replace \ref with \eqref for equations

docs/pages/configurationinteraction.md

@@ -62,7 +62,7 @@ The only thing that is needed, besides the general Configuration Interaction equ
 N\_D=\binom{n}{k}
 \end{equation}
 
-assuming $k$ is the total number of electrons, and $n$ is the total number of spinorbitals. Each determinant is formed by permuting the electrons between spinorbitals. For practical representation, it's useful to describe determinants as arrays of numbers, where each number corresponds to the index of an occupied orbitals. For example, the ground state determinant for a system with 6 electrons and 10 spinorbitals can be represented as $\left\lbrace 0,1,2,3,4,5\right\rbrace$, whereas the determinant $\left\lbrace 0,1,2,3,4,6\right\rbrace$ represents an excited state with one electron excited from orbital 5 to orbital 6. Using the determinants, the Configuration Interaction Hamiltonian matrix \ref{eq:ci-hamiltonian} can be constructed, and the eigenvalue problem \ref{eq:ci-eigenvalue-problem} can be solved to obtain the ground and excited state energies.
+assuming $k$ is the total number of electrons, and $n$ is the total number of spinorbitals. Each determinant is formed by permuting the electrons between spinorbitals. For practical representation, it's useful to describe determinants as arrays of numbers, where each number corresponds to the index of an occupied orbitals. For example, the ground state determinant for a system with 6 electrons and 10 spinorbitals can be represented as $\left\lbrace 0,1,2,3,4,5\right\rbrace$, whereas the determinant $\left\lbrace 0,1,2,3,4,6\right\rbrace$ represents an excited state with one electron excited from orbital 5 to orbital 6. Using the determinants, the Configuration Interaction Hamiltonian matrix \eqref{eq:ci-hamiltonian} can be constructed, and the eigenvalue problem \eqref{eq:ci-eigenvalue-problem} can be solved to obtain the ground and excited state energies.
 
 ## Full Configuration Interaction Implementation Code Example
 

docs/pages/generalizedeigenvalueproblem.md

@@ -20,7 +20,7 @@ where $\mathbf{C}$ is a matrix of eigenvectors and $\mathbf{\Lambda}$ is a diago
 \mathbf{B}^{-1}\mathbf{A}\mathbf{C}=\mathbf{C}\mathbf{\Lambda}.
 \end{equation}
 
-This method is not always numerically stable, especially when the matrices $\mathbf{A}$ and $\mathbf{B}$ are ill-conditioned. Should you try to use this method for the Roothaan equations in the Hartree--Fock method, you would find that the solution is is not correct. A more stable approach is to modify the equation \ref{eq:gen_eig} as
+This method is not always numerically stable, especially when the matrices $\mathbf{A}$ and $\mathbf{B}$ are ill-conditioned. Should you try to use this method for the Roothaan equations in the Hartree--Fock method, you would find that the solution is is not correct. A more stable approach is to modify the equation \eqref{eq:gen_eig} as
 
 \begin{align}
 \mathbf{A}\mathbf{C}&=\mathbf{B}\mathbf{C}\mathbf{\Lambda}\nonumber \\\\\

docs/pages/hartreefockmethod.md

@@ -65,7 +65,7 @@ and the two-electron Coulomb repulsion integrals
 J\_{\mu\nu\kappa\lambda}=\braket{\phi\_{\mu}\phi\_{\mu}|\hat{J}|\phi\_{\kappa}\phi\_{\lambda}},
 \end{equation}
 
-which play crucial roles in the Hartree--Fock calculation.<!--\cite{10.1016/S0065-3276!08!60019-2}--> The Hartree--Fock method revolves around solving the Roothaan equations \ref{eq:roothaan} iteratively. The Fock matrix is defined as
+which play crucial roles in the Hartree--Fock calculation.<!--\cite{10.1016/S0065-3276!08!60019-2}--> The Hartree--Fock method revolves around solving the Roothaan equations \eqref{eq:roothaan} iteratively. The Fock matrix is defined as
 
 \begin{equation}\label{eq:fock}
 F\_{\mu\nu}=H\_{\mu\nu}^{core}+D\_{\kappa\lambda}(J\_{\mu\nu\kappa\lambda}-\frac{1}{2}J\_{\mu\lambda\kappa\nu})
@@ -109,7 +109,7 @@ W_{\mu\nu}=2C_{\mu i}C_{\nu i}\varepsilon_i
 
 To perform most of the post-Hartree--Fock calculations, we usually need to transform the integrals to the Molecular Spinorbital basis. We will describe it here and refer to it in the post-Hartree--Fock methods sections. We will also present the post-Hartree--Fock methods using the integrals in the Molecular Spinorbital basis (and its antisymmetrized form in case of the Coulomb integrals), since it is more general.
 
-All the integrals defined in the equations \ref{eq:hamiltonian}, \ref{eq:overlap}, and \ref{eq:coulomb} and even the Fock matrix in the equation \ref{eq:fock} are defined in the basis of atomic orbitals. To transform these integrals to the Molecular Spinorbital basis, we need to use the coefficient matrix $\mathbf{C}$ obtained from the solution of the Roothaan equations \ref{eq:roothaan}. The coefficient matrix $\mathbf{C}$, which is obtained from the Restricted Hartree--Fock calculation, is calculated in the spatial molecular orbital basis. The first step is to expand the coefficient matrix $\mathbf{C}$ to the Molecular Spinorbital basis. This can be done mathematically using the tiling matrix $\mathbf{P}\_{n\times 2n}$, defined as
+All the integrals defined in the equations \eqref{eq:hamiltonian}, \eqref{eq:overlap}, and \eqref{eq:coulomb} and even the Fock matrix in the equation \eqref{eq:fock} are defined in the basis of atomic orbitals. To transform these integrals to the Molecular Spinorbital basis, we need to use the coefficient matrix $\mathbf{C}$ obtained from the solution of the Roothaan equations \eqref{eq:roothaan}. The coefficient matrix $\mathbf{C}$, which is obtained from the Restricted Hartree--Fock calculation, is calculated in the spatial molecular orbital basis. The first step is to expand the coefficient matrix $\mathbf{C}$ to the Molecular Spinorbital basis. This can be done mathematically using the tiling matrix $\mathbf{P}\_{n\times 2n}$, defined as
 
 \begin{equation}
 \mathbf{P}=