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Basic Analysis
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The basics on PELE analysis to run after the simulation is finished.


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Plot metrics
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AdaptivePELE (within the PelePlatform) and Gnuplot is need it. **To run from inside the /LIG_Pele/output/ folder**

Explanation::

    python -m AdaptivePELE.analysis.plotAdaptive pele_steps column_x (starting by 1) column_y  basename_of_report -points -zcol column_z (colorbar)  | gnuplot -p

Example::

    python -m AdaptivePELE.analysis.plotAdaptive 8 5 6 report_ -points -zcol 4 | gnuplot -p


**If you want to limit the axis of the plot** 

    You can obtain the gnuplot command by doing the next command:
        ``python -m AdaptivePELE.analysis.plotAdaptive 8 5 6 report_ -points -zcol 4``
    
    To obtain this output: 
        ``set cbrange[0:60]; plot for [i=1:127] for [j=0:60-1] ''.j.'/report_'.i u 5:8 lt 6 lc palette frac j/60. notitle``


    Then enter to gnuplot set the xrange/yrange and use the line outputted by the previous command to plot:

    .. code-block:: bash

        $ gnuplot

            > set xrange [-9600:-9400]

            > set yrange [-90:0]

            > set cbrange[0:60]; plot for [i=1:127] for [j=0:60-1] ''.j.'/report_'.i u 5:8 lt 6 lc palette frac j/60. notitle



Output:

.. image:: gnuplot.png

*****************************************
Retrieve the snapshots with best energy
*****************************************

AdaptivePELE (within PelePlatform) is need it. **To run from inside the LIG_Pele/output/ folder.**

Explanation::

    python -m AdaptivePELE.analysis.interactivePlot  columny columnx pele_steps -o output_folder

Example::

    python -m AdaptivePELE.analysis.interactivePlot  5 6 8 -o BestStructs

Once the plot is done with your left button mouse drag a square on the plot containing the structures you want to be downloaded as shown in Figure below.


.. image:: interactivePlot.png
    :align: center


This will output all snapshots contain in the square in a folder called BestStructs.


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Extract the movie of your best snapshot
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AdaptivePELE is need it.

Once you did the interactivePlot you may want to have the entrance path of your best selected structure. For this you must run the commnad below **from inside the LIG_Pele/output folder.**

Explanation::

    python -m AdaptivePELE.analysis.backtrackAdaptiveTrajectory  epoch trajectory step

Example::

    python -m AdaptivePELE.analysis.backtrackAdaptiveTrajectory  5 123 1