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
Known bugs and unimplemented features
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
|
K
|
L
|
M
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N
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O
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P
|
Q
|
R
|
S
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T
|
U
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V
|
W
|
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_nonbonded_interaction() (MDMC.MD.simulation.Universe 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_constraints() (MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse method)
apply_ensemble_fixes() (MDMC.MD.engine_facades.lammps_engine.LAMMPSEnsemble method)
array (MDMC.MD.parameters.Parameters attribute)
as_array (MDMC.MD.parameters.Parameters property)
ase_read_cif() (in module MDMC.MD.ase.cif)
ASEAtoms (class in MDMC.MD.ase.conversions)
assign() (MDMC.readers.observables.obs_reader.ObservableReader method)
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_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.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.simulation.Universe attribute)
(MDMC.MD.simulation.Universe property)
(MDMC.readers.configurations.cif.CIF property)
(MDMC.readers.configurations.conf_reader.ConfigurationReader property)
(MDMC.trajectory_analysis.trajectory.Configuration property)
B
barostat (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_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 attribute)
(MDMC.MD.simulation.Universe property)
bonded_interactions (MDMC.MD.simulation.Universe attribute)
(MDMC.MD.simulation.Universe property)
bonds (MDMC.MD.ase.conversions.ASEAtoms attribute)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSUniverse attribute)
(MDMC.MD.force_fields.ff.FileForceField property)
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)
CIF (class in MDMC.readers.configurations.cif)
components (MDMC.common.units.Unit attribute)
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)
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)
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)
density (MDMC.MD.simulation.Universe attribute)
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.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_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_lookup (MDMC.MD.simulation.Universe attribute)
(MDMC.MD.simulation.Universe property)
element_set (MDMC.trajectory_analysis.trajectory.Configuration attribute)
engine (MDMC.MD.simulation.Simulation attribute)
ensemble (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.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
faster_autocorrelation() (in module MDMC.common.mathematics)
faster_correlation() (in module MDMC.common.mathematics)
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() (MDMC.trajectory_analysis.trajectory.Configuration method)
filter_by_element() (MDMC.trajectory_analysis.trajectory.Configuration 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_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)
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_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
ID_or_Q (MDMC.readers.observables.MantidSQw.MantidSQw attribute)
import_from_alias() (MDMC.MD.engine_facades.facade_factory.MDEngineFacadeFactory static method)
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.PDFReader 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 attribute)
(MDMC.MD.simulation.Universe 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)
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)
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)
log_parameters() (MDMC.MD.parameters.Parameters method)
lorentzian() (in module MDMC.common.resolution_functions)
M
MantidSQw (class in MDMC.readers.observables.MantidSQw)
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.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.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.refinement.minimizers
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
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.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.obs_reader
MDMC.readers.observables.obs_reader_factory
MDMC.readers.observables.xml_SQw
MDMC.readers.reader
MDMC.readers.reader_factory
MDMC.refinement.FoM
MDMC.refinement.minimizers
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_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_body (MDMC.MD.force_fields.ff.WaterModel property)
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)
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 attribute)
(MDMC.MD.simulation.Universe property)
neighbor_steps (MDMC.MD.engine_facades.lammps_engine.LAMMPSSimulation property)
nonbonded_interactions (MDMC.MD.simulation.Universe attribute)
(MDMC.MD.simulation.Universe 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 attribute)
(MDMC.MD.simulation.Universe property)
parameters_values (MDMC.MD.interaction_functions.InteractionFunction property)
parent_simulation (MDMC.MD.engine_facades.facade.MDEngine property)
parse() (MDMC.readers.configurations.cif.CIF method)
(MDMC.readers.observables.LAMPSQw.LAMPSQw method)
(MDMC.readers.observables.MantidSQw.MantidSQw 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)
PDF (MDMC.readers.observables.obs_reader.PDFReader property)
PDF_err (MDMC.readers.observables.obs_reader.PDFReader property)
PDFReader (class in MDMC.readers.observables.obs_reader)
Periodic (class in MDMC.MD.interaction_functions)
physical_property (MDMC.common.units.Unit property)
plot_results() (MDMC.control.control.Control method)
PPPM (class in MDMC.MD.simulation)
pressure (MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine property)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSEnsemble 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
r (MDMC.readers.observables.obs_reader.PDFReader property)
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.LAMMPSEnsemble method)
repr_decorator() (in module MDMC.common.decorators)
rescale_step (MDMC.MD.engine_facades.lammps_engine.LAMMPSEnsemble attribute)
reset_config() (MDMC.MD.engine_facades.facade.MDEngine method)
(MDMC.MD.engine_facades.lammps_engine.LAMMPSEngine 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)
solvent_density (MDMC.MD.simulation.Universe attribute)
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)
structure_list (MDMC.MD.simulation.Universe attribute)
(MDMC.MD.simulation.Universe property)
(MDMC.trajectory_analysis.trajectory.Configuration property)
system_state (MDMC.MD.engine_facades.lammps_engine.PyLammpsAttribute property)
T
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.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.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_function_execution() (in module MDMC.common.decorators)
time_step (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)
top_level_structure_list (MDMC.MD.simulation.Universe attribute)
(MDMC.MD.simulation.Universe property)
traj_step (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)
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.trajectory_analysis.trajectory.AtomCollection property)
(MDMC.trajectory_analysis.trajectory.Configuration attribute)
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
validate_structure() (MDMC.trajectory_analysis.trajectory.Configuration method)
validate_value() (MDMC.MD.parameters.Parameter static method)
value (MDMC.MD.parameters.Parameter 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)
volume (MDMC.MD.simulation.Universe attribute)
W
w (MDMC.readers.observables.obs_reader.SQwReader property)
WaterModel (class in MDMC.MD.force_fields.ff)
weakref_cache() (in module MDMC.common.decorators)
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)