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 29 Supported initiation methods in PyRETIS¶
Method name	Description
kick	For initiating new trajectories from given initial configuration(s).
load	For loading previously generated frames/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:

Modify the velocities (e.g. new velocities are generated from a Maxwellian distribution).
Integrate the equations of motion one step forward in time. This results in a new phase point, say $y$ .
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 has 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 30 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 31 Keywords for the load method.¶
Keyword	Description
method	Selects the load method.
load_and_kick	Generate a new path by the kick method from the loaded data.
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_and_kick¶

load_and_kick = boolean

The use of load_and_kick initialization method if the keyword is set to True.

Keyword load_folder¶

load_folder = string

The load_folder keyword specifies a directory containing the initial paths to start from. In this folder there are two possibilities:

– UNFORMATTED/LOAD GENERIC FILES OPTION – When only a trajectory or/and some frames are available, they can be copied in the load folder. The load function will copy all the trajectories and frames files from such a folder into the respective folders for each ensemble (e.g. 000 001 etc). Thereafter, the order parameter and the energy will be computed and stored in the files order.txt and energy.txt, respectively. A third file, traj.txt containing the list of the frames to be used by PyRETIS, will be then also generated. Only the frames and the parts of the trajectories relevant for each ensemble will be considered by the load function. In the case that different trajectories are to be used to initialize different ensembles, the relevant files can be stored in the respective ensemble subfolders (e.g. ‘000’, ‘001’, etc) contained in the load folder. The load function searches in the load folder[000, 001, 002, etc.] for usable files. For each ensemble subfolder, if the files order.txt, energy.txt and traj.txt are present, they will be loaded, otherwise they will be re-generated. Note that if the .txt files will be loaded, a direct correspondence with the trajectory/frame files is expected (as in the forthcoming resume option section).

– FORMATTED/RESUME OPTION – Previous output can be copy and pasted in the load folder, or the here described files generated with the proper formatting. This option is usefull when simulations need to be restarted but some settings need to be changed, or when the restart files are corrupted.

The presence of subfolders named 000, 001 etc. and that these folders 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 32 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.