.. _chemiscope:

chemiscope
==========

Chemiscope is a tool for interactive exploration of databases of materials and
molecules, correlating local and global structural representations with the
properties of the systems. Chemiscope files can be viewed `online
<https://chemiscope.org/>`_, generated using a `python library
<https://pypi.org/project/chemiscope/>`_ and used inside jupyter notebooks or
sphinx documentations, which is how it's used in the cookbook examples. You can
check the `documentation <https://chemiscope.org/docs/>`_ and the `github
repository <https://github.com/lab-cosmo/chemiscope>`_.



.. grid:: 1 2 2 3
    :gutter: 1 1 2 3

    .. grid-item::
        .. card:: Generalized Convex Hull construction for the polymorphs of ROY
            :link: ../examples/roy-gch/roy-gch
            :link-type: doc
            :text-align: center
            :shadow: md

            .. image:: ../examples/roy-gch/images/thumb/sphx_glr_roy-gch_thumb.png
                :alt: This notebook analyzes the structures of 264 polymorphs of ROY, from Beran et Al, Chemical Science (2022), comparing the conventional density-energy convex hull with a Generalized Convex Hull (GCH) analysis (see Anelli et al., Phys. Rev. Materials (2018)). It uses features computed with rascaline and uses the directional convex hull function from scikit-matter to make the figure.
                :class: gallery-img

                
    .. grid-item::
        .. card:: PCA/PCovR Visualization for the rattled GaAs training dataset
            :link: ../examples/gaas-map/gaas-map
            :link-type: doc
            :text-align: center
            :shadow: md

            .. image:: ../examples/gaas-map/images/thumb/sphx_glr_gaas-map_thumb.png
                :alt: This example uses rascaline and metatensor to compute structural properties for the structures in a training for a ML model. These are then used with simple dimensionality reduction algorithms (implemented in sklearn and skmatter) to obtain a simplified description of the dataset, that is then visualized using chemiscope.
                :class: gallery-img

                
    .. grid-item::
        .. card:: Path integral metadynamics
            :link: ../examples/pi-metad/pi-metad
            :link-type: doc
            :text-align: center
            :shadow: md

            .. image:: ../examples/pi-metad/images/thumb/sphx_glr_pi-metad_thumb.png
                :alt: This example shows how to run a free-energy sampling calculation that combines path integral molecular dynamics to model nuclear quantum effects and metadynamics to accelerate sampling of the high-free-energy regions.
                :class: gallery-img

                
    .. grid-item::
        .. card:: Path integral molecular dynamics
            :link: ../examples/path-integrals/path-integrals
            :link-type: doc
            :text-align: center
            :shadow: md

            .. image:: ../examples/path-integrals/images/thumb/sphx_glr_path-integrals_thumb.png
                :alt: This example shows how to run a path integral molecular dynamics simulation using i-PI, analyze the output and visualize the trajectory in chemiscope. It uses LAMMPS as the driver to simulate the q-TIP4P/f water model.
                :class: gallery-img