add readme and examples; add timer; other small fixes

Author: Jun Yang

Manual/intro.tex

@@ -646,7 +646,7 @@ \subsubsection{Particle density matrices (pdm)}\label{sec:AppNpdm}
 
 1. Calculate these two states seperately. 
 
-2. Copy the temporary files from previous calculations into a folder. statefile, StateInfo, wave, Rotation files are needed. SpinBlock files are biggest. Fortunately, they are not needed here. Temporary files for different bra state and ket state might have the same name. The number before tmp in the file names stands for state numbers. It is convenient to change the number for tmporary files of bra as 0 and that of ket as 1. 
+2. Copy the temporary files from previous calculations into a folder. statefile, wave, Rotation files are needed. SpinBlock files are biggest. Fortunately, they are not needed here. Temporary files for different bra state and ket state might have the same name. The number before tmp in the file names stands for state numbers. It is convenient to change the number for temporary files of bra as 1 and that of ket as 0. 
 
 %\subsubsection{Restarting a calculation}
 \subsubsection{Restarting a calculation}\label{sec:AppRest}

README.md

@@ -0,0 +1,11 @@
+sym d2h 
+orbitals FCIDUMP
+
+nelec 8
+spin 0
+irrep 1
+
+hf_occ integral
+schedule default
+maxM 500 
+maxiter 30