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examples: updated output documentation
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‎docs/source/conf.py‎

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# Configuration file for the Sphinx documentation builder.
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#
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# For the full list of built-in configuration values, see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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# -- Project information -----------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
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‎docs/source/examples.md‎

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# Examples
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```{eval-rst}
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.. warning::
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.. note::
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Some examples overwrite or create files or directories. If running in the PyMCNP/examples directory, run the following command to clean the
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directory:
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‎docs/source/examples/create.md‎

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INP cell created using `__init__`:
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1 1 0.5 #(99:3) imp:n 1.0
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## Creating Material Cards
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INP surface created using `__init__`:
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## Creating INP Files
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INP file created using `__init__`:
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Create `Inp`
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1 0 +1
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1 rpp -50 50 -50 50 -50 50
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1 rpp -10 10 -10 10 -10 10
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1 so 100
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m1 007014 -0.797088 008016 -0.199514
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m1 082204 -0.014 082206 -0.241 082207 -0.221 082208 -0.524
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sdef pos 0 0 0 erg 14.4 par 1
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f4:n 2
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nps 100000.0
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rand seed 1232209489
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m21 007014 -0.797088 008016 -0.199514
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m22 008016 -0.19984179019595494 022046 -0.02472289143502082 022047 &
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-0.02229555300321877 022048 -0.22091776443511935 022049 &
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-0.016212223353146985 022050 -0.015522979107079737 008016 &
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-0.03575396279808631 082206 -0.11186230536770471 082207 &
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-0.10257912649901553 082208 -0.24321928635965673
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m23 082204 -0.014 082206 -0.241 082207 -0.221 082208 -0.524
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‎docs/source/examples/do.md‎

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## Checking INP Files
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```{eval-rst}
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.. note::
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This example requires `example_00.inp <https://github.com/FSIBT/PyMCNP/blob/master/files/inp/example_00.inp>`_.
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```
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```{eval-rst}
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.. literalinclude:: ../../../examples/do_check.py
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:language: python
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```
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Output:
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Checking INP file: `PyMCNP/files/inp/example_00.inp`
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Fixing and writing to INP file: `PyMCNP/files/inp/example_00.inp`
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## Converting OUTP Files
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```{eval-rst}
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.. note::
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This example requires `example_00.outp <https://github.com/FSIBT/PyMCNP/blob/master/files/outp/example_00.outp>`_.
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```
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```{eval-rst}
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.. literalinclude:: ../../../examples/do_convert.py
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:language: python
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```
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Output:
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Converting tally #1 from `PyMCNP/files/outp/example_00.outp` to `example_00-1.csv`
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Converting tally #1 from `PyMCNP/files/outp/example_00.outp` to `example_00-1.parquet`
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## Plotting OUTP Files
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```{eval-rst}
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.. note::
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This example requires `example_00.outp <https://github.com/FSIBT/PyMCNP/blob/master/files/outp/example_00.outp>`_.
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```
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```{eval-rst}
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Plotting tally #1 from files/outp/example_00.outp.
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Writing plots tally #1 from files/outp/example_00.outp to `example_00-1.pdf`.
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![do_plot_0](../images/do_plot_0.png)
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![do_plot_1](../images/do_plot_1.png)
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![do_plot_2](../images/do_plot_2.png)
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![do_plot_3](../images/do_plot_3.png)
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## Running INP Files
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```{eval-rst}
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.. note::
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This example requires `example_00.inp <https://github.com/FSIBT/PyMCNP/blob/master/files/inp/example_00.inp>`_, `example_01.inp <https://github.com/FSIBT/PyMCNP/blob/master/files/inp/example_01.inp>`_, and `example_02.inp <https://github.com/FSIBT/PyMCNP/blob/master/files/inp/example_02.inp>`_.
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```
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```{eval-rst}
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.. literalinclude:: ../../../examples/do_run.py
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:language: python
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```
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Output:
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Running `echo` in the current working directory:
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Calling `prehook_batch` pymcnp-2025-08-22--01-12-44
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Calling `prehook_file` pymcnp-2025-08-22--01-12-44/run-0 0
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inp=pymcnp-2025-08-22--01-12-44/run-0/run-0.inp outp=pymcnp-2025-08-22--01-12-44/run-0/run-0.outp ptrac=pymcnp-2025-08-22--01-12-44/run-0/run-0.ptrac
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Calling `prehook_file` pymcnp-2025-08-22--01-12-44/run-1 1
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inp=pymcnp-2025-08-22--01-12-44/run-1/run-1.inp outp=pymcnp-2025-08-22--01-12-44/run-1/run-1.outp ptrac=pymcnp-2025-08-22--01-12-44/run-1/run-1.ptrac
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Calling `prehook_file` pymcnp-2025-08-22--01-12-44/run-2 2
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Calling `posthook_file` pymcnp-2025-08-22--01-12-44/run-0 0
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Calling `posthook_file` pymcnp-2025-08-22--01-12-44/run-1 1
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inp=pymcnp-2025-08-22--01-12-44/run-2/run-2.inp outp=pymcnp-2025-08-22--01-12-44/run-2/run-2.outp ptrac=pymcnp-2025-08-22--01-12-44/run-2/run-2.ptrac
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Calling `posthook_file` pymcnp-2025-08-22--01-12-44/run-2 2
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Calling `posthook_batch` pymcnp-2025-08-22--01-12-44
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## Visualizing INP Files
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```{eval-rst}
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.. note::
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This example requires `valid_29.inp <https://github.com/FSIBT/PyMCNP/blob/master/files/inp/valid_29.inp>`_.
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```
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```{eval-rst}
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Visualizing all surfaces from `PyMCNP/files/inp/valid_29.inp`.
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Writing visualizations of all surfaces from `PyMCNP/files/inp/valid_29.inp` to `valid_29-surfaces.pdf`
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![do_visualize](../images/do_visualize.png)
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## Parameter Scan
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```{eval-rst}
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.. note::
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This example requires `example_01.outp <https://github.com/FSIBT/PyMCNP/blob/master/files/outp/example_01.outp>`_ and `example_04.inp <https://github.com/FSIBT/PyMCNP/blob/master/files/inp/example_04.inp>`_.
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```
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```{eval-rst}
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.. literalinclude:: ../../../examples/do_parameter_scan.py
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:language: python
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```
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Output:
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Running parameter scan `echo` in the current working directory:
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inp=pymcnp-2025-08-22--01-52-15/run-0/run-0.inp outp=pymcnp-2025-08-22--01-52-15/run-0/run-0.outp ptrac=pymcnp-2025-08-22--01-52-15/run-0/run-0.ptrac
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inp=pymcnp-2025-08-22--01-52-15/run-1/run-1.inp outp=pymcnp-2025-08-22--01-52-15/run-1/run-1.outp ptrac=pymcnp-2025-08-22--01-52-15/run-1/run-1.ptrac
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inp=pymcnp-2025-08-22--01-52-15/run-2/run-2.inp outp=pymcnp-2025-08-22--01-52-15/run-2/run-2.outp ptrac=pymcnp-2025-08-22--01-52-15/run-2/run-2.ptrac
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inp=pymcnp-2025-08-22--01-52-15/run-3/run-3.inp outp=pymcnp-2025-08-22--01-52-15/run-3/run-3.outp ptrac=pymcnp-2025-08-22--01-52-15/run-3/run-3.ptrac
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inp=pymcnp-2025-08-22--01-52-15/run-4/run-4.inp outp=pymcnp-2025-08-22--01-52-15/run-4/run-4.outp ptrac=pymcnp-2025-08-22--01-52-15/run-4/run-4.ptrac
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DONE! :)
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![do_parameter_scan_0](../images/do_parameter_scan_0.png)
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![do_parameter_scan_1](../images/do_parameter_scan_1.png)
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![do_parameter_scan_2](../images/do_parameter_scan_2.png)
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![do_parameter_scan_3](../images/do_parameter_scan_3.png)
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![do_parameter_scan_4](../images/do_parameter_scan_4.png)

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