improved docs

doc/source/api-reference/qibo.rst

@@ -1213,9 +1213,9 @@ Matrix Hamiltonian
 ^^^^^^^^^^^^^^^^^^
 
 The first implementation of Hamiltonians uses the full matrix representation
-of the Hamiltonian operator in the computational basis. This matrix has size
-``(2 ** nqubits, 2 ** nqubits)`` and therefore its construction is feasible
-only when number of qubits is small.
+of the Hamiltonian operator in the computational basis. 
+For :math:`n` qubits, this matrix has size :math:`2^{n} \times 2^{n}`.
+Therefore, its construction is feasible only when :math:`n` is small.
 
 Alternatively, the user can construct this Hamiltonian using a sparse matrices.
 Sparse matrices from the

src/qibo/derivative.py

@@ -13,41 +13,43 @@ def parameter_shift(
     nshots=None,
 ):
     """In this method the parameter shift rule (PSR) is implemented.
-    Given a circuit U and an observable H, the PSR allows to calculate the derivative
-    of the expected value of H on the final state with respect to a variational
+    Given a circuit :math:`U` and an observable :math:`H`, the PSR allows to calculate the derivative
+    of the expected value of :math:`H` on the final state with respect to a variational
     parameter of the circuit.
     There is also the possibility of setting a scale factor. It is useful when a
     circuit's parameter is obtained by combination of a variational
     parameter and an external object, such as a training variable in a Quantum
     Machine Learning problem. For example, performing a re-uploading strategy
     to embed some data into a circuit, we apply to the quantum state rotations
-    whose angles are in the form: theta' = theta * x, where theta is a variational
-    parameter and x an input variable. The PSR allows to calculate the derivative
-    with respect of theta' but, if we want to optimize a system with respect its
-    variational parameters we need to "free" this procedure from the x depencency.
-    If the `scale_factor` is not provided, it is set equal to one and doesn't
+    whose angles are in the form :math:`\\theta^{\\prime} = x \\, \\theta`, 
+    where :math:`\\theta` is a variational parameter, and :math:`x` an input variable. 
+    The PSR allows to calculate the derivative with respect to :math:`\\theta^{\\prime}`.
+    However, if we want to optimize a system with respect to its
+    variational parameters, we need to "free" this procedure from the :math:`x` depencency.
+    If the ``scale_factor`` is not provided, it is set equal to one and doesn't
     affect the calculation.
     If the PSR is needed to be executed on a real quantum device, it is important
-    to set `nshots` to some integer value. This enables the execution on the
+    to set ``nshots`` to some integer value. This enables the execution on the
     hardware by calling the proper methods.
 
     Args:
         circuit (:class:`qibo.models.circuit.Circuit`): custom quantum circuit.
         hamiltonian (:class:`qibo.hamiltonians.Hamiltonian`): target observable.
             if you want to execute on hardware, a symbolic hamiltonian must be
-            provided as follows (example with Pauli Z and ``nqubits=1``):
+            provided as follows (example with Pauli:math:`Z` and :math:`n = 1`):
             ``SymbolicHamiltonian(np.prod([ Z(i) for i in range(1) ]))``.
         parameter_index (int): the index which identifies the target parameter
             in the ``circuit.get_parameters()`` list.
         initial_state (ndarray, optional): initial state on which the circuit
-            acts. Default is ``None``.
-        scale_factor (float, optional): parameter scale factor. Default is ``1``.
+            acts. If ``None``, defaults to the zero state :math:`\\ket{\\mathbf{0}}`. 
+            Defaults to ``None``.
+        scale_factor (float, optional): parameter scale factor. Defaults to :math:`1`.
         nshots (int, optional): number of shots if derivative is evaluated on
             hardware. If ``None``, the simulation mode is executed.
-            Default is ``None``.
+            Defaults to ``None``.
 
     Returns:
-        (float): Value of the derivative of the expectation value of the hamiltonian
+        float: Value of the derivative of the expectation value of the hamiltonian
             with respect to the target variational parameter.
 
     Example:
@@ -167,27 +169,28 @@ def finite_differences(
     step_size=1e-7,
 ):
     """
-    Calculate derivative of the expectation value of `hamiltonian` on the
-    final state obtained by executing `circuit` on `initial_state` with
-    respect to the variational parameter identified by `parameter_index`
+    Calculate derivative of the expectation value of ``hamiltonian`` on the
+    final state obtained by executing ``circuit`` on ``initial_state`` with
+    respect to the variational parameter identified by ``parameter_index``
     in the circuit's parameters list. This method can be used only in
     exact simulation mode.
 
     Args:
         circuit (:class:`qibo.models.circuit.Circuit`): custom quantum circuit.
         hamiltonian (:class:`qibo.hamiltonians.Hamiltonian`): target observable.
-            if you want to execute on hardware, a symbolic hamiltonian must be
-            provided as follows (example with Pauli Z and ``nqubits=1``):
+            To execute on hardware, a symbolic hamiltonian must be
+            provided as follows (example with Pauli-:math:`Z` and :math:`n = 1`):
             ``SymbolicHamiltonian(np.prod([ Z(i) for i in range(1) ]))``.
         parameter_index (int): the index which identifies the target parameter
-            in the ``circuit.get_parameters()`` list.
+            in the :meth:`qibo.models.Circuit.get_parameters` list.
         initial_state (ndarray, optional): initial state on which the circuit
-            acts. Default is ``None``.
-        step_size (float): step size used to evaluate the finite difference
-            (default 1e-7).
+            acts. If ``None``, defaults to the zero state :math:`\\ket{\\mathbf{0}}`. 
+            Defaults to ``None``.
+        step_size (float, optional): step size used to evaluate the finite difference.
+            Defaults to :math:`10^{-7}`.
 
     Returns:
-        (float): Value of the derivative of the expectation value of the hamiltonian
+        float: Value of the derivative of the expectation value of the hamiltonian
             with respect to the target variational parameter.
     """
 

src/qibo/hamiltonians/abstract.py

@@ -57,11 +57,10 @@ def ground_state(self):
 
     @abstractmethod
     def exp(self, a):  # pragma: no cover
-        """Computes a tensor corresponding to exp(-1j * a * H).
+        """Computes a tensor corresponding to :math:`\\exp(-i \\, a \\, H)`.
 
         Args:
-            a (complex): Complex number to multiply Hamiltonian before
-                exponentiation.
+            a (complex): Complex number to multiply Hamiltonian before exponentiation.
         """
         raise_error(NotImplementedError)
 
@@ -70,27 +69,31 @@ def expectation(self, state, normalize=False):  # pragma: no cover
         """Computes the real expectation value for a given state.
 
         Args:
-            state (array): the expectation state.
-            normalize (bool): If ``True`` the expectation value is divided
-                with the state's norm squared.
+            state (ndarray): state in which to calculate the expectation value.
+            normalize (bool, optional): If ``True``, the expectation value 
+                :math:`\\ell_{2}`-normalized. Defaults to ``False``.
 
         Returns:
-            Real number corresponding to the expectation value.
+            float: real number corresponding to the expectation value.
         """
         raise_error(NotImplementedError)
 
     @abstractmethod
     def expectation_from_samples(self, freq, qubit_map=None):  # pragma: no cover
-        """Computes the real expectation value of a diagonal observable given the frequencies when measuring in the computational basis.
+        """Computes the expectation value of a diagonal observable, 
+        given computational-basis measurement frequencies.
 
         Args:
             freq (collections.Counter): the keys are the observed values in binary form
-            and the values the corresponding frequencies, that is the number
-            of times each measured value/bitstring appears.
-            qubit_map (tuple): Mapping between frequencies and qubits. If None, [1,...,len(key)]
+                and the values the corresponding frequencies, that is the number
+                of times each measured value/bitstring appears.
+            qubit_map (tuple): Mapping between frequencies and qubits. 
+                If ``None``, then defaults to 
+                :math:`[1, \\, 2, \\, \\cdots, \\, \\mathrm{len}(\\mathrm{key})]`.
+                Defaults to ``None``.
 
         Returns:
-            Real number corresponding to the expectation value.
+            float: real number corresponding to the expectation value.
         """
         raise_error(NotImplementedError)
 

src/qibo/hamiltonians/hamiltonians.py

@@ -17,14 +17,16 @@ class Hamiltonian(AbstractHamiltonian):
 
     Args:
         nqubits (int): number of quantum bits.
-        matrix (np.ndarray): Matrix representation of the Hamiltonian in the
-            computational basis as an array of shape ``(2 ** nqubits, 2 ** nqubits)``.
-            Sparse matrices based on ``scipy.sparse`` for numpy/qibojit backends
-            or on ``tf.sparse`` for the tensorflow backend are also
-            supported.
+        matrix (ndarray): Matrix representation of the Hamiltonian in the
+            computational basis as an array of shape :math:`2^{n} \\times 2^{n}`.
+            Sparse matrices based on ``scipy.sparse`` for ``numpy`` / ``qibojit`` backends
+            (or on ``tf.sparse`` for the ``tensorflow`` backend) are also supported.
+        backend (:class:`qibo.backends.abstract.Backend`, optional): backend to be used
+            in the execution. If ``None``, it uses :class:`qibo.backends.GlobalBackend`.
+            Defaults to ``None``.
     """
 
-    def __init__(self, nqubits, matrix=None, backend=None):
+    def __init__(self, nqubits, matrix, backend=None):
         from qibo.backends import _check_backend
 
         self.backend = _check_backend(backend)
@@ -50,7 +52,7 @@ def __init__(self, nqubits, matrix=None, backend=None):
     def matrix(self):
         """Returns the full matrix representation.
 
-        Can be a dense ``(2 ** nqubits, 2 ** nqubits)`` array or a sparse
+        For :math:`n` qubits, can be a dense :math:`2^{n} \\times 2^{n}` array or a sparse
         matrix, depending on how the Hamiltonian was created.
         """
         return self._matrix
@@ -68,22 +70,22 @@ def matrix(self, mat):
 
     @classmethod
     def from_symbolic(cls, symbolic_hamiltonian, symbol_map, backend=None):
-        """Creates a ``Hamiltonian`` from a symbolic Hamiltonian.
+        """Creates a :class:`qibo.hamiltonian.Hamiltonian` from a symbolic Hamiltonian.
 
-        We refer to the
-        :ref:`How to define custom Hamiltonians using symbols? <symbolicham-example>`
-        example for more details.
+        We refer to :ref:`How to define custom Hamiltonians using symbols? <symbolicham-example>`
+        for more details.
 
         Args:
-            symbolic_hamiltonian (sympy.Expr): The full Hamiltonian written
-                with symbols.
+            symbolic_hamiltonian (sympy.Expr): full Hamiltonian written with ``sympy`` symbols.
             symbol_map (dict): Dictionary that maps each symbol that appears in
-                the Hamiltonian to a pair of (target, matrix).
+                the Hamiltonian to a pair ``(target, matrix)``.
+            backend (:class:`qibo.backends.abstract.Backend`, optional): backend to be used
+                in the execution. If ``None``, it uses :class:`qibo.backends.GlobalBackend`.
+                Defaults to ``None``.
 
         Returns:
-            A :class:`qibo.hamiltonians.SymbolicHamiltonian` object
-            that implements the Hamiltonian represented by the given symbolic
-            expression.
+            :class:`qibo.hamiltonians.SymbolicHamiltonian`: object that implements the 
+            Hamiltonian represented by the given symbolic expression.
         """
         log.warning(
             "`Hamiltonian.from_symbolic` and the use of symbol maps is "
@@ -175,15 +177,16 @@ def energy_fluctuation(self, state):
         Evaluate energy fluctuation:
 
         .. math::
-            \\Xi_{k}(\\mu) = \\sqrt{\\langle\\mu|\\hat{H}^2|\\mu\\rangle - \\langle\\mu|\\hat{H}|\\mu\\rangle^2} \\,
+            \\Xi_{k}(\\mu) = \\sqrt{\\bra{\\mu} \\, H^{2} \\, \\ket{\\mu} 
+                - \\bra{\\mu} \\, H \\, \\ket{\\mu}^2} \\, .
 
-        for a given state :math:`|\\mu\\rangle`.
+        for a given state :math:`\\ket{\\mu}`.
 
         Args:
-            state (np.ndarray): quantum state to be used to compute the energy fluctuation.
+            state (ndarray): quantum state to be used to compute the energy fluctuation.
 
-        Return:
-            Energy fluctuation value (float).
+        Returns:
+            float: Energy fluctuation value.
         """
         state = self.backend.cast(state)
         energy = self.expectation(state)
@@ -311,6 +314,9 @@ class SymbolicHamiltonian(AbstractHamiltonian):
             The symbol_map can also be used to pass non-quantum operator arguments
             to the symbolic Hamiltonian, such as the parameters in the
             :meth:`qibo.hamiltonians.models.MaxCut` Hamiltonian.
+        backend (:class:`qibo.backends.abstract.Backend`, optional): backend to be used
+            in the execution. If ``None``, it uses :class:`qibo.backends.GlobalBackend`.
+            Defaults to ``None``.
     """
 
     def __init__(self, form=None, nqubits=None, symbol_map={}, backend=None):
@@ -419,7 +425,7 @@ def terms(self, terms):
     def matrix(self):
         """Returns the full matrix representation.
 
-        Consisting of ``(2 ** nqubits, 2 ** nqubits)`` elements.
+        Consisting of :math:`2^{n} \\times 2^{n}`` elements.
         """
         return self.dense.matrix
 
@@ -449,8 +455,8 @@ def _get_symbol_matrix(self, term):
             term (sympy.Expr): Symbolic expression containing local operators.
 
         Returns:
-            Numerical matrix corresponding to the given expression as a numpy
-            array of size ``(2 ** self.nqubits, 2 ** self.nqubits).
+            ndarray: matrix corresponding to the given expression as an array
+            of shape ``(2 ** self.nqubits, 2 ** self.nqubits)``.
         """
         if isinstance(term, sympy.Add):
             # symbolic op for addition
@@ -697,7 +703,7 @@ def apply_gates(self, state, density_matrix=False):
 
         Gates are applied to the given state.
 
-        Helper method for ``__matmul__``.
+        Helper method for :meth:`qibo.hamiltonians.SymbolicHamiltonian.__matmul__`.
         """
         total = 0
         for term in self.terms:
@@ -759,7 +765,8 @@ def circuit(self, dt, accelerators=None):
 
         Args:
             dt (float): Time step used for Trotterization.
-            accelerators (dict): Dictionary with accelerators for distributed circuits.
+            accelerators (dict, optional): Dictionary with accelerators for distributed circuits.
+                Defaults to ``None``.
         """
         from qibo import Circuit  # pylint: disable=import-outside-toplevel
         from qibo.hamiltonians.terms import (  # pylint: disable=import-outside-toplevel