MDMC
Overview
1. Introduction
2. Installation
3. Simulations
4. Parameter Refinement
5. Contributing to MDMC
Tutorials
Building an MDMC Universe
Reading atoms from configuration files
Units in MDMC
Applying a
ForceField
Solvating an MDMC Universe
Molecular Visualization
Running a Simulation in MDMC
Creating an Observable from a Simulation
Selecting Fitting Parameters
Running a Refinement
Argon A-to-Z
Developer Documentation
Overview
Coding Standards
Documentation Standards
Units
Testing
MDMC Software Management
Containers
Debugging inside Containers
Recipes for ‘simple’ additions
Modules
common
control
gui
MD
readers
refinement
trajectory_analysis
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)
accuracy (MDMC.MD.simulation.ConstraintAlgorithm attribute)
(MDMC.MD.simulation.KSpaceSolver attribute)
add_bonded_interaction_pairs() (MDMC.MD.simulation.Universe method)
add_force_field() (MDMC.MD.simulation.Universe method)
add_interaction() (MDMC.MD.structural_units.Atom method)
add_nonbonded_interaction() (MDMC.MD.simulation.Universe method)
add_structural_unit() (MDMC.MD.simulation.Universe method)
(MDMC.trajectory_analysis.trajectory.Configuration method)
ang_momentum_steps (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property)
angle_ID (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute)
angles (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute)
apply_constraints() (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse method)
apply_ensemble_fixes() (MDMC.MD.engine_facades.lammps_engine.Ensemble method)
ase_read_cif() (in module MDMC.MD.ase.cif)
ASEAtoms (class in MDMC.MD.ase.conversions)
Atom (class in MDMC.MD.structural_units)
atom_dict (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute)
atom_lines() (MDMC.MD.ase.conversions.X3D method)
atom_positions (MDMC.trajectory_analysis.trajectory.Configuration property)
atom_type (MDMC.MD.structural_units.Atom property)
atom_type_interactions (MDMC.MD.simulation.Universe property)
atom_type_properties (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute)
atom_types (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute)
(MDMC.MD.simulation.Universe property)
atom_velocities (MDMC.trajectory_analysis.trajectory.Configuration property)
AtomCollection (class in MDMC.trajectory_analysis.trajectory)
AtomContainer (class in MDMC.MD.container)
atoms (MDMC.MD.container.AtomContainer attribute)
(MDMC.MD.container.AtomContainer property)
(MDMC.MD.force_fields.ff.FileForceField property)
(MDMC.MD.simulation.Universe property)
(MDMC.MD.structural_units.Atom property)
(MDMC.MD.structural_units.StructuralUnit property)
(MDMC.readers.configurations.cif.CIF property)
(MDMC.readers.configurations.conf_reader.ConfigurationReader property)
(MDMC.trajectory_analysis.trajectory.Configuration property)
(MDMC.trajectory_analysis.trajectory.Trajectory property)
B
barostat (MDMC.MD.engine_facades.lammps_engine.Ensemble property)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine property)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property)
base (MDMC.common.units.Unit property)
base_class() (MDMC.readers.configurations.conf_reader_factory.ConfigurationReaderFactory static method)
(MDMC.readers.observables.obs_reader_factory.ObservableReaderFactory static method)
(MDMC.readers.reader_factory.ReaderFactory static method)
bond_angles (MDMC.MD.force_fields.ff.FileForceField property)
bond_ID (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute)
bond_lines() (MDMC.MD.ase.conversions.X3D method)
bonded_interaction_pairs (MDMC.MD.simulation.Universe property)
(MDMC.MD.structural_units.Atom property)
(MDMC.MD.structural_units.CompositeStructuralUnit property)
(MDMC.MD.structural_units.Molecule property)
(MDMC.MD.structural_units.StructuralUnit property)
bonded_interactions (MDMC.MD.simulation.Universe property)
(MDMC.MD.structural_units.StructuralUnit property)
bonds (MDMC.MD.ase.conversions.ASEAtoms attribute)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute)
(MDMC.MD.force_fields.ff.FileForceField property)
bounding_box (MDMC.MD.structural_units.StructuralUnit property)
BoundingBox (class in MDMC.MD.structural_units)
Buckingham (class in MDMC.MD.interaction_functions)
C
calculate_dt() (MDMC.trajectory_analysis.observables.SQw method)
calculate_E() (MDMC.trajectory_analysis.observables.SQw static method)
calculate_from_MD() (MDMC.trajectory_analysis.observables.obs.Observable method)
charge (MDMC.MD.structural_units.Atom property)
CIF (class in MDMC.readers.configurations.cif)
components (MDMC.common.units.Unit attribute)
CompositeStructuralUnit (class in MDMC.MD.structural_units)
Configuration (class in MDMC.trajectory_analysis.trajectory)
configuration (MDMC.MD.simulation.Universe attribute)
ConfigurationReader (class in MDMC.readers.configurations.conf_reader)
ConfigurationReaderFactory (class in MDMC.readers.configurations.conf_reader_factory)
configurations (MDMC.trajectory_analysis.trajectory.Trajectory attribute)
(MDMC.trajectory_analysis.trajectory.Trajectory property)
constraint_algorithm (MDMC.MD.simulation.Universe attribute)
ConstraintAlgorithm (class in MDMC.MD.simulation)
Control (class in MDMC.control.control)
conversion_factor (MDMC.common.units.Unit attribute)
(MDMC.common.units.Unit property)
convert_bond() (in module MDMC.MD.ase.conversions)
convert_bonds() (in module MDMC.MD.ase.conversions)
convert_from_ase_atom() (in module MDMC.MD.ase.conversions)
convert_to_ase_atom() (in module MDMC.MD.ase.conversions)
convert_trajectory() (MDMC.MD.engine_facades.facade.MDEngine method)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method)
convert_unit() (in module MDMC.MD.engine_facades.lammps_engine)
copy() (MDMC.MD.structural_units.Atom method)
(MDMC.MD.structural_units.CompositeStructuralUnit method)
(MDMC.MD.structural_units.StructuralUnit method)
copy_interactions() (MDMC.MD.structural_units.Atom method)
correlation() (in module MDMC.common.mathematics)
Coulomb (class in MDMC.MD.interaction_functions)
couls (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute)
create_facade() (MDMC.MD.engine_facades.facade_factory.MDEngineFacadeFactory static method)
create_force_field() (MDMC.MD.force_fields.force_field_factory.ForceFieldFactory static method)
create_observable() (MDMC.trajectory_analysis.observables.obs_factory.ObservableFactory class method)
create_reader() (MDMC.readers.reader_factory.ReaderFactory class method)
create_reader_from_ext() (MDMC.readers.configurations.conf_reader_factory.ConfigurationReaderFactory class method)
create_units() (in module MDMC.common.units)
D
data (MDMC.readers.observables.obs_reader.ObservableReader property)
(MDMC.trajectory_analysis.observables.obs.Observable property)
(MDMC.trajectory_analysis.trajectory.Configuration attribute)
(MDMC.trajectory_analysis.trajectory.Configuration property)
(MDMC.trajectory_analysis.trajectory.Trajectory property)
dependent_variables (MDMC.readers.observables.obs_reader.ObservableReader property)
(MDMC.readers.observables.obs_reader.SQwReader property)
(MDMC.trajectory_analysis.observables.obs.Observable property)
dependent_variables_structure (MDMC.trajectory_analysis.observables.obs.Observable property)
dict_from_element() (MDMC.readers.observables.xml_SQw.XML_SQw static method)
dimensions (MDMC.MD.simulation.Universe attribute)
(MDMC.trajectory_analysis.trajectory.AtomCollection property)
dispersions (MDMC.MD.force_fields.ff.FileForceField property)
dispersive_solver (MDMC.MD.simulation.Universe attribute)
disps (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute)
dumps (MDMC.MD.engine_facades.lammps_engine.PyLammpsAttribute property)
E
E (MDMC.readers.observables.obs_reader.SQwReader property)
electrostatic_solver (MDMC.MD.simulation.Universe attribute)
element (MDMC.MD.structural_units.Atom attribute)
element_dict (MDMC.MD.simulation.Universe property)
element_list (MDMC.MD.simulation.Universe property)
(MDMC.trajectory_analysis.trajectory.Configuration property)
(MDMC.trajectory_analysis.trajectory.Trajectory property)
element_set (MDMC.trajectory_analysis.trajectory.Configuration attribute)
(MDMC.trajectory_analysis.trajectory.Trajectory property)
engine (MDMC.MD.simulation.Simulation attribute)
Ensemble (class in MDMC.MD.engine_facades.lammps_engine)
ensemble (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine property)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation attribute)
equilibrate() (MDMC.control.control.Control method)
errors (MDMC.readers.observables.obs_reader.ObservableReader property)
(MDMC.readers.observables.obs_reader.SQwReader property)
(MDMC.trajectory_analysis.observables.obs.Observable property)
Ewald (class in MDMC.MD.simulation)
exp_datasets (MDMC.control.control.Control attribute)
extension (MDMC.readers.configurations.conf_reader.ConfigurationReader property)
F
file (MDMC.readers.observables.netCDF.netCDF attribute)
file_dep (MDMC.readers.observables.LAMPSQw.LAMPSQw attribute)
file_dep_err (MDMC.readers.observables.LAMPSQw.LAMPSQw attribute)
file_detectors (MDMC.readers.observables.MantidSQw.MantidSQw attribute)
file_indep (MDMC.readers.observables.LAMPSQw.LAMPSQw attribute)
file_name (MDMC.MD.force_fields.ff.FileForceField property)
file_variables (MDMC.readers.observables.MantidSQw.MantidSQw attribute)
FileForceField (class in MDMC.MD.force_fields.ff)
fill() (MDMC.MD.simulation.Universe method)
filter() (MDMC.MD.parameters.Parameters method)
filter_atom_attribute() (MDMC.MD.parameters.Parameters method)
filter_atoms() (in module MDMC.MD.structural_units)
(MDMC.trajectory_analysis.trajectory.Configuration method)
filter_atoms_element() (in module MDMC.MD.structural_units)
filter_by_element() (MDMC.trajectory_analysis.trajectory.Configuration method)
filter_by_time() (MDMC.trajectory_analysis.trajectory.Trajectory method)
filter_dataframe() (in module MDMC.common.df_operations)
filter_element() (MDMC.MD.force_fields.ff.FileForceField method)
filter_function() (MDMC.MD.parameters.Parameters method)
filter_interaction() (MDMC.MD.parameters.Parameters method)
filter_name() (MDMC.MD.parameters.Parameters method)
filter_ordered_dataframe() (in module MDMC.common.df_operations)
filter_structure() (MDMC.MD.parameters.Parameters method)
filter_structures() (MDMC.trajectory_analysis.trajectory.Configuration method)
filter_value() (MDMC.MD.parameters.Parameters method)
fit_parameters (MDMC.control.control.Control attribute)
fix_names (MDMC.MD.engine_facades.lammps_engine.PyLammpsAttribute property)
fix_styles (MDMC.MD.engine_facades.lammps_engine.PyLammpsAttribute property)
fixes (MDMC.MD.engine_facades.lammps_engine.PyLammpsAttribute property)
FoM_calculator (MDMC.control.control.Control attribute)
force_field (MDMC.MD.simulation.Universe attribute)
force_fields (MDMC.MD.simulation.Universe property)
ForceField (class in MDMC.MD.force_fields.ff)
ForceFieldFactory (class in MDMC.MD.force_fields.force_field_factory)
formula (MDMC.MD.structural_units.CompositeStructuralUnit property)
frames (MDMC.trajectory_analysis.trajectory.Trajectory property)
G
gaussian() (in module MDMC.common.resolution_functions)
get_ase_atoms() (in module MDMC.MD.ase.conversions)
get_bonded_interactions_atoms() (in module MDMC.MD.ase.cif)
get_bonds() (in module MDMC.MD.ase.viewer)
get_center_of_rotation() (MDMC.MD.ase.conversions.X3D method)
get_force_field_names() (MDMC.MD.force_fields.force_field_factory.ForceFieldFactory static method)
get_menu_data() (MDMC.MD.ase.viewer.Viewer method)
get_observable() (MDMC.trajectory_analysis.observables.obs_factory.ObservableFactory class method)
get_reduced_chemical_formula() (in module MDMC.MD.structural_units)
get_solvent_config() (in module MDMC.MD.solvents.solvents)
get_solvent_names() (in module MDMC.MD.solvents.solvents)
get_viewpoint_z() (MDMC.MD.ase.conversions.X3D method)
H
HarmonicPotential (class in MDMC.MD.interaction_functions)
I
improper_ID (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute)
impropers (MDMC.MD.force_fields.ff.FileForceField property)
independent_variables (MDMC.readers.observables.obs_reader.ObservableReader property)
(MDMC.readers.observables.obs_reader.SQwReader property)
(MDMC.trajectory_analysis.observables.obs.Observable property)
inter_func_decorator() (in module MDMC.MD.interaction_functions)
interaction (in module MDMC.MD.engine_facades.lammps_engine)
interaction_dictionary (MDMC.MD.force_fields.ff.FileForceField property)
(MDMC.MD.force_fields.ff.ForceField property)
(MDMC.MD.force_fields.SPC.SPC property)
(MDMC.MD.force_fields.SPCE.SPCE property)
InteractionFunction (class in MDMC.MD.interaction_functions)
interactions (MDMC.MD.parameters.Parameter property)
(MDMC.MD.simulation.Universe property)
(MDMC.MD.structural_units.StructuralUnit property)
K
kspace_solver (MDMC.MD.simulation.Universe attribute)
KSpaceSolver (class in MDMC.MD.simulation)
L
LAMMPSEngine (class in MDMC.MD.engine_facades.lammps_engine)
LAMMPSSimulation (class in MDMC.MD.engine_facades.lammps_engine)
LAMMPSUniverse (class in MDMC.MD.engine_facades.lammps_engine)
LAMPSQw (class in MDMC.readers.observables.LAMPSQw)
LennardJones (class in MDMC.MD.interaction_functions)
limit_atoms() (in module MDMC.MD.ase.viewer)
lin_momentum_steps (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property)
lmp (MDMC.MD.engine_facades.lammps_engine.PyLammpsAttribute attribute)
lorentzian() (in module MDMC.common.resolution_functions)
M
MantidSQw (class in MDMC.readers.observables.MantidSQw)
mass (MDMC.MD.structural_units.Atom property)
max (MDMC.MD.structural_units.BoundingBox property)
max_iterations (MDMC.MD.simulation.ConstraintAlgorithm property)
maximum_frames() (MDMC.trajectory_analysis.observables.obs.Observable method)
MD_steps (MDMC.control.control.Control attribute)
MDEngine (class in MDMC.MD.engine_facades.facade)
MDEngineFacadeFactory (class in MDMC.MD.engine_facades.facade_factory)
MDMC.common.constants
module
MDMC.common.decorators
module
MDMC.common.df_operations
module
MDMC.common.mathematics
module
MDMC.common.resolution_functions
module
MDMC.common.units
module
MDMC.control.control
module
MDMC.MD.ase.cif
module
MDMC.MD.ase.conversions
module
MDMC.MD.ase.viewer
module
MDMC.MD.container
module
MDMC.MD.engine_facades.facade
module
MDMC.MD.engine_facades.facade_factory
module
MDMC.MD.engine_facades.lammps_engine
module
MDMC.MD.force_fields.ff
module
MDMC.MD.force_fields.force_field_factory
module
MDMC.MD.force_fields.OPLSAA
module
MDMC.MD.force_fields.SPC
module
MDMC.MD.force_fields.SPCE
module
MDMC.MD.interaction_functions
module
MDMC.MD.parameters
module
MDMC.MD.simulation
module
MDMC.MD.solvents.solvents
module
MDMC.MD.solvents.SPC_config
module
MDMC.MD.structural_units
module
MDMC.readers.configurations.cif
module
MDMC.readers.configurations.conf_reader
module
MDMC.readers.configurations.conf_reader_factory
module
MDMC.readers.observables.LAMPSQw
module
MDMC.readers.observables.MantidSQw
module
MDMC.readers.observables.netCDF
module
MDMC.readers.observables.obs_reader
module
MDMC.readers.observables.obs_reader_factory
module
MDMC.readers.observables.xml_SQw
module
MDMC.readers.reader
module
MDMC.readers.reader_factory
module
MDMC.refinement.FoM
module
MDMC.trajectory_analysis.observables.obs
module
MDMC.trajectory_analysis.observables.obs_factory
module
MDMC.trajectory_analysis.observables.PDF
module
MDMC.trajectory_analysis.observables.SQw
module
MDMC.trajectory_analysis.observables.SQw_coh
module
MDMC.trajectory_analysis.observables.SQw_incoh
module
MDMC.trajectory_analysis.trajectory
module
min (MDMC.MD.structural_units.BoundingBox property)
minimize() (MDMC.MD.engine_facades.facade.MDEngine method)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method)
(MDMC.MD.simulation.Simulation method)
minimizer (MDMC.control.control.Control attribute)
minimum_frames() (MDMC.trajectory_analysis.observables.obs.Observable method)
mod_docstring() (in module MDMC.common.decorators)
module
MDMC.common.constants
MDMC.common.decorators
MDMC.common.df_operations
MDMC.common.mathematics
MDMC.common.resolution_functions
MDMC.common.units
MDMC.control.control
MDMC.MD.ase.cif
MDMC.MD.ase.conversions
MDMC.MD.ase.viewer
MDMC.MD.container
MDMC.MD.engine_facades.facade
MDMC.MD.engine_facades.facade_factory
MDMC.MD.engine_facades.lammps_engine
MDMC.MD.force_fields.ff
MDMC.MD.force_fields.force_field_factory
MDMC.MD.force_fields.OPLSAA
MDMC.MD.force_fields.SPC
MDMC.MD.force_fields.SPCE
MDMC.MD.interaction_functions
MDMC.MD.parameters
MDMC.MD.simulation
MDMC.MD.solvents.solvents
MDMC.MD.solvents.SPC_config
MDMC.MD.structural_units
MDMC.readers.configurations.cif
MDMC.readers.configurations.conf_reader
MDMC.readers.configurations.conf_reader_factory
MDMC.readers.observables.LAMPSQw
MDMC.readers.observables.MantidSQw
MDMC.readers.observables.netCDF
MDMC.readers.observables.obs_reader
MDMC.readers.observables.obs_reader_factory
MDMC.readers.observables.xml_SQw
MDMC.readers.reader
MDMC.readers.reader_factory
MDMC.refinement.FoM
MDMC.trajectory_analysis.observables.obs
MDMC.trajectory_analysis.observables.obs_factory
MDMC.trajectory_analysis.observables.PDF
MDMC.trajectory_analysis.observables.SQw
MDMC.trajectory_analysis.observables.SQw_coh
MDMC.trajectory_analysis.observables.SQw_incoh
MDMC.trajectory_analysis.trajectory
Molecule (class in MDMC.MD.structural_units)
molecule_list (MDMC.MD.simulation.Universe property)
(MDMC.trajectory_analysis.trajectory.Configuration property)
N
n_atoms (MDMC.MD.simulation.Universe property)
n_body (MDMC.MD.force_fields.ff.WaterModel property)
n_bonded (MDMC.MD.simulation.Universe property)
n_interactions (MDMC.MD.simulation.Universe property)
n_molecules (MDMC.MD.simulation.Universe property)
n_nonbonded (MDMC.MD.simulation.Universe property)
name (MDMC.MD.interaction_functions.InteractionFunction property)
(MDMC.MD.simulation.ConstraintAlgorithm property)
(MDMC.MD.simulation.KSpaceSolver property)
(MDMC.trajectory_analysis.observables.obs.Observable property)
nbis_by_atom_type_pairs (MDMC.MD.simulation.Universe property)
neighbor_steps (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property)
netCDF (class in MDMC.readers.observables.netCDF)
nonbonded_interactions (MDMC.MD.simulation.Universe property)
(MDMC.MD.structural_units.Atom property)
(MDMC.MD.structural_units.CompositeStructuralUnit property)
(MDMC.MD.structural_units.Molecule property)
(MDMC.MD.structural_units.StructuralUnit property)
nonbonded_mix (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse property)
O
Observable (class in MDMC.trajectory_analysis.observables.obs)
observable_pairs (MDMC.control.control.Control attribute)
ObservableFactory (class in MDMC.trajectory_analysis.observables.obs_factory)
ObservableReader (class in MDMC.readers.observables.obs_reader)
ObservableReaderFactory (class in MDMC.readers.observables.obs_reader_factory)
OPLSAA (class in MDMC.MD.force_fields.OPLSAA)
origin (MDMC.trajectory_analysis.observables.obs.Observable property)
P
Parameter (class in MDMC.MD.parameters)
parameterize_interactions() (MDMC.MD.force_fields.ff.ForceField method)
Parameters (class in MDMC.MD.parameters)
parameters (MDMC.MD.interaction_functions.InteractionFunction property)
(MDMC.MD.simulation.Universe property)
parameters_values (MDMC.MD.interaction_functions.InteractionFunction property)
parse() (MDMC.readers.configurations.cif.CIF method)
(MDMC.readers.observables.LAMPSQw.LAMPSQw method)
(MDMC.readers.observables.MantidSQw.MantidSQw method)
(MDMC.readers.observables.netCDF.netCDF method)
(MDMC.readers.observables.xml_SQw.XML_SQw method)
(MDMC.readers.reader.Reader method)
parse_all_nonbonded_styles() (in module MDMC.MD.engine_facades.lammps_engine)
parse_bonded_coefficients() (in module MDMC.MD.engine_facades.lammps_engine)
parse_bonded_styles() (in module MDMC.MD.engine_facades.lammps_engine)
parse_constraint() (in module MDMC.MD.engine_facades.lammps_engine)
parse_dep_var() (MDMC.readers.observables.LAMPSQw.LAMPSQw method)
parse_detectors() (MDMC.readers.observables.MantidSQw.MantidSQw method)
parse_dispersion_coefficients() (in module MDMC.MD.engine_facades.lammps_engine)
parse_indep_var() (MDMC.readers.observables.LAMPSQw.LAMPSQw method)
parse_kspace_solver() (in module MDMC.MD.engine_facades.lammps_engine)
parse_nonbonded_modifications() (in module MDMC.MD.engine_facades.lammps_engine)
parse_nonbonded_styles() (in module MDMC.MD.engine_facades.lammps_engine)
parse_variables() (MDMC.readers.observables.MantidSQw.MantidSQw method)
partition() (in module MDMC.MD.engine_facades.lammps_engine)
partition_interactions() (in module MDMC.MD.engine_facades.lammps_engine)
Periodic (class in MDMC.MD.interaction_functions)
physical_property (MDMC.common.units.Unit property)
position (MDMC.MD.structural_units.Molecule property)
(MDMC.MD.structural_units.StructuralUnit property)
positions (MDMC.trajectory_analysis.trajectory.Trajectory property)
PPPM (class in MDMC.MD.simulation)
pressure (MDMC.MD.engine_facades.lammps_engine.Ensemble property)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine property)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property)
proper_ID (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute)
propers (MDMC.MD.force_fields.ff.FileForceField property)
PyLammpsAttribute (class in MDMC.MD.engine_facades.lammps_engine)
Q
Q (MDMC.readers.observables.obs_reader.SQwReader property)
R
Rattle (class in MDMC.MD.simulation)
read_from_file() (MDMC.trajectory_analysis.observables.obs.Observable method)
Reader (class in MDMC.readers.reader)
reader (MDMC.trajectory_analysis.observables.obs.Observable attribute)
ReaderFactory (class in MDMC.readers.reader_factory)
refine() (MDMC.control.control.Control method)
register() (MDMC.trajectory_analysis.observables.obs_factory.ObservableFactory class method)
remove_ensemble_fixes() (MDMC.MD.engine_facades.lammps_engine.Ensemble method)
repr_decorator() (in module MDMC.common.decorators)
rescale_step (MDMC.MD.engine_facades.lammps_engine.Ensemble attribute)
reset_config() (MDMC.MD.engine_facades.facade.MDEngine method)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method)
rotate() (MDMC.MD.structural_units.CompositeStructuralUnit method)
run() (MDMC.MD.engine_facades.facade.MDEngine method)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method)
(MDMC.MD.simulation.Simulation method)
S
save_config() (MDMC.MD.engine_facades.facade.MDEngine method)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method)
saved_config (MDMC.MD.engine_facades.facade.MDEngine property)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine property)
scale() (MDMC.trajectory_analysis.trajectory.Configuration method)
set_atom_mass() (MDMC.MD.force_fields.ff.FileForceField method)
set_atoms() (MDMC.MD.ase.viewer.Viewer method)
set_config() (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse method)
set_docstring() (in module MDMC.common.decorators)
set_parameters_interactions() (MDMC.MD.interaction_functions.InteractionFunction method)
set_tie() (MDMC.MD.parameters.Parameter method)
settings (MDMC.MD.simulation.Simulation attribute)
setup_simulation() (MDMC.MD.engine_facades.facade.MDEngine method)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method)
setup_universe() (MDMC.MD.engine_facades.facade.MDEngine method)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method)
Shake (class in MDMC.MD.simulation)
Simulation (class in MDMC.MD.simulation)
simulation (MDMC.control.control.Control attribute)
skin (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property)
solvate() (MDMC.MD.simulation.Universe method)
SPC (class in MDMC.MD.force_fields.SPC)
SPCConfig (class in MDMC.MD.solvents.SPC_config)
SPCE (class in MDMC.MD.force_fields.SPCE)
SQwReader (class in MDMC.readers.observables.obs_reader)
step() (MDMC.control.control.Control method)
StructuralUnit (class in MDMC.MD.structural_units)
structure_list (MDMC.MD.simulation.Universe property)
(MDMC.MD.structural_units.CompositeStructuralUnit property)
(MDMC.trajectory_analysis.trajectory.Configuration property)
structure_type (MDMC.MD.structural_units.StructuralUnit property)
system_state (MDMC.MD.engine_facades.lammps_engine.PyLammpsAttribute property)
T
t_fraction (MDMC.MD.engine_facades.lammps_engine.Ensemble property)
t_window (MDMC.MD.engine_facades.lammps_engine.Ensemble property)
temperature (MDMC.MD.engine_facades.lammps_engine.Ensemble property)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine property)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property)
TemporalConfiguration (class in MDMC.trajectory_analysis.trajectory)
thermostat (MDMC.MD.engine_facades.lammps_engine.Ensemble property)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine property)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property)
tie (MDMC.MD.parameters.Parameter property)
tied (MDMC.MD.parameters.Parameter property)
time_step (MDMC.MD.engine_facades.lammps_engine.Ensemble property)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine property)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property)
times (MDMC.trajectory_analysis.trajectory.Trajectory property)
top_level_structure (MDMC.MD.structural_units.StructuralUnit property)
traj_step (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine property)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation attribute)
(MDMC.MD.simulation.Simulation attribute)
Trajectory (class in MDMC.trajectory_analysis.trajectory)
trajectory (MDMC.MD.simulation.Simulation property)
translate() (MDMC.MD.structural_units.StructuralUnit method)
U
uniformity_requirements (MDMC.trajectory_analysis.observables.obs.Observable property)
Unit (class in MDMC.common.units)
unit (MDMC.common.units.UnitFloat property)
(MDMC.common.units.UnitNDArray property)
unit_array() (in module MDMC.common.units)
unit_decorator() (in module MDMC.common.decorators)
unit_decorator_getter() (in module MDMC.common.decorators)
UnitFloat (class in MDMC.common.units)
UnitNDArray (class in MDMC.common.units)
Universe (class in MDMC.MD.simulation)
universe (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation attribute)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute)
(MDMC.MD.simulation.Simulation attribute)
(MDMC.MD.structural_units.Atom property)
(MDMC.MD.structural_units.CompositeStructuralUnit property)
(MDMC.MD.structural_units.StructuralUnit property)
(MDMC.trajectory_analysis.trajectory.AtomCollection property)
(MDMC.trajectory_analysis.trajectory.Configuration attribute)
(MDMC.trajectory_analysis.trajectory.Trajectory property)
update_parameters() (MDMC.MD.engine_facades.facade.MDEngine method)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine method)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse method)
use_FFT (MDMC.trajectory_analysis.observables.obs.Observable property)
V
valid_position() (MDMC.MD.structural_units.StructuralUnit method)
validate_config() (MDMC.trajectory_analysis.trajectory.Trajectory static method)
validate_structure() (MDMC.trajectory_analysis.trajectory.Configuration method)
validate_value() (MDMC.MD.parameters.Parameter static method)
value (MDMC.MD.parameters.Parameter property)
velocities (MDMC.trajectory_analysis.trajectory.Trajectory property)
velocity (MDMC.MD.structural_units.StructuralUnit property)
view() (in module MDMC.gui.__init__)
(in module MDMC.MD.ase.viewer)
view_ase() (in module MDMC.MD.ase.viewer)
view_x3dom() (in module MDMC.MD.ase.viewer)
Viewer (class in MDMC.MD.ase.viewer)
W
w (MDMC.readers.observables.obs_reader.SQwReader property)
WaterModel (class in MDMC.MD.force_fields.ff)
wrap_docstring() (in module MDMC.common.decorators)
write() (MDMC.MD.ase.conversions.ASEAtoms method)
(MDMC.MD.ase.conversions.X3D method)
X
X3D (class in MDMC.MD.ase.conversions)
XML_SQw (class in MDMC.readers.observables.xml_SQw)