updated manual & makefile

manual/manual-cn/manual-cn.tex

@@ -240,7 +240,7 @@ \section{\texttt{\$QCData}输入组} \label{sec:inp-qcdata}
 *.hess （通过\verb|HESS|），其中\verb|DDIP|是可选的，若对红外强度不感兴趣可以忽略。
 \item \textsc{CFour}
   \begin{description}
-  \item 解析频率计算（\texttt{VIB=ANALYTIC}）：*.out文件（通过\verb|FCHK|） + GRD（通过\verb|GEOM|）。
+  \item 解析频率计算（\texttt{VIB=ANALYTIC}）：*.out文件（通过\verb|FCHK|） + GRD（通过\verb|GEOM|）。\textbf{不要用于Hartree-Fock级别计算！}
   \item 数值频率（\texttt{VIB=FINDIF}）和解析频率计算：使用\textsc{Molden}文件。但是无红外强度。参见下面的\texttt{MOLDEN}。
   \item 如果没有GRD文件或\textsc{Molden}文件，或者由于某些原因导致\textsc{Molden}文件缺少频率数据，也可以仅指定*.out文件（通过\verb|FCHK|），
   \textsc{UniMoVib}将尝试从*.out中打印的原子量，振动频率，和简正模式构造Hessian矩阵。但是，由于\textsc{CFour}打印的简正模式存在一些缺陷和
@@ -445,6 +445,7 @@ \section{来自\textsc{Gaussian}的频率计算数据} \label{sec:exp2}
  $end
 \end{lstlisting}\end{colorboxed}
 
+\newpage
 \section{来自\textsc{Molpro}的频率计算数据} \label{sec:exp3}
 
 \textsc{Molpro}无法使用非阿贝尔群对称性，如 CH$_4$的$T_d$群。通过\textsc{UniMoVib}，你可以得到振动模式在最高点群下的不可约表示。
@@ -565,12 +566,16 @@ \chapter{已知问题} \label{part:problem}
 
 \item \textsc{CFour}
 
-在只有单个*.out文件使用的情况下（通过\verb|FCHK|），\textsc{UniMoVib}尝试构造Hessian矩阵。但是由于\textsc{CFour}打印的简正模式
-存在缺陷和错误，结果可能有问题：
 \begin{enumerate}
-  \item 对于高对称分子，在频率输出部分可能会重新排列原子，导致原子顺序在几何结构部分和频率部分不一致。
-  \item 对于线形多原子分子，可能会少打印一个简正模式。
-  \item 由于打印的简正模式数据精度很低（第一列只有3个有效数字，其余列4个），一些低频可能无法被\textsc{UniMoVib}复现。
+\item 在Hartree-Fock级别解析频率的情况下，*.out文件中打印的Hessian矩阵、APT矩阵可能有问题，导致错误的结果。
+
+\item 在只有单个*.out文件使用的情况下（通过\verb|FCHK|），\textsc{UniMoVib}尝试构造Hessian矩阵。但是由于\textsc{CFour}打印的简正模式
+存在缺陷和错误，结果可能有问题：
+  \begin{itemize}
+    \item[(a)] 对于高对称分子，在频率输出部分可能会重新排列原子，导致原子顺序在几何结构部分和频率部分不一致。
+    \item[(b)] 对于线形多原子分子，可能会少打印一个简正模式。
+    \item[(c)] 由于打印的简正模式数据精度很低（第一列只有3个有效数字，其余列4个），一些低频可能无法被\textsc{UniMoVib}复现。
+  \end{itemize}
 \end{enumerate}
 
 \end{itemize}

manual/manual-en/manual-en.tex

@@ -394,7 +394,7 @@ \subsection{\texttt{\$QCData} group} \label{sec:inp-qcdata}
 \item \textsc{CFour}
   \begin{description}
   \item For analytical frequency (\texttt{VIB=ANALYTIC}): *.out file (by \verb|FCHK|) + GRD
-  (by \verb|GEOM|).
+  (by \verb|GEOM|). \textbf{Not suggested for Hartree-Fock calculations!}
   \index{{Quantum chemistry program}@{Quantum chemistry program}!MOLDEN}
   \item For both numerical frequency (\texttt{VIB=FINDIF}) and analytical frequency: Use the \textsc{Molden} file. However, no IR intensities.
   See also \texttt{MOLDEN} below.
@@ -815,12 +815,17 @@ \section{Known problems} \label{part:problem}
 \index{{Quantum chemistry program}@{Quantum chemistry program}!CFour}
 \item \textsc{CFour}
 
-If only a single *.out file is specified by \verb|FCHK|, \textsc{UniMoVib} tries to construct the Hessian matrix. However this may do not work well due to some defects and errors in the printed normal modes by \textsc{CFour},
-  \begin{enumerate}
-    \item If the molecule has a high symmetry, the atoms therein may be reordered in the frequency output, and therefore the atom orderings in the geometry and frequency parts will be different.
-    \item For linear polyatomic molecules, one normal mode can be missing.
-    \item Due to very low accuracy of the printed normal mode data (3 significant digits for the first column and 4 for the others), some low frequencies cannot be well reproduced by \textsc{UniMoVib}.
-  \end{enumerate}
+\begin{enumerate}
+  \item In the case of analytical frequency by Hartree-Fock, the Hessian matrix and APT matrix printed in the *.out file can be wrong.
+
+  \item If only a single *.out file is specified by \verb|FCHK|, \textsc{UniMoVib} tries to construct the Hessian matrix. However this may do not work well due to some defects and errors in the printed normal modes by \textsc{CFour},
+  \begin{itemize}
+    \item[(a)] If the molecule has a high symmetry, the atoms therein may be reordered in the frequency output, and therefore the atom orderings in the geometry and frequency parts will be different.
+    \item[(b)] For linear polyatomic molecules, one normal mode can be missing.
+    \item[(c)] Due to very low accuracy of the printed normal mode data (3 significant digits for the first column and 4 for the others), some low frequencies cannot be well reproduced by \textsc{UniMoVib}.
+  \end{itemize}
+\end{enumerate}
+
 
 \end{itemize}
 

src/Makefile

@@ -1,7 +1,7 @@
 #
 # This Makefile may be used for gfortran under Linux or Windows-MinGW.
 #
-# Written by W. Zou <qcband@gmail.com>. May 02 2020.
+# Written by W. Zou <qcband@gmail.com>. June 13 2022.
 #
 
 #DIR        = ../win32/
@@ -26,7 +26,7 @@ MODOBJ     = $(addprefix $(OBJ)/, $(MODS:.f90=.o))
 
 all: $(MODOBJ) $(F90OBJ) $(F77OBJ)
 	@echo
-	$(FCOM) $(COMPFLAGS) $(OBJ)/*.o -o $(EXE)
+	$(FCOM) $(OBJ)/*.o $(COMPFLAGS) -o $(EXE)
 	@echo
 	@echo "  --- $(NAME) has been compiled successfully!"
 	@echo

src/Makefile-ifort_mkl

@@ -1,7 +1,7 @@
 #
 # This Makefile may be used for ifort + mkl under Linux.
 #
-# Written by W. Zou <qcband@gmail.com>. May 02 2021.
+# Written by W. Zou <qcband@gmail.com>. June 13 2022.
 #
 
 DIR        = ../
@@ -27,7 +27,7 @@ MODOBJ     = $(addprefix $(OBJ)/, $(MODS:.f90=.o))
 
 all: $(MODOBJ) $(F90OBJ)
 	@echo
-	$(FCOM) $(COMPFLAGS) $(OBJ)/*.o -o $(EXE)
+	$(FCOM) $(OBJ)/*.o $(COMPFLAGS) -o $(EXE)
 	@echo
 	@echo "  <<< $(NAME) has been compiled successfully! >>>"
 	@echo