pyretis.initiation package

This package defines methods for initiating path ensembles.

Package structure

Modules

__init__.py

This file, imports from the other modules and defines some helper methods for the initiation.

initiate_kick.py (pyretis.initiation.initiate_kick)

Methods for initiating using the kick method.

initiate_load.py (pyretis.initiation.initiate_load)

Methods for initiating by loading already existing paths from files.

initiate_restart.py (pyretis.initiation.initiate_restart)

Methods for initiating by loading PyRETIS restart files.

Important methods defined in this package

get_initiation_method (get_initiation_method())

Method to select initiation method from settings.

initiate_path_simulation (initiate_path_simulation())

Method to initiate a path simulation.

pyretis.initiation.get_initiation_method(settings)

Return the initiation method from given settings.

Parameters:settings (dict) – This dictionary contains the settings for the initiation. Returns:out (callable) – The method to be used for the initiation.

pyretis.initiation.initiate_path_simulation(simulation, settings)

Initialise a path simulation.

Parameters:

• simulation (object like PathSimulation) – The simulation we are doing the initiation for.
• settings (dict) – A dictionary with settings for the initiation.

Returns:

out (callable) – The method to be used for the initiation.

List of submodules

• pyretis.initiation.initiate_kick
• pyretis.initiation.initiate_load
• pyretis.initiation.initiate_restart

pyretis.initiation.initiate_kick module

This file contains functions used for initiation of paths.

Important methods defined here

generate_initial_path_kick (generate_initial_path_kick())

Function for generating an initial path by repeatedly kicking a phase point.

initiate_kick (initiate_kick())

Helper method, selects either initiate_kicki() or initiate_kick_max().

initiate_kicki (initiate_kicki())

A method for initiating a path ensemble by repeatedly modifying velocities to find the crossing with the interfaces.

initiate_kick_max (initiate_kick_max())

A method similar to py:meth:.initiate_kick. Here, if possible, we will use points from the previous paths, closest to the target interface.

initiate_path_ensemble_kick (initiate_path_ensemble_kick())

Method to initiate a single path ensemble.

fix_path_by_tis (fix_path_by_tis())

Method to fix an initial path that starts and ends at the wrong interface via TIS moves.

pyretis.initiation.initiate_kick._get_help(start_cond, interfaces)

Define some helper methods for fix_path_by_tis().

This method returns two methods that fix_path_by_tis() can use to determine if a new path is an improvement compared to the current path and if the “fixing” is done.

Parameters:

• start_cond (string) – The starting condition (from the TIS settings). Left or Right.
• interfaces (list of floats) – The interfaces, on form [left, middle, right].

Returns:

• out[0] (method) – The method which determines if a new path represents an improvement over the current path.
• out[1] (method) – The method which determines if we are done, that is if we can accept the current path.

pyretis.initiation.initiate_kick.fix_path_by_tis(initial_path, ensemble, tis_settings)

Fix a path that starts and ends at the wrong interfaces.

The given path is amended by performing TIS moves (shooting and time reversal). Note that this function is intended to be used in connection with the initialisation.

Parameters:

• initial_path (object like PathBase) – This is the initial path to fix. It starts & ends at the wrong interface.

• ensemble (dict.) – It contains:

  • path_ensemble : object like PathEnsemble The path ensemble to create an initial path for.
  • system : object like System System is used here since we need access to the temperature and to the particle list.
  • order_function : object like OrderParameter The class used for obtaining the order parameter(s).
  • engine : object like EngineBase The engine to use for propagating a path.
  • rgen : object like RandomGenerator This is the random generator that will be used.

• tis_settings (dict) – Settings for TIS method, here we explicitly use:

  • start_cond: string which defines the start condition.
  • maxlength: integer which gives the maximum allowed path length.

  Note that we here explicitly set some local TIS settings for use in the make_tis_step function.

Returns:

out (object like PathBase) – The amended path.

pyretis.initiation.initiate_kick.generate_initial_path_kick(ensemble, tis_settings)

Generate an initial path with the kicking method.

This function will generate an initial path by repeatedly kicking a phase-space point until the middle interface is crossed. The point before and after kicking are stored, so when the middle interface is crossed we have two points we can integrate forward and backward in time. This function is intended for use with TIS. For use with RETIS one should set the appropriate tis_settings so that the starting conditions are fine (i.e. for the [0^-] ensemble it might be different for the other ensembles).

Parameters:

• ensemble (dict.) – It contains:
  • path_ensemble : object like PathEnsemble The path ensemble to create an initial path for.
  • system : object like System System is used here since we need access to the temperature and to the particle list.
  • order_function : object like OrderParameter The class used for obtaining the order parameter(s).
  • engine : object like EngineBase The engine to use for propagating a path.
  • rgen : object like RandomGenerator This is the random generator that will be used.
• tis_settings (dict) – This dictionary contains settings for TIS. Explicitly used here:
  • start_cond: string, starting condition, ‘L’eft or ‘R’ight.
  • maxlength: integer, maximum allowed length of paths.

Yields:

• out[0] (boolean) – True if we are finished.
• out[1] (string) – The current status of this method.
• out[2] (object like PathBase or None) – If we are finished (and successful) this is the generated initial path. Otherwise, this is equal to None.

pyretis.initiation.initiate_kick.initiate_kick(simulation, settings, cycle)

Run the initiation method for several ensembles.

Please see documentation for initiate_path_ensemble_kick().

pyretis.initiation.initiate_kick.initiate_kick_max(simulation, settings, cycle)

Run the initiation for several ensembles.

This method is similar to initiate_kick(), but here we update the initial point for an ensemble to use that of the previous path (if this exist).

Please see documentation for initiate_path_ensemble_kick().

pyretis.initiation.initiate_kick.initiate_kicki(simulation, settings, cycle)

Run the initialization for several ensembles.

Please see documentation for initiate_path_ensemble_kick().

pyretis.initiation.initiate_kick.initiate_path_ensemble_kick(ensemble, tis_settings, cycle)

Run the “kick” initiate for a given ensemble.

Parameters:

• ensemble (dict) – It contains:
  • path_ensemble : object like PathEnsemble The path ensemble to create an initial path for.
  • system : object like System The system is used here since we need access to the temperature and to the particle list.
  • order_function : object like OrderParameter The class used for obtaining the order parameter(s).
  • engine : object like EngineBase The engine to use for propagating a path.
  • rgen : object like RandomGenerator This is the random generator that will be used.
• tis_settings (dict) – This dictionary contains the TIS settings.
• cycle (integer, optional) – The cycle number we are initiating at, typically this will be 0 which is the default value.

Returns:

• out[0] (boolean) – True if the initial path was accepted.
• out[1] (object like py:class:.PathBase) – The initial path.
• out[2] (string) – The status of the path.

pyretis.initiation.initiate_load module

Method for initiating paths by loading from previous simulation(s).

Important methods defined here

initiate_load (initiate_load())

A method that will get the initial path from the output of a previous simulation.

pyretis.initiation.initiate_load._check_path(path, path_ensemble, warning=True)

Run some checks for the path.

Parameters:

• path (object like PathBase) – The path we are to set up/fill.
• path_ensemble (object like PathEnsemble) – The path ensemble the path could be added to.
• warning (boolean, optional) – If True, it output warnings, else only debug info.

pyretis.initiation.initiate_load._do_the_dirty_load_job(mainfolder, edir)

Copy the files to a place where PyRETIS expects them to be.

The function checks if in the destination folder some suitable files are already present. If not, it tries to copy them from the main load folder.

Parameters:

• mainfolder (string) – The path of the main load directory with frame/trajectory files.
• edir (string) – The path of the path ensemble load directory with frame/trajectory files.

pyretis.initiation.initiate_load._generate_traj_txt_from_ext(dirname, system, accepted=True)

Generate a traj.txt file in the path ensemble folder.

Parameters:

• dirname (string) – The path of the path ensemble directory with trajectory files.
• system (object like System) – A system object we can use when calculating the order parameter(s).
• accepted (boolean, optional) – It controls where the traj files shall be located, if True in the accepted folder, if False in the main folder.

pyretis.initiation.initiate_load._load_energies_for_path(path, dirname)

Load energy data for a path.

Parameters:

• path (object like PathBase) – The path we are to set up/fill.
• dirname (string) – The path to the directory with the input files.

Returns:

None, but may add energies to the path.

pyretis.initiation.initiate_load._load_external_trajectory(dirname, engine, copy=True)

Load an external trajectory.

Here, we also do some moving of files to set up for a path simulation (if copy=True).

Parameters:

• dirname (string) – The directory where we can find the trajectory file(s).
• engine (object like ExternalMDEngine) – The engine we use, here it is used to access the directories for the new simulation.
• copy (boolean, opt) – If true, it copies the files to the main ensemble folders.

Returns:

traj (dict) – A dictionary containing the trajectory information. Here, the trajectory information is a list of files with indices and information about velocity direction.

pyretis.initiation.initiate_load._load_order_parameters(traj, dirname, system, order_function)

Load or recalculate the order parameters.

Parameters:

• traj (dictionary) – The trajectory we have loaded. Used here if we are re-calculating the order parameter(s).
• dirname (string) – The path to the directory with the input files.
• system (object like System) – A system object we can use when calculating the order parameter(s).
• order_function (object like OrderParameter) – This can be used to re-calculate order parameters in case they are not given.

Returns:

out (list) – The order parameters, each item in the list corresponds to a time frame.

pyretis.initiation.initiate_load._load_order_parameters_ext(traj, dirname, order_function, engine)

Load or re-calculate the order parameters.

For external trajectories, dumping of specific frames from a trajectory might be expensive and we here do slightly more work than just dumping the frames.

Parameters:

• traj (dictionary) – The trajectory we have loaded. Used here if we are re-calculating the order parameter(s).
• dirname (string) – The path to the directory with the input files.
• order_function (object like OrderParameter) – This can be used to re-calculate order parameters in case they are not given.
• system (object like System) – A system object we can use when calculating the order parameter(s).

Returns:

out (list) – The order parameters, each item in the list corresponds to a time frame.

pyretis.initiation.initiate_load._load_trajectory(dirname, filename='traj.txt')

Load a trajectory from a file.

Parameters:

• dirname (string) – The directory where we can find the trajectory file(s).
• filename (string) – The name of the trajectory file.

Returns:

traj (dict) – A dictionary containing the trajectory information. That is, position and velocity for each frame.

pyretis.initiation.initiate_load.clean_path(path, path_ensemble, simtype='retis')

Remove useless frames from a path.

This function removes phasepoints from a path that are not needed (e.g. the one in stable states)

Parameters:

• path (object like PathBase) – The path we try to fix.
• path_ensemble (object like PathEnsembleExt) – The path ensemble the path could be added to.
• simtype (string) – The simulation type. ‘retis’, ‘repptis’, ‘pptis’

pyretis.initiation.initiate_load.initiate_load(simulation, settings, cycle, plot_loads=False)

Initialise paths by loading already generated ones.

Parameters:

• simulation (object like Simulation) – The simulation we are setting up.
• cycle (integer) – The simulation cycles we are starting at.
• settings (dictionary) – A dictionary with settings for the initiation.

pyretis.initiation.initiate_load.read_path_files(path, dirname, ensemble)

Read data needed for a path from a directory.

Parameters:

• path (object like PathBase) – The path we are to set up/fill.
• dirname (string) – The path to the directory with the input files.
• ensemble (dictionary of objects) – It contains:
  • path_ensemble: object like PathEnsemble This is the path ensemble to perform the initialization.
  • order_function: object like OrderParameter The class used for obtaining the order parameter(s).
  • engine: object like EngineBase The engine to use for propagating a path.
  • system: object like System A system object we can use when calculating the order parameter(s).

pyretis.initiation.initiate_load.read_path_files_ext(path, dirname, ensemble)

Read data needed for a path from a directory.

Parameters:

• path (object like Path) – The path we are to set up/fill.
• path_ensemble (object like PathEnsembleExt) – The path ensemble the path could be added to.
• dirname (string) – The path to the directory with the input files.
• ensemble (dictionary of objects) – It contains:
  • path_ensemble: object like PathEnsemble This is the path ensemble to perform the initialization.
  • order_function: object like OrderParameter The class used for obtaining the order parameter(s).
  • engine: object like EngineBase The engine to use for propagating a path.
  • system: object like System A system object we can use when calculating the order parameter(s).

pyretis.initiation.initiate_load.reorderframes(path, path_ensemble)

Re-order the phase points in the input path.

This function assumes that the path needs to be fixed. It checks for the validity of the path and keeps only the frames that are useful for the region to explore e.g. [0^-].

Parameters:

• path (object like PathBase) – The path we try to fix.
• path_ensemble (object like PathEnsembleExt) – The path ensemble the path could be added to.

pyretis.initiation.initiate_load.write_order_parameters(order_file_name, orderdata, header='# Re-calculated order parameters.')

Store re-calculated order parameters to a file.

pyretis.initiation.initiate_restart module

This file contains functions used for initiation of paths.

Important methods defined here

initiate_restart (initiate_restart())

A method that will get the initial path from the output from a previous simulation.

pyretis.initiation.initiate_restart.initiate_restart(simulation, settings, cycle)

Initialise paths by loading restart data.

Parameters:

• simulation (object like Simulation) – The simulation we are setting up.
• settings (dictionary) – A dictionary with settings for the initiation.
• cycle (integer) – The simulation cycles we are starting at.