Index

_

__init__() (hymd.hamiltonian.DefaultNoChi method) (hymd.hamiltonian.DefaultWithChi method) (hymd.hamiltonian.Hamiltonian method) (hymd.hamiltonian.SquaredPhi method)

_random_chi_squared() (in module hymd.thermostat) _random_gaussian() (in module hymd.thermostat) _setup() (hymd.hamiltonian.Hamiltonian method)

A

a (hymd.input_parser.Config attribute) Angle (class in hymd.force) angle_bonds (hymd.input_parser.Config attribute) atom_1 (hymd.force.Bond attribute) (hymd.force.Chi attribute) (hymd.force.Dielectric_type attribute) (hymd.force.Dihedral attribute)

atom_2 (hymd.force.Bond attribute) (hymd.force.Chi attribute) (hymd.force.Dihedral attribute) atom_3 (hymd.force.Angle attribute) (hymd.force.Dihedral attribute) atom_4 (hymd.force.Dihedral attribute)

B

barostat (hymd.input_parser.Config attribute) barostat_type (hymd.input_parser.Config attribute)

Bond (class in hymd.force) bonds (hymd.input_parser.Config attribute) box_size (hymd.input_parser.Config attribute)

C

cancel_com_momentum (hymd.input_parser.Config attribute) check_angles() (in module hymd.input_parser) check_bonds() (in module hymd.input_parser) check_box_size() (in module hymd.input_parser) check_cancel_com_momentum() (in module hymd.input_parser) check_charges() (in module hymd.input_parser) check_charges_types_list() (in module hymd.input_parser) check_chi() (in module hymd.input_parser) check_config() (in module hymd.input_parser) check_dielectric() (in module hymd.input_parser) check_dihedrals() (in module hymd.input_parser) check_domain_decomposition() (in module hymd.input_parser) check_hamiltonian() (in module hymd.input_parser) check_integrator() (in module hymd.input_parser) check_m() (in module hymd.input_parser) check_mass() (in module hymd.input_parser) check_max_molecule_size() (in module hymd.input_parser) check_n_b() (in module hymd.input_parser) check_n_flush() (in module hymd.input_parser) check_n_particles() (in module hymd.input_parser) check_n_print() (in module hymd.input_parser) check_name() (in module hymd.input_parser)

check_NPT_conditions() (in module hymd.input_parser) check_start_and_target_temperature() (in module hymd.input_parser) check_tau() (in module hymd.input_parser) check_thermostat_coupling_groups() (in module hymd.input_parser) Chi (class in hymd.force) chi (hymd.input_parser.Config attribute) close_file() (hymd.file_io.OutDataset method) coeffs (hymd.force.Dihedral attribute) comp_pressure() (in module hymd.pressure) compute_angle_forces__plain() (in module hymd.force) compute_bond_forces__plain() (in module hymd.force) compute_dihedral_forces__plain() (in module hymd.force) compute_field_and_kinetic_energy() (in module hymd.field) compute_field_energy_q_GPE() (in module hymd.field) compute_field_force() (in module hymd.field) compute_self_energy_q() (in module hymd.field) Config (class in hymd.input_parser) conv_crit (hymd.input_parser.Config attribute) convergence_type (hymd.input_parser.Config attribute) coulomb_constant (hymd.input_parser.Config attribute) coulombtype (hymd.input_parser.Config attribute) csvr_thermostat() (in module hymd.thermostat)

D

DefaultNoChi (class in hymd.hamiltonian) DefaultWithChi (class in hymd.hamiltonian) dielectric_const (hymd.input_parser.Config attribute) Dielectric_type (class in hymd.force) dielectric_type (hymd.input_parser.Config attribute) dielectric_value (hymd.force.Dielectric_type attribute) dih_type (hymd.force.Dihedral attribute)

Dihedral (class in hymd.force) dihedrals (hymd.input_parser.Config attribute) dipole_forces_redistribution() (in module hymd.force) distribute_input() (in module hymd.file_io) domain_decomposition (hymd.input_parser.Config attribute) domain_decomposition() (in module hymd.field) dtype (hymd.input_parser.Config attribute)

E

equilibrium (hymd.force.Bond attribute)

F

file_name (hymd.input_parser.Config attribute) filter() (hymd.logger.MPIFilterAll method) (hymd.logger.MPIFilterRoot method)

find_all_paths() (in module hymd.force) flush() (hymd.file_io.OutDataset method)

G

gas_constant (hymd.input_parser.Config attribute)

H

Hamiltonian (class in hymd.hamiltonian) hamiltonian (hymd.input_parser.Config attribute) hymd.barostat module hymd.field module hymd.file_io module hymd.force module

hymd.input_parser module hymd.integrator module hymd.pressure module hymd.thermostat module

I

initial_energy (hymd.input_parser.Config attribute) initialize_pm() (in module hymd.field) integrate_position() (in module hymd.integrator) integrate_velocity() (in module hymd.integrator)

integrator (hymd.input_parser.Config attribute) interaction_energy (hymd.force.Chi attribute) is_open() (hymd.file_io.OutDataset method) isotropic() (in module hymd.barostat)

K

kappa (hymd.input_parser.Config attribute)

L

Logger (class in hymd.logger)

M

m (hymd.input_parser.Config attribute) mass (hymd.input_parser.Config attribute) max_molecule_size (hymd.input_parser.Config attribute) mesh_size (hymd.input_parser.Config attribute) module hymd.barostat hymd.field hymd.file_io hymd.force hymd.input_parser hymd.integrator hymd.pressure hymd.thermostat

MPIFilterAll (class in hymd.logger) MPIFilterRoot (class in hymd.logger)

N

n_b (hymd.input_parser.Config attribute) n_flush (hymd.input_parser.Config attribute) n_particles (hymd.input_parser.Config attribute)

n_print (hymd.input_parser.Config attribute) n_steps (hymd.input_parser.Config attribute) name (hymd.input_parser.Config attribute)

O

OutDataset (class in hymd.file_io)

P

parse_config_toml() (in module hymd.input_parser) pol_mixing (hymd.input_parser.Config attribute) prepare_bonds() (in module hymd.force)

prepare_bonds_old() (in module hymd.force) prepare_index_based_bonds() (in module hymd.force) pressure (hymd.input_parser.Config attribute) propensity_potential_coeffs() (in module hymd.force)

R

read_config_toml() (in module hymd.input_parser)

respa_inner (hymd.input_parser.Config attribute) rho0 (hymd.input_parser.Config attribute)

S

self_energy (hymd.input_parser.Config attribute) semiisotropic() (in module hymd.barostat) setup() (hymd.hamiltonian.DefaultNoChi method) (hymd.hamiltonian.DefaultWithChi method) (hymd.hamiltonian.SquaredPhi method) (hymd.logger.Logger class method) setup_time_dependent_element() (in module hymd.file_io)

sigma (hymd.input_parser.Config attribute) sort_dielectric_by_type_id() (in module hymd.input_parser) SquaredPhi (class in hymd.hamiltonian) start_temperature (hymd.input_parser.Config attribute) store_data() (in module hymd.file_io) store_static() (in module hymd.file_io) strength (hymd.force.Bond attribute)

T

tags (hymd.input_parser.Config attribute) target_pressure (hymd.input_parser.Config attribute) target_temperature (hymd.input_parser.Config attribute) tau (hymd.input_parser.Config attribute)

tau_p (hymd.input_parser.Config attribute) thermostat_coupling_groups (hymd.input_parser.Config attribute) thermostat_work (hymd.input_parser.Config attribute) time_step (hymd.input_parser.Config attribute) type_charges (hymd.input_parser.Config attribute)

U

update_field() (in module hymd.field)

update_field_force_q() (in module hymd.field) update_field_force_q_GPE() (in module hymd.field)