MDMC package
Subpackages
- MDMC.MD package
- Subpackages
- Submodules
- MDMC.MD.container module
- MDMC.MD.interaction_functions module
- MDMC.MD.interactions module
- MDMC.MD.parameters module
- MDMC.MD.simulation module
ConstraintAlgorithm
Ewald
KSpaceSolver
PPPM
Rattle
Shake
Simulation
Universe
Universe.dimensions
Universe.configuration
Universe.force_fields
Universe.kspace_solver
Universe.electrostatic_solver
Universe.dispersive_solver
Universe.constraint_algorithm
Universe.interactions
Universe.bonded_interactions
Universe.nonbonded_interactions
Universe.bonded_interaction_pairs
Universe.n_bonded
Universe.n_nonbonded
Universe.n_interactions
Universe.parameters
Universe.volume
Universe.element_list
Universe.element_dict
Universe.element_lookup
Universe.atoms
Universe.n_atoms
Universe.molecule_list
Universe.n_molecules
Universe.structure_list
Universe.top_level_structure_list
Universe.equivalent_top_level_structures_dict
Universe.force_fields
Universe.atom_types
Universe.atom_type_interactions
Universe.density
Universe.solvent_density
Universe.nbis_by_atom_type_pairs
Universe.add_bonded_interaction_pairs()
Universe.add_force_field()
Universe.add_nonbonded_interaction()
Universe.add_structure()
Universe.atom_type_interactions
Universe.atom_types
Universe.atoms
Universe.bonded_interaction_pairs
Universe.bonded_interactions
Universe.density
Universe.dimensions
Universe.element_dict
Universe.element_list
Universe.element_lookup
Universe.equivalent_top_level_structures_dict
Universe.fill()
Universe.force_fields
Universe.interactions
Universe.molecule_list
Universe.n_atoms
Universe.n_bonded
Universe.n_interactions
Universe.n_molecules
Universe.n_nonbonded
Universe.nbis_by_atom_type_pairs
Universe.nonbonded_interactions
Universe.parameters
Universe.solvate()
Universe.solvent_density
Universe.structure_list
Universe.top_level_structure_list
Universe.volume
- MDMC.MD.structures module
Atom
BoundingBox
CompositeStructure
Molecule
Structure
Structure.atoms
Structure.bonded_interaction_pairs
Structure.bonded_interactions
Structure.bounding_box
Structure.copy()
Structure.interactions
Structure.is_equivalent()
Structure.nonbonded_interactions
Structure.position
Structure.structure_type
Structure.top_level_structure
Structure.translate()
Structure.universe
Structure.valid_position()
Structure.velocity
filter_atoms()
filter_atoms_element()
get_reduced_chemical_formula()
- Module contents
- MDMC.common package
- MDMC.control package
- Submodules
- MDMC.control.control module
Control
Control.simulation
Control.exp_datasets
Control.fit_parameters
Control.minimizer
Control.observable_pairs
Control.FoM_calculator
Control.MD_steps
Control.calculate_max_FoM()
Control.engine_recovery_from_equil()
Control.equilibrate()
Control.minimize()
Control.plot_results()
Control.refine()
Control.reset_engine()
Control.step()
Control.trial_reduce_time_step()
- MDMC.control.plot_results module
- Module contents
- MDMC.exporters package
- MDMC.gui package
- MDMC.readers package
- Subpackages
- MDMC.readers.configurations package
- MDMC.readers.observables package
- Submodules
- MDMC.readers.observables.LAMPPDF module
- MDMC.readers.observables.LAMPSQw module
- MDMC.readers.observables.MDANSESQw module
- MDMC.readers.observables.MantidSQw 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
- Module contents
- Submodules
- MDMC.readers.reader module
- MDMC.readers.reader_factory module
- Module contents
- Subpackages
- MDMC.refinement package
- MDMC.resolution package
- MDMC.trajectory_analysis package
- Subpackages
- MDMC.trajectory_analysis.observables package
- Submodules
- 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
- Module contents
- MDMC.trajectory_analysis.observables package
- Submodules
- MDMC.trajectory_analysis.compact_trajectory module
CompactTrajectory
CompactTrajectory.data
CompactTrajectory.exportAtom()
CompactTrajectory.filter_by_element()
CompactTrajectory.filter_by_time()
CompactTrajectory.filter_by_type()
CompactTrajectory.labelAtoms()
CompactTrajectory.positions
CompactTrajectory.postProcess()
CompactTrajectory.preAllocate()
CompactTrajectory.setBytesPerNumber()
CompactTrajectory.setCharge()
CompactTrajectory.setDimensions()
CompactTrajectory.subtrajectory()
CompactTrajectory.times
CompactTrajectory.validateTypes()
CompactTrajectory.velocities
CompactTrajectory.writeEmptyStep()
CompactTrajectory.writeOneStep()
configurations_as_compact_trajectory()
- MDMC.trajectory_analysis.trajectory module
AtomCollection
Configuration
Configuration.element_set
Configuration.universe
Configuration.data
Configuration.add_structure()
Configuration.atom_positions
Configuration.atom_velocities
Configuration.atoms
Configuration.data
Configuration.element_list
Configuration.element_set
Configuration.filter_atoms()
Configuration.filter_by_element()
Configuration.filter_structures()
Configuration.molecule_list
Configuration.scale()
Configuration.structure_list
Configuration.validate_structure()
TemporalConfiguration
- Module contents
- Subpackages
- MDMC.utilities package
- Submodules
- 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
- Module contents
Module contents
MDMC is a Python 3 package for optimising classical molecular dynamics (MD) potential parameters by refining against experimental data, particularly dynamical data such as the dynamic structure factor. The refinement uses derivative free optimisation algorithms, e.g. Monte Carlo (MC).
Documentation
MDMC has three different forms of documentation:
docstrings provided within the code, such as this one. These can viewed from the Python command shell (REPL) by calling the
help()
function on the class, function, method or object. In an interactive (ipython) command shell,?
can also be used after a class, function, method or object.Online documentation, built from /doc, and available on the MDMC homepage.
Interactive (Jupyter notebook) tutorials, available within /doc/tutorials, which provide in dept descriptions and examples of specific features of MDMC.
Available subpackages
- common
Functions and classes common to all subpackages
- control
Uses refinement and MD subpackages to control MDMC parameter optimisation
- gui
Provides GUI functionality
- MD
Molecular dynamics tools and engine interfaces
- readers
Atomic configuration and experimental observable file readers
- refinement
Algorithms for refining parameters
- trajectory_analysis
Tools related to creating trajectories and calculating observables from them
Logging
By default MDMC will log a single process regardless of whether it is being run in serial or parallel. The process will log to ‘MDMC.log’.