Index

A

absolute_path (MDMC.MD.force_fields.ff.FileForceField property) accuracy (MDMC.MD.simulation.ConstraintAlgorithm attribute) (MDMC.MD.simulation.KSpaceSolver attribute) add_bonded_interaction_pairs() (MDMC.MD.simulation.Universe method) add_force_field() (MDMC.MD.simulation.Universe method) add_interaction() (MDMC.MD.structural_units.Atom method) add_nonbonded_interaction() (MDMC.MD.simulation.Universe method) add_structural_unit() (MDMC.MD.simulation.Universe method) (MDMC.trajectory_analysis.trajectory.Configuration method) ang_momentum_steps (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property) angle_ID (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute) angles (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute) apply_constraints() (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse method) apply_ensemble_fixes() (MDMC.MD.engine_facades.lammps_engine.Ensemble method) ase_read_cif() (in module MDMC.MD.ase.cif) ASEAtoms (class in MDMC.MD.ase.conversions) Atom (class in MDMC.MD.structural_units) atom_dict (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute) atom_lines() (MDMC.MD.ase.conversions.X3D method)

atom_positions (MDMC.trajectory_analysis.trajectory.Configuration property) atom_type (MDMC.MD.structural_units.Atom property) atom_type_interactions (MDMC.MD.simulation.Universe property) atom_type_properties (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute) atom_types (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute) (MDMC.MD.simulation.Universe property) atom_velocities (MDMC.trajectory_analysis.trajectory.Configuration property) AtomCollection (class in MDMC.trajectory_analysis.trajectory) AtomContainer (class in MDMC.MD.container) atoms (MDMC.MD.container.AtomContainer attribute) (MDMC.MD.container.AtomContainer property) (MDMC.MD.force_fields.ff.FileForceField property) (MDMC.MD.simulation.Universe property) (MDMC.MD.structural_units.Atom property) (MDMC.MD.structural_units.StructuralUnit property) (MDMC.readers.configurations.cif.CIF property) (MDMC.readers.configurations.conf_reader.ConfigurationReader property) (MDMC.trajectory_analysis.trajectory.Configuration property) (MDMC.trajectory_analysis.trajectory.Trajectory property)

B

barostat (MDMC.MD.engine_facades.lammps_engine.Ensemble property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property) base (MDMC.common.units.Unit property) base_class() (MDMC.readers.configurations.conf_reader_factory.ConfigurationReaderFactory static method) (MDMC.readers.observables.obs_reader_factory.ObservableReaderFactory static method) (MDMC.readers.reader_factory.ReaderFactory static method) bond_angles (MDMC.MD.force_fields.ff.FileForceField property) bond_ID (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute) bond_lines() (MDMC.MD.ase.conversions.X3D method) bonded_interaction_pairs (MDMC.MD.simulation.Universe property) (MDMC.MD.structural_units.Atom property) (MDMC.MD.structural_units.CompositeStructuralUnit property) (MDMC.MD.structural_units.Molecule property) (MDMC.MD.structural_units.StructuralUnit property)

bonded_interactions (MDMC.MD.simulation.Universe property) (MDMC.MD.structural_units.StructuralUnit property) bonds (MDMC.MD.ase.conversions.ASEAtoms attribute) (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute) (MDMC.MD.force_fields.ff.FileForceField property) bounding_box (MDMC.MD.structural_units.StructuralUnit property) BoundingBox (class in MDMC.MD.structural_units) Buckingham (class in MDMC.MD.interaction_functions)

C

calculate_dt() (MDMC.trajectory_analysis.observables.SQw method) calculate_E() (MDMC.trajectory_analysis.observables.SQw static method) calculate_from_MD() (MDMC.trajectory_analysis.observables.obs.Observable method) charge (MDMC.MD.structural_units.Atom property) CIF (class in MDMC.readers.configurations.cif) components (MDMC.common.units.Unit attribute) CompositeStructuralUnit (class in MDMC.MD.structural_units) Configuration (class in MDMC.trajectory_analysis.trajectory) configuration (MDMC.MD.simulation.Universe attribute) ConfigurationReader (class in MDMC.readers.configurations.conf_reader) ConfigurationReaderFactory (class in MDMC.readers.configurations.conf_reader_factory) configurations (MDMC.trajectory_analysis.trajectory.Trajectory attribute) (MDMC.trajectory_analysis.trajectory.Trajectory property) constraint_algorithm (MDMC.MD.simulation.Universe attribute) ConstraintAlgorithm (class in MDMC.MD.simulation) Control (class in MDMC.control.control) conversion_factor (MDMC.common.units.Unit attribute) (MDMC.common.units.Unit property) convert_bond() (in module MDMC.MD.ase.conversions)

convert_bonds() (in module MDMC.MD.ase.conversions) convert_from_ase_atom() (in module MDMC.MD.ase.conversions) convert_to_ase_atom() (in module MDMC.MD.ase.conversions) convert_trajectory() (MDMC.MD.engine_facades.facade.MDEngine method) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method) convert_unit() (in module MDMC.MD.engine_facades.lammps_engine) copy() (MDMC.MD.structural_units.Atom method) (MDMC.MD.structural_units.CompositeStructuralUnit method) (MDMC.MD.structural_units.StructuralUnit method) copy_interactions() (MDMC.MD.structural_units.Atom method) correlation() (in module MDMC.common.mathematics) Coulomb (class in MDMC.MD.interaction_functions) couls (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute) create_facade() (MDMC.MD.engine_facades.facade_factory.MDEngineFacadeFactory static method) create_force_field() (MDMC.MD.force_fields.force_field_factory.ForceFieldFactory static method) create_observable() (MDMC.trajectory_analysis.observables.obs_factory.ObservableFactory class method) create_reader() (MDMC.readers.reader_factory.ReaderFactory class method) create_reader_from_ext() (MDMC.readers.configurations.conf_reader_factory.ConfigurationReaderFactory class method) create_units() (in module MDMC.common.units)

D

data (MDMC.readers.observables.obs_reader.ObservableReader property) (MDMC.trajectory_analysis.observables.obs.Observable property) (MDMC.trajectory_analysis.trajectory.Configuration attribute) (MDMC.trajectory_analysis.trajectory.Configuration property) (MDMC.trajectory_analysis.trajectory.Trajectory property) dependent_variables (MDMC.readers.observables.obs_reader.ObservableReader property) (MDMC.readers.observables.obs_reader.SQwReader property) (MDMC.trajectory_analysis.observables.obs.Observable property)

dependent_variables_structure (MDMC.trajectory_analysis.observables.obs.Observable property) dict_from_element() (MDMC.readers.observables.xml_SQw.XML_SQw static method) dimensions (MDMC.MD.simulation.Universe attribute) (MDMC.trajectory_analysis.trajectory.AtomCollection property) dispersions (MDMC.MD.force_fields.ff.FileForceField property) dispersive_solver (MDMC.MD.simulation.Universe attribute) disps (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute) dumps (MDMC.MD.engine_facades.lammps_engine.PyLammpsAttribute property)

E

E (MDMC.readers.observables.obs_reader.SQwReader property) electrostatic_solver (MDMC.MD.simulation.Universe attribute) element (MDMC.MD.structural_units.Atom attribute) element_dict (MDMC.MD.simulation.Universe property) element_list (MDMC.MD.simulation.Universe property) (MDMC.trajectory_analysis.trajectory.Configuration property) (MDMC.trajectory_analysis.trajectory.Trajectory property) element_set (MDMC.trajectory_analysis.trajectory.Configuration attribute) (MDMC.trajectory_analysis.trajectory.Trajectory property) engine (MDMC.MD.simulation.Simulation attribute)

Ensemble (class in MDMC.MD.engine_facades.lammps_engine) ensemble (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation attribute) equilibrate() (MDMC.control.control.Control method) errors (MDMC.readers.observables.obs_reader.ObservableReader property) (MDMC.readers.observables.obs_reader.SQwReader property) (MDMC.trajectory_analysis.observables.obs.Observable property) Ewald (class in MDMC.MD.simulation) exp_datasets (MDMC.control.control.Control attribute) extension (MDMC.readers.configurations.conf_reader.ConfigurationReader property)

F

file (MDMC.readers.observables.netCDF.netCDF attribute) file_dep (MDMC.readers.observables.LAMPSQw.LAMPSQw attribute) file_dep_err (MDMC.readers.observables.LAMPSQw.LAMPSQw attribute) file_detectors (MDMC.readers.observables.MantidSQw.MantidSQw attribute) file_indep (MDMC.readers.observables.LAMPSQw.LAMPSQw attribute) file_name (MDMC.MD.force_fields.ff.FileForceField property) file_variables (MDMC.readers.observables.MantidSQw.MantidSQw attribute) FileForceField (class in MDMC.MD.force_fields.ff) fill() (MDMC.MD.simulation.Universe method) filter() (MDMC.MD.parameters.Parameters method) filter_atom_attribute() (MDMC.MD.parameters.Parameters method) filter_atoms() (in module MDMC.MD.structural_units) (MDMC.trajectory_analysis.trajectory.Configuration method) filter_atoms_element() (in module MDMC.MD.structural_units) filter_by_element() (MDMC.trajectory_analysis.trajectory.Configuration method) filter_by_time() (MDMC.trajectory_analysis.trajectory.Trajectory method) filter_dataframe() (in module MDMC.common.df_operations) filter_element() (MDMC.MD.force_fields.ff.FileForceField method)

filter_function() (MDMC.MD.parameters.Parameters method) filter_interaction() (MDMC.MD.parameters.Parameters method) filter_name() (MDMC.MD.parameters.Parameters method) filter_ordered_dataframe() (in module MDMC.common.df_operations) filter_structure() (MDMC.MD.parameters.Parameters method) filter_structures() (MDMC.trajectory_analysis.trajectory.Configuration method) filter_value() (MDMC.MD.parameters.Parameters method) fit_parameters (MDMC.control.control.Control attribute) fix_names (MDMC.MD.engine_facades.lammps_engine.PyLammpsAttribute property) fix_styles (MDMC.MD.engine_facades.lammps_engine.PyLammpsAttribute property) fixes (MDMC.MD.engine_facades.lammps_engine.PyLammpsAttribute property) FoM_calculator (MDMC.control.control.Control attribute) force_field (MDMC.MD.simulation.Universe attribute) force_fields (MDMC.MD.simulation.Universe property) ForceField (class in MDMC.MD.force_fields.ff) ForceFieldFactory (class in MDMC.MD.force_fields.force_field_factory) formula (MDMC.MD.structural_units.CompositeStructuralUnit property) frames (MDMC.trajectory_analysis.trajectory.Trajectory property)

G

gaussian() (in module MDMC.common.resolution_functions) get_ase_atoms() (in module MDMC.MD.ase.conversions) get_bonded_interactions_atoms() (in module MDMC.MD.ase.cif) get_bonds() (in module MDMC.MD.ase.viewer) get_center_of_rotation() (MDMC.MD.ase.conversions.X3D method) get_force_field_names() (MDMC.MD.force_fields.force_field_factory.ForceFieldFactory static method)

get_menu_data() (MDMC.MD.ase.viewer.Viewer method) get_observable() (MDMC.trajectory_analysis.observables.obs_factory.ObservableFactory class method) get_reduced_chemical_formula() (in module MDMC.MD.structural_units) get_solvent_config() (in module MDMC.MD.solvents.solvents) get_solvent_names() (in module MDMC.MD.solvents.solvents) get_viewpoint_z() (MDMC.MD.ase.conversions.X3D method)

H

HarmonicPotential (class in MDMC.MD.interaction_functions)

I

improper_ID (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute) impropers (MDMC.MD.force_fields.ff.FileForceField property) independent_variables (MDMC.readers.observables.obs_reader.ObservableReader property) (MDMC.readers.observables.obs_reader.SQwReader property) (MDMC.trajectory_analysis.observables.obs.Observable property) inter_func_decorator() (in module MDMC.MD.interaction_functions) interaction (in module MDMC.MD.engine_facades.lammps_engine)

interaction_dictionary (MDMC.MD.force_fields.ff.FileForceField property) (MDMC.MD.force_fields.ff.ForceField property) (MDMC.MD.force_fields.SPC.SPC property) (MDMC.MD.force_fields.SPCE.SPCE property) InteractionFunction (class in MDMC.MD.interaction_functions) interactions (MDMC.MD.parameters.Parameter property) (MDMC.MD.simulation.Universe property) (MDMC.MD.structural_units.StructuralUnit property)

K

kspace_solver (MDMC.MD.simulation.Universe attribute)

KSpaceSolver (class in MDMC.MD.simulation)

L

LAMMPSEngine (class in MDMC.MD.engine_facades.lammps_engine) LAMMPSSimulation (class in MDMC.MD.engine_facades.lammps_engine) LAMMPSUniverse (class in MDMC.MD.engine_facades.lammps_engine) LAMPSQw (class in MDMC.readers.observables.LAMPSQw)

LennardJones (class in MDMC.MD.interaction_functions) limit_atoms() (in module MDMC.MD.ase.viewer) lin_momentum_steps (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property) lmp (MDMC.MD.engine_facades.lammps_engine.PyLammpsAttribute attribute) lorentzian() (in module MDMC.common.resolution_functions)

M

MantidSQw (class in MDMC.readers.observables.MantidSQw) mass (MDMC.MD.structural_units.Atom property) max (MDMC.MD.structural_units.BoundingBox property) max_iterations (MDMC.MD.simulation.ConstraintAlgorithm property) maximum_frames() (MDMC.trajectory_analysis.observables.obs.Observable method) MD_steps (MDMC.control.control.Control attribute) MDEngine (class in MDMC.MD.engine_facades.facade) MDEngineFacadeFactory (class in MDMC.MD.engine_facades.facade_factory) MDMC.common.constants module MDMC.common.decorators module MDMC.common.df_operations module MDMC.common.mathematics module MDMC.common.resolution_functions module MDMC.common.units module MDMC.control.control module MDMC.MD.ase.cif module MDMC.MD.ase.conversions module MDMC.MD.ase.viewer module MDMC.MD.container module MDMC.MD.engine_facades.facade module MDMC.MD.engine_facades.facade_factory module MDMC.MD.engine_facades.lammps_engine module MDMC.MD.force_fields.ff module MDMC.MD.force_fields.force_field_factory module MDMC.MD.force_fields.OPLSAA module MDMC.MD.force_fields.SPC module MDMC.MD.force_fields.SPCE module MDMC.MD.interaction_functions module MDMC.MD.parameters module MDMC.MD.simulation module MDMC.MD.solvents.solvents module MDMC.MD.solvents.SPC_config module MDMC.MD.structural_units module MDMC.readers.configurations.cif module MDMC.readers.configurations.conf_reader module MDMC.readers.configurations.conf_reader_factory module MDMC.readers.observables.LAMPSQw module MDMC.readers.observables.MantidSQw module MDMC.readers.observables.netCDF module MDMC.readers.observables.obs_reader module MDMC.readers.observables.obs_reader_factory module MDMC.readers.observables.xml_SQw module

MDMC.readers.reader module MDMC.readers.reader_factory module MDMC.refinement.FoM module MDMC.trajectory_analysis.observables.obs module MDMC.trajectory_analysis.observables.obs_factory module MDMC.trajectory_analysis.observables.PDF module MDMC.trajectory_analysis.observables.SQw module MDMC.trajectory_analysis.observables.SQw_coh module MDMC.trajectory_analysis.observables.SQw_incoh module MDMC.trajectory_analysis.trajectory module min (MDMC.MD.structural_units.BoundingBox property) minimize() (MDMC.MD.engine_facades.facade.MDEngine method) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method) (MDMC.MD.simulation.Simulation method) minimizer (MDMC.control.control.Control attribute) minimum_frames() (MDMC.trajectory_analysis.observables.obs.Observable method) mod_docstring() (in module MDMC.common.decorators) module MDMC.common.constants MDMC.common.decorators MDMC.common.df_operations MDMC.common.mathematics MDMC.common.resolution_functions MDMC.common.units MDMC.control.control MDMC.MD.ase.cif MDMC.MD.ase.conversions MDMC.MD.ase.viewer MDMC.MD.container MDMC.MD.engine_facades.facade MDMC.MD.engine_facades.facade_factory MDMC.MD.engine_facades.lammps_engine MDMC.MD.force_fields.ff MDMC.MD.force_fields.force_field_factory MDMC.MD.force_fields.OPLSAA MDMC.MD.force_fields.SPC MDMC.MD.force_fields.SPCE MDMC.MD.interaction_functions MDMC.MD.parameters MDMC.MD.simulation MDMC.MD.solvents.solvents MDMC.MD.solvents.SPC_config MDMC.MD.structural_units MDMC.readers.configurations.cif MDMC.readers.configurations.conf_reader MDMC.readers.configurations.conf_reader_factory MDMC.readers.observables.LAMPSQw MDMC.readers.observables.MantidSQw MDMC.readers.observables.netCDF MDMC.readers.observables.obs_reader MDMC.readers.observables.obs_reader_factory MDMC.readers.observables.xml_SQw MDMC.readers.reader MDMC.readers.reader_factory MDMC.refinement.FoM MDMC.trajectory_analysis.observables.obs MDMC.trajectory_analysis.observables.obs_factory MDMC.trajectory_analysis.observables.PDF MDMC.trajectory_analysis.observables.SQw MDMC.trajectory_analysis.observables.SQw_coh MDMC.trajectory_analysis.observables.SQw_incoh MDMC.trajectory_analysis.trajectory Molecule (class in MDMC.MD.structural_units) molecule_list (MDMC.MD.simulation.Universe property) (MDMC.trajectory_analysis.trajectory.Configuration property)

N

n_atoms (MDMC.MD.simulation.Universe property) n_body (MDMC.MD.force_fields.ff.WaterModel property) n_bonded (MDMC.MD.simulation.Universe property) n_interactions (MDMC.MD.simulation.Universe property) n_molecules (MDMC.MD.simulation.Universe property) n_nonbonded (MDMC.MD.simulation.Universe property) name (MDMC.MD.interaction_functions.InteractionFunction property) (MDMC.MD.simulation.ConstraintAlgorithm property) (MDMC.MD.simulation.KSpaceSolver property) (MDMC.trajectory_analysis.observables.obs.Observable property)

nbis_by_atom_type_pairs (MDMC.MD.simulation.Universe property) neighbor_steps (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property) netCDF (class in MDMC.readers.observables.netCDF) nonbonded_interactions (MDMC.MD.simulation.Universe property) (MDMC.MD.structural_units.Atom property) (MDMC.MD.structural_units.CompositeStructuralUnit property) (MDMC.MD.structural_units.Molecule property) (MDMC.MD.structural_units.StructuralUnit property) nonbonded_mix (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse property)

O

Observable (class in MDMC.trajectory_analysis.observables.obs) observable_pairs (MDMC.control.control.Control attribute) ObservableFactory (class in MDMC.trajectory_analysis.observables.obs_factory)

ObservableReader (class in MDMC.readers.observables.obs_reader) ObservableReaderFactory (class in MDMC.readers.observables.obs_reader_factory) OPLSAA (class in MDMC.MD.force_fields.OPLSAA) origin (MDMC.trajectory_analysis.observables.obs.Observable property)

P

Parameter (class in MDMC.MD.parameters) parameterize_interactions() (MDMC.MD.force_fields.ff.ForceField method) Parameters (class in MDMC.MD.parameters) parameters (MDMC.MD.interaction_functions.InteractionFunction property) (MDMC.MD.simulation.Universe property) parameters_values (MDMC.MD.interaction_functions.InteractionFunction property) parse() (MDMC.readers.configurations.cif.CIF method) (MDMC.readers.observables.LAMPSQw.LAMPSQw method) (MDMC.readers.observables.MantidSQw.MantidSQw method) (MDMC.readers.observables.netCDF.netCDF method) (MDMC.readers.observables.xml_SQw.XML_SQw method) (MDMC.readers.reader.Reader method) parse_all_nonbonded_styles() (in module MDMC.MD.engine_facades.lammps_engine) parse_bonded_coefficients() (in module MDMC.MD.engine_facades.lammps_engine) parse_bonded_styles() (in module MDMC.MD.engine_facades.lammps_engine) parse_constraint() (in module MDMC.MD.engine_facades.lammps_engine) parse_dep_var() (MDMC.readers.observables.LAMPSQw.LAMPSQw method) parse_detectors() (MDMC.readers.observables.MantidSQw.MantidSQw method) parse_dispersion_coefficients() (in module MDMC.MD.engine_facades.lammps_engine)

parse_indep_var() (MDMC.readers.observables.LAMPSQw.LAMPSQw method) parse_kspace_solver() (in module MDMC.MD.engine_facades.lammps_engine) parse_nonbonded_modifications() (in module MDMC.MD.engine_facades.lammps_engine) parse_nonbonded_styles() (in module MDMC.MD.engine_facades.lammps_engine) parse_variables() (MDMC.readers.observables.MantidSQw.MantidSQw method) partition() (in module MDMC.MD.engine_facades.lammps_engine) partition_interactions() (in module MDMC.MD.engine_facades.lammps_engine) Periodic (class in MDMC.MD.interaction_functions) physical_property (MDMC.common.units.Unit property) position (MDMC.MD.structural_units.Molecule property) (MDMC.MD.structural_units.StructuralUnit property) positions (MDMC.trajectory_analysis.trajectory.Trajectory property) PPPM (class in MDMC.MD.simulation) pressure (MDMC.MD.engine_facades.lammps_engine.Ensemble property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property) proper_ID (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute) propers (MDMC.MD.force_fields.ff.FileForceField property) PyLammpsAttribute (class in MDMC.MD.engine_facades.lammps_engine)

Q

Q (MDMC.readers.observables.obs_reader.SQwReader property)

R

Rattle (class in MDMC.MD.simulation) read_from_file() (MDMC.trajectory_analysis.observables.obs.Observable method) Reader (class in MDMC.readers.reader) reader (MDMC.trajectory_analysis.observables.obs.Observable attribute) ReaderFactory (class in MDMC.readers.reader_factory) refine() (MDMC.control.control.Control method) register() (MDMC.trajectory_analysis.observables.obs_factory.ObservableFactory class method) remove_ensemble_fixes() (MDMC.MD.engine_facades.lammps_engine.Ensemble method)

repr_decorator() (in module MDMC.common.decorators) rescale_step (MDMC.MD.engine_facades.lammps_engine.Ensemble attribute) reset_config() (MDMC.MD.engine_facades.facade.MDEngine method) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method) rotate() (MDMC.MD.structural_units.CompositeStructuralUnit method) run() (MDMC.MD.engine_facades.facade.MDEngine method) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method) (MDMC.MD.simulation.Simulation method)

S

save_config() (MDMC.MD.engine_facades.facade.MDEngine method) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method) saved_config (MDMC.MD.engine_facades.facade.MDEngine property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine property) scale() (MDMC.trajectory_analysis.trajectory.Configuration method) set_atom_mass() (MDMC.MD.force_fields.ff.FileForceField method) set_atoms() (MDMC.MD.ase.viewer.Viewer method) set_config() (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse method) set_docstring() (in module MDMC.common.decorators) set_parameters_interactions() (MDMC.MD.interaction_functions.InteractionFunction method) set_tie() (MDMC.MD.parameters.Parameter method) settings (MDMC.MD.simulation.Simulation attribute) setup_simulation() (MDMC.MD.engine_facades.facade.MDEngine method) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method) setup_universe() (MDMC.MD.engine_facades.facade.MDEngine method) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method)

Shake (class in MDMC.MD.simulation) Simulation (class in MDMC.MD.simulation) simulation (MDMC.control.control.Control attribute) skin (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property) solvate() (MDMC.MD.simulation.Universe method) SPC (class in MDMC.MD.force_fields.SPC) SPCConfig (class in MDMC.MD.solvents.SPC_config) SPCE (class in MDMC.MD.force_fields.SPCE) SQwReader (class in MDMC.readers.observables.obs_reader) step() (MDMC.control.control.Control method) StructuralUnit (class in MDMC.MD.structural_units) structure_list (MDMC.MD.simulation.Universe property) (MDMC.MD.structural_units.CompositeStructuralUnit property) (MDMC.trajectory_analysis.trajectory.Configuration property) structure_type (MDMC.MD.structural_units.StructuralUnit property) system_state (MDMC.MD.engine_facades.lammps_engine.PyLammpsAttribute property)

T

t_fraction (MDMC.MD.engine_facades.lammps_engine.Ensemble property) t_window (MDMC.MD.engine_facades.lammps_engine.Ensemble property) temperature (MDMC.MD.engine_facades.lammps_engine.Ensemble property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property) TemporalConfiguration (class in MDMC.trajectory_analysis.trajectory) thermostat (MDMC.MD.engine_facades.lammps_engine.Ensemble property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property) tie (MDMC.MD.parameters.Parameter property) tied (MDMC.MD.parameters.Parameter property)

time_step (MDMC.MD.engine_facades.lammps_engine.Ensemble property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property) times (MDMC.trajectory_analysis.trajectory.Trajectory property) top_level_structure (MDMC.MD.structural_units.StructuralUnit property) traj_step (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation attribute) (MDMC.MD.simulation.Simulation attribute) Trajectory (class in MDMC.trajectory_analysis.trajectory) trajectory (MDMC.MD.simulation.Simulation property) translate() (MDMC.MD.structural_units.StructuralUnit method)

U

uniformity_requirements (MDMC.trajectory_analysis.observables.obs.Observable property) Unit (class in MDMC.common.units) unit (MDMC.common.units.UnitFloat property) (MDMC.common.units.UnitNDArray property) unit_array() (in module MDMC.common.units) unit_decorator() (in module MDMC.common.decorators) unit_decorator_getter() (in module MDMC.common.decorators) UnitFloat (class in MDMC.common.units) UnitNDArray (class in MDMC.common.units) Universe (class in MDMC.MD.simulation) universe (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation attribute) (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute) (MDMC.MD.simulation.Simulation attribute) (MDMC.MD.structural_units.Atom property) (MDMC.MD.structural_units.CompositeStructuralUnit property) (MDMC.MD.structural_units.StructuralUnit property) (MDMC.trajectory_analysis.trajectory.AtomCollection property) (MDMC.trajectory_analysis.trajectory.Configuration attribute) (MDMC.trajectory_analysis.trajectory.Trajectory property)

update_parameters() (MDMC.MD.engine_facades.facade.MDEngine method) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method) (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse method) use_FFT (MDMC.trajectory_analysis.observables.obs.Observable property)

V

valid_position() (MDMC.MD.structural_units.StructuralUnit method) validate_config() (MDMC.trajectory_analysis.trajectory.Trajectory static method) validate_structure() (MDMC.trajectory_analysis.trajectory.Configuration method) validate_value() (MDMC.MD.parameters.Parameter static method) value (MDMC.MD.parameters.Parameter property) velocities (MDMC.trajectory_analysis.trajectory.Trajectory property)

velocity (MDMC.MD.structural_units.StructuralUnit property) view() (in module MDMC.gui.__init__) (in module MDMC.MD.ase.viewer) view_ase() (in module MDMC.MD.ase.viewer) view_x3dom() (in module MDMC.MD.ase.viewer) Viewer (class in MDMC.MD.ase.viewer)

W

w (MDMC.readers.observables.obs_reader.SQwReader property) WaterModel (class in MDMC.MD.force_fields.ff)

wrap_docstring() (in module MDMC.common.decorators) write() (MDMC.MD.ase.conversions.ASEAtoms method) (MDMC.MD.ase.conversions.X3D method)

X

X3D (class in MDMC.MD.ase.conversions)

XML_SQw (class in MDMC.readers.observables.xml_SQw)