The initial-path section

The initial-path section specifies how the initial path for a TIS/RETIS simulation should be generated.

Example initial-path section:
Initial-path settings
---------------------
method = kick
kick-from = previous

The different methods may require different keywords and this is described below for the following supported methods:

Table 27 Supported initiation methods in PyRETIS
Method name Description
kick For initiating new trajectories from given initial configuration(s).
load For loading already generated trajectories
restart For restarting PyRETIS simulations.

The kick method

The kick method is used to generate new initial paths for the path ensembles in a simulation. As an example, consider the path ensemble [i^+]. Associated with this path ensemble is the interface \lambda_i and the kick method starts by searching for a crossing with this interface. Given that the system is in a phase point, say x, this method will search for the crossing by:

  1. Modify the velocities (e.g. new velocities are generated from a Maxwellian distribution).
  2. Integrate the equations of motion one step forward in time. This results in a new phase point, say y.
  3. If y is closer to the interface \lambda_i compared to x, then we update x = y and repeat the steps. Otherwise, the steps are just repeated without updating x.

When the crossing is found, the algorithm have produced two phase points, one immediately before the interface and one immediately after. A full path is then generated by integrating the equations of motion forward in time from the point immediately after the interfaces and backward in time from the point immediately before the interfaces.

Keywords for the kick method

For the kick method, the following keywords can be set:

Table 28 Keywords for the kick method.
Keyword Description
method Selects the kick method.
kick-from Modify how the initial point for the kick method is picked.

Keyword method

method = kick
The method keyword selects the kick initialization.

Keyword kick-from

kick-from = string

The kick-from keyword specifies what initial point we use for the kick method. This setting is used when several path ensembles are initiated at the same time. It can be set to:

  • kick-from = initial: In which we will kick from the initial configuration provided. That is, all path ensembles are initiated from the same starting point.
  • kick-from = previous: In which we kick from the point on the previous path which is closest to the next interface and still left of this interface. The first path ensemble will be initiated using the provided initial configuration for the particles.
Default:
The default value is kick-from = initial.

The load method

The load method will load previous paths from files.

Keywords for the load method

For the load method, the following keywords can be set:

Table 29 Keywords for the load method.
Keyword Description
method Selects the load method.
load_folder Selects the directory where the paths we will load are stored.

Keyword method

method = load
The method keyword selects the load initialization.

Keyword load_folder

load_folder = string

The load_folder keyword specifies a directory containing the initial paths to start from. It is assumed that this directory contains folders named 000, 001 etc. and that these folder contains the paths we are to load. The paths should be given as:

  • For internal engines:
    1. A traj.txt file containing the full path (positions and velocities).
    2. A order.txt file containing the order parameters for the path. If this file is not given, the order parameters will be re-calculated.
    3. A energy.txt file containing the energies. If this file is not given, the energies along the path will be ignored.
  • For external engines:
    1. A traj.txt file with the path.
    2. A accepted folder containing the files referenced in the traj.txt file.
    3. A order.txt file containing the order parameters for the path. If this file is not given, the order parameters will be re-calculated.
    4. A energy.txt file containing the energies. If this file is not given, the energies along the path will be ignored.
Default:
The default value is load_folder = load.

The restart method

The restart method is used to continue simulations.

Keywords for the restart method

For the restart method, the following keywords can be set:

Table 30 Keywords for the restart method.
Keyword Description
method Selects the restart method.

Keyword method

method = restart
The method keyword selects the restart initialization. Here, we load path and ensemble data from the restart files for each ensemble. These restart files are named ensemble.restart and there is one such file for each path ensemble, e.g. 001/ensemble.restart. Note that when doing a restart, the ensemble.restart files will be overwritten with new data from the continued simulation.