Merge pull request #67 from qiboteam/code-examples

Documentation: Edit and move some pages from `Getting started` to `Tutorials`

doc/source/api-reference/index.rst

@@ -7,6 +7,6 @@ In this section we document the main Qibochem components and primitives in the p
 .. toctree::
     :maxdepth: 1
 
-    driver
+    molecule
     ansatz
     measurement

doc/source/api-reference/molecule.rst

@@ -0,0 +1,12 @@
+
+.. _molecule-class:
+
+Molecule
+========
+
+Qibochem provides the ``Molecule`` class to save various properties related to the molecular system,
+and to drive the classical quantum chemistry calculation to obtain the necessary quantities for any subsequent quantum compute calculations.
+
+.. autoclass:: qibochem.driver.molecule.Molecule
+    :members:
+    :member-order: bysource

doc/source/conf.py

@@ -19,7 +19,6 @@
 import qibochem
 
 # -- Project information -----------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
 project = "qibochem"
 copyright = "The Qibo team"
@@ -33,6 +32,9 @@
 
 master_doc = "index"
 
+# 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.doctest",
@@ -69,14 +71,13 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-#
+
 html_theme = "furo"
 html_favicon = "favicon.ico"
 
 # custom title
 html_title = "Qibochem · v" + release
 
-# custom html theme options (colors and font)
 html_theme_options = {
     "top_of_page_button": "edit",
     "source_repository": "https://github.com/qiboteam/qibochem/",

doc/source/getting-started/index.rst

@@ -2,16 +2,10 @@
 Getting started
 ===============
 
-This section covers the basics of qibochem. More details are given in the following subsections.
-
+This section covers how to install Qibochem and a basic example presenting the functionality of Qibochem.
 
 .. toctree::
     :maxdepth: 1
 
     installation
-    molecule
-    hamiltonian
-    ansatz
-    measurement
-..
-    measurement
+    quickstart

doc/source/getting-started/installation.rst

@@ -1,19 +1,35 @@
-============
-Installation
-============
+Installation instructions
+=========================
 
-Using pip install:
+Supported operating systems
+---------------------------
+
+At the moment, Qibochem is only actively supported on Linux and MacOS systems.
+In principle, it should be possible to install and run Qibochem on Windows, but with the caveat that the PySCF driver for obtaining molecular integrals is not available on Windows systems.
+
+.. note::
+      Qibochem is supported for Python >= 3.9.
+
+..
+  TODO: update further when package released on pypi
+
+Installing from source
+----------------------
+
+Using ``pip install``:
 
 .. code-block::
 
     git clone https://github.com/qiboteam/qibochem.git
     cd qibochem
     pip install .
 
-Using poetry:
+Using ``poetry``:
 
 .. code-block::
 
     git clone https://github.com/qiboteam/qibochem.git
     cd qibochem
     poetry install
+
+For larger simulations, it may be desirable to install `other backend drivers <https://qibo.science/qibo/stable/getting-started/backends.html/>`_ for Qibo as well.

doc/source/getting-started/quickstart.rst

@@ -0,0 +1,35 @@
+Quick start
+-----------
+
+..
+  TODO: Add pip install when package on pypi
+
+Here is an example of building the UCCD ansatz with the H2 molecule to test your installation:
+
+.. testcode::
+    import numpy as np
+    from qibo.models import VQE
+
+    from qibochem.driver.molecule import Molecule
+    from qibochem.ansatz.hf_reference import hf_circuit
+    from qibochem.ansatz.ucc import ucc_circuit
+
+    # Define the H2 molecule and obtain its 1-/2- electron integrals with PySCF
+    h2 = Molecule([('H', (0.0, 0.0, 0.0)), ('H', (0.0, 0.0, 0.7))])
+    h2.run_pyscf()
+    # Generate the molecular Hamiltonian
+    hamiltonian = h2.hamiltonian()
+
+    # Build a UCC circuit ansatz for running VQE
+    circuit = hf_circuit(h2.nso, sum(h2.nelec))
+    circuit += ucc_circuit(h2.nso, [0, 1, 2, 3])
+
+    # Create and run the VQE, starting with random initial parameters
+    vqe = VQE(circuit, hamiltonian)
+
+    initial_parameters = np.random.uniform(0.0, 2*np.pi, 8)
+    best, params, extra = vqe.minimize(initial_parameters)
+
+
+..
+  TODO: Another example with measurements

doc/source/index.rst

@@ -6,14 +6,14 @@ What is Qibochem?
 
 Qibochem is a plugin to Qibo for quantum chemistry simulations.
 
-Qibochem key features:
+Key features of Qibochem:
 
 * General purpose Molecule class
 
   - effective Hamiltonian construction for active space
   - inline or .xyz file input for molecular geometry
 
-* PySCF or Psi4 for calculation of 1- and 2-electron integrals
+* Calculation of 1- and 2-electron integrals with PySCF
 * Unitary Coupled Cluster Ansatz
 
 
@@ -27,7 +27,7 @@ available.
 1. **Installation and Setup**: Begin by referring to the
    :doc:`/getting-started/index` guide to set up the ``Qibochem`` library in your environment.
 
-2. **Tutorials**: Explore the :doc:`/code-examples/index` section for a range of
+2. **Tutorials**: Explore the :doc:`/tutorials/index` section for a range of
    tutorials that cater to different levels of expertise. These tutorials cover
    basic examples, advanced examples and tutorials with algorithm for specific
    applications.
@@ -45,6 +45,7 @@ Contents
     :caption: Introduction
 
     getting-started/index
+    tutorials/index
 
 .. toctree::
     :maxdepth: 2