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 31 Supported initiation methods in PyRETIS
Method name Description
kick For initiating new trajectories from given initial configuration(s).
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 . Associated with this path ensemble is the interface and the kick method starts by searching for a crossing with this interface. Given that the system is in a phase point, say , 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 .
3. If is closer to the interface compared to , then we update and repeat the steps. Otherwise, the steps are just repeated without updating .

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 32 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.

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

Table 33 Keywords for the load method.
Keyword Description
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¶

The method keyword selects the load initialization.

The use of load_and_kick initialization method if the keyword is set to True. The method will select the loaded frame closest to the interface to be crossed and feeds it as starting point for the kicking initialization procedure. Once the kicking procedure will be completed, a new trajectory will be generated with 2 way shooting, fully replacing the loaded frames/trajectory.

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 ones for each ensemble (e.g. 000 001 etc). Thereafter, the order parameter will be computed and stored in the file order.txt. A second 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. The unstructured load checks if the loaded frames compose a trajectory that satisfies the relative ensemble definition. If not, the frames are sorted according to their order parameter and the ensemble definition is checked again. If the new sorted sequence still do not compose a formally valid trajectory, but some frames are present such that the ensemble definition could be satisfied, the path is mirrored in order to obtain a L to L or R to R path. This is a bookkeeping procedure to generate a formally valid path for a given ensemble. At the end of the procedure, all the frames that are not useful for the sampling are removed. The procedure will keep the two closest frames, before and after the first interface, and all the frames between the interface defining the ensemble and the last interface. In the case that this last group has no entries, the frames with the highest order parameter is kept in order to allow the load_and_kick procedure.

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 useful 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 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 34 Keywords for the restart method.
Keyword Description
method Selects the restart method.
flexible-restart Allow the modification of input before restarts.

Keyword method¶

method = restart
The method keyword selects the restart initialization. The general simulation information is stored in the file pyretis.restart. The restart file can be specified in the simulation section with the keyword restart in the simulation input file. Thereafter, path and ensemble data from restart files for each ensemble are loaded. These restart files are named ensemble.restart and there is one of 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. Note: if an ensemble has a lower number of cycles, it is possible to temporaneously prioritize it until it gets the same number of cycles by adding the keyword priority_shooting = True in the retis section.

Keyword method¶

flexible_restart = boolean

If True, the settings included in the input file will be read and used (e.g. change the number of interfaces, their position, etc). Note 1) If the settings are changed in a restart, the new options must be consistent in respect to the detail balance. If not, the pathensemble.txt files should be discarded. Note 2) If some interfaces are removed, the ensemble folders have to be relabeled by the user. PyRETIS expects a series of subfolders with a continuous numbering scheme that contains the relative ensembles. Note 3) If some ensemble have to be added, the priority_shooting option in the retis section might be considered to focus the sampling in the new ensembles.

Default:
The default value is flexible_restart = False.