Update the manual to version 1.7

doc/gpumd.tex

@@ -87,6 +87,16 @@ \section{Citations}
 Rev. B, 95:144309, Apr 2017.
 \end{itemize}
 
+
+You can cite the following paper if you use GPUMD to study heat transport using the homogeneous nonequilibrium molecular dynamics (HNEMD) method:
+\begin{itemize}
+\item 
+Zheyong Fan, Haikuan Dong, Ari Harju, and Tapio Ala-Nissila,
+Homogeneous nonequilibrium molecular dynamics method for heat transport with many-body potentials,
+https://arxiv.org/abs/1805.00277
+\end{itemize}
+
+
 \section{Feedbacks}
 
 You can e-mail the first author if you find errors in the manual or bugs in the source code, or have any suggestions/questions about the manual and code. The following email addresses can be used:
@@ -127,6 +137,7 @@ \section{Utilities for heat transport simulations}
 \item It can calculate the phonon density of states (DOS) from the velocity autocorrelation function (VAC), using the method of Dickey and Paskin \cite{dickey1969pr}.
 \item It can calculate the equilibrium heat current auto-correlation (HAC), whose time integral gives the running thermal conductivity according to the Green-Kubo relation \cite{green1954jcp,kubo1957jpsj}. As stressed in Ref. \cite{fan2015prb}, the heat current as implemented in LAMMPS \cite{plimpton1995jcp} does not apply to many-body potentials and significantly underestimates the thermal conductivity in 2D materials described by many-body potentials. GPUMD also contains the thermal conductivity decomposition method as introduced in Ref. \cite{fan2017prb}, which is essential for 2D materials.
 \item It can calculate the thermal conductivity of a system of finite length or the thermal boundary resistance (Kapitza resistance) of an interface or similar structures using non-equilibrium MD (NEMD) methods. The spectral decomposition method as described in Ref. \cite{fan2017prb} has also been implemented.
+\item It can calculate the thermal conductivity using the homogeneous nonequilibrium MD (HNEMD) method \cite{evans1982pla} for general many-body potentials \cite{fan2018submitted}
 \end{itemize}
 
 
@@ -215,7 +226,7 @@ \subsection{Major changes introduced in version 1.6}
 \subsection{Major changes introduced in version 1.7}
 \begin{enumerate}
 \item Changed about half of the code from C style to C++ style.
-\item Added the homogeneous nonequilibrium molecular dynamics method for heat transport with many-body potentials \cite{fan2018submitted,xu2018submitted,dong2018submitted}. Currently, we have only implemented this method for the Tersoff and the SW potentials. We will add this method to all the other potentials in the future. 
+\item Added the homogeneous nonequilibrium molecular dynamics (HNEMD) method for heat transport with many-body potentials \cite{fan2018submitted,xu2018submitted,dong2018submitted}. Currently, we have only implemented this method for the Tersoff and the SW potentials. We will add this method to all the other potentials in the future. 
 \end{enumerate}