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‎_sources/index.rst.txt

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Indices and tables
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==================
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* :ref:`genindex`
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* :ref:`modindex`
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* :ref:`search`
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.. toctree::
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:caption: Tutorial
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:maxdepth: 2
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:hidden:
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tutorials/tutorial
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.. toctree::
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.. toctree::
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:caption: Python modules
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:maxdepth: 2
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:hidden:
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modules/trajectorytool
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modules/boxcountingtool
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modules/countoscope
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modules/countoscope

‎_sources/tutorials/tutorial.rst.txt

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Tutorial
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========
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Installation
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------------
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In order to install the Countoscope Python tool, clone the repository using:
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.. code:: bash
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git clone https://github.com/Countoscope/countoscope.git
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Install all the required Python packages using:
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.. code:: bash
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pip install -r requirements.txt
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Then, type:
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.. code:: bash
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pip install .
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Use
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---
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In a Python script or a Jupyter Notebook, define the path to the data trajectory
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file. For instance, using the `3D-closed` dataset provided in the `datasets`
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repository:
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.. code:: python
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path_to_data = "/mpath/datasets/datasets/3D-closed/trajectory.xyz"
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Import the Countoscope as well as NumPy by typing:
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.. code:: python
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from countoscope import Countoscope
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import numpy as np
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The trajectory file `trajectory.xyz` corresponds to a system of 190 particles in
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a :math:`(30 Å)^3` box. Let us define the system size as a NumPy array:
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.. code:: python
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system_size = np.array([30, 30, 30])
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Finally, let us choose a grid size for the Countoscope measurement:
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.. code:: python
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box_size=np.array([10, 10, 10])
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Then, launch the Countoscope calculation using *trajectory_file*, *system_size*,
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and *box_size* as input parameters:
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.. code:: python
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results = Countoscope(trajectory_file = path_to_data,
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system_size=system_size,
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box_size=box_size)
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results.run()
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After the calculation is done, all the computed data can be obtained from the
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`results`object. For instance, for :math:`<N>`, type:
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.. code:: python
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print(np.round(results.mean_of_N,2))
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which will return:
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.. code:: bash
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0.84
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To plot :math:`<\Delta N^2>`, let us import Pyplot first:
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.. code:: python
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import matplotlib.pyplot as plt
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plt.loglog(results.delta_n2)

‎genindex.html

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<p class="caption" role="heading"><span class="caption-text">Tutorial</span></p>
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<li class="toctree-l1"><a class="reference internal" href="tutorials/tutorial.html">Tutorial</a></li>
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<p class="caption" role="heading"><span class="caption-text">Python modules</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="modules/trajectorytool.html">Trajectory Tool</a></li>
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<li class="toctree-l1"><a class="reference internal" href="modules/boxcountingtool.html">Box Counting Tool</a></li>
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<li class="toctree-l1"><a class="reference internal" href="modules/countoscope.html">Countoscope</a></li>

‎index.html

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<head><meta charset="utf-8"/>
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<link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="search.html" /><link rel="next" title="Trajectory Tool" href="modules/trajectorytool.html" />
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<link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="search.html" /><link rel="next" title="Tutorial" href="tutorials/tutorial.html" />
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<title>Countoscope 0.0.1 documentation</title>
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<p class="caption" role="heading"><span class="caption-text">Python modules</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="modules/trajectorytool.html">Trajectory Tool</a></li>
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<li class="toctree-l1"><a class="reference internal" href="modules/boxcountingtool.html">Box Counting Tool</a></li>
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<li class="toctree-l1"><a class="reference internal" href="modules/countoscope.html">Countoscope</a></li>
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</section>
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<section id="indices-and-tables">
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<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Link to this heading"></a></h1>
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<ul class="simple">
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<li><p><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></p></li>
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<li><p><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></p></li>
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<li><p><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></p></li>
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<script src="_static/sphinx_highlight.js?v=dc90522c"></script>
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‎modules/boxcountingtool.html

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‎modules/countoscope.html

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‎modules/trajectorytool.html

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<link rel="index" title="Index" href="../genindex.html" /><link rel="search" title="Search" href="../search.html" /><link rel="next" title="Box Counting Tool" href="boxcountingtool.html" /><link rel="prev" title="Countoscope" href="../index.html" />
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<link rel="index" title="Index" href="../genindex.html" /><link rel="search" title="Search" href="../search.html" /><link rel="next" title="Box Counting Tool" href="boxcountingtool.html" /><link rel="prev" title="Tutorial" href="../tutorials/tutorial.html" />
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‎objects.inv

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# Project: Countoscope
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# Version:
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# The remainder of this file is compressed using zlib.
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xڵUMS� ��W0��D�G{��{�Pxmp���4�zIi�$��ms�c����vh���qǚ��[�(IY��Jy$a`��pJޅ���� �˞q�8�W~&��dv�����u�+Ph��=��o-T(�����N/c*=��'�[�t*$0��r+��j�&6��Vh�4*�� &Tu�;����� ����G-�Ş�cw��sm���\a=zՋ)�ʪq3Cc@R'PO��A:��4����2t��`.�r�~x�l��>��@W��XHǸ�E�qpM ��:P9ޜv���V���BB�h|�W'�iG�ɗ� P�Sl�F�w�嶠��#��k�$��vu�#/�09�8��At|�x�cY��F8���Gr��v.��O{��=i�D<cZzx�H�b4��S��u*�Ki��o��W�5�� k��{�_�-$��N�6
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xڵUMS� ��W0��Əc�z�㌽g(�-��8��^R�6��j���x�����%�Kȗ��T�!jV�s����nY��&_��Wqsv�f���p���-���{vw����9�'( t��@k��*��Apৗq��N$�`:���k%���/A��:����D^}����!S!]���B���Go��d{̎���!�І?(��דO=�>��7 t4'�v" ����D���2le��N�"�?��Bo�Ӈ��u1�.vӱ&���i.��6�kO`
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��9�XZ/�6���)х�[�H��v(5�_Ηr�e�b����y�>nVY �I�5_�f�;֭nq�f{�Dрz������`,�Y��<GgD�W;֚Y���k���O��l�mh��K�K�$��� �7�E��м�!y�0B��Ãq-�y���|UM�q�Վ�w���޷�e߽��$

‎py-modindex.html

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<ul>
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‎search.html

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<li class="toctree-l1"><a class="reference internal" href="modules/countoscope.html">Countoscope</a></li>

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