.. _tutorial_parrep:

===================================
Running a Parallel Replica Job
===================================

A sample parallel replica simulation can be found in the directory: ``examples/parallel-replica/``. Two input files ``config.ini`` and ``pos.con`` are required for EON simlution.

The example system is the diffusion of an Al adatom on the Al(100) surface. A snapshot of the system is given below:

..  image:: fig/aladatom1.png
    :align: center

The ``config.ini`` file will run a parallel replica job with 2 replicas on one local core. 

.. literalinclude:: ../examples/parallel-replica/.config.ini.tur

Now we can run the trajectory by executing the command ``../../bin/eon``::

    $ ../../bin/eon
    simulation time is 0.000000e+00
    state list path does not exist, creating .//states/
    registering results
    0 (result) searches processed
    time in current state is 0.000000e+00
    0 searches in the queue
    making 2 searches
    job finished in .//jobs/scratch/0_0
    job finished in .//jobs/scratch/0_1
    2 searches created

Then use "../../bin/eon -n" to register the result::

    $ ../../bin/eon -n
    simulation time is 0.000000e+00
    registering results
    found transition with time 8.200e-12
    2 (result) searches processed
    Average Speedup is  1.000000
    time in current state is 0.000000e+00
    currently in state 1
    0 searches in the queue
    making 0 searches

Information from the trajectoy is written in the ``dynamics.txt`` file::

    step-number   reactant-id    process-id    product-id     step-time    total-time       barrier          rate
    ---------------------------------------------------------------------------------------------------------------
                0             0             0             1  8.200000e-12  8.200000e-12      0.000000  0.000000e+00

The first column contains the number of the trajectories which find a transition label the successful searches, in this case all the three searches are successful. The second and fouth column label the reactant and product; Column 5 and Column 6 are the transition time for each success searches and the accumulated simulation time.
    
Detailed information of the simulation is stored in the folder ``states``. where the geometric and energy of the visited states are stored in the sub-folder labeled as state id. You can find the geometric of the prodcut in ``states/1/reactant.con/``, a snapshot is shown below:

..  image:: fig/aladatom2.png 
    :align: center

Compared to the reactant geometric, we can tell that the transition we found follows the exchange mechanism.

Parallel Replica with Hyperdynamics
--------------------------------------

You can turn on the hyperdynamics method by adding the following section to your ``config.ini`` file::

    [Hyperdynamics]
    bias_potential=bond_boost       ; bond_boost bias potential
    bb_boost_atomlist=20,26,50,56,150 ; atoms that are boosted in the bias potential
    bb_rcut=3.0                     ; boost radius
    bb_rmd_time=100.0               ; MD time to obtain the equilibrium configuration
    bb_dvmax=0.4                    ; magnitude of the bond-boost bias potential
    bb_stretch_threshold=0.2        ; defines the bond-boost dividing surface
    bb_ds_curvature=0.95            ; curvature near the bond-boost dividing surface, it should be <= 1; a value of 0.9-0.98 is recommended
   
All other settings and output infomation are as in a regular parallel replica dynamics simulation.