MDMC
Overview
1. Introduction
2. Contributing to MDMC
Tutorials
Argon A-to-Z
Equilibrating simulations
Running a Refinement (in detail)
Understanding scientific units in MDMC
How-to
How to use MDMC
Installation
Reference
MDMC
Explanation
Explanation
Developer Documentation
Developer Documentation
MDMC
Index
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
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)