evaluation_util
Short description
- class pyrid.evaluation.evaluation_util.Evaluation(file_name='PyRID', path=None)[source]
The Evaluation class has several methods that are useful for evaluating simulation results such as reading observables from hdf5 files, calculating MSDs and plotting observables and reactions graphs.
- Attributes
- file_namestring
file name
- self.pathstring
file directory
- self.fig_pathstring
Figures directory
- self.Observablesdictionary
Dictionary keeping the observables / system measures (except rdf).
- self.rdfdictionary
Dictionary keeping the rdf data.
- self.Measureslist
List of all available observables / measures
- self.time_MSDdictionary
Dictionary keeping the time vectors for the MSD data.
- self.MSD_datadictionary
Dictionary keeping the MSD data for each molecule type.
- self.time_P2dictionary
Dictionary keeping the time vectors for the P2 data.
- self.P2_datadictionary
Dictionary keeping the P2 data for each molecule type.
- self.P2_tdictionary
Dictionary keeping the theoretical P2 data for each molecule type.
- self.molecules_colorsfloat64[:,4]
Molecule colors rgba [0,1].
- self.molecules_colors_rgbfloat64[:,3]
Molecule colors rgb [0,255].
- self.molecules_colors_hexlist
Molecule colors hex.
- self.reactions_colordictionary
Reactions colors used in reaction graph plots.
- self.color_palletedictionary
Color palettes used for the different observable plots (Energy, Pressure, …)
- self.unitsdictionary
Unit system
- self.Tempfloat64
Temperature
- self.box_lengthsfloat64[3]
Simulation box lengths
- self.dtfloat64
Integration time step
- self.etafloat64
Viscosity
- self.kbtfloat64
Boltzmann constant times Temperature.
- self.nstepsint64
Number of simulation steps.
- self.Moleculesdictionary
Molecule data per molecule type (bead position, bead radii, molecule volume, mobility tensors).
- self.hdfobject
hdf5 file loaded using the h5py library.
Methods
load_file(self, file_name, path = None)
Loads an hdf5 file and extracts simulation properties such as temperature and simulation box size.
read_molecule_data(self)
Reads molecule data from the hdf5 file (mobility tensor, bead position and radii, etc.)
load_hdf(self)
Loads any hdf5 file from self.path directory.
close_hdf(self)
Closes the hdf5 file.
MSD(self, time_interval, stride, Simulation, molecule)
Calculates the Mean Squared Distance (MSD) from the molecule positions and from theory.
plot_MSD(self, Simulation, molecule, save_fig = False, fig_name = None, fig_path=None)
Plots the molecules’ Mean Squared Distance (MSD).
P2(self, time_interval, stride, Simulation, molecule, theory_only = False, Delta_t = None)
Calculates the rotational time correlation function P2 from the molecule orientations and from theory.
plot_P2(self, Simulation, molecule, theory_only = False, save_fig = False, fig_name = None, fig_path=None, limits = None)
Plots the rotational time correlation function P2.
plot_rdf(self, mol_pairs, steps = [0], save_fig = False, fig_name = None , fig_path = None, average = False)
Plots the radial distribution function (RDF) from the hdf5 file.
read_observable(self, measure, sampling = None, molecules = ‘All’, educts = ‘All’, Reaction_Type = None, steps = ‘All’, file_path = None)
Reads an observable / measure from the hdf5 file.
plot_observable(self, measure, molecules = ‘All’, Reaction_Type = None, educt = None, bond_pairs = ‘All’, particle_educt = None, step = 0, save_fig = False, fig_name = None , fig_path = None, sampling = None, formats = [‘png’], show = True)
Plots an observable / measure found in the hdf5 file.
plot_reactions_graph(self, Simulation, graph_type = ‘Bimolecular’, graph_subtype = ‘’)
Plots a reactions graph using the pyvis library.
- MSD(time_interval, stride, Simulation, molecule)[source]
Calculates the Mean Squared Distance (MSD) from the molecule positions and from theory.
- Parameters
- time_intervalint64
The time step until which the molecule positions are sampled for the MSD calculation. Note: Currently sampling always starts at time step 0.
- strideint64
Stride with which the molecule positions are sampled.
- Simulationobject
Instance of the Simulation class.
- moleculestring
Name of the molecule type.
- P2(time_interval, stride, Simulation, molecule, theory_only=False, Delta_t=None)[source]
Calculates the rotational time correlation function P2 from the molecule orientations and from theory.
- Parameters
- time_intervalint64
The time step until which the molecule positions are sampled for the MSD calculation. Note: Currently sampling always starts at time step 0.
- strideint64
Stride with which the molecule positions are sampled.
- Simulationobject
Instance of the Simulation class.
- moleculestring
Name of the molecule type.
- theory_onlyboolean
If set to True, only the theoretical values for P2 are calculated. Default = False.
- Delta_tfloat64
Time step.
- load_file(file_name, path=None)[source]
Loads an hdf5 file and extracts simulation properties such as temperature and simulation box size.
- Parameters
- file_namestring
Name of the hdf5 file.
- pathstring
self.path is set to this directory. By default, self.path = Path(os.getcwd()) / ‘Files’. Default = None.
- plot_MSD(Simulation, molecule, save_fig=False, fig_name=None, fig_path=None)[source]
Plots the molecules’ Mean Squared Distance (MSD).
- Parameters
- Simulationobject
Instance of the Simulation class.
- moleculestring
Name of the molecule type.
- save_figboolean
Default = False
- fig_namestring
Default = None
- fig_pathstring
Default = None
- plot_P2(Simulation, molecule, theory_only=False, save_fig=False, fig_name=None, fig_path=None, limits=None)[source]
Plots the rotational time correlation function P2.
- Parameters
- Simulationobject
Instance of the Simulation class.
- moleculestring
Name of the molecule type.
- theory_onlyboolean
If set to True, only the theoretical values for P2 are calculated. Default = False.
- save_figboolean
Default = False
- fig_namestring
Default = None
- fig_pathstring
Default = None
- limitsfloat64[2,2]
x- and y-axis limits. Default = None.
- plot_observable(measure, molecules='All', Reaction_Type=None, educt=None, bond_pairs='All', particle_educt=None, step=0, save_fig=False, fig_name=None, fig_path=None, sampling=None, formats=['png'], show=True)[source]
Plots an observable / measure found in the hdf5 file.
- Parameters
- measurestring
observable / measure which to read from the hdf5 file.
- samplingstepwise’ or ‘binned’ or None
Sampling method used. If None, the sampling method is chosen automatically based on the measure type. Default = None.
- moleculeslist of strings
List of molecule types for which to read the observable data. If set to ‘All’, all molecules found in the hdf5 file are loaded. Default = ‘All’.
- eductlist of strings
List of reaction educts for which to read the reactions data. If set to ‘All’, all reactions found in the hdf5 file are loaded. Default = ‘All’.
- bond_pairslist of strings
List of bond pair types for which to read particle bond data. If set to ‘All’, all bonds found in the hdf5 file are loaded. Default = ‘All’.
- particle_eductslist of strings
List of particle reaction educts for which to read the reactions data. If set to ‘All’, all particle reactions found in the hdf5 file are loaded. Default = ‘All’.
- Reaction_Type‘bind’, ‘enzymatic’, ‘conversion’, ‘conversion_rb’, ‘decay_rb’, ‘production_rb’, ‘release’, ‘fusion’, ‘enzymatic_rb’
Type of the reaction whose data is read from the hdf5 file.
- stepint64
Time step at which to read the observable data. Default = 0
- save_figboolean
Default = False
- fig_namestring
Default = None
- fig_pathstring
Default = None
- samplingstepwise’ or ‘binned’ or None
Sampling method used. If None, the sampling method is chosen automatically based on the measure type. Default = None.
- formatslist of strings
File formats in which figures are saved. Default = [‘png’]
- showboolean
If True, figures are shown directly after they have been plotted. Otherwise figures are not shown (make sure to set save_fig = True). Default = True.
- Returns
- tuple(fig, ax)
figure and corresponding axes object.
- plot_rdf(mol_pairs, steps=[0], save_fig=False, fig_name=None, fig_path=None, average=False)[source]
Plots the radial distribution function (RDF) from the hdf5 file.
- Parameters
- mol_pairsnested list of strings
Molecule pairs for which the rdf is plotted.
- stepsint64[1]
Time steps. Default = [0]
- theory_onlyboolean
If set to True, only the theoretical values for P2 are calculated. Default = False.
- save_figboolean
Default = False
- fig_namestring
Default = None
- fig_pathstring
Default = None
- averageboolean
Average over rdfs at different points in time if more than one time step is given in parameter “steps”. Default = False
- Returns
- tuple(fig, ax)
figure and corresponding axes object.
- plot_reactions_graph(Simulation, graph_type='Bimolecular', graph_subtype='')[source]
Plots a reactions graph using the pyvis library.
- Parameters
- Simulationobject
Instance of Simulation class
- graph_type‘Bimolecular’, ‘Biparticle’, ‘Unimolecular’, ‘Interactions’
Reaction graph type. Default = ‘Bimolecular’
- graph_subtype‘pair relations’, ‘product relations’
Reaction graph subtype. Default = ‘product_relations’.
- read_molecule_data()[source]
Reads molecule data from the hdf5 file (mobility tensor, bead position and radii, etc.)
- read_observable(measure, sampling=None, molecules='All', educts='All', Reaction_Type=None, steps='All', file_path=None)[source]
Reads an observable / measure from the hdf5 file.
- Parameters
- measurestring
observable / measure which to read from the hdf5 file.
- samplingstepwise’ or ‘binned’ or None
Sampling method used. If None, the sampling method is chosen automatically based on the measure type. Default = None.
- moleculeslist of strings
List of molecule types for which to read the observable data. If set to ‘All’, all molecules found in the hdf5 file are loaded. Default = ‘All’.
- eductslist of strings
List of reaction educts for which to read the reactions data. If set to ‘All’, all reactions found in the hdf5 file are loaded. Default = ‘All’.
- Reaction_Type‘bind’, ‘enzymatic’, ‘conversion’, ‘conversion_rb’, ‘decay_rb’, ‘production_rb’, ‘release’, ‘fusion’, ‘enzymatic_rb’
Type of the reaction whose data is read from the hdf5 file.
- stepsint64[:] or All
Time steps at which to read the observable data. Default = All
- file_pathstring
File path. Default = None