Merge branch 'develop'

.gitignore

@@ -23,4 +23,5 @@ build
 html/
 GPATH
 GRTAGS
-GTAGS
+GTAGS
+.idea

HPhiconfig.sh

@@ -23,33 +23,33 @@ if [ -z ${1} ] || [ ${1} = "help" ]; then
 else
     if [ ${1} = "sekirei" ]; then
         cat > src/make.sys <<EOF
-CC = icc
+CC = mpiicc
 LAPACK_FLAGS = -Dlapack -mkl=parallel 
-FLAGS = -qopenmp  -O3 -xCORE-AVX2 -mcmodel=large -shared-intel
+FLAGS = -qopenmp  -O3 -xCORE-AVX2 -mcmodel=large -shared-intel -D MPI -g -traceback
 MTFLAGS = -DDSFMT_MEXP=19937 \$(FLAGS)
 INCLUDE_DIR=./include
 EOF
     elif [ ${1} = "maki" ]; then
         cat > src/make.sys <<EOF
-CC = fccpx
+CC = mpifccpx
 LAPACK_FLAGS = -Dlapack -SSL2BLAMP
-FLAGS = -Kfast,openmp,SPARC64IXfx,parallel -Kmemalias,alias_const
+FLAGS = -Kfast,openmp,SPARC64IXfx,parallel -Kmemalias,alias_const -D MPI -g
 MTFLAGS = -DDSFMT_MEXP=19937 \$(FLAGS)
 INCLUDE_DIR=./include
 EOF
     elif [ ${1} = "intel" ]; then
         cat > src/make.sys <<EOF
 CC = icc
 LAPACK_FLAGS = -Dlapack -mkl=parallel 
-FLAGS = -openmp -O3 -DHAVE_SSE2
+FLAGS = -openmp -O3 -DHAVE_SSE2 -g -traceback
 MTFLAGS = -DDSFMT_MEXP=19937 \$(FLAGS)
 INCLUDE_DIR=./include
 EOF
     elif [ ${1} = "mpicc-intel" ]; then
         cat > src/make.sys <<EOF
 CC = mpicc
 LAPACK_FLAGS = -Dlapack -mkl=parallel 
-FLAGS = -openmp -O3 -DHAVE_SSE2 -D MPI
+FLAGS = -openmp -O3 -DHAVE_SSE2 -D MPI -g -traceback
 MTFLAGS = -DDSFMT_MEXP=19937 \$(FLAGS)
 INCLUDE_DIR=./include
 EOF
@@ -99,6 +99,18 @@ EOF
     echo
 
     cat > makefile <<EOF
+help:
+	@echo ""
+	@echo "Usage :"
+	@echo "make <entry>"
+	@echo ""
+	@echo "<entry> is chosen from below"
+	@echo "      HPhi : Build simulator HPhi in src/"
+	@echo " userguide : Generate userguid_jp.pdf & userguide_en.pdf in doc/"
+	@echo "     clean : Remove all generated files excepting makefile"
+	@echo " veryclean : Remove all generated files including makefile"
+	@echo ""
+
 HPhi:
 	cd src;make -f makefile_src
 

doc/doc_origin/com.sh

@@ -0,0 +1,6 @@
+platex  main
+bibtex  main
+platex  main
+platex  main
+dvipdfmx main.dvi
+#open -a Preview.app main.pdf

doc/doc_ver0.1/com.sh

@@ -0,0 +1,6 @@
+platex  main
+bibtex  main
+platex  main
+platex  main
+dvipdfmx main.dvi
+#open -a Preview.app main.pdf

doc/en/chap01_en.tex

@@ -53,6 +53,7 @@ \subsection{Contributors}
 \label{subsec:contributors}
 This software is developed by following contributors.
 \begin{itemize}
+\item{ver.0.2 (released at 2015/12/28)}
 \item{ver.0.1 (released at 2015/10/09)}
 \begin{itemize}
 	\item{\bf Developers}

doc/en/chap02_1_en.tex

@@ -24,15 +24,16 @@ \subsection{Using \texttt{HPhiconfig.sh}}
 \item \verb|sekirei| : ISSP system-B ''sekirei''
 \item \verb|maki| : ISSP system-C ''maki''
 \item \verb|intel| : intel compiler + Linux PC
+\item \verb|mpicc-intel| : intel compiler + MPI (excepting intelMPI) + Linux PC
 \item \verb|gcc| : GCC + Linux PC
 \item \verb|gcc-mac| : GCC + Mac
 \end{itemize}
 
 \verb|make.sys| is as follows (for ISSP-system-B ''sekirei''):
 \begin{verbatim}
- CC = icc
+ CC = mpiicc
  LAPACK_FLAGS = -Dlapack -mkl=parallel 
- FLAGS = -qopenmp  -O3 -xCORE-AVX2 -mcmodel=large -shared-intel
+ FLAGS = -qopenmp  -O3 -xCORE-AVX2 -mcmodel=large -shared-intel -D MPI
  MTFLAGS = -DDSFMT_MEXP=19937 $(FLAGS)
  INCLUDE_DIR=./include
 \end{verbatim}
@@ -43,6 +44,7 @@ \subsection{Using \texttt{HPhiconfig.sh}}
 \item \verb|FLAGS| : Other compilation options.
   OpenMP utilization option (\verb|-openmp|, \verb|-fopenmp|, \verb|-qopenmp|, etc.)
   must be specified.
+  When you use MPI, please set \verb|-D MPI|.
 \item \verb|MTFLAGS|, \verb|INCLUDE_DIR| : Options for the Mersenne Twister
   and additional include directory. You do not have to modify them.
 \end{itemize}
@@ -56,7 +58,6 @@ \subsection{Using \texttt{HPhiconfig.sh}}
 and obtain an executable \verb|HPhi| in \verb|src/| directory;
 you should add this directory to the \verb|$PATH|.
 
-\subsection{Using \texttt{cmake}}
 
 
 \begin{screen}
@@ -73,3 +74,44 @@ \subsection{Using \texttt{cmake}}
 
 \end{screen}
 
+
+\subsection{Using \texttt{cmake}}
+
+\begin{screen}
+\Large 
+{\bf Tips}
+\normalsize\\
+Before using cmake for sekirei, you must type 
+\begin{verbatim}
+source /home/issp/materiapps/tool/env.sh
+\end{verbatim}
+while for maki, you must type
+\begin{verbatim}
+source /global/app/materiapps/tool/env.sh
+\end{verbatim}
+\end{screen}
+
+We can compile Hphi as
+\begin{verbatim}
+cd $HOME/build/hphi
+cmake -DCONFIG=gcc $PathTohphi
+make
+\end{verbatim}
+Here, we set a path to $\HPhi$ as \verb| $PathTohphi| and to a build directory as \verb| $HOME/build/hphi|. After compiling, a src folder is constructed below a \verb| $HOME/build/hphi |folder and obtain an executable \verb|HPhi| in \verb|src/| directory. When there is not a MPI library in your system, an executable \verb|HPhi| is automatically compiled without a MPI library.
+
+In the above example, we compile $\HPhi$ by using a gcc compiler. We can select a compiler by using following options
+\begin{itemize}
+\item \verb|sekirei| : ISSP system-B ''sekirei''
+\item \verb|fujitsu| : Fujitsu compiler (ISSP system-C ''maki'')
+\item \verb|intel| : intel compiler + Linux PC
+\item \verb|gcc| : GCC compiler + Linux PC.
+\end{itemize}
+An example for compiling $\HPhi$ by an intel compiler is shown as follows, 
+\begin{verbatim}
+mkdir ./build
+cd ./build
+cmake -DCONFIG=intel ../
+make
+\end{verbatim}
+After compiling,  a \verb|src| folder is made below the \verb|build| folder and an execute $\HPhi$ is made in the  \verb|src| folder. It is noted that  we must delete the  \verb|build| folder and do the above works again when we change the compilers.
+

doc/en/chap02_en.tex

@@ -9,6 +9,7 @@ \section{Prerequisite}
 \begin{itemize}
 \item C compiler (intel, Fujitsu, GNU, etc. )
 \item LAPACK library (intel MKL, Fujitsu TCL, ATLAS, etc.)
+\item MPI library (If you do not use MPI, it is not necessary.)
 \end{itemize}
 
 \begin{screen}
@@ -40,8 +41,13 @@ \section{Installation}
 \section{Directory structure}
 When HPhi-xxx.tar.gz is unzipped, the following directory structure is composed.\\
 \\
+├──CMakeLists.txt\\
 ├──COPYING\\
-├──doc/\\
+├──config/\\
+│~~~~~~~├──fujitsu.cmake\\
+│~~~~~~~├──gcc.cmake\\
+│~~~~~~~├──intel.cmake\\
+│~~~~~~~└──sekirei.cmake\\├──doc/\\
 │~~~~~~~├──en/\\
 │~~~~~~~├──jp/\\
 │~~~~~~~├──userguide\_en.pdf\\
@@ -68,7 +74,11 @@ \section{Directory structure}
 │~~~~~~│~~~~~~~~~~~~~~~│~~~~~~└──$\cdots$\\
 │~~~~~~│~~~~~~~~~~~~~~~├─HeisenbergSquare/\\
 │~~~~~~│~~~~~~~~~~~~~~~│~~~~~~└──$\cdots$\\
-│~~~~~~│~~~~~~~~~~~~~~~└─Kitaev/\\
+│~~~~~~│~~~~~~~~~~~~~~~├─Kagome/\\
+│~~~~~~│~~~~~~~~~~~~~~~│~~~~~~└──$\cdots$\\
+│~~~~~~│~~~~~~~~~~~~~~~├─Kitaev/\\
+│~~~~~~│~~~~~~~~~~~~~~~│~~~~~~└──$\cdots$\\
+│~~~~~~│~~~~~~~~~~~~~~~└─S1Chain/\\
 │~~~~~~│~~~~~~~~~~~~~~~~~~~~~~~└──$\cdots$\\
 │~~~~~~└──Standard/\\
 │~~~~~~~~~~~~~~~~~~├──Hubbard/\\
@@ -90,10 +100,13 @@ \section{Directory structure}
 │~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~│~~~~~~└──$\cdots$\\
 │~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~├─HeisenbergSquare/\\
 │~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~│~~~~~~└──$\cdots$\\
-│~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~└─Kitaev/\\
+│~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~├─Kitaev/\\
+│~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~│~~~~~~└──$\cdots$\\
+│~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~└─S1Chain/\\
 │~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~└──$\cdots$\\
 └──src/\\
 ~~~~~~~~~~~~~├──**.c\\
+~~~~~~~~~~~~~├──CMakeLists.txt\\
 ~~~~~~~~~~~~~├──include/\\
 ~~~~~~~~~~~~~│~~~~~~~└──**.h\\
 ~~~~~~~~~~~~~└──makefile\_src\\
@@ -124,7 +137,21 @@ \subsection{{\it Standard} mode}
 
 Run a executable \verb|HPhi| in terminal by setting option ``\verb|-s|" (or ``\verb|--standard|'') and the name of input file written in previous step.
 
-\verb|$ |\textit{Path}\verb|/HPhi -s |\textit{Input\_file\_name}
+\begin{itemize}
+
+\item Serial/OpenMP parallel
+
+  \verb|$ |\textit{Path}\verb|/HPhi -s |\textit{Input\_file\_name}
+
+\item MPI parallel/ Hybrid parallel
+
+  \verb|$ mpiexec -np |\textit{number\_of\_processes}\verb| |\textit{Path}\verb|/HPhi -s |\textit{Input\_file\_name}
+
+  When you use a queuing system in workstations or super computers, 
+  sometimes the number of processes is specified as an argument for the job-submitting command.
+  If you need more information, please refer manuals for your system.
+
+\end{itemize}
 
 \item Watch calculation logs
 
@@ -164,8 +191,18 @@ \subsection{{\it Expert} mode}
 {\bf Note:} A List file can be easily made by using standard mode.
  \item  Run\\
 Run $\HPhi$ in terminal by setting option ``\verb|-e|" (or ``\verb|--expert|'') and a file name of a list file.\\
-\verb|$ |\textit{Path}\verb|/HPhi -e |\textit{Input\_List\_file\_name}
 
+\begin{itemize}
+
+\item Serial/OpenMPI
+
+  \verb|$ |\textit{Path}\verb|/HPhi -e |\textit{Input\_List\_file\_name}
+
+\item MPI/Hybrid
+
+  \verb|$ mpiexec -np |\textit{number\_of\_processes}\verb| |\textit{Path}\verb|/HPhi -e |\textit{Input\_List\_file\_name}
+
+\end{itemize}
 
 \item Under running\\
 Log files are outputted in the ``output" folder which is automatically made in the directory for a calculation scenario.

doc/en/chap03_en.tex

@@ -2,23 +2,6 @@
 %----------------------------------------------------------
 \chapter{Tutorial}
 \label{Ch:model}
-\section{Common works}
-In this section, we describe the procedure for constructing calculation environments after installation.
-\begin{enumerate}
-\item Make a directory for a calculation scenario.
-%
-\item Move to the directory.
-\end{enumerate}
-Here, we show a simple example for commands on a terminal below.\\
-\begin{minipage}{10cm}
-\begin{screen}
-\begin{verbatim}
-mkdir ./CalcScenario
-mv ./CalcScenario
-\end{verbatim}
-\end{screen}
-\end{minipage}
-
 \section{{\it Standard} mode}
 \input{chap03_2_en.tex}
 
@@ -97,8 +80,8 @@ \subsection{Files for basic parameters}
 CParaFileHead  zqp
 --------------------
 Nsite          16   
-Nup            8    
-Ndown          8    
+Ncond          0    
+2Sz            0    
 Lanczos_max    1000 
 initial_iv     12   
 nvec           1    
@@ -112,10 +95,10 @@ \subsection{Files for basic parameters}
 \end{screen}
 \end{minipage}
 ~\\
-In this file, we set parameters for calculation such as a site number, a total number of up spin,  a total number of down spin and a number of Lanczos step etc. The details of ModPara file are shown in \ref{Subsec:modpara}.\\
+In this file, we set parameters for calculation such as a site number, {a total number of conduction electrons,  a total $S_z$} and a number of Lanczos step etc. The details of ModPara file are shown in \ref{Subsec:modpara}.\\
 
 \item {\bf Setting positions of localized spins}\\
-Positions of localized spins are defined by a LocSpin file (in this sample, locspn.def). The contents of files are shown as below.\\
+Positions {and $S$} of localized spins are defined by a LocSpin file (in this sample, locspn.def). The contents of files are shown as below.\\
 \begin{minipage}{15cm}
 \begin{screen}
 \begin{verbatim}
@@ -124,12 +107,12 @@ \subsection{Files for basic parameters}
 ================================ 
 ========i_0LocSpn_1IteElc ====== 
 ================================ 
-    0      0
-    1      0
-    2      0
-    3      0
-    4      0
-    5      0
+    0      1
+    1      1
+    2      1
+    3      1
+    4      1
+    5      1
 …
 \end{verbatim}
 \end{screen}
@@ -139,7 +122,7 @@ \subsection{Files for basic parameters}
 \end{description}
 
 \subsection{Files for constructing Hamiltonian}
-After setting basic parameters, we make input files for constructing Hamiltonian. Since calculations are done by the representation of fermion  operators in $\HPhi$, we must rewrite spin operator using the following relation
+After setting basic parameters, we make input files for constructing Hamiltonian. Since calculations are done by the representation of fermion operators in $\HPhi$, we must rewrite spin operator. {For example,  in the case of $S=1/2$, we rewrite the equation by} using the following relation
 \begin{align}
 S_z^{(i)}&=(c_{i\uparrow}^{\dag}c_{i\uparrow}-c_{i\downarrow}^{\dag}c_{i\downarrow})/2,\\
 S_+^{(i)}&=c_{i\uparrow}^{\dag}c_{i\downarrow},\\
@@ -165,7 +148,7 @@ \subsection{Files for constructing Hamiltonian}
 \end{screen}
 \end{minipage}
 ~\\
-We can use this term when an electric magnetic field is added in spin system. For example, when an magnetic field is added at a site 1 such as $-0.5 S_z^{(1)}$, this term can be rewritten as $-0.5/2(c_{1\uparrow}^{\dag}c_{1\uparrow}-c_{1\downarrow}^{\dag}c_{1\downarrow})$. Thus, the input file becomes as follows.\\
+We can use this term when an electric magnetic field is added in spin system. For example, when an magnetic field is added at a site 1 such as $-0.5 S_z^{(1)}$ { for $S=1/2$}, this term can be rewritten as $-0.5/2(c_{1\uparrow}^{\dag}c_{1\uparrow}-c_{1\downarrow}^{\dag}c_{1\downarrow})$. Thus, the input file becomes as follows.\\
 \begin{minipage}{15cm}
 \begin{screen}
 \begin{verbatim}
@@ -208,7 +191,7 @@ \subsection{Files for constructing Hamiltonian}
 \end{screen}
 \end{minipage}
 ~\\
-Here, we explain an interaction between a site $i$ and a site $j$, for simplicity. Using fermion operators, interaction terms for spin operators can be rewritten as
+Here, we explain an interaction between a site $i$ and a site $j$ {in the case of $S=1/2$}, for simplicity. Using fermion operators, interaction terms for spin operators can be rewritten as
 \begin{align}
 H_{i,i+1}&=J(S_x^{(i)}S_x^{(i+1)}+S_y^{(i)}S_y^{(i+1)}+S_z^{(i)}S_z^{(i+1)}) \nonumber\\
 &=J \left( \frac{1}{2}S_+^{(i)}S_-^{(i+1)}+\frac{1}{2}S_-^{(i)}S_+^{(i+1)}+S_z^{(i)}S_z^{(i+1)} \right) \nonumber\\