sampling.likelihood.optimization) check_basin() (transition_sampling.engines.plumed.PlumedOutputHandler method) check_warnings() (transition_sampling.engines.cp2k.CP2K_outputs.CP2KOutputHandler method) colvars (transition_sampling.likelihood.likelihood_max.Maximizer attribute) combinations (transition_sampling.likelihood.likelihood_max.MaximizerSolution attribute) copy_out_file() (transition_sampling.engines.cp2k.CP2K_outputs.CP2KOutputHandler method) cp2k_dict (transition_sampling.engines.cp2k.CP2K_inputs.CP2KInputsHandler attribute)

cp2k_inputs (transition_sampling.engines.cp2k.CP2K_engine.CP2KEngine attribute) CP2KEngine (class in transition_sampling.engines.cp2k.CP2K_engine) CP2KInputsHandler (class in transition_sampling.engines.cp2k.CP2K_inputs) CP2KOutputHandler (class in transition_sampling.engines.cp2k.CP2K_outputs) csv_name (transition_sampling.algo.aimless_shooting.ResultsLogger property) cur_index (transition_sampling.algo.aimless_shooting.ResultsLogger attribute) current_offset (transition_sampling.algo.aimless_shooting.AsyncAimlessShooting attribute) current_start (transition_sampling.algo.aimless_shooting.AsyncAimlessShooting attribute)

D

DefaultAcceptor (class in transition_sampling.algo.acceptors)

E

engine (transition_sampling.algo.aimless_shooting.AsyncAimlessShooting attribute)

execute() (in module transition_sampling.driver)

F

flip_velocity() (transition_sampling.engines.abstract_engine.AbstractEngine method) (transition_sampling.engines.cp2k.CP2K_engine.CP2KEngine method) (transition_sampling.engines.cp2k.CP2K_inputs.CP2KInputsHandler method)

fwd (transition_sampling.engines.abstract_engine.ShootingResult attribute)

G

generate_velocities() (in module transition_sampling.algo.aimless_shooting) get_atomic_mass_dict() (in module transition_sampling.util.atomic_masses)

get_engine_str() (transition_sampling.engines.abstract_engine.AbstractEngine method) (transition_sampling.engines.cp2k.CP2K_engine.CP2KEngine method) get_out_file() (transition_sampling.engines.cp2k.CP2K_outputs.CP2KOutputHandler method)

I

is_accepted() (transition_sampling.algo.acceptors.AbstractAcceptor method) (transition_sampling.algo.acceptors.DefaultAcceptor method) (transition_sampling.algo.acceptors.MultiBasinAcceptor method) (transition_sampling.algo.aimless_shooting.AsyncAimlessShooting static method)

L

log_name (transition_sampling.algo.aimless_shooting.AimlessShootingDriver attribute)

log_result() (transition_sampling.algo.aimless_shooting.ResultsLogger method)

M

main() (in module transition_sampling.driver) max (transition_sampling.likelihood.likelihood_max.MaximizerSolution attribute) maximize() (transition_sampling.likelihood.likelihood_max.Maximizer method) Maximizer (class in transition_sampling.likelihood.likelihood_max) MaximizerSolution (class in transition_sampling.likelihood.likelihood_max) md_cmd (transition_sampling.engines.abstract_engine.AbstractEngine attribute) MDPHandler (class in transition_sampling.engines.gromacs.mdp) metadata (transition_sampling.likelihood.likelihood_max.Maximizer attribute) module transition_sampling transition_sampling.algo transition_sampling.algo.acceptors transition_sampling.algo.aimless_shooting transition_sampling.colvar transition_sampling.colvar.plumed_driver transition_sampling.driver transition_sampling.engines transition_sampling.engines.abstract_engine transition_sampling.engines.cp2k transition_sampling.engines.cp2k.CP2K_engine transition_sampling.engines.cp2k.CP2K_inputs transition_sampling.engines.cp2k.CP2K_outputs transition_sampling.engines.gromacs transition_sampling.engines.gromacs.mdp transition_sampling.engines.plumed transition_sampling.likelihood transition_sampling.likelihood.likelihood_max transition_sampling.likelihood.optimization transition_sampling.util transition_sampling.util.atomic_masses transition_sampling.util.periodic_table transition_sampling.util.xyz

MultiBasinAcceptor (class in transition_sampling.algo.acceptors)

N

name (transition_sampling.algo.aimless_shooting.ResultsLogger attribute)

niter (transition_sampling.likelihood.likelihood_max.Maximizer attribute)

O

obj_func() (in module transition_sampling.likelihood.optimization)

optimize() (in module transition_sampling.likelihood.optimization)

P

parse_aimless() (in module transition_sampling.driver) parse_colvar() (in module transition_sampling.driver) parse_engine() (in module transition_sampling.driver) parse_likelihood() (in module transition_sampling.driver) pick_starting() (transition_sampling.algo.aimless_shooting.AsyncAimlessShooting method) plumed_handler (transition_sampling.engines.abstract_engine.AbstractEngine attribute)

PlumedDriver (class in transition_sampling.colvar.plumed_driver) PlumedInputHandler (class in transition_sampling.engines.plumed) PlumedOutputHandler (class in transition_sampling.engines.plumed) position_dir (transition_sampling.algo.aimless_shooting.AimlessShootingDriver attribute) (transition_sampling.algo.aimless_shooting.AsyncAimlessShooting attribute) print_freq (transition_sampling.engines.gromacs.mdp.MDPHandler attribute) products (transition_sampling.algo.acceptors.MultiBasinAcceptor attribute)

R

raw_string (transition_sampling.engines.gromacs.mdp.MDPHandler attribute) reactants (transition_sampling.algo.acceptors.MultiBasinAcceptor attribute) read_and_run() (in module transition_sampling.driver) read_frames_2_3() (transition_sampling.engines.cp2k.CP2K_outputs.CP2KOutputHandler method) read_timestep() (transition_sampling.engines.cp2k.CP2K_inputs.CP2KInputsHandler method) read_xyz_file() (in module transition_sampling.util.xyz) read_xyz_frame() (in module transition_sampling.util.xyz) req_improvement (transition_sampling.likelihood.likelihood_max.MaximizerSolution attribute) results_logger (transition_sampling.algo.aimless_shooting.AsyncAimlessShooting attribute)

ResultsLogger (class in transition_sampling.algo.aimless_shooting) rev (transition_sampling.engines.abstract_engine.ShootingResult attribute) run() (transition_sampling.algo.aimless_shooting.AimlessShootingDriver method) (transition_sampling.algo.aimless_shooting.AsyncAimlessShooting method) (transition_sampling.colvar.plumed_driver.PlumedDriver method) run_aimless() (in module transition_sampling.driver) run_colvar() (in module transition_sampling.driver) run_likelihood() (in module transition_sampling.driver) run_shooting_point() (transition_sampling.engines.abstract_engine.AbstractEngine method)

S

set_delta_t() (transition_sampling.engines.abstract_engine.AbstractEngine method) (transition_sampling.engines.cp2k.CP2K_engine.CP2KEngine method) set_plumed_file() (transition_sampling.engines.cp2k.CP2K_inputs.CP2KInputsHandler method) set_positions() (transition_sampling.engines.abstract_engine.AbstractEngine method) (transition_sampling.engines.cp2k.CP2K_engine.CP2KEngine method) (transition_sampling.engines.cp2k.CP2K_inputs.CP2KInputsHandler method) set_project_name() (transition_sampling.engines.cp2k.CP2K_inputs.CP2KInputsHandler method)

set_traj_print_file() (transition_sampling.engines.cp2k.CP2K_inputs.CP2KInputsHandler method) set_traj_print_freq() (transition_sampling.engines.cp2k.CP2K_inputs.CP2KInputsHandler method) (transition_sampling.engines.gromacs.mdp.MDPHandler method) set_velocities() (transition_sampling.engines.abstract_engine.AbstractEngine method) (transition_sampling.engines.cp2k.CP2K_engine.CP2KEngine method) (transition_sampling.engines.cp2k.CP2K_inputs.CP2KInputsHandler method) ShootingResult (class in transition_sampling.engines.abstract_engine) SingleSolution (class in transition_sampling.likelihood.likelihood_max)

T

temp (transition_sampling.algo.aimless_shooting.AimlessShootingDriver attribute) (transition_sampling.algo.aimless_shooting.AsyncAimlessShooting attribute) (transition_sampling.engines.cp2k.CP2K_inputs.CP2KInputsHandler property) timestep (transition_sampling.engines.gromacs.mdp.MDPHandler property) to_csv() (transition_sampling.likelihood.likelihood_max.MaximizerSolution method) to_dataframe() (transition_sampling.likelihood.likelihood_max.MaximizerSolution method) transition_sampling module transition_sampling.algo module transition_sampling.algo.acceptors module transition_sampling.algo.aimless_shooting module transition_sampling.colvar module transition_sampling.colvar.plumed_driver module transition_sampling.driver module transition_sampling.engines module transition_sampling.engines.abstract_engine module transition_sampling.engines.cp2k module

transition_sampling.engines.cp2k.CP2K_engine module transition_sampling.engines.cp2k.CP2K_inputs module transition_sampling.engines.cp2k.CP2K_outputs module transition_sampling.engines.gromacs module transition_sampling.engines.gromacs.mdp module transition_sampling.engines.plumed module transition_sampling.likelihood module transition_sampling.likelihood.likelihood_max module transition_sampling.likelihood.optimization module transition_sampling.util module transition_sampling.util.atomic_masses module transition_sampling.util.periodic_table module transition_sampling.util.xyz module

U

use_jac (transition_sampling.likelihood.likelihood_max.Maximizer attribute)

V

validate_inputs() (transition_sampling.engines.abstract_engine.AbstractEngine method) (transition_sampling.engines.cp2k.CP2K_engine.CP2KEngine method)

W

write_cp2k_inputs() (transition_sampling.engines.cp2k.CP2K_inputs.CP2KInputsHandler method) write_mdp() (transition_sampling.engines.gromacs.mdp.MDPHandler method)

write_plumed() (transition_sampling.engines.plumed.PlumedInputHandler method) write_xyz_frame() (in module transition_sampling.util.xyz)

X

xyz_name (transition_sampling.algo.aimless_shooting.ResultsLogger property)