Updated the documentation

Author: mesonepigreco

UserGuide/_static/about.html

@@ -0,0 +1,6 @@
+<h3>About</h3>
+<p>SSCHA code documentation</p>
+<p><a href="https://www.sscha.eu">
+	<img src="http://sscha.eu/img/SSCHA_Logo_original_Horizontala_leyeda_Gabe.png"
+		alt="www.sscha.eu" width="200" height="50" />
+</a></p>

UserGuide/advanced.rst

@@ -138,6 +138,56 @@ You can plot all the minimization path (frequencies, free energy, gradients) cal
 The sscha-plot-data.py script is automatically installed within the SSCHA code.
 
 
+Load from the output files
+--------------------------
+
+It is possible to load an ensemble directly from a list of output files from a specific program, 
+like quantum ESPRESSO.
+This is usefull when a calculation ended with an error on the cluster, 
+and the ensemble has not been saved on the disk (but you have the output files of the 
+configurations that have been already computed succesfully).
+
+In this case, you can restart the minimization using an ensemble with the following code:
+
+.. code-block:: python
+
+    # Load the dynamical matrix
+    dyn = CC.Phonons.Phonons("dyn", 4)
+
+    # Load the ensemble
+    ens = sscha.Ensemble.Ensemble(dyn, 300)
+
+    # Load the ensemble from the output of the calculator
+    # In this case, the pwo files are output of the quantum espresso program.
+    # Any output file that ASE is able to read can be used to load the ensemble.
+    ens.load_from_calculator_output(directory="data", out_ext=".pwo")
+
+
+    # Run the minimization
+    minim = sscha.SchaMinimizer.SSCHA_Minimizer(ens)
+    minim.init()
+    minim.set_minimization_step(0.01)
+    minim.run()
+    minim.finalize()
+
+An example of this procedure is provided in the ``tests/test_load_ensemble_from_calculator_output`` directory.
+
+Alternatively, you can also use the ensemble to restart a full relax procedure.
+In this case, you need to provide the key ``restart_from_ens = True`` to the
+``relax`` or ``vc_relax`` methods of the ``SSCHA`` class in the ``Relax`` module.
+
+.. code-block:: python
+
+   # Initialize the minimizer minim (see example above)
+   relax = sscha.Relax.SSCHA(minim, ase_calculator=calculator,
+                           N_configs = 100, max_pop = 20)
+   relax.relax(restart_from_ens = True)
+
+   # Or, if you want to perform a variable cell relaxation
+   relax.vc_relax(restart_from_ens = True)  
+
+
+
 Cluster configuration with a code different from Quantum ESPRESSO
 -----------------------------------------------------------------
 

UserGuide/conf.py

@@ -63,9 +63,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'1.2'
+version = u'1.4'
 # The full version, including alpha/beta/rc tags.
-release = u'1.2'
+release = u'1.4'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -93,11 +93,24 @@
 #
 html_theme = 'alabaster'
 
+
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 #
-# html_theme_options = {}
+html_theme_options = {
+        "rightsidebar": "true",
+        "relbarbgcolor": "black"
+        }
+
+html_sidebars = {
+        "**": [
+            "about.html",
+            "navigation.html",
+            "relations.html",
+            "searchbox.html"
+            ]
+        }
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -109,12 +122,12 @@
 #
 # This is required for the alabaster theme
 # refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
-html_sidebars = {
-    '**': [
-        'relations.html',  # needs 'show_related': True theme option to display
-        'searchbox.html',
-    ]
-}
+# html_sidebars = {
+#     '**': [
+#         'relations.html',  # needs 'show_related': True theme option to display
+#         'searchbox.html',
+#     ]
+# }
 
 
 # -- Options for HTMLHelp output ------------------------------------------

UserGuide/install.rst

@@ -5,11 +5,57 @@ The SSCHA code is a collection of 2 python packages: CellConstructor and python-
 In this guide, we refer to the installation of python-sscha.
 
 
+Easy installation using Anaconda
+--------------------------------
+
+The easy way to install python-sscha is to use the anaconda distribution of python.
+
+.. code-block:: console
+
+    conda create -n sscha -c conda-forge python=3.11 gfortran libblas lapack openmpi julia openmpi-mpicc pip numpy scipy spglib
+    conda activate sscha
+    pip install ase julia mpi4py
+    pip install cellconstructor python-sscha tdscha
+
+
+This will create a new environment called sscha, install all the dependencies and the packages.
+To use the code, you need to activate the environment:
+
+.. code-block:: console
+
+    conda activate sscha
+
+
+The sscha code exploits the julia language to speed up the calculation.
+To install the julia dependencies, you need to run the following command:
+
+.. code-block:: console
+
+   python -c 'import julia; julia.install()'
+
+
+And that's it! You can now run the sscha code.
+
+.. code-block:: console
+
+   sscha -h
+
+
+SSCHA also works as a library, so you can import it in your python scripts.
+To check that everything is working, you can run the following script:
+
+.. code-blocK:: python
+
+   import sscha, sscha.Ensemble
+   print("Hello world!")
+
+If it runs without problems, the SSCHA code is working correctly.
+
 Requirements
 ------------
 
 To install python-sscha you need:
-1. python (either 2.7 or 3.*)
+1. python<=3.11
 2. numpy
 3. scipy
 4. matplotlib