Index

_

_AlchemiBase (class in mcpy.calculators.alchemi)

A

Activity AlchemiBrownianMove (class in mcpy.moves)

AlchemiCalculator (class in mcpy.calculators) AlchemiFCalculator (class in mcpy.calculators) analyze_phase_diagram_results() (in module mcpy.utils)

B

BaseCalculator (class in mcpy.calculators) BaseCell (class in mcpy.cell) BaseEnsemble (class in mcpy.ensembles)

BaseMove (class in mcpy.moves) BatchedReplicaExchange (class in mcpy.ensembles) BrownianMove (class in mcpy.moves)

C

calculate_volume() (mcpy.cell.BaseCell method) (mcpy.cell.Cell method) (mcpy.cell.NullCell method) CanonicalEnsemble (class in mcpy.ensembles) Cell (class in mcpy.cell)

Chemical potential chunk_ranges() (in module mcpy.utils.chunking) configure() (in module mcpy.utils.logging) CustomCell (class in mcpy.cell)

D

de Broglie wavelength de_broglie_deletion() (mcpy.utils.SetUnits method) de_broglie_insertion() (mcpy.utils.SetUnits method) DeletionMove (class in mcpy.moves) derive_mu_bulk() (in module mcpy.utils.reference_mu) derive_mu_gas() (in module mcpy.utils.reference_mu) DisplacementMove (class in mcpy.moves) do_exchange() (mcpy.ensembles.ReplicaExchange method) do_trial_move() (mcpy.moves.AlchemiBrownianMove method) (mcpy.moves.BaseMove method) (mcpy.moves.BrownianMove method) (mcpy.moves.DeletionMove method) (mcpy.moves.DisplacementMove method) (mcpy.moves.InsertionMove method) (mcpy.moves.MoleculeDeletionMove method) (mcpy.moves.MoleculeDisplacementMove method) (mcpy.moves.MoleculeInsertionMove method) (mcpy.moves.MoveSelector method) (mcpy.moves.PermutationMove method) (mcpy.moves.ShakeMove method)

DomeCell (class in mcpy.cell)

E

Ensemble

Exchangeable region Exclusion radius

F

finalize_run() (mcpy.ensembles.BaseEnsemble method) (mcpy.ensembles.CanonicalEnsemble method) (mcpy.ensembles.GrandCanonicalEnsemble method) find_molecules() (in module mcpy.moves.molecule_utils)

Free volume free_volume() (mcpy.cell.BaseCell method) (mcpy.cell.Cell method) (mcpy.cell.NullCell method)

G

GCMC get_atoms_specie_inside_cell() (mcpy.cell.Cell method) get_custom_height_cell() (mcpy.cell.CustomCell method) get_exchange_count() (mcpy.moves.MoveSelector method) get_gaussian() (mcpy.utils.RandomNumberGenerator method) get_potential_energies() (mcpy.calculators.alchemi._AlchemiBase method) (mcpy.calculators.AlchemiFCalculator method) get_potential_energy() (mcpy.calculators.alchemi._AlchemiBase method) (mcpy.calculators.BaseCalculator method) get_random_free_point() (mcpy.cell.BaseCell method) (mcpy.cell.Cell method) (mcpy.cell.NullCell method) get_random_point() (mcpy.cell.BaseCell method) (mcpy.cell.Cell method) (mcpy.cell.DomeCell method) (mcpy.cell.NullCell method) (mcpy.cell.SphericalCell method)

get_species() (mcpy.cell.Cell method) get_uniform() (mcpy.utils.RandomNumberGenerator method) get_volume() (mcpy.cell.BaseCell method) (mcpy.cell.Cell method) (mcpy.cell.NullCell method) (mcpy.moves.BaseMove method) (mcpy.moves.DeletionMove method) (mcpy.moves.MoleculeDeletionMove method) GrandCanonicalEnsemble (class in mcpy.ensembles)

H

Hybrid GCMC

I

initialize_outfile() (mcpy.ensembles.BaseEnsemble method) (mcpy.ensembles.ReplicaExchange method) initialize_run() (mcpy.ensembles.BaseEnsemble method) (mcpy.ensembles.CanonicalEnsemble method) (mcpy.ensembles.GrandCanonicalEnsemble method) InsertionMove (class in mcpy.moves) interval_ratios() (mcpy.moves.MoveSelector method)

is_point_exchangeable() (mcpy.cell.BaseCell method) (mcpy.cell.CustomCell method) is_point_inside() (mcpy.cell.BaseCell method) (mcpy.cell.Cell method) (mcpy.cell.CustomCell method) (mcpy.cell.DomeCell method) (mcpy.cell.NullCell method) (mcpy.cell.SphericalCell method)

M

MACE_F_Calculator (class in mcpy.calculators) mc_sample_points (mcpy.cell.Cell property) mcpy.moves.molecule_utils module mcpy.utils.chunking module mcpy.utils.reference_mu module module mcpy.moves.molecule_utils mcpy.utils.chunking mcpy.utils.reference_mu

Molecular species molecule_com() (in module mcpy.moves.molecule_utils) molecule_groups() (in module mcpy.moves.molecule_utils) molecule_id MoleculeDeletionMove (class in mcpy.moves) MoleculeDisplacementMove (class in mcpy.moves) MoleculeInsertionMove (class in mcpy.moves) Move move_atoms_to_center() (mcpy.cell.SphericalCell method) MoveSelector (class in mcpy.moves) mu_h_che() (in module mcpy.utils.reference_mu) mu_o_che() (in module mcpy.utils.reference_mu)

N

NullCell (class in mcpy.cell)

P

PermutationMove (class in mcpy.moves)

plot_phase_diagram() (in module mcpy.utils)

Q

quaternion_matrix() (in module mcpy.moves.molecule_utils)

R

random_rotation_matrix() (in module mcpy.moves.molecule_utils) RandomNumberGenerator (class in mcpy.utils) relax() (mcpy.ensembles.CanonicalEnsemble method) Relaxation Replica

Replica Exchange ReplicaExchange (class in mcpy.ensembles) run() (mcpy.ensembles.BaseEnsemble method) (mcpy.ensembles.ReplicaExchange method) run_md() (mcpy.calculators.alchemi._AlchemiBase method) (mcpy.calculators.AlchemiCalculator method)

S

SetUnits (class in mcpy.utils)

ShakeMove (class in mcpy.moves) SphericalCell (class in mcpy.cell)

T

total_ratios() (mcpy.moves.MoveSelector method)

Trajectory

U

Units type

W

write_coordinates() (mcpy.ensembles.BaseEnsemble method) write_outfile() (mcpy.ensembles.BaseEnsemble method) (mcpy.ensembles.GrandCanonicalEnsemble method) (mcpy.ensembles.ReplicaExchange method)

write_xyz() (in module mcpy.ensembles.base_ensemble)