documentation refactor 1

Doc/_static/custom.css

@@ -32,7 +32,7 @@ a:hover {
 
 /* Custom styles for math elements */
 .math {
-    text-align: left;
+    text-align: center;
 }
 
 .eqno {

Doc/conf.py

@@ -65,7 +65,13 @@
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode', 'sphinx.ext.graphviz', 'sphinx.ext.inheritance_diagram', 'sphinx.ext.imgmath']#,'rst2pdf.pdfbuilder']
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.graphviz',
+    'sphinx.ext.inheritance_diagram',
+    'sphinx.ext.mathjax',
+]#,'rst2pdf.pdfbuilder']
 
 imgmath_latex_preamble = "\\usepackage{mathrsfs}"
 

Doc/index.rst

@@ -10,22 +10,17 @@ Welcome to MDANSE's documentation!
    This is the documentation of the MDANSE 2.0 release.
    The documentation, just like the code itself, is still under development.
 
-Introduction
-============
-
-`MDANSE Project Website <https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx>`_
-
-`MDANSE GitHub Page <https://github.com/ISISNeutronMuon/MDANSE>`_
+**Useful links**: `MDANSE Project Website <https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx>`_ | `MDANSE GitHub Page <https://github.com/ISISNeutronMuon/MDANSE>`_
 
 **MDANSE** (**Molecular Dynamics Analysis for Neutron Scattering Experiments**)
-is a python application designed for computing neutron observables
+is a Python application designed for computing neutron observables
 from molecular dynamics (MD) trajectories that can be directly compared with
 neutron scattering experiments, particularly inelastic and quasi-elastic
 neutron scattering spectroscopies.
 
-To do this, it interfaces with a variety of MD simulation software such
-as CASTEP, VASP, DMOL, Gromacs, DL_POLY, CHARMM, LAMMPS, PBD, DFTB etc., 
-and provides both a graphical user interface (GUI) and a command line interface. 
+MDANSE can analyse MD trajectories from a variety of MD simulation software such
+as CASTEP, VASP, DMOL, Gromacs, DL_POLY, CHARMM, LAMMPS, DFTB and etc.,
+and provides both graphical user interface (GUI) and command line interfaces.
 
 This project is built on the development published previously: \
 G. Goret, B. Aoun, E. Pellegrini, "MDANSE: An Interactive Analysis Environment for Molecular Dynamics Simulations", 
@@ -57,49 +52,51 @@ J Chem Inf Model. 57(1):1-5 (2017).
        </div>
    </div>
 
-
 .. toctree::
    :maxdepth: 5
+   :hidden:
    :caption: 💡 Explanations
 
    pages/introduction
    pages/installation
    pages/files
-   pages/gui
-   pages/cmd
    pages/workflow
    pages/dynamics
    pages/scattering
    pages/structure
    pages/analysis
-   pages/trajectory
-   pages/plotting
    pages/fca
 
 .. toctree::
    :maxdepth: 5
+   :hidden:
    :caption: ⚛️ How-To Guides
 
-   pages/H_gui
+   pages/H_start
    pages/H_cli
+   pages/H_gui
+   pages/gui
+   pages/H_trajectory
+   pages/H_gloss
    pages/H_Dynamics
    pages/H_Scattering
    pages/H_Structure
    pages/H_other
-   pages/H_gloss
-   pages/H_Plotting
    pages/H_fca
+   pages/H_Plotting
+   pages/H_Batch
 
 .. toctree::
    :maxdepth: 5
+   :hidden:
    :caption: 🧪 Tutorials
 
-   pages/T_Batch
+   pages/T_Water_IR
    pages/T_sim
-   pages/T_Analysis
 
 .. toctree::
    :maxdepth: 5
+   :hidden:
    :caption: 📚 Technical References
 
    pages/R_contact
@@ -109,7 +106,7 @@ J Chem Inf Model. 57(1):1-5 (2017).
    pages/R_further
    pages/references
 
-Indices and tables
+Indices and Tables
 ==================
 
 * :ref:`genindex`

Doc/pages/T_Batch.rst → Doc/pages/H_Batch.rst

@@ -1,5 +1,5 @@
-Running Batch Jobs in MDANSE: Tutorial
-=============================================
+Running Batch Jobs
+==================
 
 Introduction
 ------------

Doc/pages/H_Dynamics.rst

@@ -1,5 +1,5 @@
-How to Guide: Analysis Dynamics
-======================================
+Running Dynamics Calculations
+=============================
 
 Angular Correlation
 -------------------

Doc/pages/H_Plotting.rst

@@ -1,5 +1,156 @@
-How to guide: Plotting Options 
-===============================
+Plotting the Results
+====================
+
+In this section, we'll explore various plotting options tailored to MDANSE
+(Molecular Dynamics Analysis for Neutron Scattering Experiments) data, helping
+you effectively analyze and visualize your scientific findings.
+
+To learn more about how to use these plots and make the most out of MDANSE's
+visualization tools, refer to the technical references and user guides available
+in the MDANSE documentation. These resources provide in-depth instructions,
+examples, and tips on utilizing the plotting capabilities.
+
+Understanding the Plotting Options
+----------------------------------
+
+**Line Plotter:**
+    Visualize dynamic trends in MDANSE data, e.g., temperature fluctuations,
+    energy profiles, or scattering intensities over time. Customize line styles,
+    colors, and axes settings.
+
+**Image Plotter:**
+    Display MDANSE data as heatmaps or spatial distributions. Adjust aspect
+    ratios, colormaps, and settings for neutron scattering patterns, electron
+    density maps, or spatial correlations.
+
+**Elevation Plotter:**
+    Explore 3D MDANSE structures and landscapes. Zoom in on molecular
+    structures and adjust contrast for detailed examination of complex systems,
+    like biomolecules or nanomaterials.
+
+**2D Slice Plotter:**
+    Visualize specific 3D MDANSE data slices, focusing on dimensions and regions
+    of interest. Simplify density profiles, radial distribution functions, or
+    cross-sectional views of molecular assemblies.
+
+**Iso Surface Plotter:**
+    Create 3D surface visualizations with various rendering modes. Adjust opacity,
+    contours, and slice orientations to highlight features in volumetric data,
+    such as solvent density distributions or macromolecular structures.
+
+Choosing the Right Plotting Option
+----------------------------------
+
+Selecting the appropriate plotting option is crucial for meaningful insights:
+
+**Line Plotter:**
+    For tracking temporal changes like temperature and energy during simulations.
+
+**Image Plotter:**
+    To display spatial information, such as scattering patterns, electron
+    densities, or diffusion maps.
+
+**Elevation Plotter:**
+    Useful for gaining a 3D perspective on complex molecular structures,
+    nanomaterials, or biomolecules.
+
+**2D Slice Plotter:**
+    When focusing on specific 3D data sections, aiding local property analysis.
+
+**Iso Surface Plotter:**
+    Great for rendering 3D volumetric data, highlighting complex structures like
+    solvent-solute interfaces or protein conformations.
+
+
+
+Line Plotter
+-------------
+
+Figure 1 shows a Line Plot of temperature vs. time. In this Line Plotter,
+the x-axis represents time (in picoseconds), while the y-axis represents
+temperature (in Kelvin). The graph shows how the temperature of a molecular
+system evolves during a 1000 ps molecular dynamics simulation. This plot
+allows for tracking variations and trends in the system's temperature,
+revealing valuable insights into its thermal behavior over time.
+
+MDANSE's Line Plotter is an essential tool for visualizing dynamic data trends.
+It's particularly valuable for tracking changes in critical parameters, such as
+temperature fluctuations, energy profiles, or scattering intensities, as they
+evolve over time during simulations. Users can adjust line styles, colors, and
+axes settings to enhance data clarity. This tool is useful for analyzing
+temporal behavior. For instance, it can identify temperature shifts that may
+indicate phase transitions, fluctuations in energy levels signifying critical
+events, or scattering intensity variations revealing structural changes.
+
+Image Plotter
+-------------
+
+Figure 2 shows an Image Plot of a neutron scattering pattern from a
+crystalline material. It employs scattering angles (in degrees) on both
+the x and y-axes, while the colormap represents neutron scattering
+intensity. This visualization aids in the identification of
+crystallographic peaks and provides structural insights.
+
+The Image Plotter in MDANSE simplifies spatial data visualization,
+making it suitable for systems with complex data structures, including
+neutron scattering patterns or electron density maps. Its user-friendly
+interface allows you to customize aspect ratios and select colormaps
+that best highlight essential data features. This tool aids in pattern
+recognition and structural analysis. It is particularly beneficial for
+understanding structural insights within diverse systems.
+
+Elevation Plotter
+-----------------
+
+Figure 3 shows a three-dimensional elevation plot of a biomolecule. The
+x and y-axes denote spatial coordinates (in angstroms), while the z-axis
+represents elevation, offering a three-dimensional view of a protein's
+structure. It provides a view of its spatial arrangement, including bond
+angles and structural features.
+
+MDANSE's Elevation Plotter is for exploring complex three-dimensional
+structures like biomolecules and nanomaterials. Researchers can zoom in
+on molecular structures, adjust contrast settings, and navigate 3D
+topography. This tool reveals subtle spatial details often concealed in
+2D representations, aiding in visualizing surface characteristics or
+deconstructing the structure of biomolecules.
+
+2D Slice Plotter
+----------------
+
+Figure 4 shows a Density Profile Slice. The 2D Slice Plotter reveals the
+density profile of solvent molecules within a specific plane of a
+nanomaterial. Spatial coordinates (in nanometers) are depicted on the x
+and y-axes, while the color map indicates particle density. This plot is
+instrumental in understanding spatial variations in solvent distribution.
+
+The 2D Slice Plotter simplifies the visualization of cross-sectional
+views within 3D datasets. It streamlines the examination of localized
+properties, enabling in-depth analysis of factors like density profiles
+or composition within specific sections of a system. Researchers employ
+it to study particle distribution in nanomaterials or conduct
+compositional analyses of specific molecular layers.
+
+Iso Surface Plotter
+-------------------
+
+Figure 5 shows an Electron Density Iso Surface. This provides a detailed
+visualization of the electron density distribution around a molecule. It
+utilizes spatial coordinates (in angstroms) on the x, y, and z-axes,
+while the isosurface illustrates specific electron density levels.
+Researchers can manipulate parameters to emphasize molecular shapes and
+binding sites within the electron density data.
+
+MDANSE's Iso Surface Plotter effectively visualizes volumetric data.
+Researchers can customize parameters like opacity and contour levels to
+emphasize features within 3D datasets, such as solvent density
+distributions or protein conformations. This tool aids in visualizing and
+analyzing complex structures and interfaces within molecular or material
+systems, facilitating tasks like visualizing molecular binding sites or
+solvent molecule arrangements around nanoparticles. Researchers gain a
+comprehensive understanding of intricate structures and their scientific
+significance.
+
 
 Line Plotter
 ------------

Doc/pages/H_Scattering.rst

@@ -1,8 +1,8 @@
-How to Guide Analysis: Scattering
-==================================
+Running Scattering Calculations
+===============================
 
-Current Correlation Function Analysis 
-''''''''''''''''''''''''''''''''''''''
+Current Correlation Function
+''''''''''''''''''''''''''''
 **Index 1:** Current Correlation Function Analysis 
 
 **Purpose:**
@@ -69,8 +69,8 @@ of density fluctuations and propagating shear modes within the molecular system.
     - Overlay multiple CCF plots to facilitate comparisons.
 
 
-Dynamic Coherent Structure Factor Analysis 
-'''''''''''''''''''''''''''''''''''''''''''
+Dynamic Coherent Structure Factor
+'''''''''''''''''''''''''''''''''
 **Index 2:** Dynamic Coherent Structure Factor Analysis
 
 **Purpose:**
@@ -126,8 +126,8 @@ following plotting suggestions for better visualization and interpretation:
    - Use contour plots to visualize the evolution of the dynamic incoherent
    structure factor over time.
 
-Dynamic Incoherent Structure Factor Analysis 
-'''''''''''''''''''''''''''''''''''''''''''''
+Dynamic Incoherent Structure Factor
+'''''''''''''''''''''''''''''''''''
 **Index 3:** Dynamic Incoherent Structure Factor Analysis
 
 **Purpose:**
@@ -187,8 +187,8 @@ system.
      of Q and time, highlighting prominent features.
 
 
-Elastic Incoherent Structure Factor Analysis 
-'''''''''''''''''''''''''''''''''''''''''''''
+Elastic Incoherent Structure Factor
+'''''''''''''''''''''''''''''''''''
 **Index 4:** Elastic Incoherent Structure Factor Analysis
 
 **Purpose:**
@@ -243,8 +243,8 @@ and the EISF within the system.
      - Generate 2D contour plots to explore correlations between Q vectors and
        their impact on the EISF.
 
-Gaussian Dynamic Incoherent Structure Factor Analysis 
-''''''''''''''''''''''''''''''''''''''''''''''''''''''
+Gaussian Dynamic Incoherent Structure Factor
+''''''''''''''''''''''''''''''''''''''''''''
 **Index 5:** Gaussian Dynamic Incoherent Structure Factor Analysis
 
 **Purpose:**
@@ -300,8 +300,8 @@ neutron-specific studies.
        dynamic changes within the system.
 
 
-Neutron Dynamic Total Structure Factor Analysis 
-''''''''''''''''''''''''''''''''''''''''''''''''
+Neutron Dynamic Total Structure Factor
+''''''''''''''''''''''''''''''''''''''
 **Index 6:** Neutron Dynamic Total Structure Factor Analysis
 
 **Purpose:**

Doc/pages/H_Structure.rst

@@ -1,5 +1,5 @@
-How-to Guide: Analysis Structure 
-=================================
+Running Structure Calculations
+==============================
 
 Area Per Molecule
 -----------------