List of equations does not also list the ones in \align environement

Question

None of the existing examples that I found for listing equations does include the equations in the \align environement. How can I also include both equation types in the same list of equations? Here is a MWE:

    \documentclass[english]{article}
\setcounter{secnumdepth}{2}
%\setcounter{tocdepth}{1}
\usepackage{amsmath}
\usepackage{tocloft}
\usepackage{xstring}
\usepackage[unicode=true, pdfusetitle,
 bookmarks=true,bookmarksnumbered=false,bookmarksopen=false,
 breaklinks=false,pdfborder={0 0 0},backref=false,colorlinks=false]
 {hyperref}
\makeatletter
\numberwithin{equation}{section}
% we use this for our refernces as well
\AtBeginDocument{\renewcommand{\ref}[1]{\mbox{\autoref{#1}}}}
% redefinition of \equation for convenience
\let\oldequation = \equation
\let\endoldequation = \endequation
\AtBeginDocument{\let\oldlabel = \label}% \AtBeginDocument because hyperref redefines \label
\newcommand{\mynewlabel}[1]{%
  \StrBehind{#1}{eq:}[\Str]% remove "eq:" from labels
  \myequations{\Str}\oldlabel{#1}}
  \renewenvironment{equation}{%
  \oldequation
  \let\label\mynewlabel
}{\endoldequation}
% redefinition of \eqnarray for convenience
\let\oldeqnarray = \eqnarray
\let\endoldeqnarray = \endeqnarray
%\AtBeginDocument{\let\oldlabel = \label}% \AtBeginDocument because hyperref redefines \label
\newcommand{\mynewlabelarray}[1]{%
  \StrBehind{#1}{eq:}[\Str]% remove "eq:" from labels
  \myequations{\Str}\oldlabel{#1}}
  \renewenvironment{eqnarray}{%
  \oldeqnarray
  \let\label\mynewlabelarray
}{\endoldeqnarray}
\newcommand{\listequationsname}{\normalsize  List of Equations}
\newlistof{myequations}{equ}{\listequationsname}
\newcommand{\myequations}[1]{%
      \addcontentsline{equ}{myequations}{\protect\numberline{\theequation}#1}}
\setlength{\cftmyequationsnumwidth}{3em}
\makeatother
\begin{document}
%\tableofcontents
\listofmyequations
\section{Section title}
\begin{equation}
  F=q[E+(v\times B)]
  \label{eq:Force}
\end{equation}
\begin{equation}
  \tau=F\times r
  \label{eq:Torque}
\end{equation}
If the electrical force in \ref{eq:Force} is ignored,
and the remaining magnetic force is used in \ref{eq:Torque},
with the assumption that $v$ is perpendicular to $B$, we find that
\begin{equation}
      \tau=qvBrsin\theta
  \label{eq:Magnetic}
\end{equation}
\begin{align}
  \min_{u_{i}(t),y_i, i=1...N}!!!!!! J(u_i(t),y_i)  &:=  \sum_{i=1}^N \int_0^{T} R_i(u_{i}(t),t) dt \label{eq:objective function}\
+&  \xi \int_{0}^{T}  \left(\theta\frac{M - I(t)}{M}K(t)  - D(t)\right)^2 dt +  \sum_{i=1}^N \gamma_i y_i  \notag\

& \sum_{i=1}^N p_{i} \int_{T_i}^{T} u_i(t-T_i)dt \notag\

+&  h\int_{0}^T \left[\theta\frac{M - I(t)}{M}K(t) - D(t)\right]^+ dt, \notag
\end{align}
subject to
\begin{align}
  K(t)& = \sum_{i=1}^N u_i(t-T_i), & \quad t\in [0,T] \label{eq:2} \
  u_i(t) &\le  % \theta_i S_i(t) y_i =
  \theta_i (M_i - I_i(t)) y_i,  & \ \ i = 1\ldots N \quad t\in [0,T-T_i] \label{eq:ui}\
  u_i(t) & =  0, & i = 1\ldots N \quad t\in [T-T_i,T] \label{eq:uio}\
  \dot{I}_i(t)& = f_i(I_i(t)), &  i = 1 \ldots N \quad t\in [0,T]& \label{eq:dotIi}\
  \dot{I}(t)& = f(I(t)), &\quad t\in [0,T] \label{eq:dotI}\
  u_i(t) & \ge  0, & i = 1 \ldots N \quad t\in [0,T]& \label{eq:const5}\
  K(t)& \ge  0, &\quad t\in [0,T]& \
  y_i &\in  {0,1},  & i = 1 \ldots N& \label{eq:const6}
\end{align}
%where
\begin{equation}\label{eq:capacity constraint}
    u^{j}i(t) \leq Min{p\in C^{j}{i}} \sum{k \in {K^{j}_{ip}}} u^{j+1}_k(t-T_k)
\end{equation}
\end{document} 

Answer 1

I don't think it's good idea to modify the \label macro manually, as it gets used and redefined by quite a few other packages, including the hyperref and cleveref packages. I'd just apply \myequations directives directly to those equations that are supposed to be listed in the List of Equations. (When used with gather and align environments, it appears to be the case that the \myequations directives have be issued after line-break directives. Not sure why.)

Oh, and please don't use eqnarray environments; use align instead.

\documentclass[english]{article}
\setcounter{secnumdepth}{2}
\usepackage{mathtools} % for \coloneqq and \mathclap macros
\usepackage{tocloft}
\usepackage[unicode=true, pdfusetitle, bookmarks=true, 
    bookmarksnumbered=false, bookmarksopen=false, 
    breaklinks=false, backref=false, 
    colorlinks=true,allcolors=black]
   {hyperref}
\usepackage[noabbrev]{cleveref}
\counterwithin{equation}{section}
\newcommand{\listequationsname}{\normalsize List of Equations}
\newlistof{myequations}{equ}{\listequationsname}
\newcommand{\myequations}[1]{%
      \addcontentsline{equ}{myequations}%
      {\protect\numberline{\theequation}#1}}

\setlength{\cftmyequationsnumwidth}{2.5em}
\begin{document}
%\tableofcontents
\listofmyequations
\allowdisplaybreaks
\section{Section title}
\begin{gather}
   F=q[E+(v\times B)]
   \label{eq:Force}  \ \myequations{Force}
   \tau=F\times r
   \label{eq:Torque} 
\end{gather} \myequations{Torque}
If the electrical force in \cref{eq:Force} is ignored, and 
if the remaining magnetic force is used in \cref{eq:Torque}, 
with the assumption that $v$ is perpendicular to~$B$, we 
find that
\begin{equation}
   \tau=qvBr\sin\theta
   \label{eq:Magnetic} 
   \myequations{Magnetic}
\end{equation}
\begin{equation} 
   \label{eq:objective function} 
   \myequations{Objective function}
\begin{aligned}[t] 
\smash[b]{\min_{\mathclap{%
     \substack{u_{i}(t),y_i,\ i=1,\dots,N}}}}
     ,J(u_i(t),y_i)

&\coloneqq \sum_{i=1}^N \int_0^{T} R_i(u_{i}(t),t), dt 
    \
&\quad+ \xi \int_{0}^{T} \left(\theta\frac{M - I(t)}{M}K(t) - D(t)\right)^{!2} dt 
      + \sum_{i=1}^N \gamma_i y_i \
&\quad+ \sum_{i=1}^N p_{i} \int_{T_i}^{T} u_i(t-T_i),dt\
&\quad+  h\int_{0}^T \left[\theta\frac{M - I(t)}{M}K(t) - D(t)\right]^+ dt,
\end{aligned}
\end{equation}
subject to
\begin{align}
  K(t) &= \sum\nolimits_{i=1}^N u_i(t-T_i), 
    && t\in [0,T] 
       \label{eq:2} \
  u_i(t) &\le  % \theta_i S_i(t) y_i =
  \theta_i (M_i - I_i(t)) y_i,

    && i = 1,\ldots, N, 
       \quad t\in [0,T-T_i] 
       \label{eq:ui} \ \myequations{ui}
  u_i(t) &=  0, 
    && i = 1,\ldots, N, 
       \quad t\in [T-T_i,T] 
       \label{eq:uio} \ \myequations{uio}
  \dot{I}i(t) &= f_i(I_i(t)), 
    && i = 1,\ldots,N, 
       \quad t\in [0,T] 
       \label{eq:dotIi} \ \myequations{dotIi}
  \dot{I}(t) &= f(I(t)), 
    && t\in [0,T] 
       \label{eq:dotI}\ \myequations{dotI}
  u_i(t) &\ge  0, 
    && i = 1,\ldots,N, 
       \quad t\in [0,T]
       \label{eq:const5} \ \myequations{const5}
  K(t) &\ge  0, 
    && t\in [0,T] \
  y_i &\in  {0,1},

    && i = 1,\ldots,N 
      \label{eq:const6}
\end{align} \myequations{const6}
where
\begin{equation}
  \label{eq:capacity constraint}
  \myequations{Capacity constraint}
    u^{j}_i(t) \leq \min{p\in C^{j}{i}} \sum{k \in {K^{j}_{ip}}} u^{j+1}_k(t-T_k)
\end{equation}
\end{document} 

Answer 2

As Mico commented, you should not redefine \label. If you want to avoid supplying a label you can make simple command that does both. I used \ref here to pickup the correct number within ams alignments.

\documentclass[english]{article}
\setcounter{secnumdepth}{2}
\usepackage{mathtools} % for \coloneqq and \mathclap macros
\usepackage{tocloft}
\usepackage[unicode=true, pdfusetitle, bookmarks=true, 
    bookmarksnumbered=false, bookmarksopen=false, 
    breaklinks=false, backref=false, 
    colorlinks=true,allcolors=black]
   {hyperref}
\usepackage[noabbrev]{cleveref}
\counterwithin{equation}{section}
\newcommand{\listequationsname}{\normalsize List of Equations}
\newlistof{myequations}{equ}{\listequationsname}
\newcommand{\myequations}[1]{%
      \addcontentsline{equ}{myequations}%
      {\protect\numberline{\ref{eq:#1}}#1}}

\setlength{\cftmyequationsnumwidth}{2.5em}
\newcommand\myeq[1]{\label{eq:#1}\myequations{#1}}
\begin{document}
%\tableofcontents
\listofmyequations
\allowdisplaybreaks
\section{Section title}
\begin{gather}
   F=q[E+(v\times B)]
   \myeq{Force}  \
   \tau=F\times r
   \myeq{Torque} 
\end{gather}
If the electrical force in \cref{eq:Force} is ignored, and 
if the remaining magnetic force is used in \cref{eq:Torque}, 
with the assumption that $v$ is perpendicular to~$B$, we 
find that
\begin{equation}
   \tau=qvBr\sin\theta
   \myeq{Magnetic} 
\end{equation}
\begin{equation} 
   \myeq{objective function} 
\begin{aligned}[t] 
\smash[b]{\min_{\mathclap{%
     \substack{u_{i}(t),y_i,\ i=1,\dots,N}}}}
     ,J(u_i(t),y_i)

&\coloneqq \sum_{i=1}^N \int_0^{T} R_i(u_{i}(t),t), dt 
    \
&\quad+ \xi \int_{0}^{T} \left(\theta\frac{M - I(t)}{M}K(t) - D(t)\right)^{!2} dt 
      + \sum_{i=1}^N \gamma_i y_i \
&\quad+ \sum_{i=1}^N p_{i} \int_{T_i}^{T} u_i(t-T_i),dt\
&\quad+  h\int_{0}^T \left[\theta\frac{M - I(t)}{M}K(t) - D(t)\right]^+ dt,
\end{aligned}
\end{equation}
subject to
\begin{align}
  K(t) &= \sum\nolimits_{i=1}^N u_i(t-T_i), 
    && t\in [0,T] 
       \label{eq:2} \
  u_i(t) &\le  % \theta_i S_i(t) y_i =
  \theta_i (M_i - I_i(t)) y_i,

    && i = 1,\ldots, N, 
       \quad t\in [0,T-T_i] 
       \myeq{ui} \
  u_i(t) &=  0, 
    && i = 1,\ldots, N, 
       \quad t\in [T-T_i,T] 
       \myeq{uio} \
  \dot{I}i(t) &= f_i(I_i(t)), 
    && i = 1,\ldots,N, 
       \quad t\in [0,T] 
       \myeq{dotIi} \
  \dot{I}(t) &= f(I(t)), 
    && t\in [0,T] 
       \myeq{dotI}\
  u_i(t) &\ge  0, 
    && i = 1,\ldots,N, 
       \quad t\in [0,T]
       \myeq{const5} \
  K(t) &\ge  0, 
    && t\in [0,T] \
  y_i &\in  {0,1},

    && i = 1,\ldots,N 
      \myeq{const6}
\end{align}
where
\begin{equation}
  \myeq{capacity constraint}
    u^{j}_i(t) \leq \min{p\in C^{j}{i}} \sum{k \in {K^{j}_{ip}}} u^{j+1}_k(t-T_k)
\end{equation}
\end{document}