Merge branch 'develop'

Author: mitsuaki1987

.gitignore

@@ -1,3 +1,111 @@
+
+# Created by https://www.gitignore.io/api/linux,python
+
+### Linux ###
+*~
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# dotenv
+.env
+
+# virtualenv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+
+# Rope project settings
+.ropeproject
+
+#for Hphi 
 HPhi
 makefile
 Makefile
@@ -14,7 +122,7 @@ make.sys
 *.log
 *.o
 *.optrpt
-*.pdf
+userguide_*.pdf
 *.synctex.gz
 *.toc
 *~

doc/en/chap04_en.tex

@@ -157,7 +157,7 @@ \subsection{Parameters about the kind of a calculation}
 
 \begin{figure}[!tbhp]
   \begin{center}
-    \includegraphics[width=8cm]{../figs/chap04_1_lattice.eps}
+    \includegraphics[width=8cm]{../figs/chap04_1_lattice.pdf}
     \caption{Schematic illustration of
       (a) one dimensional chain lattice, 
       (b) two dimensional square lattice, and 
@@ -173,7 +173,7 @@ \subsection{Parameters about the kind of a calculation}
 
 \begin{figure}[!tbhp]
   \begin{center}
-    \includegraphics[width=15cm]{../figs/chap04_1_honeycomb.eps}
+    \includegraphics[width=15cm]{../figs/chap04_1_honeycomb.pdf}
     \caption{Schematic illustration of the anisotropic honeycomb lattice.
       The nearest neighbor 
       hopping integral, spin coupling, offsite Coulomb integral
@@ -186,7 +186,7 @@ \subsection{Parameters about the kind of a calculation}
 
 \begin{figure}[!tbhp]
   \begin{center}
-    \includegraphics[width=10cm]{../figs/kagome.eps}
+    \includegraphics[width=10cm]{../figs/kagome.pdf}
     \caption{Schematic illustration of the Kagome lattice.
     }
     \label{fig_kagome}
@@ -195,7 +195,7 @@ \subsection{Parameters about the kind of a calculation}
 
 \begin{figure}[!tbhp]
   \begin{center}
-    \includegraphics[width=10cm]{../figs/ladder.eps}
+    \includegraphics[width=10cm]{../figs/ladder.pdf}
     \caption{Schematic illustration of the ladder lattice.
     }
     \label{fig_ladder}
@@ -242,7 +242,7 @@ \subsubsection{Ladder (Fig. \ref{fig_ladder})}
 
 \begin{figure}[!tbhp]
   \begin{center}
-    \includegraphics[width=15cm]{../figs/chap04_1_unitlattice.eps}
+    \includegraphics[width=15cm]{../figs/chap04_1_unitlattice.pdf}
     \caption{The shape of the numerical cell 
       when ${\vec a}_0 = (6, 2), {\vec a}_1 = (2, 4)$
       in the triangular lattice.
@@ -703,6 +703,29 @@ \subsection{Parameters for the numerical condition}
 We specify the interval steps of calculating correlation functions in TPQ method.\\ 
 {\bf Note:} The small interval increases the time cost of calculations.
 
+\item \verb|OutputMode|
+
+{\bf Type :} Choose from \verb|"none"|, \verb|"correlation"|, and \verb|"full"|
+(\verb|correlation| as a default)
+
+{\bf Description :} Indices of correlation functions
+are specified with this keyword.
+\verb|"none"| indicates correlation functions will not calculated.
+When \verb|outputmode="correlation"|,
+$\langle c_{i \sigma}^{\dagger}c_{i \sigma} \rangle$ is computed at all $i, \sigma$,
+and
+$\langle c_{i \sigma}^{\dagger}c_{i \sigma} c_{j \sigma'}^{\dagger}c_{j \sigma'} \rangle$
+is computed at all $i, j, \sigma, \sigma'$.
+If \verb|"full"| is selected,
+$\langle c_{i \sigma}^{\dagger}c_{j \sigma'} \rangle$ is computed at all $i, j, \sigma, \sigma'$,
+and
+$\langle c_{i_1 \sigma_1}^{\dagger}c_{i_2 \sigma_2} c_{i_3 \sigma_3}^{\dagger}c_{i_4 \sigma_4} \rangle$
+is computed at all $i_1, i_2, i_3, i_4, \sigma_1, \sigma_2, \sigma_3, \sigma_4$.
+
+In spin system, 
+indices are specified as those on the Bogoliubov representation
+(See \ref{sec_bogoliubov_rep}).
+
 \end{itemize}
 
 \section{Input files for {\it Expert} mode}

doc/en/chap05_en.tex

@@ -261,4 +261,22 @@ \subsubsection*{Initial vector}
 the thread ID, the number of threads, the process ID, respectively;
 the initial vector depends both on \verb|initial_iv| and the numbber of parallelism.
 
+\section{Bogoliubov representation}\label{sec_bogoliubov_rep}
+
+In the spin system,
+the spin indices in input files of \verb|transfer|, \verb|InterAll|,
+and correlation functions are specified as those of the Bogoliubov representation.
+Spin operators are written by using creation/annihilation operators as follows:
+\begin{align}
+  S_{i z} &= \sum_{\sigma = -S}^{S} \sigma c_{i \sigma}^\dagger c_{i \sigma}
+  \\
+  S_{i}^+ &= \sum_{\sigma = -S}^{S-1} 
+  \sqrt{S(S+1) - \sigma(\sigma+1)} 
+  c_{i \sigma+1}^\dagger c_{i \sigma}
+  \\
+  S_{i}^- &= \sum_{\sigma = -S}^{S-1} 
+  \sqrt{S(S+1) - \sigma(\sigma+1)} 
+  c_{i \sigma}^\dagger c_{i \sigma+1}
+\end{align}
+
 %----------------------------------------------------------

doc/en/userguide_en.tex

@@ -11,7 +11,7 @@
 \documentclass[a4paper,12pt,openany]{../package/mybook}
 %
 \usepackage{amsmath, amsfonts, amsthm, amssymb}
-\usepackage{graphicx}
+\usepackage[dvipdfmx]{graphicx}
 \usepackage{color}
 \usepackage{bm}
 \usepackage{cite}
@@ -92,7 +92,7 @@
 \mytitlepage{%
 User guide 
 }{%
-\Huge $\HPhi$ ver.1.0%
+\Huge $\HPhi$ ver.1.1.1%
 }
 {\large
 {\it \copyright 2015- The University of Tokyo}\\