Index

A

absolute_path (MDMC.MD.force_fields.ff.FileForceField property) AbstractFQt (class in MDMC.trajectory_analysis.observables.fqt) AbstractSQw (class in MDMC.trajectory_analysis.observables.sqw) accuracy (MDMC.MD.simulation.ConstraintAlgorithm attribute) (MDMC.MD.simulation.KSpaceSolver attribute) add_atoms() (MDMC.MD.interactions.BondedInteraction method) add_bonded_interaction_pairs() (MDMC.MD.simulation.Universe method) add_box() (MDMC.MD.packmol.packmol_setup.PackmolSetup method) add_container() (MDMC.MD.packmol.packmol_setup.PackmolSetup method) add_cube() (MDMC.MD.packmol.packmol_setup.PackmolSetup method) add_fixed_structure() (MDMC.MD.packmol.packmol_setup.PackmolSetup method) add_force_field() (MDMC.MD.simulation.Universe method) add_interaction() (MDMC.MD.structures.Atom method) add_nonbonded_interaction() (MDMC.MD.simulation.Universe method) add_sphere() (MDMC.MD.packmol.packmol_setup.PackmolSetup method) add_structure() (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) append() (MDMC.MD.parameters.Parameters method) apply() (MDMC.resolution.from_file.FileResolution method) (MDMC.resolution.gaussian.GaussianResolution method) (MDMC.resolution.lorentzian.LorentzianResolution method) (MDMC.resolution.null.NullResolution method) (MDMC.resolution.resolution.Resolution method) apply_constraints() (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYUniverse method) (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse method) apply_ensemble_fixes() (MDMC.MD.engine_facades.lammps_engine.LAMMPSEnsemble method) apply_resolution() (MDMC.trajectory_analysis.observables.fqt.AbstractFQt method) array (MDMC.MD.parameters.Parameters attribute) as_array (MDMC.MD.parameters.Parameters property) ASE_to_MDMC() (in module MDMC.MD.ase.convert) ASEExporter (class in MDMC.exporters.configurations.ase)

ASEReader (class in MDMC.readers.configurations.ase) assign() (MDMC.readers.observables.LAMPPDF.LAMPPDF method) (MDMC.readers.observables.obs_reader.ObservableReader method) Atom (class in MDMC.MD.structures) atom_dict (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute) atom_positions (MDMC.trajectory_analysis.trajectory.Configuration property) atom_type (MDMC.MD.structures.Atom property) atom_type_interactions (MDMC.MD.simulation.Universe attribute) (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.interactions.BondedInteraction property) (MDMC.MD.interactions.Coulombic property) (MDMC.MD.interactions.Dispersion property) (MDMC.MD.interactions.NonBondedInteraction property) (MDMC.MD.simulation.Universe 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.interactions.BondedInteraction property) (MDMC.MD.interactions.Coulombic property) (MDMC.MD.interactions.Dispersion property) (MDMC.MD.interactions.Interaction property) (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.structures.Atom property) (MDMC.MD.structures.Structure property) (MDMC.readers.configurations.conf_reader.ConfigurationReader property) (MDMC.readers.configurations.pdb.ProteinDataBankReader property) (MDMC.trajectory_analysis.trajectory.Configuration property) auto_equilibrate() (MDMC.MD.simulation.Simulation method)

B

barostat (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYEngine property) (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYEnsemble property) (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYSimulation property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEnsemble 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 (class in MDMC.MD.interactions) bond_angles (MDMC.MD.force_fields.ff.FileForceField property) bond_ID (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute) BondAngle (class in MDMC.MD.interactions) bonded_interaction_pairs (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.structures.Atom property) (MDMC.MD.structures.CompositeStructure property) (MDMC.MD.structures.Molecule property) (MDMC.MD.structures.Structure property)

bonded_interactions (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.structures.Structure property) BondedInteraction (class in MDMC.MD.interactions) bonds (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute) (MDMC.MD.force_fields.ff.FileForceField property) (MDMC.readers.configurations.pdb.ProteinDataBankReader property) bounding_box (MDMC.MD.structures.Structure property) BoundingBox (class in MDMC.MD.structures) Buckingham (class in MDMC.MD.interaction_functions)

C

calc_CoM() (MDMC.MD.structures.CompositeStructure method) calc_incoherent_scatt_length() (in module MDMC.trajectory_analysis.observables.fqt) calculate() (MDMC.refinement.FoM.FoM_abs.FigureOfMerit method) calculate_difference() (MDMC.refinement.FoM.FoM_abs.ObservablePair method) calculate_dt() (MDMC.trajectory_analysis.observables.sqw.AbstractSQw method) calculate_E() (MDMC.trajectory_analysis.observables.sqw.AbstractSQw static method) calculate_errors() (MDMC.refinement.FoM.FoM_abs.ObservablePair method) calculate_exp_errors() (MDMC.refinement.FoM.FoM_abs.ObservablePair method) calculate_from_MD() (MDMC.trajectory_analysis.observables.fqt.AbstractFQt method) (MDMC.trajectory_analysis.observables.obs.Observable method) (MDMC.trajectory_analysis.observables.PairDistributionFunction method) (MDMC.trajectory_analysis.observables.pdf.PairDistributionFunction method) (MDMC.trajectory_analysis.observables.sqw.AbstractSQw method) calculate_max_FoM() (MDMC.control.control.Control method) calculate_resolution_functions() (MDMC.trajectory_analysis.observables.sqw.AbstractSQw method) calculate_rho() (in module MDMC.trajectory_analysis.observables.fqt) calculate_rho_config() (MDMC.trajectory_analysis.observables.fqt.AbstractFQt method) calculate_single_FoM() (MDMC.refinement.FoM.ChiSquared_experror.ChiSquaredExpError method) (MDMC.refinement.FoM.FoM_abs.FigureOfMerit method) (MDMC.refinement.FoM.RSquared_noneerror.RSquared_noneerror method) calculate_SQw() (MDMC.trajectory_analysis.observables.fqt.AbstractFQt method) calculate_volume() (in module MDMC.MD.packmol.packmol_setup) change_parameters() (MDMC.refinement.minimizers.GPO.GPO method) (MDMC.refinement.minimizers.GPR.GPR method) (MDMC.refinement.minimizers.minimizer_abs.Minimizer method) (MDMC.refinement.minimizers.MMC.MMC method) change_state() (MDMC.refinement.minimizers.MMC.MMC method) charge (MDMC.MD.structures.Atom property) (MDMC.MD.structures.Molecule property) check_dep_var() (MDMC.refinement.FoM.FoM_abs.ObservablePair method) check_errors() (MDMC.refinement.FoM.FoM_abs.ObservablePair method) check_indep_var() (MDMC.refinement.FoM.FoM_abs.ObservablePair method) check_origin() (MDMC.refinement.FoM.FoM_abs.ObservablePair method) check_types() (MDMC.refinement.FoM.FoM_abs.ObservablePair method) ChiSquaredExpError (class in MDMC.refinement.FoM.ChiSquared_experror) CIFReader (class in MDMC.readers.configurations.cif) clear() (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYEngine method) (MDMC.MD.engine_facades.facade.MDEngine method) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method) CNVS_WIDTH (in module MDMC.utilities.plotting) CODATA (in module MDMC.common.units) CODATA_VERSION (in module MDMC.common.units) CoherentDynamicStructureFactor (in module MDMC.trajectory_analysis.observables) CoherentIntermediateScatteringFunction (in module MDMC.trajectory_analysis.observables) CompactTrajectory (class in MDMC.trajectory_analysis.compact_trajectory) components (MDMC.common.units.Unit attribute)

CompositeStructure (class in MDMC.MD.structures) 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_as_compact_trajectory() (in module MDMC.trajectory_analysis.compact_trajectory) ConstrainableMixin (class in MDMC.MD.interactions) constrained (MDMC.MD.interactions.ConstrainableMixin attribute) constraint_algorithm (MDMC.MD.simulation.Universe attribute) ConstraintAlgorithm (class in MDMC.MD.simulation) constraints (MDMC.MD.parameters.Parameter property) Control (class in MDMC.control.control) conversion_factor (MDMC.common.units.Unit attribute) (MDMC.common.units.Unit property) convert_trajectory() (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYEngine method) (MDMC.MD.engine_facades.facade.MDEngine method) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method) convert_unit() (in module MDMC.MD.engine_facades.dlpoly_engine) (in module MDMC.MD.engine_facades.lammps_engine) convert_units() (in module MDMC.utilities.tinker_converter) copy() (MDMC.MD.structures.Atom method) (MDMC.MD.structures.CompositeStructure method) (MDMC.MD.structures.Structure method) copy_interactions() (MDMC.MD.structures.Atom method) core_batch() (in module MDMC.trajectory_analysis.observables.concurrency_tools) correlation() (in module MDMC.common.mathematics) Coulomb (class in MDMC.MD.interaction_functions) Coulombic (class in MDMC.MD.interactions) couls (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute) create_bond() (MDMC.readers.configurations.pdb.ProteinDataBankReader method) create_bounds() (MDMC.refinement.minimizers.GPR.GPR static method) create_cornerplot() (MDMC.control.plot_results.PlotResults method) create_executor() (in module MDMC.trajectory_analysis.observables.concurrency_tools) create_facade() (MDMC.MD.engine_facades.facade_factory.MDEngineFacadeFactory static method) create_FoM() (MDMC.refinement.FoM.FoM_factory.FoMFactory static method) create_force_field() (MDMC.MD.force_fields.force_field_factory.ForceFieldFactory static method) create_instance() (MDMC.resolution.resolution_factory.ResolutionFactory method) create_instl_test() (MDMC.utilities.installation_tests.InstlTestFactory class method) create_logger() (in module MDMC.common.log) create_minimizer() (MDMC.refinement.minimizers.minimizer_factory.MinimizerFactory static method) create_observable() (MDMC.trajectory_analysis.observables.obs_factory.ObservableFactory class method) create_parameter_point_array() (MDMC.refinement.minimizers.GPR.GPR 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) cutoff (MDMC.MD.interactions.NonBondedInteraction property)

D

data (MDMC.readers.observables.obs_reader.ObservableReader property) (MDMC.trajectory_analysis.compact_trajectory.CompactTrajectory property) (MDMC.trajectory_analysis.observables.obs.Observable property) (MDMC.trajectory_analysis.trajectory.Configuration attribute) (MDMC.trajectory_analysis.trajectory.Configuration property) data_norm_factor() (MDMC.refinement.FoM.FoM_abs.FigureOfMerit method) DataPrinter (class in MDMC.control.plot_results) density (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) dependent_variables (MDMC.readers.observables.obs_reader.ObservableReader property) (MDMC.readers.observables.obs_reader.PDFReader property) (MDMC.readers.observables.obs_reader.SQwReader property) (MDMC.trajectory_analysis.observables.fqt.AbstractFQt property) (MDMC.trajectory_analysis.observables.obs.Observable property) (MDMC.trajectory_analysis.observables.PairDistributionFunction property) (MDMC.trajectory_analysis.observables.pdf.PairDistributionFunction property) (MDMC.trajectory_analysis.observables.sqw.AbstractSQw property) dependent_variables_structure (MDMC.trajectory_analysis.observables.fqt.AbstractFQt property) (MDMC.trajectory_analysis.observables.obs.Observable property) (MDMC.trajectory_analysis.observables.PairDistributionFunction property) (MDMC.trajectory_analysis.observables.pdf.PairDistributionFunction property) (MDMC.trajectory_analysis.observables.sqw.AbstractSQw property)

dict_from_element() (MDMC.readers.observables.xml_SQw.XML_SQw static method) DihedralAngle (class in MDMC.MD.interactions) dimensions (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.trajectory_analysis.trajectory.AtomCollection property) Dispersion (class in MDMC.MD.interactions) dispersions (MDMC.MD.force_fields.ff.FileForceField property) dispersive_solver (MDMC.MD.simulation.Universe attribute) disps (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute) DISTRIBUTION (MDMC.refinement.minimizers.MMC.MMC attribute) dlpoly (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYAttribute attribute) DLPOLYAttribute (class in MDMC.MD.engine_facades.dlpoly_engine) DLPOLYEngine (class in MDMC.MD.engine_facades.dlpoly_engine) DLPOLYEnsemble (class in MDMC.MD.engine_facades.dlpoly_engine) DLPOLYSimulation (class in MDMC.MD.engine_facades.dlpoly_engine) DLPOLYUniverse (class in MDMC.MD.engine_facades.dlpoly_engine) dummy_headers() (in module MDMC.utilities.tinker_converter) dumps (MDMC.MD.engine_facades.lammps_engine.PyLammpsAttribute property) DynamicStructureFactor (in module MDMC.trajectory_analysis.observables)

E

E (MDMC.readers.observables.obs_reader.SQwReader property) (MDMC.trajectory_analysis.observables.sqw.AbstractSQw property) electrostatic_solver (MDMC.MD.simulation.Universe attribute) element (MDMC.MD.structures.Atom attribute) element_dict (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) element_list (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.trajectory_analysis.trajectory.Configuration property) element_list() (MDMC.MD.interactions.BondedInteraction method) (MDMC.MD.interactions.Coulombic method) (MDMC.MD.interactions.Dispersion method) (MDMC.MD.interactions.Interaction method) element_lookup (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) element_set (MDMC.trajectory_analysis.trajectory.Configuration attribute), [1] element_tuple() (MDMC.MD.interactions.Interaction method) enforcing_minimizer_compatibility() (MDMC.refinement.minimizers.minimizer_abs.Minimizer method) engine (MDMC.MD.simulation.Simulation attribute) engine_recovery_from_equil() (MDMC.control.control.Control method) ensemble (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYEngine property) (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYSimulation attribute) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation attribute) equilibrate() (MDMC.control.control.Control method) equivalent_top_level_structures_dict (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property)

errors (MDMC.readers.observables.obs_reader.ObservableReader property) (MDMC.readers.observables.obs_reader.PDFReader property) (MDMC.readers.observables.obs_reader.SQwReader property) (MDMC.trajectory_analysis.observables.fqt.AbstractFQt property) (MDMC.trajectory_analysis.observables.obs.Observable property) (MDMC.trajectory_analysis.observables.PairDistributionFunction property) (MDMC.trajectory_analysis.observables.pdf.PairDistributionFunction property) (MDMC.trajectory_analysis.observables.sqw.AbstractSQw property) eval() (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYEngine method) (MDMC.MD.engine_facades.facade.MDEngine method) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method) Ewald (class in MDMC.MD.simulation) execution_time (MDMC.common.time_keeper.TimeKeeper attribute) exp_datasets (MDMC.control.control.Control attribute) exp_obs (MDMC.refinement.FoM.FoM_abs.ObservablePair property) exportAtom() (MDMC.trajectory_analysis.compact_trajectory.CompactTrajectory method) Exporter (class in MDMC.exporters.exporter) extension (MDMC.readers.configurations.ase.ASEReader attribute) (MDMC.readers.configurations.cif.CIFReader attribute) (MDMC.readers.configurations.packmol_pdb.PackmolPDBReader attribute) (MDMC.readers.configurations.pdb.ProteinDataBankReader attribute) extract_partial_pdf() (MDMC.readers.observables.netCDFPDF.netCDFPDF method) extract_result() (MDMC.refinement.minimizers.GPO.GPO method) (MDMC.refinement.minimizers.GPR.GPR method) (MDMC.refinement.minimizers.minimizer_abs.Minimizer method) (MDMC.refinement.minimizers.MMC.MMC method)

F

faster_autocorrelation() (in module MDMC.common.mathematics) faster_correlation() (in module MDMC.common.mathematics) FigureOfMerit (class in MDMC.refinement.FoM.FoM_abs) file (MDMC.readers.observables.netCDFPDF.netCDFPDF attribute) (MDMC.readers.observables.netCDFSQw.netCDFSQw 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) (MDMC.MD.force_fields.OPLSAA.OPLSAA attribute) file_variables (MDMC.readers.observables.MantidSQw.MantidSQw attribute) (MDMC.readers.observables.MDANSESQw.MDANSESQw attribute) FileForceField (class in MDMC.MD.force_fields.ff) FileResolution (class in MDMC.resolution.from_file) fill() (MDMC.MD.simulation.Universe method) fill_with_packmol() (MDMC.MD.packmol.packmol_wrapper.PackmolFiller method) filled_universe (MDMC.MD.packmol.packmol_wrapper.PackmolFiller property) filter() (MDMC.MD.parameters.Parameters method) filter_atom_attribute() (MDMC.MD.parameters.Parameters method) filter_atoms() (in module MDMC.MD.structures) (MDMC.trajectory_analysis.trajectory.Configuration method) filter_atoms_element() (in module MDMC.MD.structures) filter_by_element() (MDMC.trajectory_analysis.compact_trajectory.CompactTrajectory method) (MDMC.trajectory_analysis.trajectory.Configuration method) filter_by_time() (MDMC.trajectory_analysis.compact_trajectory.CompactTrajectory method) filter_by_type() (MDMC.trajectory_analysis.compact_trajectory.CompactTrajectory 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 (MDMC.refinement.minimizers.minimizer_abs.Minimizer attribute) FoM_calculator (MDMC.control.control.Control attribute) FoM_old (MDMC.refinement.minimizers.minimizer_abs.Minimizer attribute) FoMFactory (class in MDMC.refinement.FoM.FoM_factory) force_fields (MDMC.MD.simulation.Universe attribute), [1] (MDMC.MD.simulation.Universe property) ForceField (class in MDMC.MD.force_fields.ff) ForceFieldFactory (class in MDMC.MD.force_fields.force_field_factory) format_result_string() (MDMC.refinement.minimizers.GPO.GPO method) (MDMC.refinement.minimizers.GPR.GPR method) (MDMC.refinement.minimizers.minimizer_abs.Minimizer method) (MDMC.refinement.minimizers.MMC.MMC method) formula (MDMC.MD.structures.CompositeStructure property) FQt (class in MDMC.trajectory_analysis.observables) (class in MDMC.trajectory_analysis.observables.fqt) (MDMC.trajectory_analysis.observables.fqt.AbstractFQt property) FQt_coh (in module MDMC.trajectory_analysis.observables) FQt_incoh (in module MDMC.trajectory_analysis.observables) FQtCoh (in module MDMC.trajectory_analysis.observables) FQtCoherent (class in MDMC.trajectory_analysis.observables) (class in MDMC.trajectory_analysis.observables.fqt_coh) FQtIncoherent (class in MDMC.trajectory_analysis.observables.fqt_incoh) FQtIncoherentFQtIncoh (in module MDMC.trajectory_analysis.observables) function (MDMC.MD.interactions.Interaction property) function_called() (MDMC.common.time_keeper.TimeKeeper method) function_name (MDMC.MD.interactions.Interaction property)

G

gaussian() (in module MDMC.common.resolution_functions) GaussianResolution (class in MDMC.resolution.gaussian) get_FoM_names() (MDMC.refinement.FoM.FoM_factory.FoMFactory static method) get_force_field_names() (MDMC.MD.force_fields.force_field_factory.ForceFieldFactory static method) get_max_sizes() (MDMC.MD.packmol.packmol_setup.PackmolSetup method) get_measured_points() (MDMC.control.plot_results.PlotResults method) get_minimizer_names() (MDMC.refinement.minimizers.minimizer_factory.MinimizerFactory static method) get_observable() (MDMC.trajectory_analysis.observables.obs_factory.ObservableFactory class method) get_packmol_files_path() (MDMC.MD.packmol.packmol_wrapper.PackmolFiller method) get_packmol_output_path() (MDMC.MD.packmol.packmol_wrapper.PackmolFiller method) get_packmol_path() (MDMC.MD.packmol.packmol_wrapper.PackmolFiller static method) get_parameters_old_values() (MDMC.refinement.minimizers.minimizer_abs.Minimizer method)

get_parser() (in module MDMC.utilities.cli) get_point_group() (in module MDMC.trajectory_analysis.observables.fqt) get_reduced_chemical_formula() (in module MDMC.MD.structures) get_settings() (MDMC.MD.packmol.packmol_setup.PackmolSetup method) get_solvent_config() (in module MDMC.MD.solvents.solvents) get_solvent_names() (in module MDMC.MD.solvents.solvents) get_structures() (MDMC.MD.packmol.packmol_setup.PackmolSetup method) global_minimum_position() (MDMC.refinement.minimizers.GPR.GPR static method) GPO (class in MDMC.refinement.minimizers.GPO) GPR (class in MDMC.refinement.minimizers.GPR) GPR_fit() (MDMC.refinement.minimizers.GPR.GPR method) GPR_predict() (MDMC.refinement.minimizers.GPR.GPR static method)

H

h (in module MDMC.common.constants) h_bar (in module MDMC.common.constants) HANDLED_PARAMS (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYEngine attribute) HarmonicPotential (class in MDMC.MD.interaction_functions) has_converged() (MDMC.refinement.minimizers.GPO.GPO method) (MDMC.refinement.minimizers.GPR.GPR method) (MDMC.refinement.minimizers.minimizer_abs.Minimizer method) (MDMC.refinement.minimizers.MMC.MMC method)

history (MDMC.refinement.minimizers.minimizer_abs.Minimizer attribute) (MDMC.refinement.minimizers.minimizer_abs.Minimizer property) history_columns (MDMC.refinement.minimizers.GPO.GPO attribute) (MDMC.refinement.minimizers.GPO.GPO property) (MDMC.refinement.minimizers.GPR.GPR attribute) (MDMC.refinement.minimizers.GPR.GPR property) (MDMC.refinement.minimizers.minimizer_abs.Minimizer property) (MDMC.refinement.minimizers.MMC.MMC attribute) (MDMC.refinement.minimizers.MMC.MMC property)

I

ID_or_Q (MDMC.readers.observables.MantidSQw.MantidSQw attribute) improper (MDMC.MD.interactions.DihedralAngle attribute) improper_ID (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute) impropers (MDMC.MD.force_fields.ff.FileForceField property) IncoherentDynamicStructureFactor (in module MDMC.trajectory_analysis.observables) IncoherentIntermediateScatteringFunction (in module MDMC.trajectory_analysis.observables) INDENT (MDMC.exporters.configurations.packmol_input.PackmolInputExporter attribute) independent_variables (MDMC.readers.observables.obs_reader.ObservableReader property) (MDMC.readers.observables.obs_reader.PDFReader property) (MDMC.readers.observables.obs_reader.SQwReader property) (MDMC.trajectory_analysis.observables.fqt.AbstractFQt property) (MDMC.trajectory_analysis.observables.obs.Observable property) (MDMC.trajectory_analysis.observables.PairDistributionFunction property) (MDMC.trajectory_analysis.observables.pdf.PairDistributionFunction property) (MDMC.trajectory_analysis.observables.sqw.AbstractSQw property) InstlTestBase (class in MDMC.utilities.installation_tests) InstlTestCore (class in MDMC.utilities.installation_tests) InstlTestDynamicPlottingDependencies (class in MDMC.utilities.installation_tests) InstlTestFactory (class in MDMC.utilities.installation_tests) InstlTestLAMMPS (class in MDMC.utilities.installation_tests) InstlTestX11Forwarding (class in MDMC.utilities.installation_tests) inter_func_decorator() (in module MDMC.MD.interaction_functions) Interaction (class in MDMC.MD.interactions)

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) (MDMC.MD.force_fields.TIP3P.TIP3P property) (MDMC.MD.force_fields.TIP3PFB.TIP3PFB property) InteractionFunction (class in MDMC.MD.interaction_functions) interactions (MDMC.MD.parameters.Parameter property) (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.structures.Structure property) IntermediateScatteringFunction (in module MDMC.trajectory_analysis.observables) IPythonDataPrinter (class in MDMC.control.plot_results) is_atom() (in module MDMC.utilities.structures) is_equivalent() (MDMC.MD.interactions.Bond method) (MDMC.MD.interactions.BondAngle method) (MDMC.MD.interactions.BondedInteraction method) (MDMC.MD.interactions.Dispersion method) (MDMC.MD.interactions.NonBondedInteraction method) (MDMC.MD.structures.Atom method) (MDMC.MD.structures.Molecule method) (MDMC.MD.structures.Structure method)

K

kspace_solver (MDMC.MD.simulation.Universe attribute)

KSpaceSolver (class in MDMC.MD.simulation)

L

labelAtoms() (MDMC.trajectory_analysis.compact_trajectory.CompactTrajectory method) LAMMPSEngine (class in MDMC.MD.engine_facades.lammps_engine) LAMMPSEnsemble (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) LAMPPDF (class in MDMC.readers.observables.LAMPPDF) LAMPSQw (class in MDMC.readers.observables.LAMPSQw) LennardJones (class in MDMC.MD.interaction_functions) lin_momentum_steps (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property)

lmp (MDMC.MD.engine_facades.lammps_engine.PyLammpsAttribute attribute) load_history() (MDMC.refinement.minimizers.minimizer_abs.Minimizer method) LOG_ERROR_MSG (MDMC.utilities.installation_tests.InstlTestDynamicPlottingDependencies attribute) (MDMC.utilities.installation_tests.InstlTestLAMMPS attribute) (MDMC.utilities.installation_tests.InstlTestX11Forwarding attribute) log_parameters() (MDMC.MD.parameters.Parameters method) log_test_passed() (MDMC.utilities.installation_tests.InstlTestBase method) lorentzian() (in module MDMC.common.resolution_functions) LorentzianResolution (class in MDMC.resolution.lorentzian)

M

main() (in module MDMC.utilities.cli) MantidSQw (class in MDMC.readers.observables.MantidSQw) mass (MDMC.MD.structures.Atom property) (MDMC.MD.structures.Molecule property) max (MDMC.MD.structures.BoundingBox property) max_iterations (MDMC.MD.simulation.ConstraintAlgorithm property) maximum_frames() (MDMC.trajectory_analysis.observables.obs.Observable method) (MDMC.trajectory_analysis.observables.PairDistributionFunction method) (MDMC.trajectory_analysis.observables.pdf.PairDistributionFunction method) (MDMC.trajectory_analysis.observables.sqw.SQwMixins method) MD_obs (MDMC.refinement.FoM.FoM_abs.ObservablePair property) MD_steps (MDMC.control.control.Control attribute) MDANSESQw (class in MDMC.readers.observables.MDANSESQw) MDEngine (class in MDMC.MD.engine_facades.facade) MDEngineError MDEngineFacadeFactory (class in MDMC.MD.engine_facades.facade_factory) MDMC module MDMC.common module MDMC.common.constants module MDMC.common.decorators module MDMC.common.df_operations module MDMC.common.log module MDMC.common.mathematics module MDMC.common.resolution_functions module MDMC.common.time_keeper module MDMC.common.units module MDMC.control module MDMC.control.control module MDMC.control.plot_results module MDMC.exporters module MDMC.exporters.configurations module MDMC.exporters.configurations.ase module MDMC.exporters.configurations.packmol_input module MDMC.exporters.exporter module MDMC.gui module MDMC.MD module MDMC.MD.ase module MDMC.MD.ase.convert module MDMC.MD.container module MDMC.MD.engine_facades module MDMC.MD.engine_facades.dlpoly_engine 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 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.force_fields.TIP3P module MDMC.MD.force_fields.TIP3PFB module MDMC.MD.interaction_functions module MDMC.MD.interactions module MDMC.MD.packmol module MDMC.MD.packmol.packmol_setup module MDMC.MD.packmol.packmol_wrapper module MDMC.MD.parameters module MDMC.MD.simulation module MDMC.MD.solvents module MDMC.MD.solvents.solvents module MDMC.MD.solvents.SPC_config module MDMC.MD.structures module MDMC.readers module MDMC.readers.configurations module MDMC.readers.configurations.ase module MDMC.readers.configurations.cif module MDMC.readers.configurations.conf_reader module MDMC.readers.configurations.conf_reader_factory module MDMC.readers.configurations.packmol_pdb module MDMC.readers.configurations.pdb module MDMC.readers.observables module MDMC.readers.observables.LAMPPDF module MDMC.readers.observables.LAMPSQw module MDMC.readers.observables.MantidSQw module MDMC.readers.observables.MDANSESQw module MDMC.readers.observables.netCDFPDF module MDMC.readers.observables.netCDFSQw 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 module MDMC.refinement.FoM module MDMC.refinement.FoM.ChiSquared_experror module MDMC.refinement.FoM.FoM_abs module MDMC.refinement.FoM.FoM_factory module MDMC.refinement.FoM.RSquared_noneerror module MDMC.refinement.minimizers module MDMC.refinement.minimizers.GPO module MDMC.refinement.minimizers.GPR module MDMC.refinement.minimizers.minimizer_abs module MDMC.refinement.minimizers.minimizer_factory module MDMC.refinement.minimizers.MMC module MDMC.resolution module MDMC.resolution.from_file module

MDMC.resolution.gaussian module MDMC.resolution.lorentzian module MDMC.resolution.null module MDMC.resolution.resolution module MDMC.resolution.resolution_factory module MDMC.trajectory_analysis module MDMC.trajectory_analysis.compact_trajectory module MDMC.trajectory_analysis.observables module MDMC.trajectory_analysis.observables.concurrency_tools module MDMC.trajectory_analysis.observables.fqt module MDMC.trajectory_analysis.observables.fqt_coh module MDMC.trajectory_analysis.observables.fqt_incoh 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.trajectory module MDMC.utilities module MDMC.utilities.cli module MDMC.utilities.installation_tests module MDMC.utilities.partitioning module MDMC.utilities.plotting module MDMC.utilities.structures module MDMC.utilities.tinker_converter module MDMC.utilities.trajectory_slicing module MDMC_to_ASE() (in module MDMC.MD.ase.convert) min (MDMC.MD.structures.BoundingBox property) minimize() (MDMC.control.control.Control method) (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYEngine method) (MDMC.MD.engine_facades.facade.MDEngine method) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method) (MDMC.MD.simulation.Simulation method) Minimizer (class in MDMC.refinement.minimizers.minimizer_abs) minimizer (MDMC.control.control.Control attribute) MinimizerFactory (class in MDMC.refinement.minimizers.minimizer_factory) minimum_frames() (MDMC.trajectory_analysis.observables.obs.Observable method) (MDMC.trajectory_analysis.observables.PairDistributionFunction method) (MDMC.trajectory_analysis.observables.pdf.PairDistributionFunction method) (MDMC.trajectory_analysis.observables.sqw.SQwMixins method) MMC (class in MDMC.refinement.minimizers.MMC) mod_docstring() (in module MDMC.common.decorators) module MDMC MDMC.common MDMC.common.constants MDMC.common.decorators MDMC.common.df_operations MDMC.common.log MDMC.common.mathematics MDMC.common.resolution_functions MDMC.common.time_keeper MDMC.common.units MDMC.control MDMC.control.control MDMC.control.plot_results MDMC.exporters MDMC.exporters.configurations MDMC.exporters.configurations.ase MDMC.exporters.configurations.packmol_input MDMC.exporters.exporter MDMC.gui MDMC.MD MDMC.MD.ase MDMC.MD.ase.convert MDMC.MD.container MDMC.MD.engine_facades MDMC.MD.engine_facades.dlpoly_engine MDMC.MD.engine_facades.facade MDMC.MD.engine_facades.facade_factory MDMC.MD.engine_facades.lammps_engine MDMC.MD.force_fields 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.force_fields.TIP3P MDMC.MD.force_fields.TIP3PFB MDMC.MD.interaction_functions MDMC.MD.interactions MDMC.MD.packmol MDMC.MD.packmol.packmol_setup MDMC.MD.packmol.packmol_wrapper MDMC.MD.parameters MDMC.MD.simulation MDMC.MD.solvents MDMC.MD.solvents.solvents MDMC.MD.solvents.SPC_config MDMC.MD.structures MDMC.readers MDMC.readers.configurations MDMC.readers.configurations.ase MDMC.readers.configurations.cif MDMC.readers.configurations.conf_reader MDMC.readers.configurations.conf_reader_factory MDMC.readers.configurations.packmol_pdb MDMC.readers.configurations.pdb MDMC.readers.observables MDMC.readers.observables.LAMPPDF MDMC.readers.observables.LAMPSQw MDMC.readers.observables.MantidSQw MDMC.readers.observables.MDANSESQw MDMC.readers.observables.netCDFPDF MDMC.readers.observables.netCDFSQw 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 MDMC.refinement.FoM MDMC.refinement.FoM.ChiSquared_experror MDMC.refinement.FoM.FoM_abs MDMC.refinement.FoM.FoM_factory MDMC.refinement.FoM.RSquared_noneerror MDMC.refinement.minimizers MDMC.refinement.minimizers.GPO MDMC.refinement.minimizers.GPR MDMC.refinement.minimizers.minimizer_abs MDMC.refinement.minimizers.minimizer_factory MDMC.refinement.minimizers.MMC MDMC.resolution MDMC.resolution.from_file MDMC.resolution.gaussian MDMC.resolution.lorentzian MDMC.resolution.null MDMC.resolution.resolution MDMC.resolution.resolution_factory MDMC.trajectory_analysis MDMC.trajectory_analysis.compact_trajectory MDMC.trajectory_analysis.observables MDMC.trajectory_analysis.observables.concurrency_tools MDMC.trajectory_analysis.observables.fqt MDMC.trajectory_analysis.observables.fqt_coh MDMC.trajectory_analysis.observables.fqt_incoh MDMC.trajectory_analysis.observables.obs MDMC.trajectory_analysis.observables.obs_factory MDMC.trajectory_analysis.observables.pdf MDMC.trajectory_analysis.observables.sqw MDMC.trajectory_analysis.trajectory MDMC.utilities MDMC.utilities.cli MDMC.utilities.installation_tests MDMC.utilities.partitioning MDMC.utilities.plotting MDMC.utilities.structures MDMC.utilities.tinker_converter MDMC.utilities.trajectory_slicing Molecule (class in MDMC.MD.structures) molecule_list (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.trajectory_analysis.trajectory.Configuration property)

N

n_atoms (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) n_averages (MDMC.refinement.FoM.FoM_abs.ObservablePair property) n_body (MDMC.MD.force_fields.ff.WaterModel property) (MDMC.MD.force_fields.SPC.SPC attribute) (MDMC.MD.force_fields.SPCE.SPCE attribute) (MDMC.MD.force_fields.TIP3P.TIP3P attribute) (MDMC.MD.force_fields.TIP3PFB.TIP3PFB attribute) n_bonded (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) n_interactions (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) n_molecules (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) n_nonbonded (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) N_TEXT_LINES (in module MDMC.utilities.plotting) name (MDMC.MD.interaction_functions.InteractionFunction property) (MDMC.MD.simulation.ConstraintAlgorithm property) (MDMC.MD.simulation.KSpaceSolver property) (MDMC.trajectory_analysis.observables.FQt attribute) (MDMC.trajectory_analysis.observables.fqt.FQt attribute) (MDMC.trajectory_analysis.observables.fqt_coh.FQtCoherent attribute) (MDMC.trajectory_analysis.observables.fqt_incoh.FQtIncoherent attribute) (MDMC.trajectory_analysis.observables.FQtCoherent attribute) (MDMC.trajectory_analysis.observables.obs.Observable property) (MDMC.trajectory_analysis.observables.PairDistributionFunction attribute) (MDMC.trajectory_analysis.observables.pdf.PairDistributionFunction attribute) (MDMC.trajectory_analysis.observables.SQw attribute) (MDMC.trajectory_analysis.observables.sqw.SQw attribute) (MDMC.trajectory_analysis.observables.sqw.SQwCoherent attribute) (MDMC.trajectory_analysis.observables.sqw.SQwIncoherent attribute) (MDMC.trajectory_analysis.observables.SQwCoherent attribute) (MDMC.utilities.installation_tests.InstlTestBase attribute)

nbis_by_atom_type_pairs (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) neighbor_steps (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property) netCDFPDF (class in MDMC.readers.observables.netCDFPDF) netCDFSQw (class in MDMC.readers.observables.netCDFSQw) nonbonded_interactions (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.structures.Atom property) (MDMC.MD.structures.CompositeStructure property) (MDMC.MD.structures.Molecule property) (MDMC.MD.structures.Structure property) nonbonded_mix (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse property) NonBondedInteraction (class in MDMC.MD.interactions) NullResolution (class in MDMC.resolution.null) number_of_calls (MDMC.common.time_keeper.TimeKeeper attribute)

O

obs_pairs (MDMC.refinement.FoM.FoM_abs.FigureOfMerit attribute) Observable (class in MDMC.trajectory_analysis.observables.obs) observable_pairs (MDMC.control.control.Control attribute) ObservableFactory (class in MDMC.trajectory_analysis.observables.obs_factory)

ObservablePair (class in MDMC.refinement.FoM.FoM_abs) 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

p_damp (MDMC.MD.engine_facades.lammps_engine.LAMMPSEnsemble property) PackmolFiller (class in MDMC.MD.packmol.packmol_wrapper) PackmolInputExporter (class in MDMC.exporters.configurations.packmol_input) PackmolPDBReader (class in MDMC.readers.configurations.packmol_pdb) PackmolSetup (class in MDMC.MD.packmol.packmol_setup) PairDistributionFunction (class in MDMC.trajectory_analysis.observables) (class in MDMC.trajectory_analysis.observables.pdf) 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.interactions.Interaction property) (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.refinement.minimizers.minimizer_abs.Minimizer attribute) parameters_old_values (MDMC.refinement.minimizers.minimizer_abs.Minimizer attribute) parameters_values (MDMC.MD.interaction_functions.InteractionFunction property) parent_simulation (MDMC.MD.engine_facades.facade.MDEngine property) parse() (MDMC.readers.configurations.ase.ASEReader method) (MDMC.readers.configurations.cif.CIFReader method) (MDMC.readers.configurations.packmol_pdb.PackmolPDBReader method) (MDMC.readers.configurations.pdb.ProteinDataBankReader method) (MDMC.readers.observables.LAMPPDF.LAMPPDF method) (MDMC.readers.observables.LAMPSQw.LAMPSQw method) (MDMC.readers.observables.MantidSQw.MantidSQw method) (MDMC.readers.observables.MDANSESQw.MDANSESQw method) (MDMC.readers.observables.netCDFPDF.netCDFPDF method) (MDMC.readers.observables.netCDFSQw.netCDFSQw 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_dataframe() (in module MDMC.utilities.tinker_converter) 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_header() (MDMC.readers.observables.MDANSESQw.MDANSESQw method) 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_prm() (in module MDMC.utilities.tinker_converter) parse_variables() (MDMC.readers.observables.MantidSQw.MantidSQw method) partition() (in module MDMC.utilities.partitioning) partition_interactions() (in module MDMC.utilities.partitioning) PDF (in module MDMC.trajectory_analysis.observables) (MDMC.readers.observables.obs_reader.PDFReader property) (MDMC.trajectory_analysis.observables.PairDistributionFunction property) (MDMC.trajectory_analysis.observables.pdf.PairDistributionFunction property) PDF_err (MDMC.readers.observables.obs_reader.PDFReader property) (MDMC.trajectory_analysis.observables.PairDistributionFunction property) (MDMC.trajectory_analysis.observables.pdf.PairDistributionFunction property) PDFReader (class in MDMC.readers.observables.obs_reader) Periodic (class in MDMC.MD.interaction_functions) physical_property (MDMC.common.units.Unit property) PlaintextDataPrinter (class in MDMC.control.plot_results) PLOT_HEIGHT (in module MDMC.utilities.plotting) plot_progress() (in module MDMC.utilities.plotting) plot_results() (MDMC.control.control.Control method) PlotResults (class in MDMC.control.plot_results) position (MDMC.MD.structures.Molecule property) (MDMC.MD.structures.Structure property) positions (MDMC.trajectory_analysis.compact_trajectory.CompactTrajectory property) postProcess() (MDMC.trajectory_analysis.compact_trajectory.CompactTrajectory method) PPPM (class in MDMC.MD.simulation) preAllocate() (MDMC.trajectory_analysis.compact_trajectory.CompactTrajectory method) present_result() (MDMC.refinement.minimizers.minimizer_abs.Minimizer method) pressure (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYEngine property) (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYEnsemble property) (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYSimulation property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEnsemble property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property) print_data() (MDMC.control.plot_results.DataPrinter method) (MDMC.control.plot_results.IPythonDataPrinter method) (MDMC.control.plot_results.PlaintextDataPrinter method) print_header() (MDMC.control.plot_results.DataPrinter method) (MDMC.control.plot_results.IPythonDataPrinter method) (MDMC.control.plot_results.PlaintextDataPrinter method) proper_ID (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute) propers (MDMC.MD.force_fields.ff.FileForceField property) ProteinDataBankReader (class in MDMC.readers.configurations.pdb) PyLammpsAttribute (class in MDMC.MD.engine_facades.lammps_engine)

Q

Q (MDMC.readers.observables.obs_reader.SQwReader property) (MDMC.trajectory_analysis.observables.sqw.SQwMixins property)

R

r (MDMC.readers.observables.obs_reader.PDFReader property) (MDMC.trajectory_analysis.observables.PairDistributionFunction property) (MDMC.trajectory_analysis.observables.pdf.PairDistributionFunction property) Rattle (class in MDMC.MD.simulation) read() (in module MDMC.readers.configurations) read_from_file() (MDMC.trajectory_analysis.observables.obs.Observable method) read_prm() (in module MDMC.utilities.tinker_converter) read_settings() (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYAttribute method) Reader (class in MDMC.readers.reader) reader (MDMC.trajectory_analysis.observables.obs.Observable attribute) ReaderFactory (class in MDMC.readers.reader_factory) recreated_Q (MDMC.trajectory_analysis.observables.sqw.AbstractSQw property) refine() (MDMC.control.control.Control method) register() (MDMC.trajectory_analysis.observables.obs_factory.ObservableFactory class method) (MDMC.utilities.installation_tests.InstlTestFactory class method) registry (MDMC.trajectory_analysis.observables.obs_factory.ObservableFactory attribute) (MDMC.utilities.installation_tests.InstlTestFactory attribute) remove_ensemble_fixes() (MDMC.MD.engine_facades.lammps_engine.LAMMPSEnsemble method) remove_structure() (MDMC.MD.packmol.packmol_setup.PackmolSetup method) repr_decorator() (in module MDMC.common.decorators) rescale_step (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYEnsemble attribute) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEnsemble attribute) reset_config() (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYEngine method) (MDMC.MD.engine_facades.facade.MDEngine method) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method)

reset_engine() (MDMC.control.control.Control method) reset_parameters() (MDMC.refinement.minimizers.GPO.GPO method) (MDMC.refinement.minimizers.GPR.GPR method) (MDMC.refinement.minimizers.minimizer_abs.Minimizer method) (MDMC.refinement.minimizers.MMC.MMC method) Resolution (class in MDMC.resolution.resolution) ResolutionFactory (class in MDMC.resolution.resolution_factory) resolutions (MDMC.resolution.resolution_factory.ResolutionFactory attribute) resolve_density() (MDMC.MD.packmol.packmol_setup.PackmolSetup static method) rotate() (MDMC.MD.structures.CompositeStructure method) RSquared_noneerror (class in MDMC.refinement.FoM.RSquared_noneerror) run() (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYEngine method) (MDMC.MD.engine_facades.facade.MDEngine method) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method) (MDMC.MD.simulation.Simulation method) (MDMC.utilities.installation_tests.InstlTestBase method) (MDMC.utilities.installation_tests.InstlTestCore method) (MDMC.utilities.installation_tests.InstlTestDynamicPlottingDependencies method) (MDMC.utilities.installation_tests.InstlTestLAMMPS method) (MDMC.utilities.installation_tests.InstlTestX11Forwarding method) run_installation_tests() (in module MDMC.utilities.installation_tests)

S

save_config() (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYEngine method) (MDMC.MD.engine_facades.facade.MDEngine method) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method) saved_config (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYEngine property) (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_config() (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYUniverse method) (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse method) set_docstring() (in module MDMC.common.decorators) set_parameter_values() (MDMC.refinement.minimizers.GPO.GPO method) (MDMC.refinement.minimizers.GPR.GPR method) set_parameters_interactions() (MDMC.MD.interaction_functions.InteractionFunction method) set_tie() (MDMC.MD.parameters.Parameter method) setBytesPerNumber() (MDMC.trajectory_analysis.compact_trajectory.CompactTrajectory method) setCharge() (MDMC.trajectory_analysis.compact_trajectory.CompactTrajectory method) setDimensions() (MDMC.trajectory_analysis.compact_trajectory.CompactTrajectory method) settings (MDMC.MD.simulation.Simulation attribute) setup_data (MDMC.MD.packmol.packmol_wrapper.PackmolFiller property) setup_simulation() (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYEngine method) (MDMC.MD.engine_facades.facade.MDEngine method) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method) setup_universe() (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYEngine method) (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) slice_trajectory() (in module MDMC.utilities.trajectory_slicing) solvate() (MDMC.MD.simulation.Universe method) solvent_density (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) sorted_element_list() (MDMC.MD.interactions.Interaction 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) SQw (class in MDMC.trajectory_analysis.observables) (class in MDMC.trajectory_analysis.observables.sqw) (MDMC.trajectory_analysis.observables.sqw.AbstractSQw property) SQw_coh (in module MDMC.trajectory_analysis.observables) SQw_err (MDMC.trajectory_analysis.observables.sqw.AbstractSQw property) SQw_incoh (in module MDMC.trajectory_analysis.observables) SQwCoh (in module MDMC.trajectory_analysis.observables) SQwCoherent (class in MDMC.trajectory_analysis.observables) (class in MDMC.trajectory_analysis.observables.sqw) SQwIncoherent (class in MDMC.trajectory_analysis.observables.sqw) SQwIncoherentSQwIncoh (in module MDMC.trajectory_analysis.observables) SQwMixins (class in MDMC.trajectory_analysis.observables.sqw) SQwReader (class in MDMC.readers.observables.obs_reader) standardise_alias() (MDMC.MD.engine_facades.facade_factory.MDEngineFacadeFactory static method) start_logging() (in module MDMC.common.log) started (MDMC.common.time_keeper.TimeKeeper attribute) step() (MDMC.control.control.Control method) (MDMC.refinement.minimizers.GPO.GPO method) (MDMC.refinement.minimizers.GPR.GPR method) (MDMC.refinement.minimizers.minimizer_abs.Minimizer method) (MDMC.refinement.minimizers.MMC.MMC method) Structure (class in MDMC.MD.structures) structure_list (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.structures.CompositeStructure property) (MDMC.trajectory_analysis.trajectory.Configuration property) structure_type (MDMC.MD.structures.Structure property) structures (MDMC.readers.configurations.packmol_pdb.PackmolPDBReader property) subtrajectory() (MDMC.trajectory_analysis.compact_trajectory.CompactTrajectory method) success (MDMC.utilities.installation_tests.InstlTestBase attribute) (MDMC.utilities.installation_tests.InstlTestBase property) summarise_results() (MDMC.common.time_keeper.TimeKeeper method) system_state (MDMC.MD.engine_facades.lammps_engine.PyLammpsAttribute property)

T

t (MDMC.trajectory_analysis.observables.fqt.AbstractFQt property) t_damp (MDMC.MD.engine_facades.lammps_engine.LAMMPSEnsemble property) t_fraction (MDMC.MD.engine_facades.lammps_engine.LAMMPSEnsemble property) t_window (MDMC.MD.engine_facades.lammps_engine.LAMMPSEnsemble property) temperature (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYEngine property) (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYEnsemble property) (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYSimulation attribute) (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYSimulation property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEnsemble property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property) TemporalConfiguration (class in MDMC.trajectory_analysis.trajectory) thermostat (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYEngine property) (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYEnsemble property) (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYSimulation property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEnsemble property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property) tie (MDMC.MD.parameters.Parameter property) tied (MDMC.MD.parameters.Parameter property) time (MDMC.trajectory_analysis.trajectory.TemporalConfiguration attribute) time_function_execution() (in module MDMC.common.decorators) time_passed() (MDMC.common.time_keeper.TimeKeeper method) time_step (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYSimulation attribute) (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYSimulation property) (MDMC.MD.engine_facades.facade.MDEngine property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSEnsemble property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property) (MDMC.MD.simulation.Simulation attribute) (MDMC.MD.simulation.Simulation property)

TimeKeeper (class in MDMC.common.time_keeper) times (MDMC.trajectory_analysis.compact_trajectory.CompactTrajectory property) TIP3P (class in MDMC.MD.force_fields.TIP3P) TIP3PFB (class in MDMC.MD.force_fields.TIP3PFB) tolerance (MDMC.MD.packmol.packmol_setup.PackmolSetup property) top_level_structure (MDMC.MD.structures.Structure property) top_level_structure_list (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) total_time() (MDMC.common.time_keeper.TimeKeeper method) traj_step (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYSimulation attribute) (MDMC.MD.engine_facades.facade.MDEngine property) (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation attribute) (MDMC.MD.simulation.Simulation attribute) (MDMC.MD.simulation.Simulation property) trajectory (MDMC.MD.simulation.Simulation attribute) (MDMC.MD.simulation.Simulation property) translate() (MDMC.MD.structures.Structure method) trial_reduce_time_step() (MDMC.control.control.Control method)

U

uniformity_requirements (MDMC.trajectory_analysis.observables.fqt.AbstractFQt property) (MDMC.trajectory_analysis.observables.obs.Observable property) (MDMC.trajectory_analysis.observables.PairDistributionFunction property) (MDMC.trajectory_analysis.observables.pdf.PairDistributionFunction property) (MDMC.trajectory_analysis.observables.sqw.AbstractSQw 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) UNIT_VECTOR (in module MDMC.common.mathematics) UnitFloat (class in MDMC.common.units) UnitNDArray (class in MDMC.common.units) Universe (class in MDMC.MD.simulation) universe (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYSimulation attribute) (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYUniverse attribute) (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation attribute) (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute) (MDMC.MD.interactions.BondedInteraction property) (MDMC.MD.interactions.Interaction property) (MDMC.MD.interactions.NonBondedInteraction property) (MDMC.MD.simulation.Simulation attribute) (MDMC.MD.structures.Atom property) (MDMC.MD.structures.CompositeStructure property) (MDMC.MD.structures.Structure property) (MDMC.trajectory_analysis.trajectory.AtomCollection property) (MDMC.trajectory_analysis.trajectory.Configuration attribute)

update_parameters() (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYEngine method) (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYUniverse method) (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.structures.Structure method) validate_energy() (MDMC.trajectory_analysis.observables.sqw.AbstractSQw method) validate_obs() (MDMC.refinement.FoM.FoM_abs.ObservablePair method) validate_setup() (MDMC.MD.packmol.packmol_setup.PackmolSetup method) validate_structure() (MDMC.trajectory_analysis.trajectory.Configuration method) validate_value() (MDMC.MD.parameters.Parameter static method) validate_weight() (MDMC.refinement.FoM.FoM_abs.ObservablePair static method) validateTypes() (MDMC.trajectory_analysis.compact_trajectory.CompactTrajectory method)

value (MDMC.MD.parameters.Parameter property) (MDMC.refinement.FoM.FoM_abs.FigureOfMerit attribute) VBOX_HEIGHT (in module MDMC.utilities.plotting) velocities (MDMC.trajectory_analysis.compact_trajectory.CompactTrajectory property) velocity (MDMC.MD.structures.Structure property) view() (in module MDMC.gui) volume (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.structures.BoundingBox property)

W

w (MDMC.readers.observables.obs_reader.SQwReader property) (MDMC.trajectory_analysis.observables.sqw.AbstractSQw property) WaterModel (class in MDMC.MD.force_fields.ff) weakref_cache() (in module MDMC.common.decorators) weight (MDMC.refinement.FoM.FoM_abs.ObservablePair property) window_in_t() (MDMC.resolution.gaussian.GaussianResolution method) (MDMC.resolution.lorentzian.LorentzianResolution method) window_in_w() (MDMC.resolution.gaussian.GaussianResolution method) (MDMC.resolution.lorentzian.LorentzianResolution method)

wrap_docstring() (in module MDMC.common.decorators) write() (MDMC.exporters.configurations.ase.ASEExporter method) (MDMC.exporters.configurations.packmol_input.PackmolInputExporter method) (MDMC.exporters.exporter.Exporter method) write_data() (in module MDMC.utilities.tinker_converter) write_force_field_module() (in module MDMC.utilities.tinker_converter) write_history() (MDMC.refinement.minimizers.minimizer_abs.Minimizer method) writeEmptyStep() (MDMC.trajectory_analysis.compact_trajectory.CompactTrajectory method) writeOneStep() (MDMC.trajectory_analysis.compact_trajectory.CompactTrajectory method) wyckoff_symmetries() (in module MDMC.trajectory_analysis.observables.fqt)

X

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