.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/run_mesocircuit.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_auto_examples_run_mesocircuit.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_run_mesocircuit.py:

Run mesocircuit
------------------

Main example script to run a simulation of the mesocircuit with NEST and 
subsequently analyze and plot the results.
The simulation of the spiking neuronal network can be followed by an LFP
simulation and the corresponding postprocessing and plotting.

.. GENERATED FROM PYTHON SOURCE LINES 11-17

The script `mesocircuit_framework` contains the main functionality for
parameter evalutation and job execution.
The mesocircuit framework allows for the evaluation of parameter spaces, but
here we only simulate one individual parameter combination.
Several interesting parameter combinations (overwriting default values) are
collected in a dictionary in the script `parametersets` for convenience.

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.. code-block:: Python


    from mesocircuit import mesocircuit_framework as mesoframe
    import parametersets


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Here, we choose the parameter set `mesocircuit_MAMV1` which is the default
model. It is an upscaled version of the microcircuit representing area V1 of
the Multi-Area Model (Schmidt and van Albada, 2018).
'mesocircuit_MAMV1_evoked` applies a thalamic stimulus to the center of the
same model.
For local testing, `local_microcircuit_PD` and `local_mesocircuit_PD` are good
choices. These models base on the original microcircuit
(Potjans and Diesmann, 2014) and are downscaled for execution on a laptop.

.. GENERATED FROM PYTHON SOURCE LINES 30-36

.. code-block:: Python


    name = 'mesocircuit_MAMV1'
    # name = 'local_mesocircuit_PD'
    params_key = name
    custom_params = parametersets.ps_dicts[params_key]


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Next, we instantiate a `MesocircuitExperiment` with the custom parameters.
The argument `name` can be chosen freely; here we just use the name of the
parameter set.
Upon instantiation, data directories are created, derived parameters
calculated, and job scripts written.
If an already existing experiment should be loaded, a class can be
instantiated with the arguments of the existing `name` and `load=True`.

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.. code-block:: Python


    meso_exp = mesoframe.MesocircuitExperiment(name, custom_params)


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A `MesocircuitExperiment` provides an overview over all the parameter
combinations it is holding (`parameterview`) and a list of all the individual
model instances of class `Mesocircuit`` (`circuits`).

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.. code-block:: Python


    print(meso_exp.parameterview)
    print(meso_exp.circuits)


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For each Mesocircuit jobs can finally be launched.
All provided jobs are run one after the other. `analysis_and_plotting` is for
convenience combined into one job, but `analysis` and `plotting` can also be
handled as individual jobs.
For running the full model on an HPC cluster, `machine='hpc'` is required for
submitting batch scripts via slurm; for a local test run `machine='local'`
should be selected.

.. GENERATED FROM PYTHON SOURCE LINES 63-76

.. code-block:: Python


    circuit = meso_exp.circuits[0]
    circuit.run_jobs(
        jobs=[
            'network',
            'analysis_and_plotting',
            # 'lfp_simulation',
            # 'lfp_postprocess',
            # 'lfp_plotting',
        ],
        machine='hpc',
        # machine='local'
    )


.. _sphx_glr_download_auto_examples_run_mesocircuit.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: run_mesocircuit.ipynb <run_mesocircuit.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: run_mesocircuit.py <run_mesocircuit.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: run_mesocircuit.zip <run_mesocircuit.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_