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Merge pull request #443 from ConnorWelch-OSU/update-input-file-names
Update input file names
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source/user/tutorial/add_deploy.rst

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``ExampleInstitution`` is a placeholder for your institution name, and in this scenario
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only one of each prototype will be deployed since ``n_build`` has a value of 1 for each.
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This example is now complete. Save your file as the desired file name (with ``.xml``
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extension) and run your code through |Cyclus|. If your simulation runs into errors,
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This example is now complete. Save your file as ``tutorial_deployinst.xml`` and run your code through |Cyclus|. If your simulation runs into errors,
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sample files can be found `here <https://doi.org/10.5281/zenodo.4557613>`_ under
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``input_deployinst.xml`` or ``output_deployinst.sqlite``.

source/user/tutorial/add_reg_inst.rst

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Activity: Save your input file
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------------------------------
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Save your input file as ``cyclus_intro_file.xml``
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Save your input file as ``tutorial_oncethrough.xml``
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Activity: Add an extra institution into the Region
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You are now ready to generate a full |Cyclus| input file.
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1. Save your input file as 'cyclus_intro_file.xml'
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1. Save your input file as ``tutorial_oncethrough.xml``
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Check: Full Input File

source/user/tutorial/add_second_reactor.rst

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Note: the blank space between ``</institution>`` and ``</region>`` is
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for additional institutions in the future.
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Save your input file as input_file2.xml and run the |Cyclus| simulation.
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Save your input file as ``tutorial_secondreactor.xml`` and run the |Cyclus| simulation.
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If your simulation runs into errors, sample files can be found `here
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<https://doi.org/10.5281/zenodo.4557613>`_ under ``input_secondreactor.xml``
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or ``ouput_secondreactor.sqlite``.

source/user/tutorial/mod_rxtr.rst

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Activity: Save your Input File
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--------------------
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The input for this example is now complete. Save your input file as 'recycle_input.xml'. If
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The input for this example is now complete. Save your input file as ``tutorial_recycle.xml``. If
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your simulation runs into errors, sample files can be found `here
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<https://doi.org/10.5281/zenodo.4557613>`_ under ``input_recycle.xml``
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or ``ouput_recycle.sqlite``.

source/user/tutorial/run_cyclus_native.rst

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--------------------------------------------
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1. Go to the Jupyter notebook, making sure you are in the same folder as the input file
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2. Remove any old |Cyclus| output files by: ``!rm tutorial.sqlite``
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3. Run |Cyclus| by: ``!cyclus input.xml -o tutorial_singlerx.sqlite``
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3. Run |Cyclus| by: ``!cyclus tutorial_oncethrough.xml -o tutorial_output_oncethrough.sqlite``
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.. image:: cyclus_in_IP.png
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:align: center
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:alt: Running |Cyclus| in an IPython Notebook
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When your simulation has finished, a file of the name ``tutorial_singlerx.sqlite``
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When your simulation has finished, a file of the name ``tutorial_output_oncethrough.sqlite``
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will be in your file folder. Your Jupyter Notebook can then be used with
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`Cymetric <https://fuelcycle.org/user/cymetric/index.html>`_ to analyze your
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data. Examples of how to use Cymetric can be found in the `GitHub

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