---
myst:
  html_meta:
    "description": "A tutorial on running a Parallel Replica Dynamics (PRD) job with eOn, including how to add hyperdynamics for accelerated simulations."
    "keywords": "eOn Parallel Replica tutorial, PRD, hyperdynamics, accelerated dynamics, Al(100)"
---

# 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:

```{figure} ../fig/aladatom1.png
---
alt: Al adatom on the Al(100)
class: full-width
align: center
---
Al adatom on the Al(100)
```

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 `python -m eon.server`

```{code-block} bash
eOngit/examples/parallel-replica via 🅒 eongit
➜ python -m eon.server
Eon version: 1321976b
Simulation time: 0.000000e+00 s
State list path does not exist; Creating: .//states/
Registering results
Processed results: 0
Time in current state: 0.000000e+00 s
Simulation time: 0.000000e+00 s
Queue contains: 0 searches
Making: 2 searches
Job finished: .//jobs/scratch/0_0
Job finished: .//jobs/scratch/0_1
Created: 2 searches
```

Then use the `-n` flag to register the result::

```{code-block} bash
eOngit/examples/parallel-replica via 🅒 eongit
➜ python -m eon.server -n
Eon version: 1321976b
Simulation time: 0.000000e+00 s
Registering results
Found transition with time: 5.000e-12 s
Cancelled 0 workunits from state 0
Processed results: 0
Currently in state: 1
Time in current state: 0.000000e+00 s
Simulation time: 5.000000e-12 s
Queue contains: 0 searches
Making: 0 searches
```

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

```{code-block} bash
➜ cat dynamics.txt
 step-number   reactant-id    process-id    product-id     step-time    total-time       barrier          rate        energy
-----------------------------------------------------------------------------------------------------------------------------
           0             0             0             1  5.000000e-12  5.000000e-12      0.000000  0.000000e+00   -472.909569
```

More information is obtained by running a few more times:

```{code-block} bash
➜ for i in {0..2}; python -m eon.server; done
Eon version: 1321976b
Simulation time: 5.000000e-12 s
Registering results
Processed results: 0
Time in current state: 0.000000e+00 s
Simulation time: 5.000000e-12 s
Queue contains: 0 searches
Making: 2 searches
Job finished: .//jobs/scratch/1_2
Job finished: .//jobs/scratch/1_3
Created: 2 searches
Eon version: 1321976b
Simulation time: 5.000000e-12 s
Registering results
Found transition with time: 2.000e-12 s
Cancelled 0 workunits from state 1
Processed results: 0
Currently in state: 2
Time in current state: 0.000000e+00 s
Simulation time: 7.000000e-12 s
Queue contains: 0 searches
Making: 2 searches
Job finished: .//jobs/scratch/2_4
Job finished: .//jobs/scratch/2_5
Created: 2 searches
➜ python -m eon.server -n
Eon version: None
Simulation time: 7.000000e-12 s
Registering results
Found transition with time: 3.000e-12 s
Cancelled 0 workunits from state 2
Processed results: 0
Currently in state: 3
Time in current state: 0.000000e+00 s
Simulation time: 1.000000e-11 s
Queue contains: 0 searches
Making: 0 searches
➜ cat dynamics.txt
 step-number   reactant-id    process-id    product-id     step-time    total-time       barrier          rate        energy
-----------------------------------------------------------------------------------------------------------------------------
           0             0             0             1  5.000000e-12  5.000000e-12      0.000000  0.000000e+00   -472.909569
           1             1             0             2  2.000000e-12  7.000000e-12      0.000000  0.000000e+00   -472.909577
           2             2             0             3  3.000000e-12  1.000000e-11      0.000000  0.000000e+00   -472.909572
```

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:

```{figure} ../fig/aladatom2.png
---
alt: Al adatom on the Al(100)
class: full-width
align: center
---
Al adatom on the Al(100)
```

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

## Adding Hyperdynamics

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


```{code-block} ini
[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.