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.ConstraintAlgorithm attribute) (MDMC.MD.KSpaceSolver attribute) (MDMC.MD.simulation.ConstraintAlgorithm attribute) (MDMC.MD.simulation.KSpaceSolver attribute) add_atoms() (MDMC.MD.BondedInteraction method) (MDMC.MD.interactions.BondedInteraction method) add_bonded_interaction_pairs() (MDMC.MD.simulation.Universe method) (MDMC.MD.Universe method) add_box() (MDMC.MD.packmol.packmol_setup.PackmolSetup method) (MDMC.MD.packmol.PackmolSetup method) add_container() (MDMC.MD.packmol.packmol_setup.PackmolSetup method) (MDMC.MD.packmol.PackmolSetup method) add_cube() (MDMC.MD.packmol.packmol_setup.PackmolSetup method) (MDMC.MD.packmol.PackmolSetup method) add_fixed_structure() (MDMC.MD.packmol.packmol_setup.PackmolSetup method) (MDMC.MD.packmol.PackmolSetup method) add_force_field() (MDMC.MD.simulation.Universe method) (MDMC.MD.Universe method) add_interaction() (MDMC.MD.Atom method) (MDMC.MD.structures.Atom method) add_nonbonded_interaction() (MDMC.MD.simulation.Universe method) (MDMC.MD.Universe method) add_sphere() (MDMC.MD.packmol.packmol_setup.PackmolSetup method) (MDMC.MD.packmol.PackmolSetup method) add_structure() (MDMC.MD.simulation.Universe method) (MDMC.MD.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 method) (MDMC.MD.parameters.Parameters method) apply() (MDMC.resolution.FileResolution method) (MDMC.resolution.from_file.FileResolution method) (MDMC.resolution.gaussian.GaussianResolution method) (MDMC.resolution.GaussianResolution method) (MDMC.resolution.lorentzian.LorentzianResolution method) (MDMC.resolution.LorentzianResolution method) (MDMC.resolution.null.NullResolution method) (MDMC.resolution.NullResolution method) (MDMC.resolution.Resolution 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 attribute) (MDMC.MD.parameters.Parameters attribute) as_array (MDMC.MD.Parameters property) (MDMC.MD.parameters.Parameters property) ASE_to_MDMC() (in module MDMC.MD.ase.convert) ASEExporter (class in MDMC.exporters.configurations) (class in MDMC.exporters.configurations.ase) ASEReader (class in MDMC.readers.configurations) (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) (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.Atom property) (MDMC.MD.structures.Atom property) atom_type_interactions (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.Universe attribute) (MDMC.MD.Universe property) atom_type_properties (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute) atom_types (MDMC.MD.BondedInteraction property) (MDMC.MD.Coulombic property) (MDMC.MD.Dispersion property) (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.NonBondedInteraction property) (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.Universe attribute) (MDMC.MD.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.Atom property) (MDMC.MD.BondedInteraction property) (MDMC.MD.container.AtomContainer attribute) (MDMC.MD.container.AtomContainer property) (MDMC.MD.Coulombic property) (MDMC.MD.Dispersion property) (MDMC.MD.force_fields.ff.FileForceField property) (MDMC.MD.Interaction 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.Structure property) (MDMC.MD.structures.Atom property) (MDMC.MD.structures.Structure property) (MDMC.MD.Universe attribute) (MDMC.MD.Universe property) (MDMC.readers.configurations.conf_reader.ConfigurationReader property) (MDMC.readers.configurations.pdb.ProteinDataBankReader property) (MDMC.readers.configurations.ProteinDataBankReader property) (MDMC.trajectory_analysis.trajectory.Configuration property) auto_equilibrate() (MDMC.control.Control method) (MDMC.control.control.Control method) (MDMC.MD.Simulation method) (MDMC.MD.simulation.Simulation method) available_names() (MDMC.common.factory.Factory class 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) BEST (MDMC.control.control.Dump attribute) Bond (class in MDMC.MD) (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) (class in MDMC.MD.interactions) bonded_interaction_pairs (MDMC.MD.Atom property) (MDMC.MD.CompositeStructure property) (MDMC.MD.Molecule property) (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.Structure property) (MDMC.MD.structures.Atom property) (MDMC.MD.structures.CompositeStructure property) (MDMC.MD.structures.Molecule property) (MDMC.MD.structures.Structure property) (MDMC.MD.Universe attribute) (MDMC.MD.Universe property)

bonded_interactions (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.Structure property) (MDMC.MD.structures.Structure property) (MDMC.MD.Universe attribute) (MDMC.MD.Universe property) BondedInteraction (class in MDMC.MD) (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) (MDMC.readers.configurations.ProteinDataBankReader property) bounding_box (MDMC.MD.Structure property) (MDMC.MD.structures.Structure property) BoundingBox (class in MDMC.MD) (class in MDMC.MD.structures) Buckingham (class in MDMC.MD) (class in MDMC.MD.interaction_functions)

C

calc_CoM() (MDMC.MD.CompositeStructure method) (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 method) (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.Atom property) (MDMC.MD.Molecule property) (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) (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) (class in MDMC.MD.structures) Configuration (class in MDMC.trajectory_analysis.trajectory) configuration (MDMC.MD.simulation.Universe attribute) (MDMC.MD.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) (class in MDMC.MD.interactions) constrained (MDMC.MD.ConstrainableMixin attribute) (MDMC.MD.interactions.ConstrainableMixin attribute) constraint_algorithm (MDMC.MD.simulation.Universe attribute) (MDMC.MD.Universe attribute) ConstraintAlgorithm (class in MDMC.MD) (class in MDMC.MD.simulation)

constraints (MDMC.MD.Parameter property) (MDMC.MD.parameters.Parameter property) Control (class in MDMC.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.Atom method) (MDMC.MD.CompositeStructure method) (MDMC.MD.Structure method) (MDMC.MD.structures.Atom method) (MDMC.MD.structures.CompositeStructure method) (MDMC.MD.structures.Structure method) copy_interactions() (MDMC.MD.Atom method) (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) (class in MDMC.MD.interaction_functions) Coulombic (class in MDMC.MD) (class in MDMC.MD.interactions) couls (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute) create() (MDMC.common.factory.Factory class method) (MDMC.trajectory_analysis.observables.obs_factory.ObservableFactory class method) (MDMC.utilities.installation_tests.InstlTestFactory class method) create_bond() (MDMC.readers.configurations.pdb.ProteinDataBankReader method) (MDMC.readers.configurations.ProteinDataBankReader method) create_bounds() (MDMC.refinement.minimizers.GPR.GPR static method) create_box_data() (in module MDMC.exporters.trajectories.H5MD_build) create_cornerplot() (MDMC.control.plot_results.PlotResults method) (MDMC.control.PlotResults method) create_empty_groups() (in module MDMC.exporters.trajectories.H5MD_build) create_executor() (in module MDMC.trajectory_analysis.observables.concurrency_tools) create_facade() (MDMC.MD.engine_facades.facade_factory.MDEngineFacadeFactory static method) create_from_h5md() (MDMC.trajectory_analysis.compact_trajectory.CompactTrajectory static method) create_instance() (MDMC.resolution.resolution_factory.ResolutionFactory class method) (MDMC.resolution.ResolutionFactory class method) create_list_of_element_objects() (in module MDMC.common.periodictable_objects) create_logger() (in module MDMC.common.log) create_metadata_group() (in module MDMC.exporters.trajectories.H5MD_build) create_parameter_data() (in module MDMC.exporters.trajectories.H5MD_build) create_parameter_point_array() (MDMC.refinement.minimizers.GPR.GPR method) create_reader_from_ext() (MDMC.readers.configurations.conf_reader_factory.ConfigurationReaderFactory class method) create_simulation_data() (in module MDMC.exporters.trajectories.H5MD_build) create_units() (in module MDMC.common.units) curr_pack (MDMC.common.factory.ModuleFactory attribute), [1] (MDMC.MD.force_fields.force_field_factory.ForceFieldFactory attribute) (MDMC.readers.configurations.conf_reader_factory.ConfigurationReaderFactory attribute) (MDMC.readers.observables.obs_reader_factory.ObservableReaderFactory attribute) (MDMC.refinement.FoM.FoM_factory.FoMFactory attribute) (MDMC.refinement.minimizers.minimizer_factory.MinimizerFactory attribute) (MDMC.resolution.resolution_factory.ResolutionFactory attribute) (MDMC.resolution.ResolutionFactory attribute) curr_path (MDMC.common.factory.ModuleFactory attribute), [1] (MDMC.MD.force_fields.force_field_factory.ForceFieldFactory attribute) (MDMC.readers.configurations.conf_reader_factory.ConfigurationReaderFactory attribute) (MDMC.readers.observables.obs_reader_factory.ObservableReaderFactory attribute) (MDMC.refinement.FoM.FoM_factory.FoMFactory attribute) (MDMC.refinement.minimizers.minimizer_factory.MinimizerFactory attribute) (MDMC.resolution.resolution_factory.ResolutionFactory attribute) (MDMC.resolution.ResolutionFactory attribute) cutoff (MDMC.MD.interactions.NonBondedInteraction property) (MDMC.MD.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) (MDMC.MD.Universe attribute) (MDMC.MD.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) (class in MDMC.MD.interactions) dimensions (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.Universe attribute) (MDMC.MD.Universe property) (MDMC.trajectory_analysis.trajectory.AtomCollection property) Dispersion (class in MDMC.MD) (class in MDMC.MD.interactions) dispersions (MDMC.MD.force_fields.ff.FileForceField property) dispersive_solver (MDMC.MD.simulation.Universe attribute) (MDMC.MD.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) Dump (class in MDMC.control.control) dump_h5md() (MDMC.control.Control method) (MDMC.control.control.Control method) 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) (MDMC.MD.Universe attribute) element (MDMC.MD.Atom attribute) (MDMC.MD.structures.Atom attribute) element_dict (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.Universe attribute) (MDMC.MD.Universe property) element_list (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.Universe attribute) (MDMC.MD.Universe property) (MDMC.trajectory_analysis.trajectory.Configuration property) element_list() (MDMC.MD.BondedInteraction method) (MDMC.MD.Coulombic method) (MDMC.MD.Dispersion method) (MDMC.MD.Interaction method) (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) (MDMC.MD.Universe attribute) (MDMC.MD.Universe property) element_set (MDMC.trajectory_analysis.trajectory.Configuration attribute), [1] element_tuple() (MDMC.MD.Interaction method) (MDMC.MD.interactions.Interaction method) enforcing_minimizer_compatibility() (MDMC.refinement.minimizers.minimizer_abs.Minimizer method) engine (MDMC.MD.Simulation attribute) (MDMC.MD.simulation.Simulation attribute) engine_recovery_from_equil() (MDMC.control.Control method) (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 method) (MDMC.control.control.Control method) equivalent_top_level_structures_dict (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.Universe attribute) (MDMC.MD.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) EVERY (MDMC.control.control.Dump attribute) Ewald (class in MDMC.MD) (class in MDMC.MD.simulation) exclude (MDMC.common.factory.ModuleFactory attribute), [1] (MDMC.MD.force_fields.force_field_factory.ForceFieldFactory attribute) (MDMC.readers.configurations.conf_reader_factory.ConfigurationReaderFactory attribute) (MDMC.readers.observables.obs_reader_factory.ObservableReaderFactory attribute) (MDMC.refinement.FoM.FoM_factory.FoMFactory attribute) (MDMC.refinement.minimizers.minimizer_factory.MinimizerFactory attribute) (MDMC.resolution.resolution_factory.ResolutionFactory attribute) (MDMC.resolution.ResolutionFactory attribute) execution_time (MDMC.common.time_keeper.TimeKeeper attribute) exp_datasets (MDMC.control.Control attribute) (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.ASEReader attribute) (MDMC.readers.configurations.cif.CIFReader attribute) (MDMC.readers.configurations.CIFReader attribute) (MDMC.readers.configurations.packmol_pdb.PackmolPDBReader attribute) (MDMC.readers.configurations.PackmolPDBReader attribute) (MDMC.readers.configurations.pdb.ProteinDataBankReader attribute) (MDMC.readers.configurations.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

Factory (class in MDMC.common.factory) 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.configurations.ASEReader attribute) (MDMC.readers.configurations.CIFReader attribute) (MDMC.readers.configurations.PackmolPDBReader attribute) (MDMC.readers.configurations.ProteinDataBankReader attribute) (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) (class in MDMC.resolution.from_file) fill() (MDMC.MD.simulation.Universe method) (MDMC.MD.Universe method) fill_with_packmol() (MDMC.MD.packmol.packmol_wrapper.PackmolFiller method) (MDMC.MD.packmol.PackmolFiller method) filled_universe (MDMC.MD.packmol.packmol_wrapper.PackmolFiller property) (MDMC.MD.packmol.PackmolFiller property) filter() (MDMC.MD.Parameters method) (MDMC.MD.parameters.Parameters method) filter_atom_attribute() (MDMC.MD.Parameters method) (MDMC.MD.parameters.Parameters method) filter_atoms() (in module MDMC.MD) (in module MDMC.MD.structures) (MDMC.trajectory_analysis.trajectory.Configuration method) filter_atoms_element() (in module MDMC.MD) (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 method) (MDMC.MD.parameters.Parameters method) filter_interaction() (MDMC.MD.Parameters method) (MDMC.MD.parameters.Parameters method)

filter_name() (MDMC.MD.Parameters method) (MDMC.MD.parameters.Parameters method) filter_ordered_dataframe() (in module MDMC.common.df_operations) filter_structure() (MDMC.MD.Parameters method) (MDMC.MD.parameters.Parameters method) filter_structures() (MDMC.trajectory_analysis.trajectory.Configuration method) filter_value() (MDMC.MD.Parameters method) (MDMC.MD.parameters.Parameters method) fit_parameters (MDMC.control.Control attribute) (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 attribute) (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) (MDMC.MD.Universe attribute), [1] (MDMC.MD.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.CompositeStructure property) (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.Interaction property) (MDMC.MD.interactions.Interaction property) function_called() (MDMC.common.time_keeper.TimeKeeper method) function_name (MDMC.MD.Interaction property) (MDMC.MD.interactions.Interaction property)

G

gaussian() (in module MDMC.common.resolution_functions) GaussianResolution (class in MDMC.resolution) (class in MDMC.resolution.gaussian) get() (MDMC.common.factory.Factory class method) get_max_sizes() (MDMC.MD.packmol.packmol_setup.PackmolSetup method) (MDMC.MD.packmol.PackmolSetup method) get_measured_points() (MDMC.control.plot_results.PlotResults method) (MDMC.control.PlotResults method) get_packmol_files_path() (MDMC.MD.packmol.packmol_wrapper.PackmolFiller method) (MDMC.MD.packmol.PackmolFiller method) get_packmol_output_path() (MDMC.MD.packmol.packmol_wrapper.PackmolFiller method) (MDMC.MD.packmol.PackmolFiller method) get_packmol_path() (MDMC.MD.packmol.packmol_wrapper.PackmolFiller static method) (MDMC.MD.packmol.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) (in module MDMC.MD.structures) get_settings() (MDMC.MD.packmol.packmol_setup.PackmolSetup method) (MDMC.MD.packmol.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) (MDMC.MD.packmol.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) H5MD_DATA (in module MDMC.exporters.trajectories.H5MD_build) h_bar (in module MDMC.common.constants) HANDLED_PARAMS (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYEngine attribute) HarmonicPotential (class in MDMC.MD) (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.DihedralAngle attribute) (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) (MDMC.exporters.configurations.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) (in module MDMC.MD.interaction_functions) Interaction (class in MDMC.MD) (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) (class in MDMC.MD.interaction_functions) interactions (MDMC.MD.Parameter property) (MDMC.MD.parameters.Parameter property) (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.Structure property) (MDMC.MD.structures.Structure property) (MDMC.MD.Universe attribute) (MDMC.MD.Universe property) IntermediateScatteringFunction (in module MDMC.trajectory_analysis.observables) IPythonDataPrinter (class in MDMC.control.plot_results) is_atom() (in module MDMC.utilities.structures) is_best_FoM() (MDMC.refinement.minimizers.minimizer_abs.Minimizer method) is_equivalent() (MDMC.MD.Atom method) (MDMC.MD.Bond method) (MDMC.MD.BondAngle method) (MDMC.MD.BondedInteraction method) (MDMC.MD.Dispersion method) (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.Molecule method) (MDMC.MD.NonBondedInteraction method) (MDMC.MD.Structure method) (MDMC.MD.structures.Atom method) (MDMC.MD.structures.Molecule method) (MDMC.MD.structures.Structure method)

K

kspace_solver (MDMC.MD.simulation.Universe attribute) (MDMC.MD.Universe attribute)

KSpaceSolver (class in MDMC.MD) (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) (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 method) (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) (class in MDMC.resolution.lorentzian)

M

main() (in module MDMC.utilities.cli) MantidSQw (class in MDMC.readers.observables.MantidSQw) mass (MDMC.MD.Atom property) (MDMC.MD.Molecule property) (MDMC.MD.structures.Atom property) (MDMC.MD.structures.Molecule property) max (MDMC.MD.BoundingBox property) (MDMC.MD.structures.BoundingBox property) max_iterations (MDMC.MD.ConstraintAlgorithm property) (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 attribute) (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.factory module MDMC.common.log module MDMC.common.mathematics module MDMC.common.periodictable_objects 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.exporters.trajectories module MDMC.exporters.trajectories.H5MD_build 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.H5MD_reader 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.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.BoundingBox property) (MDMC.MD.structures.BoundingBox property) minimize() (MDMC.control.Control method) (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 method) (MDMC.MD.simulation.Simulation method) Minimizer (class in MDMC.refinement.minimizers.minimizer_abs) minimizer (MDMC.control.Control attribute) (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.factory MDMC.common.log MDMC.common.mathematics MDMC.common.periodictable_objects 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.exporters.trajectories MDMC.exporters.trajectories.H5MD_build 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.H5MD_reader 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.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 ModuleFactory (class in MDMC.common.factory) Molecule (class in MDMC.MD) (class in MDMC.MD.structures) molecule_list (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.Universe attribute) (MDMC.MD.Universe property) (MDMC.trajectory_analysis.trajectory.Configuration property)

N

n_atoms (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.Universe attribute) (MDMC.MD.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) (MDMC.MD.Universe attribute) (MDMC.MD.Universe property) n_interactions (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.Universe attribute) (MDMC.MD.Universe property) n_molecules (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.Universe attribute) (MDMC.MD.Universe property) n_nonbonded (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.Universe attribute) (MDMC.MD.Universe property) N_TEXT_LINES (in module MDMC.utilities.plotting) name (MDMC.MD.ConstraintAlgorithm property) (MDMC.MD.interaction_functions.InteractionFunction property) (MDMC.MD.InteractionFunction property) (MDMC.MD.KSpaceSolver property) (MDMC.MD.simulation.ConstraintAlgorithm property) (MDMC.MD.simulation.KSpaceSolver property) (MDMC.trajectory_analysis.observables.obs.Observable property) (MDMC.utilities.installation_tests.InstlTestBase attribute)

nbis_by_atom_type_pairs (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.Universe attribute) (MDMC.MD.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.Atom property) (MDMC.MD.CompositeStructure property) (MDMC.MD.Molecule property) (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.Structure property) (MDMC.MD.structures.Atom property) (MDMC.MD.structures.CompositeStructure property) (MDMC.MD.structures.Molecule property) (MDMC.MD.structures.Structure property) (MDMC.MD.Universe attribute) (MDMC.MD.Universe property) nonbonded_mix (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse property) NonBondedInteraction (class in MDMC.MD) (class in MDMC.MD.interactions) NONE (MDMC.control.control.Dump attribute) NullResolution (class in MDMC.resolution) (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 attribute) (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) (class in MDMC.MD.packmol.packmol_wrapper) PackmolInputExporter (class in MDMC.exporters.configurations) (class in MDMC.exporters.configurations.packmol_input) PackmolPDBReader (class in MDMC.readers.configurations) (class in MDMC.readers.configurations.packmol_pdb) PackmolSetup (class in MDMC.MD.packmol) (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) (class in MDMC.MD.parameters) parameterize_interactions() (MDMC.MD.force_fields.ff.ForceField method) Parameters (class in MDMC.MD) (class in MDMC.MD.parameters) parameters (MDMC.MD.Interaction property) (MDMC.MD.interaction_functions.InteractionFunction property) (MDMC.MD.InteractionFunction property) (MDMC.MD.interactions.Interaction property) (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.Universe attribute) (MDMC.MD.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) (MDMC.MD.InteractionFunction property) parent_simulation (MDMC.MD.engine_facades.facade.MDEngine property) parse() (MDMC.readers.configurations.ase.ASEReader method) (MDMC.readers.configurations.ASEReader method) (MDMC.readers.configurations.cif.CIFReader method) (MDMC.readers.configurations.CIFReader method) (MDMC.readers.configurations.packmol_pdb.PackmolPDBReader method) (MDMC.readers.configurations.PackmolPDBReader method) (MDMC.readers.configurations.pdb.ProteinDataBankReader method) (MDMC.readers.configurations.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) particles_file_path() (in module MDMC.readers.H5MD_reader) 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) (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 method) (MDMC.control.control.Control method) PlotResults (class in MDMC.control) (class in MDMC.control.plot_results) position (MDMC.MD.Molecule property) (MDMC.MD.Structure property) (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) (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) (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) (class in MDMC.MD.simulation) read() (in module MDMC.readers.configurations) read_all_data() (in module MDMC.readers.H5MD_reader) read_box_property() (in module MDMC.readers.H5MD_reader) read_dataset() (in module MDMC.readers.H5MD_reader) read_from_file() (MDMC.trajectory_analysis.observables.obs.Observable method) read_number_steps() (in module MDMC.readers.H5MD_reader) read_prm() (in module MDMC.utilities.tinker_converter) read_settings() (MDMC.MD.engine_facades.dlpoly_engine.DLPOLYAttribute method) read_times() (in module MDMC.readers.H5MD_reader) read_units() (in module MDMC.readers.H5MD_reader) Reader (class in MDMC.readers.reader) reader (MDMC.trajectory_analysis.observables.obs.Observable attribute) recreated_Q (MDMC.trajectory_analysis.observables.sqw.AbstractSQw property) refine() (MDMC.control.Control method) (MDMC.control.control.Control method) register() (MDMC.common.factory.RegisterFactory class method) RegisterFactory (class in MDMC.common.factory) registry (MDMC.common.factory.Factory attribute) (MDMC.MD.force_fields.force_field_factory.ForceFieldFactory attribute) (MDMC.readers.configurations.conf_reader_factory.ConfigurationReaderFactory attribute) (MDMC.readers.observables.obs_reader_factory.ObservableReaderFactory attribute) (MDMC.refinement.FoM.FoM_factory.FoMFactory attribute) (MDMC.refinement.minimizers.minimizer_factory.MinimizerFactory attribute) (MDMC.resolution.resolution_factory.ResolutionFactory attribute) (MDMC.resolution.ResolutionFactory attribute) (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) (MDMC.MD.packmol.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 method) (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) (class in MDMC.resolution.resolution) ResolutionFactory (class in MDMC.resolution) (class in MDMC.resolution.resolution_factory) resolve_density() (MDMC.MD.packmol.packmol_setup.PackmolSetup static method) (MDMC.MD.packmol.PackmolSetup static method) rotate() (MDMC.MD.CompositeStructure method) (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 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) (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) scan() (MDMC.common.factory.ModuleFactory class method) (MDMC.refinement.FoM.FoM_factory.FoMFactory class 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) (MDMC.MD.InteractionFunction method) set_tie() (MDMC.MD.Parameter method) (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 attribute) (MDMC.MD.simulation.Simulation attribute) setup_data (MDMC.MD.packmol.packmol_wrapper.PackmolFiller property) (MDMC.MD.packmol.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) (class in MDMC.MD.simulation) Simulation (class in MDMC.MD) (class in MDMC.MD.simulation) simulation (MDMC.control.Control attribute) (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) (MDMC.MD.Universe method) solvent_density (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.Universe attribute) (MDMC.MD.Universe property)

sorted_element_list() (MDMC.MD.Interaction method) (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 method) (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) (class in MDMC.MD.structures) structure_list (MDMC.MD.CompositeStructure property) (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.structures.CompositeStructure property) (MDMC.MD.Universe attribute) (MDMC.MD.Universe property) (MDMC.trajectory_analysis.trajectory.Configuration property) structure_type (MDMC.MD.Structure property) (MDMC.MD.structures.Structure property) structures (MDMC.readers.configurations.packmol_pdb.PackmolPDBReader property) (MDMC.readers.configurations.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) supported_types() (MDMC.common.factory.Factory class 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.Parameter property) (MDMC.MD.parameters.Parameter property) tied (MDMC.MD.Parameter property) (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 attribute) (MDMC.MD.Simulation 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) (MDMC.MD.packmol.PackmolSetup property) top_level_structure (MDMC.MD.Structure property) (MDMC.MD.structures.Structure property) top_level_structure_list (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.Universe attribute) (MDMC.MD.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 attribute) (MDMC.MD.Simulation property) (MDMC.MD.simulation.Simulation attribute) (MDMC.MD.simulation.Simulation property) trajectory (MDMC.MD.Simulation attribute) (MDMC.MD.Simulation property) (MDMC.MD.simulation.Simulation attribute) (MDMC.MD.simulation.Simulation property) translate() (MDMC.MD.Structure method) (MDMC.MD.structures.Structure method) trial_reduce_time_step() (MDMC.control.Control method) (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) (class in MDMC.MD.simulation) universe (MDMC.MD.Atom property) (MDMC.MD.BondedInteraction property) (MDMC.MD.CompositeStructure property) (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.Interaction property) (MDMC.MD.interactions.BondedInteraction property) (MDMC.MD.interactions.Interaction property) (MDMC.MD.interactions.NonBondedInteraction property) (MDMC.MD.NonBondedInteraction property) (MDMC.MD.Simulation attribute) (MDMC.MD.simulation.Simulation attribute) (MDMC.MD.Structure property) (MDMC.MD.structures.Atom property) (MDMC.MD.structures.CompositeStructure property) (MDMC.MD.structures.Structure property) (MDMC.trajectory_analysis.trajectory.AtomCollection property)

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.Structure method) (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) (MDMC.MD.packmol.PackmolSetup method) validate_structure() (MDMC.trajectory_analysis.trajectory.Configuration method) validate_value() (MDMC.MD.Parameter static method) (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.Parameter property) (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.Structure property) (MDMC.MD.structures.Structure property) view() (in module MDMC.gui) volume (MDMC.MD.BoundingBox property) (MDMC.MD.simulation.Universe attribute) (MDMC.MD.simulation.Universe property) (MDMC.MD.structures.BoundingBox property) (MDMC.MD.Universe attribute) (MDMC.MD.Universe 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.GaussianResolution method) (MDMC.resolution.lorentzian.LorentzianResolution method) (MDMC.resolution.LorentzianResolution method) window_in_w() (MDMC.resolution.gaussian.GaussianResolution method) (MDMC.resolution.GaussianResolution method) (MDMC.resolution.lorentzian.LorentzianResolution method) (MDMC.resolution.LorentzianResolution method)

wrap_docstring() (in module MDMC.common.decorators) write() (MDMC.exporters.configurations.ase.ASEExporter method) (MDMC.exporters.configurations.ASEExporter method) (MDMC.exporters.configurations.packmol_input.PackmolInputExporter method) (MDMC.exporters.configurations.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_H5MD() (in module MDMC.exporters.trajectories.H5MD_build) 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)