Index

A

adapt_stepsize_to_energy_change() (riigid.optimizer.GDWAS.GDWAS method) adapt_stepsize_to_prevent_too_large_steps() (riigid.optimizer.GDWAS.GDWAS method) add_force_and_torque_on_fragments() (riigid.optimization_step.OptimizationStep method) add_updated_structure() (riigid.optimization_step.OptimizationStep method) allowed_rotation (riigid.fragment.Fragment attribute) allowed_translation (riigid.fragment.Fragment attribute)

angle_between_vectors() (in module riigid.library.rotation) angle_r0 (riigid.optimizer.GDWAS.GDWAS attribute) angles_between_principal_axes_and_xyz() (in module riigid.library.rotation) apply_boundaries() (riigid.fragment.Fragment method) atoms (riigid.fragment.Fragment attribute) (riigid.structure.Structure attribute)

C

calculate_energy_and_forces() (riigid.structure.Structure method) calculate_net_force_on_fragment() (riigid.fragment.Fragment method) calculate_torque_on_fragment() (riigid.fragment.Fragment method) calculator (riigid.optimizer.GDWAS.GDWAS attribute) check() (riigid.convergence.criterion.Compound_Criterion method) (riigid.convergence.criterion.Criterion method) (riigid.convergence.displacement.Criterion_Displacement method) Compound_Criterion (class in riigid.convergence.criterion)

convergence_criterion (riigid.optimizer.GDWAS.GDWAS attribute) copy_docstring() (in module riigid.library.misc) Criterion (class in riigid.convergence.criterion) Criterion_Displacement (class in riigid.convergence.displacement) current_energy (riigid.optimizer.GDWAS.GDWAS attribute) current_forces (riigid.optimizer.GDWAS.GDWAS attribute) current_structure (riigid.optimizer.GDWAS.GDWAS attribute) cutoff (riigid.convergence.displacement.Criterion_Displacement attribute)

D

define_fragment_by_adding_atoms() (riigid.structure.Structure method) define_fragment_by_indices() (riigid.structure.Structure method)

displacement_r0 (riigid.optimizer.GDWAS.GDWAS attribute) drop_last_step_if_energy_got_larger() (riigid.optimizer.GDWAS.GDWAS method)

E

energy (riigid.optimization_step.OptimizationStep attribute)

euler_angles (riigid.fragment.Fragment attribute)

F

forces_on_atoms (riigid.optimization_step.OptimizationStep attribute)

Fragment (class in riigid.fragment) fragments (riigid.structure.Structure attribute)

G

GDWAS (class in riigid.optimizer.GDWAS) get_atoms_indices_by_height() (in module riigid.library.misc)

get_indices_of_atoms1_in_atoms2() (in module riigid.library.misc) get_normal_vector_fragment() (in module riigid.library.rotation)

I

indices_in_structure (riigid.fragment.Fragment attribute) initialize_stepsize_in_first_iteration() (riigid.optimizer.GDWAS.GDWAS method) is_converged (riigid.convergence.criterion.Compound_Criterion attribute) (riigid.convergence.criterion.Criterion attribute) (riigid.convergence.displacement.Criterion_Displacement attribute)

iteration (riigid.optimizer.GDWAS.GDWAS attribute) (riigid.optimizer.optimizer.Optimizer attribute)

M

max_iter (riigid.optimizer.GDWAS.GDWAS attribute) (riigid.optimizer.optimizer.Optimizer attribute) max_rot (riigid.optimizer.GDWAS.GDWAS attribute) max_trans (riigid.optimizer.GDWAS.GDWAS attribute) module riigid.convergence.criterion riigid.convergence.displacement riigid.fragment riigid.library.misc riigid.library.rotation riigid.optimization_step riigid.optimizer.GDWAS riigid.optimizer.optimizer riigid.structure

move() (riigid.structure.Structure method) move_by_forces() (riigid.fragment.Fragment method) move_random_step() (riigid.fragment.Fragment method) (riigid.structure.Structure method)

O

operator (riigid.convergence.criterion.Compound_Criterion attribute) optimization_history (riigid.optimizer.GDWAS.GDWAS attribute) (riigid.optimizer.optimizer.Optimizer attribute)

OptimizationStep (class in riigid.optimization_step) Optimizer (class in riigid.optimizer.optimizer)

P

print_reason_for_end_of_optimization() (riigid.optimizer.optimizer.Optimizer method)

R

redirect_stdout_to_file() (in module riigid.library.misc) remove_updated_structure() (riigid.optimization_step.OptimizationStep method) respect_restrictions_r0 (riigid.optimizer.GDWAS.GDWAS attribute) rest_fragment (riigid.structure.Structure attribute) riigid.convergence.criterion module riigid.convergence.displacement module riigid.fragment module riigid.library.misc module riigid.library.rotation module

riigid.optimization_step module riigid.optimizer.GDWAS module riigid.optimizer.optimizer module riigid.structure module rotate_by_angle_and_axis() (riigid.fragment.Fragment method) rotate_by_euler_angles() (riigid.fragment.Fragment method) rotate_by_torque() (riigid.fragment.Fragment method) rotmat() (in module riigid.library.rotation) run() (riigid.optimizer.GDWAS.GDWAS method) (riigid.optimizer.optimizer.Optimizer method)

S

seed_r0 (riigid.optimizer.GDWAS.GDWAS attribute) set_to_euler_angles() (riigid.fragment.Fragment method) shift_and_rotate_a_fragment() (riigid.structure.Structure method) signed_angle_between_vectors() (in module riigid.library.rotation) start_structure (riigid.optimizer.GDWAS.GDWAS attribute)

start_with_random_step (riigid.optimizer.GDWAS.GDWAS attribute) stepsize (riigid.optimizer.GDWAS.GDWAS attribute) stepsize_factor_dn (riigid.optimizer.GDWAS.GDWAS attribute) stepsize_factor_up (riigid.optimizer.GDWAS.GDWAS attribute) Structure (class in riigid.structure) structure (riigid.optimization_step.OptimizationStep attribute)

T

translate_by_force() (riigid.fragment.Fragment method)

translate_by_shift() (riigid.fragment.Fragment method)

U

update_atoms_attribute_from_fragments() (riigid.structure.Structure method) update_body_fixed_axes() (riigid.fragment.Fragment method) update_euler_angles() (riigid.fragment.Fragment method)

update_inertia_matrix() (riigid.fragment.Fragment method) update_rotation_properties() (riigid.fragment.Fragment method) update_structure (riigid.optimization_step.OptimizationStep attribute)